Horticulture

For those less familiar with the Apprenticeship, it is a six month, full-time organic training for up to 38 apprentices from around the world. The roots of the program extend to the arrival of Alan Chadwick at UCSC 40 years ago, when he and a group of student “apprentices” created the Student Garden Project . Apprentices have traditionally been allowed to live on the farm in their own tents for the six months, sharing cooking and other chores in the Farm Center kitchen and dining room. As a past apprentice and staff member, Boyce-Abel said that for her the planned apprentice housing demonstrated a new level of support from UCSC and a new, more permanent status for the Apprenticeship. When the campus approved the apprentice housing project, Garden Manager Orin Martin said, “This represents staying power.” The apprentice tent cabins, planned as “light-on-the-land,” appropriate technology structures tucked in behind the plum orchard, will give the program a solid foundation. Olivia’s challenge inspired a $20,000 gift from 1978-79 apprentice Meg Cadoux Hirshberg and her husband Gary Hirshberg , whose gift amount allows them to name one of the cabins. Phyllis Anderson, a 1967-70 apprentice and a Friends member, large square planting pots pledged $5,000 which entitles her to name one room of a cabin, as will Jeannine Bonstelle Bassett’s $5,000 gift through the Silent Gong Fund.

Many other apprenticeship graduates and Friends of the Farm & Garden members have also supported the project with gifts and pledges. With these gifts, added to the Center facilities funds set aside for this purpose and funds brought in through this summer’s Back 40 event, more than half the needed $487,000 has been raised. Should you be inspired to donate now, please send a check to the above address made out to the UCSC Foundation with “Apprentice Housing Project” in the memo line.To subsist as an herbivore, an organism must overcome substantial barriers in the form of physical or chemical plant defenses and less than optimal nutrient availability. In some instances, the plant defenses interact directly with nutrient availability by decreasing uptake or impeding digestion , although myriad mechanisms have been described for how herbivores adapt to or avoid defenses. In addition to these deterrents, plant tissues typically maintain high carbon to nitrogen ratios, and plant fluids are depleted in many essential amino acids, making it more difficult for herbivores to acquire nitrogen-based nutrients. To overcome these dietary limitations, herbivores evolved partnerships with bacteria that facilitated transitions to new feeding niches, e.g., on phloem or xylem, or otherwise augmented plant palatability by attenuating defenses. Symbioses can fail, however, when symbiont genomes degrade or limit host range . Thus, there is likely selection pressure to either replace symbionts with more efficient ones, or to evolve novel feeding strategies to avoid symbiont dependence. Indeed, several hemipteran lineages, including leaf hoppers and the Phylloxeridae , have transitioned to novel plant-feeding strategies and lost their obligate symbiont associations.

The transitions in and out of symbioses have left genomic signatures such as reduced genome structure and function for many obligate symbionts, although the effects of symbiosis on herbivore genomes with or without symbionts is unknown.The metabolic coordination in amino acid synthesis and usage between bacteria and host requires amino acid transporters that function in transporting amino acids across the insect/symbiont interface, membranes that separate the cytoplasm of symbionts from insect hemolymph. Two types of AATs mediate this transport: the amino acid polyamine organocation transporter superfamily and the amino acid/auxin permease transporters family . Although both groups belong to the APC superfamily, members of the AAAP family have relatively divergent amino acid sequences, varying substrate specificities, and 11 transmembrane domains, compared to other transporters of the APC family. Expression profiles of these two families of AAT genes for several herbivorous species and their bacterial endosymbionts support a role for these transporters in the evolution of nutritional endosymbiosis. A growing body of evidence has demonstrated that insects induce nutrient sinks in plants in the form of galls that abundantly supply minerals, carbohydrates, and free amino acids. Given that numerous insect taxa form galls, an intriguing question arises: how does the accessibility of gall-enriched nutritive compounds influence the evolution of insect hosts and/or their symbionts? Among the Sternorrhyncha, few lineages secondarily lost endosymbionts concurrent with a shift to parenchyma feeding, and some taxa, such as the Phylloxeridae also induce galls. Insects within the Phylloxeridae are considered sister to the aphids and adelgids , groups that also retain galling and free-living species.

In contrast with aphids and adelgids that harbor symbionts in bacteriocytes, Phylloxeridae species lack stable intracellular symbionts. Further, Phylloxeridae comprises numerous life history strategies, including galling and free-living species that allow a phylogenetically controlled comparison to understand how these strategies arose with respect to their nutrient acquisition and metabolism. As an important grape pest worldwide, the grape phylloxera is capable of making leaf and root galls and its interaction with plant hosts has been the most investigated among the Phylloxeridae. Studies showed that infestation of D. vitifoliae reprograms plant metabolism, leading to the accumulation of nutrients such as carbohydrates and free amino acids. Recently, D. vitifoliae AATs were compared to paralogs in aphids to help pinpoint which transporters underlie the maintenance of nutrient symbiosis between aphids and Buchnera with an emerging conclusion that ecological context may contribute to AAT gene copy number and evolution. To expand the understanding of amino acid metabolism associated with herbivorous insects, we compared species that manipulate plant host amino acid content by gall forming to free-living species, and among species with and without stable nutritional endosymbionts. We sequenced the transcriptomes of nine Phylloxeridae species including D. vitifoliae and eight from the genus Phylloxera. Oak phylloxera has a free-living life history and thus was compared to other galling phylloxerid species regarding AAT evolution whereas two aphid species whose genomes are sequenced were compared to four other galling aphids. Our results indicated that galling insects, in Phylloxeridae and among aphidomorphs, experienced increased constraints on the evolution of AATs likely because of their ability to manipulate plant host metabolism.We collected nine known species within the Phylloxeridae for RNA sequencing. Phylloxeridae is a sister family of Adelgidae under the superfamily Phylloxeroidea, which is sister to the Aphidoidea: Aphididae all within the suborder Sternorrhyncha . These nine species include three that gall stems/petioles , one that feeds across hosts causing crinkles/folds in leaf veins , three that form spheres on leaves , one freely living , and one that galls both roots and leaves of Vitis species . In contrast to P. quercus that lives freely on oak trees , all the other Phylloxera species induce galls on different hickory species and/or tissues . Although the description of P. foveata places it on C. cordiformis and the individuals collected in this study came from C. glabra, we are considering the insects to be the same species for this study because of similarity in the induced phenotype. The Phylloxeridae represents an unresolved taxon , where ongoing research is delineating species. All Carya originating phylloxerids were collected from the Arnold Arboretum of Harvard University, Boston, Massachusetts. Phylloxera quercus was collected from Quercus sp. at a horticultural nursery in Bellevue, WA. Daktulosphaira vitifoliae was collected from native grapes near Madera Canyon, Arizona. Collected insect samples were stored in RNAlater solution at room temperature initially, transferred to 4 °C within eight hours for temporal storage , plastic square planter pots and later kept at −80 °C until RNA isolation. Insects at all stages were collected initially but separated to include only juveniles and adults for sequence analysis.Amino acid uptake, transport, and catabolism underlie the success of herbivory as a life history strategy. Here we present the first multigene tree for members within the Phylloxeridae; a family with both galling and free-living herbivores. We also present transcript profiles across fluid feeding herbivores that support plant host constraint on insect amino acid transporter evolution. Galling sap-feeding insects show fewer AAT transcripts than free-living species within the same insect families and within the same genus of Phylloxera. The ability of galling insects to manipulate plant nutrient content likely altered selection to retain or duplicate the number of functioning AATs within the insect.

Previous research suggests some AATs facilitate the evolution of endosymbioses but also that ecological context may interact with nutrient transporter evolution to shape adaptive duplication or loss. Our data advance this idea by highlighting how complex the selective environment is and suggest specialized interactions with plants play a large role in determining the evolution of herbivore genomes, especially when nutrient manipulating strategies are involved. Previous research on some AATs correlates gene expression and presence with the maintenance of endosymbioses; however, phylloxerids lack stable endosymbionts and still retain many of these same AATs. We found members of the Phylloxeridae family retain at least one copy of each APC found among other aphidomorphs with the exception of two clades that show duplications. Otherwise, phylloxerids retained at least one APC similar to many other Sternorrhyncha insects and D. melanogaster. Interestingly, free-living P. quercus often showed multiple AAT copies within clades where galling phylloxerids possessed only one copy . Free-living aphids also show a similar pattern compared to galling aphids for many clades . This increase within clades suggests that these paralogs may function generally to support nutrient transport when feeding on host parenchyma, atissue where nutrients are lower than when feeding on gall tissue where nutrients can be enriched by and for the galling insect. We hypothesize then that host nutrient manipulation altered the selection environment to maintain certain AATs. In support of this we identified fewer AATs in galling insects than free-living relatives. In some instances, galling phylloxerids did not accumulate specific AAT transcripts; however, lack of accumulation may result from a missing gene or lack of conditions under which expression occurs. While we recognize the limitations of transcriptome information to resolve this, the use of the D. vitifoliae and M. persicae genomes suggests all phylloxerid and nearly all aphid genes were accounted for, and that variation in AATs among genera occurs within aphidomorphs. Some Phylloxera species show accumulation of AATs absent from the D. vitifoliae genome whereas galling Phylloxera species show different numbers of AAT transcripts across clades. Similarly, some galling aphids also lack transcripts for some clades where free-living aphids retain one if not more transcripts. This provides support that differences in the nutrient environments across plant hosts differentially alter selection to retain certain AATs. Little information exists for comparing extensive metabolite profiles of hosts across galled taxa, but the diversity in morphology, color, and specialized tissues that are induced in plant hosts by galling insects suggests nutrient pools that insects feed upon differ widely. Future studies examining metabolite pools among closely related taxa will help resolve what limitations, if any, are present in induced plant phenotypes, and provide additional tests of the role of host nutrient manipulation in the evolution of insect AATs. The microbial community plays a fundamental role in animal nutrient acquisition from food, especially for sapfeeding insects where coevolution with endosymbiotic bacteria alleviates low amino acid content provided by phloem diets. Galling or less apparent manipulation of host nutrients increases nutrient flux to feeding sites, potentially altering selection on the stability of endosymbiotic relationships. Our data and previous transcriptome profiles support increases in paralogs for two free-living aphids, but no galling aphids share these increases. This pattern suggests lineage specificity; however, until more insects are profiled in a way that controls for phylogeny while spanning the range of plant nutrient manipulation, either host manipulation, lineage specific evolution, or both may alter selection on AAT gene evolution. Prior transcriptome assessments correlated transcript abundance and presence with maintaining endosymbiosis. By examining more phylloxerids, we increased resolution of slimfast gene evolution, providing support for previous data that all aphidomorphs experienced slimfast duplication . Thus, slimfast expansions likely occurred in the ancestral aphidomorph. Because the ancestral state of phylloxerids is unresolved without a phylogeny, it is possible that the ancestor lost AATs with the evolution of galling or gained AATs with the transition away from galling. Either scenario would link this clade to nutrient acquisition strategies. Although phylloxerids lack stable nutritional endosymbionts, numerous microbial partners exist within the gut microbiome .

Jardineand Sampson were quickly elevated from “special agents” to permanent positions in the Forest Service, becoming “the two pioneers in national forest-range research” . Jardine was promoted to Inspector of Grazing in charge of the new Office of Grazing Studies in 1910, overseeing range research and directing the monumental task of “range reconnaissance” throughout the national forests over the following decade . He later served as chief of the Office of Experiment Stations and Director of Research for the USDA. Sampson was appointed to head the new Utah Experiment Station on the Manti National Forest, where he worked until 1922, when he accepted a newly created academic post in range science at the University of California-Berkeley. Both authored reports in 1919 that rank among the most influential in the history of US rangelands: Jardine’s “Range Management on the National Forests” was the first comprehensive statement of the policies and principles guiding forest rangeland management. It was still in use at his retirement in 1945—having been “three times reprinted without change”—when he was described as having “brought out the principles on which are founded the standards of good grazing practice over the whole western range country” .

Sampson’s “Plant Succession in Relation to Range Management” established range science on the basis of Clementsian ecological theory. For governmental and scientific purposes, blueberry packaging box respectively, Jardine and Sampson became the principal architects of the dominant paradigm affecting US rangelands in the 20th century. It relied on fencing and predator control not only to remake the physical landscape in favor of livestock production, but also to modifly the social landscape, reducing livestock owners’ dependence on herders to tend and protect their animals. In this realm and many others, the policies of the Forest Service benefited some people at the expense of others, and the agency relied heavily on “science,” howsoever flawed, to buttress its legitimacy . With the creation of the Office of Grazing Studies within the Forest Service, moreover, a critical bureaucratic shift took place, apparently without comment or resistance. The scientific challenge of studying grasses, grazing, and rangelands passed from the Bureau of Plant Industry into the hands of the Forest Service, first under the umbrella of the Branch of Grazing and, after 1926, the Branch of Research. There is no indication that Coville objected to this transfer of research authority, and perhaps he could not have foreseen its longer-term consequences. Foremost among these consequences was the permanent subordination of range research to the Forest Service’s core mandate, timber production, and to its corollary imperative of fire suppression. What this meant, in practice, was that range researchers would be discouraged, if not prohibited outright, from investigating the possible benefits of fire to grasslands, savannas and forests throughout the West for most of the 20th century.

It is impossible to know what might have happened had range research remained in the portfolio of the BPI, but there is reason to believe that fire might well have been viewed in a more favorable light, at least in certain parts of the country such as the Southwest .The effects of the Coyote-Proof Pasture Experiment extend down to the present and across literally hundreds of millions of acres of rangelands in the US and elsewhere. It contributed directly to policies of fencing the land into pastures and eradicating predators of all kinds in the belief that these measures would benefit both livestock production and rangeland conditions. Fencing has since become ubiquitous and almost unquestioned as a basic tool of ranching and rangeland management, subsidized by US government agencies and aggressively promoted in pastoral development projects overseas; Netz , who acknowledges that the US West was where barbed wire fencing found its first widespread use, goes so far as to view it as fundamental to the “ecology of modernity.” Many predators continue to be persecuted by the BBS’s descendent agency, Wildlife Services; even those that are not, persist only at much reduced numbers. Perhaps most importantly, the Wallowa experiment contributed indirectly to institutionalizing range research in an agency whose primary mission lay elsewhere, inhibiting scientific recognition of the ecological importance of recurrent fires. The ecological effects of fencing probably cannot be disentangled from the other factors it enables or accompanies, such as water development, reduced herd mobility, and land tenure rationalization; suffice to say that fragmentation is considered a major threat to rangelands worldwide .

The magnitude of the influence of predators on ecosystem processes is controversial , but there is wide agreement that the consequences of long-term fire suppression are profound .Critical physical geography reveals the concatenation of particular events that influenced the Coyote-Proof Pasture Experiment, while simultaneously illuminating the institutional and political conditions that enabled it to have such widespread effects. We can then ask new questions about present-day issues and debates concerning rangeland conservation and management. In recent decades, scientists and environmentalists have challenged many predator control programs, and some extirpated predators, such as wolves, have been protected and/or reintroduced in portions of their former species ranges. But fencing is rarely challenged. In view of the history recounted here, one has to wonder if restoring predators can only be compatible with continued range livestock production if herding, too, is restored—in which case fences may no longer be necessary.Bronson’s words proved prophetic: the Student Garden Project that Alan Chadwick and his student apprentices brought to life at UC Santa Cruz starting in 1967—and all that has grown from it—have indeed had a major impact on food and farming systems over the past four decades. Chadwick and his apprentices not only created a vibrant organic garden—they set a precedent for forty years of groundbreaking work in sustainable food and agriculture education, research, and public service at UCSC. The garden sparked the growth of a 25-acre organic campus farm and an internationally known apprentice training course, as well as cutting edge programs in food systems and organic farming research and extension, national and international work in agroecology, a model farm-to-college program, an award-winning children’s garden, and much more. “We are small but mighty—an incubator for innovation,” says Sheldon Kamieniecki, dean of the Division of Social Sciences at UCSC. “Our influence proves you don’t have to be a big ag school to have major impacts on farming and food distribution.” In this article we’ll take a brief look back at the Farm & Garden’s history and examine some of the innovative ways that the Center for Agroecology & Sustainable Food Systems continues to stay at the cutting edge of sustainable food and agriculture research, education, and public service.Beginning in 1967, long before sustainability became part of the vernacular, students at UC Santa Cruz were practicing organic gardening under Chadwick’s exacting direction. Chadwick had been brought aboard at the fledgling campus to start a garden project that would help give students a “sense of place” amidst the chaos of construction at the newest of the University of California campuses. Chadwick’s students formed the core of an informal student “apprenticeship,” working alongside him to transform a chaparral-covered slope in what was then the heart of the growing campus into a lush, vibrant organic garden. This apprenticeship approach to teaching—in which instructors worked side-by-side with the students, gradually giving them increased responsibility—would become a hallmark of the training approach used at UC Santa Cruz. Inspired by the garden’s success, students lobbied for a larger plot of ground on which to put Chadwick’s organic practices to work. In 1971, seventeen acres on the lower campus were set aside for an organic campus farm. Later expanded to twenty-five acres, blueberry packaging containers the UCSC Farm became a demonstration and teaching site for small- and medium-scale organic farming techniques. Faculty and student involvement in the garden and farm grew in the 1970s with courses in organic horticulture and agriculture offered as “practicums” through the Environmental Studies Department, as well as appropriate technology and natural history classes based at the farm. Students took advantage of opportunities provided by the farm and garden to design thesis projects and learn through independent studies. Students and staff planted orchards, windbreaks, and perennial borders, creating a diversified organic farm on the growing campus.

In 1975, the loosely organized apprenticeship that began under Chadwick’s direction was formalized into a full time, year-round program offered through UC Santa Cruz Extension. The Apprenticeship Program was the first university-based program to offer students intensive academic and experiential training in organic gardening and farming techniques. With a dedicated work force, the original Garden Project expanded and the farm grew to include tractor-cultivated row crops, as well as hand-worked garden beds, generating enough produce to support a small direct marketing and wholesale effort, and establishing one of California’s first organic “farmers’ markets.”The late 1970s saw increasing concern over the environmental and social effects of conventional farming, from pesticide pollution and soil erosion to the impoverished status of farm workers. The Environmental Studies faculty recognized that the UCSC Farm & Garden projects held potential for wider academic and research applications that could address such issues. To help develop that potential, Steve Gliessman was hired in 1980 to create the Agroecology Program—this was the first University of California program to focus specifically on what would come to be called “sustainable” agriculture. Recognizing that sustainability required social as well as environmental changes, the Agroecology Program hired social scientist Patricia Allen in 1984. Allen initiated the nation’s first work on social issues in sustainable agriculture, addressing topics such as labor, gender, and access to food. Allen also organized and spearheaded the first University of California systemwide conference on agricultural sustainability in 1985. In addition to its work with academic groups, the Agroecology Program also created ties with local, small-scale growers. In 1989 the program hired entomologist Sean Swezey and began a Farm Extension effort to serve growers interested in organic farming techniques. This was the first public organic extension service offered in the U.S. Program researchers worked with local growers on their farms on studies examining the transition from conventional to organic management in crops such as strawberries, apples, artichokes, and cotton. This work took a unique “whole systems” approach that included research on soil fertility, pest control, and economic impacts. In 1994 the Agroecology Program was renamed the Center for Agroecology & Sustainable Food Systems, to better reflect its blend of natural and social sciences work. In 1997, agroecologist Carol Shennan was hired as the center’s director. Shennan brought an interest in agroecosystems and landscape ecology and developed a focus on intersections among agroecology, environment, and community. In 2007 Patricia Allen was appointed director, and continues her work to address various social issues in sustainable agriculture .Over the past decade the growing interest in organic food and alternative food initiatives, such as farmers’ markets, community supported agriculture , farm-to-college programs, and school gardens has heightened the need for research and education in these areas. Building on its history of innovations, CASFS has expanded its work to respond to these needs. Center members provide training materials and expertise to college programs around the country; conduct research to analyze and improve organic farming practices and minimize farming’s impact on natural resources; and analyze the latest trends in consumer interests, food equity issues, and alternative food systems. The growing Farm-to-College effort at UCSC is creating new ways for CASFS to work with students, staff, and faculty to develop a food system that is environmentally sound and socially just. Some of the highlights of work now taking place at CASFS include: High school students in a new youth empowerment program based at the UCSC Farm, with flowers from their farm plot; these were donated to a Santa Cruz family shelter. Trend-setting research and scholarship on social issues in the agrifood system, with current fields of study including perceptions of and priorities for social justice in the agrifood system, farm-to-institution programs, food-system localization efforts, gender issues in agrifood systems, priorities and pedagogies in sustainable agriculture education, and consumer interests and preferences. Basic and applied natural science research on ways to conserve nutrients on organic farms, minimize the impacts of farming on surrounding ecosystems, and manage pests and diseases with organically acceptable techniques, including an innovative approach to minimizing pest damage in strawberries .

Due to the low concentration of resveratrol specified within the Japanese knotweed rhizome used to simulate the base case model, approximately 6,000 kg of Japanese knotweed rhizomes is needed per batch. While ethanol is widely used across the simulated facility, a large quantity of ethanol at an approximate 1:1 ratio is required during the extraction process, largely attributing to the high cost for ethanol. To demonstrate the relationship between resveratrol concentration and the quantity and cost of ethanol in the process, we calculated ethanol consumption as we increased the concentration. Here, Figure 4.2 illustrates the change in the total cost of ethanol and amount of ethanol used when the concentration of resveratrol per knotweed rhizome is increased up to 3 mg/g.The increase of resveratrol found within the rhizomes led to an exponential decrease in the quantity of ethanol needed for processing. In comparison to the base case model, there’s a reduction of $1.6 million to the overall cost of ethanol when the concentration of resveratrol is increased an order of magnitude to 1mg/g. When resveratrol concentration is as high as 3 mg/g, ethanol cost decrease by $2.1 million, a 53% decrease from the base case model results. When the cost of total ethanol used is compared between 1 mg/g and 3 mg/g models, wholesale grow bags the difference is only about $575 thousand or a 23% decrease.

A simple method to evaluate the effect of the concentration in rhizomes, we measured the mass of knotweed rhizomes needed for processing as concentration was varied. As expected, an increase in knotweed concentration results in fewer knotweed rhizomes needed for processing. Figure 4.3 shows the change in mass of knotweed rhizomes needed and ethanol consumption per increasing concentration of resveratrol within the knotweed.Notably, ethanol is a commodity which has experienced some volatility in price during the last few years. A commodity tracker provided by trading economics.com tracks the cost of ethanol per gallon in USD daily . Trading Economics demonstrates that the price of ethanol per gallon reached a low of about $0.95 in April of 2020 and a high of $3.43 on November of 2021, with a current price of about $2.65 per gallon during the time this report was written 2 . The initial jump in ethanol price was over 260% in only a time span of one year and seven months. The price has since dropped about 23% since its peak in a span of 4 months with financial analysts at Trading Economics forecasting a further reduction in price in the near future. This fluctuation in price ultimately limits the ability to effectively assess the effect that the cost of ethanol has towards resveratrol production and similar bio-manufacturing facilities utilizing large quantities of ethanol.

In effort to assess the effect the ethanol price has on the OPEX, the price of ethanol was varied by increments of $0.50 from $1.00 to $3.00. The corresponding OPEX values for each scenario is demonstrated in Figure 4.4 below.In the scenario where ethanol was priced towards its low price of $1.00 per gallon, the annual operating cost to produce 100 MT of resveratrol is reported to be $13.2 and $9.2 million, with and without depreciation, respectively. In the same simulation file, where ethanol is now priced at $3.0 per gallon, the annual operating cost increases to $17.0 and $13.2 million, with and without depreciation, respectively. The base case scenario was performed using a price of $2.00 per gallon of ethanol. The annual operating cost for the base case model is $15.0 and $11.2 million, with and without depreciation, respectively. The difference in annual operating cost is roughly 16% when compared to the $1.00 per gallon scenario and 11.5% when compared to the $3.00. With each increment of $0.50, the annual operating costs steadily increases an average of 6.8% from the last. To assess the cost of ethanol to the COGS, the COGS values was plotted against the change in ethanol price, shown below in Figure 4.5.As expected, the COGS was shown in increase in a linear fashion, in a similar trend to that shown in the relationship between OPEX and ethanol price. An incremental increase of $0.50 from $1.0 to $3.0 per gallon of ethanol increased the COGS an average value of $10.

The COGS value for the optimistic case of $1.0 per gallon case is reported to be $131 and $92 including and not including depreciation, respectively. The variation in price is about $20 for both COGS values and a percentage difference of 13.5% and 18.1%, includingand not including depreciation, respectively. While ethanol is understood to change in price due to many unprecedented factors, it is recommended that the price of ethanol be discussed and be agreed upon for long periods of time with commercial supplies in efforts to hedge against the variation in price in the global market.Another commodity deemed essential to produce 100 MT of resveratrol is the cellulase enzymes used for hydrolysis in the process. Patents released by three resveratrol manufacturers in China detail steps on how to utilize ß-glucosidase for hydrolyzing polydatin into resveratrol to increase production . Here, the simulation for the base case model was designed in a similar fashion to incorporate the utilization of ß-glucosidase found in cellulase. As a result, the annual cost of cellulase enzymes was expected to be $71,436 or 1.3% of the annual operating cost. However, the price of cellulase enzymes used within the model was retrieved using literature values derived from a techno-economic analysis on enzymes costs for bio-fuel production3 . This value was not discussed or confirmed with a large-scale commercial manufacturer of industrial enzymes. The use of industrial enzymes remains a challenge as prices remain inconsistent due to enzymes being reported in terms of dollars per gallon of biofuels3,4. These prices often account for factors beyond the cost of enzymes themselves, such as overall bio-fuel yield, feedstock choice, and enzyme loading 3 . Consequently, a wide range of prices for industrial cellulase enzymes exists. Notably, an analysis performed by scientists at the United States National Renewable Energy Laboratory mention retrieving a Multi-Year Program Plan from the Office of the Biomass Program, Energy Efficiency and Renewable Energy, U.S. Department of Energy where the price of cellulase enzymes was anticipated to be within the range of $0.35/gal in 2007 and $0.12/gal by 2012. The same authors at the NREL performed a techno-economic analysis on thedesign and economics for conversion of lignocellulosic biomass to ethanol and concluded they were able to retrieve a price of $0.34/gal when using their own on-site enzyme production section, aligning their cost with the expectations of the DOE. Novozymes, an industry leader in industrial enzyme production, released a press release titled “New enzymes turn waste into fuel” in February of 2010 mentioning they can offer cellulase enzyme at a competitive price of $0.50 per gallon of cellulosic ethanol5 . Using the pricing information retrieved by the techno-economic analysis on cellulase enzymes for industrial applications mentioned above3 , grow bags for gardening a range of prices for cellulase enzymes per gallon of ethanol can be found to be between $0.68-$1.47. The difference in price is understood to be attributed to using the maximum theoretical yields of sugar consumption and if yields were based on saccharification and fermentation yields found in literature3 .

Since the price of enzymes are another variable cost which attribute to the cost of production, a sensitivity analysis was performed to assess the impact of such a large spread between enzyme cost. A scatter plot demonstrating the relationship between the COGS and enzymes cost is shown below in Figure 4.6.The range of ethanol used for this analysis were chosen from the values retrieved during our search for enzymes costs and a case where the enzymes are supplied at no additional cost. The list is as follows, $0.00/gal, $0.12/gal, $0.35/gal, $0.50/gal, $0.68/gal, $0.85/gal, and $1.47/gal. A large change in COGS values was not seen. The largest change in COGS when comparing to the base case occurred when the price of enzymes increased an order of magnitude to $1.47/gal. Here, the change in total cost was 188%, or a price increase of $134,000 a year when compared to the base case model. The low cost of enzymes for resveratrol production can be expected since the amount of enzymes being loaded to the reaction vessel is relatively small compared to the total mass also entering the reactor . To ensure the model was appropriately modeled, the percentage of enzyme costs was measured as the enzyme cost was varied, shown in Figure 4.7. As expected, as the cost of enzymes increase, as did the percentage of total enzymes cost to the total raw material costs.An alternative to single use enzymes highlighted in other Rsv production patents and scientific literature is the use of fermentation. Rather than purchasing and mixing pure enzymes with plant tissue, this approach mixes plant tissue with microbial cultures, utilizing the enzymes secreted within the solution, ultimately reducing operating costs and raw material cost associated to the addition of water for mixing. This method’s feasibility has already been demonstrated by Wang, H. et al., who effectively compares hydrolyzing P. cuspidatum herbs using fermented fungi versus using acid hydrolysis was performed and dubbed using fungi as an effective and feasible alternative6 . Arguably, applying this method for large scale production might not be practical, as one patent reports the time for fermentation ranges from 10 to 15 days7 , significantly reducing processing time and annual production throughput. Additionally, other researchers argue that the activity of the β-glucosidase enzyme responsible for converting polydatin to Rsv does not perform optimally under fermentation conditions 8 . Another alternative which can be utilized to address high enzyme costs was demonstrated in the analysis performed by the U.S. NREL. Design a bio-processing facility with its own on-site enzyme production section4 . This approach is one that has already been utilized in Rsv literature where the feasibility of fermenting Aspergillus oryzae and separating the β-glucosidase enzyme from solution to hydrolyze P. cuspidatum plant tissue was demonstrated8 . The use of on-site enzyme production is expected to reduce purchasing costs and provide a consistent supply of enzymes available for industrial use.As described above, the most utilized approach when extracting resveratrol from Japanese knotweed is the use of an enzymatic hydrolysis step to convert any existing polydatin to resveratrol. However, data surrounding large scale processing of Japanese knotweed is limited, therefore, bioprocessing parameters such as percent conversion was retrieved using literature on laboratory scale experiments. It should be noted that literature describes an efficient process where conversions can yield values as high as 100%9 . Rather than initializing 100% conversion within the simulation, another conservative approach was taken, and 90% conversion was specified within the base case model. To evaluate the impact that the percent conversion had on the CAPEX and COGS, the percentage was varied from 90 to 100 by increments of two, shown in Figure 4.8.Increasing the enzymatic conversion led to a reduction in both CAPEX and COGS. Utilizing the 90 and 100 percent conversion results for comparison, the difference in COGS is $3.1 and a $200 thousand difference in CAPEX. The largest drop in CAPEX among the different percent conversions occurred between 92 and 94 percent conversion, yielding a decrease in CAPEX of 55 thousand . Here, the reduction in price is attributed to 3 factors: the reduction in equipment size, the reduction of units needed for processing knotweed, and lastly, the reduction in raw materials such as water and ethanol entering the process at a 1:1 mass ratio with the mass of knotweed. The relationship between Japanese knotweed and COGS to increasing enzymatic conversion percentages is shown in Figure 4.9. One specific example where the reduction in CAPEX is seen is the reduction of reactor size needed to perform the enzymatic hydrolysis. The size of the reactor in the base case model is 13,621 L but the reactor is resized to 12,925 L when the conversion was increased to 94%. While there is a price decrease in both the CAPEX and COGS when 100% conversion is initialized, the author would advise against expecting to replicate similar values as 100 percent conversion may not be practical at large scale.

A total of 6,236 SNPs were detected as being significantly associated with the host Vitis using the Bonferroni correction for multiple hypothesis testing with p-values <0.05. However, this still does not exclude the possibility of significance via phylogenetic proximity across the tree. Given the few clades of Vitis-associated bacteria, this dataset did not offer the power to use the most conservative method used by Scoary, the worst pairwise comparison p-value, which would identify only SNPs that have arisen independently across the phylogeny. However, data presented here , show genes that have a significant corrected P-value, and also have a best pairwise comparison P <=.125, showing some indication of independent emergence. 22 SNPs fit those criteria. Out of those 22, there were 9 genes in which several SNPs within them emerged as significant, seedling starter pot likely due to linkage disequilibrium. Amongst the then total of 13 genes identified with significant SNPs, 5 are only identified to the level of hypothetical protein. Most genes that had multiple SNPs detected as significant also had identical frequencies of those SNPs across the populations, showing high linkage of those sites. Due to this, only one SNP is shown per gene and included in the enrichment tests.

The 8 non-hypothetical significant genes are azu , carA, , clpP , nadD , mutY , ubiJ , exbD_1/2 , IpxD3/4 . KEGG orthologies show that 5 of the 8 identified and named genes are classified in the metabolism family in terms of their molecular functions . All identified SNPs were present at lower frequencies in strains from Vitis than other hosts, with a mean frequency of 0.047 in Vitis derived strains and a mean frequency of 0.49 in non-Vitis derived strains. Gene gain and loss was also tested using Scoary for host associations and the same pvalue corrections to go from 473 genes with Bonferroni p <0.05 to 37 genes that also had a best pairwise comparison p <= 0.125 . Out of the 37 identified genes, 33 are only identified as hypothetical proteins. The four named genes are xerC_1/2 , hcaB , mdtA_1/2/3 , and a cluster identified using Panaroo that includes the three genes CnrA , swrC_2 , and acrF_2 .These genes each belong to a different KEGG orthology .Information about X. fastidiosa ssp. fastidiosa infections in coffee in Central America is still limited – little symptomatology is associated with the disease; however, there are persistent infections in the field . The results of this work suggest that the host jump included adaptation of the X. fastidiosa strains to Vitis and lessened the ability of the U.S. strains to infect C. arabica. However, the ability for the pathogen to move throughout the C. arabica plants’ xylem vessels demonstrates a higher infectivity than expected in a fully resistant plant.

Movement of the strains away from the inoculation point was observed, which shows the ability of the bacteria to successfully degrade the pit membrane, which is often a barrier to colonization. However, in contrast to that finding, there was a reduction of positive-testing C. arabica plants over the course of the year after the inoculation. This demonstrates a lower infectivity in C. arabica than the strains have to V. vinifera where infections in a greenhouse are sustained post-inoculation. This could demonstrate a reduction in the ability to create chronic infections in C. arabica by the Vitis-adapted strains. It is possible that the chronic infections of X. fastidiosa in C. arabica plants observed in situ may be caused by high rates of re-inoculation by insect vectors rather than strain level variation in infectivity. That is not the case for ssp. fastidiosa in V. vinifera, just one inoculation is sufficient for high virulence, and only cold winter temperatures have been known to cure infections that are otherwise chronic . The virulence of the U.S. strains to C. arabica is not as high as to V. vinifera, as shown by the lack of severe symptoms in C. arabica. Given that, this study does not offer evidence that the California ssp. fastidiosa strains are generally more virulent than the ancestral strains in Central America. While not a likely scenario, there is a possibility that instead of experiencing adaptation to a specific host, the introduced strains became generally more virulent, which has been hypothesized about the globally spreading ssp. pauca strain infecting olive in Italy . In this paper, we present hypervirulence as a possible scenario, but as it is not supported by the data, we were able to rule it out. Symptom development in infected C. arabica plants consists of minor stunted growth, compared to the severe leaf scorch, matchstick petioles, shriveled fruit, and often plant death that occurs in V. vinifera. There are records of virulence of X. fastidiosa in C. arabica, such as evaluation of ssp. pauca in Brazil. In inoculation experiments with those strains, C. arabica may still develop symptoms slowly, and the proportion of positive plants does also reduce, however after 8 months the percentage positive was around 30% , not entirely dissimilar to the results from this project, which extends some uncertainty about this system.

All methods used detected genetic signatures of adaptation, and many genetic candidates were identified by multiple methods. We were able to identify genes and SNPs associated with the host Vitis as well as genes under positive selection in strains isolated from Vitis. These genes included many hypothetical proteins, however genes with known functions pertaining to infections by X. fastidiosa were also identified.The genes identified by multiple methods included those whose functions in X. fastidiosa have been previously investigated, while many still have unknown functions . ClpX, the gene for the ATP-dependent protease ATP binding subunit, was previously identified as being upregulated 4x during induction of biofilm condition , a physiological state that is vital for virulence and vector colonization . Mutations in the copper related gene copA have been found to drastically alter copper tolerance in X. fastidiosa, which is vital for agricultural survival given the frequency of copper in treating fungal infections in the vineyard, a fungicide that has been in use since the 18th century . It is conceivable that after a host jump into a vineyard, it would be necessary for pathogens to survive higher levels of copper exposure. DegP has been found to be upregulated upon heat shock in X. fastidiosa . TolB encodes for a translocation protein involved in membrane integrity and has been shown to be important for biofilm development, an important aspect of pathogenicity . These are among a suite of other genes that are both hypothetical proteins, or just understudied in X. fastidiosa but show evidence of being involved in the process of this climate and host shift. Now that these genes have been identified, they are prime candidates for targeting in future experiments to determine their effects on host range and climate adaptation. This study also includes one hypothesis that lies outside the general narrative of the introduction event, round nursery pots namely the evaluation of infectivity of ssp. multiplex towards C. arabica, which has not been tested before. While in California, ssp. multiplex has never been found infecting grapevine in the field, it has been shown to generate non persistent infections, similar to what we observed in C. arabica, in the greenhouse . Recently, infections of grapevine by ssp. fastidiosa have been detected in the field in Virginia . While the ssp. multiplex infections were not highly virulent, they were just as persistent as the ssp. fastidiosa strains. In conclusion, we have identified a suite of genes that are related to a host switch to Vitis with a corresponding reduction in the ability to infect an ancestral host. These data support the hypothesis that the shift was not a host range expansion of the subspecies, but a reduction of ability to infect a former host while optimizing the ability to infect a new host species.The results of in-situ experiments can differ greatly from those conducted in controlled laboratory conditions, especially in applied biological systems. In pathology specifically, there are often ethical and regulatory hurdles that prevent the introduction of disease-causing pathogens into naïve systems, whether it is for human health, food security, or in natural systems.

Researchers are therefore typically constrained to using controlled or model systems that are ethically, financially, and logistically feasible. For example, mice are often used to understand human disease, and quarantine greenhouses are used to study plant disease . These proxy systems are imperfect, as we intuitively know that there are differences between a mouse and a human, so there are differences between the potted plant on your windowsill and the towering redwoods of California. These differences are intuitive, but also biological as the effects of interactions between organisms and their complex environments are impossible to recreate, and these environmental and physiological differences directly affect the outcomes of research in plant pathology . The chances to experimentally infect plants in accurate conditions are few and far between, so rare opportunities provide critical research windows. One such system that suffers from a lack of realistic experimental control is Pierce’s disease of grapevines , a persistent burden to the vineyards of California since the introduction of the etiological agent into North America in the late 1800s . The pathogenic bacterial strains that colonized Vitis vinifera and cause PD have since spread to Taiwan, Europe, and the Eastern United States . Although the relationship between Xylella fastidiosa and PD has been understood since 1978 , this study is the first to document the progression of symptoms in mature commercial grapevines under field conditions over the course of several years with a known inoculation time and location on the plant. Despite the challenges of conducting this work in-situ, predominantly concern from the proprietors about infection spreading, we have made insights that counter much of the classic understanding of this disease system and deepen our understanding of symptom development and bacterial multiplication and movement in PD. Several studies have documented PD, which collectively create expectations for the progression of this disease. The pathogen is known to move through mature grapevines at least fast enough to enter the cordon from the shoot within the first year of infection . However, given that removal of the cordon does not reduce disease severity in subsequent years , the pathogen must be moving further into the plant, presumably into the trunk during the first year. It is also well established that there are differences in response to X. fastidiosa infection based on Vitis vinifera cultivar, with some cultivars more susceptible than others . Symptoms are presumed to first appear late in the season that infection occurred, except in especially susceptible cultivars, such as Chardonnay, in which they can arise sooner. Characteristic symptoms have been described as leaf scorch, uneven lignification of the shoots, shriveled berries, and “matchstick” petioles, a situation in which the leaf blade becomes detached from the petiole. In this system, disease symptoms and pathogen infection do not always persist through the winter, a phenomenon called overwinter curing. However, the mechanism for recovery has not yet been determined, and current explanations range from pathogen temperature susceptibility to plant defensive responses. Expectations for overwinter curing are both temperature and cultivardependent, and in Napa Valley, the expected recovery rate for early-season inoculations is around 30% . Progression of PD symptoms has been monitored under controlled conditions . However, such data may not translate to plants grown in the vineyard for various biotic and abiotic reasons. Greenhouse conditions do not account for the complex nutritional, pest, and other biotic  and abiotic pressures of the field , and greenhouse assays of grapevines are typically conducted with an excised shoot, rather than a mature plant. Observational studies are similarly limited because they often miss aspects such as recovery, asymptomatic infections, or unexpected symptoms by not relying on controls, but instead seeking out expected symptoms. These studies have given us a view on characteristics of PD and its progression that we were able to experimentally test.Three commercial vineyard blocks were selected as trial sites at two locations in Napa Valley. Plots were set up with permission from vineyard managers; however, the identity and specific locations of sites must be kept confidential. Each block was planted with one of three wine grape cultivars, Vitis vinifera cv. Cabernet Sauvignon, Chardonnay or Merlot.

While there are three distinctive subspecies of X. fastidiosa, and it would be desirable to be able to use those subspecies for management decisions, so far the subspecies have not been found to have sufficient resolution to define host range or to infer risk . Understanding the molecular basis of plant host specificity in X. fastidiosa is vital for predicting and acting upon host shifts, but these are processes yet to be described . Xylella fastidiosa is a member of the group Xanthomonadaceae, and phylogenetically clusters sister to Xanthomonas albilineans, technically within the paraphyletic genus Xanthomonas, although Xylella is considered a separate genus . Xylella spp., and Xanthomonas albilineans, are the only xylem limited Xanthomonadaceae and have convergently reduced genomes compared to the rest of the genus . Xylella also lacks a Type III Secretion system , a loss compared to its higher order taxonomic group. As the purpose of the T3SS in phytopathogens is to deliver effectors into living plant cells the loss has been hypothesized to be due to X. fastidiosa primarily interacting with non-living tissue; insect cuticle and mature xylem vessels . While the molecular basis of host range is not understood, cut flower bucket there are consistent patterns in the ability of particular X. fastidiosa isolates to infect specific plant hosts regardless of their environmental condition .

This implies that genetics, as opposed to only environmental conditions, underlie the relationship between isolates and plant hosts that allow for colonization. Recurring pathogen specificity to a particular host can be either explained through phylogenetic signal, where members of a clade have shared traits that allow for pathogenesis in that host, or by pathological convergence, where more distantly related strains have separately acquired mechanisms for virulence. Both processes have underlying genetics but each shows different phylogenetic patterns . Lastly, we have seen that deletion of rpfF, which controls cell-cell signaling via a diffusible signal factor , can expand the host range of X. fastidiosa . For example, removing the O-antigen from the exterior of X. fastidiosa cells allows the plant to quickly recognize X. fastidiosa and initiate immune responses, thus decreasing its likelihood of colonization of the plant . O-antigens are highly variable and evolve rapidly, and often are shown to have coevolutionary histories between symbiotic organisms as they are the first exposed part of any bacterium . In terms of phylogenetic methods, cophylogenies have shown no cospeciation between plant hosts and X. fastidiosa or any other congruence between the evolutionary histories of X. fastidiosa and its plant hosts . Based on the current data, it is not generally possible to tell if X. fastidiosa is undergoing host jumps or range expansions, however the data available so far suggests that both are occurring given that in certain situations we see strains able to infect multiple hosts while in other situations we see multiple strains co-existing in nature but no cross infections of hosts .

Using the influx of whole genome data generated in the past several years, we searched the genomes of X. fastidiosa for correlations with plant host species. The first method we pursued was conducting ancestral state reconstructions. Ancestral state reconstructions use genetic data , with a known phenotype for each taxon, to characterize the most likely state that each ancestral node of the tree would have possessed for the phenotype of interest. This tool has been used to understand host-pathogen interactions via ancestral state reconstructions in fungi and trematodes parasite systems . Ideally, we would be able to ask: what was the most likely ancestral host of the ancestor of all X. fastidiosa? If we can understand patterns in the past, it can help us better build models to predict future hosts based on the genomic changes associated with historical host shifts. Following the ancestral state reconstructions, we looked further into the pan-genome by calculating correlations between plant host types and the presence/absence of each gene. This study aimed to compare the commonly used genetic datasets available for phylogenetic analyses of X. fastidiosa both to compare phylogenetic topologies as well as ancestral host states from each dataset. We hypothesized that the pathogen phylogeny would be correlated with hosthistory and that we could observe this trend through ancestral state reconstruction. If there is no relationship between host and the phylogeny, there should not be conclusive ancestral state reconstruction results. We hypothesize that by using either the core genome of X. fastidiosa, pangenome phylogenetic tree, or both, it would be possible to estimate the likelihood of hypothetical plant hosts for ancestral nodes of inTherest .

This would show that the host is largely dependent and predictable based on the phylogeny of bacterial relationships and would lead to further pursuing allelic differences in core-genome and/or gene gain/loss in the pan-genome and estimate how either or both are correlated with plant host identity. While not biologically meaningful, since MLST data is still frequently used in X. fastidiosa management, we included that datatype in our analysis for comparison as well.Phylogenetic reconstruction of disparate regions and sizes are topologically similar The pan-genome of all sequences and the outgroup X. taiwanensis – Wufong1_PLS229 contained 17,024 genes . The alignment of MLST genes totaled 4,146 bp in length, while the core genome comprised 1,411 concatenated regions in a total of 354,816 bp. Non-recombinant regions identified with ClonalFrameML comprised only 32% of the core genome , leaving an alignment consisting of only 112,819 base pairs . The alignment contained 130 pairs of sequences that were completely identical to each other, highly reducing the amount of within subspecies differentiation that is possible with this dataset and creating large polytomies of indistinguishable sequences within subspecies fastidiosa as well as within subsp. pauca . Due to this lack of within-subspecies resolution, the phylogeny with recombinant regions removed is only suitable for between subspecies comparisons due to the extensive data loss in removing recombinant regions. The strains and locations in the alignment with recombination can be visualized in the supplemental materials . While between subspecies topologies are similar among the four trees generated, they are not identical. The core genome tree shows consensus of taxonomic division into three subspecies, however, subsp. sandyi and morus could be either part of subsp. fastidiosa or each their own small subspecies without affecting the monophyly of subsp. fastidiosa. . The non-recombinant tree is similar except that subsp. morus is clusThered within subsp. fastidiosa. The pan-genome splits the most basal of the three subspecies, subsp. pauca, into a paraphyletic cluster, however places multiplex, fastidiosa, morus, and sandyi similarly to the core phylogeny . The MLST tree shows subsp. morus as the outgroup to subsp. fastidiosa while subsp. sandyi falls within subsp. fastidiosa. The other difference among the four topologically similar trees is variation in branch length. Since the pangenome tree was built with gene presence/absence data, it was calculated in gene changes per site. Phylogeny and alignment information is summarized in Table 1. A 16S rDNA phylogeny was also built as a comparison , but the phylogeny provided very poor differentiation among strains .Within subspecies fastidiosa, the core genome rearticulates the three PD clades that were found in Castillo et al. . Within the clade defined as PD-III, the sequence similarity in the core has led to extensive polytomies, with many sequences indistinguishable in the core . The three PD clades are also articulated in the non-recombinant phylogeny, and the pan-genome phylogeny, however the MLST tree does not differentiate these clades from one another. Not poorly resolved, the MLST does have high bootstrap support for clades that conflict with trees constructed with core and pan genome trees, flower display buckets suggesting that using MLST genes has the potential to subvert the analysis of relationships between taxa, while showing strong bootstrap support. Within subspecies multiplex, there have typically been considered two groups, the non-recombining “non-IHR”, multiplex, as well as the recombining outgroup “IHR” multiplex .

The core genome tree as well as the MLST tree both articulate these two groups, the clade “non-IHR”, as well as the non-monophyletic recombining group, “IHR”. The non-recombinant tree and the pan-genome tree do not re-create these groupings . All phylogenies but the pan genome show a consistent split in subsp. pauca between the strains isolated from the Italian OQDS outbreak and the mixed host strains from Brazil. Within the OQDS strains, as well as several very closely related strains from Costa Rica, there is no clear resolution at this genomic scale. Within the Brazilian clade, strain Hib4 is the outgroup in all phylogenies except the MLST. subsp.Interrogating the results of the ancestral state reconstruction to the genus level of the core-genome phylogeny shows undetermined hosts at the deepest nodes . However, the ancestral node of the subspecies fastidiosa has a significant association with the plant genus Coffea, which persists throughout subspecies fastidiosa as the most likely ancestral host for all strains isolated from South and Central America. This changes for the Pierce’s disease of grapevines clade, where the ancestral host of all nodes except one is Vitis, the one exception being an ancestral Prunus node. Subspecies sandyi and morus are undetermined in ancestral hosts. Subspecies multiplex has a more dynamic history, with Vaccinium shown to be the most likely ancestral host for the subspecies, and then within the clade, a switch to a large group of nodes whose most likely host in Prunus, as well as two nodes depicting Platanus and Olea. Subspecies pauca does not have a determined ancestral host of the whole subspecies, and internal nodes switch several times between Citrus and Coffea, and once to Olea. In terms of the genera across the reconstructions, while the deep nodes , are often undetermined, there is more resolution within subspecies . The node that is consistent across the four reconstructions is that there is a high likelihood of the genus Coffea being the ancestral host of the node representing the introduction of subsp. fastidiosa from Central to North America. The genus Vaccinium was predicted as the most likely ancestral host of subsp. multiplex in the core genome phylogeny, whereas in the nonrecombinant phylogeny, the ancestor of all but one strain of subsp. multiplex is the genus Prunus. All four trees agree upon the ancestor of the internal “non-IHR” multiplex clade being Prunus. In terms of the transition models chosen for each reconstruction, most trees had lower AIC scores when using the equal rates model with fewer parameters than the symmetrical rates model, the exception being for the pan-genome super order reconstruction having a lower AIC score with the symmetric model than the equal rates .At the node representing the ancestor of the species X. fastidiosa, both the nonrecombinant core and pan-genome phylogenies predict that the clade Rosid is the most likely ancestral host . The core and MLST phylogenies predict Asterid to be the ancestral host, but at lower likelihoods of 87 and 78%, respectively, which are visualized, along with all likelihoods under 95%, as undetermined . There is enough discordance between reconstructions a consistent pattern at this host depth is unlikely.Bacteria isolated from the genera Coffea and Vitis as well as the super-orders Asterid and Rosid have X. fastidiosa genes with which they are significantly correlated; totaling 30 genes . Ten of these 30 genes are significantly correlated with both Asterids and Rosids, with paired, opposite relationships . Some correlations are of significance due to elevated presence of the gene among strains found in a particular host, while most are significant due to an absence of particular genes in the host of interest. Since lineage-specific interdependencies are accounted for with the phylogeny, the correlated genes are representative of convergent processes, either evolutionarily or via lateral gene transfer, not shared ancestry by descent. Genes that are significant mark repeated non-vertical descent changes in the pan-genome of strains in convergent patterns specific to the hosts of interest. While most identified genes are hypothetical proteins, genes shown to be correlated with host were fitB_1 system, involved in in-host migration, vbhT , socA , and a HTH-type transcriptional regulator .In this paper, we show that there is a genetic basis to the host range of X. fastidiosa. We demonstrate that both the phylogeny and gene gain and loss in the pan-genome are connected to plant host of the diverse species X. fastidiosa, and that an Asterid of undetermined genus was the most likely ancestral plant host of X. fastidiosa.

Alleviation of thermal limitations on Pc growth rates increased the predicted Pc risk in an 470 000 km2 area for the high emissions scenario with a projected mean increase of 0.08. For the low emissions scenario, Pc risks increase over a 390 000 km2 area for the low emissions scenario, with an average 0.05 increase in the Pc risk. Overall, the total area where Pc risks exceed 0.5 declines to approximately 164 000 km2 or 13% of the study region for the B1 scenario. The decline in spatial extent under a high emissions scenario is actually slightly less pronounced, with the predicted Pc range being 170 000 km2 or 13.7% of the region. This occurs even though the area where there is sufficient water for high spring Pc activity declines more for the high emissions scenario than for a low emissions scenario. The results reflect the importance of a trade off between increased winter survival range and decreased spring water availability. At the scale of the Bay Area, future climate projections contain considerable uncertainty associated with climatic down scaling. Broadly, however, the B1 scenario represents a case with warmer spring temperatures but without considerable reduction in rainfall,while the A2 scenario represents a situation with reduced rainfall and warmer temperatures. As shown in Fig. 3, cut flower transport bucket the effects are quite striking: an increase in temperature without a large decrease in rainfall results in an increase in the area that is vulnerable to Pc by approximately 20% .

Conversely, a decline in rainfall and increase in temperature result in a large decline in Pc risk, to approximately 3800 km2 , about half of its contemporary range.The modeling study indicated four different controls on modeled Pc range, which interacted to generate complex spatial patterns of Pc response to projected climatic changes. The first control was the proportion of soil organic carbon, which provided a static template of areas in which Pc would not establish. The second control was winter temperatures which impede pathogen over-winter survival. The range over which the pathogen survived winter expanded sequentially from contemporary conditions to the B1 and then A2 climate scenarios. The third and fourth controls on pathogen range lay in spring temperature and rainfall which together controlled spring Pc activity. The implications of drier climatic conditions in the study area varied depending on the absolute local Pc risk in a given area. Thus, little change in Pc risk was predicted in wet regions such as the northern coast, where drier spring conditions under B1 and A2 climate futures were still wet enough to support Pc activity. In the driest limits of the current Pc range, contemporary rainfall was too limited to support Pc activity, and further drying of the climate under B1 and A2 scenarios did not alter the pathogen risk. In mesic regions, progressively dry springs reduced overall Pc risk under the B1 scenario, relative to contemporary conditions.

Despite further reductions in rainfall under the A2 scenario, however, only minor further decreases in Pc spring risk were predicted compared to the B1 scenario. This we attribute to increasing spring temperatures enhancing the rate of Pc expansion during spring, which increased disease risk over part of the model range. The spatial locations where warmer spring temperatures under the B1 and A2 scenarios caused increases in Pc risk were spatially separated from the locations where decreases in rainfall reduced Pc risk, so the overall pattern of Pc risk during spring under contemporary, B1 and A2 scenarios differs: the B1 case primarily reflects reductions in the contemporary area of high risk, while the A2 scenario continues this reduction but also leads to expanded regions of moderate Pc risk in the north-eastern part of the study region. The interactions of these controls lead to a decrease in Pc range under both B1 and A2 scenarios compared to contemporary conditions, but, surprisingly, less of a reduction in total Pc range under the more extreme warming scenario. The modeling study ignored several factors that impact dynamic Pc risk – that is, the risk of Pc developing in uninfected areas. It has not considered pathways of introduction of Pc into natural communities. Proximity to roads, streams, soil disturbance, innoculum sources, and high vehicle or pedestrian traffic are highly likely to impact these risks. Similarly, the diversity of Californian vegetation and its variable sensitivity to Pc has not been considered: higher resolution studies considering differentials of vegetation susceptibility could provide a far more nuanced picture of the spatial extent of Pc, and could, for instance, eliminate areas of risk in primarily urbanized environments in the San Francisco Bay Area.

However, in the absence of improved data regarding host–pathogen interactions for dominant vegetation types in the area, there is limited basis on which to make such a high-resolution suite of assumptions about vegetation susceptibility. Despite this missing information, the damped sensitivity of Pc range relative to changes in assumed host resistance across the region in conjunction with field observations confirming that a wide range of regional species are susceptible to Pc, suggests that the overall conclusions of the modeling study regarding climate sensitivity should be robust. Finally, we have assumed that the local environmental conditions experienced by Pc are determined solely by climate, which is not true in the irrigated agricultural areas in California’s Central and Imperial Valleys. In these regions, irrigation regimes that are sufficiently frequent to sustain high water potentials in the root zone would alleviate the environmental water stress, as indicated by the observation of Pc occurrence within the Imperial Valley. If water stress is alleviated in these regions, temperatures are warm enough in both winter and spring to support high levels of Pc activity. Thus, irrigated agricultural land should be considered at risk of Pc infestation under both present and future scenarios. Overall, the modeling analysis suggests that Pc has a much larger potential range in the US southwest than could be inferred purely from current observations of the locations of infected sites. At present, despite the high awareness of Phytophthora ramorum and sudden oak death in the US southwest, there is limited public awareness, policy or scientific attention given to Pc . Sources of Pc are known to exist in agricultural and nursery settings in California , and appear to be the source of Pc infection in native ecosystems in several cases . However, no current phytosanitation certification programs, protocols for reducing soil movement from infected to clean sites, or recognized successful spot treatment approaches to minimizing Pc spread are in place in California . While the number of native species in California that are susceptible to Pc remains unclear, estimates in comparably biodiverse southwestern Australia suggest that over 3000 of the 5700 indigenous plant species are susceptible . Pc has already demonstrated its potential to reshape plant communities and entire ecologies . In the absence of detailed information about host susceptibility in California, the large ranges that appear to be supported by contemporary climates in conjunction with the severe effects of Pc in comparable ecosystems point to a critical need to improve risk assessment, procona flower transport containers phytosanitation and awareness of Pc disease. Despite its relatively simple ecology, Pc nonetheless displays non-monotonic responses to climatic warming at regional and local scales, with spatially distinct regions having opposite trends in Pc risk. Although the modeling framework presented accounts for many different aspects of climate, other changes including carbon fertilization due to enhanced atmospheric [CO2], changing land use and ecological thresholds have been neglected, and linking disease risk models to ecosystem outcomes remains challenging. For example, in Western Australia a 40 year drying trend has reduced Pc activity, but with the effect of replacing Pc induced mortality with drought stress stress . Considering that Pc mortality is linked to periods of drought stress that follow wet periods in which Pc causes root damage , limitation of Pc range due to drying, while beneficial for limiting expansion of the pathogen, may come at the expense of increased mortality for infected ecosystems.

The idea that one should be eating healthy to stay healthy is not a debate. Numerous studies show how particular foods individualistically effect human health, but none thus far, to our knowledge, have investigated about the combined impact of a specific diet on the human body as a whole. It is critical for us to understand which kinds of things we should eat and the ways in which their collective consumption will impact our bodies. According to Dr. Tomas J. Carlson, a distinguished pediatrician and ethnobotany researcher, choosing foods from every color in the rainbow is the key to good health. Each fruit and vegetable gets its natural color from the chemical composition of the exclusive phytonutrient in it. Interestingly, the presence of one molecule in one fruit/ vegetable does not necessarily reflect the same color in another type of fresh produce. For instance, although the rich red color in most red fruits and vegetables is naturally derived from the phytonutrient lycopene, most berries such as strawberries and raspberries do not contain lycopene. Instead, they contain brightly colored chemicals called anthocyanins, which are made in plants during ripening season through the joining of a molecule of a sugar with a molecule of their colorless “anthocyanidin” precursors. Anthocyanins are also found in raspberries, which are high in dietary fiber and vitamin C and have a low glycemic index because they contain 6% fiber and only 4% sugar per total weight. Higher quantities of fiber in the fruit, when consumed, helps lower the levels of low-density lipoprotein or the ‘unhealthy’ cholesterol to enhance the functionality of our heart and potentially induce weight loss. The exact pigment that anthocyanins reflect is partly dependent on the variance in acidity or alkalinity in different plants. Because of the relatively high pH of the tissues in blueberry plants, these chemicals turn blue in color during the ripening process of the fruit. Recent research in the Journal of Nutrition suggests that the abundant antioxidant properties in wild blueberries contributes to the reduction in the development of such disorders as Alzheimer’s Dementia and cognitive loss. A type of antioxidants selectively found in yellow and orange colored foods are called cryptoxanthins. In a study conducted by Bovier et al., it is shown that the combination of the beta form of these carotenoids with other sources of nutrients such as lutein and zeaxanthin in carrots, oranges, and corn leads to improved visual processing speed with regular consumption in young healthy subjects.10, 18While green produce mainly derives its pigmentation from chlorophyll, its white counterparts get their natural color from anthoxanthins, favonoid pigments that exhibit antioxidant properties. Among green fruits and vegetables, broccoli stands apart as the most nutritious because of the special combination in which its 3 glucosinolate phytonutrients are found. This “dynamic trio” makes what are called Isothiocyanates , the detox-regulating molecules in broccoli that enhance vitamin A in the form of beta-carotene. Many recent studies claim that the antioxidants in ITCs not only regulate metabolism and cholesterol levels when consumed but also act as cancer chemopreventive phytochemicals. Fruits that are on the same level as broccoli with regards to health in the white-produce family are bananas. Japanese Scientists reveal that the high amounts of vitamin B6, manganese, potassium and fiber in the ripened versions of these fruits can help prevent high blood pressure, protect against atherosclerosis, and improve immunity levels in regular eaters. Despite an enormous amount of scientific knowledge and evidence for the overall beneficial effect of a single fruit/vegetable and/or phytonutrient at a time on human health, no study so far, to our knowledge, has been able to conclusively link the validity of these claims to the whole human body. This offers the opportunity for one to test the combined impact of eating a colorful diet on humans through a systematic study. The purpose of our investigation is to apply a more holistic approach to the study of how the human body is effected as a result of a diet that is composed of all the colors of the rainbow. In other words, in addition to exploring the individual food stuf’s role in improving health, we want to analyze the outcome of the regular incorporation of a whole pack of colorful foods into one’s meals.

They contrast markedly with the mean estimate of / 0.02 with an upper bound of 0.06 obtained for the non-IHR group . Recombination in clade A. As noted earlier, Nunney et al. proposed that the two clades A and B in the X. fastidiosa subsp. multiplex tree of Parker et al. corresponded to isolates that had been subject to IHR versus those largely free of IHR . However, this hypothesis is undermined by the absence of evidence of intersubspecific introgression from X. fastidiosa subsp. fastidiosa to X. fastidiosa subsp. multiplex in the analysis of clade A by Parker et al. . However, in our reanalysis of these data using the targeted introgression test , we found that out of the 9 loci, 6 showed statistically significant evidence of IHR in alleles found in the clade A isolates . Furthermore, in this reanalysis, all of the 6 clade A genotypes carried recombinant alleles in at least 4 of these loci, while none of the 9 clade B genotypes showed any similar evidence of IHR. As noted previously, the 6 recombinant group isolates common to both studies were all classified into group A . They encompassed 4 of the genotypes identified by Parker et al. : Almond2 , the Blueberry1 group , the Blueberry2 group , 25 liter pot plastic and the Ragweed group . They showed significant evidence of IHR at 4 or 5 of the 9 loci , so that in total they showed significant evidence of IHR in 6 or 7 out of the 17 genes examined.

Plant hosts of the recombinant group. Given the identification of a discrete recombinant subgroup within X. fastidiosa subsp. multiplex, we investigated the possibility that it corresponded with a shift in the plant hosts that were infected. Among the 33 isolates defining 9 STs, there were 5 plant hosts represented more than once: ST27 on almond , ST27 and ST40 on purple leaf plum , ST22, ST28, ST42, and ST58 on giant ragweed , ST32 on blackberry , and ST42 and ST43 on blueberry , to which we can add American elm by including the 4 additional clade A isolates from Parker et al. . Closer examination of X. fastidiosa subsp. multiplex isolates from these host plants, using the 143 isolates subjected to MLST , showed that almond and purple leaf plum isolates were recombinant types only about one-quarter of the time . The ratios in American elm from Washington, DC , and western ragweed from Texas were substantially higher , but it was only in blackberry , and blueberry that 100% of the isolates were recombinant. While the sample size for blackberry was very small, the isolates were geographically separate and defined a single sequence type that was found on no other host. ST32 differed from all other STs in the recombinant group, except ST41, in carrying the nonrecombinant pilU3 allele . Blueberry isolates were better represented and again were isolated from two different states, Florida and Georgia. The 7 isolates that we typed defined two STs: ST43, which was found in both Florida and Georgia and was unique to these blueberry isolates, and ST42, which was isolated in Georgia on blueberry but also in Texas on western ragweed .

Analysis of the recombinant group ofX. fastidiosa subsp. multiplex showed three important results. First, intersubspecific recombination was shown to have occurred in 50% of 8 loci scatThered throughout the genome that were chosen independently of the data . Second, it was shown that the donor of the introgressed sequence was X. fastidiosa subsp. fastidiosa, a subspecies introduced from Central America into the United States as a single strain . However, the introgressed sequence at two of the loci did not come from any of the X. fastidiosa subsp. fastidiosa genotypes that have been found in the United States. This result suggests that another introduction of X. fastidiosa subsp. fastidiosa must have occurred, an introduction that resulted in successful IHR, after which the donor genotype seems to have disappeared. This involvement of an unexpected X. fastidiosa subsp. fastidiosa strain supports the hypothesis that the members of the recombinant group share a single ancestral IHR event. Third, the hypothesis that IHR has facilitated a shift to new hosts is strongly supported by the example of blueberry, where 10 isolates have been typed and potentially supportedby the example of blackberry . A link between the shift to a novel plant host and homologous recombination has not been previously identified. Of course, the direct causation of this link can never be proved without knowledge of the genetic changes driving this shift. It can always be argued that the link is fortuitous and that one or more point mutations in the nonrecombined X. fastidiosa subsp. multiplex genome are causal in the host shift. First, both blueberry and blackberry are native to the United States, so if only a simple genetic change was required to infect these species, why did the native nonrecombinant X. fastidiosa subsp. multiplex apparently never acquire these changes? Second, a similar but even more extensive mixing of the genomes of X. fastidiosa subspp. fastidiosa and multiplex is found in the only form of X. fastidiosa that infects another U.S. native plant, mulberry . Furthermore, in other bacterial species, it has been demonstrated that recombination can drive rapid evolution, both in the laboratory and, in the case of Helicobacter pylori, in mice .

Similarly, McCarthy et al. concluded that lineages of Campylobacter jejuni in chickens versus cattle and sheep were able to shift host type, because rapid adaptation was facilitated by recombination with the resident host population. In the study by Nunney et al. , it was shown that the recombinant genotypes formed a well-defined group , demonstrating that intersubspecific homologous recombination was not randomly distributed across the X. fastidiosa subsp. multiplex isolates. This work was based on a survey of 143X. fastidiosa subsp. multiplex isolates using just 8 loci. There were 33 isolates that showed some evidence of IHR in at least 1 locus: all but 2 showed statistically significant evidence in at least 2 loci, while the remaining 110 showed no such evidence . The generality of this discrete group of recombinant forms was supported by our analysis presented here of the sequence data from 9 more loci sequenced by Parker et al. . These loci divided isolates into 2 groups that appeared to correspond to the recombinant and non-IHR groups, respectively , even though Parker et al. found no evidence of IHR. Upon reanalysis, we found statistically significant IHR in 6 of the 9 loci in the clade A data but no evidence of IHR in the clade B data. Clade A included 6 isolates that we had typed in the present study, and each of these showed evidence of IHR in 4 or 5 of the additional 9 loci. Thus, 25 litre plant pot in two independent samplings that together examined 17 loci, there was clear evidence of substantial genomewide IHR in the recombinant group iso-lates, amounting to 50% of the genes showing IHR across the MLST locis plus the pilU locus . The average was higher when based on the loci sequenced by Parker et al. ; however, this was probably biased upwards by the manner in which the loci were chosen . None of the IHR events in 6 of the 9 loci identified using the targeted introgression test, or in the case of complete introgression, a chi-square test, were detected by Parker et al. using PHI and the 9 tests implemented in RDP . This failure of the standard tests of recombination to detect IHR was previously noted by Nunney et al. , motivating the development of their introgression test. We examined the hypothesis that the recombinant group STs were derived from a single IHR event involving a X. fastidiosa subsp. multiplex recipient and an X. fastidiosa subsp. fastidiosa donor. The distribution of allelic differences among the recombinant STs was consistent with them all being derived from a single initial event, but a small number of other intersubspecific and intrasubspecific recombination events would also be needed . More importantly, the genotypes seen in the recombinant group can be accounted for entirely, or very nearly so, based on a single X. fastidiosa subsp. fastidiosa donor genotype. For example, the substantial variation in cysG can all be accounted for by an ancestral introgression of X. fastidiosa subsp. fastidiosa allele 12 followed by subsequent intrasubspecific recombination of X. fastidiosa subsp. multiplex sequence to form the other two alleles . In contrast, variation at pilU could be accounted for by a second donor contributing the X. fastidiosa subsp. fastidiosa pilU9 allele, but it could also have arisen by a single mutation in pilU1 unique to the recombinant group.

A possible single X. fastidiosa subsp. multiplex recipient genotype was also identified . This genotype is consistent with a known ST: setting cysG to allele 3 makes the recipient identical to ST45, which was sampled from the states of California, Kentucky, and Texas . Elsewhere, we consider a slightly different hypothesis regarding the origin of the recombinant group in which the donor and recipient subspecies are reversed—i.e., that it was derived from a single IHR event, but involving an X. fastidiosa subsp. multiplex donor and an X. fastidiosa subsp. fastidiosa recipient; however, apart from the role reversal, the conclusions are unalThered . The ancestral reconstruction allows us to consider the second question posed earlier: is the donor consistent with the X. fastidiosa subsp. fastidiosa genotypes found in the United States? The answer is very clearly “no.” The original donor carried cysG12 and holC19 . These alleles are both found in isolates from Central America, but no X. fastidiosa subsp. fastidiosa isolate found in the United States comes close to matching this criterion: the most similar U.S. ST has a 12-bp mismatch. There has been extensive sampling of X. fastidiosa subsp. fastidiosa within the United States, based on 85 isolates sampled across the United States from 15 different host plants . There is very little variation within X. fastidiosa subsp. fastidiosa isolates from the United States, consistent with the hypothesis that all X. fastidiosa subsp. fastidiosa isolates currently found in the United States are derived from a single strain introduced from Central America . Based on these data, we conclude that the X. fastidiosa subsp. fastidiosa donor was introduced into the United States from Central America and recombined with a native X. fastidiosa subsp. multiplex genotype similar to ST45; however, this donor lineage of X. fastidiosa subsp. fastidiosa was ultimately unsuccessful and died out. We can never conclusively prove the absence of this genotype from North America. However, X. fastidiosa has been extensively sampled from many plant species throughout the United States, and no isolates of X. fastidiosa subsp. fastidiosa have been found that carry alleles similar to the inferred donor alleles cysG12 and holC19 ; indeed all X. fastidiosa subsp. fastidiosa isolates so far found in the United States are consistent with the introduction into the United States of just a single genotype . The transient presence of the donor genotype is consistent with a single large-scale introgression event founding the recombinant group. This raises the possibility that conjugation might have been involved; however, if this was the case, the genomic DNA was broken into pieces prior to homologous recombination, since the data show short regions of recombination. The data from the MLST loci plus pilU show 7 significant recombination events , and 3 of them included at least one recombination breakpoint. Since these loci range in length from roughly 400 to 700 bp, this result would be consistent with an average recombination length of no more than a few kb, similar to the 2.6-kb average length observed by Nunney et al. in a comparison of two X. fastidiosa subsp. fastidiosa genomes . Similarly, the regions identified from the data of Parker et al. showed the same pattern, with a high proportion of recombination breakpoints identified within the sequenced loci . In this context, it is important to note that Rogers and Stenger have found a conjugative plasmid in X. fastidiosa. Furthermore, a high rate of transformation has been demonstrated in the lab , and it has been shown that this process can result in efficient recombination with only a few hundred bases of homologous sequence .

We included all structurally intact moss and lichen tissue in the live biomass category. This was determined by tugging gently on the brown part of the moss or lichen ramet; the part that broke off was determined to be litter. Large samples were chopped into small pieces, mixed, and then subsampled for fresh and dry weights. Tissues were then dried at 60C for 48 h or more before weighing. Above ground vascular net primary production was estimated as the sum of the current year‘s apical growth, including leaves and stems. We did not measure secondary growth for understory plants and thus our ANPP values represent an underestimate for shrubs where secondary growth is likely important, mainly Salix spp. and trees less than 1.37 m tall. Apical growth was defined as that produced from apical or intercalary meristems during the current growing season; it was calculated by summing the masses of all current year‘s leaf, stem, grow raspberries in a pot and reproductive tissues in the quadrat harvested. Harden and others measured moss production in these sites by measuring the apical growth of individual species and then scaling growth to the plot level with digital mapping. At each site, an average of ten 60 · 60 cm2 moss plots were arranged along greater than 100 m transects with plots spaced every 20–40 m.

Percent cover values for up to five dominant moss species within each plot were recorded in fall 2001 via digital photos, extensive field notation, and digitization with Arcview 8.0 software . Apical growth for each species within each plot was based on growth between June and September of 2001. Within each plot, 10 cm2 dense, generally single-species patches of moss were dyed with a fluorescent brightener in early June. Sprayed moss samples were harvested in late September using a coring device of known area and refrigerated until measurement. Apical growth of each ramet was measured individually under a black light using calipers and new growth was harvested, dried, and weighed to estimate per ramet production. The density of stems per m2 was determined from the % cover plots described above. Moss NPP per species was then estimated on a per plot basis as the mass of apical growth per ramet times the ramet density per unit area times the areal coverage. To validate this method of estimating moss NPP, Harden and others compared estimates of H. splendens productivity to estimates based on a morphological growth marker . They found that the fluorescent dye method underestimated H. splendens production relative to the morphological method, possibly due to an offset in the timing of harvest of the two methods. We have chosen to report the fluorescent dye methods here because these estimates likely represent the most conservative estimate of moss NPP.

Compared with mature tundra, the disturbed ground associated with bear digs generally has lower vascular plant species richness. In contrast, Shannon-Weaver diversity levels are indistinguishable between mature tundra and digs, suggesting that the lower overall plant cover in bear digs allows a more even distribution of the abundances of plant species that are present. The results of this direct comparison are intuitive, but grizzlies’ cumulative effect on community richness and structure is more appropriately thought of as marginal addition to the mature tundra community than as a contrast to it. At any given time, recognizable bear digs make up only a small fraction of the ground cover in mature tundra areas. In the northern portion of our study area, Christian found between 7 and 23 bear digs within sight of each kilometer-long transect through ground squirrel habitat, and grizzlies digging for glacier lily bulbs excavate no more than 6% of suitable meadow habitat in a given year in Glacier National Park . The results of our pairwise comparison show that overall, mature tundra alone has fewer plant species than mature tundra with bear digs. The difference in our plots was small but statistically significant. So, although mature tundra harbors more plant species at the landscape level than bear digs, a potentially important effect emerges at the smaller scales relevant to most plants and many animals.

Square meter by square meter, repeated samples from a landscape of mature tundra dotted with bear digs will exhibit greater species richness than samples from a landscape of pure bear digs but also greater richness than samples from purely undisturbed tundra. Although our data cannot define the optimum level of disturbance, they suggest strongly that moderate levels of bear digging will modestly enhance local species richness. In alpine tundra, grizzly bear digs undergo transient increases in plant species richness and diversity that develop over time as recolonization of the dig occurs. This result is consistent with other studies of mammalian disturbance. In desert , coastal prairie , and serpentine annual grasslands , digging mammals have significant impacts on species richness and diversity, with species numbers usually rising after a disturbance event. In some cases, richness and diversity appear to decline as digs undergo succession back to mature tundra. This pattern fits that predicted by the intermediate disturbance hypothesis , with highest diversity or richness at an intermediate stage in succession following the bear digging. We note this result with caution, however, because our data indicate relative richness and diversity of bear digs and because our proxy for dig age is inherently imprecise. As recolonization occurs, in any case, we have shown that species composition of bear digs remains very similar to that of the immediately surrounding tundra, implying that throughout the successional recovery of bear digs most colonization comes from nearby plants.In addition to changing community diversity, bear digs have differential impacts on plants with different life histories. In particular, these disturbances appear to favor plants with certain clonal growth strategies. The biological significance of these effects differs between the two plant communities we studied. In snowbed areas, all clonal types except the most dominant one were favored by digging, suggesting that the statistically significant reduction in above ground guerrilla species may release species of other clonal types from competition, leading to the observed increases in species richness and diversity. In mesic meadows, by contrast, species of the dominant below ground phalanx clonal type were actually favored by digging, while two of the less common clonal types, above ground guerrilla and phalanx species, were suppressed. In this case, it is possible that bear digs are frequent enough to prevent the dominance of above ground species, even in what appears to be mature tundra. Our observations suggest that grizzly bear digs are very concentrated in some areas, but we cannot speculate on the recurrence interval for bear digs in any given location. Ultimately, several of the changes in group dominance by plant species of different clonal types were statistically insignificant. Given the broad range of plant morphologies and strategies grouped within each of our coarsely classified clonal types, we expected to find more significant differences at the scale of individual species. In a study of short-grass prairie communities, for example, Platt showed that a small suite of ‘‘fugitive’’ plant species depended entirely upon badger disturbances for recruitment and reproduction. Unlike Platt, but in common with other studies of digging mammals , we did not find individual species that appeared to absolutely require bear digs for establishment or reproduction. In retrospect, this result is not surprising, given the large number of abiotic disturbances that affect alpine communities; avalanches, frost heaving, solifluction, best grow pots and freeze-thaw ground tears are all significant forces in shaping tundra communities . Indeed, although the species most dependent on bear digs in this study, Epilobium anagallidifolium, also occurred in mature tundra plots, it did so almost exclusively in the cracks caused by frost heaving and ground tears.

The degree to which bear digs’ effects on biotic communities resemble the effects of these other, abiotic disturbances is not well understood, but it seems clear that the ground disturbance associated with bear foraging is not wholly unique in this environment. Still, we found several plant species that showed a statistically significant difference in abundance between bear digs and mature tundra. Furthermore, both species dominant on bear digs were of the phalanx clonal type, while five of the six more common in mature tundra were guerrilla species. These results raise questions about the role of clonal growth form in mediating competitive interactions. Theoretical work has emphasized that differences in clonal form can mediate competitive interactions , and Boeken and Shachak’s work in the Negev desert documented various plant traits favored by disturbances, including seed size and dispersal characteristics. Given the low seedling recruitment rates and long life spans thought to be typical of most tundra species, we suggest that grizzly bear digs may provide critical microsites for reproduction and survival of phalanx-type plants that are at a competitive disadvantage relative to aggressively spreading guerrilla species in densely vegetated mature tundra. Clearly, though, these interactions occur within a diverse plant community where species with widely varying clonal forms interact on small spatial scales. This diversity is probably maintained by the interaction between a diversity of clonal growth forms in the context of numerous microand mesoscale disturbance events. Our observation that the second most common species in a study plot frequently differs in clonal form from the dominant species supports the possibility that the varying clonal forms common in this system may help to allow coexistence of species.The growth of the “critical zone” paradigm has added impetus to closer investigation of soil-plant atmosphere interactions in ecohydrology . This follows from work emphasizing the importance of vegetation in regulating the global terrestrial hydrological cycle, with transpiration being the dominant “green water” flux to the atmosphere compared to evaporation from soils and canopy interception in most environments . More locally, the role vegetation plays in partitioning precipitation into such “green water” fluxes and alternative “blue water” fluxes to groundwater and streamflow has increased inTherest in the feedbacks between vegetation growth and soil development in different geographical environments . The emerging consequences of climatic warming to changes in vegetation characteristics and the implications of land use alterations add further momentum to the need to understand where plants get their water from, and how water is partitioned and recycled in soil-plant systems . Stable isotopes in soil water and plant stem water have been invaluable tools in elucidating ecohydrological interactions over the past decade . Earlier work by Ehleringer and Dawson explained the isotope content of xylem water in trees in terms of potential plant water sources. Building on that, Brooks et al. showed that the isotope characteristics of xylem water did not always correspond to bulk soil water sources as plant xylem water was fractionated and offset relative to the global meteoric water line compared to mobile soil water, groundwater and stream flow signatures. This led to the “Two Water Worlds” hypothesis which speculated that plant water was drawn from a “pool” of water that was “ecohydrologically separated” from the sources of groundwater recharge and stream flow . Research at some sites has found similar patterns of ecohydrologic separation and suggested it may be a ubiquitous characteristic of plant-water systems . Others have found that differences between plant water and mobile water may be limited only to drier periods , or may be less evident in some soil-vegetation systems . Direct hypothesis testing of potential processes that may explain the difference between the isotopic composition of xylem water and that of potential water sources has been advanced by detailed experiments in controlled environments, often involving the use of Bayesian mixing models which assume all potential plant water sources have been sampled . However, as field data become increasingly available from critical zone studies, more exploratory, inferential approaches can be insightful in terms of quantifying the degree to which xylem water isotopes can or cannot be attributed to measured soil water sources . As this research field has progressed, it has become apparent that extraction of soil and plant waters for isotope analysis is beset with a number of methodological issues . Soil waters held under different tensions may have different isotopic characteristics: for example, freely moving water sampled by suction lysimeters often shows a much less marked evaporative fractionation signal than bulk soil waters dominated by less mobile storage extracted by cryogenic or equilibration methods .

One metric especially stands out —positive predictive value for D. melanogaster was nearly 95% . In other words, given that an 11-day egg-laying segment of this species is classified as terminal, there is nearly a 95% chance that this classification is correct. The value of this performance metric in this fruit fly species contrasts to that for the values from data on the tephritid species where it ranged between around 66% to just under 75% depending on species and whether the database was complete or censored.We believe that there were a number of important results from this study. The first was the revelation that daily egg-laying patterns in fruit flies can be used to distinguish periods in a female fly’s life that end in death from those that do not . Most of the previous analyses and models concerned with individual-level egg laying in fruit flies at or near the end of life focused primarily on classification of end-of-life stage such as senescent, terminal or retired stage. Our approach differed in that we made specific predictions that could be quantified according to performance metrics. A second important result was that the overall performance metrics such as precision, container raspberries accuracy and false positives and negatives were heavily species-dependent. This was because of between-species differences in the consistency of egg laying patterns in both the midlife and terminal segments.

Among the three species the best performing metrics including accuracy and precision were those produced using data on D. melanogaster. A third important outcome of our study was that it shed important light on the challenges inherent in predicting the timing of death. As we noted earlier, one reason for some of the low-performing metrics was that the egg-laying patterns indicative of flies that are at the end of their lives are also present in midlife. Consequently the segments in which these occur are misclassified as terminal rather than midlife. Another problem of misclassification occurred when flies either died at the height of their egg laying or very old flies produced larger numbers of eggs close to their day of death. In other words, patterns of egg laying that were more common in midlife than at or near the end of life. These types of misclassifications were rare in D. melanogaster but occurred around one third of the time in the Mexfly as was reflected in the much higher rates of false negatives for this species relative to the other two. A fourth important and what we consider to be the overarching outcome of our study was “proof-of-principle”—patterns of reproduction at the individual level contain information that can be used to predict impending death in fruit flies. This general finding is important since it suggests that there are likely identifiable individual-level age-specific life history data ranging from information on respiratory, metabolic and locomotor activity to sleep, circadian, and mating patterns that can be used singly or in various combinations to predict the timing of death, not only in fruit flies, but in a range of other organisms including in humans.

Indeed, the egg laying patterns we used to identify impending death may be the rudimentary equivalents of clinical prediction rules in humans used to calibrate the timing of deaths across age groups and between sexes. A unique strength of our study was in its multi-level comparisons involving two different fruit fly families , two different genera within one of these families and three different species overall . Our results demonstrated that the same independent variables could be used across families, genera and species to classify egg-laying segments ; but that the performance metrics such as accuracy and precision were family-, genus- and species-dependent. A caveat that applies to all studies like ours involving contingency tables is that performance metrics including PPV and NPV depend upon the relative numbers of positive and negative cases. Because the proportion of negatives influences the number of both false positives and true negatives, as the proportion of negatives increases, PPV decreases and NPV increases. For example, in disease epidemiology the if the prevalence of infection were low, the PPV might be very small but will be much larger in a population with moderate or high prevalence. So the fraction of true positives relative to false positives will be lower in the former hypothetical scenario than in the latter but in both cases the TPR remains the same.

This sample size-dependent relationship for some performance metrics in the contingency table was one of the primary reasons we used equal numbers of mid life and terminal segments for each fruit fly species rather than the number of mid-life segments possible for each species. For example, after a 10-day maturation period, flies that live 25, 50 and 100 days each have only a single 11-day terminal segment but 4, 29 and 68 possible mid-life 11- day segments, respectively. Because both the cohort sizes and life expectancies differed among the three fly species, the relative numbers of possible mid-life versus terminal 11-day segments also differed. Thus using different relative numbers of mid-life versus terminal segments for each species rather than equal numbers would have confounded comparisons. This perspective underscores the caution required in the interpretation of contingency table performance metrics such as sensitivity and specificity where one is much higher than theother. Indeed, this is the case for the Medfly and Mexfly in which sensitivity ranges from 40 to 60% for both but specificity is substantially higher for both species—i.e., 90 and 70%, respectively. This we conclude that our findings are robust but that the specific values of the performance metrics are subject aspects of the sample including size and details such as segment length. An entirely different aspect of this large concept and one we don’t address in this study is that of distinguishing between mid-life and terminal segments when, for example, age-specific reproductive patterns are altered by changing food quality modifying availability . We believe that research on the classification and timing of death in non-human species has the potential to provide important insights into approaches on similar research in humans. This includes research in contexts ranging from estimations of time to death after withdrawal of life-sustaining treatment in patients including for organ transplants , in nursing homes where 50% die within 3 years and over 30% need palliative care within a year , in hospice end-of-life care where one of the key criteria for entry and Medicare eligibility is that the patient has 6 months or less to live if the disease takes its natural course , and for physicians and their patients who are considering euthanasia for what is referred to as “dying on time” for dementia patients who may not wish to continuing living in advanced stages of any number of dementia-related diseases, but the symptoms conflict with the due care criteria . Lowbush “wild” blueberries are considered a nutrient-rich healthy food, due in large part to their exceptional phenolic content and antioxidant activity. Lowbush blueberries are particularly rich in anthocyanins and the anthocyanin profile is complex compared with other fruits. They contain five of the six anthocyanidins commonly found in nature , which can have three different sugar moieties attached as well as acyl groups such as acetyl-, malonyl-, or coumaryl- also attached to the sugar moieties. Blueberries are also rich in proanthocyanidins, chlorogenic acid, and flavonols. Diets rich in blueberries or their polyphenolic-rich extracts have been associated with lower cardiovascular risk, weight gain and metabolic syndrome, draining pots and neurological diseases . In addition, studies involving blueberries have identified polyphenolic-derived phenolic acids that improve cell differentiation and proliferation of osteoblasts in vitro and promote bone growth and limit bone loss in rodents. These health-promoting effects are due to a myriad of mechanisms associated with blueberry polyphenolics, including prevention of oxidative stress and inflammation, and vaso- and lipid modulation.

Many human studies reporting positive health outcomes have used freeze-dried wild blueberry powder, which is a natural source of concentrated polyphenolics. However, the freeze-dried WBB powder may be tart or astringent and not always palatable to consume. This can be problematic in feeding trials in children and adults. In our previous work, we developed five food products prepared with freeze-dried WBB powder that were evaluated for children’s acceptability and desire to eat . These results are useful in designing food products as well as menu items that could be used in clinical trials of WBB-rich diets. In addition to evaluating sensory properties, it is important to validate the storage stability of polyphenolics in these products, before use in clinical trials, to ensure that a consistent dose of polyphenolics can be maintained. Blueberry polyphenolics, especially anthocyanins, are unstable in various processed forms such as juices, jams, purees, and canned berries when stored at ambient temperature. Additionally, anthocyanins in freeze-dried WBB powder are susceptible to degradation when stored at ambient temperature with a reported half-life of 139 days at 25 ◦C. The mechanism responsible for loss of anthocyanins during storage is unknown, but anthocyanin losses are commonly accompanied by increased polymeric color values, suggesting that anthocyanins form polymers with proanthocyanidins. In addition to polymerization, many other factors can affect the stability of anthocyanins including exposure to elevated temperatures, light, oxygen, metals, sugars, and ascorbic acid. At present, refrigeration of blueberry products such as jam and juices is the best approach to mitigate polyphenolic losses during storage. This study was undertaken to determine the stability of anthocyanins, flavonols, chlorogenic acid, and percent polymeric color in five blueberry products prepared with freeze-dried WBB powder. Gummy, oatmeal bar, graham cracker cookie, and juice were stored at 21 ◦C and 4.4 ◦C and evaluated for anthocyanin, flavonol, and chlorogenic acid content and percent polymeric color over eight weeks of storage. An ice pop product stored at −20 ◦C was evaluated for its anthocyanin and chlorogenic acid content over eight weeks of storage.Samples of juice, ice pop, gummy, oatmeal bar, and graham cracker cookie, each containing 15 g of WBB powder per serving, were prepared and packaged as previously described. One serving of oatmeal bar, ice pop, and graham cracker cookie was equivalent to one piece each , a juice serving was 135 g, and a gummy serving was 7 pieces, or 113 g. The amount of 15 g of WBB powder used in product formulations was calculated and converted from previous animal studies to humans. This involved only the use of brief microwave heating to solubilize the ingredients in order to avoid thermal loss of phenolic compounds, but still obtain a ready-to-consume non-baked product. The blueberry juice and ice pop were prepared with an anthocyanin concentrate, previously extracted from the WBB powder. This procedure was used to produce juice and ice pop products with no particulates. The formulation was adjusted with water so the anthocyanin content ofthe products was equivalent to that found in 15 g of WBB powder per serving. The preparation and processing of the samples for the storage study were performed in two separate experiments, using the same sample of wild freeze-dried blueberries obtained from FutureCeuticals Inc. . The WBB powder was stored at 15.5 ◦C for four months between the two experiments. The samples from Experiment 1 were stored at 21 ◦C and the samples from Experiment 2 were stored at 4.4 ◦C. The ice pop products prepared in Experiment 1 were stored at −20 ◦C. Three samples of each packaged product were evaluated at time 0 and after 2, 4, 6, and 8 weeks of storage.Polyphenolics were extracted by homogenizing 5 g of WBB-containing food product or 1 g of WBB powder in 25 mL of extraction solution containing methanol/water/formic acid , to the smallest particle size using a Euro Turrax T18 Tissuemizer for 1 min. Homogenates were centrifuged for 5 min at 10,864 × g. The pellet was re-extracted two additional times with 25 mL of extraction solution and centrifuged for 5 min at 10,864 × g. The filtrates were pooled and adjusted to 100 mL with extraction solvent in a volumetric flask. Prior to HPLC analysis, 5 mL of extract were dried in a Thermo Savant Speed Vac Plus SC210A and reconstituted in 1 mL 5% formic acid in water. All samples were passed through 0.45 µm nylon syringe filters into 1 mL HPLC vials prior to HPLC analysis.

The division of cultures into those with shorter incubation times and longer ones persists across the CLR transformation, though the magnitude of the differences decreases . Notably, the results here, which should mathematically represent trends that are valid in Euclidean space, also correspond to trends from the PCA analysis of the relative abundances still in simplex space. The agreement between the PCA results from the untransformed and those from the transformed datasets indicates that these results are very unlikely to be mathematical artifacts. In fact, they seem to carry enough biological significance to persist through extensive mathematical and statistical manipulation, including rarefaction, relative abundance calculations, and logratio transformation. Results from PCoA, dot plot of abundances, and PCA together serve as exceptional evidence of the compositional changes in the temporal cultures as well as the compositional “neutrality” of plaque. They also point to the lack of host driven differences, implicating the possibility of a baseline in vitro culture that can be developed by manipulating incubation times. A clear difference between the untransformed and CLR-transformed PCA that is worth some exposition is the number of factors shown graphically and accounted for mathematically.

In the untransformed PCA, blueberry pot size the first two components account for almost 90% of the variation in the samples while in the CLR-transformed PCA, the first two components only account for 45% of the total variation. Untransformed PCA on the temporal samples attributes variations to mostly the Streptococcus, Veillonella, and Pseudomonas OTUs while CLR-transformed PCA includes contributions from the Actinobacillus and Acinetobacter OTUs, along with a number of other genera. Even in the most prevalent and abundant genera, the PCA on the untransformed dataonly accounts for two of the three more prominent Streptococcus OTUs and one of the two Veillonella OTUs. On the other hand, results from the CLR-transformed PCA are much more consistent with the dot plot. Regardless of whether PCA on relative abundance data led to spurious trends in the temporal cultures, it is clear that performing PCA on simplex spaces can obscure the observation of important factors. For these reasons, we elected to keep performing PCA on CLR-transformed relative abundances in subsequent experiments, in order to gain a more complete understanding of what contributes to compositional differences.The results from the analyses of the temporal cultures confirm that our culturing procedures helped avoid contamination.

We discovered that controls in the temporal cultures were much more difficult to keep clean than those in the preliminary cultures. This may be due to the physical proximity of the control wells to the culture wells, which enables accidental splashing during feeding and moving of the plates, though we took great care to avoid doing so. As in the preliminary experiments, OTUs in the controls fell entirely within the taxa expected from either the E. coli spike-in or from the cultures, with no sign of external contamination. In terms of diversity, the temporal samples seemed slightly higher than the preliminary samples , though by what quantitative extent we do not know. We may estimate the differences between the preliminary cultures and the temporal cultures by observing the differences between the 24-hour cultures and the more aged cultures from the temporal samples. This particular comparison shows that the more aged cultures contained different distribution of OTUs and more OTUs in some cases. The increased diversity with increased incubation times was very much expected, and the procedures we used in to generate the temporal cultures were capable of capturing early colonizers as well as some of the middle colonizers from the oral bacterial community. In terms of procedural differences between the preliminary and temporal experiments, we used rarefaction to standardize and make samples comparable to one another, as rarefaction was once again shown to be a defensible approach in the temporal experiments.

We also opted not to separate the liquid from the sedimentary cells in the temporal experiment because of the lack of biological significance of the liquid samples. During the preliminary experiments, we confirmed that the liquid samples did not contain aberrant OTUs, i.e. OTUs belonging to neither the human oral bacterial community nor to the spike-in E. coli, and that the liquid samples contained low biomass. These observations led us to believe that the liquid was simply an extension of the sedimented cells, not a saliva-like substance that helps inoculate the cultures, especially given the lack of liquid movement in the cultures at all. As for the composition of the temporal cultures, we observed a shift from Streptococcus OTUs to Veillonella OTUs followed by the rise of Prevotella OTUs in all three hosts. This observation corroborates previous research on the succession of microbes in the colonization of the human dental surface, where Streptococcus spp. serve as the earliest colonizers of dental enamel, followed by microbes from several other genera that include Veillonella and Prevotella. This order of succession of species is in large part explained by the attachment capabilities of streptococcal bacteria. The two most abundant streptococcal OTUs in this study have been shown to produce surface proteins that bind to salivary amylase, human extra parotid glycoprotein, salivary surface lectins, human salivary antigen C fibrillar glycoprotein, and Veillonella fibrillar antigen B. Clearly, organisms in these streptococcal OTUs can act as intermediaries between the salivary pellicle deposited on dental enamel and other bacteria, and our methods provided appropriate conditions for this temporal succession observed in humans as well as in other in vivo and in vitro models of the human oral microbiome. We may be able to observe finer details of temporal development if we increase the sampling frequency, i.e. add more time points to the 5 existing ones during the 168-hour interval. However, it is not clear how the increased aerobic exposure would affect the purity and the development of the cultures. We will likely have to introduce additional measures to avoid contamination should we choose to sample the cultures more frequently. The E. coli spike-in in the temporal experiments served as a qualitative approach for estimating the biomass of the controls. For controls not contaminated by oral bacterial OTUs, the Escherichia-Shigella OTU dominated the relative abundance as in preliminary experiments . Even in controls that had been internally contaminated, the Escherichia-Shigella OTU still occupied 50% or more of the total abundance until the 168-hour incubation. At this time, we have confirmed that up to 168 hours of incubation time, the culturing procedure does not introduce microbes that interfere greatly with the in vitro compositions; both the OTUs and the estimated biomass in the controls, relative to the E. coli spike-in, imply that the OTUs and their distributions in the cultures were likely minimally affected by any potential cross-contamination between the wells. In future experiments, plant raspberry in container we may quantify the biomass directed by weighing the cells from the controls and cultures to gain an understanding of how much cross-contamination in a single plate affects the culture compositions in that plate, though we may not need to do so with the E. coli spike-in. Since the original purpose of the E. coli spike-in – developing a quantitative internal standard that would allow us to estimate the number of cells of the OTUs in the in vitro bacterial community – has been shown to be infeasible, we will eliminate this step to improve procedural efficiency as well as increase the sequencing depths of the cultures. Interestingly, a somewhat recent paper details a quantitative approach that links the number of cells per gram to the differences in gut microbiota.

The authors use flow cytometry cell-counting and 16S copy number corrections to bypass issues stemming from the fixed depth of Illumina MiSeq 16S rRNA sequencing process. The results from this quantitative profiling experiment showed that microbial load is significantly associated with changes in the microbiota, underscoring the importance of the ability to quantify sample biomass. It may be useful to incorporate this particular quantitation approach into future experiments, though the differences in microbial load are likely to be much higher in direct fecal samples across different hosts than the differences generated by cellular growth in in vitro cultures inoculated by similar amount of host plaque. Another potential improvement, should we reinstitute the spike-in procedure, may be using a species or type of bacteria other than E. coli. Ideally, the spike-in should be absent from the human oral microbiome while simultaneously demonstrating extraction and amplification efficiencies similar to members of the oral microbiome.

Because E. coli, a Gram-negative bacterium, has been shown to extract more efficiently than Grampositive bacteria such as S. aureus , E. coli K12 ER2738 may be a non-ideal choice for spike-ins. In this respect, we may be able to use the phi X 174 DNA sequences employed by the UC Davis Host-Microbe Systems Biology Core, as the sequences from that bacteriophage have been shown not to interfere much with the sequencing processes of microbes. Another key quantification step for reinstituting a spike-in would be to compare extraction efficiencies across different Gram-positive species in the oral bacterial community so that we understand potential extraction bias. With that information, we may be able to devise corrective measures to estimate the number of cells in each OTU more accurately. For the temporal cultures, we did not perform an in-depth analysis of host plaque because the goal for this phase of the project was not to generate in vitro cultures with composition that exactly matched that of host plaque. The purpose of this phase was to establish a baseline community that contained organisms common to oral and dental plaque microbiome, with some mimicry of the organismal succession observed in hosts. In this case, though the composition of plaque is useful for making comparisons, the absolute plaque composition from any single host and the precise replication of host specific oral communities were not of central importance. Furthermore, we have been prepared for the fact that unless able to perfectly reproduce the natural conditions, anyin vitro culturing process inevitably selects for a subset of organisms from the microbial community in nature. The short incubation time of one week and an environment absent of host nutrient sources and immune systems in this model make it extremely unlikely that we would be able to replicate the formation of a mature oral or dental plaque community. However, should we look to cultivate communities with higher diversity, we can now build upon this simple yet robust methodology by varying and/or adding nutrients, and regularly re-inoculating the cultures to increase the presence of middle and later colonizers. Here, re-inoculation may be the key to mimicking host variation in the “base” in vitro cultures. In any case, our methodology seemed capable of establishing communities with compositional developments that mimicked in vivo bacterial successions as well as capturing host differences in a qualitative, limited manner. As a last comment on the bio-informatics analyses: As we continued to augment the statistical methods from the preliminary experiments, we adopted the centered-logratio transformation to make PCA a mathematically sound process. This transformation helped confirm the biological significance of the patterns observed in the temporal cultures. The comparison between Figures 24 and 25 shows that CLR helps correct some potential artifacts created by working with relative abundance data, i.e. working in simplex space. For instance, the differences between clusters of samples in the PCA plot before transformation were much more pronounced than those after transformation . Given that CLR has been shown to reduce false discovery rates substantially, the decrease in the effect size in the temporal experiments as a result of the CLR transformation is simultaneously expected and highly desirable. Hence, we will use this method as a tool and a check on patterns observed in PCoA of relative abundance data going forward.In the temporal experiments, we expanded upon the previously established culturing procedures by extending the incubation time and implementing a feeding regimen. Analysis wise, we were able to characterize the community composition of the temporal cultures by using the established, validated bio-informatics pipeline. We also gained the capability to scrutinize and correct the results from Principal Component Analysis on relative abundance datasets, with the addition of the centered-log-ratio transformation.