Future work could explore the genomes of these ASVs to discern why they are important in their respective agricultural systems and test the hypothesis that they serve as keystone species using synthetic communities. Concluding whether adaptive plant-microbe feed backs result in an M × R interaction leading to shifts in other rhizosphere processes is complicated by the importance of poorly understood fungal communities and methodological limitations of this study. Numerous fungal taxa respond to the M × R interaction according to our differential abundance analysis , yet knowledge of these taxa remains limited due in part to the constraints of culture-dependent methods prevalent in the past. Nonetheless, fungi influence inter-kingdom interactions and agriculturally relevant processes in the rhizosphere, and novel molecular biology tools could be used to improve our understanding of key fungal regulators identified in these analyses. Metagenomics and -transcriptomics would facilitate a much more comprehensive analysis of potential functional shifts. A highly useful starting point would be to delve into dynamic variation in microbial genes involved in carbon metabolism and nitrogen cycling in the rhizosphere,30 litre plant pots in combination with root exudate metabolomics and measurements of root N uptake.
Stable isotope labeling and in situ visualization methods could further complement our understanding of how management, plant roots, and their interactive effects shape rhizosphere processes. The scope of this study was intentionally restricted to a single genotype of one crop in two management systems to limit the main sources of variation to the management and rhizosphere effects that were of primary interest, but the limits to inference of this small-scale study must be considered. Other studies in maize have found that strong legacy effects of soil managementhistory are generally acted upon in a similar manner by two maize cultivars and that rhizosphere bacterial community composition varies only slightly among hybrids from different decades of release.Testing whether these limited effects of plant selection hold true for additional contrasting genotypes and genetic groups of maize would further complement this work. Furthermore, variation in root system architecture across crop genotypes might interact with tillage and soil properties responsive to management effects. Management practices such as the inclusion of forage or cover crops planted in stands rather than rows might affect the differentiation of bulk and rhizosphere soil uniquely from systems based on perennial crops, successive plantings of row crops in the same locations, and/or minimal tillage. Study designs incorporating more genotypes, management systems, and cultivation environments would therefore be highly useful to test how results of this study may be extrapolated to other settings. Future studies should also identify functional genes that are upregulated or downregulated in the rhizosphere under specific agricultural management practices.
Whether such functional shifts are adaptive will provide insight into the relationship between agroecology and ecology. Positive eco-evolutionary feed backs resulting in adaptive microbial communities have been described in unmanaged ecosystems, for example, habitat-adapted symbiosis in saline or arid environments. If similar adaptive recruitment can occur with annual crops in the context of agroecosystems, maximizing this process should be added to the list of rhizosphere engineering strategies and targets for G × E breeding screens. Finally, while our results provide evidence that management and plant influence interact to shape microbial communities at one sampling point, we highlight the need to reframe the M × R interaction as a dynamic process. Rhizosphere communities may be more different from one another than bulk soil communities because roots develop right after tillage and fertilization, when management systems are most distinct . Plants are not static entities, but active participants in the ongoing process of rhizosphere recruitment. As an alternative to the “rhizosphere snapshot,” we propose a “rhizosphere symphony” model that acknowledges the active role of root exudates in orchestrating the composition and function of microbial communities. Altered root exudation during development and in response to water and nutrient limitation can upregulate or downregulate microbial taxa and functions, as a conductor brings together different sections of instruments in turn during a symphony.
Although it is unknown whether this plasticity in exudate composition occurs in response to agricultural management, observations of changed exudate quantity and quality in response to soil type and long-term N fertilization suggest that it is possible. Differences in the timing of nutrient availability between management systems, such as delayed N release from cover crop mineralization compared to mineral fertilizer, could thus result in management-system-specific exudate dynamics and rhizosphere microbial communities, i.e., an M × R interaction. If true, this mechanism suggests that we may be able to manipulate the sound of the symphony by talking to the conductor: plant-driven strategies may be instrumental in maximizing beneficial rhizosphere interactions throughout the season.The Elkhorn Slough is located in the Central Monterey Bay area and feeds into the head of the Monterey Submarine Canyon in the newly designated Monterey Bay National Marine Sanctuary. The slough is described by the Department of Fish and Game as “one of the most ecologically important estuarine systems in California” . Elkhorn Slough was designated as an environmentally sensitive habitat in the 1976 California Coastal Plan and over 1400 acres of the slough are in the National Estuarine Research Reserve System. Water quality in the Elkhorn Slough is heavily influenced by both past and present human activities on the land surrounding the slough. This is especially true of agriculture. Non-point source pollutants from farm use of chemical fertilizers and pesticides have been identified as a primary cause of water quality degradation in the Elkhorn Slough. Agriculture is one of the main land uses in the slough watershed with about 26% of the local watershed in agricultural production. Of this land, strawberry production accounts for the greatest area under production . Field testing and monitoring of alternative farming practices that decrease dependence on synthetic chemical inputs has been extremely limited. What is needed is the development of farming systems that are economically as well as environmentally sustainable. The Azevedo Ranch site encompasses 137 acres, approximately 120 of which are currently in strawberry cultivation. The land is jointly owned by The Nature Conservancy and the Monterey County Agricultural and Historical Land Conservancy, whose stated goal is to keep this property in open space in perpetuity. The property will be divided into a wetlands buffer zone surrounding three “pocket marshes,” and an upland agricultural zone. The marshes are separated from the main channel of the slough by a railroad berm. They are connected to tidal water by culverts through the berm,25 liter pot plastic making each independent. The buffer zone, which is currently in cultivation, will be restored with native vegetative cover including native bunch grasses, Coast Live Oaks, and maritime chaparral. The upper agricultural zone will encompass 83 acres and will eventually be converted to low-input sustainable agriculture. The management of the agricultural lands will be guided by an advisory committee, but the overall goal is to develop models, for the greater watershed, of ecologically and economically sustainable methods for crop production.
An additional research site is located on the Elkhorn Slough National Estuarine Research Reserve. The site includes a small pond drained by sloping uplands. It is very similar to the three drainages on the Azevedo ranch, with the important exception that it has never been cultivated. Although the pond is larger than any of the Azevedo marshes and is subject to greater flushing, it provides the opportunity to obtain background data on soils, sediments, and biota in the absence of agricultural disturbances. During the first two years of the study we established critical measurements, protocols, and characterizations of these watersheds under standard cultivation practices. These data will serve as a baseline for comparison once the property is converted to low-input sustainable agricultural management and habitat restoration is completed in the wetland buffer. Conversion and restoration will occur in 2 to 4 years, once the land has been fully paid for. The project is guided by a Technical Advisory Committee which meets monthly. Although this report marks the end of Project Number UCAL-WRC-W-801, the project is ongoing. Our long term goal is the investigation oflinkages between different farm management practices and health of the adjacent slough, as monitored by sedimentation, input of anthropogenic chemicals, water quality, and the response of wetlands flora and fauna. In the future, we will implement and test alternative farming practices that lessen or eliminate the dependence on synthetic chemical inputs. We will also be able to assess the influence of border zones at the land-water margin as buffers between agricultural uplands and estuarine receiving waters. The lead author recently submitted a proposal to the UC Water Resources Center entitled, “Evaluating Vegetated Buffer Zones Between Commercial Strawberry Fields and the Elkhorn Slough Estuary.” Erosion of soils from strawberry fields is a major mechanism of transport of agricultural chemical residues into slough surface waters. About 75% of the anthropogenic erosion in the Eu.horn Slough watershed is attributed to strawberry production . While a background rate of erosion for most soils is about 1 ton/acre/year, erosion from these strawberry lands ranges from 8 to 145 tons/acre/year, with the highest rates occurring during heavy rains. Costs of erosion and sediment damages are estimated at over $3 million/year, or $7911acre of strawberry land . These estimates do not include any factor for environmental damage to the estuary. The Soil Conservation Service has recommended a variety of management practices designed specifically to address the problem of erosion from strawberry fields in the Elkhorn Slough watershed . Unfortunately, many local growers have not yet implemented these practices. A demonstration project can test and report on these and other practices to convince reluctant growers that these techniques work. A recent report on farming practices in the Elkhorn Slough watershed showed that growing practices are strongly correlated with grower ethnicity, and that outreach programs must be targeted for specific under served groups to be effective . Growers apply synthetically and naturally compounded forms of nitrogen, potassium, phosphorous, and other plant nutrients to soils. Some portion of these minerals is taken up by the crop, some is retained in the soil, and some is subject to export from the system through downward leaching, surface runoff, or erosion. Nitrogen, in the form of nitrate, is especially prone to leaching and is a significant problem in groundwater in the Elkhorn Slough watershed. A significant percentage of wells in the Elkhorn Slough watershed are contaminated with unacceptable levels of nitrate . High levels of nitrate in groundwater are associated with agricultural activities, especially strawberry production around the slough. Other nutrients, such as phosphorous, tend to associate closely with soil colloids, and are prone to transport on eroded sediments. There are little or no data to address the potential of fertilizer nutrients being transported into the slough. Research by Broenkow and Smith suggests that tidal water may be the major source of nitrogen in the slough, as local nitrogen concentrations seem to be controlled mainly by the tide. Strong pulses of nitrogen enter the slough after winter rains, but they are soon flushed by the tide. Past measurements have shown low nitrate and phosphate levels in slough water, though no new measurements of slough channel surface water have been made since 1980. Soil water and nitrate movement through the surface soil were studied using porous cup lysimeters. In the first year, twelve lysimeters were installed in the Central Field and six in the grassland control site at the Elkhorn Slough NERR. Lysimeters were place in pairs at one foot and two foot depths to sample the root zone and below the principal root zone. In the crop field, three pairs were placed low on the slope, and three pairs higher up on the slope. In the grassland all three pairs were placed at a similar slope position. First year results showed a great deal of variation in nitrate-nitrogen levels in strawberry bed soil-water. It was not possible to determine the direction of movement or any strong response to seasonality. Furthermore, we found that surface runoff was extremely significant in nutrient loading into the pocket marshes.