Microfluidic platforms have also been successfully employed to study the interactions between the root, microbiome and nematodes in real time . In the systems, additional vertical side channels are connected perpendicularly to the main micro-channel to enable introduction of microorganisms and solutes to the roots in a spatially and temporally defined manner . A recent microfluidic design incorporated a nano-porous interface which confines the root in place while enabling metabolite sampling from different parts of the root . These studies demonstrated the potential of microfluidics in achieving spatiotemporal insights into the complex interaction networks in the rhizosphere. Despite several advantages of microfluidics in rhizosphere research as described above, some challenges remain. All the microfluidic applications grow plants in hydroponic systems where clear media is necessary for the imaging applications and packing solid substrates in the micro-channels is not trivial.Thus,vertical grow rack interrogating the micro-scale interactions in bigger, more developed plants is not possible with current micro-fluidic channel configurations.
In addition, technical challenges such as operating the micro-valves and micro-fabrication present a barrier to device design and construction for non-specialists. Fabricated ecosystems aim to capture critical aspects of ecosystem dynamics within highly controlled laboratory environments . They hold promise in accelerating the translation of lab-based studies to field applications and advance science from correlative and observational insights to mechanistic understanding. Pilot scale enclosed ecosystem chambers such as EcoPODs, EcoTrons and EcoCELLs have been developed for such a purpose . These state-of-the-art systems offer the ability to manipulate many parameters such as temperature, humidity, gas composition, etc., to mimic field conditions and are equipped with multiple analytical instruments to link below ground rhizosphere processes to above ground observations and vice versa . Currently, however, accessibility to such systems is low as there are only several places in the world which can host such multifaceted facilities due to the requirement of significant financial investments. Switching back to lab-scale systems, a recent perspective paper calls for the need to standardize devices, microbiomes and laboratory techniques to create model ecosystems to enable elucidation of molecular mechanisms mediating observed plant-microbe interactions e.g., exudate driven bacterial recruitment . Toward this goal, open source 3D printable chambers, termed Ecosystem Fabrication devices, have been released with detailed protocols to provide controlled laboratory habitats aimed at promoting mechanistic studies of plant-microbe interactions . Similar to a rhizotron setup, these flowth rough systems are designed to provide clear visual access to the rhizosphere with flexibility of use with either soil or liquid substrates.
Certainly, there are many limitations to these devices in that they are limited to relatively small plants and limit the 3D architecture of the root system. Still, an advantage with the EcoFAB is that its 3D printable nature allows for adaptations and modifications to be made and shared on public data platforms such as Github for ease of standardization across different labs and experiments . In fact, a recent multi-lab effort showed high reproducibility of root physiological and morphological traits in EcoFAB-grown Brachypodium distachyon plants . The development of comparable datasets through the use of standardized systems is crucial to advancing our understanding of complex rhizosphere interactions. Open science programs such as the EcoFAB foster a transparent and collaborative network in an increasingly multidisciplinary scientific community. Specialized plant chamber systems are necessary for nondestructive visualization of rhizosphere processes and interactions as all destructive sampling approaches tend to overestimate the rhizosphere extent by 3–5 times compared to those based on visualization techniques . Nonetheless, plants in such chambers are still grown in defined boundaries and suffer from inherent container impacts. For instance, studies have pointed out that container design significantly influences root growth during early developmental stages and leaves lasting impacts on plant health and phenotype . The majority of the lab-based chambers are also centimeter scale and are unlikely to replicate exact field conditions in terms of soil structure, water distribution, redox potential or root zone temperatures . While comparisons between chamber-grown and pot-grown plants show similar outputs , studies comparing plants grown in confined spaces to those directly grown in the field are missing. A recent review mapped the gradient boundaries for different rhizosphere aspects and found that despite the dynamic nature of each trait, the rhizosphere size and shape exist in a quasi-stationary state due to the opposing directions of their formation processes . The generalized rhizosphere boundaries were deducted to be within 0.5–4 mm for most rhizosphere processes except for gases which exceeds > 4 mm and interestingly, they are independent of plant type, root type, age or soil . Bearing this in mind, our assessment of the different growth chambers revealed possible overestimation of rhizosphere ranges in some chamber set ups.
For instance, the use of root-free soil pouches representing rhizosphere soil despite being cm-distance away from the rhizoplane. This prompts the need for careful evaluation of new growth chamber designs to ensure accurate simulation of natural rhizosphere conditions. To date, many rhizosphere microbiome studies and growth chambers systems focus on the impact of plant developmental stage, genotype and soil type on microbial composition and function . On the other hand, predation as a driver in the rhizosphere microbiome remains understudied. For instance, protists are abundant in the soil and are active consumers of bacteria and fungi and play a role in nutrient cycling yet remain an overlooked part of the rhizosphere . Viruses are also pivotal in modulating host communities thereby affecting bio-geochemical cycles but their influence in the rhizosphere is poorly studied . These predatorprey interactions in the rhizosphere deserve in-depth studies which can be facilitated by these specialized growth chambers. Another area worth investigating in the rhizosphere is in anaerobic microbial ecology. At microbially relevant scales, soils primarily exist as aggregates . Aggregation creates conditions different from bulk soil, particularly in terms of oxygen diffusion and water flow resulting in anoxic spaces within aggregates and influences the microbial community.The rhizosphere is also rich in a wide range of compounds which can serve as alternative electron acceptors such as nitrate, iron, sulfate and humic substances in the absence of oxygen . However, most anaerobic studies in the rhizosphere focus only on aqueous environments such as water-logged paddy soils despite biochemical and metatranscriptomic evidence pointing to the possibility of anaerobic respiration in the rhizosphere . To fully understand biogeochemical cycles in the rhizosphere, it is imperative to investigate rhizosphere processes in the microscale and to include localized redox conditions as one of the influencing parameters. Microfluidic platforms with its fast prototyping capabilities can be helpful in creating growth chambers designed to stimulate these redox changes. In the study of the rhizosphere microbiome, genetic manipulation strategies are foundational in deep characterization of microbial mechanisms and current manipulation techniques require axenic isolates. However, the uncultivability of a significant portion of soil microorganisms continues to hamper efforts in gaining mechanistic knowledge. Even for culturable isolates,vertical grow table the process of isolation introduces selective pressure and disturbance to the community with inevitable loss of information on spatial interactions. A recent innovation in gene editing technologies using CRISPR-cas systems demonstrated in situ editing of genetically tractable bacteria within a complex community . Coupled with the use of transparent soil-like substrates , the application of such a technique for the editing of in situ rhizosphere microbiome while preserving spatial and temporal associations would indeed bring invaluable insights. Specialized growth chambers using 3D fabrication and microfluidic technologies are primed to facilitate such innovations. Finally, this review revealed that while similarities exist among the different growth chamber systems, many of these systems are bespoke. This makes it difficult to replicate experiments and determine reproducibility which are important cornerstones of scientific advancement. The complexity of rhizosphere interactions also warrant that computational models are essential to gain a better understanding of system level processes . However, predictive modeling requires data from standardized approaches to be comparable between experiments. Thus, future growth chamber systems and designs are encouraged to follow the open science framework to enable standardization to an extent, such as in the case of EcoFABs .
In the 1960s, the state of Punjab led in the adoption of new high-yielding varieties of wheat and rice. Production of these new varieties required innovations in the use of fertilizer and water, which occurred in a complementary manner to the innovation in seed choices. Mechanization of several aspects of farming also became a supporting innovation. Agricultural extension services based in Punjab’s public universities guided farmers in their transition to the new modes of production. Furthermore, an infrastructure of local roads and market towns had been developed by the state government: these, along with central government procurement guarantees, gave farmers access and security in earning income from their produce. In the private sector, new providers of seeds and fertilizer, as well as farm equipment and equipment maintenance services also arose. All of these conditions together created what has been known as the Green Revolution economy. With the Green Revolution, Punjab quickly became the state with the highest per capita income. This ranking persisted into the 1990s, but underlying conditions became less favorable well before then. Gains in agricultural yields and productivity slowed, due to diminishing returns. While India began to grow faster after trade and industrial policy liberalization of 1991 and subsequent creeping reforms in other sectors, agriculture remained locked into the old policies, and Punjab mostly into the old equilibrium. The relative failure of Punjab to transition from agriculture to industry or to modern services means that the state still faces a major challenge in effecting this classical structural transformation needed for growth. This failure has been a major reason in the state’s decline toward the middle of the per capita income rankings of India’s major states. However, agriculture also desperately needs attention, even if it cannot be the only sector that must change to address Punjab’s economic problems. The reasons for not neglecting agriculture are several. First, there is the immediate problem of economic distress in the sector, concentrated among small farmers and agricultural laborers. Second, the current pattern of cropping and water use is leading to a rapid decline in the groundwater table, threatening complete ecological collapse of much of the state’s agriculture. Third, the Green Revolution economy has little or no room for further innovation that would enhance productivity and rural incomes. Any one of these reasons is significant, but put together, they imply a compelling case for considering how innovation in Punjab agriculture can be spurred. This paper considers five challenges to effecting meaningful innovation in Punjab’s agricultural economy. It does not present solutions, but it is hoped that an analysis of obstacles to change can provide fundamental inputs into the process of seeking positive change. The first challenge to innovation is that, in contrast to the 1960s Green Revolution, a post-innovation agricultural economy will be much more complex, with a wider range of crops, requiring more sophisticated production technologies, as well as greater complexity in the entire supply chain. The second challenge is that this more complex agriculture will need more sophisticated infrastructure, since fruits and vegetables are much more perishable than grains such as wheat and rice . Other complementary inputs, such as water, fertilizer, farm equipment and management, will also need to be provided in innovative ways. A third challenge flows from the first two characteristics of complexity and complementarity: the costs of switching to new products and modes of production will entail significant one-time switching costs, as well as new and ongoing risks. Future risks, even if partly covered by insurance, represent a kind of switching cost, albeit less direct than explicit expenditures on shifting farm operations from one set of routines and activities to another. The fourth challenge considered here is more subtle, in that it concerns questions of appropriate balance, rather than movement to a well-defined post-innovation future. Indeed, the challenge is to assess what kinds of innovations can best be implemented in which contexts or situations: in some cases, incremental innovations or adaptation of existing frontier techniques from elsewhere may work, while in other cases, frontier innovations spurred by fundamental research may be required.