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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Switchgrass-associated soil microbes have subtle but distinct effects on germination vs. growth under drought

Soil microbial communities can play a large role in plant fitness, including plants’ response to drought. How microbes mediate drought response may also differ across the plants’ life stage, but studies rarely study causal effects of microbes on plant fitness at multiple stages. We conducted a greenhouse experiment on switchgrass (Panicum virgatum L.) to investigate how microbial presence (sterile bulk vs. live bulk soils) and microbial source (communities from bulk vs. rhizosphere soil) affect germination and seedling growth (life-stage) during drought. We also investigated how drought and life-stage alter the assembly of the inoculated communities. Both drought conditions and the absence of microbes reduced germination (49% and 50% fewer seedlings, respectively, p < 0.05), but there were few effects of microbial presence on older seedlings. In addition, microbial source had no effect on the evaluated plant traits, but interestingly, the initially similar bulk and rhizosphere communities became compositionally distinct after 34 days with germinating seeds, but not with seedlings. Therefore, it may be that the plants did respond to microbial source through changes in seed or root exudates, and calls for further study. Finally, while sometimes microbes did benefit plants under drought, we did not find evidence that they are especially beneficial in this condition. We suggest that microbes’ effects differ across plant life stage, and may be both positive and negative. Further research should advance understanding of plant stress tolerance within a framework of plant-microbiome co-development.

drought↗
DOE OSTI2022

Uptake of individual and mixed per- and polyfluoroalkyl substances (PFAS) by soybean and their effects on functional genes related to nitrification, denitrification, and nitrogen fixation

Here in this study, we set up a soil-microbe-soybean system spiked with PFOA, PFOS, or a PFAS mixture of eight PFAS and investigated the distribution of PFAS in the system and impacts on the abundance and expression level of genes involved in the nitrogen (N) cycle. When soybean was exposed to the PFAS mixtures, synergistic uptake by shoots was detected. PFAS exhibited remarkable impacts on abundance of nitrification and denitrification genes in both bulk soil and rhizosphere as well as expression of N fixation gene in soybean nodules. The abundance of nitrification genes AOA and AOB amoA and denitrification gene nirK was significantly reduced (p < 0.05) in almost all treatments in bulk soil, except PFOA at 10 μg/kg. The abundance of other functional genes, such as nirS and norZ was affected differently depending on PFAS concentrations and sample location, either bulk soil or the rhizosphere. Interestingly, the N fixation gene nifH in soybean nodules was overexpressed by a PFAS mixture at 100 μg/kg. Hence, this work provided in-depth knowledge regarding the distribution of PFAS and their impacts on the N cycle for the studied system. Results from this study provide insights on assessing risks posed by individual or mixed PFAS to soybean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Scrambling Signal Modularity in Bottom-up Assembled Synthetic Pseudomonas Consortia Reveals Robust Information Transfer

There is immense potential in crafting synthetic microbial communities for application in human health, agriculture, the environment, and even biomanufacturing where an appropriately constructed consortium can be assembled with tremendous biosynthetic or degradative capabilities. In many of these cases, bacterial signaling serves as a form of intercellular information transfer that guides the collective’s behavior. Such communication is complex, as many signals, signal disruptors, microbial species, physical barriers, and spatiotemporal constraints may be involved. Here, in this work, we demonstrate that a multisignal pathway for molecular information transfer within a consortium of several Pseudomonas spp. can be scrambled (genetically and organizationally) while the original message is still effectively conveyed. Assembled from the bottom up, we have employed two types of signaling molecules (i) a redox active secondary metabolite (rhizospheric signal, phloroglucinol), and (ii) a bacterial quorum sensing signal (3-oxo-C12 acylhomoserine lactone, AI-1). These signals can be intraconverted and acted upon by designated community members. We show how the order in which the signals are received, transduced, and subsequently transmitted can be rearranged with minimal impact on the intended outcome. In the consortial context, we found this messaging structure can be remarkably robust. Inspired by rhizospheric molecular signaling mechanisms, this work provides a conceptual framework for designing signaling and information transfer processes within assembled communities.

Biological and medical sciences↗
DOE OSTI2021

Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors

Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors.

16S rRNA↗
DOE OSTI2024

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition

ABSTRACT Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Abstract Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid ( Adelges tsugae , HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii , that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

16S rRNA↗
DOE OSTI2023

Long-Term Persistence of Three Microbial Wildfire Biomarkers in Forest Soils

Long-term monitoring of microbial communities in the rhizosphere of post-fire forests is currently one of the key knowledge gaps. Knowing the time scale of the effects is indispensable to aiding post-fire recovery in vulnerable woodlands, including holm oak forests, that are subjected to a Mediterranean climate, as is the case with forests that are found in protected areas such as the Sierra Nevada National and Natural Park in southeastern Spain. We took rhizosphere soil samples from burned and unburned holm oak trees approximately 3, 6, and 9 years after the 2005 fire that devastated almost 3500 ha in southeastern Spain. We observed that the prokaryotic communities are recovering but have not yet reached the conditions observed in the unburned forest. A common denominator between this fire and other fires is the long-term persistence of three ecosystem recovery biomarkers—specifically, higher proportions of the genera Arthrobacter, Blastococcus, and Massilia in soil microbial communities after a forest fire. These pyrophilous microbes possess remarkable resilience against adverse conditions, exhibiting traits such as xerotolerance, nitrogen mineralization, degradation of aromatic compounds, and copiotrophy in favorable conditions. Furthermore, these biomarkers thrive in alkaline environments, which persist over the long term following forest fires. The relative abundance of these biomarkers showed a decreasing trend over time, but they were still far from the values of the control condition. In conclusion, a decade does not seem to be enough for the complete recovery of the prokaryotic communities in this Mediterranean ecosystem.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Synthetic microbial communities: Bridging research and application in second-generation bioenergy feedstock microbiomes

The sustainable production of purpose-grown bioenergy feedstocks is essential in transitioning away from fossil fuels. Synthetic communities (SynComs) are consortia of microorganisms that can be used as biological interventions to support objectives like plant growth and stress tolerance. This review examines the state of knowledge regarding microbiomes and SynComs of second-generation bioenergy feedstocks, focusing on the rhizosphere. We first provide an overview of second-generation feedstocks, including switchgrass (Panicum virgatum), miscanthus (Miscanthus × giganteus), sorghum (Sorghum spp.), sugarcane (Saccharum spp.), and poplar (Populus spp.), and summarize our current understanding of their plant-soil-microbiome ecology. We next discuss considerations in the objectives, design, and evaluation of SynComs to enhance feedstock production, and then critically review the literature around their use. Our literature analysis revealed that SynCom performance varied substantially between controlled pilot experiments and field trials, possibly due to system complexity that could not be fully considered in their design and pilot evaluation. We identified a gap in the use of SynComs to support the unique sustainability objectives of biofuel feedstock agriculture, presenting an opportunity to leverage these additional microbial traits in SynCom designs. Finally, we emphasize the importance of targeted research to identify the ecological principles that govern the assembly, activation, and persistence of microbes in the feedstock rhizosphere, thereby enhancing our capacity to manage microbiomes under diverse environmental conditions and ensure their functionality. Beyond biofuels, SynComs are a promising microbiome management strategy for crop production; however, an ecologically informed design and evaluation of SynComs are advised.

SynCom↗
DOE OSTI2025

Belowground plant carbon and nitrogen exchange: plant-derived carbon inputs and pore structure formation

Belowground plant transfer of carbon (C) and nitrogen (N) can benefit soil ecosystems, increasing soil C gains and plant N availability, while improving soil pore structure. We explored such transfers among three plant species of North American prairie, where C and N were transferred from a grass (Panicum virgatum L., switchgrass (Sgrass)) to either a legume (Lespedeza capitata Michx., bush clover (Bclover)), a forb (Rudbeckia hirta L., black-eyed Susan (BSforb)), or a mixture of the two. The plants were grown either with/out direct root contact, thus allowing assessment of the relative contributions of fungal- and root-based transfer pathways. The Sgrass was labeled with 13 C and 15 N, and C and N transfers were assessed by measuring isotope enrichment of roots and aboveground biomass of neighboring plants. Soil inputs of plant-derived C and N were assessed by isotope analyses of the rhizosphere soil. X-ray computed tomography was used for pore structure analyses. Carbon transfer was much higher in the presence of direct/close root contact between source and recipient plants, yet N transfers appeared to be mainly fungal driven. Here, while C and N were readily transferred from Sgrass to other Sgrass and Bclover neighbors, transfers to BSforb were negligible. However, in a three species system, the presence of the legume enhanced C and N transfers to BSforb, suggesting non-additive influences of diverse plant community composition. The more plant-derived C and N was found in the rhizosphere of recipient plants, the greater C and N transfers through roots. Greater C and N transfers were associated with increases in 8–30 μm diameter pores and decreases in >150 μm pores. Summarily, diverse plant communities, especially those with legumes, increase C and N transfers, which then benefit soil C inputs and its protection via changes in pore structure.

13 CO 2 pulse labeling↗
DOE OSTI2023

Structure-Driven Liquid Microjunction Surface-Sampling Probe Mass Spectrometry

The rhizosphere is the narrow region of soil surrounding the roots of plants that is influenced by root exudates, root secretions, and associated microbial communities. This region is crucial to plant growth and development and plays a critical role in nutrient uptake, disease resistance, and soil transformation. Understanding the function of exogenous compounds in the rhizosphere starts with determining the spatiotemporal distribution of these molecular components. Using liquid microjunction surface-sampling probe mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes enables in situ, nondisruptive, and nondestructive spatiotemporal measurement of exogenous compounds from plant roots. However, long imaging times (>2 h) can negatively affect plant heath and limit temporal studies. Here, we present a novel strategy to optimize the number and location of sampling sites on these microporous membrane-covered microfluidic devices. In conclusion, this novel, “structure-driven” sampling workflow takes into consideration the channel structure of the microfluidic device to maximize sampling from the channels and minimize acquisition time (~4× less time in some cases while providing similar chemical image accuracy), thus reducing stress on plants during in situ LMJ-SSP-MS analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques

As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific 13C-pyruvate root-labeling experiment. Further, washed (rhizosphere-depleted) and unwashed roots were examined to test the impact of microbial presence on root metabolic pathways. Drought had a species-specific impact on the metabolic profiles and spatial distribution in Piper sp. and Hibiscus rosa sinensis roots, signifying different defense mechanisms; Piper sp. enhanced root structural defense via recalcitrant compounds including lignin, while H. rosa sinensis enhanced biochemical defense via secretion of antioxidants and fatty acids. In contrast, Clitoria fairchildiana, a legume tree, was not influenced as much by drought but rather by rhizosphere presence where carbohydrate storage was enhanced, indicating a close association with symbiotic microbes. This study demonstrates how multiple techniques can be combined to identify how plants cope with drought through different drought-tolerance strategies and the consequences of such changes on below-ground organic matter composition.

Drought, Carbon cycle, MALDI-MSI, Metabolomics, Na↗
DOE OSTI2020

Carbon Dioxide Production in Bedrock Beneath Soils Substantially Contributes to Forest Carbon Cycling

Abstract Soils are widely considered the primary terrestrial organic matter pool mediating carbon transactions with the atmosphere and groundwater. Because soils are both a host and a product of rhizosphere activity, they are thought to mark the location where photosynthetic fixation of carbon dioxide (CO 2 ) is balanced by the oxidation of organic matter. However, in many terrestrial environments, the rhizosphere extends below soils and into fractured bedrock, and it is unknown if the resulting biological and hydrologic dynamics in bedrock have a significant impact on carbon cycling. Here we show substantial production of CO 2 in weathered bedrock at 4–8 m below the thin soils (<0.5 m thick) of a Northern California forest using innovative monitoring technology for sampling gases and water in fractured rock. The deep CO 2 production supports a persistent upward flux of CO 2(g) year‐round from bedrock to soil, constituting between 2% and 29% of the average daily CO 2 efflux from the land surface. When water is rapidly transported across the fractured bedrock vadose zone, nearly 50% of the CO 2 produced in the bedrock dissolves into water, promoting water‐rock interaction and export of dissolved inorganic carbon (DIC) from the unsaturated zone to groundwater, constituting as much as 80% of the DIC exiting the hillslope. Such CO 2 production in weathered bedrock is subject to unique moisture, temperature, biological, and mineralogical conditions which are currently missing from terrestrial carbon models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Reparameterizing Litter Decomposition Using a Simplified Monte Carlo Method Improves Litter Decay Simulated by a Microbial Model and Alters Bioenergy Soil Carbon Estimates

Litter decomposition determines soil organic matter (SOM) formation and plant-available nutrient cycles. Therefore, accurate model representation of litter decomposition is critical to improving soil carbon (C) projections of bioenergy feedstocks. Soil C models that simulate microbial physiology (i.e., microbial models) are new to bioenergy agriculture, and their parameterization is often based on small datasets or manual calibration to reach benchmarks. Here, we reparameterized litter decomposition in a microbial soil C model (CORPSE - Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment) using the continental-scale Long-term Inter-site Decomposition Experiment Team (LIDET) dataset which documents decomposition across a range of litter qualities over a decade. Here, we conducted a simplified Monte Carlo simulation that constrained parameter values to reduce computational costs. The LIDET-derived parameters improved modeled C and nitrogen (N) remaining, decomposition rates, and litter mean residence times as compared to Baseline parameters. We applied the LIDET litter decomposition parameters to a microbial bioenergy model (Fixation and Uptake of Nitrogen – Bioenergy Carbon, Rhizosphere, Organisms, and Protection) to examine soil C estimates generated by Baseline and LIDET parameters. LIDET parameters increased estimated soil C in bioenergy feedstocks, with even greater increases under elevated plant inputs (i.e., by increasing residue, N fertilization). This was due to the integrated effects of plant litter quantity, quality, and agricultural practices (tillage, fertilization). Collectively, we developed a simple framework for using large-scale datasets to inform the parameterization of microbial models that impacts projections of soil C for bioenergy feedstocks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy

Root biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free, in situ imaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With simultaneously recorded 3PF signal, we demonstrated our ability to investigate root-microbe interactions by achieving single-bacterium tracking and subcellular imaging of fungal spores and hyphae in the rhizosphere.

Pan, Daisong [University of California, Berkeley, ↗
DOE OSTI2023

Drought Shifts Sorghum Root Metabolite and Microbiome Profiles and Enriches for Pipecolic Acid

Plant-associated microbial communities shift in composition as a result of environmental perturbations, such as drought. It has been shown that Actinobacteria are enriched in plant roots and rhizospheres during drought stress. However, the correlations between microbiome dynamics and plant response to drought are poorly understood. Here we apply a combination of bacterial community composition analysis and plant metabolite profiling in Sorghum bicolor roots, rhizospheres, and soil during drought and drought recovery to investigate potential contributions of host metabolism to shifts in bacterial composition. Our results provide a detailed view of metabolic shifts across the plant root during drought and show that the response to rewatering differs between root and soil; additionally, we identify drought-responsive metabolites that are highly correlated with the observed changes in Actinobacteria abundance. Furthermore, we find that pipecolic acid is a drought-enriched metabolite in sorghum roots, and that exogenous application of pipecolic acid inhibits root growth. Finally, we show that this activity functions independent of the systemic acquired resistance pathway and has the potential to impact Actinobacterial taxa within the root microbiome.

165 RRNA↗
DOE OSTI2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Filling gaps in our understanding of belowground plant traits across the world: an introduction to a Virtual Issue

The belowground world is one of the final frontiers in terrestrial ecology. The tangling of plant roots with the surrounding soil below is a lifeline for the humble forbs and towering trees above, and roots play a key role in shaping ecosystem carbon, water and nutrient cycling (Bardgett et al., 2014). Ecologists have long sought to better understand the ecosystem-scale consequences of differing plant strategies, above- and belowground, by relating plant characteristics, or traits, to plant function (Grime, 1977; Pregitzer, 2002). While developing trait–function linkages is arguably more difficult for plant traits that are hidden belowground, root and rhizosphere ecologists continue to fan out across grasslands and forests with their shovels, isotopes, and specialized cameras, seeking a better understanding of the secret lives of roots. Over the years, New Phytologist has served as a virtual town square for scientists to discuss their hard-won observations on the interplay among belowground plant traits, microbial activity, and edaphic and environmental conditions from biomes around the world (Norby & Jackson, 2000; Pregitzer, 2002; Matamala & Stover, 2013; Norby & Iversen, 2017). In this Editorial we highlight the newest papers that update and add to our understanding of the role of root and rhizosphere traits in broader ecosystem processes. We focused on papers published in New Phytologist between 1 January 2019 and 31 December 2020 and extended this window to papers still in ‘early view’ up to the time of writing. Because of the overwhelming number of papers, we did not include those with a decidedly genomic focus or that served primarily as data syntheses, reviews, insights or commentaries.

59 BASIC BIOLOGICAL SCIENCES↗