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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Plant root exudates and rhizosphere bacterial communities shift with neighbor context

A plant's neighborhood context can alter its interactions with other organisms, but little is known about how these dynamics occur belowground, especially with soil microbes. Microbial communities in rhizosphere soil are influenced by many factors, including abiotic conditions and root-derived signals. In particular, root exudates have strong effects on rhizosphere assembly, respond to changes in abiotic conditions, and help plants interact with neighbors. Therefore, we predicted that root exudates likely play a central role in neighbor-induced shifts in rhizosphere communities. We conducted a greenhouse experiment to test this and determine how the rhizosphere bacterial community of a focal plant, Panicum virgatum, changed when beside different neighbors, and whether these shifts were mediated by neighbor-induced changes in root exudation. We found that neighbor altered both focal plant exudates and rhizosphere community, and that changes were largest when the focal plant was beside the most competitive neighbor, Rudbeckia hirta, which reduced both focal plant growth and nitrogen uptake. Several factors contributed to neighbor impacts on rhizosphere assembly, including neighbor-induced changes in root exudates during nitrogen-limitation and microbial spillover from roots of larger neighbors. Using an additional soil incubation, we also found that these changes in exudates can have even greater effects on soil nutrients than on microbial assembly. Overall, we show that neighbors influence one another's microbiomes, and highlight neighbor-induced changes in root exudates as one mechanism through which this may occur. Furthermore, this work suggests that rhizosphere assembly may differ in mixed-species communities and thus emphasizes a need for microbiome studies that consider neighborhood context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites

Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites

Trichoderma spp. are ubiquitous rhizosphere fungi capable of producing several classes of secondary metabolites that can modify the dynamics of the plant-associated microbiome. However, the bacterial-fungal mechanisms that mediate these interactions have not been fully characterized. Here, a random barcode transposon-site sequencing (RB-TnSeq) approach was employed to identify bacterial genes important for fitness in the presence of Trichoderma atroviride exudates. We selected three rhizosphere bacteria with RB-TnSeq mutant libraries that can promote plant growth: the nitrogen fixers Klebsiella michiganensis M5aI and Herbaspirillum seropedicae SmR1, and Pseudomonas simiae WCS417. As a non-rhizosphere species, Pseudomonas putida KT2440 was also included. From the RB-TnSeq data, nitrogen-fixing bacteria competed mainly for iron and required the siderophore transport system TonB/ExbB for optimal fitness in the presence of T . atroviride exudates. In contrast, P . simiae and P . putida were highly dependent on mechanisms associated with membrane lipid modification that are required for resistance to cationic antimicrobial peptides (CAMPs). A mutant in the Hog1-MAP kinase (Δ tmk 3) gene of T . atroviride showed altered expression patterns of many nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters with potential antibiotic activity. In contrast to exudates from wild-type T . atroviride , bacterial mutants containing lesions in genes associated with resistance to antibiotics did not show fitness defects when RB-TnSeq libraries were exposed to exudates from the Δ tmk3 mutant. Unexpectedly, exudates from wild-type T . atroviride and the Δ tmk 3 mutant rescued purine auxotrophic mutants of H . seropedicae , K . michiganensis and P . simiae . Metabolomic analysis on exudates from wild-type T . atroviride and the Δ tmk 3 mutant showed that both strains excrete purines and complex metabolites; functional Tmk3 is required to produce some of these metabolites. This study highlights the complex interplay between Trichoderma -metabolites and soil bacteria, revealing both beneficial and antagonistic effects, and underscoring the intricate and multifaceted nature of this relationship.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Summary Biocrusts are phototroph‐driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth‐promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host–microbe co‐culture experiments between biocrust communities/biocrust isolates and a model grass ( Brachypodium distachyon ) or a dominant biocrust cyanobacterium ( Microcoleus vaginatus ), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates ( Bosea sp._L1B56, Pseudarthrobacter sp. _ L1D14 and Pseudarthrobacter picheli_ L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B . distachyon exudates, and supplementation of plant growth medium with this metabolite increased B . distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth‐promoting microbes and metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

ABSTRACT The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography–mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas . Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress. IMPORTANCE The development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Abstract Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome

Camelina ( Camelina sativa L.) is a potential biofuel crop and beneficial rotation crop in dryland cropping systems. Little is known about camelina microbiota or the legacy effect of soil origin/cropping system zones on camelina-associated microbiome assembly. To explore camelina-microbe associations, we grew camelina in the greenhouse using soil transplanted from 33 locations in the dryland wheat production area of eastern Washington. Bacterial, archaeal, and fungal communities from bulk soil, rhizosphere, and endosphere were characterized with 16S rRNA and internal transcribed spacer amplicon sequencing and were analyzed alongside site-specific climatic and edaphic data. We found that soil from the highest precipitation zone had higher alpha diversity than soil from the driest zone, but this effect was not seen in the greenhouse rhizosphere or endosphere. Plant compartment, cropping system zone, and soil origin all significantly influenced microbial composition, with soil pH and organic matter, as well as precipitation at origin, as major predictors. Analysis of abundance–occupancy distributions showed that the Actinobacteriota Aeromicrobium and Marmoricola and the fungus Pseudogymnoascus in the rhizosphere were plant-selected, while the endosphere was characterized by a number of Actinobacteriota, Rhizobium, and Clostridium. Sphingomonas amplicon sequence variants were also consistently enriched in the rhizosphere, suggesting that they are present in soils collected throughout eastern Washington and may represent good candidate biostimulants. Several lignin decomposing fungi had site-specific rhizospheric distributions, suggesting that they may be dispersal-limited or result from the legacy effect of long-term wheat cropping. Overall, this study contributes to our understanding of microbiome assembly in and on camelina roots while also highlighting the potential impact of cropping history on soil- and plant-associated microbiomes. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.

Barnes, Elle M↗
DOE OSTI2021

Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi

Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor’s microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with Pinus taeda (native host) and Populus trichocarpa (non-native host). Gene expression of interacting fungal and bacterial rhizosphere communities was compared among three plant-pairs: Populus growing with Populus , Populus with Pinus , and Pinus with Pinus . Our results demonstrate that heterospecific plant partners affect the assembly of root microbiomes, including the changes in the structure of host specific community. Comparative metatranscriptomics reveals that several species of ectomycorrhizal fungi (EMF) and saprotrophic fungi exhibit different patterns of functional and regulatory gene expression with these two plant hosts. Heterospecific plants affect the transcriptional expression pattern of EMF host-specialists (e.g., Pinus -associated Suillus spp.) on both plant species, mainly including the genes involved in the transportation of amino acids, carbohydrates, and inorganic ions. Alteration of root microbiome by neighboring plants may help regulate basic plant physiological processes via modulation of molecular functions in the root microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Abiotic Stress Reorganizes Rhizosphere and Endosphere Network Structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses, such as water and nutrient limitation. Although the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe–microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments, as well as an increase in the modularity and proportion of positive associations, which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. Although stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks, likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

09 BIOMASS FUELS↗
DOE OSTI2024

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

ABSTRACT Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change. IMPORTANCE Microbiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus ), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla

Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition

Protists, in particular bacterivores, are essential players in the rhizosphere; thus, how their interactions with bacteria and fungi affect plant productivity and soil nutrient cycles warrants more attention. Using next-generation sequencing of the 18 S rRNA gene, we investigated the distribution of two major protistan phyla, Cercozoa and Endomyxa, across four seasons, and four soil compartments - rhizosphere, root, soil and litter. The sampling was replicated in two forests in Norway and the Czech Republic, in order to test our results across biogeographic scales. Compartment had a major influence in shaping protistan communities, over and above spatial distance and seasonal variation. Protistan diversity was highest in the bulk soil while lowest in the roots, suggesting that the plants select for restricted assemblages of protists. Accordingly, only the root compartment harboured a subset of the bulk soil protistan diversity. In addition, protistan communities showed markedly different distributions according to their feeding modes, with opposite patterns for bacterivores versus omnivores and eukaryvores. The small bacterivorous flagellates (mostly Glissomonadida) were more abundant in roots, while the larger amoeboid eukaryvores (e.g. some of the Cryomonadida and vampyrellids) dominated in soil and in the rhizosphere, and the omnivores (e.g. Euglyphida and part of the Cercomonadida), also large and mostly amoeboid, were more abundant in litter. The current view of the soil microbiome is mostly focused on bacteria and fungi: this detailed study on the community distribution of protists according to their feeding modes reveals the essential role they play in each of the soil compartments, an essential precondition for a detailed understanding of the soil food web and nutrient cycling in forest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities

ABSTRACT Terpenes are among the oldest and largest class of plant-specialized bioproducts that are known to affect plant development, adaptation, and biological interactions. While their biosynthesis, evolution, and function in aboveground interactions with insects and individual microbial species are well studied, how different terpenes impact plant microbiomes belowground is much less understood. Here we designed an experiment to assess how belowground exogenous applications of monoterpenes (1,8-cineole and linalool) and a sesquiterpene (nerolidol) delivered through an artificial root system impacted its belowground bacterial and fungal microbiome. We found that the terpene applications had significant and variable impacts on bacterial and fungal communities, depending on terpene class and concentration; however, these impacts were localized to the artificial root system and the fungal rhizosphere. We complemented this experiment with pure culture bioassays on responsive bacteria and fungi isolated from the sorghum rhizobiome. Overall, higher concentrations (200 µM) of nerolidol were inhibitory to Ferrovibrium and tested Firmicutes. While fungal isolates of Penicillium and Periconia were also more inhibited by higher concentrations (200 µM) of nerolidol, Clonostachys was enhanced at this higher level and together with Humicola was inhibited by the lower concentration tested (100 µM). On the other hand, 1,8-cineole had an inhibitory effect on Orbilia at both tested concentrations but had a promotive effect at 100 µM on Penicillium and Periconia . Similarly, linalool at 100 µM had significant growth promotion in Mortierella , but an inhibitory effect for Orbilia . Together, these results highlight the variable direct effects of terpenes on single microbial isolates and demonstrate the complexity of microbe-terpene interactions in the rhizobiome. Importance Terpenes represent one of the largest and oldest classes of plant-specialized metabolism, but their role in the belowground microbiome is poorly understood. Here, we used a “rhizobox” mesocosm experimental set-up to supply different concentrations and classes of terpenes into the soil compartment with growing sorghum for 1 month to assess how these terpenes affect sorghum bacterial and fungal rhizobiome communities. Changes in bacterial and fungal communities between treatments belowground were characterized, followed by bioassays screening on bacterial and fungal isolates from the sorghum rhizosphere against terpenes to validate direct microbial responses. We found that microbial growth stimulatory and inhibitory effects were localized, terpene specific, dose dependent, and transient in time. This work paves the way for engineering terpene metabolisms in plant microbiomes for improved sustainable agriculture and bioenergy crop production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic Distribution

Switchgrass (Panicum virgatum L.) has been championed as a promising bioenergy crop due to its high productivity across a wide environmental range. The switchgrass microbiome—including bacteria, archaea, fungi, and other microbiota inhabiting soil and plant tissues—can influence plant function substantially. We conducted a review of the literature investigating switchgrass microbiome structure, key functional roles, and taxa isolated from field-grown plants. Although site conditions and plant compartment (i.e., location within shoots, roots, or root-influenced soil) appear to be the strongest drivers of switchgrass microbiome structure, the microbiome is also shaped by climate, season, and host genotype. Studies comparing across plant species show that the switchgrass microbiome is more similar to the microbiomes of other perennial plants than to the microbiomes of annual plants. Members of the switchgrass microbiome confer several benefits to their host. Most notably, mycorrhizal fungi can increase plant biomass many-fold, associative nitrogen-fixing bacteria can provide a substantial portion of the plant’s nitrogen demand, and fungal endophytes can improve plant tolerance to drought. Although the fungi and bacteria cultured from switchgrass represent only a portion of the microbiome, these serve as a valuable resource for researchers interested in investigating functional outcomes of the switchgrass microbiome. We highlight areas where additional research is necessary for a more comprehensive understanding of switchgrass microbiome structure, function, and potential to enhance sustainable bioenergy production. Key gaps include the role of understudied organisms (e.g., viruses, microeukaryotes, and nonmycorrhizal fungi), multitrophic relationships, mechanisms underpinning switchgrass–microbiome interactions, and field-scale validation of experimental findings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Fabricated devices for performing bacterial-fungal interaction experiments across scales

Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress

Cowpea is one of the major legumes cultivated in arid and semiarid regions of the world. Four soil-microbial samples (SS-1 through SS-4) collected from semiarid soils in Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, which were grown under salinity stress to analyze bacterial composition in the rhizosphere and within nodules using cultivation-dependent and -independent methods. Two varieties, 603 and the salt-tolerant CB 46, were each inoculated with or without the four different native soil samples or grown in medium either N-deficient (-N) or supplemented with N (+N). Plants inoculated with soil samples SS-2 and SS-4 grew better than plants inoculated with SS-1- and SS-3 and grew comparably with the +N controls. Environmental DNA (eDNA) was isolated from SS-1 and SS-4, and, by 16S ribosomal RNA sequencing, the soil microbiomes consisted mainly of Actinobacteria, Firmicutes, Proteobacteria, and other nonproteobacterial genera. However, analysis of eDNA isolated from cowpea nodules established by the trap plants showed that the nodule microbiome consisted almost exclusively of proteobacterial sequences, particularly species of Bradyrhizobium. Bacteria were isolated from both soils and nodules, and 34 of the 51 isolates tested positive for plant-growth-promoting rhizobacteria traits in plate assays. Many could serve as future inocula for crops in arid soils. The discrepancy between the types of bacteria isolated by culturing bacteria isolated from surface-sterilized cowpea nodules (proteobacteria and nonproteobacteria) versus those detected by sequencing DNA isolated from the nodules (proteobacteria) from cowpea nodules (proteobacteria and nonproteobacteria) versus those detected in the nodule microbiome (proteobacteria) needs further study.

59 BASIC BIOLOGICAL SCIENCES↗