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At least 199 records · Page 11

How deep should we go to understand roots at the top of the world?

Harsh environmental conditions and the short summers of northern, high-latitude biomes impose unique constraints on the plants that live in the arctic tundra and the boreal forest. To escape the harsh aboveground environment, plants in these habitats often allocate a large portion of their biomass belowground to facilitate nutrient acquisition. In turn, the proximity of living plant roots to vast stores of sequestered soil carbon in these biomes means that shifts in rooting depth distribution and the size of the root–soil interface could significantly contribute to ongoing climate change. Indeed, plant ‘priming’ of rhizosphere decomposition via root exudation, particularly from shallowly distributed roots, can lead to losses of carbon from tundra soils. While we have a hard-won understanding of the distribution of plant communities across the arctic tundra and the boreal forest from direct field observations scaled to the landscape level using climate-informed mapping techniques (i.e. the Circumpolar Arctic Vegetation Map (CAVM); Walker et al. , 2005), these vegetation maps are only the tip of the iceberg (Iversen et al. , 2015). Root form and function remain hidden beneath the land surface. In an article recently published in New Phytologist , Blume-Werry et al. (2023, 10.1111/nph.18998) asked whether rooting depth distribution, and ensuing carbon emissions, could be inferred from commonly used vegetation mapping classifications across the pan-Arctic. An important question to guide our understanding, mapping, and prediction of belowground characteristics and ecosystem feedbacks at the top of the world. Unfortunately, they found that the answer was ‘not quite’. While rooting depth distribution varied demonstrably, in turn causing substantial changes in modeled carbon emissions via rhizosphere ‘priming’, variation across rooting depth profiles did not correspond with vegetation mapping classes. If we are unable to predict belowground rooting depth distributions across large spatial scales by leveraging aboveground vegetation community distributions, how then should belowground researchers proceed?

59 BASIC BIOLOGICAL SCIENCES↗

Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO 2 in northern peatlands

Warming and elevated CO 2 (eCO 2 ) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO 2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO 2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO 2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

59 BASIC BIOLOGICAL SCIENCES↗

Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical and biotic properties of soil. However, cover crops, a group of plants that provide ecosystem services, can be utilised during fallow periods or used as an intercrop to restore soil health. The effectiveness of ecosystem services provided by cover crops varies widely as very little breeding has occurred in these species. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. In this study, we provide an overview of the range of belowground ecosystem services provided by cover crop roots: (1) soil structural remediation, (2) capture of soil resources and (3) maintenance of the rhizosphere and building of organic matter content. Based on the ecosystem services described, we outline current and promising phenotyping technologies and breeding strategies in cover crops that can enhance agricultural sustainability through improvement of root traits.

54 ENVIRONMENTAL SCIENCES↗

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↗

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↗

Data for Immediate Impacts of Soybean Cover Crop on Bacterial Community Composition and Diversity in Soil Under Long-Term Saccharum Monoculture

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.

Field Data↗

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth’s ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infectingKlebsiellasp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNAKlebsiellaphage genomes. Taxonomic analyses revealed that theseKlebsiellaphages belong to three known phage families (Autographiviridae,Drexlerviridae, andStraboviridae) and two newly proposed phage families (CandidatusMavericviridaeand Ca.Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages’ ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families,Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1–14 of our 22 bacterial strain panel that included pathogenicKlebsiellaandRaoultellastrains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build theKlebsiellamodel system for studying phage-host interactions of rhizosphere-associated bacteria.

Science & Technology - Other Topics↗

Comparing the Recovery of Arbuscular and Ectomycorrhizal Stands from Long-Term Nitrogen Fertilization at the Fernow Experimental Forest, WV (2021 and 2022)

This data was generated to answer the research question: After the end of a 30-year nitrogen (N) fertilization experiment in an Eastern temperate forest, to what extent do plant microbial interactions and carbon cycling in arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) dominated stands follow different recovery trajectories?The soil and the roots used in this dataset were sampled from two watersheds (N-fertilized watershed 3 and Reference watershed 7) with 6 AM and 6 ECM dominated stands each, over the course of three months (June, July, August) in 2021 and 2022. The "All_Roots.csv" data includes fine root biomass (in g) scaled to sampled soil (m2) (Scaled_Rt_Bm_gm2), and AM and ECM root colonization (%) in two soil fractions: the organic horizon (O) and the mineral horizon (B). The "All_Enzymes.csv" data includes extracellular soil enzyme activity (N-acetyl-glucosaminidase (NAG), acid phosphatase (AP), β-glucosidase (BG), phenol oxidase and peroxidase), and the ratios of BG to AP (BG:AP) and BG to NAG (BG:NAG) in three soil fractions: the organic horizon (O), the bulk soil (B), and the rhizosphere (R).The "All_Nmin" data includes inorganic N (NO3- and NH4+) pools (unit: μg of N per g of dry soil) measured pre- (I_Nitrate_ugNgsoil and I_Ammonia_ugNgsoil) and post-incubation (F_Nitrate_ugNgsoil and F_Ammonia_ugNgsoil), as well as calculated nitrification (Nitrification_day) and nitrogen mineralization (Mineralization_day) rates per day, in three soil fractions: the organic horizon (O), the bulk soil (B), and the rhizosphere (R).

54 ENVIRONMENTAL SCIENCES↗

Biomolecular and Characterization Imaging Science Program: 2023 Principal Investigator Meeting Proceedings

The 2023 U.S. Department of Energy (DOE) Biological and Environmental Research (BER) program’s Biomolecular Characterization and Imaging Science (BCIS) Principal Investigator Meeting expanded in scope from previous Bioimaging Science Program (BSP) meetings to include BER Structural Biology and Imaging Resources, which are located largely at DOE Office of Science national laboratories. The BCIS meeting was part of BER’s Biological Systems Science Division (BSSD) annual PI meeting, which was held April 17–19, 2023, and featured parallel meetings of the BCIS and Genomic Science programs (GSP). The meetings were held together to encourage networking and idea exchange across technologies and biological application areas, forging new multidisciplinary collaborations among researchers from adjacent BSSD programmatic areas. Two joint BCIS-GSP sessions were held: “BCIS Technologies for Investigating the Rhizosphere” and “Joint Emerging Topics and Technologies.” The rhizosphere session focused on scientific findings from BCIS and GSP PIs, including national laboratory collaborations. The intent was to identify new opportunities to measure and understand the complex community of microbes, roots, and soils that support plant growth under challenging environmental conditions. The emerging technologies session highlighted forward-looking approaches and tools to tackle challenges within the scope of BSSD research on investigating and modifying genomic and molecular function. A final interactive discussion of the BCIS program was led by plenary session chairs.

59 BASIC BIOLOGICAL SCIENCES↗

Testing mechanisms of how mycorrhizal associations affect forest soil carbon and nitrogen cycling (Final Technical Report)

Trees are in a symbiotic partnership with mycorrhizal fungi in which they provide the fungi with carbon from photosynthesis and the fungi provide the trees with nutrients and water. In temperate forests, the vast majority of trees form symbioses with one of two types of mycorrhizal fungi—arbuscular mycorrhizal (AM) fungi or ectomycorrhizal (EcM) fungi. These fungi differ in their morphology, hyphal length, and nutrient acquisition strategies. Many studies have found systematic differences in soil organic matter and nitrogen availability between forest stands dominated by AM-associating trees versus EcM-associating trees. For instance, there is a larger proportion of organic matter that is mineral-associated, more available nitrogen, and lower soil carbon to nitrogen ratios in AM forest stands relative to EcM forests stands. However, the mechanisms driving these patterns are not known, which complicates our ability to model soil organic matter dynamics in forested ecosystems. The main objective of this research was to understand the degree to which the observed differences in soil C and N dynamics between AM and EcM dominated forests are driven by tree traits like litter decomposability and root exudation versus mycorrhizal fungal nutrient acquisition strategies. We investigated these mechanisms using observations and targeted experiments and incorporated this knowledge into a process-based soil organic matter model. The observational studies compared the importance of leaf litter decomposability versus fungal identity on soil organic matter processes. We found that often fungal identity and traits were more important drivers of soil organic matter patterns than leaf litter decomposability. We ran two novel experiments: 1) a growth chamber experiment across four EcM and four AM tree species using a 13 C-labeled atmosphere to trace seedling-derived C into hyphae, the rhizosphere, and soil; and 2) an in situ decomposition experiment of six different 13 C and 15 N labeled litters that ranged in decomposability incubated across a gradient of EcM dominance at three sites that capture important variation in climate, soils, and forest species composition. In the first experiment, we found no significant differences of seedling mycorrhizal association on soil carbon sequestration over a growing season, but we did find that mycorrhizal association affected rhizodeposition with EcM-associating seedlings depositing more carbon in response to increased nitrogen availability. The decomposition experiment is still ongoing, but thus far, we have found slower litter decomposition in only one of three EcM-dominated forests which suggests that differences between AM- and EcM-dominated forests depend on the environmental context and identity of the EcM fungi. Lastly, we explicitly incorporated mycorrhizal processes into the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model creating Myco-CORPSE. By including the different nutrient acquisition strategies of AM and EcM fungi, we explored the conditions under which EcM fungi can slow decomposition rates and lead to greater soil organic carbon accumulation compared to AM fungi. We found that the effect of EcM fungi was highly context dependent and that EcM fungi decreased decomposition in colder forests with recalcitrant litter inputs and when they produced oxidases and necromass-degrading enzymes. Our research highlights the importance of fungal nutrient acquisition in driving soil organic matter patterns and the need to move beyond the AM-EcM dichotomy to consider the identity and traits of the specific fungi participating in the symbiosis. Overall, this research has resulted in six, peer-reviewed published papers in journals such as Global Change Biology, Ecology (2), Soil Biology and Biochemistry, and Ecosystems (2). There are at least two more papers in progress on this research including one that was recently submitted to Global Change Biology.

54 ENVIRONMENTAL SCIENCES↗

Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis

Background: Investigators using metagenomic sequencing to study microbiomes often trim and decontaminate reads without knowing their effect on downstream analyses. Objective: This study was designed to evaluate the impacts JGI trimming and decontamination procedures have on assembly and binning metrics, placement of MAGs into species trees, and functional profiles of MAGs extracted from complex rhizosphere metagenomes, as well as how more aggressive trimming impacts these binning metrics. Methods: Twenty-three Miscanthus x giganteus rhizosphere metagenomes were subjected to different combinations and thresholds of force, kmer, and quality trimming and decontamination using BBDuk. Reads were assembled and binned in KBase. Phylogenomic and statistical analyses were applied to evaluate the effects of trimming and decontamination on downstream analyses. Results: We found that JGI trimmed and decontaminated reads had significant impacts on assembly and binning metrics compared to raw reads, including significantly higher total contig counts, more contigs greater than 10k bp in length, and larger total lengths of raw assemblies compared to QC assemblies, and 2.0% lower average contamination of QC MAGs compared to raw MAGs. We also found that differences in the placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. Furthermore, aggressive trimming (Q20) was found to significantly reduce MAG counts. Conclusion: Trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing?” However, mild trimming and decontamination of metagenomic reads with high-quality scores are recommended for removing sample processing and sequencing artifacts.

Whitham, Jason M.↗

16s Amplicon Analysis of Soil Data for Interactive effects of depth and differential irrigation on soil microbiome composition and functioning

Genomic DNA was isolated from soil and rhizosphere samples using the Zymo Quick-DNA fecal/soil microbe miniprep kit (catalog no. D6010) according to the manufacturer’s instructions (Zymo Research; Irvine, CA) with the modification of eluting in 100 uL elution buffer. Sample concentrations were quantified using the Qubit dsDNA HS assay kit (Thermo Fisher). For rhizosphere samples only, DNA was subsequently purified using Zymo’s ZR-96 DNA Clean & Concentrator kit (catalog no. D4024) to account for low DNA concentrations of these samples. . In each replicate block, there were five drip irrigation treatments (T1 = 100% normal irrigation, T2 = 56.25%, T3 = 37.5%, T4 = 18.75% and T5=no irrigation. On July 20, the strength of the drought treatments was increased: T1 remained at 100%, whereas T2 changed from 75% to 56.25%, T2 changed from 50% to 37.5%, and T4 changed from 25% to 18.75%. Sequencing was performed as described previously (Naylor, Fansler, et al. 2020). Sequences were amplified on the MiSeq platform (Illumina, San Diego, CA) using 16S primers (515F and 806R) specific to the V4 region. Raw sequence data was processed with the pipeline Hundo for amplicon quality control and annotation. Downstream statistical analyses on 16S datasets were performed using the program R and the packages ‘phyloseq’ and ‘vegan’.

Soil microbiome, metatranscriptomics↗

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↗

A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress

Introduction: Rhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging. Methods: Here, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla. Genomic analysis of the individual strains was performed to reveal encoded plant growth-promoting traits, including genes for the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ transporters, and some predicted traits were validated by laboratory phenotypic assays. Results: The SynCom demonstrates strong stability both in vitro and in planta. Most strains encoded multiple plant growth-promoting functions, and several of these were confirmed experimentally. The presence of osmoprotectant and ion transporter genes likely contributed to the observed resilience of Brachypodium to drought stress, where plants amended with the SynCom recovered better than those without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria. Discussion: Our results demonstrate that trait-informed construction of synthetic communities can yield stable, functionally diverse consortia that enhance plant resilience under drought. Preferential colonization near root tips points to active, localized plant-microbe signaling as a component of stress-responsive recruitment. This stable SynCom provides a scalable platform for probing mechanisms of plant-microbe interaction and for developing microbiome-based strategies to improve soil and crop performance in variable environments.

Yadav, Archana↗

Soil organic matter and plant carbon allocated to nitrogen acquisition simulated by the FUN-BioCROP model

This data package contains the model input, results, and validation data from Juice et al (citation below). The FUN-BioCROP model (Fixation and Uptake of Nitrogen- Bioenergy Carbon, Rhizosphere, Organisms, and Protection) advances the field of bioenergy modeling by integrating new empirical paradigms of the role of belowground processes in shaping coupled carbon (C) and nitrogen (N) cycles. It was developed by modifying the FUN-CORPSE model (Fixation and Uptake of Nitrogen- Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment, Sulman et al. 2017 Ecology Letters) for use in bioenergy systems by including mechanistic tillage, organic matter addition, nitrogen fertilization, harvest, and feedstock-specific parameters, and to be driven by DayCent plant productivity and biomass data.

biofuel sustainability↗

Hollow fiber mid-ID spectrometer with UV laser ablation sampling for fine spatial reoslution of isotope ratios in solids

We describe a system that combines isotope ratio analysis via mid-infrared (Mid-IR) laser absorption spectroscopy with fine spatial resolution sampling using a UV pulsed laser. The UV laser ablates a pit in a solid on the order of 10 microns in diameter. The sample-derived particulates resulting from laser ablation pass through a micro-combustor, and the resulting gas is analyzed using Mid-IR laser absorption spectroscopy in a capillary absorption spectrometer (CAS). The CAS uses a hollow fiber optic waveguide with a reflective inner coating and a small internal volume on the order of 1ml. The hollow fiber both guides the laser light from source to detector and contains the gas sample at reduced pressure. Near unity overlap between the laser beam and sample enables sensitive analysis with ultra-small sample size. A prototype system has been demonstrated to enable stable carbon isotopic analysis (d13C) with 1 per mil precision using <1 picomole of carbon and is currently being used to study nutrient exchange in soil/root/microbial rhizosphere studies. The smaller sample size of this system is enabling fine spatial resolution analysis (on the order of 10 microns), which is roughly an order of magnitude smaller than was possible with an isotope ratio mass spectrometer (IRMS). In addition to rhizosphere studies, the system can provide a useful tool for fine scale isotope analysis with applications in biological, forensic, and environmental science.

capillary absorption spectroscopy, laser ablation,↗

Simulated plant-mediated oxygen input has strong impacts on fine-scale porewater biogeochemistry and weak impacts on integrated methane fluxes in coastal wetlands

Methane (CH 4 ) emissions from wetland ecosystems are controlled by redox conditions in the soil, which are currently underrepresented in Earth system models. Plant-mediated radial oxygen loss (ROL) can increase soil O 2 availability, affect local redox conditions, and cause heterogeneous distribution of redox-sensitive chemical species at the root scale, which would affect CH 4 emissions integrated over larger scales. In this study, we used a subsurface geochemical simulator (PFLOTRAN) to quantify the effects of incorporating either spatially homogeneous ROL or more complex heterogeneous ROL on model predictions of porewater solute concentration depth profiles (dissolved organic carbon, methane, sulfate, sulfide) and column integrated CH 4 fluxes for a tidal coastal wetland. From the heterogeneous ROL simulation, we obtained 18% higher column averaged CH 4 concentration at the rooting zone but 5% lower total CH 4 flux compared to simulations of the homogeneous ROL or without ROL. This difference is because lower CH 4 concentrations occurred in the same rhizosphere volume that was directly connected with plant-mediated transport of CH 4 from the rooting zone to the atmosphere. Sensitivity analysis indicated that the impacts of heterogeneous ROL on model predictions of porewater oxygen and sulfide concentrations will be more important under conditions of higher ROL fluxes or more heterogeneous root distribution (lower root densities). Despite the small impact on predicted CH 4 emissions, the simulated ROL drastically reduced porewater concentrations of sulfide, an effective phytotoxin, indicating that incorporating ROL combined with sulfur cycling into ecosystem models could potentially improve predictions of plant productivity in coastal wetland ecosystems.

54 ENVIRONMENTAL SCIENCES↗