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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Genomic signatures in Variovorax enabling colonization of the Populus endosphere

Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.

comparative genomics↗
DOE OSTI2022

Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles

Lava caves, tubes, and fumaroles in Hawai‘i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing methods, we investigated the phylogenetic distinctness and diversity and identified microbial interactions and consortia through co-occurrence networks in 70 samples from lava tubes, geothermal lava caves, and fumaroles on the island of Hawai‘i. Our data illustrate that lava caves and geothermal sites harbor unique microbial communities, with very little overlap between caves or sites. We also found that older lava tubes (500–800 yrs old) hosted greater phylogenetic diversity (Faith's PD) than sites that were either geothermally active or younger (<400 yrs old). Geothermally active sites had a greater number of interactions and complexity than lava tubes. Average phylogenetic distinctness, a measure of the phylogenetic relatedness of a community, was higher than would be expected if communities were structured at random. This suggests that bacterial communities of Hawaiian volcanic environments are phylogenetically over-dispersed and that competitive exclusion is the main driver in structuring these communities. This was supported by network analyses that found that taxa (Class level) co-occurred with more distantly related organisms than close relatives, particularly in geothermal sites. Network “hubs” (taxa of potentially higher ecological importance) were not the most abundant taxa in either geothermal sites or lava tubes and were identified as unknown families or genera of the phyla, Chloroflexi and Acidobacteria. These results highlight the need for further study on the ecological role of microbes in caves through targeted culturing methods, metagenomics, and long-read sequence technologies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

UFMP and CAW Bioreactor Metagenome

CSTR anaerobic bioreactors fed UltraFiltered Milk Permeate (UFMP) and Cottage cheese Acid Whey (CAW) were inoculated with acid sludge microbial communities and monitored overtime for lactic acid production. Samples were taken for metagenomics analyses.

bioreactor metagenome↗
DOE OSTI2021

The Influence of Bacteria on the Growth, Lipid Production, and Extracellular Metabolite Accumulation by Phaeodactylum tricornutum (Bacillariophyceae)

Here, to examine the impact of heterotrophic bacteria on microalgal physiology, we co-cultured the diatom Phaeodactylum tricornutum with six bacterial strains to quantify bacteria-mediated differences in algal biomass, total intracellular lipids, and for a subset, extracellular metabolite accumulation. A Marinobacter isolate significantly increased algal cell concentrations, dry biomass, and lipid content compared to axenic algal cultures. Two other bacterial strains from the Bacteroidetes order, of the genera Algoriphagus and Muricauda, significantly lowered P. tricornutum biomass, leading to overall decreased lipid accumulation. These three bacterial co-cultures (one mutualistic, two competitive) were analyzed for extracellular metabolites via untargeted liquid chromatography mass spectrometry to compare against bacteria-free cultures. Over 80% of the extracellular metabolites differentially abundant in at least one treatment were in higher concentrations in the axenic cultures, in agreement with the hypothesis that the co-cultured bacteria incorporated algal-derived organic compounds for growth. Furthermore, the extracellular metabolite profiles of the two growth-inhibiting cultures were more similar to one another than the growth-promoting co-culture, linking metabolite patterns to ecological role. Our results show that algal–bacterial interactions can influence the accumulation of intracellular lipids and extracellular metabolites, and suggest that utilization and accumulation of compounds outside the cell play a role in regulating microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Microdiverse bacterial clades prevail across Antarctic wetlands

Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genomes to ecosystem function: Targeting critical knowledge gaps in methanogenesis and translation to updated global biogeochemical models

Natural freshwater temperate wetland systems currently represent the largest natural source of atmospheric methane, but are relatively understudied using systems biology tools (e.g. meta-omics) compared to other high producing methane systems (e.g. peat, tropical, or reconstructed wetlands). Using field investigations at the NOAA operated sentinel site on Lake Erie, methane producing activities and responses to geochemical conditions will be determined along seasonal and spatial gradients (Objective 1). Here, a combination of high-throughput activity and gas measurements, combined with high-resolution systems biology and analytical methods, will provide in depth knowledge of the microbiological, chemical, and physical constraints on methane production in wetlands. Using laboratory microcosms, the formation of anoxic microsites and their capacity to facilitate methane production in wetland soils will be simulated (Objective 2). This objective will validate the findings from the field investigations, offering a more controlled environment for teasing out the role of different yet interrelated variables. Lastly, these field and laboratory data will be used for multi-scale, process-level evaluation of an ecosystem biogeochemical model that accommodates these newly identified processes and parameterizes representation of these processes along relevant environmental gradients (Objective 3).This research will identify multiple interacting geochemical, ecological, and metabolic constraints that are poorly understood, oversimplified, or missing in global biogeochemical methane models. This proposal targets the role of oxygen limitation on methane processes in soil domains, to improve reactive transport models of microbial carbon cycling across terrestrial-aquatic soils and generate data on nutrient cycling activities in Great Lake wetlands. This information could provide new insights into the microbial controllers of Lake Erie eutrophication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Integrating microbial communities into algal biotechnology: a pathway to enhanced commercialization

Microalgae are increasingly recognized for their potential in wastewater treatment and the sustainable production of feedstock for fuel, feed, food, and other bioproducts. Like conventional agricultural systems, algal cultivation involves complex microbial communities. However, despite their pivotal role in cultivation outcomes, especially at the commodity-scale, the critical interactions between microalgae and their microbiomes are often overlooked. Here we synthesize current knowledge on the taxonomic diversity, ecological roles, and biotechnological potential of algal microbiomes, with a focus on their interactions with algal hosts through nutrient exchange, growth modulation, pathogen defense, and environmental conditioning. We also examine how environmental factors such as nutrient availability, salinity, and temperature influence these interactions. Advances in microbiome engineering, including synthetic biology and ecological approaches, offer opportunities to enhance beneficial algal-microbiome interactions, thereby improving growth, resilience, and yield. These advancements could lead to more sustainable and economically viable microalgae cultivation, with far-reaching implications for environmental management and biotechnological innovation. By addressing key economic and environmental barriers, microbiome engineering holds transformative potential to revolutionize large-scale algae cultivation and provide sustainable solutions to global challenges.

Microbiology↗
DOE OSTI2024

Soil microbiome interventions for carbon sequestration and climate mitigation

Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Climate, soil mineralogy and mycorrhizal fungi influence soil organic matter fractions in eastern US temperate forests

Identifying the primary controls of particulate (POM) and mineral-associated organic matter (MAOM) content in soils is critical for determining future stocks of soil carbon (C) and nitrogen (N) across the globe. However, drivers of these soil organic matter fractions are likely to vary among ecosystems in response to climate, soil type and the composition of local biological communities. We tested how soil factors, climate and plant–fungal associations influenced the distribution and concentrations of C and N in MAOM and POM in seven temperate forests in the National Ecological Observatory Network (NEON) across the eastern United States. Samples of upper mineral horizon soil within each forest were collected in plots representing a gradient of dominant tree–mycorrhizal association, allowing us to test how plant and microbial communities influenced POM and MAOM across sites differing in climate and soil conditions. We found that concentrations of C and N in soil organic matter were primarily driven by soil mineralogy, but the relative abundance of MAOM versus POM C was strongly linked to plot-level mycorrhizal dominance. Furthermore, the effect of dominant tree mycorrhizal type on the distribution of N among POM and MAOM fractions was sensitive to local climate: in cooler sites, an increasing proportion of ectomycorrhizal-associated trees was associated with lower proportions of N in MAOM, but in warmer sites, we found the reverse. As an indicator of soil carbon age, we measured radiocarbon in the MAOM fraction but found that within and across sites, Δ 14 C was unrelated to mycorrhizal dominance, climate, or soil factors, suggesting that additional site-specific factors may be primary determinants of long-term SOM persistence. Our results indicate that while soil mineralogy primarily controls SOM C and N concentrations, the distribution of SOM among density fractions depends on the composition of vegetation and microbial communities, with these effects varying across sites with distinct climates. Here we also suggest that within biomes, the age of mineral-associated soil carbon is not clearly linked to the factors that control concentrations of MAOM C and N.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Soil viruses: Understudied agents of soil ecology

Over the past couple decades there has been intense exploration of the soil microbiome using modern sequencing and bioinformatics approaches. These studies have revealed a vast diversity of microorganisms across a variety of habitats (Thompson et al., 2017) and how differences in the environment, for example with climate change, influence the soil microbial community composition (Jansson and Hofmockel, 2020). The focus of these studies has primarily been on microbial cellular organisms, including bacteria, archaea and fungi. By contrast, in depth study of soil viruses has been largely neglected, until recently. There are several reasons that soil viruses are less studied, including difficulties with extraction of viruses from soil particles, difficulties with classification of soil viruses based on microscopic imaging, and reliance on the small proportion of microbial hosts that can be cultivated. Now that comprehensive soil metagenomes are available the current trend has been to survey the metagenomes for viral sequences. This approach has revealed that soil viruses are incredibly abundant, highly diverse, and largely uncharacterized (Paez-Espino et al., 2016). This so-called ‘viral dark matter’ presents an incredible research opportunity for the future. Here I will highlight some of these potential research avenues based on what is known to date.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Hyporheic Oxygen Dynamics in the East River, Colorado: Insights From an In–Situ, High Frequency Time Series During Two Distinct Flow Seasons

Dissolved oxygen (DO) is critical for aquatic ecosystems, however, few studies have focused on the long-term DO dynamics in hyporheic zones, which are a function of both transport (hydrologic exchange between river and hyporheic zone) and uptake by biogeochemical reactions or respiration. We explore the dynamics of temperature and DO at 10, 20, and 35 cm depth beneath the East River, Colorado, from July–October 2017 (relatively normal water year) and April to October 2018 (comparatively low flow year), enabled by distinctive, in-situ, high frequency (Δt = 5 min) sensors that provided continuous time-series from the undisturbed study site over 14 months. We expect that hyporheic DO, which has a regular daily fluctuation pattern, is supplied by the surface water (at all times we estimate downwelling) and that diurnal hyporheic DO temporal patterns should be aligned with diurnal hyporheic temperature patterns. However, this was not found to be the case. Hyporheic DO becomes depleted briefly at 20 and 35 cm depths in 2017, and at all three hyporheic depths for extended periods in 2018. Whereas diurnal temperature fluctuations have consistent timings of maxima and minima, hyporheic DO rarely has as regular a pattern, and daily ranges are inconsistent. Rainfall events caused some of these changes to diurnal hyporheic DO patterns without repeatable effects. Antecedent snowpack conditions influence streamflow dynamics and therefore hyporheic DO dynamics in this alpine river. These results also point to the strong and variable influence of hyporheic microbial communities regulating hyporheic DO.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean.

Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. Here, we showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Rapid eco‐phenotypic feedback and the temperature response of biomass dynamics

Biomass dynamics capture information on population dynamics and ecosystem-level processes (e.g., changes in production over time). Understanding how rising temperatures associated with global climate change influence biomass dynamics is thus a pressing issue in ecology. The total biomass of a species depends on its density and its average mass. Consequently, disentangling how biomass dynamics responds to increasingly warm and variable temperatures ultimately depends on understanding how temperature influences both density and mass dynamics. Here, we address this issue by keeping track of experimental microbial populations growing to carrying capacity for 15 days at two different temperatures, and in the presence and absence of temperature variability. We develop a simple mathematical expression to partition the contribution of changes in density and mass to changes in biomass and assess how temperature responses in either one influence biomass shifts. Moreover, we use time-series analysis (Convergent Cross Mapping) to address how temperature and temperature variability influence reciprocal effects of density on mass and vice versa. We show that temperature influences biomass through its effects on density and mass dynamics, which have opposite effects on biomass and can offset each other. We also show that temperature variability influences biomass, but that effect is independent of any effects on density or mass dynamics. Last, we show that reciprocal effects of density and mass shift significantly across temperature regimes, suggesting that rapid and environment-dependent eco-phenotypic dynamics underlie biomass responses. Overall, our results connect temperature effects on population and phenotypic dynamics to explain how biomass responds to temperature regimes, thus shedding light on processes at play in cosmopolitan and abundant microbes as the world experiences increasingly warm and variable temperatures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling

The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N 2 O) from the tropics. Toward closing these knowledge gaps, in this study we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N 2 O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N 2 O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ~45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta

The choanoflagellate Salpingoeca rosetta exemplifies the capacity of marine microeukaryotes to integrate environmental cues into their life histories. Some of the cues that S. rosetta detects are lipids from their bacterial prey that induce the development of multicellular colonies called rosettes. In the aquatic environments where S. rosetta would encounter bacterial cues, microbial communities gain refuge and food from algae. For example, microbes in coastal environments benefit from macroalgae that annually release ∼10 14 g of carbon, primarily in the form of polysaccharides that comprise ∼80% of dissolved organic carbon in surface waters. Despite the ecological impact of algae and historical descriptions of choanoflagellates attached to algae, the influence of algae on choanoflagellate life history transitions has remained unexplored. Here, we report that porphyran, a polysaccharide produced by the red macroalga Porphyra umbilicalis, induces multicellular development in S. rosetta. We first noticed this response when S. rosetta formed multicellular rosette colonies while growing in media prepared from P. umbilicalis, even though rosette-inducing bacteria were absent. By biochemically purifying extracts of P. umbilicalis, we identified porphyran as the rosette-inducing factor. This response provides a biochemical insight that indicates algal polysaccharides may serve as cues to mediate associations between choanoflagellates and algae. Moreover, this observation complements evidence from environmental and geochemical studies that show the impact that algae have exerted on the ecology and evolution of eukaryotes, including a rise in algal productivity during the origin of animals, the closest living relatives of choanoflagellates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

59 BASIC BIOLOGICAL SCIENCES↗