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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition

Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800–3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2–3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. Furthermore, during a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The rhizosphere and cropping system, but not arbuscular mycorrhizae, affect ammonia oxidizing archaea and bacteria abundances in two agricultural soils

Arbuscular mycorrhizal fungi (AMF) form symbioses with roots that can enhance plant nutrition. While AMF have been shown to have a role in soil nitrogen (N) cycling, it is unclear whether AMF affect N cycling microbes such as ammonia-oxidizing bacteria (AOB) and archaea (AOA), which convert ammonium into nitrite in the first step of nitrification. In this study, we examined the effects of AMF on AOA and AOB abundances within the corn rhizosphere and bulk soil of conventional (corn-soybean rotation with inorganic fertilizer) and diversified (cornsoybean- oats/alfalfa-oats rotation with composted manure) systems. We hypothesized that AMF would decrease AOA and AOB abundances in a cropping-system dependent manner, possibly due to competition for ammonium. We grew corn deficient or proficient in AMF symbiosis in microcosms for 10 weeks. At the end of the experiment, both soils planted with the AMF-proficient corn genotype had higher ammonium and lower nitrate pool sizes compared to the same soils planted with the AMF-deficient corn genotype. Likewise, total plant N was higher in the AMF-proficient genotype compared to the AMF-deficient genotype. Despite changes in soil inorganic N pool sizes, AOA and AOB abundances were unaffected by plant AMF-proficiency. Instead, AOA abundance was greater in the rhizosphere than in the bulk soil regardless of cropping system, and AOB abundance was greater in the conventional than the diversified cropping system soil regardless of proximity to the root. These data indicate that 1) AMF did not affect AOA or AOB abundance in these N-rich soils but other factors such as root proximity and inorganic fertilization did and 2) AOA and AOB have differing ecological niches within rhizosphere and bulk soil that should be considered when managing for nitrogen losses.

Wattenburger, Cassandra↗
DOE OSTI2023

Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform

Abstract Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae . We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.

09 BIOMASS FUELS↗
DOE OSTI2021

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants ( Panicum virgatum ) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The direct and indirect drivers shaping RNA viral communities in grassland soils

ABSTRACT Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Urbanization drives convergence in soil profile texture and carbon content

Urban development has driven extensive modification of the global landscape. This shift in land use and land cover alters ecological functioning, and thereby affects sustainable management agendas. Urbanization fundamentally reshapes the soils that underlay landscapes, and throughout the soil profile, extends impacts of urbanization far below the landscape surface. The impacts of urbanization on deeper soils that are beyond the reach of regular land management are largely unknown, and validation of general theories of convergent ecosystem properties are thwarted by a dearth of both level of measurement effort and the substantial heterogeneity in soils and urban landscapes. Here, we examined two soil properties with strong links to ecological functioning—carbon and mineral-fraction particle size—measured in urban soils, and compared them to their pre-urbanization conditions across a continental gradient encompassing global soil diversity. We hypothesized that urbanization drove convergence of soils properties from heterogeneous pre-urban conditions towards homogeneous urban conditions. Based on our observations, we confirm the hypothesis. Both soil carbon and particle size converged toward an intermediate value in the full data distribution, from pre-urban to urban conditions. These outcomes in urban soils were observed to uniformly be fine textured soils with overall lower carbon content. Although these properties are desirable for supporting urban infrastructure (e.g. buildings, pipes), they constrain the potential to render ecosystem services. Since soil profile texture and carbon content were convergent and observed across 11 cities, we suggest that these property profiles can be used as a universal urban soil profile to: 1) provide a clear prediction for how urbanization will shift soil properties from pre-urban conditions, 2) facilitate the adoption of commonly-accepted soil profiles for process models, and 3) offer a reference point to test against urban management strategies and how they impact soil resources.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal-associated trees

Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait-based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon-specific and community-wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition-induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. In conclusion, our study also highlights the potential of employing qSIP in conjunction with trait-based analytical approaches to inform how ecological processes of microbial communities influence soil functioning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

ABSTRACT Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics. IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

DPSIR-ESA Vulnerability Assessment (DEVA) Framework: Synthesis, Foundational Overview, and Expert Case Studies

Land resources are central to understanding the relationship between humans and their environment. We broadly define a land resource to include all the ecological resources of climate, water, soil, landforms, flora, and fauna, and all the socioeconomic systems that interact with agriculture, forestry, and other land uses within some system boundary. Understanding the vulnerability of land resources to changes in land management or climate forcing is critical to developing sustainable land management strategies. Vulnerability assessments are complex given the multiple uses of the assessments, the multi-disciplinary nature of the problem, limited understanding, the dynamic structure of vulnerability, scale issues, and problems with identifying effective vulnerability indicators. Here, we propose a novel conceptual framework for vulnerability assessments of land resources that combines the driver– pressure–state–impact–response (DPSIR) framework adopted by the European Environment Agency to describe interactions between society and the environment, and the exposure-sensitivity-adaptive capacity (ESA) framework used by the Intergovernmental Panel on Climate Change to assess impacts of climate change. The DPSIR-ESA Vulnerability Assessment (DEVA) framework operationalizes the process of assessing the vulnerability of a target system to external stressors. The DEVA framework includes the following elements: 1) Definition of the target system (Land resource), 2) Description of internal characteristics of the target system (State), 3) Description of target system vulnerability indicators (Adaptive capacity, Sensitivity), 4) Description of stressor characteristics (Drivers, Pressures), 5) Description of stressor vulnerability indicators (Exposure), 6) Description of target system response to stressors (Impacts), and 7) Description of modifications to target systems or stressors (Responses). In stating that they have “applied the DEVA framework”, analysts acknowledge that they have (a) considered the full breadth of each DEVA element, (b) have made conscious decisions to limit the scope and complexity of certain elements, and (c) can communicate both the rationale for these decisions and the impact of these decisions on the vulnerability assessment results and recommendations. The DEVA framework was refined during invited presentations and follow-up discussions from a series of Special Sessions with leading experts at two successive ASABE Annual International Meetings. Six case studies drawn from the sessions elaborate upon the DEVA framework and provide concrete examples of the key concepts. The DEVA approach gives engineers, planners, and analysts a new, flexible framework to apply a broad array of useful tools toward assessment of land resource system vulnerability.

Anandhi, Aauvadi↗
DOE OSTI2024

Genomic fingerprints of the world’s soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Multidecadal Biological Monitoring and Abatement Program assessing human impacts on aquatic ecosystems within the Oak Ridge Reservation in eastern Tennessee, USA

Human activities can be powerful drivers of ecosystem change within catchments. While most long-term catchment studies have been conducted at pristine sites, such studies are less common from sites more impacted by human activity. The Oak Ridge National Laboratory's Biological Monitoring and Abatement Program (BMAP) was developed in the mid-1980s to (1) assess compliance with environmental regulations, (2) identify causes of adverse ecological impacts, (3) provide data for human and ecological risk assessments, and (4) evaluate the effectiveness of remedial actions taken to mitigate the impacts of contaminants in soils, groundwater, and surface water by documenting ecological recovery on the Oak Ridge Reservation (ORR), a federally owned 33,476-acre site in eastern Tennessee, USA, managed by the U.S. Department of Energy. The ORR is composed of multiple watersheds containing many small to mid-size streams. BMAP uses an integrated approach for determining stream health; its databases include long-term seasonal records of contaminant concentrations in water and biota, data from aquatic toxicity testing, and surveys of macroinvertebrate and fish assemblages from impacted and reference streams. These long-term data provide valuable records of degradation and recovery in catchment ecosystems. Our objective in this work is to describe our study system and data series in order to increase awareness of the availability of these long-term data to the catchment science community.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Future increase in compound soil drought-heat extremes exacerbated by vegetation greening

Compound soil drought and heat extremes are expected to occur more frequently with global warming, causing wide-ranging socio-ecological repercussions. Vegetation modulates air temperature and soil moisture through biophysical processes, thereby influencing the occurrence of such extremes. Global vegetation cover is broadly expected to increase under climate change, but it remains unclear whether vegetation greening will alleviate or aggravate future increases in compound soil drought-heat events. Here, using a suite of state-of-the-art model simulations, we show that the projected vegetation greening will increase the frequency of global compound soil drought-heat events, equivalent to 12-21% of the total increment at the end of 21st century. This increase is predominantly driven by reduced albedo and enhanced transpiration associated with increased leaf area. Although greening-induced transpiration enhancement has counteracting cooling and drying effects, the excessive water loss in the early growing season can lead to later soil moisture deficits, amplifying compound soil drought-heat extremes during the subsequent warm season. These changes are most pronounced in northern high latitudes and are dominated by the warming effect of CO 2 . Our study highlights the necessity of integrating vegetation biophysical effects into mitigation and adaptation strategies for addressing compound climate risks.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2023

New York Ecological Conservation: Evaluating Agricultural Conservation Easement Impact Using Earth Observations to Examine Avoided Soil Carbon Loss to Development

Farmland provides ecosystems and communities with services ranging from habitat conservation to food security. As total U.S. farmland continues to decline, agricultural lands near urban areas are especially vulnerable. Our project partners—Finger Lakes Land Trust, Genesee Land Trust, and Saratoga Preserving Land and Nature (PLAN)—can use study results to better profile farmland vulnerability, issuing conservation easements to protect maximum acreage in Saratoga County and the Finger Lakes Region of New York. Multiple existing studies effectively use remote sensing imagery to analyze historical land cover and forecast future change. This study examined soil carbon stocks and land cover change to estimate avoided soil carbon loss. We also predicted farmland vulnerability. We completed these analyses using European Space Agency (ESA) and NASA Earth observations that include Landsat 5 Thematic Mapper (TM), Landsat 8 Operational Land Imager (OLI), Landsat 9 OLI-2, Sentinel-2 Multispectral Instrument (MSI), and Suomi National Polar-Orbiting Partnership (NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) for nighttime lights data that aided in the land change model analysis. We determined that the conversion of agriculture to development from 1990 to 2022 occurred at rates of 0.91% (Finger Lakes) and 7% (Saratoga). Urban development is predicted to increase surrounding urban centers through 2030 and 2050. We also estimate that between 26.5 and 348,101 kilotons (Finger Lakes) and 3.7 and 58,006 kilotons (Saratoga) of soil carbon losses have been avoided through agricultural easements. Findings from this study will support our partners in determining agricultural conservation easement benefits and prioritizing the acquisition of future easement sites.

Agriculture↗
DOE OSTI2021

Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy

Abstract In studying problems like plant‐soil‐microbe interactions in environmental biogeochemistry and ecology, one usually has to quantify and model how substrates control the growth of, and interaction among, biological organisms (and abiotic factors, e.g., adsorptive mineral soil surfaces). To address these substrate‐consumer relationships, many substrate kinetics and growth rules have been developed, including the famous Monod kinetics for single‐substrate‐based growth and Liebig's law of the minimum for multiple‐nutrient‐colimited growth. However, the mechanistic basis that leads to these various concepts and mathematical formulations and the implications of their parameters are often quite uncertain. Here, we show that an analogy based on Ohm's law in electric circuit theory is able to unify many of these different concepts and mathematical formulations. In this Ohm's law analogy, a resistor is defined by a combination of consumers’ and substrates’ kinetic traits. In particular, the resistance is equal to the mean first passage time that has been used to derive the Michaelis‐Menten kinetics under substrate replete conditions for a single substrate as well as the predation rate of individual organisms. We further show that this analogy leads to important insights on various biogeochemical problems, such as (a) multiple‐nutrient‐colimited biological growth, (b) denitrification, (c) fermentation under aerobic conditions, (d) metabolic temperature sensitivity, and (e) the legitimacy of Monod kinetics for describing bacterial growth. We expect that our approach will help both modelers and nonmodelers to better understand and formulate hypotheses when studying certain aspects of environmental biogeochemistry and ecology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Abstract Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12 family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗