Biology subjects

Barnett, S. E.

Publications and source records attributed to Barnett, S. E..

10 recordsLinked to original sources

bioRxiv2026

Biotic versus environmental controls on microbial degradation of permafrost organic matter

Permafrost thaw exposes ancient organic matter to microbial degradation, which is predicted to release globally significant quantities of greenhouse gases into the atmosphere. Though microorganisms drive these processes, the relative importance of biotic (taxonomic and functional community composition) versus environmental (e.g., soil physicochemistry) drivers and their interactions are unknown. Using a novel in situ thaw experiment conducted at the Cold Regions Research and Engineering Laboratorys Permafrost Tunnel near Fairbanks, Alaska, we experimentally separated the effects of soil physicochemistry and microbial communities under "real-world" thaw conditions. To simulate thaw, active layer soil, Holocene permafrost (2 kya), and Pleistocene permafrost (40 kya) were sterilized, inoculated with microbial communities from the different soils, enclosed in 0.22 {micro}m membrane bags to prevent immigration, and buried in the active layer. We retrieved the bags after two weeks and two months of thaw and characterized microbial community structure (16S rRNA and ITS2 amplicon sequencing), functional potential (metagenome sequencing), and soil organic matter (OM) composition at the molecular level (FT-ICR MS). Soil had a stronger effect on bacterial community and gene assemblages than inoculum, and the effects of inoculum were stronger and longer-lasting on community structure than functional potential. Pleistocene permafrost initially contained approximately eleven times more dissolved organic carbon than the other soils, and was enriched in OM derived from microbial necromass and low molecular weight organic acids. This carbon was rapidly depleted during thaw and OM compositional characteristics became increasingly similar to active layer and Holocene permafrost, paralleling shifts in Pleistocene permafrost functional gene profiles and bacterial community structure towards those of other soils. Overall, this work provides new insights into the susceptibility of OM to microbial degradation in compositionally distinct permafrost soils, and ways in which Pleistocene Yedoma permafrost carbon is likely to be particularly vulnerable to permafrost thaw.

microbiology↗

bioRxiv2025

Disturbance increases soil microbiome functional redundancy but decreases capacity for insurance via winnowed environmental responsiveness

Redundancy is the capacity of coexisting populations to perform similar functions, supporting stable outputs under disturbance. The insurance hypothesis proposes that diverse communities are more resilient because they can respond to varied environmental stressors. Both redundancy and insurance likely shape resilience, but their relative contributions and potential interactions remain unclear. Here, we examined functional redundancy and potential for insurance in soil microbial communities disturbed by an ongoing underground fire in Centralia, Pennsylvania, USA, using seven years of deep metagenome sequencing from heated and reference sites. Analyses of taxonomic and functional diversity showed that functional redundancy increased with disturbance intensity, driven by declines in both diversity and average genome size. Biogeochemistry-relevant metabolisms, such as carbohydrate and nitrogen pathways, showed greater per-genome investment with disturbance intensity, indicating enhanced redundancy. However, transcription factor evenness - linked to community environmental responsiveness- was lower in heated soils. Thus, prolonged disturbance that imposes a strong selection can increase redundancy and near-term stability while simultaneously diminishing insurance potential against future stress, revealing tradeoffs between these mechanisms in microbial community resilience.

ecology↗

bioRxiv2024

Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

Viruses are important components of the soil microbiome, influencing microbial population dynamics and the functions of their hosts. However, the relationships and feedbacks between virus dynamics, microbial host dynamics, and environmental disturbance is not understood. Centralia, PA, USA, is the site of an underground coal seam fire that has been burning for over 60 years. As the fire moves along the coal seam, previously heated soils cool to ambient temperature, creating a gradient of heat disturbance intensity and recovery. We examined annual soil viral population dynamics over seven consecutive years in Centralia using untargeted metagenome sequencing. Viral communities changed over time and were distinct between fire-affected and reference sites. Dissimilarity in viral communities was greater across sites (space) than within a site across years (time), and cumulative viral diversity more rapidly stabilized within a site across years than within a year across sites. There also were changes in CRISPR investment as soils cooled, corresponding to shifts in viral diversity. Finally, there were also differences in viral-encoded auxiliary metabolic genes between fire-affected and reference sites. These results indicate that despite high site-to-site soil viral diversity, there was surprising viral community consistency within a site over the years and shifting host-viral interactions in soils recovering from disturbance. Together, these results provide insights into how viral and host communities collectively respond to unpredicted environmental disturbance. HighlightsO_LIIn a seven-year annual study of temperate soils affected by an underground fire, viral communities displayed greater variability across sites (spatial) than over time (temporal). C_LIO_LIViral communities were distinct between heated and unheated soils throughout sampling. C_LIO_LISoil bacterial community composition correlated to viral community composition, though this relationship weakened when accounting for edaphic properties of soil temperature and pH. C_LIO_LISoil viral communities may be less resilient to press disturbance than their host bacterial communities. C_LIO_LIViral-host interactions may shift during soil recovery from long-term heating. C_LI

microbiology↗

bioRxiv2023

Accounting for active populations provides a new perspective on the degree and mechanisms of soil microbiome resilience

Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the "whole" bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.

microbiology↗

bioRxiv2022

Genomic features predict bacterial life history strategies in soil, as identified by metagenomic stable isotope probing

Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on tradeoffs in energy allocation to growth, resource acquisition, and survival. Such tradeoffs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multi-substrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic tradeoffs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil.

microbiology↗

bioRxiv2022

Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil

Tracking the metabolic activity of whole soil communities can improve our understanding of the transformation and fate of carbon in soils. We used stable isotope metabolomics to trace 13C from nine labeled carbon sources into the water-soluble metabolite pool of an agricultural soil over time. Soil was amended with a mixture of all nine sources, with one source isotopically labeled in each treatment. We compared changes in the 13C-enrichment of metabolites with respects to carbon source and time over a 48-day incubation and contrasted differences between soluble versus insoluble sources. Whole soil metabolite profiles varied singularly by time, while the composition of 13C-labeled metabolites differed primarily by carbon source (R2 = 0.68) rather than time (R2 = 0.07) with source-specific differences persisting throughout incubations. The 13C-labeling of metabolites from insoluble carbon sources occurred at a slower rate than soluble sources but yielded a higher average atom % 13C in metabolite markers of biomass (amino acids and nucleic acids). The 13C-enrichment of metabolite markers of biomass stabilized at between 5 - 15 atom % 13C by the end of incubations. Temporal patterns in the 13C-enrichment of TCA cycle intermediates, nucleobases (uracil and thymine), and by-products of DNA salvage (allantoin) closely tracked microbial activity. Our results demonstrate that metabolite production in soils is driven by the carbon source supplied to the community, and that the fate of carbon in metabolite profiles do not tend to converge over time as a result of ongoing microbial processing and recycling. ImportanceCarbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking 13C from supplied carbon sources into metabolite pools and biomass. We show that differences in the metabolism of sources influences the fate of carbon in soils. Heterogeneity in 13C-metabolite profiles corresponded with compositional differences in the metabolically active populations, providing a basis for how microbial community composition is correlated with the quality of soil carbon. Our study demonstrates the application of SIP-metabolomics in studying soils and identifies several metabolite markers of growth, activity, and other aspects of microbial function.

microbiology↗

bioRxiv2022

Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history

Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of 13C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are predictable from soil DNA content. Soil DNA yield is easy to measure and it predicts microbial community dynamics linked to soil carbon cycling. Originality-Significance StatementSoil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Microbial communities vary with respect to land-use, but we still have an incomplete understanding of how variation in community structure links to variation in community function. DNA stable isotope probing (DNA-SIP) is a high-resolution method that can identify specific microbial taxa that assimilate carbon in situ. We conducted a large-scale multi-substrate DNA-SIP experiment to explore differences in bacterial activity across land-use regimes. We show that microbial community dynamics vary with land-use, that these dynamics are linked to soil carbon cycling, and that they are predicted from easily measured soil properties.

microbiology↗

bioRxiv2021

Life history strategies explain bacterial activity in the soil carbon cycle

Soil microorganisms determine the fate of soil organic matter (SOM), and their activities comprise a major component of the global carbon (C) cycle. We employed a multi-substrate DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interact within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 days. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds comprised of taxa that had similar 13C assimilation dynamics. We show that C source bioavailability explained significant variation in both C mineralization dynamics and guild structure. In addition, guild structure explained significant variation in bacterial growth dynamics. We demonstrate that the observed guild structure is consistent with predictions made by bacterial life history theory. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. We interpret these findings in the context of bacterial life history strategies and their relationship to terrestrial C-cycling.

microbiology↗

bioRxiv2019

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

BackgroundDNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, MetaSIPSim, to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment.\n\nResultsThrough simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G+C content impacted the assembly of labeled genomes and subsequent binning, where high community G+C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance.\n\nConclusionsMetagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.

bioinformatics↗

bioRxiv2017

HTSSIP: an R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (q-SIP), and {Delta}BD. Currently, the computational tools to perform these analyses are either not publicly available or lack documentation, testing, and developer support. To address this shortfall, we have developed the HTSSIP R package, a toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/nick-youngblut/HTSSIP.

bioinformatics↗