Biology subjects

Sessions, A.

Publications and source records attributed to Sessions, A..

4 recordsLinked to original sources

bioRxiv2026

SIP-enabled multi-omics reveals soil microbiome responses to drought and rehydration

The activity of the soil microbiome, and its balance of anabolic (organic C consuming) and catabolic (CO2-releasing) reactions, determines the magnitude and direction of soil carbon fluxes. Over half a century of research has revealed that soil water dynamics are key controllers of microbial activity. With increasing hydroclimate volatility expected across many regions of the Earth, there is a greater need to describe and quantify microbial responses to drought and rehydration cycles. In this study, we conducted rainfall exclusion experiments at two archetypical Mediterranean-type field sites. After rainfall exclusion and subsequent soil rehydration, we applied a SIP-enabled, multi-omics methodology to generate a multi-faceted case study of microbial growth, greenhouse gas fluxes, and the forms of carbon that drive both. Our results indicate that rehydration increases microbial anabolic processes by orders of magnitude, shifting cell generation times from years to days within just minutes. High-intensity drought increases the lag period before microbial growth resumes, but both stable-isotope probing and metagenomic inference agree that microbial communities exhibit greater capacity for rapid growth following drought stress. Furthermore, significant shifts in the soil metabolome are observed following drought and rehydration, implicating specific osmolytes as key to the microbial response and indicating metabolite diversity as a key modulator of microbiome functioning. Together, our results provide constraints on microbial activity rates in soil and mechanisms underpinning microbial responses to drought and rewetting. These findings motivate further research into microbial responses under increasingly volatile hydroclimate regimes and downstream contributions to the global carbon cycle. Significance StatementSoil is a major global store and source of carbon. The microbiome determine the fate of soil organic carbon, and the microbiome is ultimately controlled by soil water dynamics. Early, innovative experiments by H.F. Birch defined "The Birch Effect" - the observation that soils emit CO2 following drying and subsequent rehydration. However, it remains unclear when, and to what magnitude, soil microorganisms are actively growing following this rehydration, and what biological mechanisms explain the observed CO2 pulse. In this work, we apply an array of methodologies to address this question, describing rates of microbial growth during drought and rewetting. Our results provide crucial insights into how soil microbiomes will respond to increasing hydroclimate volatility across the globe.

microbiology↗

bioRxiv2025

Cycling of sulfur redox intermediates drives microbial activity in the sulfate-methane transition zone of cold methane seeps

Microbial sulfate reduction is a cornerstone of marine sediment biogeochemistry, driving carbon remineralization and fueling the anaerobic oxidation of methane (AOM). Yet in zones of high methane flux, sulfate limitations may constrain the sulfate-reducing bacteria (SRB) and anaerobic methanotrophic archaea (ANME) that typically perform AOM. Although often overlooked, sulfur redox intermediates are readily utilized by diverse microorganisms, potentially driving AOM in sulfate-limited zones. To resolve the microbial mechanisms underlying cryptic sulfur cycling in such sediments, Monterey Canyon cold methane seeps were investigated through an integrated geochemical, isotopic, and metatranscriptomic approach. High-resolution electrochemical measurements confirmed intense sulfide production in seep sites, and long-term anoxic incubations were conducted with sediment from the SMTZ amended with elemental sulfur, thiosulfate, or sulfate as the sole sulfur source, with or without methane. Over 650 days, sulfide accumulation was greatest in elemental sulfur treatments, followed by thiosulfate and sulfate; in all cases methane addition enhanced sulfide production. Isotopic measurements showed modest S-isotope fractionation indicating that the large fractionations typical of slow sulfate reduction were muted by additional sulfur transformations. In elemental sulfur treatments, isotopic and geochemical patterns suggested that disproportionation was unlikely. Metatranscriptomes revealed broad expression of sox genes and abundant dsr/apr across treatments, along with thiosulfate-linked phs upregulation. While ANME-2c and SEEP-SRB2 activity increased with methane, transcriptomic and isotopic data together highlighted the roles of Desulfocapsaceae, Desulfobulbaceae, and Sulfurovaceae lineages in mediating sulfur transformations. Taken together, these results demonstrate how cryptic sulfur cycling may sustain microbial communities in sulfate-depleted deep-sea sediments and contribute to AOM.

ecology↗

bioRxiv2025

Shifts in ruminant fermentation during inhibition of methanogenesis are reflected in the isotope compositions of volatile fatty acids.

Ruminant animals are a major source of the potent greenhouse gas methane, but they are also a tractable target for climate solutions. Several strategies have been developed to lower methane emissions from ruminants, including feed additives that inhibit methanogenic archaea. Sustainable solutions must eliminate methane emissions without hampering the microbial fermentation of plant material, which the animal host relies on for carbon and energy. However, current tools cannot directly quantify or characterize the metabolic pathways of in vivo ruminant fermentation. To fill this gap, we developed an electrospray (ESI) Orbitrap mass spectrometry technique to measure the stable isotope ratios (13C /12C and 2H/1H) of volatile fatty acids (VFAs) at their natural isotopic abundances directly from rumen fluid. We tested this technique on in vitro incubations of rumen fluid fed three different substrates with and without the additive Asparagopsis taxiformis. We found that the isotope composition of VFAs changed and reflected a remodeling of microbial fermentation pathways. Specifically, acetates{delta} 13C value increased when methanogens were inhibited, suggesting a lower relative rate of acetate synthesis and a lack of acetogenic activity. Furthermore, the{delta} 2H value of propionate decreased, which may indicate a change in the balance between the two pathways of propionate synthesis toward the less energetic acrylate pathway. Both signals were consistent across feed types. Taken together, our results provide evidence that fermentative metabolism is remodeled during methanogenesis inhibition and decreases relative fluxes through ATP-generating pathways. More broadly, this study demonstrates the utility of ESI-Orbitrap-based isotopic analysis for studying rumen microbial ecology. IMPORTANCESlowing methane production from ruminant animals (e.g. cows) is a major target for mitigation of anthropogenic climate change. While strategies that eliminate microorganisms producing methane have been successful, they have cascading impacts on the microbial ecology of the rumen, possibly affecting animal health and productivity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/682381v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1368f20org.highwire.dtl.DTLVardef@ee87baorg.highwire.dtl.DTLVardef@10f714org.highwire.dtl.DTLVardef@1cd4f6a_HPS_FORMAT_FIGEXP M_FIG C_FIG Of particular importance is microbial fermentation, which generates easily digested volatile fatty acids (VFAs) from hard-to-breakdown plant matter. To better understand how fermentation responds to methane mitigation strategies, we measured the isotope composition of VFAs in cow rumen. Our results indicate that fermentation changes pathways when methane production is inhibited to those that generate less energy for the cell. As methane mitigation strategies are developed in the coming decade, isotopic analysis of VFAs may be a useful and accessible contribution to our understanding of rumen microbiology.

microbiology↗

bioRxiv2024

Nondestructive Seed Genotyping via Microneedle-Based DNA Extraction

Crop breeding plays an essential role in addressing food security by enhancing crop yield, disease resistance, and nutritional value. However, the current crop breeding process faces multiple challenges and limitations, especially in genotypic evaluations. Traditional methods for seed genotyping remain labor-intensive, time-consuming, and cost-prohibitive outside of large-scale breeding programs. Here, we present a handheld microneedle (MN)-based seed DNA extraction platform for rapid, nondestructive, and in-field DNA isolation from crop seeds for instant marker analysis. Using soybean seeds as a case study, we demonstrated the use of polyvinyl alcohol (PVA) MN patches for the successful extraction of DNA from softened soybean seeds. This extraction technology maintained high seed viability, showing germination rates of 82% and 79%, respectively, before and after MN sampling. The quality of MN-extracted DNA was sufficient for various genomic analyses, including PCR, LAMP, and whole genome sequencing. Importantly, this MN patch method also allowed for the identification of specific genetic differences between soybean varieties. Additionally, we designed a 3D-printed extraction device, which enabled multiplexed seed DNA extraction in a microplate format. In the future, this method could be applied at scale and in-field for crop seed DNA extraction and genotyping analysis.

plant biology↗