Biology subjects

Tfaily, M. M.

Publications and source records attributed to Tfaily, M. M..

11 recordsLinked to original sources

bioRxiv2026

Soil viral response to drought disturbance and ecosystem recovery in an artificial rainforest

Anthropogenic climate change is driving increased temperature and altered precipitation patterns in tropical rainforests, yet the impact of severe drought on soil viral communities and their recovery capacity remains poorly understood. Soil viruses can exert strong controls on bacterial populations impacting microbially-mediated soil processes such as carbon cycling. At the same time, viruses are very sensitive to changes in the soil environment. We leverage meta-omics data from soils collected during a two-month drought and one-month recovery experiment carried in the Biosphere 2 Tropical Rainforest artificial biome. Our results indicate that soil viral community structure responds to small scale soil habitat heterogeneity more strongly than on overall changes in moisture. Additionally, the abundance of soil viruses was associated with a higher diversity of metabolites in the soil, suggesting viruses play a key role in soil biogeochemical processes. Altogether, our study suggests that soil viruses are an active part of tropical rainforest soil microbial communities and that is necessary to understand their response to drought.

microbiology↗

bioRxiv2026

Microbial communities in tropical soils are highly resilient to fluctuating redox conditions

Many wet tropical soils alternate frequently between fully oxygenated and anaerobic conditions, constraining the terminal electron acceptors available for microbial metabolism, and the mineral-organic matter interactions that regulate many aspects of soil carbon (C) cycling. However, it is still unclear how fluctuating soil redox conditions influence the microbial community composition and if microbially mediated C flux is sensitive to extended oxic or anoxic periods like those observed during drought and flooding respectively. Using a 44-day redox manipulation of tropical soils that experience daily-to-weekly oxygen (O2) fluctuations in the field, we measured how different redox regimes shape soil biogeochemistry and microbial and metabolite composition. Replicate microcosms were exposed to four treatments (static oxic, static anoxic, high frequency fluctuation (4 day oxic/4 day anoxic), or low frequency fluctuation (8 day oxic/4 day anoxic)) regimes, and harvested for microbial, metabolite, carbon dioxide (CO2) flux, and biogeochemical assays at multiple timepoints. Oxic and fluctuating redox conditions caused the microbial community to shift in a manner correlated with soil iron content and directly orthogonal to communities from anoxic soils. The identity of both iron oxidizers and iron reducers was distinct in static anoxic soils but was resilient to redox fluctuation and prolonged O2 exposure. The total amount of CO2 respired was similar across all four redox regimes. Water-extractable organic matter composition was distinct across redox treatments, with anoxic soils accumulating higher levels of carbohydrate-, proteins-, amino sugar-, and lignin-like compounds consistent with reduced enzymatic decomposition and release of mineral-associated organic matter via iron reduction, while oxic soils showed elevated lipid- and unsaturated hydrocarbon-like compounds indicative of greater microbial biomass turnover. The microbial community adapted to dynamic redox conditions and the results substantiate cycling of distinct C compounds under varying redox conditions resulting from varying bioavailability (driven by mineral-OM dynamics) and/or shifted microbial metabolism.

microbiology↗

bioRxiv2025

Transcriptional and metabolic stasis define desiccation-induced dormancy in a soil bacterium until water vapor initiates resuscitation.

Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration on the composition of cellular RNA and metabolites are still poorly understood. Here, we describe how slow drying and rehydration with water vapor influence the composition of RNAs and metabolites in a soil Arthrobacter. While drying reduced cultivability relative to hydrated controls, water vapor rehydration fully restored it. Ribosomal RNA proportions remained constant throughout all treatments, and mRNA profiles showed stable composition during desiccation--changing only during transitions into and out of desiccation-induced dormancy. Six transcriptional modules displayed distinct expression patterns in desiccated-rehydrated samples relative to hydrated controls, including desiccation-rehydration responsive and rehydration-specific profiles. Targeted intracellular metabolomics revealed similarly static profiles during desiccation, with a cluster of ribonucleosides and nucleobases increasing in response to desiccation and returning to baseline levels upon rehydration with water vapor. These findings demonstrate that both mRNA and metabolite profiles remain essentially frozen in desiccated Arthrobacter, with dynamic changes occurring only during state transitions. These results have important implications in environments with frequent drying cycles where stable mRNA in dormant cells combined with intracellular RNA recycling may obscure interpretations of RNA-based environmental analyses that use RNA as a marker of microbial activity. Our results suggest that RNA-based activity assessments in periodically dry environments require careful consideration of dormancy-associated molecular preservation. SIGNIFICANCE STATEMENTMetabolic activity quickly ceases in drying bacteria as they enter desiccation-induced dormancy. We show mRNA and metabolite profiles were variable during drying and rewetting but did not change while desiccated. Additionally, water vapor stimulated the shift from the static to active state when exiting desiccation-induced dormancy. These shifts coincided with increased cultivability, indicating water vapor resuscitated dry cells. Because RNAs are transient, labile molecules that are turned over rapidly in growing bacteria, the presence of RNA in the environment is used as a marker for microbial activity. Our research shows this assumption may not hold for desiccated cells, indicating reliance on RNA as a marker of activity in environments that experience drying may obscure estimates of in situ microbial activity.

microbiology↗

bioRxiv2025

Continental-scale integration of soil metagenomes and metabolomes reveals ubiquitous microbial capacity for recalcitrant carbon decomposition.

Soil organic matter (SOM) decomposition by microorganisms represents one of the largest uncertainties in predicting terrestrial carbon-atmosphere feedbacks. Yet we lack systematic understanding of the microbial taxa that drive decomposition of chemically distinct carbon pools and of the metabolic pathways they employ across environmental gradients. Here, we address this critical gap using the first continental-scale soil dataset pairing shotgun metagenomes with high-resolution molecular characterization of SOM chemistry. We use data from 47 standardized soil cores - selected using microbial respiration rates from 106 soils across the United States - to assemble 0.76 terabases (Tbs) of prokaryotic metagenome-assembled genomes (828 MAGs) and identify 66,727 distinct SOM molecules. Integrating these datasets revealed widespread microbial potential for depolymerizing chemically-recalcitrant carbon compounds previously considered stable. Notably, we uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of chemically-complex carbon through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our continental-scale integration of microbial genotypes with their chemical substrates reveals that a substantial fraction of SOM that is considered to be relatively stable harbors decomposition potential that current Earth system models fail to capture. These findings provide mechanistic insight for incorporating microbial metabolic pathways into carbon cycle predictions and highlight an underappreciated vulnerability of soil carbon to environmental variability.

microbiology↗

bioRxiv2025

Stable states in an unstable landscape: microbial resistance at the front line of climate change

Microbiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. Because the rapid thaw of permafrost peatlands makes a very large store of soil carbon available to microbial metabolism, understanding microbiome dynamics in these systems is particularly urgent. We quantified microbial warming response over seven years across three habitats in a thawing permafrost peatland, using large-scale multi-omics data. We integrated analyses of organisms (via taxonomy), functions (via metabolic pathways and proteins), and community organization (via network structure and ecological assembly) to deeply characterize response mechanisms. We consistently found a pattern of within-habitat microbiome stability, with virtually no signal of gradual change in the warming period studied. The resistance to change appeared bolstered by habitat-specific dispersal processes and community-level functional redundancy, particularly via versatile carbon generalists. Our findings also reveal key genome-inferred metabolic processes that underlie microbiome stability. Together, our results highlight the importance of understanding the limits of these stabilizing processes and suggest that future research should reorient towards critical habitat transitions.

microbiology↗

bioRxiv2024

Polyphenol rewiring of the microbiome reduces methane emissions

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens--either through direct toxic effects or by diverting their substrates and energy--to gain traction. Problematically, current microbial methane mitigation knowledge derives from rumen studies and lacks detailed microbiome-centered insights, limiting translation across ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane- emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a novel catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes also co-expressed hydrogen-uptake genes, suggesting that hydrogenases may act as a hydrogen sink during catechin degradation, depriving methanogens of substrates. This was supported by decreased gene expression in hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. We also saw reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.

microbiology↗

bioRxiv2023

Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolisms is incomplete, which compromises prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire, in arctic Sweden. In quadrupling the genomic representation of the sites methanogens and examining their encoded metabolisms, we revealed that nearly 20% (72) of the metagenome-assembled genomes (MAGs) encoded potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy, and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activity. Methanogenesis across increasing permafrost thaw is thus revised from sole dominance of hydrogenotrophic production, and the appearance of acetoclastic at full thaw, to consider co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.

microbiology↗

bioRxiv2021

Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues

1.Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a 13CO2 labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using 13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon, 13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a "transient fraction" of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids. SynopsisThis study explores the interaction of rhizosphere carbon, minerals, and microbial influence on the fate of soil carbon. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/436628v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@17ce1bborg.highwire.dtl.DTLVardef@1c7c2e8org.highwire.dtl.DTLVardef@1cd0e41org.highwire.dtl.DTLVardef@162ff90_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2020

Unification of Environmental Metabolomics with Metacommunity Ecology

Environmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis meta-metabolome ecology and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed -diversity and {beta}-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and {beta}NTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.

ecology↗

bioRxiv2018

Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils

Oscillating redox conditions are the norm in tropical soils; driven by an ample supply of reductants, high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. Yet the net result of variable soil redox regimes on iron-organic matter (Fe-OM) associations in tropical soils owing to changing climate is poorly understood. Using a 44-day redox incubation experiment with humid tropical soils from Puerto Rico, we examined patterns of Fe and C transformation under four redox regimes: static anoxic, flux 4-day (4d oxic, 4d anoxic), flux 8-day (8d oxic, 4d anoxic) and static anoxic. Prolonged anoxia promoted reductive dissolution of Fe-oxides and an increase in short-range ordered (SRO) Fe oxides. Preferential dissolution of this less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to anoxic), and coincided with increased dissolved organic carbon, presumably due to acidification or direct release of OM from dissolving Fe(III) mineral phases. Average nominal oxidation state of water-soluble carbon was lowest under persistent anoxic conditions, suggesting more reduced OC is microbially preserved under reducing conditions. Anoxic soil compounds had high H/C values (similar to lignin-like metabolites) whereas oxic soil compounds had higher O/C values, akin to tannin- and cellulose-like components. Cumulative respiration derived from native soil organic carbon was highest in static oxic soils. These results highlight the volatility of mineral-OM interactions in tropical soils, and suggest that short-term impacts of shifting soil O2 availability control exchanges of C between mineral-sorbed and aqueous pools, implying that the periodicity of low-redox moments may control the fate of C in wet tropical soils.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC=\"FIGDIR/small/312108_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (23K):\norg.highwire.dtl.DTLVardef@add07borg.highwire.dtl.DTLVardef@15269bforg.highwire.dtl.DTLVardef@19ca034org.highwire.dtl.DTLVardef@1d9d793_HPS_FORMAT_FIGEXP M_FIG Toc Art C_FIG

ecology↗

bioRxiv2018

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities

Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw, however studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from factors that influence non-permafrost soil communities. To test this hypothesis, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the relative importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16), and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2=0.14, p=0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings reveal that the processes shaping microbial communities in permafrost are distinct from those in non-permafrost soils, as the stability of the permafrost environment imposes dispersal and thermodynamic constraints on permafrost communities. Models of permafrost community composition will need to account for these unique drivers in order to predict community characteristics across permafrost landscapes, and in efforts to understand how pre-thaw conditions will influence post-thaw ecological and biogeochemical processes.

ecology↗