Biology subjects

Leleiwi, I.

Publications and source records attributed to Leleiwi, I..

8 recordsLinked to original sources

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↗

bioRxiv2026

Deciphering the microbial contributors to methane cycling in coastal wetlands

Although wetlands are increasingly recognized as important contributors to the global methane budget, the microorganisms and processes involved methane cycling are poorly characterized, particularly in coastal brackish and saline systems. Here, we investigated microbial and geochemical factors contributing to methane dynamics in three coastal wetlands with different salinities, dominant vegetation types, and soil chemical characteristics. These included a freshwater flotant marsh, a cypress swamp, and a mesohaline salt marsh. Specifically, we paired methane porewater concentrations, surface fluxes, geochemistry, and 16S rRNA gene sequencing to address how microbial community composition links to porewater concentrations and its potential effects on emissions. We found that porewater methane concentrations across sites were the highest in the swamp, followed by the salt marsh and the flotant marsh, and were explained by methanogen richness and abundance. While methane-cycling microbial communities were significantly structured by salinity, two microbial taxa (Methanosaeta and Methanomicrobiaceae) were present across all sites. Hydrogenotrophs were the most abundant methanogen functional group, with Methanomicrobiaceae and Methanobacterium discriminant among wetlands. In contrast, methanotroph functional types varied among wetlands. Type I dominated the freshwater flotant marsh, while the anaerobic methanotrophic archaea the saltwater marsh. These findings contribute to an enhanced understanding of the microbiological contributions to methane emissions from coastal wetlands. Scientific Significance Statement TopicThis study provides critical insights into the microbial and geochemical controls on methane emissions across coastal wetlands along a salinity gradient. Challenging the prevailing paradigm, methane porewater concentrations did not inversely correlate with salinity, as the swamp site with intermediate salinity exhibited the highest concentrations. Methanogen richness and abundance emerged as strong predictors of methane concentrations, while methanotroph richness had no predictive value. Two core methanogens, Methanosaeta and Methanomicrobiaceae, were consistently present across all wetland types. The findings highlight potential role of the water column as a biological methane filter, especially in saline environments. This study significantly advances the understanding of methane cycling in coastal wetlands by decoupling methane emissions from salinity gradients and emphasizing the role of microbial communities and local environmental factors. These insights are essential for refining biogeochemical models to forecast greenhouse gas emissions under sea-level rise and saltwater intrusion scenarios. Scientific Significance Statement OutletThis work integrates microbial ecology, geochemistry, and ecosystem structure to address interdisciplinary questions relevant to the limnological community. Here, we reveal how microbial community composition, rather than salinity alone, predicts methane emissions, offering a fresh perspective into carbon cycling in estuarine and coastal environments. The findings also provide critical insights for improving greenhouse gas emission models to predict climate change feedback from coastal areas.

microbiology↗

bioRxiv2026

Divergent successional patterns and infection dynamics in virion and transcriptionally active soil viral communities following phosphorus amendment and wet-up

Viruses are key regulators of terrestrial carbon, nitrogen, and phosphorus cycling, yet how environmental perturbations structure viral activity remains poorly resolved. Rewetting of seasonally dry soils triggers rapid microbial and viral responses, but the relationships between virion-associated and transcriptionally active viral communities, and the role of phosphorus in these dynamics, remain unclear. Here, we integrated viromics, metatranscriptomics, environmental DNA (eDNA), and amplicon sequencing to track viral succession and virus-host interactions over three weeks following soil rewetting, with and without phosphorus amendment. We identified 13,840 viral populations (vOTUs), of which 3,803 were transcriptionally active, representing ongoing infections. Wet-up significantly altered virion and transcriptionally active viral communities, while phosphorus selectively influenced prokaryotic and transcriptionally active viral communities but not virion composition. Virus-host linkages were predicted for 32% of vOTUs, with transcriptionally active bacteriophages infecting Actinomycetota increasing under phosphorus amendment. Following wet-up, virion abundance decreased [~]3-fold while virocells increased [~]5-fold, indicating a shift from viral persistence in dry soils to active infection. Phosphorus further enhanced virocell abundance. eDNA captured rapid viral turnover and revealed transient dynamics not resolved by viromes or metatranscriptomes alone. Together, these results demonstrate that soil viral communities are structured by distinct but complementary molecular pools that operate over different ecological timescales. Wet-up activates a reservoir of persistent virions, while phosphorus availability regulates infection dynamics and host-virus coupling. These findings highlight viruses as dynamic drivers of microbial turnover and nutrient cycling following environmental perturbation, advancing a more predictive understanding of soil ecosystem responses to changing resource availability.

ecology↗

bioRxiv2024

Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils

BackgroundWet tropical forest soils store a vast amount of organic carbon and cycle over a third of terrestrial net primary production. The microbiomes of these soils have a global impact on greenhouse gases and tolerate a remarkably dynamic redox environment--driven by high availability of reductant, high soil moisture, and fine-textured soils that limit oxygen diffusion. Yet tropical soil microbiomes, particularly virus-host interactions, remain poorly characterized, and we have little understanding of how they will shape future soil carbon cycling as high-intensity drought and precipitation events make soil redox conditions less predictable. ResultsTo investigate the effects of shifting soil redox conditions on active viral communities and virus-microbe interactions, we conducted a 44-day redox manipulation experiment using soils from the Luquillo Experimental Forest, Puerto Rico, amended with 13C-enriched plant biomass. We sequenced 10 bulk metagenomes and 85 stable isotope probing targeted metagenomes generated by extracting whole community DNA, performing density fractionation, and conducting shotgun sequencing. Viral and microbial genomes were assembled resulting in 5,420 viral populations (vOTUs) and 927 medium-to-high-quality metagenome-assembled genomes across 25 bacterial phyla. Notably, over half (54%) of the vOTUs were 13C-enriched, highlighting their active role in microbial degradation of plant litter. These active vOTUs primarily infected bacterial phyla Pseudomonadota, Acidobacteriota, and Actinomycetota, and 57% were unique to a particular redox treatment. The anoxic samples exhibited the most distinct viral communities, with an increased potential for modulating host metabolism by carrying redox-specific glycoside hydrolases. However, over a third of the vOTUs were present in all redox conditions, suggesting selection for cosmopolitan viruses occurs in these soils that naturally experience dynamic redox conditions. ConclusionsOur study demonstrates how redox conditions shape viral communities and virus-host interactions in soils. By applying different DNA assembly methods on stable isotope probing targeted metagenomes and incubating soils under various redox regimes, we identified distinct viral populations and observed significant variations in viral community composition and function. These findings highlight the specialized roles of viruses in microbial carbon degradation under diverse environmental conditions, providing important insights into their contributions to carbon cycling and the broader implications for climate change.

microbiology↗

bioRxiv2024

Time resolved multi-omics reveals diverse metabolic strategies of Salmonella during diet-induced inflammation

With a rise in antibiotic resistance and chronic infection, the metabolic response of Salmonella enterica serovar Typhimurium to various dietary conditions over time remains an understudied avenue for novel, targeted therapeutics. Elucidating how enteric pathogens respond to dietary variation not only helps us decipher the metabolic strategies leveraged for expansion but also assists in proposing targets for therapeutic interventions. Here, we use a multi-omics approach to identify the metabolic response of Salmonella enterica serovar Typhimurium in mice on both a fibrous diet and high-fat diet over time. When comparing Salmonella gene expression between diets, we found a preferential use of respiratory electron acceptors consistent with increased inflammation of the high-fat diet mice. Looking at the high-fat diet over the course of infection, we noticed heterogeneity of samples based on Salmonella ribosomal activity, which separated into three infection phases: early, peak, and late. We identified key respiratory, carbon, and pathogenesis gene expression descriptive of each phase. Surprisingly, we identified genes associated with host-cell entry expressed throughout infection, suggesting sub-populations of Salmonella or stress-induced dysregulation. Collectively, these results highlight not only the sensitivity of Salmonella to its environment but also identify phase-specific genes that may be used as therapeutic targets to reduce infection. ImportanceIdentifying novel therapeutic strategies for Salmonella infection that occur in relevant diets and over time is needed with the rise of antibiotic resistance and global shifts towards Western diets that are high in fat and low in fiber. Mice on a high-fat diet are more inflamed compared to those on a fibrous diet, creating an environment that results in more favorable energy generation for Salmonella. Over time on a high-fat diet, we observed differential gene expression across infection phases. Together, these findings reveal the metabolic tuning of Salmonella to dietary and temporal perturbations. Research like this, exploring the dimensions of pathogen metabolic plasticity, can pave the way for rationally designed strategies to control disease.

microbiology↗

bioRxiv2024

Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection

Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.

genomics↗

bioRxiv2023

A functional microbiome catalog crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial processes governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling, sequencing, and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. Specifically, GROWdb encompasses 1,469 microbial species from 27 phyla, including novel lineages from 10 families and 128 genera, and defines the core river microbiome for the first time at genome level. GROWdb analyses coupled to extensive geospatial information revealed local and regional drivers of microbial community structuring, while also presenting a myriad of foundational hypotheses about ecosystem function. Building upon the previously conceived River Continuum Concept1, we layer on microbial functional trait expression, which suggests the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures2, 3 so that it can be widely accessed across disciplines for watershed predictive modeling and microbiome-based management practices.

microbiology↗

bioRxiv2022

Exposing New Taxonomic Variation with Inflammation-A Murine Model-Specific Genome Database for Gut Microbiome Researchers

BackgroundThe murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. ResultsHere we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~42.4 Gbps/sample), we reconstructed 2,281 bacterial and 4,129 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation resistant strains. ConclusionsThis CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.

microbiology↗