Biology subjects

Meredith, L. K.

Publications and source records attributed to Meredith, L. K..

5 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↗

bioRxiv2025

Aridity drives global convergence of desert microbiomes and biogeochemical activities

Deserts cover a third of the worlds surface, supporting unique biomes and ecosystem services. Yet, we lack a comprehensive assessment of what defines and drives the microbial communities that dominate life in these regions. Here, we conducted a standardized field survey in contrasting cold, hot, and polar deserts across the seven continents, and observed geographically distant deserts share similar structure, function, and activities. Desert communities are dominated by genomically streamlined Actinobacteriota and Chloroflexota, and compared with non-desert soils, are significantly enriched with stress tolerance genes, mobile genetic elements, and antiviral strategies, revealing previously unknown ecological and evolutionary dynamics. Metabolically, these communities exhibit reduced capacity for carbohydrate and protein degradation, and instead are enriched for chemosynthetic carbon fixation, continuous energy harvesting using atmospheric trace gases and sunlight, and energy reserve biosynthesis. All sampled soils mediated respiration, trace gas oxidation, and carbon fixation, with detectable activity even in hyper-arid Atacama and Antarctic soils at the margins of life. Driver analyses identified aridity as the primary overriding driver of the microbial communities and biogeochemical activities. Collectively, these findings suggest that aridity selects for metabolically self-sufficient taxa capable of continuously meeting energy and carbon needs independently of vegetation-derived inputs, while enduring physicochemical stressors and potentially elevated viral pressure. These new insights are integral to forecast the future of soils amid increasing desertification. Significance statementDesert soils occupy a vast and expanding portion of Earth, yet what defines and governs their dominant microbial life remains incompletely defined. By assessing the composition, capabilities, and activities of microbial communities across deserts on all seven continents, we identify unifying signatures of life under extreme water limitation. We show microbial communities are highly self-sufficient, capable of acquiring energy and carbon even where plant inputs are minimal. This planetary-scale understanding of the desert microbiome has important ramifications for forecasting potential shifts of microbial communities and the services they provide as desertification intensifies.

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

Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome-specificity

Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have convergently evolved multiple times from phylogenetically distant organisms into structurally unrelated classes (, {beta}, {gamma},{delta} ,{zeta} , , {theta}, {iota}) with conserved physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57,218 -, {beta}-, and {gamma}-CA sequences from 24,184 metagenomes and genomes, including the first detection of -CA from an Archaeal species. CA sequences formed 3,859 protein clusters (1,188 with [≥] 3 sequences) that were taxonomically conserved at higher levels (i.e., Superkingdom, Phylum, Class). When viewed within a phylogenetic framework, the majority of subclades contained CAs representing multiple Superkingdoms, although numerous novel {beta}-CA clades appear unique to Fungi. Queries of CA Hidden Markov models (HMMs) against all public meta-genome and -transcriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared environment-specific, generating high CA diversity. This work represents an important contribution to the evolution, diversity, and environmental distribution of an enzyme that is key for life and has broad environmental and industrial applications.

genomics↗

bioRxiv2020

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink that is threatened by agricultural conversion. Rainforest-to-pasture conversion leads to the release of a potent greenhouse gas by converting soil from a methane sink into a source. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarem, Para and Ariquemes, Rondonia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could explain the greater methane flux. Furthermore, we found that secondary rainforests recovered as methane sinks, indicating the potential for reforestation to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

microbiology↗