Biology subjects

Pratama, A. A.

Publications and source records attributed to Pratama, A. A..

4 recordsLinked to original sources

bioRxiv2025

Hidden viral players: Diversity and ecological roles of viruses in groundwater microbiomes

Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.26 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) ([≥]5 kb), with 99% classified as novel, highlighting extensive uncharacterized viral diversity. Viruses exhibited a distinct host range, primarily targeting Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea. Notably, CPR lineages displayed low virus-host ratios and viral CRISPR targeting multiple hosts, suggesting a "virus decoy" mechanism where they may absorb viral pressure, protecting bacteria hosts. Additionally, 3,378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling, with viruses targeting 31.5% of host metabolic modules. These findings demonstrate viruses influence on microbial metabolic reprogramming and nutrient cycling in groundwater, shaping subsurface biogeochemistry.

microbiology↗

bioRxiv2025

Mobile genetic elements that shape microbial diversity and functions inthawing permafrost soils

The worlds ecosystems are shaped by microbiota. Their niches and their impacts depend on functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, quantitative field data on the rates and impacts of MGE activity remains scarce. Here we leverage large-scale soil meta-omic data to develop and apply analytics for studying MGEs in complex natural systems. In our model permafrost-thaw ecosystem, Stordalen Mire, we identify [~]2.1 million MGE recombinases across 89 microbial phyla to assess ecological distributions, affected functions, past mobility, and current activity. This revealed MGEs shaping natural genetic diversity via differential impacts on major phyla; affecting a wide range of functions, including diverse regulatory and metabolic genes affecting carbon flux and nutrient cycling; and moving at rates that should significantly influence the realized functional profiles of natural microbiomes. These findings and this systematic meta-omic framework open new avenues to better investigate MGE diversity, activity, mobility, and impacts in nature.

microbiology↗

bioRxiv2025

RNA virus ecogenomics along a subarctic permafrost thaw gradient

Climate change thaws permafrost, which releases greenhouse gases partly from dormant microorganisms awakening and metabolizing organic matter. Though DNA viruses that infect these soil microbes have been studied, little is known on soil RNA viruses, which typically infect microeukaryotes. Here we identify and characterize 2,651 RNA viruses from a 4-year time series of bulk soil metatranscriptomes derived from the climatically fragile Stordalen Mire ecosystem --a long studied permafrost peatland. RNA virus diversity was structured by habitat (palsa, bog, and fen), and these patterns correlated with pH and carbon dioxide and methane emissions. Further, host prediction, virus-encoded metabolite-transforming and information-processing functions suggested roles in ecosystem-scale carbon fluxes and contribute to greenhouse gases emissions. Together, these RNA virus ecogenomic data in permafrost provide essential baseline information for integration into predictive models to support hypothesis testing.

microbiology↗

bioRxiv2022

Unraveling the viral dark matter of the rumen microbiome with a new global virome database

Like in the human gut and other environments, viruses are probably also diverse and modulate the microbiome (both population and function) in the rumen of ruminants, but it remains largely unknown. Here we mined 975 published rumen metagenomes for viral sequences, created the first rumen virome database (RVD), and perform ecogenomic meta-analyses of these data. This identified 397,180 species-level viral operational taxonomic units (vOTUs) and allowed for a 10-fold increase in classification rate of rumen viral sequences compared with other databases. Most of the classified vOTUs belong to the order Caudovirales, but distinct from those in the human gut. Rumen viruses likely have ecosystem impacts as they were predicted to infect dominant fiber degraders and methane producers, and they carry diverse auxiliary metabolic genes and antibiotic resistance genes. Together, the RVD database and these findings provide a baseline framework for future research on how viruses may impact the rumen ecosystem.

microbiology↗