Biology subjects

Bhatnagar, J. M.

Publications and source records attributed to Bhatnagar, J. M..

4 recordsLinked to original sources

bioRxiv2025

Improved detection of fungi and uncultivated microorganisms in soil metagenomes using a comprehensive genome database

Soils harbor diverse microbial communities crucial for ecosystem functioning, but poor genomic representation of many uncultured soil microorganisms limits the utility of existing databases to address some of the most pressing questions in environmental microbiology. To address this, we developed the SoilMicrobeDB, a comprehensive, genome-based reference database to enhance metagenomic classification for soil ecosystems, with a focus on previously underrepresented fungal taxa and uncultured organisms. We evaluated the database using a large soil metagenome dataset, comparing classification rates, analyzing fungal-bacterial ratios against phospholipid fatty acid (PLFA) estimates, and validating lineage abundances with rRNA amplicon sequencing data. Mock community analysis was also conducted to test the precision of community classification and the prevalence of false positives. The SoilMicrobeDB workflow improved metagenomic read classification by over 20% and provided more accurate fungal abundance estimates, particularly for nutrient cycling groups such as ectomycorrhizal fungi. Metagenomic-derived fungal-bacterial ratios were correlated with PLFA and qPCR estimates, and lineage proportions were aligned with relative abundances estimates from rRNA amplicon sequencing. Uncultured taxa represented up to 50% of classifiable soil microbial communities in certain biomes. SoilMicrobeDB offers robust taxonomic and functional profiling of soil communities and provides a scalable and updatable tool for soil microbial ecology research. SoilMicrobeDB is accessible through an interactive platform linking genomes to environmental factors, enabling researchers to explore microbial distributions across soil conditions and potentially leading to new insights into soil ecology and management practices.

bioinformatics↗

bioRxiv2024

Microbial functional guilds and genes are key to explaining soil nutrient cycling alongside soil and plant variables

Microbes play central roles in soil nutrient cycling, yet a limited range of microbial community characteristics have been used to explain ecosystem nutrient cycling rates and their importance relative to plant and abiotic factors remains unclear. In this study, we assessed which of 126 commonly measured soil fungal and bacterial community characteristics best explained soil nitrogen (N) and phosphorus (P) cycling rates in temperate forests in the Northeastern U.S., as well as the relative contributions of microbial, plant, and abiotic factors. Using boosted regression tree modeling, we identified the microbial variables with the highest contributions to models explaining nutrient cycling rates: the relative abundances of ectomycorrhizal fungi and N-decomposition genes from oligotrophic bacteria were the most important for net ammonification, the relative abundances of indicator taxa in bacterial networks, nitrifying bacteria, and copiotrophic bacteria were the most important for net nitrification, and the relative abundance of fungal P-cycling oxidoreductase genes was the most important for net soil phosphate change. Microbial variables explained more variation than plant and abiotic variables in multivariate linear models of net nitrification and net phosphate release rates, but not net ammonification rates, which were largely explained by soil edaphic factors. Leaf litter traits were also important in explaining variation in net nitrification rates, and soil temperature was important in explaining rates of net phosphate release in soil. Collectively, our findings suggest that the N-cycling capacity of microbial functional guilds and fungal community P-cycling capacity should be incorporated into ecosystem biogeochemical models to improve our predictions and understanding of nutrient cycling and related ecological processes.

ecology↗

bioRxiv2023

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by the metabolites available in their environment, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. To this end, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the diverse assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively smaller ones, is necessary and sufficient to recapitulate all of our experimental observations. In addition to pointing to a fundamental principle of community assembly, the divergence-complexity effect has important implications for microbiome engineering applications, as it can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions.

ecology↗

bioRxiv2018

The foliar endophyte Phialocephala scopiformis DAOMC 229536 secretes enzymes supporting growth on wood as sole carbon source

The conifer needle endophyte, Phialocephala scopiformis, was cultivated in media containing ground Pinus contorta wood as sole carbon source. After five and seven days growth, concentrated extracellular fluids were subjected to LC-MS/MS analyses. A total of 590 proteins were identified of which 99 were assigned to glycoside hydrolase families within the Carbohydrate Active Enzyme (CAzyme) system. Multiple isozymes of exo-and endo-acting cellulases were among the most abundant proteins, and oxidative degradation of cellulose was supported by the presence of lytic polysaccharide monooxygenases, glucooligosaccharide oxidase and cellobiose dehydrogenase. Oxidoreductases were also plentiful and included GMC oxidoreductases, alcohol dehydrogenases, laccases, copper radical oxidases, tyrosinases and catalase. The expression and diversity of extracellular oxidoreductases indicates a capacity to metabolize alcohols and aromatic compounds.

microbiology↗