About

Jennifer Bhatnagar is an Associate Professor of Biology and the Director of the Biogeoscience Program at Boston University. Her research focuses on the ecology, chemistry, and biology of microorganisms in the environment, with particular emphasis on fungi. She studies the biochemical mechanisms that microbes use to drive large-scale processes such as carbon and nutrient cycling within ecosystems. Her work employs biochemical analyses and sequencing technologies to identify direct, mechanistic links between the genetic architecture, community structure, and biochemical functions of microbes in complex environments. Her current research includes investigating the molecular mechanisms and biogeochemical consequences of fungal species interactions, the biochemical processes involved in plant-fungal symbioses, and the responses of microbial communities to climate change. She aims to understand how microbial interactions influence ecosystem-level biogeochemistry, the molecular basis of functional diversity among mycorrhizal fungi, and how microbial communities drive ecosystem responses to climate-induced changes. Her contributions advance understanding of microbial roles in environmental processes and their responses to global change.

Research topics

• Biology
• Computational biology
• Genetics
• Computer Science
• Ecology
• Evolutionary biology
• Astronomy
• Environmental science
• Agroforestry
• World Wide Web
• Physics
• Library science
• Data science
• Geography

Selected publications

• Soil nitrogen cycling rates are linked to microbial functional and taxonomic groups across the United States

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-04

  articleSenior author

  ABSTRACT Soil microbes support life on Earth by regulating the availability of nutrients in soils, yet we lack a fundamental, baseline knowledge of which fungi and bacteria are associated with specific soil nitrogen (N) cycling processes across ecosystems. We identified functional and taxonomic groups of fungi and bacteria that are associated with net ammonification and nitrification rates in soils from diverse ecosystems across the United States, including the environmental contexts where these relationships exist. To accomplish this, we co-analyzed soil, microbial, plant, and climatic data from 19 sites across the U.S. National Ecological Observatory Network (NEON). Distinct microbial groups were associated with net ammonification versus nitrification rates, highlighting the need to measure and model these two processes separately. The relative abundance of several microbial groups known for their N-decomposition abilities (i.e., Acidobacteriae, Bacteroidia, Saccharomycetes yeasts, ectomycorrhizal fungi) were positively associated with net ammonification rates across diverse environmental conditions. Meanwhile, pathogenic fungi, copiotrophic bacteria, and bacterial classes containing denitrifying bacteria were positively associated with net nitrification rates in many wet, hot, and high-N environments. These results deepen our understanding of soil microbiome ecology and represent a practical starting point to develop microbial-explicit biogeochemical cycling models at large spatial scales.

  PublisherDOI

• Evidence for invasional meltdown in plant-fungal co-invasions

  Biological Invasions · 2026-04-21

  articleSenior author
  PublisherDOI

• A DNA Amplicon Sequence Data Processing and Analysis Pipeline for Environmental Microbiomes v1

  2025-08-06 · 1 citations

  preprintOpen accessSenior author

  Amplicon sequencing is a widely used method to characterize microbial communities across environmental and host-associated sample types. However, variation in DNA extraction methods, sequencing batch effects, contamination, and low-quality samples can introduce biases that hinder reproducibility and cross-sample comparisons. Here, we present a modular and reproducible protocol for amplicon sequence cleaning that accommodates diverse sample types and experimental designs. This workflow standardizes quality filtering, contaminant removal, batch correction, and functional annotation to enable robust downstream analyses of bacterial and fungal communities. The protocol integrates the BU16S-ITS pipeline for ASV inference with R-based tools for data cleaning and normalization and is suitable for projects using Illumina sequencing platforms. Code and documentation are available at https://github.com/k-atherton/Amplicon_Sequence_Data_Processing.

  PublisherOA PDFDOI

• A Climate BioStress Sentinel System: Identifying climate impacts from the genome to the urbanized biosphere

  Cell Reports Sustainability · 2025-11-01 · 2 citations

  articleOpen access
  PublisherDOI

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

  Ecosphere · 2025-11-01 · 3 citations

  articleOpen accessSenior author

  Abstract 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 net soil ammonium, nitrate, and phosphate mineralization rates in temperate forests in the Northeastern United States, 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 nitrogen (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 phosphorus (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 P‐cycling capacity of fungi should be incorporated into ecosystem biogeochemical models to improve our predictions and understanding of nutrient cycling and related ecological processes.

  PublisherDOI

• Inorganic nitrogen and organic matter jointly regulate ectomycorrhizal fungi‐mediated iron acquisition

  New Phytologist · 2025-01-22 · 7 citations

  articleOpen access

  Summary Ectomycorrhizal fungi (EMF) play a crucial role in facilitating plant nutrient uptake from the soil although inorganic nitrogen (N) can potentially diminish this role. However, the effect of inorganic N availability and organic matter on shaping EMF‐mediated plant iron (Fe) uptake remains unclear. To explore this, we performed a microcosm study on Pinus taeda roots inoculated with Suillus cothurnatus treated with +/−Fe‐coated sand, +/−organic matter, and a gradient of NH 4 NO 3 concentrations. Mycorrhiza formation was most favorable under conditions with organic matter, without inorganic N. Synchrotron X‐ray microfluorescence imaging on ectomycorrhizal cross‐sections suggested that the effect of inorganic N on mycorrhizal Fe acquisition largely depended on organic matter supply. With organic matter, mycorrhizal Fe concentration was significantly decreased as inorganic N levels increased. Conversely, an opposite trend was observed when organic matter was absent. Spatial distribution analysis showed that Fe, zinc, calcium, and copper predominantly accumulated in the fungal mantle across all conditions, highlighting the mantle's critical role in nutrient accumulation and regulation of nutrient transfer to internal compartments. Our work illustrated that the liberation of soil mineral Fe and the EMF‐mediated plant Fe acquisition are jointly regulated by inorganic N and organic matter in the soil.

  PublisherDOI

• Molecular mechanisms of mycorrhizal‐decomposer interactions and impacts on terrestrial biogeochemistry (Final Technical Report)

  2025-06-24

  report
  PublisherDOI

• Dysbiosis in the urban tree microbiome

  Research Square · 2025-03-25

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Disruption of the oak tree microbiome with urbanization

  Nature Cities · 2025-10-03 · 1 citations

  articleSenior author
  PublisherDOI

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-25

  preprintOpen access

  Abstract 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.

  PublisherOA PDFDOI

Recent grants

• Collaborative Research: Molecular mechanisms and biogeochemical consequences of decomposer species interactions during succession in ecosystems

  NSF · $661k · 2015–2021

Frequent coauthors

• Colin Averill

  Lawrence Livermore National Laboratory

  224 shared

• Rytas Vilgalys

  Duke University

  219 shared

• Hui-ling Liao

  216 shared

• Ryan Tappero

  Brookhaven National Laboratory

  189 shared

• Edward Brzostek

  West Virginia University

  187 shared

• Haihua Wang

  186 shared

• Nahuel Policelli

  Centro Científico Tecnológico Patagónico

  168 shared

• Nahuel Policelli

  10 shared