About

Debashish Bhattacharya is a Distinguished Professor in the Department of Biochemistry and Microbiology at Rutgers University, School of Environmental and Biological Sciences. His research interests encompass computational biology, evolution, gene regulation, organelle biology, and virology. His lab focuses on the diversity of life, with long-standing interests in algal/protist and coral evolution and genomics. Key projects include elucidating the endosymbiotic origin of photosynthetic organelles (plastids), coral biology and conservation, erecting the eukaryotic tree of life, and developing engineering solutions for field monitoring of threatened species. His research aims to explain the origin of intracellular organelles of foreign origin, investigate the integration of plastid function within cellular biochemistry, and contribute to coral reef conservation amid climate change. His team generates coral genome data to study stress response pathways and disease susceptibility, and is building portable stress monitoring devices for wild coral health assessment. Additionally, his work involves using phylogenetic and phylogenomic approaches to infer the eukaryotic tree of life and understand how horizontal gene transfer has influenced genome evolution and adaptation in microbial eukaryotes.

Research topics

• Biology
• Ecology
• Genetics
• Evolutionary biology
• Computer Science
• Computational biology
• Botany
• Biochemistry
• Bioinformatics

Selected publications

• A portable, low-cost, point-of-care DNA amplification kit with impedance-based detection for decentralized antimicrobial resistance diagnostics

  Lab on a Chip · 2026-01-01 · 1 citations

  articleOpen accessCorresponding

  copies per μl) in a complex background DNA mixture demonstrated detection results that strongly correlated with quantitative PCR (qPCR). These findings demonstrate that the amplification kit achieves performance parity with gold-standard nucleic acid detection methods while offering portability, affordability, and ease of use. By enabling accurate, rapid, and decentralized diagnostics without reliance on laboratory infrastructure, this combined workflow holds promise for advancing infectious disease monitoring and antimicrobial resistance surveillance, among other applications, at the point of care.

  PublisherOA PDFDOI

• Rafts of change: microbial and functional dynamics in simulated <i>Sargassum</i> strandings

  Applied and Environmental Microbiology · 2026-03-31

  articleOpen accessSenior author

  ABSTRACT Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum -derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future. IMPORTANCE This work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum , which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.

  PublisherDOI

• Metaproteome analysis of short-term thermal stress in three sympatric coral species reveals divergent host responses

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-26 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Abstract The accelerating loss of coral reefs worldwide due to anthropogenic climate change has led to a myriad of studies aimed at understanding the basis of coral resilience to support reef conservation. Here, we integrate physiological measurements with proteomic and metabolomic profiles to examine species-specific responses to increased temperature in three sympatric reef-building corals from the Great Barrier Reef: Acropora hyacinthus , Porites lobata , and Stylophora pistillata . We find species-specific stress response strategies with A. hyacinthus , a thermally sensitive species, exhibiting rapid decline in endosymbiont physiology, coupled with a one-third reduction in protein abundance. In contrast, P. lobata displayed a delayed physiological response to stress and a muted proteome response, suggesting greater resilience. S. pistillata initially showed minor shifts in the proteome followed by colony “bail-out”. Overall, we observed markedly different responses in most biochemical pathways in the three coral species. Nonetheless, some known biomarkers of stress, including heat-shock proteins, showed conserved responses to thermal stress with differences in temporal abundance reflecting bleaching resistance. Our results underscore the species-specific nature of coral responses to thermal stress and highlight proteomic signatures associated with symbiosis breakdown, offering mechanistic insights into coral bleaching susceptibility and resilience.

  PublisherOA PDFDOI

• Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef

  Research Square · 2025-07-17

  preprintOpen accessSenior author
  PublisherDOI

• Genome Evolution of Two Intertidal <i>Sargassum</i> Species (<i>S. fusiforme</i> and <i>S. thunbergii</i>) and Their Response to Abiotic Stressors

  Genome Biology and Evolution · 2025-04-30 · 2 citations

  articleOpen access

  Sargassum fusiforme and Sargassum thunbergii are ecologically and commercially important seaweeds that thrive in intertidal zones and are frequently exposed to extreme variation in environmental stress. Despite their importance, limited genomic information exists for these species, which hinders a comprehensive understanding of the evolution and adaptation of the genus Sargassum to marine coastal habitats. Two Sargassum genomes were generated in this study. The genome sizes of S. fusiforme and S. thunbergii were 438 and 376 Mbp, respectively, which are larger than the published genomes of the brown seaweed group, Ectocarpales. Expansion of the Sargassum genomes was significantly explained by the spread of transposable elements (TEs). Additionally, extensive gene duplications and their diversification occurred particularly through tandem, proximal, and dispersed duplications, which likely played an important role in response to environmental stress. Differentially expressed gene analysis under ambient and desiccation stress conditions confirmed that some duplicated genes respond to stress. We identified enhanced disease susceptibility 1 (EDS1) genes that promote salicylic acid (SA) biosynthesis, and their expansion is likely linked to TEs. We also confirmed the potential role of EDS1 by analyzing its subcellular localization (in Arabidopsis thaliana) and quantified the increased SA levels under desiccation conditions. This study demonstrates that the genomic evolution has played a critical role in allowing S. fusiforme and S. thunbergii to adapt to harsh intertidal conditions. The genomic resources of Sargassum species provided here will be instrumental in advancing future research, aiding in the understanding of adaptive evolution in brown algae.

  PublisherOA PDFDOI

• Gene expression and co-expression heterogeneity patterns and biodemography analyses during the cell cycle encourage aging studies in archaea

  GeroScience · 2025-07-04 · 1 citations

  articleOpen access
  PublisherOA PDFDOI

• Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes

  Nature Communications · 2025-07-01 · 9 citations

  articleOpen access

  Similar to many eukaryotes, the thermoacidophilic archaeon Saccharolobus islandicus follows a defined cell cycle program, with two growth phases, G1 and G2, interspersed by a chromosome replication phase (S), and followed by genome segregation and cytokinesis (M-D) phases. To study whether and which other processes are cell cycle-coordinated, we synchronized cultures of S. islandicus and performed an in-depth transcriptomic analysis of samples enriched in cells undergoing the M-G1, S, and G2 phases, providing a holistic view of the S. islandicus cell cycle. We show that diverse metabolic pathways, protein synthesis, cell motility and even antiviral defense systems, are expressed in a cell cycle-dependent fashion. Moreover, application of a transcriptome deconvolution method defined sets of phase-specific signature genes, whose peaks of expression roughly matched those of yeast homologs. Collectively, our data elucidates the complexity of the S. islandicus cell cycle, suggesting that it more closely resembles the cell cycle of certain eukaryotes than previously appreciated.

  PublisherDOI

• Gene transfer drives community cooperation in geothermal habitats

  Trends in Microbiology · 2025-06-20 · 2 citations

  reviewOpen access1st authorCorresponding

  Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.

  PublisherDOI

• Genetic Transfer in Action: Uncovering <scp>DNA</scp> Flow in an Extremophilic Microbial Community

  Environmental Microbiology · 2025-02-01 · 3 citations

  articleOpen accessSenior author

  Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.

  PublisherOA PDFDOI

• Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef

  Coral Reefs · 2025-11-09

  articleOpen accessSenior author

  Abstract GFP-like and RFP-like proteins serve diverse functional roles in corals, including photoprotection, prey capture, and algal symbiont attraction. This study investigated the diversity of biofluorescence patterns in 27 coral colonies of Porites cf. lutea and Porites cf. lobata from the Great Barrier Reef, Australia. We used comparative methods to characterize the extant fluorescence patterns under blue and green light for excitation, their relationship to the Porites phylogeny built using host animal 18S-28S rDNA sequence data. We also studied the impact of thermal stress on green and red fluorescence in a single coral genotype to assess stability of the observed signal. Overall, we identified six broad fluorescence patterns: star, uniform, absent, tentacles, oral region, and tentacle tips. Population analyses demonstrate that a single lineage of Porites may express divergent and distinct GFP-like patterns that are shared by all polyps in a colony. This suggests that biofluorescent proteins may confer an array of adaptive functions that allow Porites species to thrive in different ecosystems under different stressors. The reorganization of both green and red fluorescence distributions to uniform patterning under thermal stress suggests these proteins may provide a biomarker of thermal stress. Thus, the potential for GFP/green fluorescence and RFP/red fluorescence screening as a non-invasive tool to assess reef health and adaptive responses warrants further investigation, particularly in the context of climate change-driven stress events.

  PublisherOA PDFDOI

Recent grants

• Collaborative Research: Edge CMT: Polygenic traits of heat stress phenome in coral "dark genes" from genome to functional applications

  NSF · $509k · 2021–2026

• NIH Grant R01ES013679

  NIH · $1.1M · 2011

• NSFOCE-BSF: COLLABORATIVE RESEARCH: Elucidating adaptive potential through coral holobiont functional integration

  NSF · $611k · 2018–2023

• Collaborative Research: Using Transcriptomics to Understand Mechanisms of Stress Response and Toxin Production in Pathogenic and Toxigenic Microbes in Tropical Marine Waters

  NSF · $277k · 2011–2015

• Collaborative Research, RedToL: Phylogenetic and Genomic Approaches to Reconstructing the Red Algal (Rhodophyta) Tree of Life

  NSF · $744k · 2009–2014

Frequent coauthors

• Cheong Xin Chan

  Monash University

  115 shared

• Hwan Su Yoon

  Sungkyunkwan University

  112 shared

• Timothy G. Stephens

  Rutgers, The State University of New Jersey

  54 shared

• Dana C. Price

  Rutgers, The State University of New Jersey

  54 shared

• Erika Lindquist

  Lawrence Berkeley National Laboratory

  44 shared

• Pedro M. Coutinho

  44 shared

• Huan Qiu

  Anhui Medical University

  43 shared

• Igor V. Grigoriev

  Lawrence Berkeley National Laboratory

  42 shared

Education

• PhD, Biology

  Simon Fraser University

  1989