Arijit Mukherjee | HHMI Postdoctoral Fellow

About

I am an HHMI Postdoctoral Fellow in the Department of Biology at the University of North Carolina at Chapel Hill, working with Prof. Jeffery L. Dangl. My work focuses on plant–microbe interactions in the context of disease, currently investigating how commensal bacteria prime plant immunity against the obligate biotrophic pathogen Hyaloperonospora arabidopsidis (downy mildew) in Arabidopsis.

I completed my Ph.D. in Biological Sciences at the National University of Singapore (NUS), where I worked with Assoc. Prof. Sanjay Swarup on the role of plant–associated microbiomes in sulfur nutrition, uncovering a trans-kingdom fitness trade-off between plants and their microbiome. Before that, I earned an M.Sc. in Biotechnology at the Indian Institute of Technology Bombay, working with Prof. Sanjeeva Srivastava on proteomics of formalin-fixed, paraffin-embedded clinical tissue.

I am currently on the academic job market seeking faculty positions in plant biology, plant–microbe interactions, and microbiome research.

5 (co-)first-author publications 4 co-authored publications 4 editorial publications 1 granted patent 67 citations h-index: 5

Research

My research addresses how plant–associated microbiomes shape plant nutrition, fitness, and immunity. Using approaches spanning synthetic bacterial communities, high-throughput screening, and molecular genetics, I study how microbial partners can both compete with and protect their plant hosts — from trans-kingdom trade-offs in sulfur nutrition to commensal-mediated priming of innate immunity against pathogens. A central goal of my future lab will be to dissect the molecular mechanisms by which beneficial microbes reprogram plant immune and metabolic pathways, with an eye toward translating these principles into more resilient, sustainable crop systems.

Publications

* denotes equal contribution · Google Scholar profile

(Co-)First-Author Publications

In Silico Prediction and In Vitro Validation of Bacterial Interactions in the Plant Rhizosphere Using a Synthetic Bacterial Community

Mukherjee A, Tan BH, Swarup S

Bio-protocol, 15(21):e5496, 2025.

DOI PubMed

A bacterial signal coordinates plant–microbe fitness trade-off to enhance sulfur deficiency tolerance in plants

Mukherjee A, Mazumder M, Verma A, Tikariha H, Bhattacharya R, Ooi QE, Swarup S

Cell Host & Microbe, 33(10):1748–1764.e6, 2025.

DOI PubMed

Sulfur traits in the plant microbiome: implications for sustainable agriculture

Mukherjee A, Han L, Mukhopadhyay S, Kopriva S, Swarup S

Trends in Microbiology, 33(6):635–649, 2025. (Review)

DOI PubMed

Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes

Mukherjee A*, Tikariha H*, Bandla A, Pavagadhi S, Swarup S

mSystems, 8(4):e00387-23, 2023.

DOI PubMed

Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples

Mukherjee A*, Ghosh S*, Biswas D, Rao A, Shetty P, Epari S, Moiyadi A, Srivastava S

OMICS: A Journal of Integrative Biology, 26(9):512–520, 2022.

DOI PubMed

Co-authored Publications

Xenobiotic dynamics in mangroves and peatlands: Microbial mechanisms for nature-based mitigation

Mukhopadhyay S, Ooi QE, Mukherjee A, Bhattacharya R, Sarkar P, Tan ZD, Phang B, Chey SL, Lupascu M, Bandla A, Swarup S

Journal of Hazardous Materials, 511:142149, 2026. (Review)

DOI PubMed

Live-exudation assisted phytobiome culturomics system (LEAP-CS): a high-throughput culturomics system for studying plant–microbiome interactions through diffusible metabolites

Mazumder M, Pavagadhi S, Bhattacharya R, Mukherjee A, Majedi SM, Hin ITC, Swarup S

Plant Methods, 2026. (Epub ahead of print)

DOI PubMed

Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita

Nissa MU, Pinto N*, Mukherjee A*, Reddy PJ, Ghosh B, Sun Z, Ghantasala S, Chetanya C, Shenoy SV, Moritz RL, Goswami M, Srivastava S

Journal of Proteome Research, 21(2):420–437, 2022.

DOI PubMed

Editorial Publications

Beyond water transport: aquaporins mediate systemic ROS signalling to enhance stress resilience in rice roots

Mukherjee A, Sharma G

Plant Physiology, 2026. kiag362. (Epub ahead of print)

DOI PubMed

A plant–microbe treaty: coordinated action of plant and microbial proteins strengthens immunity in apple

Mukherjee A

Plant Physiology, 200(4):kiag156, 2026.

DOI PubMed

Distinct effects of Citric Acid on Primary and Anchor Roots

Mukherjee A

Plant Physiology, 2026. kiag309.

DOI

Curriculum Vitae

⇓ Download Full CV (PDF)

Education

2020 – 2024

National University of Singapore (NUS)

Ph.D. in Biological Sciences

Advisor: Assoc. Prof. Sanjay Swarup · Dissertation: “Role of Microbiomes in Plant Sulfur Nutrition”

2017 – 2019

Indian Institute of Technology Bombay (IIT Bombay), India

M.Sc. in Biotechnology

Advisor: Prof. Sanjeeva Srivastava · Dissertation: “Formalin-fixed Paraffin Embedded (FFPE) Tissue-based Proteomics Workflow: A Case Study on Brain Tumor”

2013 – 2017

Banaras Hindu University (BHU), India

B.Sc. in Agriculture

Research & Professional Experience

Apr 2025 – Present

Howard Hughes Medical Institute · University of North Carolina at Chapel Hill

Postdoctoral Researcher · Advisor: Prof. Jeffery L. Dangl

Project: Deciphering the immune priming mechanisms of commensal bacteria against the downy mildew pathogen of Arabidopsis.

Developed an in vitro method to screen for direct interaction between obligate biotroph pathogen and commensal bacterial strains
Developed a high-throughput method for large-scale screening of commensal bacteria–mediated immune priming against the downy mildew pathogen of Arabidopsis

Jan 2020 – Dec 2024

National University of Singapore (NUS), Singapore

Graduate Student Researcher · Advisor: Assoc. Prof. Sanjay Swarup

Pioneered the concept of trans-kingdom fitness trade-off in plant–microbiome systems while studying plant sulfur nutrition in the presence of complex microbial communities (Cell Host & Microbe, 2025)
Identified conserved sets of specialized metabolites produced by plant-associated microbial members (mSystems, 2025)
Provided a systems-level understanding of sulfur at the plant–atmosphere–microbe crossroads, with insights into applications (Trends in Microbiology, 2025)

May 2019 – Dec 2019

Indian Institute of Technology Bombay (IIT Bombay)

Junior Research Fellow · Advisor: Prof. Sanjeeva Srivastava

Proteome Atlas of a widely cultivated fish: contributed to developing a comprehensive and in-depth Proteome Atlas of Rohu, a widely cultivated fish in India (Journal of Proteome Research, 2022)
Label-free proteomics workflow from clinically relevant formalin-fixed and paraffin-embedded (FFPE) tissues

Jun 2018 – Apr 2019

Indian Institute of Technology Bombay (IIT Bombay)

Master’s Student Researcher · Advisor: Prof. Sanjeeva Srivastava

Formalin-fixed and paraffin-embedded (FFPE) tissue-based proteomics: developed a workflow for proteomic profiling of meningioma FFPE tissues (OMICS: A Journal of Integrative Biology, 2022)
Collaborative leadership: worked with clinicians to accrue FFPE specimens from cancer hospitals

Granted Patent

Granted Jul 2026

Protein extraction methods and quantification assay for biologically important proteins in Labeo rohita

Indian Patent No. 596493 · Application No. 202021021988

Awards & Fellowships

2026

Travel Award

American Society of Plant Biologists (ASPB)

2020

Graduate Research Fellowship

Jointly awarded by Singapore Centre for Environmental Life Sciences Engineering (SCELSE) and National University of Singapore (NUS)

2019

All India Rank 3 out of ~12,000 candidates

Junior Research Fellowship (JRF) Examination, Council of Scientific and Industrial Research (CSIR)

2019

All India Rank 17 out of ~14,000 candidates

Graduate Aptitude Test in Engineering (GATE), Life Sciences category

2017

All India Rank 2 & 4 out of ~7,000 candidates

Joint Admission Test for M.Sc. (JAM), Biological Science and Biotechnology categories, IITs

Teaching

2022

Molecular Biology

Graduate Student Instructor · NUS

Taught molecular biology to sophomore undergraduate students and assessed exam papers

2023 – 2024

Microbial Ecology

Graduate Student Instructor · NUS

Supervised 70–80 master’s students on introductory microbiome data analysis

2022 – 2023

Biological Data Analysis Using R

Graduate Student Instructor · NUS

Led the course for master’s and undergraduate students to learn R programming for statistical analysis of biological data

Mentorship

2026 – Present

Xie Yuanchen, Undergraduate Student · UNC Chapel Hill

Screening Arabidopsis mutants to identify conserved signaling pathways for rhizobacteria-mediated immune priming

Jul–Aug 2026

Ichiho Hige, High School Student · UNC Chapel Hill

Identification of direct inhibition of candidate bacterial strains towards the obligate biotroph downy mildew pathogen in Arabidopsis

2025 – 2026

Sanya Arya, Undergraduate Student · UNC Chapel Hill

Development of a high-throughput screening system to identify candidate bacterial strains that protect against Hyaloperonospora arabidopsidis

2024 – 2025

Boon Hao Tan, Undergraduate Student · National University of Singapore

Mapping bacterial interactions in a synthetic rhizosphere bacterial community (published)

2022 – 2023

Li Han, Undergraduate Student

Diversity and distribution of sulfur metabolic genes in phytobiomes (published)

Selected Talks & Presentations

Jul 2025

“Fitness Tradeoffs Between Plants and Their Microbiome”

Invited Talk · National University of Singapore (Inviter: Dr. Yuchen Long)

Jul 2026

Poster Presentation

Plant Biology 2026

Jul 2023

Poster Presentation

Plant Biology 2023

Jul 2022

Poster Presentation

SCELSE Retreat 2022

Professional Service & Leadership

2026 – 2028

Assistant Feature Editor

Plant Physiology

Writing news & views articles for published research in the journal; collaborating with peer researchers and editorial teams

2024 – 2025

Plantae Fellow

American Society of Plant Biologists (ASPB)

Writing summaries of published articles broadly related to plant biology

Ongoing

Reviewer

Microbial Ecology

2022 – 2023

Coordinator, Gap Summit 2022

University of Cambridge, UK

Coordinated 100 Leaders of Tomorrow (LoT) for an entrepreneurial pitching competition; recruited startup CEOs and staff as mentors; prepared competition themes

2022 – 2024

Resident Assistant

University Town Residence, National University of Singapore

Planned and organized wellness events for ~450 student residents; provided peer support through counselling; managed a volunteer team and expenses for resident housing

2022 – 2023

Placement Coordinator

Graduate Students’ Society, NUS

Contacted companies to participate in campus placement program; managed a team of six volunteers spearheading campus recruitment

2022 – 2023

President

DBS Graduate Students’ Society, Department of Biological Sciences, NUS

Managed a team of eight volunteers spearheading events for graduate student well-being; arranged sponsorship for departmental events

2024 – 2025

Coordinator, Plant Forum

Department of Biological Sciences, NUS

Conducted monthly seminars with plant science researchers (graduate students and postdocs) within the department

Outreach

Jul 2018

Instructor, Proteomics Bootcamp

IIT Bombay

Developed and taught hands-on modules on computational biology and plant immunity to ~50 high school and university students from underrepresented backgrounds

2024

“Expanding My Horizons” (personal essay)

Science, 378(6616), 218

Worked with a Science editor to share how co-curricular activities can shape personal development and career outcomes

Contact

I welcome inquiries from search committees. The best way to reach me is by email.

Email: arijitm@unc.edu
Office: Department of Biology
University of North Carolina at Chapel Hill
Chapel Hill, NC
Google Scholar: View profile →
ORCID: 0000-0003-3329-3535
LinkedIn: View profile →
GitHub: github.com/arijitnus

Letters of reference available upon request.