Microbial Ecologist & Computational Biologist

Plants choose their microbes. What happens to that choice as the climate changes?

I study the microbes living in and around plant roots and leaves — the ones that help plants take up nutrients, tolerate drought and heat, and resist disease — and how that partnership shifts under a changing climate and different soil management.

Max Planck Institute of Colloids and Interfaces, Potsdam Guest Scientist, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)
About

Bridging microbial ecology and plant science

I am a microbial ecologist and computational biologist currently working as a postdoctoral researcher at the Max Planck Institute of Colloids and Interfaces, and as a Guest Scientist at the Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam. My work focuses on the ecological mechanisms underlying plant–microbiome interactions and their role in soil health, plant resilience, and sustainable agricultural systems.

Before this, I spent over two years at the University of Western Australia's School of Agriculture and Environment, working within the Soil Science Challenge as a microbial ecologist studying plant–microbe interactions under soil organic and biological amendments — running pot and field trials, handling bioinformatics and statistical analysis, and supervising Master's and PhD students.

I completed my PhD at the Hawkesbury Institute for the Environment, Western Sydney University, where my doctoral research explored the drivers and mechanisms of plant microbiome assembly — integrating microbial ecology, plant biology, and computational approaches across glasshouse and large-scale field experiments spanning eucalypts to native and exotic Australian grasses.

I'm always keen to engage in collaborative research across disciplines and institutions.

Collecting soil samples in a eucalypt woodland during a field trial
Current role
Postdoctoral Researcher, Max Planck Institute of Colloids and Interfaces
Also affiliated with
Guest Scientist, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)
PhD
Hawkesbury Institute for the Environment, Western Sydney University (2024)
Based in
Potsdam, Germany
Research focus

What I study

Diagram illustrating plant microbiome research: tree and soil profile, root cross-section, and a word cloud of ecosystem function terms

Plant–microbiome interactions

How host plants select, recruit, and shape the microbial communities living in and around them, across species from eucalypts to cereal crops.

Soil and rhizosphere microbiome ecology

Tracing how soil organic amendments — biochar, compost, digestate-based products — reshape microbial communities and soil function over time.

Microbiome-mediated stress tolerance

Identifying how microbial partners help plants withstand drought, heat, and other abiotic stress, and what that means for resilient agriculture.

Functional and taxonomic profiling

Applying amplicon sequencing, shotgun metagenomics, and transcriptomics to characterise microbial communities at both taxonomic and functional resolution.

Integrating ecology with molecular biology

Combining microbial ecology with plant physiological and molecular responses to build a mechanistic picture of host–microbiome relationships.

Experience

Academic & professional appointments

06/2026 — Present
Postdoctoral Researcher
Max Planck Institute of Colloids and Interfaces, Potsdam, Germany · Guest Scientist, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)
Working on ecological mechanisms of plant–microbiome interactions and their role in soil health, plant resilience, and sustainable agricultural systems.
10/2023 — 05/2026
Postdoctoral Research Associate
School of Agriculture and Environment, University of Western Australia, Perth
Microbial ecologist on the Soil Science Challenge, focused on plant–microbe interactions under soil organic and biological amendments. Ran pot and field trials, performed bioinformatics and statistical analysis, managed project data, and supervised Master's and PhD students.
11/2016 — 09/2019
Senior Research Assistant
Bose Institute, Kolkata, India
DBT West Bengal-sponsored project on genome-wide transcriptome analysis of MYMIV-stress related genomic resources in blackgram — transcriptome profiling of differentially expressed genes and identification of SSR-based resistance markers.
07/2015 — 10/2016
Training in Charge, Computational Biology Division
The Biome, Kolkata
R&D activities, delivered bioinformatics training modules, and coordinated workshops.
04/2015 — 10/2017
Guest Lecturer
Ambit Education Centre, Sikkim Manipal University, Kolkata
Lecturer for biotechnology and bioinformatics courses.
12/2013 — 06/2015
Project Assistant
DBT Centre for Bioinformatics, Presidency University, Kolkata
DBT-funded "RNAiIDB" project — secondary and tertiary structure analysis of microRNA sequences and target identification; resource person for workshops.
Education

Educational qualifications

Doctor of Philosophy
10/2019 — 06/2024
Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
Thesis: "Drivers and mechanisms of microbiome assembly in plants" — explored ecological processes underpinning plant microbiome assembly across eucalypts and native/exotic Australian grasses, combining glasshouse and large-scale field experiments with soil measures, host traits, and amplicon sequencing.
M.Sc. in Biotechnology
07/2011 — 06/2013
Vidyasagar University, Midnapore, India
Cell and Molecular Biology, Biochemistry, Microbiology, Immunology, Bioinformatics, Biostatistics, Plant Tissue Culture.
B.Sc. (Honours) in Biotechnology
07/2008 — 06/2011
Burdwan University, West Bengal, India
Publications

Selected & complete publication record

30 works across peer-reviewed journals and conference proceedings. Click a section to expand.

Peer-reviewed publications 24 +
Jayaramaiah, R.H., Singh, P.K., Kaur, S., Maisnam, P., Singh, B.K. Microbiome genomics and climate resilience. Genomic Solutions for Breeding Climate-Resilient Crops (Accepted)
Singh, P.K., Martins, C., Jayaramaiah, R.H., Egidi, E., Macdonald, C., Wang, J., Xiong, C., Batista, B., Qui, G., Reich, P.B., Delgado-Baquerizo, M., Singh, B.K. (2026). Plant phylogenetic relatedness explains host microbiome assembly. Plant and Soil · doi.org/10.1007/s11104-026-08318-9
Liu, H., Martins, C.S.C., Zhou, G., Jayaramaiah, R.H., Zhang, H., Li, J., Singh, P.K., Yan, Z., Wang, J., Reich, P., Eisenhauer, N., Delgado-Baquerizo, M., Singh, B.K. The diversity of soil protists shapes ecosystem functions under climate change. Global Change Biology · doi.org/10.1111/gcb.70692
Zhang, Z., Sharma, M., O'Connor, J., Singh, P.K., Waite, I., Mickan, B., Bolan, N., Abbott, L., Jenkins, S., Gurung, SK. (2025). Co-application of struvite with phosphorus-solubilising bacteria enhances soil microbial activity and bioavailable phosphorus in alkaline soil. Journal of Environmental Management · doi.org/10.1016/j.jenvman.2025.128408
Rajapakshe, O.L., Gurung, S.K., O'Connor, J., Mickan, B.S., Singh, P.K., Waite, I.S., De Mascio, C., Abbott, L.K., Jenkins, S.N. (2025). Lauric acid controls nitrogen release and inhibits nitrification in wastewater-enriched compost. Journal of Environmental Management · doi.org/10.1016/j.jenvman.2025.126778
Zheng, Y., Abbott, L., Bolan, N., Singh, P., Jenkins, S., Mickan, B. (2025). Evaluating the potential of digestate-loaded biochar in improving soil biological health and plant nutrition with less greenhouse gas emissions. Environmental Pollution · dx.doi.org/10.1016/j.envpol.2025.126431
Li, J., Liu, H., Wang, J., Macdonald, C., Singh, P., Cong, V., Klein, M., Baquerizo, M., Singh, B. (2025). Enhancing plant drought resistance through specific enrichments in plant microbiomes. Cell Host & Microbe · doi.org/10.1016/j.chom.2025.05.002
Ahmed, S., Singh, P., Middleton, J., Merritt, D., Jenkins, S., Nichols, P. (2025). Impact of seed maturation on the morphological characteristics, nutritional elements, microbiome community composition, and germinability of subterranean clover seeds. Grass and Forage Science · doi.org/10.1111/gfs.12725
Zarezadeh, S., Zheng, Y., Jenkins, S.N., Mercer, G.D., Moheimani, N.R., Singh, P.K., Mickan, B.S. (2025). Sustainable soil management in agriculture under drought stress: utilizing waste-derived organic soil amendments and beneficial impacts on soil bacterial communities. Applied Soil Ecology · doi.org/10.1016/j.apsoil.2025.105870
Gurung, S.K., Mickan, B.S., Middleton, J., Singh, P.K., Jenkins, S.N., Rengel, Z., Siddique, K.H.M., Solaiman, Z.M. (2024). Manure-derived black soldier fly frass enhanced the growth of chili plants (Capsicum annuum L.) and altered rhizosphere bacterial community. Applied Soil Ecology · doi.org/10.1016/j.apsoil.2024.105605
Birnbaum, C., Dearnaley, J., Egidi, E., Frew, A., Hopkins, A., Powell, J., Aguilar-Trigueros, C., Liddicoat, C., Albornoz, F., Heuck, M.K., Dadzie, F.A., Florence, L., Singh, P.K., Mansfield, T., Rajapaksha, K., Stewart, J., Rallo, P., Peddle, S.D., Chiarenza, G. (2023). Integrating soil microbial communities into fundamental ecology, conservation, and restoration: examples from Australia. New Phytologist · doi.org/10.1111/nph.19440
Singh, P.K., Egidi, E., Macdonald, C., Singh, B. (2023). Host selection has a stronger impact on leaf microbiome assembly compared to land-management practices. Journal of Sustainable Agriculture and Environment · doi.org/10.1002/sae2.12043
Sengupta, S., Singh, P.K., Ganguli, S. (2022). Insights into the core bacterial consortia of root endophytes in two cultivated varieties of rice in West Bengal. Environmental and Experimental Biology · doi.org/10.22364/eeb.20.19
Ganguli, S., Singh, P.K., Pal, A. (2020). Transcriptome based identification of small RNA in plants: the need for robust prediction algorithms. In: Guleria, P. (Ed.), Plant Small RNA: Biogenesis, Regulation and Application, Elsevier · doi.org/10.1016/B978-0-12-817112-7.00004-3
Kundu, A.*, Singh, P.K.*, Dey, A., Ganguli, S., Pal, A. (2019). Complex molecular mechanisms underlying MYMIV-resistance in Vigna mungo revealed by comparative transcriptome profiling. Scientific Reports (equal contributions) · doi.org/10.1038/s41598-019-45383-w
Ghosh, U.D., Ghosh, M.M., Singh, P.K., Ganguli, S. (2019). Comparative profiling of the rhizospheric soil of Typha angustifolia L. from heavy metal contaminated and free sites reveals the selective abundance of γ-Proteobacteria and β-Proteobacteria. Indian Journal of Experimental Biology
Singh, P.K., Ganguli, S., Pal, A. (2018). Functions of long non-coding RNAs in plants: a riddle to explore. The Nucleus · doi.org/10.1007/s13237-018-02494
Singh, P.K., Ganguli, S., Pal, A. (2018). Screening and identification of putative long noncoding RNAs from transcriptome data of a high yielding blackgram (Vigna mungo) cv. T9. Data in Brief · doi.org/10.1016/j.dib.2018.01.043
Singh, P.K., Patel, A., Ganguli, S., Pal, A. (2017). Molecular modeling and simulation of three important components of plant–pathogen interaction cascade in Vigna mungo. Bioinformation · doi.org/10.6026/97320630013323
Ganguli, S., Rahaman, S., Bera, A.R., Vishal, V., Malik, S., Roopalakshmi, K., Singh, P.K. (2017). Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans. Genomics Data · doi.org/10.1016/j.gdata.2017.09.001
Sengupta, S., Ganguli, S., Singh, P.K. (2017). Metagenome analysis of the root endophytic microbial community of Indian rice (O. sativa L.). Genomics Data · doi.org/10.1016/j.gdata.2017.02.010
Singh, P.K., Ghoshal, J.R., Ganguli, S., Basu, P., Vishal, V., Bera, A.R., Pandey, A., Banik, R. (2016). Identification of conserved regulatory motif signatures in human miRNA upstream regions. 2016 International Conference on Bioinformatics and Systems Biology (BSB), IEEE Xplore · doi.org/10.1109/BSB.2016.7552128
Ganguli, S., Gupta, M.K., Basu, P., Banik, R., Singh, P.K., Vishal, V., Bera, R.A., Hirak, J., Das, S.G. (2014). Intelligent Access to Sequence and Structure Databases (IASSD) — an interface for accessing information from major web databases. Bioinformation · doi.org/10.6026/97320630010764
Singh, P.K., Banik, R., Chakraborty, H.J., Das, S.G., Ganguli, S., Datta, A. (2014). Identifying overlapping phylogenetic and geographic roots of HIV-1 evolution through computational analyses. International Letters of Natural Sciences · doi.org/10.18052/www.scipress.com/ILNS.7.23
Conference presentations 6 +
Singh, P.K., Zheng, Y., Bolan, N., Abbott, L., Siddique, K.H.M., Mickan, B., Jenkins, S. Organic amendments enhance root microbiome resistance and wheat yield in drought. Symposium for the Use of Organic Soil Amendments, 2025, Queensland, Australia (poster presentation)
Zaman, M., Shaukat, H., Singh, P.K., Abbott, L. Legacy effects of organic amendments and pastures on soil microbial communities. Symposium for the Use of Organic Soil Amendments, 2025, Queensland, Australia
Shaukat, H., Singh, P.K., Abbott, L., Jenkins, S. Impact of compost-fertiliser co-application on soil function and economic returns. Symposium for the Use of Organic Soil Amendments, 2025, Queensland, Australia
Singh, P.K., Martins, C., Jayaramaiah, R.H., Egidi, E., Macdonald, C., Reich, P.B., Delgado-Baquerizo, M., Singh, B.K. Plant phylogenetic relatedness explains host microbiome assembly. JAM 12, Annual Joint Academic Microbiology Seminars, 2023 (oral presentation)
Singh, P.K., Egidi, E., Macdonald, C., Singh, B. Differential response of soil, root, and leaf microbiome of Eucalyptus saligna after decade-long management. ESA-SCBO 2022, Joint Conference of the Ecological Society of Australia and the Society for Conservation Biology Oceania (oral presentation)
Singh, P.K., Martins, C., Jayaramaiah, R.H., Egidi, E., Macdonald, C., Singh, B.K. Deciphering the ecological processes that underpin microbial colonization of plants. ASPS 2021, Australian Society of Plant Scientists — NSW Node (oral presentation)
Skills

Technical & methodological toolkit

Wet Lab
Gas Chromatography–Mass Spectrometry DNA / RNA isolation PCR & qPCR Gel Electrophoresis Haematological Parameters Assay Soil Nutrient Analysis Plant Tissue Culture Microbial Culture
Dry Lab — Metagenomics
Shotgun Metagenomics Mothur QIIME2 SourceTracker USEARCH LEfSe iVikodak MEGAN PICRUSt CLC Metagenomics Workbench MG-RAST DADA2 Differential Abundance Analysis Network Analysis
Ecological & Statistical Packages
Phyloseq VEGAN Microbiome Random Forest indicspecies
RNA-Seq
BLAST2GO CLC Genomics Workbench Galaxy Transcriptomic Packages MapMan GEO2R EdgeR DESeq2 Salmon Kallisto Trinity Bowtie StringTie CPC2 GATK MiRDeep2
Programming
Perl Python R
Field-based
Large-scale biodiversity & crop experiments Plant & soil sample collection Phenotyping Plant trait estimation
Funding & awards

Recognition

Canada Impact Research and Training Award (CIRTA)
2026
Prestigious global postdoctoral fellowship for "Deciphering mechanisms underpinning cultivar-dependent responses of the Canadian winter wheat microbiome for improving soil health and nitrogen use efficiency." Declined due to a commitment to the Max Planck Institute position.
CAD 140,000
School Citizen Award
2024
For conducting a statistics workshop for HDR students, School of Agriculture and Environment, University of Western Australia.
Western Sydney Postgraduate Research Scholarship
2019
For research on plant–soil microbiome interactions — AUD 90,000 stipend plus AUD 120,000 fee waiver.
AUD 210,000 total value
Peer review activities
PLOS ONE Journal of Protein Research and Bioinformatics Journal of Sustainable Agriculture and Environment (Wiley) Environmental Microbiology Nucleus (India)
Mentorship

Workshops organised

Introductory workshop on statistical data analysis using R — UWA School of Agriculture and Environment, May 2024
Introductory workshop on bioinformatics and amplicon sequencing analysis — UWA School of Agriculture and Environment, July 2024
15 additional workshops delivered across prior appointments
Contact

Let's talk research.

Open to collaborations across disciplines and institutions — in soil microbial ecology, plant–microbiome interactions, or sustainable agriculture. Reach out by email or connect through the links.