Contact Dr Rachel Samson P
Areas of expertise
- Environment and Health
- Water Science and Engineering
Background
Dr Rachel Samson P. is a Research Fellow at Cranfield University with expertise in microbial ecology, riverine microbiomes, and phage-enabled approaches for water and environmental health. Her research examines bacteriophages and microbial communities across connected matrices, including water, wastewater, bioaerosols and soil, with emphasis on surveillance, source attribution, and intervention design for pathogen and antimicrobial resistance risk reduction. She integrates culture-based phage methods with sequencing-led microbiome and virome profiling to generate actionable outputs for treatment performance assessment and environmentally responsible mitigation.
This research aligns with the United Nations Sustainable Development Goals through defined pathways. It supports SDG 3 by improving detection and control of waterborne pathogens and AMR-relevant risks. It supports SDG 6 by advancing viral indicators and biologically grounded treatment verification. It supports SDG 14 by reducing the discharge of antibiotic-resistant bacteria and associated genetic determinants into receiving waters. It supports SDG 15 by promoting eco-compatible interventions that protect freshwater habitats and microbial biodiversity.
Research Focus (Highlights)
1. Somatic coliphages and viral indicators for water safety
Evaluated somatic coliphages as culture-based viral indicators of treatment performance and and characterised coliphage diversity... using sequencing-enabled plaque and community approaches.
2. Microbial ecology and riverine microbiomes
Investigated microbial diversity and resistome dynamics along 2,500 km of the Ganges River.
3. Phage-enabled biotechnologies
Applied bacteriophages for biofouling control and AMR-relevant risk reduction in water and environmental systems.
Key Objective
Advance cross-matrix microbiome and virome research through next-generation sequencing and translate this evidence into phage-enabled tools for environmental monitoring and microbial risk assessment.
Impact and Vision
- Environmental and Public Health
Advancing eco-compatible, phage-based solutions that strengthen microbial risk assessment across water, wastewater and connected environments.
- Innovation and Translation
Translating microbiome and virome findings into decision-relevant outputs for utilities and stakeholders, including viral indicators and sequencing-enabled profiling of bacteriophage diversity.
- Engagement and advocacy
Supporting sustainable phage applications in water treatment, biofilm control, and pathogen surveillance through clear evidence thresholds and fit-for-purpose guidance
Recent research streams
Bioaerosols and cross-matrix integration (September 2025 to present)
-Developing low-input microbiome and virome workflows for bioaerosols with next-generation sequencing.
-Comparing airborne microbial and viral signatures with corrresponding environmental reservoirs for source attribution and cross-matrix interpretation of microbial risk
Somatic Coliphage Diversity in Drinking Water
-Characterising coliphage populations across treatment stages.
-Assessing phages as natural indicators for water quality monitoring.
Core Techniques and Tools
- Molecular Biology: DNA/RNA extraction (environmental and phage samples); PCR, Sanger sequencing, quantitative RT-PCR for validation.
- Multiomics and Sequencing: Nanopore sequencing of Environmental samples, and viral concentrates, DNA amplification, Genome assembly and annotation pipelines.
- Phage Isolation and Quantification: plaque assays, water/water saturated sediment concentration, and filtration protocol
- Biofilm Assays and Microscopy: In vitro biofilm formation/disruption assays; light, inverted, and confocal microscopy to observe phage-bacteria interactions
Education
1. PhD Biological Sciences
– NCIM Resource Centre, CSIR-National Chemical Laboratory (Jan 2020 – July 2024)
– Thesis: Exploring The Microbiome of River Ganges and Harnessing the Potentials of Novel Phages Under One Health
2. MSc Microbiology
– Savitribai Phule Pune University (Jun 2015 – May 2017)
– Dissertation: Biochemical degradation of p-nitrophenol using bacterial isolates.
3. BSc in Microbiology
– B.P.H.E. Society’s Ahmednagar College (Jun 2012 – May 2015)
Research opportunities
- Microbiology
- Phage Biology
- Environmental Virology
- Multiomics through Nanopore Sequencing
- Microbiome
- River Biofilms
- River Ecology
- One Health
- SDG 3, 6, 14, 15
Current activities
- Leading the investigation of somatic coliphage diversity across drinking water treatment stages using culture-based and multiomics approaches.
- Associate Editor, npj Biofilms and Microbiomes
- Peer Reviewer for Environment International, Environmental Microbiology, Science of the Total Environment
Online Profiles
1. Google Scholar: Rachel Samson. P - Google Scholar
2. Scopus: Samson, Rachel - Author details - Scopus
3. ORCID: Dr Rachel Samson P (0009-0004-8901-2864) - ORCID
Publications
Articles In Journals
- Samson R, Pawar A, Khairnar K & Dharne M. (2025). Characterization of a novel Tequatrovirus phage from pristine stretch of the Ganges River, India, in reducing bacterial load from sewage water. Journal of Environmental Chemical Engineering, 13(3)
- Dandekar SS, Thanikkal S, Londhe A, Bhutada P, Saha U, .... (2025). Characterization of novel phages KPAФ1, KP149Ф1, and KP149Ф2 for lytic efficiency against clinical MDR Klebsiella pneumoniae infections. Microbial Pathogenesis, 202
- Mahajan V, Samson R & Dharne M. (2025). Genome mining, probiotic characteristics, and in-silico safety assessment of Limosilactobacillus fermentum AV7 isolated from Avocado fruit pulp. LWT, 216
- Samson R, Kumar S, Dastager S, Khairnar K & Dharne M. (2025). Deciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health. Microbiology Spectrum, 13(8)
- Pramanik R, Rajput V, Malik V, Nannaware K, Matra S, .... (2025). Long-Term Genomic Surveillance of SARS-CoV-2 in Campus Wastewater Depicts Lineage Trends and Public Health Implications during and after Omicron Waves. Environment & Health, 3(8)
- Singh S, Samson R & Hassard F. (2025). Phage therapy for environmental biotechnology applications. Frontiers in Microbiology, 16
- Mahale M, Samson R, Dharne M & Kodam K. (2024). Harnessing the potential of Achromobacter sp. M1 to remediate heavy metals from wastewater: Genomic insights and environmental applications. Journal of Hazardous Materials, 480
- Samson R, Dharne M & Khairnar K. (2024). Bacteriophages: Status quo and emerging trends toward one health approach. Science of The Total Environment, 908
- Rajput V, Pramanik R, Malik V, Yadav R, Samson R, .... (2023). Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India. Environmental Science and Pollution Research, 30(56)
- Samson R, Rajput V, Yadav R, Shah M, Dastager S, .... (2023). Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India. Science of The Total Environment, 872
- Rajput V, Samson R, Yadav R, Dastager S, Khairnar K, .... (2022). Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential. 3 Biotech, 12(6)
- Singh P, Ujjainiya R, Prakash S, Naushin S, Sardana V, .... (2022). A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys. Computers in Biology and Medicine, 146
- Samson R & Dharne M. (2022). COVID-19 associated mucormycosis: evolving technologies for early and rapid diagnosis. 3 Biotech, 12(1)
- Gohil K, Samson R, Dastager S & Dharne M. (2021). Probiotics in the prophylaxis of COVID-19: something is better than nothing. 3 Biotech, 11(1)
- Samson R, Rajput V, Shah M, Yadav R, Sarode P, .... (2020). Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities. Chemosphere, 252
- Samson R, Navale GR & Dharne MS. (2020). Biosensors: frontiers in rapid detection of COVID-19. 3 Biotech, 10(9)
- Samson R, Bodade R, Zinjarde S & Kutty R. (2019). A novel Sphingobacterium sp. RB, a rhizosphere isolate degrading para-nitrophenol with substrate specificity towards nitrotoluenes and nitroanilines. FEMS Microbiology Letters, 366(14)
- Samson R, Shah M, Yadav R, Sarode P, Rajput V, .... (2019). Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges. Science of The Total Environment, 674