Functional Redundancy and Metabolic Flexibility of Microbial Communities in Two Mid-Atlantic Bays

🧠 Background & Motivation

Species and communities respond differently to environmental stress depending on the extent of functional redundancy within the system. In microbial ecosystems, functional redundancy (FRed) can buffer ecosystem processes against disturbance by allowing multiple taxa to perform similar functions. However, the relationship between functional redundancy, metabolic flexibility, and ecosystem resilience remains poorly understood, particularly in dynamic coastal systems.

Estuaries are ideal natural laboratories for studying these relationships. They experience rapid environmental fluctuations driven by seasonality, nutrient inputs, salinity gradients, hypoxia, and anthropogenic stress, often leading to long-term ecosystem degradation. Comparing geographically proximate yet biologically distinct estuaries allows disentangling how community composition and function respond to similar stressors.

In this project, I integrated metagenomics, metatranscriptomics, and genome-resolved analyses across seasonal samples to quantify microbial composition, metabolic potential, activity, and functional redundancy in the Chesapeake and Delaware Bays (USA). This work combines ecological theory with large-scale multi-omics data and statistical modeling to explore how microbial communities maintain ecosystem function under disturbance.

🎯 Research Questions & Objectives

• How does functional redundancy vary across seasons and between estuarine systems?
• Do microbial communities rely on metabolic flexibility (e.g., photoheterotrophy, lithoheterotrophy) to maintain ecosystem processes under stress?
• Are specific metabolic pathways (e.g., energy acquisition) more functionally redundant than others?
• How do DNA-based metabolic potential and RNA-based activity differ in shaping functional redundancy?
• Are communities with high functional diversity but low redundancy more vulnerable to disturbance?
• Does higher functional redundancy necessarily translate to greater ecosystem resilience?

👨‍🔬 My Role

This project represents my primary postdoctoral research.

• Designed the conceptual framework linking functional redundancy, metabolic flexibility, and ecosystem resilience
• Performed metagenomic and metatranscriptomic analyses across seasonal datasets
• Quantified functional redundancy metrics at gene, pathway, and metabolic-module levels
• Conducted genome-resolved metagenomics, including MAG reconstruction, annotation, and taxonomy
• Led statistical modeling, regression analyses, and multivariate ecological analyses
• Interpreted results in the context of ecological theory and estuarine biogeochemistry
• Primary author of the manuscript and conference presentations

🧩 Challenges & Solutions

Challenge 1: Transitioning to fully independent, large-scale bioinformatics without senior technical support
Solution: Systematically evaluated and benchmarked multiple pipelines, optimizing workflows using a subset of samples before scaling analyses to full datasets.

Challenge 2: Lack of established, standardized methods for quantifying microbial functional redundancy
Solution: Developed a customized analytical framework through extensive literature review, interdisciplinary collaboration, and iterative discussions with ecologists and statisticians.

Challenge 3: Interpreting functional redundancy in the absence of directly comparable prior studies
Solution: Integrated environmental metadata, diversity metrics, and metabolic pathway analyses to contextualize FRed patterns within known estuarine gradients and ecological theory.

Challenge 4: Integrating DNA-based potential with RNA-based activity across uneven sequencing depths
Solution: Applied normalization strategies, pathway-level aggregation, and comparative DNA:RNA analyses to robustly link metabolic capacity and expression.

🛠 Methods & Tools

*Data & Sequencing

• Shotgun metagenomics
• Metatranscriptomics
• Metagenome-assembled genomes (MAGs)
• Read mapping and expression quantification
• Functional redundancy modeling

*Bioinformatics & Statistics

• Genome annotation and pathway reconstruction
• Taxonomic classification and MAG quality assessment
• Multivariate statistics and regression modeling
• Diversity metrics (alpha, beta, functional diversity)

*Tools & Software

• MetaWRAP
• GTDB-Tk
• DRAM / DRAM-v
• CoverM
• Bowtie2
• SAMtools
• R (tidyverse, vegan, ggplot2, lme4)

*Languages & Workflow

• Python
• Bash
• R
• Snakemake
• SLURM (HPC scheduling)

📄 Publications

• Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
  ISME Communications — under revision (Round 2)
  Preprint available upon request.

🎤 Conferences & Talks

• Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
  Jojy John, Maximiliano Ortiz, Barbara J. Campbell
  ASLO Aquatic Sciences Meeting, Charlotte, USA, 2025

• Microbial functional redundancy in response to substrate and energy utilization in estuarine ecosystems
  Jojy John, Maximiliano Ortiz, Pierre Ramond, Barbara J. Campbell
  ISME19, Cape Town, South Africa, 2024

• Does the microbiome insure ecosystem function?
  Jojy John, Maximiliano Ortiz, Barbara J. Campbell
  Clemson University 3rd Postdoctoral Symposium, South Carolina, USA, 2024

🧑‍🔬 Collaborators / References

Dr. Barbara J. Campbell
Dean’s Distinguished Professor
Department of Biological Sciences, Clemson University
Email: bcampb7@clemson.edu

Dr. Pierre Ramond
Postdoctoral Scientist
Institut de Ciències del Mar (ICM-CSIC)
Email: pierre@icm.csic.es

🖼 Image Gallery