Functional Redundancy and Synthetic Biofilm Design in Marine Communities under Environmental Stress

🧠 Background & Motivation

Marine microbes are key drivers of biogeochemical cycling, nutrient turnover, and ecosystem resilience. Many marine bacterial taxa share overlapping metabolic functions, a phenomenon known as functional redundancy, which can stabilize ecosystem processes when environmental conditions change. At the same time, marine microorganisms commonly form biofilms on natural and artificial surfaces, where community interactions influence attachment, persistence, and stress tolerance.

Anthropogenic pressures such as pollution, marine debris, and environmental change are reshaping coastal microbial communities, yet there is still limited genome-level understanding of how functional redundancy and biofilm-forming potential contribute to resilience under stress. This project addresses that gap by combining genomics, pangenomics, biofilm trait screening, and synthetic community design to evaluate marine isolates collected from biofilms associated with unmanned underwater vehicles.

The broader goal is to identify and assemble beneficial synthetic biofilm communities with stable biomass, strong attachment, and functional redundancy under environmental stress.

🎯 Research Questions & Objectives

*📌 Study 1: Genome-Based Characterization of Marine Isolates

• Which metabolic and ecological traits distinguish generalist and specialist marine bacteria?
• Which isolates encode genes associated with biofilm formation, EPS production, and substrate utilization?

*📌 Study 2: Functional Redundancy at the Genome Level

• To what extent do multiple isolates share overlapping metabolic traits related to carbon utilization and ecological persistence?
• Can genome-derived functional profiles be used to quantify functional redundancy among isolates?

*📌 Study 3: Synthetic Community Design

• Which combinations of isolates are most likely to produce stable and beneficial synthetic biofilms?
• How can comparative genomics and pangenomics guide isolate selection for synthetic community assembly?

🤝 Project Context

This work builds on marine isolates generated as part of the DARPA Arcadia Program, which focuses on developing beneficial biofilms for applied marine systems. The isolates used in this study were recovered from biofilms formed on autonomous navy gliders collected at Key West Naval Air Base.

I am contributing to this project through bioinformatics support, workflow development, and mentoring, while mentoring Alisha as this work forms a major component of her master’s thesis.

👨‍🔬 My Role

My role in this project centers on genome-resolved bioinformatics, comparative analysis, and synthetic community screening, including:

• Mentoring Alisha on project design, genome analysis, and interpretation
• Bioinformatics support for short-read, long-read, and hybrid genome assembly
• Functional annotation of marine isolate genomes
• Screening genomes for:
  • antibiotic resistance genes
  • secondary metabolite production potential
  • biofilm-associated genes
  • EPS production potential
• Comparative genomics and pangenome analysis
• Bioinformatic screening to identify candidate members for beneficial synthetic biofilm communities
• Quantifying functional redundancy at the genomic level

🧬 Analytical Framework

This project integrates isolate genomics with ecological screening to classify marine strains as generalists or specialists and guide synthetic community construction.

Key analytical layers include:

1. Genome Characterization
   Assembly, annotation, and trait-based screening of marine bacterial isolates

2. Trait Screening
   Identification of genes related to substrate utilization, EPS production, biofilm formation, and stress response

3. Comparative Genomics & Pangenomics
   Assessment of core and accessory functions across selected isolates to refine ecological categorization

4. Functional Redundancy Analysis
   Quantification of overlapping metabolic traits across genomes to estimate the potential for functional buffering within synthetic communities

🛠 Methods & Tools

*Genome Analysis

• Short-read assembly
• Long-read assembly
• Hybrid assembly
• Genome quality assessment
• Functional annotation

*Trait Screening

• Biofilm and EPS gene screening
• Antibiotic resistance screening
• Secondary metabolite / biosynthetic potential screening
• Carbon utilization trait profiling

*Comparative Genomics

• Pangenome analysis using PanX
• Comparative functional profiling
• Generalist vs specialist categorization

*Functional Redundancy

• Genome-level trait matrix construction
• Functional redundancy quantification across selected isolates

*Infrastructure

• Reproducible bioinformatics workflows
• Linux / HPC-based analysis

🧩 Challenges & Solutions

Challenge 1: Selecting isolates for synthetic communities from a large and functionally diverse marine culture collection
Solution: Combined genomic trait screening, pangenome analysis, and ecological categorization to prioritize isolates with desirable and complementary traits.

Challenge 2: Distinguishing beneficial biofilm-forming strains from strains carrying undesirable features
Solution: Screened genomes for biofilm/EPS traits alongside antibiotic resistance and secondary metabolite potential to balance function, safety, and ecological relevance.

Challenge 3: Quantifying functional redundancy in isolate-based synthetic communities
Solution: Constructed genome-level functional trait matrices to estimate shared and unique metabolic capacities across candidate community members.

🌊 Biological System**

The project focuses on 137 marine bacterial isolates recovered from biofilms associated with naval vehicles in South Florida. These isolates represent a diverse set of marine taxa relevant to coastal biofilms, carbon cycling, and surface-associated microbial communities.

A subset of isolates is further evaluated to design synthetic biofilm communities and test their performance under environmental stress conditions, including:

• temperature shifts
• growth on plastic-associated surfaces
• potential changes in nutrient conditions

🌍 Perspective**

This project links microbial ecology, genomics, and synthetic community design to understand how marine bacteria form stable biofilms and maintain functional redundancy under stress. Beyond basic ecological insight, the work supports the development of beneficial marine biofilms with potential applications in marine infrastructure, environmental resilience, and engineered microbiome systems.

More broadly, this project demonstrates how genome-informed selection of microbial isolates can guide the assembly of synthetic communities that are not only functionally capable, but also resilient to environmental change.

Outcome

Functional redundancy of marine synthetic biofilm communities under different environmental stresses;Alisha M. Paul, Jojy John, Diptee Chaulagain, David Karig, Barbara J. Campbell;ASM Biofilms, Oregon, 2025

Reference

Dr. Barbara J. Campbell,📧 bcampb7@clemson.edu Dr. David K. Karig,📧 dkarig@clemson.edu Alisha M. Paul,MS Research Student, Campbell Lab, Clemson University,📧 apaul3@clemson.edu