Microbial Biofouling Interactions on Autonomous Navy Gliders

** 🧠 Background & Motivation**

Biofouling is the process by which microorganisms and multicellular organisms colonize submerged surfaces, negatively impacting marine vessels by increasing drag and reducing operational efficiency. This challenge is particularly critical for battery-powered Unmanned Underwater Vehicles (UUVs), including Autonomous Navy Gliders, where increased drag leads to significant energy loss and reduced mission duration.

Rather than relying on toxic antifouling coatings, this project explores an eco-friendly alternative: engineering a smooth, invasion-resistant, and stable synthetic microbial community (Eco-Coating) composed of naturally occurring marine bacteria. By understanding the genomic, metabolic, and biofilm-forming traits of native biofouling communities, this work aims to rationally design microbial consortia that outcompete harmful fouling organisms while maintaining surface stability.

*🎯 Research Questions & Objectives8

• What microbial taxa colonize the body and tail sections of autonomous underwater vehicles?
• Which genes and pathways are associated with biofilm formation, EPS production, and antagonistic activity?
• How do isolate genomes and metagenome-assembled genomes (MAGs) inform the design of a synthetic biofilm community?
• Can genome-resolved traits predict community stability and antifouling potential?

👨‍🔬 My Role

• Provided full bioinformatics support for the project
• Performed metagenomic and genome-resolved analyses of UUV-associated biofilms
• Conducted whole-genome assembly, hybrid assembly, and long-read assembly of >100 bacterial isolates
• Genome annotation, functional screening, and comparative genomics
• Screening genomes for biofilm formation, EPS production, antibiotic biosynthesis, and antagonistic traits
• Prepared genomes and metadata for NCBI submission
• Contributed to synthetic community design using genomic and functional criteria

🧩 Challenges & Solutions

Challenge 1: Choosing appropriate assembly strategies for 200+ genomes with varying read quality and genome complexity
Solution: Implemented a tiered assembly strategy:

• Short-read–only assemblies using Shovill/SPAdes for high-quality Illumina datasets
• Long-read assemblies using Flye for structurally complex genomes
• Hybrid assemblies (Illumina + Nanopore) using Unicycler for isolates with fragmented short-read assemblies

Challenge 2: Resolving misassemblies, plasmids, and repetitive regions in hybrid assemblies
Solution:

• Used Bandage for assembly graph visualization and manual validation
• Evaluated contiguity and structural accuracy using assembly graphs and coverage profiles
• Iteratively refined assemblies prior to downstream annotation and submission

Challenge 3: Handling metagenome complexity and distinguishing isolate genomes from MAGs
Solution:

• Applied genome-resolved metagenomic workflows to separate MAGs and isolate genomes
• Cross-validated taxonomy and completeness using marker genes and coverage patterns
• Standardized QC across datasets before comparative analyses

🛠 Methods & Tools

*Data & Sequencing

• Shotgun metagenomics (biofilm samples from UUV body and tail)
• Whole-genome sequencing of bacterial isolates
• Short-read, long-read, and hybrid genome assemblies
• Functional annotation of isolate genomes and MAGs
• Taxonomic classification and genome quality assessment

*Bioinformatics & Visualization

• Assembly & QC: Flye, SPAdes, Shovill, Unicycler, NanoPlot
• Assembly validation: Bandage
• Annotation: Prokka, InterProScan, DRAM
• Metagenomics: Genome-resolved metagenomics workflows
• Infrastructure: High-performance computing (HPC)

*Languages & Workflow

• Python
• Bash
• R
• Snakemake

Publications

• Chaulagain D, John J, Paul B, Harrington EG, McCarthy G, Sathe M, Shamabadi NS, Carter E, Leonhardt J, Nawaz MS, Suleman M, Campbell BJ, Karig DK.
  Genome assemblies of bacterial isolate collections from marine biofilm and water explore microbial diversity.
  Microbiology Resource Announcements (submitted).

(Additional manuscripts in preparation.)

🎤 Conferences & Talks

• 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

• Genomic insights into antibiotic production and resistance in environmental bacteria
  Sophia Rudolph, Jojy John, Barbara J. Campbell
  Regional ASM Meeting, South Carolina, 2025

• Microbial biofouling interactions on Autonomous Navy Gliders: Insights from metagenome analysis
  Jojy John, David Karig, Barbara J. Campbell
  DARPA Meeting, 2024

• Isolation and identification of marine bacteria to enhance antifouling strategies in UUVs via a biofilm engineering approach
  ASM, Atlanta, 2024

• Optimizing a stable and smooth biofilm-forming bacterial community to reduce drag on UUVs
  ICME, 2024

🧑‍🔬 Collaborators / References

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

Dr. David K. Karig
Associate Professor, Bioengineering
Clemson University
Email: dkarig@clemson.edu

Dr. Diptee Chaulagain
Research Assistant Professor
Department of Bioengineering, Clemson University
Email: dchaula@clemson.edu