Whole Genome Analysis of Escherichia coli and Pseudomonas aeruginosa Mixed Culture Biofilms Grown for 117 Days in Spaceflight

Biofilms tend to have an increased tolerance to physical and chemical stressors. They are capable of damaging water-associated infrastructure not only on Earth but on spacecraft in space as well. Biofilms can also act as a source of infections for crew members on spacecraft. In an unexpected event, an experiment where mixed-culture biofilms of Escherichia coli strain F11 and Pseudomonas aeruginosa strain PA01 sent into space with SpaceX CRS-21 to analyze the effects of microgravity were left untouched for 117 days. Viable cells were found in some samples leading to a unique opportunity to analyze the effects of spaceflight on extended growth and microbial evolution of the biofilms. Of 24 spaceflight samples, 17 still had viability. Of those, E. coli was found only in non-treated (0ppb AgF) samples while P. aeruginosa survived the silver treatment (400ppb AgF). A total of 19 spaceflight isolates were chosen to undergo whole genome sequencing to be compared to the ancestral strain genomes. Illumina and Nanopore reads were used obtain draft genomes via a hybrid assembly. Whole genome alignment was used to identify differences, including SNPs, amongst the spaceflight genomes. Genome annotation helped to identify proteins and their functions based on the predicted protein sequences. Differences amongst the spaceflight genomes were elucidated by comparing module completeness of metabolic pathways. Some E. coli genomes had minor changes in a lipid metabolism module. Only the P. aeruginosa silver-treated samples showed changes in module completeness while all others P. aeruginosa were identical. All four shared a 75% completeness of the pyruvate oxidation pathway compared to a 50% completeness in the others. The whole genome comparison of these 117-day spaceflight bacterial cultures reveals minor changes within the genome as a result of long-term growth in space. This project shows a glimpse of the effect spaceflight has on the direction of microbial evolution of biofilms.

Name thesis:degree_name

Master of Science

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Biology

Grantor

Texas State University

Year dc:date.issued

2023

Author dc:creator

• Valdez, Aron

Advisor dc:contributor.advisor

• McLean, Robert J. C.

Committee members dc:contributor.committeemember

• Kakirde, Kavita
• Smyth, Davida

• biofilms
• spaceflight
• whole genome sequencing
• silver

Language dc:language.iso

en

Handle dc:identifier.uri

https://hdl.handle.net/10877/20265

OAI identifier oai:identifier

oai:digital.library.txst.edu:10877/20265