Genomic Insights into Chemotaxis of the Ubiquitous SAR324 Bacteria in the Pelagic Deep Ocean

In the deep, cold, pelagic ocean, where organic matter is typically scarce, chemotaxis likely plays a crucial role in enabling heterotrophic microorganisms to locate and acquire it. Here, we examine the genomic features of chemotaxis machinery under high hydrostatic pressure conditions. Single Amplified Genomes (SAGs) of the Atacama Trench water column were analyzed, focusing on the SAR324 bacteria lineage. This lineage was detected at all sampled depths and exhibited genetic potential to encode a complete set of proteins related to chemotaxis, similar to those found in model bacteria. Phylogenomic analysis clustered SAR324 SAGs into two groups: one associated with Antarctic Intermediate Water (AAIW; 500 and 1,000 m) and the other with deep Pacific Ocean Water masses (PWD; >2,000 m). Notably, PWD samples contained a higher proportion of SAGs with sequences related to chemoreceptors and intracellular signaling components, including CheA, CheB, CheW, and CheR. This finding suggests a potential strategy for capturing attractant compounds, such as organic matter via chemotaxis in the dark ocean. Read recruitment of SAR324 chemotaxis-related sequences to public ocean metagenomes and metatranscriptomes revealed a cluster enriched in bathypelagic waters (>2,800 m). The predicted amino acid composition of these sequences was similar to those found in shallower waters for most of the genes. However, notable exceptions included the predicted proteins MCP (chemoreceptors), FlhF (flagellar biosynthesis), FliN (flagellar motor switch), and FliK (flagellar hook-length control), which exhibited distinct differences in the deep-bathypelagic waters. Additionally, sequences enriched in deep metagenomes exhibited distinct nucleotide compositions and significant differences in synonymous codon usage patterns. These findings suggest specific adaptations of the chemotaxis system to low temperatures and high pressures, providing SAR324 with a selective advantage in extreme deep-sea environments.

Presentation Preference: Oral

Primary Presenter: Paula Ruiz-Fernández, Instituto Milenio de Oceanografía IC120019 (sofpaula@gmail.com)

Authors:

Edgart Flores, University of Colorado Boulder  (edgart.floresrafael@colorado.edu)

Pamela Hidalgo, Instituto Milenio de Oceanografía  (pahidalg@udec.cl)

Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences  (rstepanauskas@bigelow.org)

Osvaldo Ulloa, Instituto Milenio de Oceanografía  (oulloa@udec.cl)