Coronavirus Information for the UC San Diego Community

Our leaders are working closely with federal and state officials to ensure your ongoing safety at the university. Stay up to date with the latest developments. Learn more.

Single cells within the Puerto Rico Trench suggest hadal adaptation of microbial lineages

A look at the collection system;  Phylogenetic tree of 16S rRNA gene sequence.
TitleSingle cells within the Puerto Rico Trench suggest hadal adaptation of microbial lineages
Publication TypeJournal Article
Year of Publication2015
AuthorsLeon-Zayas R., Novotny M., Podell S, Shepard C.M, Berkenpas E., Nikolenko S., Pevzner P., Lasken R.S, Bartlett DH
JournalApplied and Environmental Microbiology
Date Published2015/12
Type of ArticleArticle
ISBN Number0099-2240
Accession NumberWOS:000365212800003
Keywordsatlantic-ocean; bacterium photobacterium-profundum; deepest ocean; escherichia-coli; genomic; insights; metagenomic analysis; nitrous-oxide; pacific-ocean; ribosomal-rna genes; shewanella-violacea dss12

Hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. The microbial communities and metabolic potential in these ecosystems are largely uncharacterized. Here, we present four single amplified genomes (SAGs) obtained from 8,219 m below the sea surface within the hadal ecosystem of the Puerto Rico Trench (PRT). These SAGs are derived from members of deep-sea clades, including the Thaumarchaeota and SAR11 clade, and two are related to previously isolated piezophilic (high-pressure-adapted) microorganisms. In order to identify genes that might play a role in adaptation to deep-sea environments, comparative analyses were performed with genomes from closely related shallow-water microbes. The archaeal SAG possesses genes associated with mixotrophy, including lipoylation and the glycine cleavage pathway. The SAR11 SAG encodes glycolytic enzymes previously reported to be missing from this abundant and cosmopolitan group. The other SAGs, which are related to piezophilic isolates, possess genes that may supplement energy demands through the oxidation of hydrogen or the reduction of nitrous oxide. We found evidence for potential trench-specific gene distributions, as several SAG genes were observed only in a PRT metagenome and not in shallower deep-sea metagenomes. These results illustrate new ecotype features that might perform important roles in the adaptation of microorganisms to life in hadal environments.


When we looked at the presence and abundance of SAG genes in different metagenomes, specific genes were uniquely found to be associated with the Puerto Rico Trench (PRT). Many of these encoded functions associated with transport or transcription. Also, PRT SAR11 and PRT NitrosopumilusSAG genes were more abundant in the meta-genomes examined from deeper-dwelling organisms. Overall, thesingle cells collected from the PRT suggest that the development ofadded metabolic capabilities might be advantageous for survival in this and perhaps other hadal locations.

Student Publication: