Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments.

Authors:
Jordan T Bird
Jordan T Bird
The University of Tennessee
Eric D Tague
Eric D Tague
University of Tennessee
Laura Zinke
Laura Zinke
University of Southern California
Andrew D Steen
Andrew D Steen
Aarhus University
Denmark
Brandi Reese
Brandi Reese
Texas A&M University Corpus Christi
Gordon Webster
Gordon Webster
Cardiff University
United Kingdom

MBio 2019 04 16;10(2). Epub 2019 Apr 16.

University of Tennessee, Knoxville, Tennessee, USA

Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured , , group OPB41, , , , , , and marine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested that and group OPB41 catabolized sugars, whereas and catabolized peptides. Metabolite and transcript data suggested that utilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps. single-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies. Much of life on Earth exists in a very slow-growing state, with microbes from deeply buried marine sediments representing an extreme example. These environments are like natural laboratories that have run multi-thousand-year experiments that are impossible to perform in a laboratory. We borrowed some techniques that are commonly used in laboratory experiments and applied them to these natural samples to make hypotheses about how these microbes subsist for so long at low activity. We found that some methods for stabilizing proteins and nucleic acids might be used by many members of the community. We also found evidence for niche differentiation strategies, and possibly cross-feeding, suggesting that even though they are barely growing, complex ecological interactions continue to occur over ultralong timescales.

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Source
http://mbio.asm.org/lookup/doi/10.1128/mBio.02376-18
Publisher Site
http://dx.doi.org/10.1128/mBio.02376-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469976PMC

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April 2019
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