The Enduring Questions: What's for Dinner? Where's My Knife? …and Can I Use My Fingers? (Unanswered) Questions Related to Organic Matter and Microbes in Marine Sediments

• Published in: Frontiers in Marine Science 2019-10, Vol.6
• Main Authors: Arnosti, Carol, Hinrichs, Kai-Uwe, Coffinet, Sarah, Wilkes, Heinz, Pantoja, Silvio
• Format: Article
• Language: English
• Subjects: Bacteria; Biodiversity and Ecology; Biosphere; deep biosphere; degradation; Dissolved organic carbon; Environmental Sciences; Fungi; Geochemistry; heterotrophic prokaryotes; Marine sediments; Metabolism; Microbial activity; Microbiology; Microorganisms; Nucleotide sequence; Organic matter; organic matter characterization; Petroleum; Physiology; Protein turnover; Proteins; Sediment; Sediments
• ISSN: 2296-7745; 2296-7745
• DOI: 10.3389/fmars.2019.00629

Work over the past decades has revealed much information about sedimentary microbial communities: their overall composition (Bacteria and Archaea), the sequence of terminal respiration processes occurring with progressive burial depth in sediments, and the depth to which they can be detected; research on the members and metabolism in the “deep biosphere” has assumed a central position in organic geochemistry, environmental microbiology, and molecular ecology (Orcutt et al., 2013; D'Hondt et al., 2019). Bulk measurements of organic matter are often not particularly enlightening in this respect; we do not understand the constraints on the microbial populations found in sediments with high dissolved organic carbon (DOC) or high sedimentary organic matter concentrations, where activity apparently is low. Isolating bacteria in the lab tears apart degradative networks, so we have a very incomplete picture of microbial interactions, but such isolates provide the opportunity for detailed physiological investigations that cannot be carried out in the environment. Better identification of proteins produced by sedimentary communities would provide much-needed insight into their metabolism. Since current protein databases overwhelmingly do not represent organisms from marine sediments (much less the deep biosphere), and organisms in these environments probably have metabolic solutions to physiological/geochemical “problems” that are not found in more-typically investigated environments, we end up with a substantial fraction of unclassified proteins.