A New Class of Marine Euryarchaeota Group II From the Mediterranean Deep Chlorophyll Maximum

ISME J. 2015 Jul;9(7):1619-34. doi: 10.1038/ismej.2014.249. Epub 2014 Dec 23.

Abstract

We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Chlorophyll / genetics*
  • Chlorophyll / physiology
  • Euryarchaeota / classification
  • Euryarchaeota / genetics*
  • Gene Expression Regulation, Archaeal
  • Genomics
  • Mediterranean Sea
  • Metagenome
  • Metagenomics / methods
  • RNA, Ribosomal, 16S / genetics
  • Species Specificity

Substances

  • RNA, Ribosomal, 16S
  • Chlorophyll