Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

Abstract

BackgroundThe photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment.ResultsOur results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth.ConclusionsAlthough limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0513-5) contains supplementary material, which is available to authorized users.

Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes

“…Recently, we characterized variations in the marine microbiome at different depths within the photic zone during a period of strong thermal stratification of the water column (Haro‐Moreno et al, ). Results showed that marine Thaumarchaeota were only found below the deep chlorophyll maximum (accounted for up to 10% of the community at 90 m), coinciding with the increase of available ammonia that is practically non‐existent at shallower depths.…”

Undinarchaeota illuminate the evolution of DPANN archaea

“…In particular, we screened publicly available metagenomes using ribosomal protein sequences of the previously reconstructed UAP2 MAGs and assembled and binned UAP2-positive samples yielding six additional MAGs belonging to the UAP2 lineage ( Table 1, Supplementary Tables 1-2 , see Methods for details). Four of the newly assembled MAGs were recovered from metagenomes of a groundwater aquifer located adjacent to the Colorado River 42 , while the two others as well as six previously reconstructed MAGs, derived from metagenomes of marine waters in the Atlantic 41,43 and Indian Oceans 44 as well as the Mediterranean Sea 45 ( Supplementary Table 2 ). UAP2 representatives were detected in samples from various depths in the water column (85-5000 m), fluctuating oxygen conditions (anoxic to oxic) and temperatures (sampling sites had temperatures from 18 up to 106°C) ( Supplementary Figure 1, Supplementary Table 1 ).…”

Associations between depth and micro-diversity within marine viral communities revealed through metagenomics

“…Scaffolds predicted to infect Proteobacteria were among the most abundant in all depths with abundances ranging from 0.5% to 2.4% of mapped reads. Previous investigation of the metagenomes from the cellular fraction revealed shifts in taxonomic composition of prokaryotic communities throughout the depth gradient [8]. These were dominated, at all depths, by Proteobacteria, mostly from the classes Alphaproteobacteria and Gammaproteobacteria.…”

“…In response, viruses adapt to those changes to guarantee their survival. The depth gradient of stratified water masses displays marked changes in environmental conditions mainly driven by light availability and temperature [8]. Thus it is an ideal habitat to study associations between environmental parameters, viruses, and their hosts.…”