Fine stratification of microbial communities through a metagenomic profile of the photic zone

Abstract

Most marine metagenomic studies of the marine photic zone analyze only samples taken at one or two depths. However, when the water column is stratified, physicochemical parameters change dramatically 25 over relatively short depth intervals. We sampled the photic water column every 15m depth at a single point of an off-shore Mediterranean site during a period of strong stratification (early autumn) to evaluate the effects of small depth increases on the microbiome. Using genomic assembly and metagenomic read recruitment, we found major shifts in the community structure over small variations of depth, with most microbes showing a distribution limited to layers approximately 30 meters thick (stenobathic). Only some 30 representatives of the SAR11 clade and the Sphingomonadaceae appeared to be eurybathic, spanning a greater range of depths. These results were confirmed by studying a single gene (rhodopsin) for which we also found narrow depth distributions. Our results highlight the importance of considering vertical distribution as a major element when analyzing the presence of marine clades and species or comparing the microbiome present at different locations. 35

High Prevalence of Quorum-Sensing and Quorum-Quenching Activity among Cultivable Bacteria and Metagenomic Sequences in the Mediterranean Sea

“…Eight seawater samples from different depths were collected for metagenomic analyses as described previously [ 55 , 56 ] on October 15, 2015 at a single point in the Mediterranean Sea (37.35361° N, 0.286194° W) by the research vessel ‘García del Cid’. Samples from 90 and 2000 m depth were also used for bacterial isolation and functional screening.…”

“…The 90 m sample is considered the limit of the photic zone, with a chlorophyll-a (Chl-a) value of 0.13 mg/m 3 , a total organic carbon (TOC) of 1.35 mgC/L, total N of 6.9 µM, total P of 0.25 µM, and 1.37 × 10 5 heterotrophic bacteria counts. The 2000 m sample was characterized by an almost undetectable Chl-a concentration (0.01 mg/m 3 ), lower TOC (0.94 mg C/L), higher total N and p -values (8.62 and 0.5 µM, respectively), and lower heterotrophic bacteria counts (4.5 × 10 4 ) [ 55 , 56 ]. Both rich and oligotrophic culture media were used for bacterial isolation as previously described [ 47 ].…”

“…Eight samples (Med-OCT2015-15 m, Med-OCT2015-30 m, Med-OCT2015-45 m, Med-OCT2015-60 m, Med-OCT2015-75 m, Med-OCT2015-90 m, Med-OCT2015-1000 m, and Med-OCT2015-2000 m) [ 55 , 56 ] from different depths were taken for metagenomic analyses on October 15, 2015 at a single sampling site in the Western Mediterranean (37.35361° N, 0.286194° W). Six samples were obtained from the uppermost 100 m at 15 m intervals using a hose attached to a CTD (Seabird).…”

“…The metagenomic analysis (read pre-processing, assembly and gene prediction and annotation) was carried out as previously described [ 56 ]. In brief, each metagenome was assembled independently using IDBA-UD [ 69 ].…”

Structure and Function of the Arctic and Antarctic Marine Microbiota as Revealed by Metagenomics

“…Recent advances in molecular ecological techniques, such as metagenomics, have enabled a more efficient pathway to address the taxonomic and functional composition of marine microbiota, including the free-living bacterioplankton [1,2,3], the sediment-dwelling microbes [4,5,6], the surface-attached biofilms [7,8,9], and the animal-associated symbionts [10,11,12]. Pursuing the goal characterisng the global seawater microbiota, the Tara Oceans expedition collected seawater samples from 68 locations, representing all main oceanic regions, and performed metagenomics to study the structure and function of the global ocean microbiota [1].…”