Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea

Ghiglione, Jean François; Palacios, Carmen; Marty, J.; Mével, Geneviève; Labrune, Céline; Conan, Pascal; Pujo‐Pay, Mireille; Garcia, Nicole; Goutx, Madeleine

doi:10.5194/bg-5-1751-2008

Cited by 58 publications

(56 citation statements)

References 88 publications

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“…We hypothesized that different microbes may adapt to these two contrasting environments differentially, leading to compositional variations in microbial community in the sea water. However, our findings rejected this hypothesis and showed a different trend from those in other water bodies in which bacterioplankton communities were reported to be highly diverse and environment driven (Giovannoni and Stingl, 2005;Martiny et al, 2006;Pommier et al, 2007;Ghiglione et al, 2008). In our study, high similarities in the indigenous bacterial communities among different sampling sites were strongly supported by tag pyrosequencing and T-RFLP analysis (Figure 1; Supplementary Table S3).…”

Section: Influence Of Environment On Microbial Communitiescontrasting

confidence: 32%

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

et al. 2010

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Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored.

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Section: Influence Of Environment On Microbial Communitiescontrasting

confidence: 32%

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

et al. 2010

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“…Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram and Multidimensional Scaling (MDS) based on Bray Curtis similarities between normalized DGGE profiles (presence/absence and intensity matrix) were constructed by using the PRIMER v6.0 software (PRIMER-E, Ltd., UK). To investigate relationships between bacterial community structure and environmental parameters, we used a direct gradient approach, canonical correspondence analysis (CCA), using the software package CANOCO version 4.5 for Windows, as previously described by Ghiglione et al (2008).…”

Section: Discussionmentioning

confidence: 99%

“…These assays were done under aerobic growth conditions on a modified R2A medium (Gomila et al, 2007), containing for 1 l of distilled water: CaCl 2 (0.1 g), MgSO 4 ·7H 2 O (0.0492 g), NaCl (5 g), yeast extract (0.5 g), sodium pyruvate (0.3 g), acid hydrolysate of casein (0.5 g), pancreatic digest of casein (0.25 g), meat extract (0.3 g) and PIPES buffer (3.4 g). The pH was adjusted to 7.2 before autoclaving.…”

Section: Enrichment and Isolation Of Microbial Strainsmentioning

confidence: 99%

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

et al. 2012

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Abstract. An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion). Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG), within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG) and Halobacteria) within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence analyses (CCA) showed that the availability of electron acceptors and the quality of electron donors (indicated by age) strongly influenced the community structure. In contrast, within the Gulf of Lion core, characterized by a homogeneous lithological structure of upper-slope environment, most detected groups were Bacteroidetes and, to a lesser extent, Betaproteobacteria. At both site, the detection of Betaproteobacteria coincided with increased terrestrial Published by Copernicus Publications on behalf of the European Geosciences Union. 3492M.-C. Ciobanu et al.: Sedimentological imprint on subseafloor microbial communities inputs, as confirmed by the geochemical measurements (Si, Sr, Ti and Ca). In the Gulf of Lion, geochemical parameters were also found to drive microbial community composition. Taken together, our data suggest that the palaeoenvironmental history of erosion and deposition recorded in the Western Mediterranean Sea sediments has left its imprint on the sedimentological context for microbial habitability, and then indirectly on structure and composition of the microbial communities during the late Quaternary.

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“…In the oceans, bacterial taxonomy and metabolic potential strongly vary with depth (DeLong et al, 2006;Ghiglione et al, 2008), suggesting that viral taxonomy and AMGs should also have depthdependent distribution. Indeed, whole-viral genome fingerprinting shows that viral communities change with depth in the ocean (Steward et al, 2000;Brum, 2005), but to our knowledge, this depth-related genetic variability has not been further explored.…”

Section: Introductionmentioning

confidence: 99%

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

2014

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Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core’ (180 PCs; one-third new to science) and ‘flexible’ (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron–sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.

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Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea

Cited by 58 publications

References 88 publications

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

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