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Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria.

Szafranski KM, Deschamps P, Cunha MR, Gaudron SM, Duperron S - Front Microbiol (2015)

Bottom Line: Communities in long-term deployments were different, and their composition was mainly influenced by the geographical location where devices were deployed.Numerous sequences related to horizontally-transmitted chemosynthetic symbionts of metazoans were identified.Results suggest that some free-living forms of metazoan symbionts or their close relatives, such as Epsilonproteobacteria associated with the shrimp Rimicaris exoculata, are efficient colonizers of plant substrates at vents and seeps.

View Article: PubMed Central - PubMed

Affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR 7208, Adaptation aux Milieux Extrêmes Paris, France ; UMR MNHN UPMC CNRS IRD UCBN 7208, Biologie des Organismes Aquatiques et Ecosystèmes Paris, France.

ABSTRACT
Reducing conditions with elevated sulfide and methane concentrations in ecosystems such as hydrothermal vents, cold seeps or organic falls, are suitable for chemosynthetic primary production. Understanding processes driving bacterial diversity, colonization and dispersal is of prime importance for deep-sea microbial ecology. This study provides a detailed characterization of bacterial assemblages colonizing plant-derived substrates using a standardized approach over a geographic area spanning the North-East Atlantic and Mediterranean. Wood and alfalfa substrates in colonization devices were deployed for different periods at 8 deep-sea chemosynthesis-based sites in four distinct geographic areas. Pyrosequencing of a fragment of the 16S rRNA-encoding gene was used to describe bacterial communities. Colonization occurred within the first 14 days. The diversity was higher in samples deployed for more than 289 days. After 289 days, no relation was observed between community richness and deployment duration, suggesting that diversity may have reached saturation sometime in between. Communities in long-term deployments were different, and their composition was mainly influenced by the geographical location where devices were deployed. Numerous sequences related to horizontally-transmitted chemosynthetic symbionts of metazoans were identified. Their potential status as free-living forms of these symbionts was evaluated based on sequence similarity with demonstrated symbionts. Results suggest that some free-living forms of metazoan symbionts or their close relatives, such as Epsilonproteobacteria associated with the shrimp Rimicaris exoculata, are efficient colonizers of plant substrates at vents and seeps.

No MeSH data available.


Percentage of pyrosequencing reads representing the most abundant OTUs (more than 1% of the total number of sequences, i.e., >3000 reads) and assigned to different bacterial phylotypes. Taxonomic classification was based on comparison of sequences within the SILVA database with OTU identity threshold at 97%. More details on taxonomic assignment of OTUs analyzed is provided in Table S3. Refer to Table 1 for sample ID.
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Figure 3: Percentage of pyrosequencing reads representing the most abundant OTUs (more than 1% of the total number of sequences, i.e., >3000 reads) and assigned to different bacterial phylotypes. Taxonomic classification was based on comparison of sequences within the SILVA database with OTU identity threshold at 97%. More details on taxonomic assignment of OTUs analyzed is provided in Table S3. Refer to Table 1 for sample ID.

Mentions: For further community analyses at the OTU level, we focused on the most abundant OTUs, which represented above 1% of the total number of sequences in the dataset (>3000 amplicons; Table S3). 15 OTUs within the Proteobacteria and 1 within the Bacteroidetes matched this criterion, representing 131712 sequences (almost 43% of the total sequences) (Figure 3; Table S3). All were related to marine bacteria. Four major OTUs (OTU_00201, OTU_11277, OTU_00411 and OTU_00023) were abundant in almost all long-term samples and constituted altogether 38 to 86% of the total number of sequences in each sample (Table S3). Communities from short-term experiments were different from the long-term ones, comprising 6 highly abundant OTUs that were rare to absent in long-term deployments (Figure 3; Table S3).


Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria.

Szafranski KM, Deschamps P, Cunha MR, Gaudron SM, Duperron S - Front Microbiol (2015)

Percentage of pyrosequencing reads representing the most abundant OTUs (more than 1% of the total number of sequences, i.e., >3000 reads) and assigned to different bacterial phylotypes. Taxonomic classification was based on comparison of sequences within the SILVA database with OTU identity threshold at 97%. More details on taxonomic assignment of OTUs analyzed is provided in Table S3. Refer to Table 1 for sample ID.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4343019&req=5

Figure 3: Percentage of pyrosequencing reads representing the most abundant OTUs (more than 1% of the total number of sequences, i.e., >3000 reads) and assigned to different bacterial phylotypes. Taxonomic classification was based on comparison of sequences within the SILVA database with OTU identity threshold at 97%. More details on taxonomic assignment of OTUs analyzed is provided in Table S3. Refer to Table 1 for sample ID.
Mentions: For further community analyses at the OTU level, we focused on the most abundant OTUs, which represented above 1% of the total number of sequences in the dataset (>3000 amplicons; Table S3). 15 OTUs within the Proteobacteria and 1 within the Bacteroidetes matched this criterion, representing 131712 sequences (almost 43% of the total sequences) (Figure 3; Table S3). All were related to marine bacteria. Four major OTUs (OTU_00201, OTU_11277, OTU_00411 and OTU_00023) were abundant in almost all long-term samples and constituted altogether 38 to 86% of the total number of sequences in each sample (Table S3). Communities from short-term experiments were different from the long-term ones, comprising 6 highly abundant OTUs that were rare to absent in long-term deployments (Figure 3; Table S3).

Bottom Line: Communities in long-term deployments were different, and their composition was mainly influenced by the geographical location where devices were deployed.Numerous sequences related to horizontally-transmitted chemosynthetic symbionts of metazoans were identified.Results suggest that some free-living forms of metazoan symbionts or their close relatives, such as Epsilonproteobacteria associated with the shrimp Rimicaris exoculata, are efficient colonizers of plant substrates at vents and seeps.

View Article: PubMed Central - PubMed

Affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR 7208, Adaptation aux Milieux Extrêmes Paris, France ; UMR MNHN UPMC CNRS IRD UCBN 7208, Biologie des Organismes Aquatiques et Ecosystèmes Paris, France.

ABSTRACT
Reducing conditions with elevated sulfide and methane concentrations in ecosystems such as hydrothermal vents, cold seeps or organic falls, are suitable for chemosynthetic primary production. Understanding processes driving bacterial diversity, colonization and dispersal is of prime importance for deep-sea microbial ecology. This study provides a detailed characterization of bacterial assemblages colonizing plant-derived substrates using a standardized approach over a geographic area spanning the North-East Atlantic and Mediterranean. Wood and alfalfa substrates in colonization devices were deployed for different periods at 8 deep-sea chemosynthesis-based sites in four distinct geographic areas. Pyrosequencing of a fragment of the 16S rRNA-encoding gene was used to describe bacterial communities. Colonization occurred within the first 14 days. The diversity was higher in samples deployed for more than 289 days. After 289 days, no relation was observed between community richness and deployment duration, suggesting that diversity may have reached saturation sometime in between. Communities in long-term deployments were different, and their composition was mainly influenced by the geographical location where devices were deployed. Numerous sequences related to horizontally-transmitted chemosynthetic symbionts of metazoans were identified. Their potential status as free-living forms of these symbionts was evaluated based on sequence similarity with demonstrated symbionts. Results suggest that some free-living forms of metazoan symbionts or their close relatives, such as Epsilonproteobacteria associated with the shrimp Rimicaris exoculata, are efficient colonizers of plant substrates at vents and seeps.

No MeSH data available.