Limits...
Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling.

Pfister CA, Meyer F, Antonopoulos DA - PLoS ONE (2010)

Bottom Line: When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes.Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes.In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America. cpfister@uchicago.edu

ABSTRACT
Mussels are conspicuous and often abundant members of rocky shores and may constitute an important site for the nitrogen cycle due to their feeding and excretion activities. We used shotgun metagenomics of the microbial community associated with the surface of mussels (Mytilus californianus) on Tatoosh Island in Washington state to test whether there is a nitrogen-based microbial assemblage associated with mussels. Analyses of both tidepool mussels and those on emergent benches revealed a diverse community of Bacteria and Archaea with approximately 31 million bp from 6 mussels in each habitat. Using MG-RAST, between 22.5-25.6% were identifiable using the SEED non-redundant database for proteins. Of those fragments that were identifiable through MG-RAST, the composition was dominated by Cyanobacteria and Alpha- and Gamma-proteobacteria. Microbial composition was highly similar between the tidepool and emergent bench mussels, suggesting similar functions across these different microhabitats. One percent of the proteins identified in each sample were related to nitrogen cycling. When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes. In some instances, the nitrogen-utilizing profile of this assemblage was more concordant with soil metagenomes in the Midwestern U.S. than for open ocean system. Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes. In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes.

Show MeSH
The number of proteins involved in CO2 fixation, including those of the Calvin-Benson cycle among a selection of marine metagenomes.To facilitate comparison among studies, the number of matches is normalized to the ‘discovery rate’ for proteins in the dataset (number of protein matches per 100 fragments). The point symbols represent the percent of all proteins identified that are used in CO2 fixation.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2865538&req=5

pone-0010518-g004: The number of proteins involved in CO2 fixation, including those of the Calvin-Benson cycle among a selection of marine metagenomes.To facilitate comparison among studies, the number of matches is normalized to the ‘discovery rate’ for proteins in the dataset (number of protein matches per 100 fragments). The point symbols represent the percent of all proteins identified that are used in CO2 fixation.

Mentions: Proteins related to CO2 fixation were also well represented in the mussel shell samples, including enzymes of the Calvin cycle (primarily RUBISCO) and exceeded those in Georgia waters and the 4 Global Ocean samples (Figure 4). We matched 232 CO2 fixation-related proteins in the tidepool sample (0.65% of all proteins) and nearly twice that in the bench sample (456 for 1.26% of all proteins). The Line Islands had a variable amount of CO2 fixation proteins with Palmyra and Kiritimati (Christmas Island) having the greatest number. The percent of proteins identified for CO2 fixation out of the entire protein pool of all metagenomes ranged between 0.0 and 1.38 across all metagenomes.


Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling.

Pfister CA, Meyer F, Antonopoulos DA - PLoS ONE (2010)

The number of proteins involved in CO2 fixation, including those of the Calvin-Benson cycle among a selection of marine metagenomes.To facilitate comparison among studies, the number of matches is normalized to the ‘discovery rate’ for proteins in the dataset (number of protein matches per 100 fragments). The point symbols represent the percent of all proteins identified that are used in CO2 fixation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2865538&req=5

pone-0010518-g004: The number of proteins involved in CO2 fixation, including those of the Calvin-Benson cycle among a selection of marine metagenomes.To facilitate comparison among studies, the number of matches is normalized to the ‘discovery rate’ for proteins in the dataset (number of protein matches per 100 fragments). The point symbols represent the percent of all proteins identified that are used in CO2 fixation.
Mentions: Proteins related to CO2 fixation were also well represented in the mussel shell samples, including enzymes of the Calvin cycle (primarily RUBISCO) and exceeded those in Georgia waters and the 4 Global Ocean samples (Figure 4). We matched 232 CO2 fixation-related proteins in the tidepool sample (0.65% of all proteins) and nearly twice that in the bench sample (456 for 1.26% of all proteins). The Line Islands had a variable amount of CO2 fixation proteins with Palmyra and Kiritimati (Christmas Island) having the greatest number. The percent of proteins identified for CO2 fixation out of the entire protein pool of all metagenomes ranged between 0.0 and 1.38 across all metagenomes.

Bottom Line: When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes.Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes.In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America. cpfister@uchicago.edu

ABSTRACT
Mussels are conspicuous and often abundant members of rocky shores and may constitute an important site for the nitrogen cycle due to their feeding and excretion activities. We used shotgun metagenomics of the microbial community associated with the surface of mussels (Mytilus californianus) on Tatoosh Island in Washington state to test whether there is a nitrogen-based microbial assemblage associated with mussels. Analyses of both tidepool mussels and those on emergent benches revealed a diverse community of Bacteria and Archaea with approximately 31 million bp from 6 mussels in each habitat. Using MG-RAST, between 22.5-25.6% were identifiable using the SEED non-redundant database for proteins. Of those fragments that were identifiable through MG-RAST, the composition was dominated by Cyanobacteria and Alpha- and Gamma-proteobacteria. Microbial composition was highly similar between the tidepool and emergent bench mussels, suggesting similar functions across these different microhabitats. One percent of the proteins identified in each sample were related to nitrogen cycling. When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes. In some instances, the nitrogen-utilizing profile of this assemblage was more concordant with soil metagenomes in the Midwestern U.S. than for open ocean system. Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes. In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes.

Show MeSH