Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis
Summary Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on unde...
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| Published in | Environmental microbiology Vol. 18; no. 5; pp. 1452 - 1469 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Blackwell Publishing Ltd
01.05.2016
Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
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| Summary: | Summary
Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, ‘who’ is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites. |
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| Bibliography: | ark:/67375/WNG-MFT5L5HV-7 Florida Space Grant Consortium istex:47E3EDA6AB764F70055640E42B44447573622A12 Fig. S1. Krona plot depicting the taxonomic composition of Archaea based on analysis of the whole shotgun metagenome sequences. Rings are associated with different taxonomy ranks (phylum, class, order and family respectively). Sequences have been filtered and only those OTUs with relative abundance greater than 0.1% are reported. Fig. S2. Krona plot depicting the taxonomic composition of Eukaryota based on analysis of the whole shotgun metagenome sequences. Rings are associated with different taxonomy ranks (phylum, class, order and family respectively). Sequences have been filtered, and only those OTUs with relative abundance greater than 0.1% are reported. Fig. S3. Phylogenetic affiliation of metagenomic reads associated with the Cyanobacteria phylum collapsed at genus level in Little Darby stromatolites. Absolute abundances (in parentheses) are reported as the total number of reads associated at each taxonomic level, including unclassified taxon. Fig. S4. Genus level distribution of reads associated with phosphate sensing, scavenging, and regulation based on MetaCV analysis. KEGG orthology groups included in the tree were as follows: K01077, K01113, K02040, K07636, K07657, K07658, K07659, K07638. Tree created in megan using the annotated read abundance, which is given in parentheses for each taxa. Fig. S5. Changes in alpha diversity within rarefaction curves computed as Shannon diversity (A) and Faith's phylogenetic diversity (B) metrics comparing microbial mats derived from different locations. Bars represent standard deviation. Diversity analyses were computed at a rarefaction depth of 450 sequences/sample. NASA Astrobiology: Exobiology and Evolutionary Biology Program Element - No. NNX14AK14G ArticleID:EMI13094 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1462-2912 1462-2920 |
| DOI: | 10.1111/1462-2920.13094 |