2007 Annual Science Report

Marine Biological Laboratory Reporting  |  JUL 2006 – JUN 2007

Microbial Diversity in the Deep Ocean

Project Summary

Microbial life exerts a profound influence on habitability of Earth where it drives all of the major biogeographical transformations including the fixation of carbon and production of atmospheric gases.

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

Microbial life exerts a profound influence on habitability of Earth where it drives all of the major biogeographical transformations including the fixation of carbon and production of atmospheric gases. Metagenomic surveys promise to describe the metabolic repertoire, evolutionary dynamics, and microbial processes that drive ecosystem function. However, the analytical power of environmental DNA sequences for modeling microbial ecosystems depends on accurate assessments of population structure, including diversity (richness) and relative abundance (evenness). We have described both aspects of population structure for microbial communities at diffuse flow vents, Marker 52 and Bag City, from Axial Seamount (45.92° N, 130° W), an active volcano at 1520 m in the northeast Pacific Ocean and the site of multi-year interdisciplinary investigations. Analysis of more than 900,000 microbial SSU amplicons demonstrated differences between the two communities at high taxonomic resolution that are consistent with dissimilar geochemical regimes between vents.

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Table 1. Chemical and SSU rRNA tag characteristics of the two sites.

  FS312 FS396
Vent Name Bag City Marker 52
Sample Year 2003 2004
Volume Filtered (mL) 1003 2000
Cells ml-1 (range) 1.21 × 105 1.57 × 105
  (9.77 × 104-1.26 × 105) (1.02 × 105-2.12 × 105)
Culturablea Hyper/Thermophilic Heterotrophs L-1    
  140-4200 20-720
DNA recovered (μg) 0.9 2.4
Total number of Archaeal V6 Tag Sequencesb 200,199 16,428
Total number of Bacterial V6 Tag Sequencesb 442,058 442,058
Total number of ε-proteobacterial V6 Tag Sequencesb 122,823 147,515
Depth (m) 1,537 1,529
Latitude °N, Longitude °W 45.92, -129.99 45.94, -129.99
Average Temperature (°C) 31.2 24.4
Maximum Temperature (°C) 31.4 24.9
H2S/ΔT (μmol kg-1 °C-1) 7.2 18.9
Mg (mmol/kg) 48.3 50.8
Alkalinity (mEq/L) 2.4 3.7
Mn (μmol/kg) 19.8 4.8
Fe (μmol/kg) 0.8 7.9
Silica (mmol/kg) 1.46 1.07

There is very little overlap in the community composition of these two sites. Descriptions of archaeal diversity are nearly exhaustive and suggest the presence of 2,700 archaeal phylotypes. In contrast, despite examining nearly 690,000 tags identified as bacterial, rarefaction curves indicate that our sampling of bacterial richness is far from complete.

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We observed more than 30,000 unique sequences that form ~18,500 phylotypes, and nonparametric estimates suggest the presence ~37,000 phylotypes, some of which represent the “rare biosphere”.

Table 2. Sequencing information and diversity estimates for all Bacteria and Archaea.

  Bacteria Archaea
Total number of V6 Tag Sequencesa 689,720 216,627
Total Unique V6 Tag Sequences 30,108 5,979
Total OTUs at 3% Difference (phylotypes) 18,537 1,931
Chao1 Estimator of Richness at 3% Difference (95% C.I.) 36,869 (36,108-37,663) 2,754 (2,594-2,952)
ACE Estimator of Richness at 3% Difference (95% C.I.) 37,038 (36,613-37,473) 2,678 (2,616-2,745)
Bray-Curtis Similarity Index at 3% Differenceb 0.08 0.01
Jaccard Similarity Index at 3% Differenceb 0.12 0.08

Extensive quality control of tag sequences ensured that the total error from PCR and pyroseqencing is less than 0.0025 per base and that fewer than 1% of tags are misassigned to phylotypes due to sequencing error. While this study only examines two sites in the deep ocean, it has important implications for our ability to sample and identify all the ecologically relevant members of microbial communities in other high-diversity habitats, such as soils and microbial mat, and communities where low abundant taxa may play crucial roles, such as human microbiota. It provides what may be the first example of a comparative population structure analysis with statistically significant descriptions of diversity, richness, and distribution of microbial populations. The huge amount of phylogenetic diversity documented here also provides a note of caution as we proceed into the age of large-scale microbial community genomic surveys. Our results suggest that even the largest of published metagenomic investigations inadequately represent the full extent of microbial diversity, as they survey only the most highly-abundant taxa.