Exploring Microbial Community Diversity


Sequencing of 16S rRNA genes directly from environmental samples has revolutionized our understanding of microbial diversity and provided valuable insights into the ecological roles of microbial communities. In this work we consider the influence of spatial proximity and environmental factors on the diversity of microbial communities. Specifically, we analyzed 15 samples from the Global Ocean Sampling (GOS) project which are situated along the Atlantic seaboard at an average interval of 320 km [1].

We characterize differences in microbial communities using two distinct diversity measures: the Bray-Curtis index (BCI) [2] which quantifies differences in taxon-level structures and the unique fraction (UniFrac) measure [3] which considers the amount of divergent evolution that has occurred between communities. Patterns in the relationships between microbial communities imply factors influencing microbial diversity.

Identifying factors which contribute to microbial diversity is of fundamental ecological importance and critical for implementing proper conservation measures. Substantial research effort has been allocated to this problem and our work is directly influenced by:

  • Fuhrman et al. [4] who identified a latitudinal cline where the richness of marine microbial communities is inversely correlated with latitude
  • Lozupone et al. [5] who identified salinity as being a major environmental factor in determining microbial community composition

We divided the 15 Atlantic seaboard samples into 4 environment types as specified by metadata provided with the GOS dataset. Of the 15 samples, 4 are identified as non-coastal samples. Three of these were identified as estuary samples. However, we have separated the Bay of Fundy estuary sample from the other estuary samples as its salinity content is more indicative of a costal environment. The other non-coastal sample is from the Halifax Harbour embayment which is of particular interest since the water in the harbour is well-known to be polluted.



We found no evidence supporting an Atlantic seaboard cline regardless of whether differences between microbial communities are characterized by taxon-level differences (BCI) or evolutionary divergence (UniFrac). More generally, in our dataset where the distance between samples is on the order of several hundred kilometers, we found no correlation between spatial proximity and community composition. It would be interesting to investigate at what scale community composition and spatial proximity begin to strongly correlate.

The hypothesis that salinity is a major determinant of microbial community composition is strongly supported by our results. We also found limited evidence suggesting that pollution can influence the composition of a microbial community and recommend continued research be performed to further support this hypothesis. These conclusions are supported by both our weighted UniFrac analysis and our BCI analysis for all taxonomical ranks from and including class to genus.

Further Reading

[1] Rusch DB et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biology, Vol. 5, No. 3, 2007, e77.
[2] Bray R and Curtis T. An Ordination of the Upland Forest Communities of Southern Wisconsin. Ecological Monographs, Vol. 27, 1957, pp 325-49.
[3] Lozupone C et al. UniFrac - An Online Tool for Comparing Microbial Community Diversity in a Phylogenetic Context. BMC Bioinformatics, Vol. 7, 7 August 2006, 371.
[4] Fuhrman JA et al. A Latitudinal Diversity Gradient in Planktonic Marine Bacteria. PNAS, Vol. 105, No. 22, 2008, pp 7774-7778.
[5] Lozupone C and Knight R. Global Patterns in Bacterial Diversity. PNAS, Vol. 104, No. 27, 2007, pp. 11436-11440.

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