NASA Astrobiology Institute (NAI)

The sub-tropical open ocean is an extreme environment that presents the opportunity to examine the factors affecting microbial community structure across a number of environmental gradients. We have developed and utilized a novel assay that allows us to simultaneously determine the taxonomic composition of Archaea, Bacteria and microbial Eucarya in DNA extracted from environmental samples. Samples analyzed represent the epi-, meso- and bathy-pelagic zones of the ocean, which display gradients in temperature, pressure, oxygen content, nutrient content and photosynthetically available radiation.

We have undertaken a massively-parallel pyrosequencing study to concomitantly examine the marine microbial diversity of all 3 domains of life: the Eucarya, Bacteria and Archaea. The ~90-120 base pair V9 region of the small subunit ribosomal RNA gene (SSU rDNA) was amplified and sequenced from samples representing the epi- (10 m), meso- (800 m), and bathy-pelagic (4,400 m) zones of the Sub-Tropical North Pacific at the Hawaii Ocean Time-Series (HOT) Station ALOHA. Phylogenetic affiliations of the assemblages shifted between al depths and all domains.

Unique sequence richness estimates, determined by parametric modeling methods, revealed much higher richness of Bacteria (10 m = 79 653, 800 m = 64 064, 4 400 m = 43 639) and Eucarya (56,292, 65,703, 37,746) than Archaea (2,013, 4,256, 4,091). Observed numbers, richness estimates and richness lower bounds indicate trends of decreasing Bacteria and Eucarya “pecies” diversity with depth, along with increasing Archaea diversity. However, at higher phylogenetic levels (>0.5 SSU rDNA dissimilarity) Bacteria richness was equal or greater in the meso- and bathypelagic than at the surface. We show a consistent shift in the composition of deep-sea phylum and class level Bacteria assemblages, when compared to surface waters.

In total, 61.8% of Bacteria, and 42.1% of Eucarya phylotypes were rare, contributing < 0.01% to the total tag sequence abundance at any depth, highlighting the importance of rare Eucarya in the make up of microbial assemblages. Furthermore, Eucarya tag sequences showed a level of microdiversity equivalent to that of the Bacteria, and displayed the greatest novelty. The decreased phylogenetic convergence of Eucarya communities in the meso- and bathypelagic, compared to those of Bacteria and Archaea assemblages, indicate that different factors may affect distribution of Eucarya with depth than those shaping Bacteria and Archaea assemblages. The closest database matches to many rare sequences, particularly those in deeper samples, were from Bacteria from sediment, soil and other non-pelagic environments, indicating deep-sea or rare marine microbes have been only poorly characterized in terms of their phylogeny and distribution.