Microbial community structure in the North Pacific ocean

Abstract

We report a ribosomal tag pyrosequencing study of the phylogenetic diversity of Archaea, Bacteria and Eucarya over a depth profile at the Hawaii Ocean Time-Series Station, ALOHA. The V9 region of the SSU rRNA gene was amplified from samples representing the epi-(10 m), meso-(800 m) and bathy-(4400 m) pelagia. The primers used are expected to amplify representatives of B80% of known phylogenetic diversity across all three domains. Comparisons of unique sequences revealed a remarkably low degree of overlap between communities at each depth. The 444 147 sequence tags analyzed represented 62 975 unique sequences. Of these, 3707 (5.9%) occurred at two depths, and only 298 (0.5%) were observed at all three depths. At this level of phylogenetic resolution, Bacteria diversity decreased with depth but was still equivalent to that reported elsewhere for different soil types. Archaea diversity was highest in the two deeper samples. Eucarya observations and richness estimates are almost one order of magnitude higher than any previous marine microbial Eucarya richness estimates. The associations of many Eucarya sequences with putative parasitic organisms may have significant impacts on our understanding of the mechanisms controlling host population density and diversity, and point to a more significant role for microbial Eucarya in carbon flux through the microbial loop. We posit that the majority of sequences detected from the deep sea that have closest matches to sequences from non-pelagic sources are indeed native to the marine environment, and are possibly responsible for key metabolic processes in global biogeochemical cycles.

Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

“…5) demonstrates that multiple environmental factors affect diversity and composition in the ETNP. This is consistent with previous work indicating that temperature has a strong influence on marine microbial diversity 35,36 (Supplementary Discussion). For instance, Thomas et al 18 project a 50% decline in phytoplankton diversity in the ETNP associated with future ocean warming.…”

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

“…Genome analysis also shows that SM9913 lacks the molybdopterin metabolism that results in ROS production, implying that SM9913 typically faces low ROS concentrations. Consistent with this finding, the oxygen concentration in sea water at a depth of 1800 m is about one third of that in surface sea water (Brown et al, 2009). Furthermore, the oxygen concentration in deep sea sediment is even lower than that in the surrounding deep-sea water (Glud, 2008).…”

“…Currently, only a few species of deep-sea bacteria have been subjected to sequence analyses. Considering the high diversity of deep-sea bacteria (Toffin et al, 2004;Sogin et al, 2006;Brown et al, 2009), more genomic sequences of representative bacterial strains must be analyzed to fully characterize the special features required for adaptation to deep-sea sediments.…”

Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean

“…Relevant linkers were attached to primers, as were eight-base barcodes (Hamady et al, 2008) used to sort individual samples; for the 60 samples, we recovered 714 245 sequences with a median read length of 475 bp. We used the approach of Huse et al (2007) that is commonly used in the literature for quality control (Brown et al, 2009;Galand et al, 2009). Using the program mothur (http://www.mothur.org; Schloss et al 2009), we discarded sequences: 4 ± 100 bp from the median sequence length, containing any ambiguous bases, containing homopolymers 48 bp, of o25 average quality score, and that did not exactly match the forward primer and barcode sequence.…”