Bacterial diversity and community composition from seasurface to subseafloor - PubMed (original) (raw)

Bacterial diversity and community composition from seasurface to subseafloor

Emily A Walsh et al. ISME J. 2016 Apr.

Abstract

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450,104 pyrotags representing 29,814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.

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Figures

Figure 1

Locations of sampling stations. Superimposed chlorophyll a content is annual average data (mean from September 1994–December 2004) from the SeaWiFS satellite uploaded into GeoMapApp (Behrenfeld and Falkowski, 1997; Gregg et al., 2005).

Figure 2

Scatterplot of sequencing and CTD data including (from left to right): OTUs (97%), oxygen, chlorophyll a, temperature and density.

Figure 3

(a) Non-metric multidimensional scaling (nMDS) plot of the water column and sediment community compositions. Axes do not represent any measured parameter, but define a 2-D space that allows the best spatial representation of sample similarity, based on Bray–Curtis similarity indices. (b) Enlargement of the nMDS plot for the water-column communities with a superimposed color gradient representing depth from seasurface (red) to the abyssopelagic water of EQP-8 and EQP-11 (blue).

Figure 4

Heatmap clustering visualization of water column and sediment bacterial communities (x axis) and class-level GAST taxonomy (y axis). The heatmap is color coded by the percentage contributed by a given taxon to any given sample. Hierarchal clustering is based on the Morista–Horn similarity index.

Figure 5

Rank abundance histograms of community overlap between (a) water column and shallow sediment (0–10 cmbsf), (b) shallow sediment and deep sediment (≥1.5 mbsl) and (c) water column and deep sediment (≥1.5 mbsl). OTUs highlighted in pink are shared between compared environments, whereas OTUs highlighted in blue are unique to each environment.

Figure 6

Rank abundance histograms for the top OTUs shared (x axis) between the oceanic and sedimentary environments. The y axis indicates the percentage of the total number of reads per OTU within our subseafloor sediment samples (⩾1.5 mbsf, red), shallow sediment samples (orange) and water-column samples (blue).

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Bacterial diversity and community composition from seasurface to subseafloor - PubMed (original) (raw)