Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone

Abstract

Microbial communities play central roles in ocean biogeochemical cycles, and are particularly important in in oceanic oxygen minimum zones (OMZs). However, the key carbon, nitrogen, and sulfur (S) cycling processes catalyzed by OMZ microbial communities are poorly constrained spatially, temporally, and with regard to the different microbial groups involved. Here we sample across dissolved oxygen (DO) gradients in the oceans' largest OMZ by volume-the eastern tropical North Pacific ocean, or ETNP-and quantify 16S rRNA and functional gene transcripts to detect and constrain the activity of different S-cycling groups. Based on gene expression profiles, putative dissimilatory sulfite reductase (dsrA) genes are actively expressed within the ETNP OMZ. dsrA expression was limited almost entirely to samples with elevated nitrite concentrations, consistent with previous observations in the Eastern Tropical South Pacific OMZ. dsrA and 'reverse' dissimilatory sulfite reductase (rdsrA) genes are related and the associated enzymes are known to operate in either direction-reducing or oxidizing different S compounds. We found that rdsrA genes and soxB genes were expressed in the same samples, suggestive of active S cycling in the ETNP OMZ. These data provide potential thresholds for S cycling in OMZs that closely mimic recent predictions, and indicate that S cycling may be broadly relevant in OMZs.

Keywords: oxygen minimum zone; sulfate reduction; sulfur cyling; sulfur oxidation; transcriptomics.

FIGURE 1

Map of sampling stations in the eastern tropical North Pacific Ocean (ETNP). Station locations are plotted on dissolved oxygen (DO) concentrations (μmol L^-1) at 100 m depth from the World Ocean Atlas (plotted in Ocean Data View).

FIGURE 2

Oceanographic sections of (A) DO (μmol kg^-1) and (B) nitrite (nmol L^-1). The location of individual sampling stations is indicated along the horizontal axis; vertical axes display depth down to 400 m; color scales show concentrations. Small black dots denote the depths of bottle samples collected for nitrite measurements, and discrete oxygen data for the same depths were extracted from the Winkler-corrected CTD data. Data were gridded in Ocean Data View.

FIGURE 3

Quantitative PCR (qPCR) data for (A)Chromatiales 16S rRNA, (B) SUP05 16S rRNA, and (C)dsrA genes and transcripts (expressed per mL). Station and depth of sample collected are shown, and gene or transcript abundances are displayed along the horizontal axes (log scale). Abundances in DNA are shown in blue, and abundances in RNA (i.e., cDNA) are shown in orange. Error bars denote SD of the triplicate measurement.

FIGURE 4

Bubble plot of qPCR data for (A) SUP05 16S rRNA and (B)dsrA plotted versus DO and nitrite. The size of the bubbles is proportional to level of expression. Gray datapoints indicate that no expression was detected.