Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico

Abstract

SummaryAreas of low oxygen have spread exponentially over the past 40 years, and are cited as a key stressor on coastal ecosystems. The world's second largest coastal hypoxic (≤2 mg of O2 l −1 ) zone occurs annually in the northern Gulf of Mexico. The net effect of hypoxia is the diversion of energy flow away from higher trophic levels to microorganisms. This energy shunt is consequential to the overall productivity of hypoxic water masses and the ecosystem as a whole. In this study, water column samples were collected at 39 sites in the nGOM, 21 of which were hypoxic. Analysis of the microbial community along a hypoxic to oxic dissolved oxygen gradient revealed that the relative abundance (iTag) of Thaumarchaeota species 16S rRNA genes (> 40% of the microbial community in some hypoxic samples), the absolute abundance (quantitative polymerase chain reaction; qPCR) of Thaumarchaeota 16S rRNA genes and archaeal ammonia-monooxygenase gene copy number (qPCR) were significantly higher in hypoxic samples. Spatial interpolation of the microbial and chemical data revealed a continuous, shelfwide band of low dissolved oxygen waters that were dominated by Thaumarchaeota (and Euryarchaeota), amoA genes and high concentrations of phosphate in the nGOM, thus implicating physicochemical forcing on microbial abundance.

Methane and microbial dynamics in the Gulf of Mexico water column

“…King et al (2013) also analyzed bacterioplankton in the coastal northern GOM, but their study extended to the mesopelagic. They reported that depth, temperature and, similar to Gillies et al (2015), oxygen were the primary drivers influencing microbial abundances in the GOM. Together these studies suggest that similar organizing principles as those discussed above shape microbal communities in the GOM, but hydrocarbon concentrations were not considered in these studies.…”

“…Sterivex filters were sparged and filled with RNAlater. DNA was extracted directly off of the filter by placing half of the Sterivex filter in a Lysing matrix E (LME) glass/zirconia/silica beads Tube (MP Biomedicals, Santa Ana, CA) using the protocol described in Gillies et al (2015) which combines phenol:chloroform:isoamyalcohol (25:24:1) and bead beating. Genomic DNA was stored at −80 • C until purified.…”

“…Recently, Gillies et al (2015) found that dissolved oxygen concentrations played a significant role in influencing microbial abundances in the northern GOM coastal hypoxic zone. King et al (2013) also analyzed bacterioplankton in the coastal northern GOM, but their study extended to the mesopelagic.…”

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves

“…Genomic DNA was extracted from the pellet by suspension in a modified CTAB extraction buffer ((10% CTAB [hexadecyltrimethylammonium bromide], 1 M NaCl and 0.5 M phosphate buffer, pH 8) with 0.1 M ammonium aluminum sulfate, 25:24:1 phenol: chloroform:isoamyl alcohol) and subjecting it to bead beating using a FastPrep-24 (MP Biomedicals, Solon, OH) following the protocol as described by Gillies et al (2015) with the following modification: the first and second extractions were combined after the ethanol wash with 50 lL EB buffer to maximize DNA yields. Genomic DNA was extracted from the pellet by suspension in a modified CTAB extraction buffer ((10% CTAB [hexadecyltrimethylammonium bromide], 1 M NaCl and 0.5 M phosphate buffer, pH 8) with 0.1 M ammonium aluminum sulfate, 25:24:1 phenol: chloroform:isoamyl alcohol) and subjecting it to bead beating using a FastPrep-24 (MP Biomedicals, Solon, OH) following the protocol as described by Gillies et al (2015) with the following modification: the first and second extractions were combined after the ethanol wash with 50 lL EB buffer to maximize DNA yields.…”

Hydrography shapes community composition and diversity of amoA‐containing Thaumarchaeota in the coastal waters off central Chile

“…Thaumarchaea are often observed in relatively high abundances in the oxic-anoxic interfaces of marine environments (Molina et al, 2010;Belmar et al, 2011;Stewart et al, 2012;Gillies et al, 2015). A recent kinetic study of nitrification in the seasonally anoxic central Chilean waters reported active ammonia oxidation at 5 nM dissolved oxygen, a value significantly lower than that associated with cultivated representatives, indicative of populations that likely differ phylogenetically and physiologically (Bristow et al, 2016).…”