Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia

Abstract

Coastal sediments accumulate metals from anthropogenic sources and as a consequence industry is required to monitor sediment health. The total concentration of a metal does not necessarily reflect its potential toxicity or biological impact, so biological assessment tools are useful for monitoring. Rapid biological assessment tools sensitive enough to detect relatively small increases in metal concentrations would provide early warning of future ecosystem impact. The authors investigated in situ populations of Archaea and Bacteria as potential tools for rapid biological assessment in sediment at 4 northern Australian coastal locations over 2 yr, in both wet and dry seasons. The 1 M HCl-extractable concentrations of metals in sediment were measured, and Archaeal and Bacterial community profiles were obtained by next-generation sequencing of sediment deoxyribonucleic acid (DNA). Species response curves were used to identify several taxonomic groups with potential as biological indicators of metal impact. Spatial variation, sediment grain size, water depth, and dissolved oxygen also correlated with microbial population shifts. Seasonal variation was less important than geographic location. Metal-challenge culture trials supported the identification of metal-resistant and -sensitive taxa. In situ Archaea and Bacteria are potentially sensitive indicators for changes in bioavailable concentrations of metals; however, the complexity of the system suggests it is important to identify metal-specific functional genes that may be informed by these sequencing surveys, and thus provide a useful addition to identity-based assays.

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

“…2). This is consistent with biogeographic surveys that have detected this group in anoxic estuarine sediments (unpublished data, accession number: JN672646), OMZs (unpublished data, accession number: MG875625), and marine sediments [79]. However, the DEV007 clade is also found in oxic seawater attached to particles [35].…”

Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria

“…SAR324 and SAR406 are considered oligotrophic bacteria (Cho and Giovannoni, 2004), which could also explain an adaptation toward low levels of trace metal concentrations. Consistent with our findings, the Verrucomicrobia DEV007 was recently identified among the most sensitive taxa to multiple metals in a molecular screening of microbial communities for candidate indicators of multiple metal impacts performed in marine sediments from northern Australia (Cornall et al, 2016).…”

Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages

“…However, we observed that the proximity to the aquaculture site was associated with the reduction of the Verrucomicrobia uncultured family DEV007 in the limpet microbiome of limpets. DEV007 is a marine group of bacteria recently pointed out as particularly sensitive to metal pollution in surface waters and marine sediments [68,69]. Its decrease in limpets growing in adhesion to the aquaculture cage might be related to the increase in heavy metal accumulation that often accompanies aquaculture practices [1], which can indirectly affect the most sensitive species in the microbiome of nearby wild organisms.…”