Analysis of microbial nitrite-dependent oxidation of methane and ammonium in different niches by molecular techniques

Abstract

Nitrogen is an essential element to all living organisms, and the biochemical transformation steps are mediated by a network of metabolically versatile microorganisms. Nitrite-dependent anaerobic methane oxidation (n-damo) and anaerobic ammonium oxidation (anammox) are two new biochemical pathways coupling nitrite reduction to methane oxidation and ammonium oxidation, respectively, to generate dinitrogen gas as a product. The distribution and diversity of n-damo microorganisms were investigated in the lakes of Badain Jaran Desert of China by retrieving specific 16S rRNA and pmoA gene sequences. The occurrence of n-damo bacteria was widely detected in both brine and freshwater lakes with high diversity, while the bacterial abundance in sediment was one order of magnitude higher than that in water. Depth, salinity and the different inorganic nitrogen species were the main environmental factors responsible for the n-damo community distribution, diversity and abundance in the desert lakes. Furthermore, the global distribution pattern of the n-damo community was summarized based on 2,343 16S rRNA gene sequences and 2,555 pmoA gene sequences collected from public databases available. The constructed phylogenetic trees showed that the distribution of this kind of bacteria in marine notably distinguished from other habitats, and the 16S rRNA gene sequences amplified from enrichment cultures established a separate phylogenetic group. Marine and coastal habitats presented higher richness and diversity among all the habitats, and marine ecosystems showed a significant community difference from the freshwater ones. In addition to habitat specificity, n-damo community composition was also shaped by salinity or anthropogenic influence. Anammox bacteria as a main nitrogen removal microbial contributor in the marine ecosystem are widely occurring in the coastal container ports and shipping channels of Hong Kong. A general distribution pattern is clear in which Ca. Scalindua species were detected as the dominant ones in ocean water influenced sites while non-Scalindua species were detected frequently in ports and channels connected with inland river discharge. The distribution of specific anammox bacteria was associated closely to the environmental quality in terms of available inorganic nitrogen and anthropogenic influence. A better understanding of the anammox bacterial community composition may advance delineation of environmental pollution history, providing a new forensic strategy to unravel the past information using sensitive DNA-based technology. In order to gain a better knowledge of n-damo and anammox processes, protection of culture heritage from biodeterioration of nitric/nitrous acid was investigated by analyzing microbial contribution to damage of the sandstone Angkor monuments in Cambodia. Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi were the most common and dominant bacterial phyla in the biofilm and exfoliated sandstone samples with each above 3.7% of the total abundance. Cyanobacteria, Thaumarchaeota, Nitrospirae and Tectomicrobia were the ones responsible for the nitrification process by forming acidity. In addition, human activities including access to visitors may contribute to the damage of the sandstone UNESCO cultural heritage in Southeast Asia. Heritage.