Molecular detection and ecology of newly emerging bacterial and archaeal groups in coastal wetland and ocean sediments

Abstract

New microorganisms discovered recently are important players in global carbon and nitrogen cycling; they include anaerobic methanotroph (ANME) and nitrite-dependent anaerobic methane oxidizing (n-damo) bacteria for anaerobic methane oxidation, anaerobic ammonium oxidizing (anammox) bacteria and Thaumarchaeota for nitrogen cycling, and Bathyarchaeota for versatile organics metabolism. Because of their worldwide distribution, knowledge on their diversity and ecological distribution patterns is important to the understanding of their ecophysiological significance. The objectives of this study were to investigate their molecular ecology through designing new PCR primers for detecting and quantifying these microorganisms and to reveal the ecological distribution pattern and potential factors regulating such pattern in the coastal mangrove wetland of Hong Kong and also South China Sea sediments.

New PCR primers for retrieving more ANME mcrA gene and improving clone library diversity coverage, and qPCR primers for ANME mcrA gene group g-h for filling the gap of detecting all ANME subgroups were designed and evaluated successfully. Two sets of primers targeting hydrazine synthase and cytochrome c biogenesis protein encoding genes were developed, and the best ones in detecting and quantifying anammox bacteria were used for further clone library and qPCR analysis. hzsB gene primers could well delineate the coastal-ocean distribution pattern of anammox bacteria in nSCS sediment samples; hzsB and hzsC gene primers, which exclusively detected anammox bacteria were recommended to be applied in combination with 16S rRNA gene primers.

Based on clone library and qPCR analysis, Methanomicrobiales, Methanosarcinales clade 1, 2 and Methanomassiliicoccus-like groups of methanogens were dominant in nSCS sediments; and close mcrA gene abundances in surface layers of mangrove field and intertidal mudflats and more abundant mcrA gene in subsurface layers were found; ANME groups were also observed in these sediments with lower proportion.

MiSeq-16S rRNA gene profiling of Mai Po wetland and nSCS sediments was performed. Stratified distribution of bacterial community was evident at Mai Po wetland. Thaumarchaeota MG-I was dominant in surface layer while Bathyarchaeota and MBG-B in subsurface layer for the archaea. Sediment depth and seasonality, and pH value were the most important factors affecting the bacterial and archaeal community structure and diversity, respectively.

The proportion of Thaumarchaeota in the total archaeal community increased with seawater depth in nSCS. Partitioned distribution of Bathyarchaeota fraction in the whole archaeal community was firstly reported with Subgroups 6 and 8 enriched in shallow-sea sediments. Temperature, seawater depth and salinity were the three most influential factors correlated with the bacterial communities observed, but less with archaeal communities. Co-existence and abundance of marine anammox and n-damo bacteria in deep-sea sediments was observed for the first time. SRBs were enriched in shallow-sea sediments, co-occurring with nitrite oxidizing Nitrospira and potential sulfide-oxidizing shallow-sea specific JTB255 clade. The global deep-sea cosmopolitans OM1 and deep-sea specific JTB255 clade were also at high abundance in deep-sea sediments of nSCS.

Molecular ecological characteristics of these newly discovered microorganisms provide further new insights on their diversity, distribution pattern and adaption to different niches.