Molecular Diversity Of Microbial Communities In Continental Margin Sediments And Contaminant Environments

Microorganisms play a key role in global cycle of carbon, nitrogen, sulfur, and heavy metal and so on. The continental margin occupies only 22%of the total ocean floor, but they are among the most productive ecosystems known. Oceanic nitrogen budget is unbalanced primarily due to denitrification which completed by denitrifying bacteria. Sulfate reduction is a dominant anaerobic carbon oxidation pathway along the margins which provide a very good anaerobic condition. Bioremediation using living organisms to degrade or transform pollutants remains potentially the most cost-effective cleanup technology for treating mixed wastes. The transformation of environmental contaminants is a complex process that is influenced by the nature and amount of the contaminant present, the structure and dynamics of the indigenous microbial community and so on.Traditional culture enrichment techniques for studying microbial communities have proven difficult and ultimately, provide an extremely limited view of microbial heterogeneity. The development and application of nucleic acid-based techniques largely eliminated the reliance on culture-dependent methods and consequently, greatly advanced the detection and characterization of microorganisms in natural habitatis.l6SrDNA or RNA was usually be used as a molecular maker for the phylogenetic analysis of microbial communities but it can not represent the functional activities. Recently, functional genes that code the key enzyme involved in a variety of metabolic pathway such denitrification, sulfate reduction and biodegradation were used to study the microbial communities.There are a lot of molecular methods such as PCR, fingerprinting, DNA/RNA hybridization and sequencing, have been used to assess microbial community structure and activities. But these techniques are labor-intensive and not adequate for real-time field application.Rapid, quantitative, and cost-effective tools that can be operated in real time and in field-scale heterogeneous environments are needed for measuring and evaluating bioremediation strategies and endpoints. Microarrays are a powerful genomic technology and are widely used to study various biological processes. It is only recently that microarray-based genomic technology has been extended to study microbial communities in the environment and bring some challenges such as specificity, sensitivity and quantification.In this study, a PCR-based cloning and sequencing approach was used to investigated the molecular diversity of nirS ,nirK in the xygen deficient continental margin and diversity of dsrAB in the continental margin systems of oxygen deficient and oxygen minimum zone and uranium contaminated aquifer. Further, we developed a comprehensive 50-mer oligonucleotide microarrays containing probes (1 670) from all of the known genes (2,402) involved in biodegradation and metal resistance to monitor biodegrading populations. The key results from these studies are summarized as bellow.1. Molecular Diversity of Denitrifying Genes in Continental Margin Sediments within the Oxygen-Deficient Zone off the Pacific Coast of Mexico.To understand the composition and structure of denitrifying communities in theoxygen-deficient zone off the Pacific coast of Mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a PCR-based cloning approach. A total of 50 operational taxonomic units (OTUs) for nirK and 82 OTUs for nirS were obtained from all samples. Forty-four of the nirS clones and 31 of the nirK clones were sequenced; the levels of similarity of the nirS clones were 52 to 92%, and the levels of similarity of the nirS clones were 50 to 99%. The percentages of overlapping OTUs between stations were 18 to 30% for nirS and 5 to 8% for nirK. Sequence analysis revealed that 26% of the nirS clones were related to the nirS genes of Alcaligenes faecalis (80 to 94% similar) andPseudomonas stutzeri (80 to 99%), whereas 3 to 31% of the nirK clones were closely related to the nirK genes of Pseudomonas sp.