Human Genetics - Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses

 At 2014-03-18 02:05:18 AM  |   95

The study of the ecophysiology of archaea is currently one of the most exciting research areas in the field of environmental microbiology. Many uncultivated archaeal groups have been discovered as microbial diversity surveys have expanded and improved, but the physiological properties of most of these uncultivated archaea remain to be determined. For instance, uncultivated archaeal lineages such as Marine benthic group B (also known as deep-sea archaeal group), Miscellaneous Crenarchaeota group (MCG) or South African gold mine Euryarchaeota group were found widespread in marine sediments (Teske and Sørensen, 2008); however, the functions of these archaea in the environments are still unknown.

MCG archaea live in diverse habitats, including terrestrial and marine, hot and cold, surface and subsurface environments (Biddle et al., 2006Teske, 2006;Kubo et al., 2012). The label ‘miscellaneous’ appears to represent the difficulty in categorizing the wide terrestrial and marine habitat range of this group (Inagaki et al., 2003). Sørensen and Teske (2006) divided hundreds of MCG clones into smaller and more manageable subgroups—MCG-1 to MCG-4. Jiang and Li, (2011)performed a comprehensive phylogenetic analysis and divided MCG archaea into seven subgroups (MCG-A to MCG-G), whereas Kubo et al. (2012) divided MCG archaea into 17 subgroups. In addition to its cosmopolitan distribution, the MCG group of archaea is one of the most abundant groups in the subsurface sedimentary biosphere based on the 16S rRNA gene abundance: the MCG clones account for 33% of all clones from 47 16S rRNA gene libraries obtained from 11 published studies of the deep marine biosphere (Fry et al., 2008). Moreover, the MCG was found to be one of the most active groups in the deep marine biosphere (Fry et al., 2008Li et al., 2012b). Parallel 16S rRNA and rDNA analyses of Ocean Drilling Program site 1229 on the Peru Margin indicated that the MCG dominated the archaeal clone libraries based on PCR-amplified 16S rDNA genes (Parkes et al., 2005) and on reverse-transcribed 16S rRNA (Biddle et al., 2006). At the Ocean Drilling Program site 1227 on the Peru Margin, MCG archaea were abundant in 16S rRNA gene clone libraries from all depths (Inagaki et al., 2006) and they dominated the reverse-transcribed 16S rRNA pool in all sediment layers except the deep-sea archaeal group/Marine benthic group B horizon (Sørensen and Teske, 2006). In addition, the carbon isotope signatures of archaeal cells and polar lipids from MCG-dominated sediment horizons indicate that these anaerobes utilize buried organic carbon substrates (Biddle et al., 2006). The widespread distribution, high abundance and metabolic activities of MCG archaea all indicate that these organisms might be significant players in biogeochemical cycles. However, the paucity of representative pure cultures has hindered our understanding of the physiological properties of these archaea as well as their ecological functions and evolutionary position. Environmental genomics provides an approach to explore the potential physiological characteristics and genomic information of uncultivated microbes in the context of indigenous microbial communities. Just recently, single-cell genome analysis suggested that members of the MCG archaea are specializing in extracellular protein degradation (Lloyd et al., 2013). Till now, only a few MCG fosmid and cosmid clones have been identified. One MCG fosmid clone was reported containing a functional bacteriochlorophyll a synthase (bchG) gene, a key enzyme for bacteriochlorophyll a biosynthesis. However, the in vivophysiological functions of BchG in MCG are still unknown, although it was supposed that containing a presumptive Bchl a synthase gene, may give the archaea more flexibility to survive or adapt to various environments (Meng et al., 2009). The other three analyzed fosmid clones contain homologous to potentially important functional genes involving in lipid biosynthesis, energy metabolism and resistance to oxidants (Li et al., 2012a). But the physiological properties and the roles of these organisms in natural biogeochemical cycles are still remaining to be determined.

In this study, we investigated the phylogenetic position and potential ecophysiological properties of this little understood MCG archaeal group using an environmental metagenomic method. A member of the MCG was hypothesized to be aromatic compound degrader based on genome information. This hypothesis was further supported by target gene expression analysis after substrate supplementation.


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