Abstract
The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.
Highlights
The phylum Actinobacteria is composed of a large group of morphologically and physiologically diverse Gram-positive bacteria with high genomic G+C contents, which are ubiquitous in nature (Ensign, 1992; Goodfellow et al, 2012)
The results showed a high diversity and a relatively comprehensive community structure of actinobacteria in the deep-sea surface sediments and water along the Southwest Indian Ridge (SWIR), which significantly correlated with environmental factors
The 16S rRNA gene pyrosequencing data showed that the relative abundance of actinobacteria in the sediments collected from the SWIR was higher than that found in the sediments of the deep Arctic and Atlantic Oceans (0.1–3.0%, 0–2.32 mbsf), but less than that reported in the deep Pacific Ocean (Inagaki et al, 2006; Schauer et al, 2010; Jorgensen et al, 2012)
Summary
The phylum Actinobacteria is composed of a large group of morphologically and physiologically diverse Gram-positive bacteria with high genomic G+C contents, which are ubiquitous in nature (Ensign, 1992; Goodfellow et al, 2012) Members of this phylum are successful colonizers of different extreme environments, often occurring as abundant populations (Bull, 2011). As for planktonic actinobacteria in the ocean, it was shown that their global distribution changed along latitudinal gradients (Pommier et al, 2007); their composition in the brackish northern Baltic Sea was related to environmental gradients including total phosphorus (TP), dissolved organic carbon, chlorophyll a, and bacterial production (Holmfeldt et al, 2009). Little is known about the actinobacterial diversity and biogeography in deep-sea habitats
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