Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria

Abstract

Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2 m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this cluster was only detected on aggregates up to a few meters above the sediment surface, but never in the fraction of free-living bacteria. A quantitative real-time PCR approach revealed that the MMC constituted up to 13% of total bacterial 16S rRNA genes in surface sediments of the North Sea. In a global survey, including sediments from the Mediterranean Sea, the Atlantic, Pacific and Indian Ocean and various climatic regions, the MMC was detected in most samples and to a water depth of 4300 m. Two fosmids of a library from sediment of the southern North Sea containing 16S rRNA genes affiliated with the MMC were sequenced. Both fosmids have a single unlinked 16S rRNA gene and no complete rRNA operon as found in most bacteria. No synteny to other myxobacterial genomes was found. The highest numbers of orthologues for both fosmids were assigned to Sorangium cellulosum and Haliangium ochraceum. Our results show that the MMC is an important and widely distributed but largely unknown component of marine sediment-associated bacterial communities.

Figure 1

(a). Stations (St) in the North Sea visited during a cruise with RV Heincke in September 2005 and analysed for the presence of the MMC. (b). Abundance of 16S rRNA genes of the MMC (percent (%) of total bacterial 16S rRNA genes) in sediment surface samples of the various stations. Numbers on the y-axis refer to stations given in a.

Figure 2

Neighbour-joining tree showing the phylogenetic relationships of bacteria of the MMC within the Myxococcales based on 16S rRNA gene sequence similarity. Sequences of at least 1300 bp were considered. Only bootstrap values >50% (derived from 2000 replicates) at main nodes are shown. Filled circles indicate that nodes were also recovered reproducibly with maximum-likelihood. Selected members of the Cyanobacteria were used as outgroup (not shown) to define the root of the tree. GenBank sequence accession numbers are given in parentheses. In addition, the sampling site is indicated. The two clones of the fosmids sequenced in this study and the two new Myxococcus spp. are shown in bold. Bar, 0.10 substitutions per nucleotide position.

Figure 3

Map showing the world-wide distribution of the MMC. ▴, detection by the MMC specific PCR, •, detection by sequencing and phylogenetic analysis of 16S rRNA genes obtained in this study and by other authors. The map was adopted from http://www.smithlifescience.com and subsequently modified.

Figure 4

Alignment of fosmids MMCf1 and MMCf2. Protein coding ORFs are depicted in light-grey, the 16S rRNA genes in dark-grey. Alignment of the two fosmids is generated by the GenomeMatcher software. The identity score of BLASTn of each block is given in grey scale; white: no similarity; black: highest similarity.