Jiang DM, Kato C, Zhou XW, Wu ZH, Sato T, Li YZ.. Phylogeographic separation of marine and soil myxobacteria at high levels of classification. ISME J 4: 1520-1530

Shandong University, Jinan, PR China.
The ISME Journal (Impact Factor: 9.3). 12/2010; 4(12):1520-30. DOI: 10.1038/ismej.2010.84
Source: PubMed


Microorganisms are globally dispersed and are able to proliferate in any habitat that supports their lifestyles, which, however, has not yet been explored in any specific microbial taxon. The social myxobacteria are considered typical soil bacteria because they have been identified in various terrestrial samples, a few in coastal areas, but none in other oceanic environments. To explore the prevalence of marine myxobacteria and to investigate their phylogenetic relationships with their terrestrial counterparts, we established myxobacteria-enriched libraries of 16S rRNA gene sequences from four deep-sea sediments collected at depths from 853 to 4675 m and a hydrothermal vent at a depth of 204 m. In all, 68 different myxobacteria-related sequences were identified from randomly sequenced clones of the libraries of different samples. These myxobacterial sequences were diverse but phylogenetically similar at different locations and depths. However, they were separated from terrestrial myxobacteria at high levels of classification. This discovery indicates that the marine myxobacteria are phylogeographically separated from their terrestrial relatives, likely because of geographic separation and environment selection.

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Available from: Chiaki Kato, Dec 22, 2014
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    • "Moreover, particle samples (>5 µm) taken in a time series at one station near Helgoland during a tidal cycle demonstrated the consistent presence of MMC in the nepheloid layer (which contains a high concentration of suspended particles) from 5 m depth to the bottom. Additionally, Jiang et al. (2010) found evidence for myxobactieral life in deep-sea sediments (up to 4675 m) and at a hydrothermal vent. A major impediment to understanding the ecology and evolution of marine myxobacteria is the difficulty of cultivating them and studying them under ecologically relevant conditions. "
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    ABSTRACT: Recent discoveries have found the myxobacteria to be much more diverse - both across and within species - than previously known, from global to micrometer spatial scales. Evolutionary analysis of such extant diversity promises to reveal much about how myxobacteria have adapted to natural ecological habitats in the past and continue to evolve in the present, particularly with regard to their intriguing social phenotypes. Experimental populations propagated under defined laboratory conditions undergo very rapid evolution at cooperative traits in a manner that radically changes their social composition. Analysis of such experimentally evolved populations allows detailed characterization of social evolutionary dynamics in real time. Moreover, traditional genetic tools and new genome sequencing technologies together allow deep investigation of the molecular basis of adaptation by experimental populations to known ecological habitats, which in turn can lead to new discoveries regarding the molecular mechanisms governing social behavior.
    Myxobacteria: Genomics, Cellular and Molecular Biology, Edited by Zhaomin Yang, Penelope I. Higgs, 02/2014: chapter Whence Comes Social Diversity? Ecological and Evolutionary Analysis of the Myxobacteria: pages 1-28; Caister Academic Press., ISBN: 978-1908230348
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    • "Order with both terrestrial and marine members that exist primarily in surface - attached swarms ( Shimkets et al . , 2006 ; Jiang et al . , 2010 ) , were up to 95 - fold more abundant on prefilters ( relative to Sterivex ) from depths below the oxycline . Marine myxobacteria have been found in anoxic sediments , but are associated primarily with oxic habitats ( Brinkhoff et al . , 2012 ) , and the Order as a whole is dominated by strictly aerobic heterotrophs ( Shimkets et al . "
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    ABSTRACT: Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.The ISME Journal advance online publication, 12 September 2013; doi:10.1038/ismej.2013.144.
    The ISME Journal 09/2013; 8(1). DOI:10.1038/ismej.2013.144 · 9.30 Impact Factor
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    • "Myxobacteria are well known for their social behavior and as producers of secondary metabolites89. These microorganisms inhabit almost every environment on earth, including soils, river mud, deep-sea sediments, and hydrothermal vents101112. Although the anaerobic myxobacteria, which at present consist of only one genus, Anaeromyxobacter, have simple life cycles and relatively small genomes (5–6 Mb)13, all of the sequenced aerobic myxobacteria have genomes larger than 9 Mb, including the 13.03 Mb genome of S. cellulosum So ce562. "
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    ABSTRACT: Complex environmental conditions can significantly affect bacterial genome size by unknown mechanisms. The So0157-2 strain of Sorangium cellulosum is an alkaline-adaptive epothilone producer that grows across a wide pH range. Here, we show that the genome of this strain is 14,782,125 base pairs, 1.75-megabases larger than the largest bacterial genome from S. cellulosum reported previously. The total 11,599 coding sequences (CDSs) include massive duplications and horizontally transferred genes, regulated by lots of protein kinases, sigma factors and related transcriptional regulation co-factors, providing the So0157-2 strain abundant resources and flexibility for ecological adaptation. The comparative transcriptomics approach, which detected 90.7% of the total CDSs, not only demonstrates complex expression patterns under varying environmental conditions but also suggests an alkaline-improved pathway of the insertion and duplication, which has been genetically testified, in this strain. These results provide insights into and a paradigm for how environmental conditions can affect bacterial genome expansion.
    Scientific Reports 07/2013; 3:2101. DOI:10.1038/srep02101 · 5.58 Impact Factor
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