Lanzen A, Jorgensen SL, Bengtsson MM, Jonassen I, Ovreas L, Urich T.. Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiol Ecol 77: 577-589

Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway.
FEMS Microbiology Ecology (Impact Factor: 3.57). 05/2011; 77(3):577-89. DOI: 10.1111/j.1574-6941.2011.01138.x
Source: PubMed

ABSTRACT DNA sequencing technology has proven very valuable for analysing the microbiota of poorly accessible ecosystems such as hydrothermal vents. Using a combination of amplicon and shotgun sequencing of small-subunit rRNA and its gene, we examined the composition and diversity of microbial communities from the recently discovered Jan Mayen vent field, located on Mohn's Ridge in the Norwegian-Greenland Sea. The communities were dominated by the epsilonproteobacterial genera Sulfurimonas and Sulfurovum. These are mesophiles involved in sulphur metabolism and typically found in vent fluid mixing zones. Composition and diversity predictions differed systematically between extracted DNA and RNA samples as well as between amplicon and shotgun sequencing. These differences were more substantial than those between two biological replicates. Amplicon vs. shotgun sequencing differences could be explained to a large extent by bias introduced during PCR, caused by preferential primer-template annealing, while DNA vs. RNA differences were thought to be caused by differences between the activity levels of taxa. Further, predicted diversity from RNA samples was consistently lower than that from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights.

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Available from: Steffen Leth Jørgensen, Sep 26, 2015
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    • "Sequences were filtered using LUCY (Chou and Holmes, 2001) to remove short (< 150 bp) and low-quality sequences (> 0.2% error probability). SSU ribosomal RNA sequences of eukaryotes were identified by MEGAN analysis of BLASTn files against a SSU rRNA reference database (Lanzén et al., 2011; parameters: min. bit score 150, min. "
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    ABSTRACT: Soils host the most complex communities on Earth, including the most diverse and abundant eukaryotes, i.e. heterotrophic protists. Protists are generally considered as bacterivores, but evidence for negative interactions with nematodes both from laboratory and field studies exist. However, direct impacts of protists on nematodes remain unknown. We isolated the soil-borne testate amoeba Cryptodifflugia operculata and found a highly specialized and effective pack-hunting strategy to prey on bacterivorous nematodes. Enhanced reproduction in presence of prey nematodes suggests a beneficial predatory life history of these omnivorous soil amoebae. Cryptodifflugia operculata appears to selectively impact the nematode community composition as reductions of nematode numbers were species specific. Furthermore, we investigated 12 soil metatranscriptomes from five distinct locations throughout Europe for 18S ribosomal RNA transcripts of C. operculata. The presence of C. operculata transcripts in all samples, representing up to 4% of the active protist community, indicates a potential ecological importance of nematophagy performed by C. operculata in soil food webs. The unique pack-hunting strategy on nematodes that was previously unknown from protists, together with molecular evidence that these pack hunters are likely to be abundant and widespread in soils, imply a considerable importance of the hitherto neglected trophic link ‘nematophagous protists’ in soil food webs.
    Environmental Microbiology 06/2015; 17. · 6.20 Impact Factor
    • "Sequences were first filtered using LUCY (Chou and Holmes, 2001), removing short (o150 bp) and low-quality sequences (40.2% error probability). SSU ribosomal RNA sequences of eukaryotes were identified by MEGAN analysis of BLASTn files against a 3-domain SSU rRNA reference database (Lanzén et al., 2011; parameters: min. bit score 150, min. "
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    ABSTRACT: The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.
    The ISME Journal 03/2015; DOI:10.1038/ismej.2015.30 · 9.30 Impact Factor
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    • "The 16S rRNA gene-based approach has been readily adopted in the past three decades by the absolute majority of the scientific community, and extensively utilized to study the microbial diversity in ecosystems ranging from large global habitats, e.g. oceans [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40], and soil [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60], to hardly accessible extreme environments such as deep sea hydrothermal vents [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76], Antarctic lakes [32,62,77–82], and Antarctic soils [33,62,83–90]. Collectively, these studies have demonstrated that the scope of phylogenetic diversity is much broader than previously implied from culture-based studies. "
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    ABSTRACT: Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.
    Journal of Advanced Research 11/2014; 6(3). DOI:10.1016/j.jare.2014.10.005
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