Blog
About

  • Record: found
  • Abstract: found
  • Article: found
Is Open Access

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

Read this article at

Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O 2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO 2, CH 4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H 2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H 2 in acidic suboxic macroscopic growths.

      Related collections

      Most cited references 59

      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

      Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Availability: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license. Contact: epruesse@mpi-bremen.de Supplementary information: Supplementary data are available at Bioinformatics online.
        Bookmark
        • Record: found
        • Abstract: found
        • Article: not found

        Community structure and metabolism through reconstruction of microbial genomes from the environment.

        Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: not found

          The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.

          The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project that has been conceived to provide a useful tool especially for the scientific microbial taxonomist community. The aim of what we have called "The All-Species Living Tree" is to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. This tree is to be regularly updated by adding the species with validly published names that appear monthly in the Validation and Notification lists of the International Journal of Systematic and Evolutionary Microbiology. For this purpose, the SAM executive editors, together with the responsible teams of the ARB, SILVA, and LPSN projects (www.arb-home.de, www.arb-silva.de, and www.bacterio.cict.fr, respectively), have prepared a 16S rRNA database containing over 6700 sequences, each of which represents a single type strain of a classified species up to 31 December 2007. The selection of sequences had to be undertaken manually due to a high error rate in the names and information fields provided for the publicly deposited entries. In addition, from among the often occurring multiple entries for a single type strain, the best-quality sequence was selected for the project. The living tree database that SAM now provides contains corrected entries and the best-quality sequences with a manually checked alignment. The tree reconstruction has been performed by using the maximum likelihood algorithm RAxML. The tree provided in the first release is a result of the calculation of a single dataset containing 9975 single entries, 6728 corresponding to type strain gene sequences, as well as 3247 additional high-fquality sequences to give robustness to the reconstruction. Trees are dynamic structures that change on the basis of the quality and availability of the data used for their calculation. Therefore, the addition of new type strain sequences in further subsequent releases may help to resolve certain branching orders that appear ambiguous in this first release. On the web sites: www.elsevier.de/syapm and www.arb-silva.de/living-tree, the All-Species Living Tree team will release a regularly updated database compatible with the ARB software environment containing the whole 16S rRNA dataset used to reconstruct "The All-Species Living Tree". As a result, the latest reconstructed phylogeny will be provided. In addition to the ARB file, a readable multi-FASTA universal sequence editor file with the complete alignment will be provided for those not using ARB. There is also a complete set of supplementary tables and figures illustrating the selection procedure and its outcome. It is expected that the All-Species Living Tree will help to improve future classification efforts by simplifying the selection of the correct type strain sequences. For queries, information updates, remarks on the dataset or tree reconstructions shown, a contact email address has been created (living-tree@arb-silva.de). This provides an entry point for anyone from the scientific community to provide additional input for the construction and improvement of the first tree compiling all sequenced type strains of all prokaryotic species for which names had been validly published.
            Bookmark

            Author and article information

            Affiliations
            [1 ]Departamento de Biología Funcional—IUBA, Universidad de Oviedo , Oviedo, Spain
            [2 ]Department of Biochemistry and Molecular Biology, University of Southern Denmark , Odense, Denmark
            [3 ]Ribocon GmbH , Bremen, Germany
            [4 ]Chair of Systems and Synthetic Biology, Wageningen University , Wageningen, The Netherlands
            [5 ]Department of Bioremediation, Bio-Iliberis R&D , Granada, Spain
            [6 ]Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis , Madrid, Spain
            [7 ]School of Biological Sciences, Bangor University , Gwynedd, UK
            [8 ]Consejo Superior de Investigaciones Científicas (CSIC), Estación Experimental del Zaidín , Granada, Spain
            [9 ]Departamento de Explotación y Prospección de Minas—IUBA, Universidad de Oviedo , Oviedo, Spain
            [10 ]Centro Nacional de Investigaciones Metalúrgicas, CSIC , Madrid, Spain
            Author notes
            [* ]Departamento de Biología Funcional—IUBA, Universidad de Oviedo , Julián Clavería s/n, 33006 Oviedo, Asturias, Spain. E-mail: jsm@ 123456uniovi.es or Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis , Marie Curie 2, 28049 Madrid, Spain. E-mail: mferrer@ 123456icp.csic.es
            [11]

            These authors contributed equally to this work.

            Journal
            ISME J
            ISME J
            The ISME Journal
            Nature Publishing Group
            1751-7362
            1751-7370
            June 2014
            16 January 2014
            1 June 2014
            : 8
            : 6
            : 1259-1274
            24430486
            4030236
            ismej2013242
            10.1038/ismej.2013.242
            Copyright © 2014 International Society for Microbial Ecology

            This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/

            Categories
            Original Article

            Microbiology & Virology

            acid mine drainage, metagenomics, omic, biofilm, arman, metaproteomics

            Comments

            Comment on this article