Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-11-04

AUTHORS

Daniela S Aliaga Goltsman, Luis R Comolli, Brian C Thomas, Jillian F Banfield

ABSTRACT

A fundamental question in microbial ecology relates to community structure, and how this varies across environment types. It is widely believed that some environments, such as those at very low pH, host simple communities based on the low number of taxa, possibly due to the extreme environmental conditions. However, most analyses of species richness have relied on methods that provide relatively low ribosomal RNA (rRNA) sampling depth. Here we used community transcriptomics to analyze the microbial diversity of natural acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Our analyses target deep pools of rRNA gene transcripts recovered from both natural and laboratory-grown biofilms across varying developmental stages. In all, 91.8% of the ∼254 million Illumina reads mapped to rRNA genes represented in the SILVA database. Up to 159 different taxa, including Bacteria, Archaea and Eukaryotes, were identified. Diversity measures, ordination and hierarchical clustering separate environmental from laboratory-grown biofilms. In part, this is due to the much larger number of rare members in the environmental biofilms. Although Leptospirillum bacteria generally dominate biofilms, we detect a wide variety of other Nitrospira organisms present at very low abundance. Bacteria from the Chloroflexi phylum were also detected. The results indicate that the primary characteristic that has enabled prior extensive cultivation-independent ‘omic’ analyses is not simplicity but rather the high dominance by a few taxa. We conclude that a much larger variety of organisms than previously thought have adapted to this extreme environment, although only few are selected for at any one time. More... »

PAGES

1014-1023

References to SciGraph publications

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  • 2008-10-09. Natural acidophilic biofilm communities reflect distinct organismal and functional organization in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2009-12-24. Cultivation and quantitative proteomic analyses of acidophilic microbial communities in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2008-10-23. Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2004-06-30. Acid mine drainage biogeochemistry at Iron Mountain, California in GEOCHEMICAL TRANSACTIONS
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  • 2011-05-19. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data in GENOME BIOLOGY
  • 2010-02-18. AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2013-11-15. Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains in BMC MICROBIOLOGY
  • 2006-09-05. RNA:protein ratio of the unicellular organism as a characteristic of phosphorous and nitrogen stoichiometry and of the cellular requirement of ribosomes for protein synthesis in BMC BIOLOGY
  • 2010-07-15. Microbial community structure across the tree of life in the extreme Río Tinto in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ismej.2014.200

    DOI

    http://dx.doi.org/10.1038/ismej.2014.200

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1036023470

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25361394


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