Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS

Appl Environ Microbiol. 2016 Apr 18;82(9):2656-2668. doi: 10.1128/AEM.03493-15. Print 2016 May.

Abstract

Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458-1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochromec system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochromecand multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Autotrophic Processes
  • Computer Simulation
  • Culture Media
  • DNA, Bacterial / genetics
  • Electron Transport
  • Ferrous Compounds / metabolism*
  • Fresh Water
  • Gallionellaceae / enzymology
  • Gallionellaceae / genetics*
  • Gallionellaceae / metabolism*
  • Geologic Sediments / chemistry
  • Hydrogen / metabolism
  • Metabolic Networks and Pathways
  • Metagenomics / methods
  • Nitrates / metabolism*
  • Oxidation-Reduction
  • Oxidoreductases / genetics
  • Oxidoreductases / metabolism
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis
  • Sequence Analysis, DNA

Substances

  • Culture Media
  • DNA, Bacterial
  • Ferrous Compounds
  • Nitrates
  • RNA, Ribosomal, 16S
  • Hydrogen
  • Oxidoreductases
  • nitrous oxide reductase

Grants and funding

This work, including the efforts of Shaomei He and Eric Roden, was funded by NASA Astrobiology Institute (NNA13AA94A). This work, including the efforts of Eric Roden, was funded by University of Wisconsin-Madison (UW) (Vilas Associateship award). This work, including the efforts of Andreas Kappler, was funded by the European Research Council under the European Union's Seventh Framework Program (FP/2007–2013)/ERC grant, agreement no. 307320 – MICROFOX.