Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems

FEMS Microbiol Ecol. 2015 Oct;91(10):fiv105. doi: 10.1093/femsec/fiv105. Epub 2015 Aug 30.

Abstract

The diversity and distribution of methylotrophic bacteria have been investigated in the oceans and lakes using the methanol dehydrogenase mxaF gene as a functional marker. However, pelagic marine (OM43) and freshwater (LD28 and PRD01a001B) methylotrophs within the Betaproteobacteria lack mxaF, instead possessing a related xoxF4-encoded methanol dehydrogenase. Here, we developed and employed xoxF4 as a complementary functional gene marker to mxaF for studying methylotrophs in aquatic environment. Using xoxF4, we detected OM43-related and LD28-related methylotrophs in the ocean and freshwaters of North America, respectively, and showed the coexistence of these two lineages in a large estuarine system (St Lawrence Estuary). Gene expression patterns of xoxF4 supported a positive relationship between xoxF4-containing methylotroph activity and spring time productivity, suggesting phytoplankton blooms are a source of methylotrophic substrates. Further investigation of methanol dehydrogenase diversity in pelagic ecosystems using comparative metagenomics provided strong support for a widespread distribution of xoxF4 (as well as several distinct xoxF5) containing methylotrophs in marine and freshwater surface waters. In total, these results demonstrate a geographical distribution of OM43/LD28-related methylotrophs that includes marine and freshwaters and suggest that methylotrophy occurring in the water column is an important component of lake and estuary carbon cycling and biogeochemistry.

Keywords: C1 metabolism; LD28; marine OM43 clade; metagenomics; methanol oxidation; methylotrophy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alcohol Oxidoreductases / metabolism*
  • Betaproteobacteria / classification*
  • Betaproteobacteria / enzymology
  • Betaproteobacteria / genetics
  • Ecosystem
  • Estuaries*
  • Genetic Markers / genetics
  • Lakes / microbiology*
  • Methanol / metabolism*
  • North America
  • Phytoplankton / classification*
  • Phytoplankton / enzymology
  • Phytoplankton / genetics

Substances

  • Genetic Markers
  • Alcohol Oxidoreductases
  • alcohol dehydrogenase (acceptor)
  • Methanol