Friederike Marie Luise Grundger

Enhanced gene detection assays for fumarate-adding enzymes allow uncovering of anaerobic hydrocarbon degraders in terrestrial and marine systems

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DOI

  • Frederick von Netzer, Helmholtz Zentrum München - German Research Center for Environmental Health
  • ,
  • Giovanni Pilloni, Helmholtz Zentrum München - German Research Center for Environmental Health
  • ,
  • Sara Kleindienst, Max Planck Institute for Marine Microbiology
  • ,
  • Martin Krüger, Federal Institute for Geosciences and Natural Resources
  • ,
  • Katrin Knittel, Max Planck Institute for Marine Microbiology
  • ,
  • Friederike Gründger
  • Tillmann Luedersa, Helmholtz Zentrum München - German Research Center for Environmental Health

The detection of anaerobic hydrocarbon degrader populations via catabolic gene markers is important for the understanding of processes at contaminated sites. Fumarate-adding enzymes (FAEs; i.e., benzylsuccinate and alkylsuccinate synthases) have already been established as specific functional marker genes for anaerobic hydrocarbon degraders. Several recent studies based on pure cultures and laboratory enrichments have shown the existence of new and deeply branching FAE gene lineages, such as clostridial benzylsuccinate synthases and homologues, as well as naphthylmethylsuccinate synthases. However, established FAE gene detection assays were not designed to target these novel lineages, and consequently, their detectability in different environments remains obscure. Here, we present a new suiteof parallel primer sets for detecting the comprehensive range of FAE markers known to date, includingclostridial benzylsuccinate, naphthylmethylsuccinate, and alkylsuccinate synthases. It was not possible to develop one single assay spanning the complete diversity of FAE genes alone. The enhanced assays were tested with a range of hydrocarbon-degrading pure cultures, enrichments, and environmental samples of marine and terrestrial origin. They revealed the presence of several, partially unexpected FAE gene lineages not detected in these environments before: distinct deltaproteobacterial and also clostridial bssA homologues as well as environmental nmsA homologues. These findings were backed up bydual-digest terminal restriction fragment length polymorphism diagnostics to identify FAE gene populations independently of sequencing. This allows rapid insights into intrinsic degrader populations anddegradation potentials established in aromatic and aliphatic hydrocarbon-impacted environmental systems.

OriginalsprogEngelsk
TidsskriftApplied and Environmental Microbiology
Vol/bind79
Nummer2
Sider (fra-til)543-552
Antal sider10
ISSN0099-2240
DOI
StatusUdgivet - 1 jan. 2013
Eksternt udgivetJa

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