Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters.
Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics.
Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
Alyse K
AK
Hawley
Sam
S
Kheirandish
Andreas
A
Mueller
Hilary T C
HT
Leung
Angela D
AD
Norbeck
Heather M
HM
Brewer
Ljiljana
L
Pasa-Tolic
Steven J
SJ
Hallam
D001105:Archaea / Q000235:genetics*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics; D059013:Microbial Consortia / Q000235:genetics*; D010100:Oxygen / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000737:chemistry
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D010100:Oxygen
Environmental proteomics; Metaproteomics; Microbial ecology; Oxygen minimum zone; Quantitative PCR