title: Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments.
abstract: The microbial ecology of a range of anaerobic biological assemblages (granular sludge) from full- and laboratory-scale wastewater treatment bioreactors, and of crop-growing and peat soils, was determined using a variety of 16S rRNA gene-based techniques, including clone library, terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis (DGGE) analyses. Fluorescent in situ hybridization (FISH) using 16S rRNA gene-targeted probes was employed to complete a "full-cycle rRNA approach" with selected biomass. Genetic fingerprinting (TRFLP and DGGE) was effectively used to elucidate community structure-crop relationships, and to detect and monitor trends in bioreactor sludge and specific enrichment cultures of peat soil. Greater diversity was resolved within bacterial than within archaeal communities, and unexpected reservoirs of uncultured Crenarchaeota were detected in sludge granules. Advanced radiotracer incubations and micro-beta imaging were employed in conjunction with FISH to elucidate the eco-functionalism of these organisms. Crenarchaeota clusters were identified in close associated with methanogenic Archaea and both were localised with acetate uptake in biofilm structure.
authors.affiliation: Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute (ECI), National University of Ireland, Galway (NUI, Galway), University Road, Galway, Ireland.
authors.forename: Gavin
authors.initials: G
authors.lastname: Collins
authors.forename: Siobhán
authors.initials: S
authors.lastname: Kavanagh
authors.forename: Sharon
authors.initials: S
authors.lastname: McHugh
authors.forename: Sean
authors.initials: S
authors.lastname: Connaughton
authors.forename: Aileen
authors.initials: A
authors.lastname: Kearney
authors.forename: Olivia
authors.initials: O
authors.lastname: Rice
authors.forename: Cora
authors.initials: C
authors.lastname: Carrigg
authors.forename: Colm
authors.initials: C
authors.lastname: Scully
authors.forename: Niamh
authors.initials: N
authors.lastname: Bhreathnach
authors.forename: Thérèse
authors.initials: T
authors.lastname: Mahony
authors.forename: Pádhraig
authors.initials: P
authors.lastname: Madden
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Enright
authors.forename: Vincent
authors.initials: V
authors.lastname: O'flaherty
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D001483:Base Sequence; D018441:Biofilms; D018533:Biomass; D019149:Bioreactors / Q000382:microbiology; D019615:Crenarchaeota / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D019641:DNA, Archaeal / Q000032:analysis / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D017753:Ecosystem; D004587:Electrophoresis, Agar Gel; D008697:Methane / Q000737:chemistry / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics*; D012722:Sewage / Q000382:microbiology*; D012988:Soil Microbiology; D014865:Waste Disposal, Fluid / Q000379:methods*
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012722:Sewage; D008697:Methane