Isolates of Thermoanaerobacter thermohydrosulfuricus from decaying wood compost display genetic and phenotypic microdiversity

• Published in: FEMS microbiology ecology Vol. 78; no. 3; pp. 473 - 487
• Main Authors: Verbeke, Tobin J., Dumonceaux, Tim J., Wushke, Scott, Cicek, Nazim, Levin, David B., Sparling, Richard
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.12.2011; Blackwell; Oxford University Press
• Subjects: Animal, plant and microbial ecology; Bacteriology; Biodiversity; biofuels; Biological and medical sciences; chaperonin‐60; Composts; DNA Fingerprinting; Ecology; ecotypes; Fermentation; Fundamental and applied biological sciences. Psychology; Metabolome; Microbial ecology; Microbiology; Miscellaneous; Molecular Sequence Data; niche specialization; Niches; Phenotype; Phylogeny; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; Soil; Soil Microbiology; Substrate Specificity; Thermoanaerobacter; Thermoanaerobacter - classification; Thermoanaerobacter - genetics; Thermoanaerobacter - growth & development; Thermoanaerobacter - isolation & purification; Wood - microbiology; chaperonin-60; biofuels; niche specialization; ecotypes; Compost; Wood; Biofuel; Thermoanaerobacter; Protein; Phenotype; Specialization; Ecological niche; Biotype; Bacteria; Genetics; Isolate; Ecotype
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/j.1574-6941.2011.01181.x

Abstract In this study, 12 strains of Thermoanaerobacter were isolated from a single decaying wood compost sample and subjected to genetic and phenotypic profiling. The 16S rRNA encoding gene sequences suggested that the isolates were most similar to strains of either Thermoanaerobacter pseudethanolicus or Thermoanaerobacter thermohydrosulfuricus. Examination of the lesser conserved chaperonin-60 (cpn60) universal target showed that some isolates shared the highest sequence identity with T. thermohydrosulfuricus; however, others to Thermoanaerobacter wiegelii and Thermoanaerobacter sp. Rt8.G4 (formerly Thermoanaerobacter brockii Rt8.G4). BOX-PCR fingerprinting profiles identified differences in the banding patterns not only between the isolates and the reference strains, but also among the isolates themselves. To evaluate the extent these genetic differences were manifested phenotypically, the utilization patterns of 30 carbon substrates were examined and the niche overlap indices (NOI) calculated. Despite showing a high NOI (> 0.9), significant differences existed in the substrate utilization capabilities of the isolates suggesting that either a high degree of niche specialization or mechanisms allowing for non-competitive co-existence, were present within this ecological context. Growth studies showed that the isolates were physiologically distinct in both growth rate and the fermentation product ratios. Our data indicate that phenotypic diversity exists within genetically microdiverse Thermoanaerobacter isolates from a common environment.