Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand

Authors

  • Matthew B. Stott,

    1. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand.
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  • Michelle A. Crowe,

    1. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand.
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  • Bruce W. Mountain,

    1. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand.
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  • Angela V. Smirnova,

    1. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand.
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  • Shaobin Hou,

    1. Advanced Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, 2565 McCarthy Mall, Keller Hall #319, Honolulu, HI 96822, USA.
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  • Maqsudul Alam,

    1. Advanced Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, 2565 McCarthy Mall, Keller Hall #319, Honolulu, HI 96822, USA.
    2. Department of Microbiology, University of Hawai'i, Snyder Hall, 2538 The Mall, Honolulu, HI 96822, USA.
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  • Peter F. Dunfield

    Corresponding author
    1. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand.
    2. Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, T2N 1N4, Canada.
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*E-mail pfdunfie@ucalgary.ca; Tel. (+1) 403 220 2469; Fax (+1) 403 289 9311.

Summary

We examined bacterial diversity of three geothermal soils in the Taupo Volcanic Zone of New Zealand. Phylogenetic analysis of 16S rRNA genes recovered directly from soils indicated that the bacterial communities differed in composition and richness, and were dominated by previously uncultured species of the phyla Actinobacteria, Acidobacteria, Chloroflexi, Proteobacteria and candidate division OP10. Aerobic, thermophilic, organotrophic bacteria were isolated using cultivation protocols that involved extended incubation times, low-pH media and gellan as a replacement gelling agent to agar. Isolates represented previously uncultured species, genera, classes, and even a new phylum of bacteria. They included members of the commonly cultivated phyla Proteobacteria, Firmicutes, Thermus/Deinococcus, Actinobacteria and Bacteroidetes, as well as more-difficult-to-cultivate groups. Isolates possessing < 85% 16S rRNA gene sequence identity to any cultivated species were obtained from the phyla Acidobacteria, Chloroflexi and the previously uncultured candidate division OP10. Several isolates were prevalent in 16S rRNA gene clone libraries constructed directly from the soils. A key factor facilitating isolation was the use of gellan-solidified plates, where the gellan itself served as an energy source for certain bacteria. The results indicate that geothermal soils are a rich potential source of novel bacteria, and that relatively simple cultivation techniques are practical for isolating bacteria from these habitats.

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