Advertisement
  • Open Access

Culturing captures members of the soil rare biosphere

Authors

  • Ashley Shade,

    1. Department of Molecular, Cellular and Developmental Biology, Yale University, Kline Biology Tower, 219 Prospect St, New Haven, CT 06520, USA
    Search for more papers by this author
  • Clifford S. Hogan,

    1. Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA
    2. Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
    Search for more papers by this author
  • Amy K. Klimowicz,

    1. Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA
    2. Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
    Search for more papers by this author
  • Matthew Linske,

    1. Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA
    2. Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
    Search for more papers by this author
  • Patricia S. McManus,

    1. Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA
    Search for more papers by this author
  • Jo Handelsman

    Corresponding author
    1. Department of Molecular, Cellular and Developmental Biology, Yale University, Kline Biology Tower, 219 Prospect St, New Haven, CT 06520, USA
      E-mail jo.handelsman@yale.edu; Tel. (+1) 203 432 9119; Fax (+1) 203 432 6161.
    Search for more papers by this author

E-mail jo.handelsman@yale.edu; Tel. (+1) 203 432 9119; Fax (+1) 203 432 6161.

Summary

The ecological significance of rare microorganisms within microbial communities remains an important, unanswered question. Microorganisms of extremely low abundance (the ‘rare biosphere’) are believed to be largely inaccessible and unknown. To understand the structure of complex environmental microbial communities, including the representation of rare and prevalent community members, we coupled traditional cultivation with pyrosequencing. We compared cultured and uncultured bacterial members of the same agricultural soil, including eight locations within one apple orchard and four time points. Our analysis revealed that soil bacteria captured by culturing were in very low abundance or absent in the culture-independent community, demonstrating unexpected accessibility of the rare biosphere by culturing.

Ancillary