Culturing captures members of the soil rare biosphere

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.

[1]  R. Knight,et al.  The Western English Channel contains a persistent microbial seed bank , 2011, The ISME Journal.

[2]  C. Pedrós-Alió.  The rare bacterial biosphere. , 2012, Annual review of marine science.

[3]  L. Riemann,et al.  Recruitment of Members from the Rare Biosphere of Marine Bacterioplankton Communities after an Environmental Disturbance , 2011, Applied and Environmental Microbiology.

[4]  Susan M. Huse,et al.  24. Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere” , 2011 .

[5]  A. Reid,et al.  The Rare Biosphere , 2011 .

[6]  J. Faith,et al.  Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice , 2011, Proceedings of the National Academy of Sciences.

[7]  J. Lennon,et al.  Microbial seed banks: the ecological and evolutionary implications of dormancy , 2011, Nature Reviews Microbiology.

[8]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[9]  Susan M. Huse,et al.  Ironing out the wrinkles in the rare biosphere through improved OTU clustering , 2010, Environmental microbiology.

[10]  Rob Knight,et al.  Direct sequencing of the human microbiome readily reveals community differences , 2010, Genome Biology.

[11]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[12]  Rob Knight,et al.  PyNAST: a flexible tool for aligning sequences to a template alignment , 2009, Bioinform..

[13]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[14]  S. Epstein.  Microbial awakenings , 2009, Nature.

[15]  Noha H. Youssef,et al.  Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere , 2008, Applied and Environmental Microbiology.

[16]  J. Handelsman,et al.  The last word: books as a statistical metaphor for microbial communities. , 2007, Annual review of microbiology.

[17]  F. Bushman,et al.  Short pyrosequencing reads suffice for accurate microbial community analysis , 2007, Nucleic acids research.

[18]  G. Casella,et al.  Pyrosequencing enumerates and contrasts soil microbial diversity , 2007, The ISME Journal.

[19]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[20]  R. B. Jackson,et al.  Toward an ecological classification of soil bacteria. , 2007, Ecology.

[21]  Les Dethlefsen,et al.  Performance of the Translational Apparatus Varies with the Ecological Strategies of Bacteria , 2007, Journal of bacteriology.

[22]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[23]  Song-Bae Kim,et al.  Numerical analysis of bacterial transport in saturated porous media , 2006 .

[24]  P. Janssen.  Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes , 2006, Applied and Environmental Microbiology.

[25]  J. Foster,et al.  Relaxed Neighbor Joining: A Fast Distance-Based Phylogenetic Tree Construction Method , 2006, Journal of Molecular Evolution.

[26]  R. Knight,et al.  UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.

[27]  Jo Handelsman,et al.  Integration of Microbial Ecology and Statistics: a Test To Compare Gene Libraries , 2004, Applied and Environmental Microbiology.

[28]  M. Clayton,et al.  Use of cluster and discriminant analyses to compare rhizosphere bacterial communities following biological perturbation , 1996, Microbial Ecology.

[29]  A. Bull,et al.  Microbial diversity , 2004, Biodiversity & Conservation.

[30]  S. Giovannoni,et al.  The uncultured microbial majority. , 2003, Annual review of microbiology.

[31]  J. Adams,et al.  Culturability as an Indicator of Succession in Microbial Communities , 2001, Microbial Ecology.

[32]  J. Handelsman,et al.  Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms , 2000, Applied and Environmental Microbiology.

[33]  W. Whitman,et al.  Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[34]  N. Pace,et al.  Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. , 1996, Trends in biotechnology.

[35]  J. Buyer.  A Soil and Rhizosphere Microorganism Isolation and Enumeration Medium That Inhibits Bacillus mycoides , 1995, Applied and environmental microbiology.

[36]  N. Pace,et al.  Microbial ecology and evolution: a ribosomal RNA approach. , 1986, Annual review of microbiology.

[37]  N. Pace,et al.  Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Peter Chesson,et al.  Coexistence Mediated by Recruitment Fluctuations: A Field Guide to the Storage Effect , 1985, The American Naturalist.