Cultivation of unculturable soil bacteria

Vartoukian, 2010, Strategies for culture of ‘unculturable’ bacteria, FEMS Lett., 309, 1

Auguet, 2010, Global ecological patterns in uncultured Archaea, ISME J., 4, 1, 10.1038/ismej.2009.109

Alain, 2009, Cultivating the uncultured: limits, advances and future challenges, Extremophiles, 13, 583, 10.1007/s00792-009-0261-3

Rastogi, 2011, Molecular techniques to assess microbial community structure, 29

Uphoff, 2001, The microbial diversity in picoplankton enrichment culture: a molecular screening of marine isolates, FEMS Microbiol. Ecol., 35, 249, 10.1111/j.1574-6941.2001.tb00810.x

Tyson, 2005, Cultivating the uncultivated: a community genomics perspective, Trends Microbiol., 13, 411, 10.1016/j.tim.2005.07.003

Button, 1993, Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results, Appl. Environ. Microbiol., 59, 881, 10.1128/aem.59.3.881-891.1993

Connon, 2002, High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates, Appl. Environ. Microbiol., 68, 3878, 10.1128/AEM.68.8.3878-3885.2002

Sangwan, 2005, Detection and cultivation of soil Verrucomicrobia, Appl. Environ. Microbiol., 71, 8402, 10.1128/AEM.71.12.8402-8410.2005

Watve, 2000, The ‘K’ selected oligophilic bacteria: a key to uncultured diversity?, Curr. Sci., 78, 1535

Kim, 2011, Review and future development of new culture methods for unculturable soil bacteria, Korean J. Microbiol., 47, 179

Janssen, 2002, Improved culturability of soil bacteria and isolation in pure culture of novel numbers of the divisions Acidobacteria, Acidobacteria, Proteobacteria and Verrucomicrobia, Appl. Environ. Microbiol., 68, 2391, 10.1128/AEM.68.5.2391-2396.2002

Stevenson, 2004, New strategies for cultivation and detection of previously uncultured microbes, Appl. Environ. Microbiol., 70, 4748, 10.1128/AEM.70.8.4748-4755.2004

Hamaki, 2005, Isolation of novel bacteria and actinomycetes using soil-extract agar medium, J. Biosci. Bioeng., 99, 485, 10.1263/jbb.99.485

Kawanishi, 2011, New detection systems of bacteria using highly selective media designed by SMART: selective medium-design algorithm restricted by two constraints, PLoS ONE, 6, 1, 10.1371/journal.pone.0016512

Janssen, 2008, New cultivation strategies for terrestrial microorganisms, 173

Leaderbetter, 1999, Acetogenesis from H2 plus CO2 by spirochetes from termite guts, Science, 283, 686, 10.1126/science.283.5402.686

Tamaki, 2005, Cultivation of uncultured fastidious microbes, Microbes Environ., 20, 85, 10.1264/jsme2.20.85

Tamaki, 2005, Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques, Appl. Environ. Microbiol., 71, 2162, 10.1128/AEM.71.4.2162-2169.2005

Davis, 2005, Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria, Appl. Environ. Microbiol., 71, 826, 10.1128/AEM.71.2.826-834.2005

Sait, 2002, Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys, Environ. Microbiol., 4, 654, 10.1046/j.1462-2920.2002.00352.x

Stott, 2008, Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand, Environ. Microbiol., 10, 2030, 10.1111/j.1462-2920.2008.01621.x

Davis, 2011, Acidobacteria, Rubrobacteridae and Chloroflexi are abundant among very slow-growing and mini-colony forming soil bacteria, Environ. Microbiol., 13, 798, 10.1111/j.1462-2920.2010.02384.x

Kataoka, 1996, Enrichment culture and isolation of slow-growing bacteria, Appl. Microbiol. Biotechnol., 45, 771, 10.1007/s002530050761

Nadell, 2009, The sociobiology of biofilms, FEMS Microbiol. Rev., 33, 206, 10.1111/j.1574-6976.2008.00150.x

West, 2007, The social lives of microbes, Annu. Rev. Ecol. Evol. Syst., 38, 53, 10.1146/annurev.ecolsys.38.091206.095740

Plugge, 2002, Enrichment of thermophilic syntrophic anaerobic glutamate-degrading consortia using a dialysis membrane reactor, Microb. Ecol., 43, 379, 10.1007/s00248-001-0047-3

Crocetti, 2002, Glycogen-accumulating organisms in laboratory-scale and full-scale wastewater treatment processes, Microbiology, 148, 3353, 10.1099/00221287-148-11-3353

Nichols, 2008, Short peptide induces an ‘uncultivable’ microorganism to grow in vitro, Appl. Environ. Microbiol., 74, 4889, 10.1128/AEM.00393-08

Pagnier, 2008, Isolation and identification of amoeba-resisting bacteria from water in human environment by using an Acanthamoeba polyphaga co-culture procedure, Environ. Microbiol., 10, 1135, 10.1111/j.1462-2920.2007.01530.x

Evstigneeva, 2009, Amoebae co-culture of soil specimens recovered 33 different bacteria, including 4 new species and Streptococcus pneumoniae, Microbiology, 155, 657, 10.1099/mic.0.022970-0

Frey-Klett, 2007, The mycorrhiza helper bacteria revisited, New Phytol., 176, 22, 10.1111/j.1469-8137.2007.02191.x

Svenning, 2003, Isolation of methane oxidizing bacteria from soil by use of a soil substrate membrane system, FEMS Microbiol. Ecol., 44, 347, 10.1016/S0168-6496(03)00073-4

Amanullah, 2010, Novel micro-bioreactor high throughput technology for cell culture process development: reproducibility and scalability assessment of fed-bath CHO culture, Biotechnol. Bioeng., 1, 57, 10.1002/bit.22664

Leadbetter, 2003, Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21th century laboratory, Curr. Opin. Microbiol., 6, 274, 10.1016/S1369-5274(03)00041-9

Lewis, 2010, Uncultured microorganisms as a source of secondary metabolites, J. Antibiot., 63, 468, 10.1038/ja.2010.87

Ferrari, 2005, Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria, Appl. Environ. Microbiol., 71, 8714, 10.1128/AEM.71.12.8714-8720.2005

Ferrari, 2008, Cultivating previously uncultured soil bacteria using a soil substrates membrane system, Nat. Protoc., 3, 1261, 10.1038/nprot.2008.102

Bollmann, 2007, Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates, Appl. Environ. Microbiol., 73, 6386, 10.1128/AEM.01309-07

Kaeberlein, 2002, Isolating ‘uncultivable’ microorganisms in pure culture in a simulated natural environment, Science, 296, 1127, 10.1126/science.1070633

Aslam, 2009, Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.), Int. J. Syst. Evol. Microb., 59, 675, 10.1099/ijs.0.000588-0

Aslam, 2010, Miniview: too much bacteria still unculturable, Crop Environ., 1, 59

Ferrari, 2009, Cultivation of fastidious bacteria by viability staining and micromanipulation on a soil substrate membrane system, Appl. Environ. Microbiol., 75, 3352, 10.1128/AEM.02407-08

Ishii, 2011, Identification and isolation of active N2O reducers in rice paddy soil, ISME J., 5, 1936, 10.1038/ismej.2011.69

Ashida, 2010, Isolation of functional single cells from environments using a micromanipulator: application to study denitrifying bacteria, Appl. Microbiol. Biotechnol., 85, 1211, 10.1007/s00253-009-2330-z

Brady, 2000, Long-chain N-acyl amino acid antibiotics isolated from heterologously expressed environmental DNA, J. Am. Chem. Soc., 122, 12903, 10.1021/ja002990u

Courtois, 2003, Lead-induced downregulation of soluble guanylate cyclase in isolated rat segments mediated by reactive oxygen species and cyclooxygenase-2, J. Am. Soc. Nephrol., 14, 1464, 10.1097/01.ASN.0000064947.14997.69

Rondon, 2000, Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms, Appl. Environ. Microbiol., 66, 2541, 10.1128/AEM.66.6.2541-2547.2000

Dauga, 2005, Expanding the known diversity and environmental distribution of cultured and uncultured bacteria, Med. Sci. (Paris), 21, 290, 10.1051/medsci/2005213290

Handelsman, 2004, Metagenomic: application of genomics to uncultured microorganisms, Microbiol. Mol. Biol. Rev., 4, 669, 10.1128/MMBR.68.4.669-685.2004

Tyson, 2004, Community structure and metabolism through reconstruction of microbial genomes from the environment, Nature, 428, 37, 10.1038/nature02340

Venter, 2004, Environmental shotgun sequencing of the Sargasso Sea, Science, 304, 66, 10.1126/science.1093857

Oremland, 2005, Whither or wither geomicrobiology in the era of ‘community metagenomics’, Nat. Rev. Microbiol., 3, 572, 10.1038/nrmicro1182

Amann, 2001, The identification of microorganisms by fluorescence in situ hybridization, Curr. Opin. Biotech., 12, 231, 10.1016/S0958-1669(00)00204-4

Amann, 1995, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev., 59, 143, 10.1128/mr.59.1.143-169.1995

Ferrari, 2006, Catalyzed reporter deposition-fluorescence in situ hybridization allows for enrichment-independent detection of microcolony forming soil bacteria, Appl. Environ. Microbiol., 72, 918, 10.1128/AEM.72.1.918-922.2006

Vartoukian, 2009, Diversity and morphology of members of the phylum ‘Synergistetes’ in periodontal health and disease, App. Environ. Microbiol., 75, 3777, 10.1128/AEM.02763-08

McCaig, 2001, Impact of cultivation on characterisation of species composition of soil bacterial communities, FEMS Microbiol. Ecol., 35, 37, 10.1111/j.1574-6941.2001.tb00786.x

Head, 1998, Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms, Microb. Ecol., 35, 1, 10.1007/s002489900056

Whitman, 1998, Prokaryotes: the unseen majority, Proc. Natl. Acad. Sci. U.S.A., 95, 6578, 10.1073/pnas.95.12.6578

Joseph, 2003, Laboratory cultivation of widespread and previously uncultured soil bacteria, Appl. Environ. Microbiol., 69, 7210, 10.1128/AEM.69.12.7210-7215.2003

Camilli, 2006, Bacterial small-molecule signaling pathways, Science, 311, 1113, 10.1126/science.1121357

Durbin, 1961, Techniques for the observation and isolation of soil microorganisms, Bot. Rev., 27, 522, 10.1007/BF02860105

Köpke, 2005, Microbial diversity in coastal subsurface sediments: a cultivation approach using various election acceptors and substrate gradients, Appl. Environ. Microbiol., 71, 7819, 10.1128/AEM.71.12.7819-7830.2005

Sharma, 2005, ‘Unculturable’ bacterial diversity: an untapped resource, Curr. Sci., 89, 72

Kamagata, 2005, Cultivation of uncultured fastidious microbes, Microbes Environ., 20, 85, 10.1264/jsme2.20.85

Janssen, 1997, Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil, Appl. Environ. Microbiol., 63, 1382, 10.1128/aem.63.4.1382-1388.1997

Angle, 2011, Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen, PLoS ONE, 6, 1

Riemann, 2010, Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters, Aquat. Microb. Ecol., 61, 235, 10.3354/ame01431

Vishnivetskaya, 2000, Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments, Extremophiles, 4, 165, 10.1007/s007920070031

Miteva, 2005, Detection and isolation of ultrasmall microorganisms from a 120,000-year-old Greenland glacier ice core, Appl. Environ. Microbiol., 71, 7806, 10.1128/AEM.71.12.7806-7818.2005

Dedysh, 2011, Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps, Front. Microbiol., 2, 1, 10.3389/fmicb.2011.00184

Sait, 2006, Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil, Appl. Environ. Microbiol., 72, 1852, 10.1128/AEM.72.3.1852-1857.2006

Brenner, 2008, Engineering microbial consortia: a new frontier in synthetic biology, Trends Biotechnol., 26, 483, 10.1016/j.tibtech.2008.05.004

Fröhlich, 2000, New techniques for isolation of single prokaryotic cells, FEMS Microbiol. Rev., 24, 567, 10.1016/S0168-6445(00)00045-0

Zhang, 2008, Optical tweezers for single cells, J. R. Soc. Interface, 5, 671, 10.1098/rsif.2008.0052

Zengler, 2002, Cultivating the uncultured, Proc. Natl. Acad. Sci. U.S.A., 99, 15681, 10.1073/pnas.252630999

Zengler, 2005, High-throughput cultivation of microorganisms using microcapsules, Methods Enzymol., 397, 124, 10.1016/S0076-6879(05)97007-9

Ingham, 2007, The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms, Proc. Natl. Acad. Sci. U.S.A., 104, 18217, 10.1073/pnas.0701693104

Kushmaro, A. et al. (2010) Method for isolating and culturing unculturable microorganisms, C12N 1/00, Ben Gurion University of Negev Research and Development Authority

Dennis, 2003, Monitoring gene expression in mixed microbial communities by using DNA microarrays, Appl. Environ. Microbiol., 69, 769, 10.1128/AEM.69.2.769-778.2003

Zvyagintsev, 2002, Composition of soil bacterial communities: new insight from old and new technologies, 297