The metagenomics of soil

[1]  T. Abe,et al.  Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes , 2005, Nature Biotechnology.

[2]  V. Torsvik,et al.  Total bacterial diversity in soil and sediment communities—A review , 1996, Journal of Industrial Microbiology.

[3]  J. Davies,et al.  Genetic diversity of soil microorganisms assessed by analysis ofhsp70 (dnaK) sequences , 1996, Journal of Industrial Microbiology.

[4]  Hyunjin Yoon,et al.  Characterization of a Novel Amylolytic Enzyme Encoded by a Gene from a Soil-Derived Metagenomic Library , 2004, Applied and Environmental Microbiology.

[5]  J. Handelsman,et al.  Metagenomics: genomic analysis of microbial communities. , 2004, Annual review of genetics.

[6]  Sean F. Brady,et al.  Long-Chain N-Acyltyrosine Synthases from Environmental DNA , 2004, Applied and Environmental Microbiology.

[7]  Seon-Woo Lee,et al.  Screening for novel lipolytic enzymes from uncultured soil microorganisms , 2004, Applied Microbiology and Biotechnology.

[8]  Pascal Simonet,et al.  Phylogenetic Analysis of Polyketide Synthase I Domains from Soil Metagenomic Libraries Allows Selection of Promising Clones , 2004, Applied and Environmental Microbiology.

[9]  C. Schleper,et al.  Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. , 2004, Environmental microbiology.

[10]  D. Janssen,et al.  Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. , 2004, Environmental microbiology.

[11]  J. Handelsman,et al.  Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. , 2004, Environmental microbiology.

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

[13]  Rolf Daniel,et al.  The soil metagenome--a rich resource for the discovery of novel natural products. , 2004, Current opinion in biotechnology.

[14]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[15]  Eric Mathur,et al.  Exploring Nitrilase Sequence Space for Enantioselective Catalysis , 2004, Applied and Environmental Microbiology.

[16]  Joern Hopke,et al.  Genetically Modified Bacterial Strains and Novel Bacterial Artificial Chromosome Shuttle Vectors for Constructing Environmental Libraries and Detecting Heterologous Natural Products in Multiple Expression Hosts , 2004, Applied and Environmental Microbiology.

[17]  C. Kuske,et al.  Diazotrophic Community Structure and Function in Two Successional Stages of Biological Soil Crusts from the Colorado Plateau and Chihuahuan Desert , 2004, Applied and Environmental Microbiology.

[18]  R. C. Foster Microenvironments of soil microorganisms , 1988, Biology and Fertility of Soils.

[19]  P. Hugenholtz,et al.  Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria , 2003, Applied and Environmental Microbiology.

[20]  Vincent J. Denef,et al.  Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. , 2003, Environmental microbiology.

[21]  Jürgen Eck,et al.  Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics , 2003, Molecular microbiology.

[22]  S. Voget,et al.  Prospecting for Novel Biocatalysts in a Soil Metagenome , 2003, Applied and Environmental Microbiology.

[23]  J. Sebat,et al.  Metagenomic Profiling: Microarray Analysis of an Environmental Genomic Library , 2003, Applied and Environmental Microbiology.

[24]  Rolf Daniel,et al.  Identification and Characterization of Coenzyme B12-Dependent Glycerol Dehydratase- and Diol Dehydratase-Encoding Genes from Metagenomic DNA Libraries Derived from Enrichment Cultures , 2003, Applied and Environmental Microbiology.

[25]  E. Wellington,et al.  Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. , 2003, Current opinion in microbiology.

[26]  J. Murrell,et al.  Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. , 2003, Current opinion in biotechnology.

[27]  Jo Handelsman,et al.  A Census of rRNA Genes and Linked Genomic Sequences within a Soil Metagenomic Library , 2003, Applied and Environmental Microbiology.

[28]  Dick B Janssen,et al.  Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. , 2003, FEMS microbiology ecology.

[29]  Rolf Daniel,et al.  Metagenomes of Complex Microbial Consortia Derived from Different Soils as Sources for Novel Genes Conferring Formation of Carbonyls from Short-Chain Polyols on Escherichia coli , 2003, Journal of Molecular Microbiology and Biotechnology.

[30]  Rolf Daniel,et al.  Construction and Screening of Metagenomic Libraries Derived from Enrichment Cultures: Generation of a Gene Bank for Genes Conferring Alcohol Oxidoreductase Activity on Escherichia coli , 2003, Applied and Environmental Microbiology.

[31]  J. Clardy,et al.  Synthesis of long-chain fatty acid enol esters isolated from an environmental DNA clone. , 2003, Organic letters.

[32]  Pascale Jeannin,et al.  Recombinant Environmental Libraries Provide Access to Microbial Diversity for Drug Discovery from Natural Products , 2003, Applied and Environmental Microbiology.

[33]  T. Richardson,et al.  Soil-based gene discovery: a new technology to accelerate and broaden biocatalytic applications. , 2003, Advances in applied microbiology.

[34]  C. Schleper,et al.  Metagenome—a challenging source of enzyme discovery , 2002 .

[35]  K. Zengler,et al.  Cultivating the uncultured , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  C. Sensen,et al.  First insight into the genome of an uncultivated crenarchaeote from soil. , 2002, Environmental microbiology.

[37]  Jo Handelsman,et al.  Isolation of Antibiotics Turbomycin A and B from a Metagenomic Library of Soil Microbial DNA , 2002, Applied and Environmental Microbiology.

[38]  J. Clardy,et al.  New natural product families from an environmental DNA (eDNA) gene cluster. , 2002, Journal of the American Chemical Society.

[39]  Lawrence O. Ticknor,et al.  Empirical and Theoretical Bacterial Diversity in Four Arizona Soils , 2002, Applied and Environmental Microbiology.

[40]  Dorothea K. Thompson,et al.  Challenges in applying microarrays to environmental studies. , 2002, Current opinion in biotechnology.

[41]  L. Øvreås,et al.  Microbial diversity and function in soil: from genes to ecosystems. , 2002, Current opinion in microbiology.

[42]  K. Lewis,et al.  Isolating "Uncultivable" Microorganisms in Pure Culture in a Simulated Natural Environment , 2002, Science.

[43]  Q. Beg,et al.  Bacterial alkaline proteases: molecular approaches and industrial applications , 2002, Applied Microbiology and Biotechnology.

[44]  J. Tiedje,et al.  Quantitative Detection of Microbial Genes by Using DNA Microarrays , 2002, Applied and Environmental Microbiology.

[45]  Anthony V. Palumbo,et al.  Spatial and Resource Factors Influencing High Microbial Diversity in Soil , 2002, Applied and Environmental Microbiology.

[46]  T. Martin Embley,et al.  Grassland Management Regimens Reduce Small-Scale Heterogeneity and Species Diversity of β-Proteobacterial Ammonia Oxidizer Populations , 2002, Applied and Environmental Microbiology.

[47]  J. Short,et al.  A Novel, High Performance Enzyme for Starch Liquefaction DISCOVERY AND OPTIMIZATION OF A LOW pH, THERMOSTABLE -AMYLASE* , 2002 .

[48]  Dorothea K. Thompson,et al.  Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment , 2001, Applied and Environmental Microbiology.

[49]  G. Gottschalk,et al.  Screening of Environmental DNA Libraries for the Presence of Genes Conferring Na+(Li+)/H+Antiporter Activity on Escherichia coli: Characterization of the Recovered Genes and the Corresponding Gene Products , 2001, Journal of bacteriology.

[50]  K. M. Helena Nevalainen,et al.  Gene Cassette PCR: Sequence-Independent Recovery of Entire Genes from Environmental DNA , 2001, Applied and Environmental Microbiology.

[51]  R. Duran,et al.  Rapid and specific identification of nitrile hydratase (NHase)-encoding genes in soil samples by polymerase chain reaction. , 2001, FEMS microbiology letters.

[52]  Jizhong Zhou,et al.  Simultaneous Recovery of RNA and DNA from Soils and Sediments , 2001, Applied and Environmental Microbiology.

[53]  Jonathan D. Trent,et al.  DNA from Uncultured Organisms as a Source of 2,5-Diketo-d-Gluconic Acid Reductases , 2001, Applied and Environmental Microbiology.

[54]  P. Simonet,et al.  Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. , 2001, Environmental microbiology.

[55]  J. Clapp,et al.  PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods. , 2001, FEMS microbiology ecology.

[56]  J. Handelsman,et al.  Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. , 2001, Organic letters.

[57]  G. Soulas,et al.  DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods , 2001, Applied and Environmental Microbiology.

[58]  M. Gilman,et al.  Expression and isolation of antimicrobial small molecules from soil DNA libraries. , 2001, Journal of Molecular Microbiology and Biotechnology.

[59]  Wolfgang Liebl,et al.  Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia , 2001, Applied and Environmental Microbiology.

[60]  G. Lloyd-Jones,et al.  Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils , 2001 .

[61]  D. Santosa Rapid extraction and purification of environmental DNA for molecular cloning applications and molecular diversity studies , 2001, Molecular biotechnology.

[62]  J. Clardy,et al.  Long-Chain N-Acyl Amino Acid Antibiotics Isolated from Heterologously Expressed Environmental DNA , 2000 .

[63]  James Borneman,et al.  Bacterial Functional Redundancy along a Soil Reclamation Gradient , 2000, Applied and Environmental Microbiology.

[64]  J Davies,et al.  Novel natural products from soil DNA libraries in a streptomycete host. , 2000, Organic letters.

[65]  G. Gottschalk,et al.  Screening of Environmental DNA Libraries for the Presence of Genes Conferring Lipolytic Activity onEscherichia coli , 2000, Applied and Environmental Microbiology.

[66]  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.

[67]  L. Øvreås,et al.  Population and community level approaches for analysing microbial diversity in natural environments , 2000 .

[68]  E. Madsen,et al.  Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples , 1999, Applied and Environmental Microbiology.

[69]  J. Handelsman,et al.  The Earth's bounty: assessing and accessing soil microbial diversity. , 1999, Trends in biotechnology.

[70]  G. Gottschalk,et al.  Construction of Environmental DNA Libraries inEscherichia coli and Screening for the Presence of Genes Conferring Utilization of 4-Hydroxybutyrate , 1999, Applied and Environmental Microbiology.

[71]  Doolittle Wf Phylogenetic Classification and the Universal Tree , 1999 .

[72]  John Dunbar,et al.  Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning , 1999, Applied and Environmental Microbiology.

[73]  L. Orgel,et al.  Phylogenetic Classification and the Universal Tree , 1999 .

[74]  J. Handelsman,et al.  Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. , 1998, Chemistry & biology.

[75]  R. Sandaa,et al.  Novel techniques for analysing microbial diversity in natural and perturbed environments. , 1998, Journal of biotechnology.

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

[77]  J Davies,et al.  A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms , 1997, Journal of bacteriology.

[78]  J. Borneman,et al.  Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation , 1997, Applied and environmental microbiology.

[79]  J. Tiedje,et al.  DNA recovery from soils of diverse composition , 1996, Applied and environmental microbiology.

[80]  D. Markewitz,et al.  How Deep Is Soil?Soil, the zone of the earth's crust that is biologically active, is much deeper than has been thought by many ecologists , 1995 .

[81]  L. Shimkets,et al.  Comparison of methods of DNA extraction from stream sediments , 1995, Applied and environmental microbiology.

[82]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[83]  L. Bakken,et al.  Evaluation of methods for extraction of bacteria from soil , 1995 .

[84]  W. Vahjen,et al.  Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast , 1993, Applied and environmental microbiology.

[85]  L. Brussaard,et al.  Relationships between habitable pore space, soil biota and mineralization rates in grassland soils , 1993 .

[86]  W. Liesack,et al.  Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment , 1992, Journal of bacteriology.

[87]  O. Rasmussen,et al.  Development and Application of a New Method To Extract Bacterial DNA from Soil Based on Separation of Bacteria from Soil with Cation-Exchange Resin , 1992, Applied and environmental microbiology.

[88]  B H Olson,et al.  Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction , 1992, Applied and environmental microbiology.

[89]  V. Torsvik,et al.  High diversity in DNA of soil bacteria , 1990, Applied and environmental microbiology.

[90]  E. Paul,et al.  Soil microbiology and biochemistry. , 1998 .

[91]  E. Paul Chapter 1 – Soil Microbiology and Biochemistry in Perspective , 1989 .

[92]  R M Atlas,et al.  Recovery of DNA from soils and sediments , 1988, Applied and environmental microbiology.

[93]  J. Tiedje,et al.  DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community , 1988, Applied and environmental microbiology.

[94]  G. Sayler,et al.  The extraction and purification of microbial DNA from sediments , 1987 .

[95]  M. Firestone,et al.  Microbial biomass response to a rapid increase in water potential when dry soil is wetted , 1987 .