Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

[1]  J. Banfield,et al.  Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil , 2020, bioRxiv.

[2]  S. Abedon,et al.  Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics , 2020, Soil Systems.

[3]  P. Engel,et al.  Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota , 2020, Proceedings of the National Academy of Sciences.

[4]  F. Rodríguez-Valera,et al.  Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil , 2020, Microbiome.

[5]  T. Whitman,et al.  Pyrogenic organic matter effects on soil bacterial community composition , 2020 .

[6]  Chao Deng,et al.  Identifying viruses from metagenomic data using deep learning , 2020, Quantitative Biology.

[7]  T. Northen,et al.  Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust , 2019, mBio.

[8]  Tetsuya Hayashi,et al.  Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes , 2019, DNA research : an international journal for rapid publication of reports on genes and genomes.

[9]  Luiz Irber,et al.  Large-scale sequence comparisons with sourmash , 2019, bioRxiv.

[10]  H. Weon,et al.  A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments , 2019, Scientific Reports.

[11]  A. Shade,et al.  Abundance-occupancy distributions to prioritize plant core microbiome membership. , 2019, Current opinion in microbiology.

[12]  J. Emerson Soil Viruses: A New Hope , 2019, mSystems.

[13]  Evelien M. Adriaenssens,et al.  Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks , 2019, Nature Biotechnology.

[14]  M. Sullivan,et al.  Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils , 2019, PeerJ.

[15]  J. Banfield,et al.  Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil , 2019, Proceedings of the National Academy of Sciences.

[16]  Yuting Li,et al.  Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application , 2019, Viruses.

[17]  M. Catellani,et al.  Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants , 2019, Phytobiomes Journal.

[18]  Natalia N. Ivanova,et al.  Minimum Information about an Uncultivated Virus Genome (MIUViG) , 2018, Nature Biotechnology.

[19]  S. Ruwanza The Edge Effect on Plant Diversity and Soil Properties in Abandoned Fields Targeted for Ecological Restoration , 2018, Sustainability.

[20]  Y. Kuzyakov,et al.  Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions , 2018, Soil Biology and Biochemistry.

[21]  J. V. van Elsas,et al.  The 'Neglected' Soil Virome - Potential Role and Impact. , 2018, Trends in microbiology.

[22]  Changsheng Li,et al.  Host-linked soil viral ecology along a permafrost thaw gradient , 2018, Nature Microbiology.

[23]  S. Saleska,et al.  Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing , 2018, mSystems.

[24]  M. Doebeli,et al.  Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem , 2018, Microbiome.

[25]  V. Sundaresan,et al.  Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice , 2018, PLoS biology.

[26]  R. L. Harrison,et al.  Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018) , 2017, Archives of Virology.

[27]  Rick L. Stevens,et al.  A communal catalogue reveals Earth’s multiscale microbial diversity , 2017, Nature.

[28]  A. Chatzinotas,et al.  Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD) , 2017, Front. Microbiol..

[29]  Kurt E. Williamson,et al.  Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory. , 2017, Annual review of virology.

[30]  Emiley A. Eloe-Fadrosh,et al.  Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity , 2017, PeerJ.

[31]  N. Fierer Embracing the unknown: disentangling the complexities of the soil microbiome , 2017, Nature Reviews Microbiology.

[32]  Katherine C DeRuff,et al.  Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages , 2017, PloS one.

[33]  Guanghua Wang,et al.  Changes of bacterial community compositions after three years of biochar application in a black soil of northeast China. , 2017 .

[34]  J. DiRuggiero,et al.  Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper‐arid polar desert , 2017, Environmental microbiology.

[35]  Alexander E Gorbalenya,et al.  Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017) , 2017, Archives of Virology.

[36]  A. Vardi,et al.  Virocell Metabolism: Metabolic Innovations During Host-Virus Interactions in the Ocean. , 2016, Trends in microbiology.

[37]  Luiz Irber,et al.  sourmash: a library for MinHash sketching of DNA , 2016, J. Open Source Softw..

[38]  Georgios A. Pavlopoulos,et al.  Uncovering Earth’s virome , 2016, Nature.

[39]  M. Sullivan,et al.  Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient , 2016, PeerJ.

[40]  Brian C. Thomas,et al.  A new view of the tree of life , 2016, Nature Microbiology.

[41]  C. Pepe-Ranney,et al.  Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter , 2015, The ISME Journal.

[42]  S. Tringe,et al.  Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species , 2015, The New phytologist.

[43]  James C. Stegen,et al.  The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle , 2015, Front. Microbiol..

[44]  J. Fuhrmann,et al.  Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation. , 2015, FEMS microbiology ecology.

[45]  Matthew B. Sullivan,et al.  VirSorter: mining viral signal from microbial genomic data , 2015, PeerJ.

[46]  Matthew B. Sullivan,et al.  Rising to the challenge: accelerated pace of discovery transforms marine virology , 2015, Nature Reviews Microbiology.

[47]  Stephen Joseph,et al.  Biochar for environmental management: an introduction , 2015 .

[48]  Cameron Johnson,et al.  Structure, variation, and assembly of the root-associated microbiomes of rice , 2015, Proceedings of the National Academy of Sciences.

[49]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[50]  S. Yooseph,et al.  Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle , 2014, Proceedings of the National Academy of Sciences.

[51]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[52]  J. Gilbert,et al.  Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilisers , 2014 .

[53]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[54]  S. Tringe,et al.  Tackling soil diversity with the assembly of large, complex metagenomes , 2014, Proceedings of the National Academy of Sciences.

[55]  Daniel J. Nasko,et al.  Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome , 2014, Microbiome.

[56]  S. Hallam,et al.  Sequencing platform and library preparation choices impact viral metagenomes , 2013, BMC Genomics.

[57]  S. Tringe,et al.  Diversity and heritability of the maize rhizosphere microbiome under field conditions , 2013, Proceedings of the National Academy of Sciences.

[58]  Hélène Touzet,et al.  SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data , 2012, Bioinform..

[59]  R. Amann,et al.  Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota , 2012, Nature.

[60]  Robert C. Edgar,et al.  Defining the core Arabidopsis thaliana root microbiome , 2012, Nature.

[61]  Kurt E. Williamson,et al.  Viruses in Soil Ecosystems , 2011 .

[62]  Katherine H. Huang,et al.  Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. , 2011, Proceedings of the National Academy of Sciences of the United States of America.

[63]  E. Boyle,et al.  A simple and efficient method for concentration of ocean viruses by chemical flocculation , 2011, Environmental microbiology reports.

[64]  Paul Blackwell,et al.  Effect of banded biochar on dryland wheat production and fertiliser use in south-western Australia: an agronomic and economic perspective , 2010 .

[65]  Ying Gao,et al.  Bioinformatics Applications Note Sequence Analysis Cd-hit Suite: a Web Server for Clustering and Comparing Biological Sequences , 2022 .

[66]  Forest Rohwer,et al.  Laboratory procedures to generate viral metagenomes , 2009, Nature Protocols.

[67]  A. Klute,et al.  Methods of soil analysis , 2015, American Potato Journal.

[68]  C. Jeon,et al.  Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil , 2008, Applied and Environmental Microbiology.

[69]  M. Kimura,et al.  Ecology of viruses in soils: Past, present and future perspectives , 2008 .

[70]  Kurt E. Williamson,et al.  Incidence of lysogeny within temperate and extreme soil environments. , 2007, Environmental microbiology.

[71]  C. Suttle Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.

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

[73]  D. Radune,et al.  Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1 , 2006, PLoS genetics.

[74]  Luke R. Thompson,et al.  Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts , 2006, PLoS biology.

[75]  Kurt E. Williamson,et al.  Abundance and Diversity of Viruses in Six Delaware Soils , 2005, Applied and Environmental Microbiology.

[76]  R. Edwards,et al.  Viral metagenomics , 2005, Nature Reviews Microbiology.

[77]  Andrew C. Tolonen,et al.  Transfer of photosynthesis genes to and from Prochlorococcus viruses. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[78]  S. Langton Avoiding edge effects in agroforestry experiments; the use of neighbour-balanced designs and guard areas , 1990, Agroforestry Systems.

[79]  M. Clokie,et al.  Marine ecosystems: Bacterial photosynthesis genes in a virus , 2003, Nature.

[80]  J. Fry,et al.  Elevated Abundance of Bacteriophage Infecting Bacteria in Soil , 2003, Applied and Environmental Microbiology.

[81]  B. Andresen,et al.  Genomic analysis of uncultured marine viral communities , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[82]  J. Fry,et al.  Seasonal Population Dynamics and Interactions of Competing Bacteriophages and Their Host in the Rhizosphere , 2000, Applied and Environmental Microbiology.

[83]  J. Fry,et al.  In Situ Population Dynamics of Bacterial Viruses in a Terrestrial Environment , 1999, Applied and Environmental Microbiology.

[84]  L. E. Ensminger,et al.  METHODS OF SOIL ANALYSIS , 1965 .