Brum JR, Sullivan MB. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol. 2015;13:147–59.
Google Scholar
Danovaro R, Corinaldesi C, Dell’Anno A, Fuhrman JA, Middelburg JJ, Noble RT, et al. Marine viruses and global climate change. Fems Microbiol Rev. 2011;35:993–1034.
Google Scholar
Suttle CA. Marine viruses – major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12.
Google Scholar
Suttle CA. Viruses in the sea. Nature. 2005;437:356–61.
Google Scholar
Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature. 2016;532:465–70.
Google Scholar
Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, et al. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol. 2020;18:21–34.
Google Scholar
Peduzzi P, Weinbauer MG. Effect of Concentrating the Virus-Rich 2-200-Nm Size Fraction of Seawater on the Formation of Algal Flocs (Marine Snow). Limnol Oceanogr. 1993;38:1562–5.
Wilhelm SW, Suttle CA. Viruses and Nutrient Cycles in the Sea – Viruses play critical roles in the structure and function of aquatic food webs. Bioscience. 1999;49:781–8.
Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature. 1999;399:541–8.
Google Scholar
Sullivan MB, Weitz JS, Wilhelm S. Viral ecology comes of age. Env Microbiol Rep. 2017;9:33–5.
Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol. 2018;3:870–80.
Google Scholar
Starr EP, Nuccio EE, Pett-Ridge J, Banfield JF, Firestone MK. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc Natl Acad Sci USA. 2019;116:25900–8.
Google Scholar
Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems. 2018;3:e0076–18.
Williamson KE, Fuhrmann JJ, Wommack KE, Radosevich M. Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annu Rev Virol. 2017;4:201–19.
Google Scholar
Emerson JB. Soil viruses: a new hope. mSystems. 2019;4:e00120–19.
Google Scholar
Liang XL, Zhang YY, Wommack KE, Wilhelm SW, DeBruyn JM, Sherfy AC, et al. Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity. Soil Biol Biochem. 2020;144:107767.
Google Scholar
Liang XL, Wang YS, Zhang Y, Zhuang J, Radosevich M. Viral abundance, community structure and correlation with bacterial community in soils of different cover plants. Appl Soil Ecol. 2021;168:104138.
Roy K, Ghosh D, DeBruyn JM, Dasgupta T, Wommack KE, Liang X, et al. Temporal dynamics of soil virus and bacterial populations in agricultural and early plant successional soils. Front. Microbiol. 2020;11:1494.
Google Scholar
Williamson KE, Radosevich M, Wommack KE. Abundance and diversity of viruses in six Delaware soils. Appl Environ Microb. 2005;71:3119–25.
Google Scholar
Lee S, Sieradzki ET, Nicolas AM, Walker RL, Firestone MK, Hazard C, et al. Methane-derived carbon flows into host-virus networks at different trophic levels in soil. Proc Natl Acad Sci USA. 2021;118:e2105124118.
Google Scholar
ter Horst AM, Santos-Medellin C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, et al. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome. 2021;9:233.
Google Scholar
Wu RN, Davison MR, Gao YQ, Nicora CD, Mcdermott JE, Burnum-Johnson KE, et al. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun Biol. 2021;4:992.
Google Scholar
Trubl G, Kimbrel J, Liquet-Gonzalez J, Nuccio E, Weber P, Pett-Ridge J, et al. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome. 2021;9:1–15.
Van Goethem MW, Swenson TL, Trubl G, Roux S, Northen TR. Characteristics of wetting-induced bacteriophage blooms in biological soil crust. Mbio. 2019;10:e02287–19.
Google Scholar
Braga LPP, Spor A, Kot W, Breuil MC, Hansen LH, Setubal JC, et al. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Microbiome. 2020;8:52.
Google Scholar
Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, et al. Identifying viruses from metagenomic data using deep learning. Quant Biol. 2020;8:64–77.
Google Scholar
Santos-Medellin C, Zinke LA, Ter Horst AM, Gelardi DL, Parikh SJ, Emerson JB. Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities. ISME J. 2021;15:1956–70.
Google Scholar
Srinivasiah S, Lovett J, Ghosh D, Roy K, Fuhrmann JJ, Radosevich M, et al. Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation. Fems Microbiol Ecol. 2015;91:fiv063.
Google Scholar
Schimel DS, House JI, Hibbard KA, Bousquet P, Ciais P, Peylin P, et al. Recent patterns and mechanisms of carbon exchange by terrestrial ecosystems. Nature. 2001;414:169–72.
Google Scholar
Glassman SI, Weihe C, Li JH, Albright MBN, Looby CI, Martiny AC, et al. Decomposition responses to climate depend on microbial community composition. Proc Natl Acad Sci USA. 2018;115:11994–9.
Google Scholar
Strickland MS, Lauber C, Fierer N, Bradford MA. Testing the functional significance of microbial community composition. Ecology. 2009;90:441–51.
Google Scholar
Matulich KL, Martiny JBH. Microbial composition alters the response of litter decomposition to environmental change. Ecology. 2015;96:154–63.
Google Scholar
Schimel JP, Schaeffer SM. Microbial control over carbon cycling in soil. Front Microbiol. 2012;3:348.
Google Scholar
Anthony MA, Crowther TW, Maynard DS, van den Hoogen J, Averill C. Distinct assembly processes and microbial communities constrain soil organic carbon formation. One Earth. 2020;2:349–60.
Albright MBN, Johansen R, Thompson J, Lopez D, Gallegos-Graves LV, Kroeger ME, et al. Soil bacterial and fungal richness forecast patterns of early pine litter decomposition. Front Microbiol. 2020;11:542220.
Google Scholar
Kuzyakov Y, Mason-Jones K. Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions. Soil Biol Biochem. 2018;127:305–17.
Google Scholar
Trubl G, Hyman P, Roux S, Abedon ST. Coming-of-age characterization of soil viruses: a user’s guide to virus isolation, detection within metagenomes, and viromics. Soil Syst. 2020;4:23.
Google Scholar
Goller PC, Haro-Moreno JM, Rodriguez-Valera F, Loessner MJ, Gomez-Sanz E. Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil. Microbiome. 2020;8:17.
Google Scholar
Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc. 2009;4:470–83.
Google Scholar
Lo CC, Chain PSG. Rapid evaluation and quality control of next generation sequencing data with FaQCs. Bmc Bioinform. 2014;15:366.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Google Scholar
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Current protocols in bioinformatics. 2020;70:e102.
Google Scholar
Kieft K, Zhou ZC, Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8:90.
Google Scholar
Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2021;39:578–85.
Google Scholar
Nayfach S, Paez-Espino D, Call L, Low SJ, Sberro H, Ivanova NN, et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol. 2021;6:960–70.
Google Scholar
McNair K, Zhou C, Dinsdale EA, Souza B, Edwards RA. PHANOTATE: a novel approach to gene identification in phage genomes. Bioinformatics. 2019;35:4537–42.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat. Methods. 2015;12:59–60.
Google Scholar
de Souza RS, Okura VK, Armanhi JS, Jorrin B, Lozano N, da Silva MJ, et al. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci Rep. 2016;6:28774.
Google Scholar
Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, MacPhee R, et al. Microbiome profiling by illumina sequencing of combinatorial sequencetagged PCR products. PLoS ONE. 2010;5:e15406.
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Google Scholar
Albright MBN, Sevanto S, Gallegos-Graves L, Dunbar J. Biotic interactions are more important than propagule pressure in microbial community invasions. Mbio. 2020;11:e02089–20.
Google Scholar
Oksanen J, Blanchet F, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2020. R package version 2.5-7. https://CRAN.Rproject.org/package=vegan
Team RC R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2021.
De Caceres M, Legendre P. Associations between species and groups of sites: indices and statistical inference. Ecology. 2009;90:3566–74.
Google Scholar
Frank E Harrell Jr. wcfCDamo. Hmisc: Harrell Miscellaneous. 2021. R packageversion 4.6-0. https://CRAN.R-project.org/package=Hmisc
Kuhn M, Jackson S, Cimentada J corrr: Correlations in R. 2020. R package version 0.4.3. https://CRAN.R-project.org/package=corrr
Spearman C. The7proof and measurement of association7between two things. Am J Psychol. 1904;15:72–101.
Epskamp S, Cramer AOJ, Waldorp LJ, Schmittmann VD, Borsboom D. qgraph: network visualizations of relationships in psychometric data. J Stat Softw. 2012;48:1–18.
Kimura M, Jia ZJ, Nakayama N, Asakawa S. Ecology of viruses in soils: Past, present and future perspectives. Soil Sci Plant Nutr. 2008;54:1–32.
Williamson KE, Schnitker JB, Radosevich M, Smith DW, Wommack KE. Cultivationbased assessment of lysogeny among soil bacteria. Microb Ecol. 2008;56:437–47.
Google Scholar
Berns AE, Philipp H, Narres HD, Burauel P, Vereecken H, Tappe W. Effect of gammasterilization and autoclaving on soil organic matter structure as studied by solid state NMR, UV and fluorescence spectroscopy. Eur J Soil Sci. 2008;59:540–50.
Google Scholar
Tian QX, He HB, Cheng WX, Zhang XD. Pulse-dynamic and monotonic decline patterns of soil respiration in long term laboratory microcosms. Soil Biol Biochem. 2014;68:329–36.
Google Scholar
Emerson JB, Adams RI, Roman CMB, Brooks B, Coil DA, Dahlhausen K, et al. Schrodinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome. 2017;5:86.
Google Scholar
Halgasova N, Ugorcakova J, Gerova M, Timko J, Bukovska G. Isolation and characterization of bacteriophage PhiBP from Paenibacillus polymyxa CCM 7400. FEMS Microbiol Lett. 2010;305:128–35.
Google Scholar
Klyczek KK, Bonilla JA, Jacobs-Sera D, Adair TL, Afram P, Allen KG, et al. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages. PLoS ONE. 2017;12:e0180517.
Google Scholar
Li P, Bhattacharjee P, Wang S, Zhang L, Ahmed I, Guo L. Mycoviruses in fusarium species: an update. Front Cell Infect Microbiol. 2019;9:257.
Google Scholar
Ghabrial SA, Caston JR, Jiang DH, Nibert ML, Suzuki N. 50-plus years of fungal viruses. Virology. 2015;479:356–68.
Google Scholar
Lopez-Mondejar R, Zuhlke D, Vetrovsky T, Becher D, Riedel K, Baldrian P. Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199. Biotechnol Biofuels. 2016;9:104.
Google Scholar
Thakur V, Kumar V, Kumar S, Singh D. Diverse culturable bacterial communities with cellulolytic potential revealed from pristine habitat in Indian trans-Himalaya. Can J Microbiol. 2018;64:798–808.
Google Scholar
Panagiotou G, Kekos D, Macris BJ, Christakopoulos P. Production of cellulolytic and xylanolytic enzymes by Fusarium oxysporum grown on corn stover in solid state fermentation. Ind Crop. Prod. 2003;18:37–45.
Google Scholar
Zheng HP, Yang TJ, Bao YZ, He PP, Yang KM, Mei XL, et al. Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics. Soil Biol Biochem. 2021;157:108230.
Google Scholar
Zhou ZH, Wang CK, Zheng MH, Jiang LF, Luo YQ. Patterns and mechanisms of responses by soil microbial communities to nitrogen addition. Soil Biol Biochem. 2017;115:433–41.
Google Scholar
Peters BM, Jabra-Rizk MA, O’May GA, Costerton JW, Shirtliff ME. Polymicrobial interactions: impact on pathogenesis and human disease. Clin Microbiol Rev. 2012;25:193.
Google Scholar
Carreira C, Lonborg C, Kuhl M, Lillebo AI, Sandaa RA, Villanueva L, et al. Fungi and viruses as important players in microbial mats. Fems Microbiol Ecol. 2020;96(11):fiaa187.
Google Scholar
Hurwitz BL, Hallam SJ, Sullivan MB. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol. 2013;14:R123.
Google Scholar
Sieradzki ET, Ignacio-Espinoza JC, Needham DM, Fichot EB, Fuhrman JA. Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nat Commun. 2019;10:1169.
Google Scholar
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