Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions

Ackermann, 1998, Tailed bacteriophages: the order Caudovirales, Advances in Virus Research, 51, 135, 10.1016/S0065-3527(08)60785-X Adl, 2006, Protists in soil ecology and forest nutrient cycling, Canadian Journal of Forest Research, 36, 1805, 10.1139/x06-056 Alphaville, 1984, Forever young Ankrah, 2014, Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition, The ISME Journal, 8, 1089, 10.1038/ismej.2013.216 Armanious, 2016, Viruses at solid–water interfaces: a systematic assessment of interactions driving adsorption, Environmental Science & Technology, 50, 732, 10.1021/acs.est.5b04644 Bales, 1991, Bacteriophage adsorption during transport through porous media: chemical perturbations and reversibility, Environmental Science & Technology, 25, 2088, 10.1021/es00024a016 Barylski, 2014, The discovery of phiAGATE, a novel phage infecting Bacillus pumilus, leads to new insights into the phylogeny of the subfamily Spounavirinae, PloS One, 9, e86632, 10.1371/journal.pone.0086632 Basler, 2015, Microbial carbon recycling: an underestimated process controlling soil carbon dynamics – Part 2: a C3-C4 vegetation change field labelling experiment, Biogeosciences, 12, 6291, 10.5194/bg-12-6291-2015 Benitez-Nelson, 2000, The biogeochemical cycling of phosphorus in marine systems, Earth-Science Reviews, 51, 109, 10.1016/S0012-8252(00)00018-0 Blagodatskaya, 2013, Active microorganisms in soil: critical review of estimation criteria and approaches, Soil Biology and Biochemistry, 67, 192, 10.1016/j.soilbio.2013.08.024 Bonnain, 2016, The Ferrojan Horse hypothesis: iron-virus interactions in the ocean, Frontiers in Marine Science, 3, 82, 10.3389/fmars.2016.00082 Bowatte, 2010, High frequency of virus-infected bacterial cells in a sheep grazed pasture soil in New Zealand, Soil Biology and Biochemistry, 42, 708, 10.1016/j.soilbio.2009.12.013 Brady, 2004 Breitbart, 2012, Marine viruses: truth or dare, Annual Review of Marine Science, 4, 425, 10.1146/annurev-marine-120709-142805 Brewer, 1964 Brookes, 2009, Soil Biology and Biochemistry, 41, 440, 10.1016/j.soilbio.2008.09.002 Brookes, 2017, Is the rate of mineralization of soil organic carbon under microbiological control?, Soil Biology and Biochemistry, 112, 127, 10.1016/j.soilbio.2017.05.003 Brum, 2015, Patterns and ecological drivers of ocean viral communities, Science, 348, 10.1126/science.1261498 Brum, 2016, Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics, The ISME Journal, 10, 437, 10.1038/ismej.2015.125 Brussow, 2005, Phage ecology, 129 Campbell, 1995, Large Pseudomonas phages isolated from barley rhizosphere, FEMS Microbiology Ecology, 18, 63, 10.1111/j.1574-6941.1995.tb00164.x Clarholm, 1985, Interactions of bacteria, protozoa and plants leading to mineralization of soil nitrogen, Soil Biology and Biochemistry, 17, 181, 10.1016/0038-0717(85)90113-0 Clasen, 2008, The effect of host Chlorella NC64A carbon: phosphorus ratio on the production of Paramecium bursaria Chlorella Virus 1, Freshwater Biology, 52, 112, 10.1111/j.1365-2427.2006.01677.x Clokie, 2011, Phages in nature, Bacteriophage, 1, 31, 10.4161/bact.1.1.14942 Cui, 2014, An allometric relationship between the genome length and virion volume of viruses, Journal of Virology, 88, 6403, 10.1128/JVI.00362-14 Danovaro, 2008, Major viral impact on the functioning of benthic deep-sea ecosystems, Nature, 454, 1084, 10.1038/nature07268 Dijkstra, 2011, Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate, Soil Biology and Biochemistry, 43, 1848, 10.1016/j.soilbio.2011.05.001 Dippold, 2016, Direct incorporation of fatty acids into microbial phospholipids in soils: position-specific labeling tells the story, Geochimica et Cosmochimica Acta, 174, 211, 10.1016/j.gca.2015.10.032 Ekschmitt, 2008, Soil-carbon preservation through habitat constraints and biological limitations on decomposer activity, Journal of Plant Nutrition and Soil Science, 171, 27, 10.1002/jpln.200700051 Emerson, 2018, Host-linked soil viral ecology along a permafrost thaw gradient, Nature Microbiology, 3, 870, 10.1038/s41564-018-0190-y Engelberg-Kulka, 2006, Bacterial programmed cell death and multicellular behavior in bacteria, PLoS Genetics, 2, 10.1371/journal.pgen.0020135 Erez, 2017, Communication between viruses guides lysis–lysogeny decisions, Nature, 541, 488, 10.1038/nature21049 Faruque, 2005, Self-limiting nature of seasonal cholera epidemics: role of host-mediated amplification of phage, Proceedings of the National Academy of Sciences, 102, 6119, 10.1073/pnas.0502069102 Fierer, 2017, Embracing the unknown: disentangling the complexities of the soil microbiome, Nature Reviews Microbiology, 15, 579, 10.1038/nrmicro.2017.87 Findlay, 2016, The chemical ecology of predatory soil bacteria, ACS Chemical Biology, 11, 1502, 10.1021/acschembio.6b00176 Fischer, 2010, Microbial uptake of low-molecular-weight organic substances out-competes sorption in soil, European Journal of Soil Science, 61, 504, 10.1111/j.1365-2389.2010.01244.x Fuhrman, 1999, Marine viruses and their biogeochemical and ecological effects, Nature, 399, 541, 10.1038/21119 Ghosh, 2008, Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA, Applied and Environmental Microbiology, 74, 495, 10.1128/AEM.01435-07 Gomez, 2011, Bacteria-phage antagonistic coevolution in soil, Science, 332, 106, 10.1126/science.1198767 Gunina, 2015, Sugars in soil and sweets for microorganisms: review of origin, content, composition and fate, Soil Biology and Biochemistry, 90, 87, 10.1016/j.soilbio.2015.07.021 Gupta, 1989, Influence of bacterial-amoebal interactions on sulfur transformations in soil, Soil Biology and Biochemistry, 21, 921, 10.1016/0038-0717(89)90081-3 Guttman, 2005, Basic phage biology, 29 Haaber, 2009, Viral lysis of Phaeocystis pouchetii: implications for algal population dynamics and heterotrophic C, N and P cycling, The ISME Journal, 3, 430, 10.1038/ismej.2008.125 Hewson, 2003, Viriobenthos production and virioplankton sorptive scavenging by suspended sediment particles in coastal and pelagic waters, Microbial Ecology, 46, 337, 10.1007/s00248-002-1041-0 Howard-Varona, 2017, Lysogeny in nature: mechanisms, impact and ecology of temperate phages, The ISME Journal, 11, 1511, 10.1038/ismej.2017.16 Jílková, 2015, The role of bacteria and protists in nitrogen turnover in ant nest and forest floor material: a laboratory experiment, European Journal of Soil Biology, 69, 66, 10.1016/j.ejsobi.2015.05.004 Joergensen, 2018, Alive and kicking: Why dormant soil microorganisms matter, Soil Biology and Biochemistry, 116, 419, 10.1016/j.soilbio.2017.10.022 Jones, 2005, Rapid intrinsic rates of amino acid biodegradation in soils are unaffected by agricultural management strategy, Soil Biology and Biochemistry, 37, 1267, 10.1016/j.soilbio.2004.11.023 Jover, 2014, The elemental composition of virus particles: implications for marine biogeochemical cycles, Nature Reviews Microbiology, 12, 519, 10.1038/nrmicro3289 Kallenbach, 2016, Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls, Nature Communications, 7, 10.1038/ncomms13630 Kemmitt, 2008, Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass – a new perspective, Soil Biology and Biochemistry, 40, 61, 10.1016/j.soilbio.2007.06.021 Kimura, 2008, Ecology of viruses in soils: past, present and future perspectives, Soil Science & Plant Nutrition, 54, 1, 10.1111/j.1747-0765.2007.00197.x 2011 Koskella, 2014, Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities, FEMS Microbiology Reviews, 38, 916, 10.1111/1574-6976.12072 Kravchenko, 2017, Soil pores and their contributions to soil carbon processes, Geoderma, 287, 31, 10.1016/j.geoderma.2016.06.027 Kravchenko, 2014, Intra-aggregate pore structure influences phylogenetic composition of bacterial community in macroaggregates, Soil Science Society of America Journal, 78, 1924, 10.2136/sssaj2014.07.0308 Kumbhar, 2014, Widespread predatory abilities in the genus Streptomyces, Archives of Microbiology, 196, 235, 10.1007/s00203-014-0961-7 Kuzyakov, 2013, Tansley Review: competition between roots and microorganisms for N: mechanisms and ecological relevance, New Phytologist, 198, 656, 10.1111/nph.12235 Kuzyakov, 2009, Soil Biology and Biochemistry, 41, 435, 10.1016/j.soilbio.2008.07.023 Lee, 2012, Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: examination by stable isotope probing (SIP) method, Soil Science & Plant Nutrition, 58, 161, 10.1080/00380768.2012.658739 Leendertz, 2006, Pathogens as drivers of population declines: the importance of systematic monitoring in great apes and other threatened mammals, Biological Conservation, 131, 325, 10.1016/j.biocon.2006.05.002 Lennon, 2011, Microbial seed banks: the ecological and evolutionary implications of dormancy, Nature Reviews Microbiology, 9, 119, 10.1038/nrmicro2504 Li, 2013, Identification of the major capsid gene (g23) of T4-type bacteriophages that assimilate substrates from root cap cells under aerobic and anaerobic soil conditions using a DNA-SIP approach, Soil Biology and Biochemistry, 63, 97, 10.1016/j.soilbio.2013.03.026 Liang, 2017, The importance of anabolism in microbial control over soil carbon storage, Nature Microbiology, 2, 17105, 10.1038/nmicrobiol.2017.105 Lipson, 1986, Effect of kaolinite on the specific infectivity of reovirus, FEMS Microbiology Letters, 37, 83, 10.1111/j.1574-6968.1986.tb01771.x Madigan, 2017 Maire, 2013, An unknown oxidative metabolism substantially contributes to soil CO2 emissions, Biogeosciences, 10, 1155, 10.5194/bg-10-1155-2013 Michen, 2010, Isoelectric points of viruses, Journal of Applied Microbiology, 10.1111/j.1365-2672.2010.04663.x Miltner, 2009, Fate of microbial biomass-derived amino acids in soil and their contribution to soil organic matter, Organic Geochemistry, 40, 978, 10.1016/j.orggeochem.2009.06.008 Miltner, 2012, SOM genesis: microbial biomass as a significant source, Biogeochemistry, 111, 41, 10.1007/s10533-011-9658-z Nam, 1998, Role of nanoporosity and hydrophobicity in sequestration and bioavailability: tests with model solids, Environmental Science and Technology, 32, 71, 10.1021/es9705304 Neher, 2010, Ecology of plant and free-living nematodes in natural and agricultural soil, Annual Review of Phytopathology, 48, 371, 10.1146/annurev-phyto-073009-114439 Odum, 2005 Ogunseitan, 1992, Application of DNA probes to analysis of bacteriophage distribution patterns in the environment, Applied and Environmental Microbiology, 58, 2046, 10.1128/AEM.58.6.2046-2052.1992 Parada, 2006, Viral burst size of heterotrophic prokaryotes in aquatic systems, Journal of the Marine Biological Association of the UK, 86, 613, 10.1017/S002531540601352X Parikka, 2017, Deciphering the virus-to-prokaryote ratio (VPR): insights into virus-host relationships in a variety of ecosystems: deciphering the virus-to-prokaryote ratio, Biological Reviews, 92, 1081, 10.1111/brv.12271 Paterson, 2009, Comments on the regulatory gate hypothesis and implications for C-cycling in soil, Soil Biology and Biochemistry, 41, 1352, 10.1016/j.soilbio.2009.02.012 Paul, 2008, Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?, The ISME Journal, 2, 579, 10.1038/ismej.2008.35 Pausch, 2016, Small but active – pool size does not matter for carbon flow in belowground food webs, Functional Ecology, 30, 479, 10.1111/1365-2435.12512 Postma, 1990, Habitable pore space and survival of Rhizobium leguminosarum biovartrifolii introduced into soil, Microbial Ecology, 19, 149, 10.1007/BF02012096 Potapov, 2017, Arthropods in the subsoil: abundance and vertical distribution as related to soil organic matter, microbial biomass and plant roots, European Journal of Soil Biology, 82, 88, 10.1016/j.ejsobi.2017.09.001 Prigent, 2005, A diversity of bacteriophage forms and genomes can be isolated from the surface sands of the Sahara Desert, Extremophiles, 9, 289, 10.1007/s00792-005-0444-5 Proctor, 1990, Viral mortality of marine bacteria and cyanobacteria, Nature, 343, 60, 10.1038/343060a0 Ranjard, 2001, Quantitative and qualitative microscale distribution of bacteria in soil, Research in Microbiology, 152, 707, 10.1016/S0923-2508(01)01251-7 Reavy, 2015, Distinct circular single-stranded DNA viruses exist in different soil types, Applied and Environmental Microbiology, 81, 3934, 10.1128/AEM.03878-14 Redfield, 1934, On the proportions of organic derivations in sea water and their relation to the composition of plankton, 176 Rillig, 2006, Mycorrhizas and soil structure, New Phytologist, 171, 41, 10.1111/j.1469-8137.2006.01750.x Rønn, 2012, Interactions between bacteria, protozoa and nematodes in soil, Acta Protozoologica, 51, 223 Roossinck, 2015, Plants, viruses and the environment: ecology and mutualism, Virology, 479–480, 271, 10.1016/j.virol.2015.03.041 Rutherford, 1992, Influence of texture on habitable pore space and bacterial-protozoan populations in soil, Biology and Fertility of Soils, 12, 221, 10.1007/BF00336036 Schimel, 2017, Estimating decay dynamics for enzyme activities in soils from different ecosystems, Soil Biology and Biochemistry, 114, 5, 10.1016/j.soilbio.2017.06.023 Schurig, 2012, Microbial cell-envelope fragments and the formation of soil organic matter: a case study from a glacier forefield, Biogeochemistry, 113, 595, 10.1007/s10533-012-9791-3 Sim, 2000, Virus transport in unsaturated porous media, Water Resources Research, 36, 173, 10.1029/1999WR900302 Sobeck, 2002, Examination of three theories for mechanisms of cation-induced bioflocculation, Water Research, 36, 527, 10.1016/S0043-1354(01)00254-8 Sterner, 2002 Steward, 2013, Are we missing half of the viruses in the ocean?, The ISME Journal, 7, 672, 10.1038/ismej.2012.121 Suttle, 1994, The significance of viruses to mortality in aquatic microbial communities, Microbial Ecology, 28, 237, 10.1007/BF00166813 Suttle, 2007, Marine viruses – major players in the global ecosystem, Nature Reviews Microbiology, 5, 801, 10.1038/nrmicro1750 Suttle, 2005, Viruses in the sea, Nature, 437, 356, 10.1038/nature04160 Swanson, 2009, Viruses in soils: morphological diversity and abundance in the rhizosphere, Annals of Applied Biology, 155, 51, 10.1111/j.1744-7348.2009.00319.x Takahashi, 2011, High frequency of phage-infected bacterial cells in a rice field soil in Japan, Soil Science & Plant Nutrition, 57, 35, 10.1080/00380768.2010.550864 Takahashi, 2013, Comparison of the frequency of visibly infected bacterial cells between the soil and the floodwater in two Japanese rice fields, Soil Science & Plant Nutrition, 59, 331, 10.1080/00380768.2013.778176 Tipping, 2016, The C: N:P: S stoichiometry of soil organic matter, Biogeochemistry, 130, 117, 10.1007/s10533-016-0247-z Trap, 2016, Ecological importance of soil bacterivores for ecosystem functions, Plant and Soil, 398, 1, 10.1007/s11104-015-2671-6 Vainio, 2017, Occurrence of similar mycoviruses in pathogenic, saprotrophic and mycorrhizal fungi inhabiting the same forest stand, FEMS Microbiology Ecology, 93, 3 van Bodegom, 2007, Microbial maintenance: a critical review on its quantification, Microbial Ecology, 53, 513, 10.1007/s00248-006-9049-5 Vidakovic, 2018, Dynamic biofilm architecture confers individual and collective mechanisms of viral protection, Nature Microbiology, 3, 26, 10.1038/s41564-017-0050-1 Watt, 2006, Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH), Environmental Microbiology, 8, 871, 10.1111/j.1462-2920.2005.00973.x Wei, 2015, Genetic signatures indicate widespread antibiotic resistance and phage infection in microbial communities of the McMurdo Dry Valleys, East Antarctica, Polar Biology, 38, 919, 10.1007/s00300-015-1649-4 Weinbauer, 2004, Ecology of prokaryotic viruses, FEMS Microbiology Reviews, 28, 127, 10.1016/j.femsre.2003.08.001 Weinbauer, 1998, Significance of viral lysis and flagellate grazing as factors controlling bacterioplankton production in a eutrophic lake, Applied and Environmental Microbiology, 64, 431, 10.1128/AEM.64.2.431-438.1998 Williamson, 2005, Abundance and diversity of viruses in six Delaware soils, Applied and Environmental Microbiology, 71, 3119, 10.1128/AEM.71.6.3119-3125.2005 Williamson, 2007, Incidence of lysogeny within temperate and extreme soil environments, Environmental Microbiology, 9, 2563, 10.1111/j.1462-2920.2007.01374.x Williamson, 2008, Cultivation-based assessment of lysogeny among soil bacteria, Microbial Ecology, 56, 437, 10.1007/s00248-008-9362-2 Williamson, 2013, Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods, Biology and Fertility of Soils, 49, 857, 10.1007/s00374-013-0780-z Williamson, 2017, Viruses in soil ecosystems: an unknown quantity within an unexplored territory, Annual Review of Virology, 4, 201, 10.1146/annurev-virology-101416-041639 Wommack, 2000, Virioplankton: viruses in aquatic ecosystems, Microbiology and Molecular Biology Reviews, 64, 69, 10.1128/MMBR.64.1.69-114.2000 Wommack, 2015, Counts and sequences, observations that continue to change our understanding of viruses in nature, Journal of Microbiology, 53, 181, 10.1007/s12275-015-5068-6 Xiao, 2014, Effect of different bacterial-feeding nematode species on soil bacterial numbers, activity, and community composition, Pedosphere, 24, 116, 10.1016/S1002-0160(13)60086-7 Yuan, 2017, Jumbo bacteriophages: an overview, Frontiers in Microbiology, 8, 10.3389/fmicb.2017.00403 Zhao, 2013, Abundant SAR11 viruses in the ocean, Nature, 10.1038/nature11921 Zwart, 1994, Rhizosphere protozoa: their significance in nutrient dynamics, 93 Łusiak-Szelachowska, 2017, Bacteriophages in the gastrointestinal tract and their implications, Gut Pathogens, 9, 10.1186/s13099-017-0196-7