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Soil Microbiological Recycling and the Virome Role in a Hectare Grassland

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Soil and Recycling Management in the Anthropocene Era

Part of the book series: Environmental Science and Engineering ((ENVSCIENCE))

Abstract

Viruses need a host for replication. In a hectare grassland, for example, a huge amount of diverse cells, majorly microbial cells are present, in which viral inserts replicate either lysogenically with the host genome or lytically after reprogramming the host metabolism towards virus particle production. A third replication mode is “chronic extrusion”. Thereby single stranded (ss) viral DNA is channelled through the cytoplasmic membrane into the surrounding environment and double stranded DNA (ds) reintegrates in new host genomes. During lytic virus replication the host cell bursts. The produced virus particles, now termed virions, and the cell nutrients are released and potential pro- and eukaryotic hosts are attracted. In a nutrient enriched environment virions find easier a new genome for reintegrating by using their inherent infectivity and autoinduced quorum-sensing. After having entered a new host lysogenic, lytic replication switching starts. During “chronic extrusion” and lytic replication cycles set free virions can absorb epigenetic information, which then may be spread by horizontal gene transfers. Lysogenic, lytic replication switchings, termed viral shunts, are temperate. Host cell multiplication regulator, carefully controlled in nature. Assumed 1% of the wealth of host cells in a hectare grassland burst lytic virus replication mediated a significant influence on the gross primary production (GPP) is inevitable. Epigenetic genetic information exchanges may improve host’s health and correspondingly the focus of this chapter lies on virus mediated nutrient side drain estimates, calculated in their importance for a hectare grassland.

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References

  1. Abeles, S.R., Pride, D.T.: Molecular bases and role of viruses in the human microbiome. J. Mol. Biol. 426, 3892–3906 (2014). https://doi.org/10.1016/j.jmb.2014.07.002

    Article  CAS  Google Scholar 

  2. Aberle, E.D., Forrest, J., Gerrard, D.E, Mills, E.W.: Principles of Meat Science, 4th edn. Kendall/Hunt Publishing Company, Dubuque, Iowa, 354 p, (2001)

    Google Scholar 

  3. Abo-Senna, A.S.M.: Occurrence of Bacillus thuringensis bacteriophages in the Egyptian arid soil. Int. J. Virol. Mol. Biol. 6, 1–8 (2017). https://doi.org/10.5923/j.ijvmb.20170601.01

    Article  Google Scholar 

  4. Adachi, A.: Grand challenge in human/animal virology: Unseen smallest replicative entities shape the whole globe. Front Microbiol (2020). https://doi.org/10.3389/fmicrb.2020.00431

    Article  Google Scholar 

  5. Amann, R.I., Ludwig, W., Schleifer, K.H.: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 (1995)

    Google Scholar 

  6. Andersen, P.C., Mizell, R.F., Brodbeck, B.V., et al.: Abundance and consumption rate of glassy-winged sharpshooter (Hemiptera: Cicadellidae) on peaches and plums. J. Entomol. Sd. 43, 394–407. naldc.nal.usda.gov/download/22693/PDF2002 (2008)

    Google Scholar 

  7. Andersson, A.F., Banfield, J.F.: Virus population dynamics and acquired virus resistance in natural microbial communities. Science 23, 1047–1050 (2008). https://doi.org/10.1126/science.1157358

    Article  CAS  Google Scholar 

  8. Angers, D.A., Eriksen-Hamel, N.S.: Full-inversion tillage and organic carbon distribution in soil profiles: a meta-analysis. SSSAJ 72, 1370–1374 (2008). https://doi.org/10.2136/sssaj2007.0342

    Article  CAS  Google Scholar 

  9. Asano, M., Wagai, R.: Evidence of aggregate hierarchy at micro- to submicron scales in an allophanic Andisol. Geoderma 216, 62–74 (2014). https://doi.org/10.1016/j.geoderma.2013.10.005

    Article  CAS  Google Scholar 

  10. Ashraf, U., Benoit-Pilven, C., Lacroix, V., Navratil, V., Naffakh, N.: Advances in analyzing virus-induced alterations of host cell splicing. Trends Microbiol. 27, 268–281 (2018). https://doi.org/10.1016/j.tim.2018.11.004

    Article  CAS  Google Scholar 

  11. Aurelie, K.K., Guy, M.M., Bona, N.F., Charles, K.M., Mawupemor, A.P., Shixue, L.: A historical review of Ebola outbreaks. An open peer reviewed chapter (2017). https://doi.org/10.5772/intechopen72660

  12. Bahar, B., Monahan, F.J., Moloney, A.P., O’Kiely, P., Scrimgeour, C.M., Schmidt, O.: Alteration of the carbon and nitrogen stable isotope composition of beef by substitution of grass silage with maize. Rapid Commun. Mass Spectrom. 19, 1937–1942 (2005). https://doi.org/10.1002/rcm.2007

    Article  CAS  Google Scholar 

  13. Bahar, B., Schmidt, O., Moloney, A.P., Scrimgeour, C.M., Begley, I.S., Monaha, F.J.: Seasonal variation in the C, N and S stable isotope composition of retail organic and conventional Irish beef. Food Chem. 106, 1299–1305 (2008). https://doi.org/10.1016/j.foodchem.2007.07.053

    Article  CAS  Google Scholar 

  14. Bahram, M., Hildebrand, F., Forslund, S.K., et al.: Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018). https://doi.org/10.1038/s41586-018-0386-6

    Article  CAS  Google Scholar 

  15. Bamforth, S.S.: Protozoa: recyclers and indicators of agroecosystem quality. In: Benckiser, G. (ed.) Fauna in Soil Ecosystems—Recycling Processes, Nutrient Fluxes, and Agricultural Production. Marcel Dekker, New York, USA) (1997)

    Google Scholar 

  16. Bamforth, S.S.: Diversity of protozoa. In: Benckiser, G., Schnell, S. (eds.) Biodiversity in agricultural production systems, pp. 205–213. Taylor and Francis, Boca Raton pp (2007)

    Google Scholar 

  17. Baraniya, D., Nannipieri, P., Kublik, S., Vestergaard, G., Schloter, M., Schöler, A.: The impact of the diurnal cycle on the microbial transcriptome in the rhizosphere of barley. Microb. Ecol. 75, 830–833 (2017). https://doi.org/10.1007/s00248-017-1101-0

    Article  CAS  Google Scholar 

  18. Baric, R.S., Crosson, S., Damania, B., Miller, S.I., Rubin, E.J.: Next-generation high-throughput functional annotation of microbial genomes. mBio, 7, e01245–16 (2016). https://doi.org/10.1128/mbio.01245-16

  19. Battini, F., Agostini, A., Tabaglio, V., Amaducci, S.: Environmental impacts of different dairy farming systems in the Po valley. J. Clean. Product. 112, 91–102 (2016). https://doi.org/10.1016/j.jclepro.2015.09.062

  20. Baudoin, E., Philippot, L., Brauman, A., Villenave, C.: Shifts in size, genetic structure and activity of the soil denitrifier community by nematode grazing. Eur. J. Soil Biol. 46, 112e118 (2010). https://doi.org/10.1016/j.ejsobi.2009.12.001

  21. Beer, C., Reichstein, M., Tomelleri, E., Ciais, P., Jung, M., Carvalhais, N., Rodenbeck, C., Arain, M., Baldocchi, D., Bonan, G.B., Bondeau, A., Cescatti, A., Lasslop, G., Lindroth, A., Lomas, M.R., Luyssaert, S., Margolis, H.A., Oleson, K., Roupsard, O., Veenendaal, E., Viovy, N., Williams, C., Woodward, I., Papale, D.: Terrestrial gross carbon dioxide uptake: global distribution and covariation with climate. Science 329, 834–838 (2010). https://doi.org/10.1126/science.1184984

  22. Benckiser, G.: Organic inputs and soil metabolism. In: Benckiser, G. (ed.) Fauna in Soil Ecosystems—Recycling Processes, Nutrient Fluxes, and Agricultural Production. Marcel Dekker, New York (1997)

    Chapter  Google Scholar 

  23. Benckiser, G., Santiago, S., Neue, H.U., et al.: Effect of fertilization on exudation, dehydrogenase activity, iron reducing populations in the rhizosphere of rice (Oryza sativa L.) in relation to iron toxicity. Plant Soil 79, 305–316 (1984). https://doi.org/10.1007/bf02184324

    Article  CAS  Google Scholar 

  24. Benckiser, G., Schnell, S.: Biodiversity in agricultural production systems. Taylor and Francis, Boca Raton (2007)

    Google Scholar 

  25. Benckiser, G., Syring, K.-M.: Erfassung und Modellierung gasförmiger N Verluste einer Parabraunerde. Z. dt geol. Ges. 136, 1–6 (1985)

    Google Scholar 

  26. Benckiser, G., Ladha, J.K., Wiesler, F.: Climate change and nitrogen turnover in soils and aquatic environments. In: Marxsen, J. (ed.) Climate Change and Microbial Ecology: Current Research and Future Trends (Chap. 8). Caister Academic Press, Norfolk, UK, p. 22

    Google Scholar 

  27. Benckiser, G.: Plastics, micro- and nanomaterials, and virus-soil microbe-plant interactions in the environment. In: Prassad, R. (ed.) Plant Nanobionics (Chap. 4). Nanotechnology in the Life Science, pp. 83–96. Springer, Heidelberg (2019)

    Google Scholar 

  28. Benckiser, G.: Biofilm surrounded hexachlorobenzene (HCB) crystals and wastewater purification. Examines Mar Biol Oceanogr. 3 (5) (2020). https://doi.org/10.31031/EIMBO.2020.03.000574

  29. Bergkemper, F., Kublik, S., Lang, F., Krüger, J., Vestergaard, G., Schloter, M., Schulz, S.: Novel oligonucleotide primers reveal a high diversity of microbes which drive phosphorous turnover in soil. J. Microbiol. Methods 125, 91–97 (2016). https://doi.org/10.1016/j.mimet.2016.04.011

    Article  CAS  Google Scholar 

  30. Berry, D., Mader, E., Lee, T.K., Woebken, D., Wang, Y., Zhu, D., Palatinszky, M., Schintlmeister, A., Schmid, M.C., Hanson, B.T., Shterzer, N., Mizrahi, I., Rauch, I., Decker, T., Bocklitz, T., Popp, J., Gibson, C.M., Fowler, P.W., Huang, W.E., Wagner, M.: Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. PNAS 112, E194–E203 (2015). https://doi.org/10.1073/pnas.1420406112

    Article  CAS  Google Scholar 

  31. Bettarel, Y., Sime-Ngando, T., Amblard, C., Dolan, J.: Viral activity in two contrasting lake ecosystems Appl. Environ. Microbiol. 70, 2941–2951 (2004). https://doi.org/10.1128/aem.70.5.2941-2951.200

    Article  CAS  Google Scholar 

  32. Beutin, L., Hammerl, J.A., Strauch, E., et al.: Spread of a distinct Stx2-encoding phage prototype among Escherichia coli O104:H4 strains from outbreaks in Germany, Norway, and Georgia. J. Virol. 86, 10444–1055 (2012). https://doi.org/10.1128/jvi.00986-12

    Article  CAS  Google Scholar 

  33. Bhowmik, A., Fortuna, A.-M., Cihacek, L.J., Bary, A.I., Cogger, C.G.: Use of biological indicators of soil health to estimate reactive nitrogen dynamics in long-term organic vegetable and pasture systems. Soil Biol. Biochem. 103, 308–319 (2016). https://doi.org/10.1016/j.soilbio.2016.09.004

    Article  CAS  Google Scholar 

  34. Bhowmik, A., Fortuna, A.-M., Cihacek, L.J., Bary, A.I., Cogger, C.G.: Potential carbon sequestration and nitrogen cycling in long-term organic management systems. Renew. Agri. Food. Syst. 1–13 (2017). https://doi.org/10.1017/si742170516000429

  35. Blagodatskaya, E., Kuzyakov, Y.: Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol. Biochem. 67, 192–211 (2013). https://doi.org/10.1016/j.soilbio.2013.08.024

    Article  CAS  Google Scholar 

  36. Bloom, J.D., Arnold, F.H.: In the light of directed evolution: pathways of adaptive protein evolution PNAS 16, 106 (Supplement 1): 9995–10000 (2009). https://doi.org/10.1073/pnas.0901522106

  37. Boenigk, J., Pfandl, K., Stadler, P., Chatzinotas, A.: High diversity of the ‘Spumella-like’ flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions. Environ. Microbiol. 7, 685–697 (2005). https://doi.org/10.1111/j.1462-2920.2005.00743.x

  38. Borriello, G., Werne, E., Roe, F., Kim, A.M., Ehrlich, G.D., Stewart, P.S.: Oxygen limitation contributes to antibiotic tolerance of Pseudomonas aeruginosa in biofilms. Antimicrobial agents and chemotherapy 48, 2659–2664 (2004). https://doi.org/10.1128/aac.48.7.2659-2664.2004

  39. Bouwman, L.A., Zwart, K.B.: The ecology of bacterivorous protozoans and nematodes in arable soil. Agri. Ecosys. Environm. 51, 145–160 (1994). https://doi.org/10.1016/0167-8809(94)9004

    Article  Google Scholar 

  40. Bratbak, G., Heldal, K.: Significance of algal viruses and ecology of Phaeocystis host-virus interactions. In: Bell, C., Brylinsky, M., Johnson-Green, P. (eds.) Microbial Biosystems. Atlantic Canada Society for Microbial Ecology, Halifax, pp. 571–575 (2000)

    Google Scholar 

  41. Brault, V., Uzest, M., Monsion, B., et al.: Aphids as transport devices for plant viruses. Compt. Rend. Biol. 333, 524–538 (2010). https://doi.org/10.1016/j.crvi.2010.04.001.epub2010

  42. De Bruyn, J.: The dead and their microbes. Microbe 11, 119–124 (2016)

    Google Scholar 

  43. Caesar-TonThat, T.C., Lenssen, A.W., Caesar, A.J., Sainju, U.M., Gaskin, J.F.: Effects of tillage on microbial populations associated to soil aggregation in dryland spring wheat system. Eur. J. Soil Biol. 46, 119 (2010). https://doi.org/10.1016/j.ejsobi.2009.12.004

    Article  Google Scholar 

  44. Carvalhais, L.C., Dennis, P.G., Fedoseyenko, D., et al.: Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency. J. Plant Nutr. Soil Sci. 174, 3–11 (2011). https://doi.org/10.1002/jpln.201000085

    Article  CAS  Google Scholar 

  45. Casjens, S.: Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49, 277–300 (2003). https://doi.org/10.1046/j.1365-2958.2003.03580.x

    Article  CAS  Google Scholar 

  46. Cela, S., Ketterings, Q.M., Czymmek, K., et al.: Characterization of nitrogen, phosphorus, and potassium mass balances of dairy farms in New York State. J. Dairy Sci. 97, 7614–7632 (2014)

    Article  CAS  Google Scholar 

  47. Chen, J.G., Crooks, R.M., Seefeldt, L.C., Bren, K.L., Bullock, R.M., Darensbourg, Y., Holland, P.L., Hoffman, B., Janik, M.J., Jones, A.K., Kanatzidis, M.G., King, P., Lancaster, M., Lymar, S.V., Pfromm, P., Schneider, W.F., Schrock, R.R.: Beyond fossil fuel–driven nitrogen transformations. Science 360, 6391 (2018). https://doi.org/10.1126/science.aar6611

    Article  CAS  Google Scholar 

  48. Chen, H.Y., Di Mascio, M., Perelson, A.S., et al.: Determination of virus burst size in vivo using a single-cycle SIV in rhesus macaques. PNAS 104, 19079–19084 (2007). https://doi.org/10.1073/pnas.0707449104

    Article  Google Scholar 

  49. Chen, Y., Lee, P., Lee, G., Mariko, S., Oikawa, T.: Simulating root responses to grazing of a Mongolian grassland ecosystem Plant Ecology 183, 265–275 (2006). https://doi.org/10.1007/s11258-005-9038-7

  50. Colangelo-Lillis, J., Wing, B.A., Raymond-Bouchard, I., Whyte, L.G.: Viral induced microbial mortality in arctic hypersaline spring sediments. Front. Microbiol. (2017). https://doi.org/10.3389/fmicb.2016.02158

  51. Colson, P., La Scola, B., Raoult, D.: Viruses of amoebae: a journey through innovative research and paradigm changes. Ann. Rev. Virol. 4, 61–85 (2017). https://doi.org/10.1146/annurev-virology-101416-04181

    Article  CAS  Google Scholar 

  52. Corinaldesi, C., Dell’Anno, A., Danovaro, R.: Viral infections stimulate the metabolism and shape prokaryotic assemblages in submarine mud volcanoes. ISME J. 6, 1250–1259 (2012). https://doi.org/10.1038/ismej.2011.185

    Article  CAS  Google Scholar 

  53. Coupland, R.T. (ed.): Ecosystems of the World: 8A and B Natural Grasslands. Elsevier, Amsterdam (1993)

    Google Scholar 

  54. Craswell, E.T., Godwin, D.C.: The efficiency of nitrogen fertilizers applied to cereals in different climates. Adv. Plant Nutrit. 1, 1–55 (1984)

    Google Scholar 

  55. Cubo, M.T., Alías-Villegas, C., Balsanelli, E., Mesa, D., de Souza, E., Espuny, M.R.: Diversity of Sinorhizobium (Ensifer) meliloti bacteriophages in the rhizosphere of Medicago marina: Myoviruses, filamentous and N4-Like Podovirus. Front. Microbiol. (2020). https://doi.org/10.3389/fmicb.2020.00022

  56. Cycoń, M., Mrozik, A., Piotrowska-Seget, Z.: Antibiotics in the soil environment—degradation and their impact on microbial activity and diversity. Front. Microbiol. 10, 338 (2019). https://doi.org/10.3389/fmicb.2019.00338

  57. Czajkowski, R.: May the phage be with you? Prophage-Like elements in the genomes of soft rot Pectobacteriaceae: Pectobacterium spp. and Dickeya spp. Front. Microbiol. (2019). https://doi.org/10.3389/fmicb.2019.00138

  58. Daims, H., Lebedeva, E.V., Pjevac, P., Han, P., Herbold, C., Albertsen, M., Jehmlich, N., Palatinszky, M., Vierheilig, J., Bulaev, A., Kirkegaard, R.H., von Bergen, M., Rattei, T., Bendinger, B., Nielsen, P.H., Wagner, M.: Complete nitrification by Nitrospira bacteria. Nature 528, 504–509 (2015). https://doi.org/10.1038/nature16461

    Article  CAS  Google Scholar 

  59. Darvishzadeh, R., Skidmore, A., Schlerf, M., Atzberger, C., Corsi, F., Cho, M.: Estimation of leaf area index and Chlorophyll For a mediterranean grassland using hyperspectral data. In: The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, vol. 27, Part B7, Beijing (2008)

    Google Scholar 

  60. Debnath, A., Reed, S.L.: Entamoeba histolytica: from high-throughput technology to new drugs. In: De Pablos Torró, L.M., Morales, J.-L. (eds.) Protozoan Parasitism: From Omics to Prevention and Control. Caister Academic Press, UK, pp. 157–170 (2018). https://doi.org/10.21775/9781910190838;

  61. Ding, G., Radl, V., Schloter-Hai, B., Jechalke, S., Heuer, H., Smalla, K., Schloter, M.: Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine. PLoS ONE 9, e92958. https://doi.org/10.1371/journal.pone.0092958

  62. Djigal, D., Baudoin, E., Philippot, L., Brauman, A., Villenave, C.: Shifts in size, genetic structure and activity of the soil denitrifier community by nematode grazing. Eur. J. Soil Biol. 46, 112e118 (2010). https://doi.org/10.1016/j.ejsobi.2009.12.001

  63. Dou, D., Hernandez-Neuta, I., Wang, H., Ostbye, H., Qian, X., Thiele, S., Resa-Infante, P., Kouassi, N.M., Sender, V., Hentrich, K., Mellroth, P., Henriques-Normark, B., Gabriel, G., Nilsson, M., Daniels, R.: Analysis of IAV replication and co-infection dynamics by a versatile RNA viral genome labeling method. Cell Rep. 20, 251–263 (2017). https://doi.org/10.1016/j.celrep.2017.06.021

    Article  CAS  Google Scholar 

  64. Van Driesche, R.G., Carruthers, R.I., Center, T., Hoddle, M.S., Hough-Goldstein, J., Morin, L., Smith, L., Wagner, D.L., Blossey, B., BrancatiniV, Casagrande R., Causton, C.E., Coetzee, J.A., Cuda, J., Ding, J., Fowler, S.V., Frank, J.H., Fuester, R., Goolsby, J., Grodowitz, M., Heard, T.A., Hill, M.P., Hoffmann, J.H., Huber, J., Julien, M., Kairo, M.T.K., Kenis, M., Mason, P., Medal, J., Messing, R., Miller, R., Moore, A., Neuenschwander, P., Newman, R., Norambuena, H., Palmer, W.A., Pemberton, R., Perez-Panduro, A., Pratt, P.D., Rayamajhi, M., Salom, S., Sands, D., Schooler, S., Schwarzländer, M., Sheppard, A., Shaw, R., Tipping, P.W., van Klinken, R.D.: Classical biological control for the protection of natural ecosystems. Biol. Control 54, 2–33 (2010). https://doi.org/10.1016/j.biocontrol.2010.03.003

    Article  Google Scholar 

  65. Dávila-Ramos, S., Castelán-Sánchez, H.G., Martínez-Ávila, L., del Rayo Sánchez-Carbente, M., Peralta, R., Hernández-Mendoza, A, Dobson, A.D.W., Gonzalez, R.A., Pastor, N., Batista-García, R.A.: A review on viral metagenomics in extreme environments. Front. Microbiol. (2019). https://doi.org/10.3389/fmicb.2019.02403

  66. Eiland, F., Klamer, M., Lind, A.-M., Leth, M., Bååth, E.: Influence of initial C/N ratio on chemical and microbial composition during long term composting of straw. Microbi. Ecol. 41, 272–280 (2001). https://www.jstor.org/stable/4251820

  67. FAO.: The State of Food and Agriculture 2019 (2019). http://www.fao.org/3/CA6030EN/CA6030EN.pdf

  68. Fageria, N.K., Baligar, V.C.: Enhancing nitrogen use efficiency in crop plants Adv. Agronomy 88, 97–185 (2005). https://doi.org/10.1016/S0065-2113(05)88004-6

    Article  CAS  Google Scholar 

  69. Fang, J.: A world without mosquitoes. Nature 466, 432–434 (2010). https://doi.org/10.1038/466432a

    Article  CAS  Google Scholar 

  70. Farlow, J., Bolkvadze, D., Leshkasheli, L., Kusradze, I., Kotorashvili, A., Kotaria, N., Balarjishvili, N., Kvachadze, L., Nikolich, M., Kutateladze, M.: Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis. BMC Genom. 19, 685 (2018). https://doi.org/10.1186/s12864-018-5056-4

    Article  CAS  Google Scholar 

  71. Field, C.B., Raupach, M.R.: The global carbon cycle. Scope Series 62. Island Press, Washington DC (2004)

    Google Scholar 

  72. Fierer, N., Jackson, R.B.: The diversity and biogeography of soil bacterial communities. PNAS 103, 626–631 (2006). https://doi.org/10.1073/pnas.0507535103

  73. Filippis, V., Villareal, L.: Lateral gene transfers or viral colonization? Science 293, 1048 (2001). https://doi.org/10.1126/science.293.5532.1048a

    Article  Google Scholar 

  74. Fink, A.: Pflanzenernährung in Stichworten. Hirt-Verlag, Kiel (1969)

    Google Scholar 

  75. Finke, J.F., Hunt, B.P.V., Winter, C., Carmack, E.C., Suttle, C.A.: Nutrients and other environmental factors influence virus abundances across oxic and hypoxic marine environments. Viruses 9, 152 (2017). https://doi.org/10.3390/v9060152

    Article  CAS  Google Scholar 

  76. Fischer, G.: Diversity of soil fungi. In: Benckiser, G., Schnell, S. (eds.) Biodiversity in Agricultural Production Systems, pp. 149–163. Taylor and Francis, Boca Raton pp (2007)

    Google Scholar 

  77. Flemming, H.-C., Wingender, J., Szewzyk, U., Steinberg, P.D., Rice, S.C., Kjelleberg, S.: Biofilms: an emergent form of bacterial life. Nat. Rev. Microbiol. 14, 563–575 (2016). https://doi.org/10.1038/nrmicro.2016.94

    Article  CAS  Google Scholar 

  78. Flemming, H.-C., Wuertz, S.: Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). https://doi.org/10.1038/s41579-019-0158-9ature

    Article  CAS  Google Scholar 

  79. Flemming, H.-C., Tamachkiarowa, A., Klahre, J., Schmitt, J.: Monitoring of fouling and biofouling in technical systems. Water Sci Technol 38, 291–298 (1998). https://doi.org/10.1016/S0273-1223(98)00704-5

  80. Forterre, P.: The universal tree of life: an update. Front. Microbiol. 6, 717 (2015). https://doi.org/10.3389/fmicb.2015.00717

    Article  Google Scholar 

  81. Fuchs, G.: Allgemeine Mikrobiologie. Georg Thieme Verlag, Germany (2007)

    Book  Google Scholar 

  82. Gans, J., Wolinsky, M., Dunbar, J.: Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387–1390 (2005). https://doi.org/10.1126/science.1112665

    Article  CAS  Google Scholar 

  83. Garnett, T., Conn, V., Kaiser, B.N.: Root based approaches to improving nitrogen use efficiency in plants Plant. Cell Environ. 32, 1272–1283 (2009). https://doi.org/10.1111/j.1365-3040.2009.02011.x

    Article  CAS  Google Scholar 

  84. Garrett, R.A., Klenk, H.‐P. (eds.): Archaea: evolution, physiology, and molecular biology (2007). Online ISBN: 9780470750865, Blackwell Publishing Ltd. https://doi.org/10.1002/9780470750865

  85. Giarrizzo, E., Burrascano, S., Chiti, T., de Bello, F., Lepš, J., Zavattero, L., Blasi, C.: Re-visiting historical semi-natural grasslands in the Apennines to assess patterns of changes in species composition and functional traits Appl. Veget. Sci. 20, 247–258 (2017). https://doi.org/10.1111/avsc.12288

    Article  Google Scholar 

  86. Gilbert, C., Peccoud, J., Chateigner, A., Moumen, B., Cordaux, R., Herniou, E.A.: Continuous influx of genetic material from host to virus populations. PLoS Genet. 12, e1005838 (2016). https://doi.org/10.1371/journal.pgen.100583

    Article  Google Scholar 

  87. Gillis, A., Mahillon, J.: Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future. Viruses 6, 2623–2672 (2014). https://doi.org/10.3390/v6072623

    Article  CAS  Google Scholar 

  88. Good, A.G., Beatty, P.H.: Fertilizing nature: a tragedy of excess in the commons. PLoS Biol. 9, e1001124 (2011). https://doi.org/10.1371/journal.pbio.1001124

    Article  CAS  Google Scholar 

  89. Grafe, M., Goers, M., von Tucher, S., Baum, C., Zimmer, D., Leinweber, P., Vestergaard, G., Kublik, S., Schloter, M., Schulz, S.: Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes. Environment. Microbiol. Rep. 10(3): 320–327 (2018). https://doi.org/10.1111/1758-2229.12651

  90. Graham, E.B., Paez-Espino, D., Brislawn, C., Neches, R.Y., Hofmockel, K.S., Wu, R., et al.: Untapped viral diversity in global soil metagenomes. biorxiv. [preprint] (2019). https://doi.org/10.1101/583997

  91. Grayston, S.J., Griffith, G.S., Mawdsley, J.L., Campbell, C.D., Bardgett, R.D.: Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol. Biochem. 33, 533–551 (2001). https://doi.org/10.1016/s0038-0717(00)00194-2

    Article  CAS  Google Scholar 

  92. Griffiths, R.I., Whiteley, A.S., O’Donnell, A.S., Bailey, M.J.: Influence of depth and sampling time on bacterial community structure in an upland grassland soil. FEMS Microbiol. Ecol. 43, 35–43 (2003). https://doi.org/10.1111/j.1574-6941.2003.tb01043.x

    Article  CAS  Google Scholar 

  93. Grossmann, L., Bock, C., Schweikert, M., Boenigk, J.: Small but manifold-hidden diversity in “Spumella-like flagellates”. J. Eukaryot Microbiol. 63, 419–439 (2016). https://doi.org/10.1111/jeu.12287

  94. Grujcic, V., Nuy, J.K., Salcher, M.M., Shabarova, T., Kasalicky, V., Boenigk, J., Jensen, M., Simek, K.: Cryptophyta as major bacterivores in freshwater summer plankton. ISME J. 12, 1668–1681 (2018). https://doi.org/10.1038/s41396-018-0057-5)

    Article  CAS  Google Scholar 

  95. Hartmann, A., Smalla, K., Soerensen, J.: Microbial diversity in the rhizosphere: methodology to study plant-beneficial bacteria. In: Benckiser, G., Schnell, S. (eds.) Biodiversity in Agricultural Production Systems, pp. 101–131. Taylor and Francis, Boca Raton pp (2007)

    Google Scholar 

  96. Hayes, S., Mahony, J., Nauta, A., Van Sinderen, D.: Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses 9, E127 (2017). https://doi.org/10.3390/v9060127

    Article  CAS  Google Scholar 

  97. Hellweger, F.L.: Carrying photosynthesis genes increases ecological fitness of cyanophage in silico. Environ. Microbiol. 11, 1386–1394 (2009). https://doi.org/10.1111/j.1462-2920.2009.01866.x. Epub 2009 Jan 23

    Article  CAS  Google Scholar 

  98. Herzog, S., Wemheuer, F., Wemheuer, B., Daniel, R.: Effects of fertilization and sampling time on composition and diversity of entire and active bacterial communities in German grassland soils. PLoS ONE 10, e0145575 (2015). https://doi.org/10.1371/journal.pone.0145575

    Article  CAS  Google Scholar 

  99. Hillesland, K.L., Stahl, D.A., Harcombe, W.: Measuring the cost of microbial mutualism. Microbe 6, 427–434 (2011)

    Google Scholar 

  100. Hirmas, D.R., Gimenez, D., Nemes, A., et al.: Climate—induced changes in continental—scale soil macroporosity may intensify water cycle. Nature 651, 100–103 (2018). https://doi.org/10.1038/s41596.018.0463.x

  101. Hobbie, J.E., Hobbie, E.A.: Microbes in nature are limited by carbon and energy: the starving-survival lifestyle in soil and consequences for estimating microbial rates. Front. Microbiol. (2013). https://doi.org/10.3389/fmicb.2013.00324

  102. Howard-Varona, C., Hargreaves, K.R., Abedon, S.T., Sullivan, M.B.: Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 11, 1511–1520 (2017). https://doi.org/10.1038/ismej.2017.16

    Article  Google Scholar 

  103. Hu, Z., Wessels, H.J.C.T., van Alen, T., Jetten, M.S.M., Kartal, B.: Nitric oxide-dependent anaerobic ammonium oxidation. Nat. Commum. 10, 1244 (2019). https://doi.org/10.1038/s41467-019-09268-w

    Article  CAS  Google Scholar 

  104. Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman Finstad, K.M., Amundson, R., Thomas, B.C., Banfield, J.F.: A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016). https://doi.org/10.1038/nmicrobiol.2016.48

  105. Humphrey, P.T., Nguyen, T.T., Villalobos, M.M., Whiteman, N.K.: Diversity and abundance of phyllosphere bacteria are linked to insect herbivory. Mol. Ecol. 23, 1497–1515 (2014). https://doi.org/10.1111/mec.12657

    Article  CAS  Google Scholar 

  106. Humphreys, I.R., Sebastian, S.: Novel viral vectors in infectious diseases. Immunology 153, 1–9 (2018). https://doi.org/10.1111/imm.12829

    Article  CAS  Google Scholar 

  107. Hyman, P., Abedon, S.T. (eds.): Viruses of Microorganisms. Caister Academic Press (2018). https://doi.org/10.21775/9781910190852

  108. Igler, C., Abedon, S.T.: Commentary: a host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Front. Microbiol. 10, 1171 (2019). https://doi.org/10.3389/fmicb.2019.01171

    Article  Google Scholar 

  109. Ito, A., Oikawa, T.: Global mapping of terrestrial primary productivity and light-use efficiency with a process-based model. In: Shiyomi, M., et al. (eds.), Global Environmental Change in the Ocean and on Land, TERRAPUB, pp. 343–358 (2004)

    Google Scholar 

  110. Iwami, S., Holder, B.P., Beauchemin, C.A.A., et al.: Quantification system for the viral dynamics of a highly pathogenic simian/human immunodeficiency virus based on an in vitro experiment and a mathematical model. Retrovirology 9, 18 (2012). https://doi.org/10.1186/1742-4690-9-18

    Article  Google Scholar 

  111. Jackson, W.T., Coyne, C.B. (eds.): Enteroviruses: Omics, Molecular Biology, and Control (2018). Caister Academic Press. https://doi.org/10.21775/9781910190739

  112. Jackson, R.B., Mooney, H.A., Schulze, E.-D.: A global budget for fine root biomass, surface area, and nutrient contents. Proc. Natl. Acad. Sci. USA 94, 7362–7366 (1997). www.pnas.org

  113. Jacoby, R., Peukert, M., Succurro, A., Koprivova, A., Kopriva, S.: The role of soil microorganisms in plant mineral nutrition—current knowledge and future directions. Front Plant. Sci. 8, 1617 (2017). https://doi.org/10.3389/fpls.2017.01617

    Article  Google Scholar 

  114. Jan, P., Calabrese, C., Lips, M.: Determinants of nitrogen surplus at farm level in Swiss agriculture. Nutr. Cycl. Agroecosyst. 109, 133–148 (2017). https://doi.org/10.1007/s10705-017-9871-9

    Article  Google Scholar 

  115. Jeltsch, A.: Oxygen, epigenetic signaling, and the evolution of early life. Trends Biochem. Sci. 38, 172–176 (2013). https://doi.org/10.1016/j.tibs.2013.02.001

    Article  CAS  Google Scholar 

  116. Jover, L.F., Effler, T.C., Buchan, A., Wilhelm, S.W., Weitz, J.S.: The elemental composition of virus particles: implications for marine biogeochemical cycles. Nat. Rev. Microbiol. 12, 519–528 (2014). https://doi.org/10.1038/nrmicro3289

  117. Karlen, D.L., Lal, R., Follett, R.F., Kimble, J.M., Hatfield, J.L., Miranowski, J.M., Cambardella, C.A., Manale, A., Anex, R.P., Rice, C.W.: Crop residues: the rest of the story. Environ. Sci. Technol. 43, 8011–8015 (2006). https://doi.org/10.1021/es9011004

    Article  CAS  Google Scholar 

  118. Katzourakis, A., Gifford, R.J.: Endogenous viral elements in animal genomes. PLoS Genet. 6, e1001191 (2010). https://doi.org/10.1371/journal.pgen.1001191

    Article  CAS  Google Scholar 

  119. Keen, E.C.: A century of phage research: Bacteriophages and the shaping of modern biology. BioEssays 37, 6–9 (2015). https://doi.org/10.1002/bies.20140015230

    Article  Google Scholar 

  120. Keil, D., Meyer, A., Berner, D., Poll, C., Schützenmeister, A., Piepho, H.P., VlasenkoA, Philippot L., Schloter, M., Kandeler, E., Marhan, S.: Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils. FEMS Microbiol. Ecol. 77, 95–106 (2011). https://doi.org/10.1111/j.1574-6941.2011.01091.x ( Epub 2011 Apr 15)

    Article  CAS  Google Scholar 

  121. Khalifa, M.E., MacDiarmid, R.M.: A novel totivirus naturally occurring in two different fungal genera. Front. Microbiol. (2019). https://doi.org/10.3389/fmicb.2019.02318

  122. Kim, K.-H., Chang, H.-W., Nam, Y.-D., Roh, S.W., Kim, M.-S., Sung, Y., Jeon, C.O., Oh, H.-M., Bae, J.-W.: Amplification of uncultured single-stranded DNA viruses from rice paddy soil Appl. Environm. Microbiol. 74, 5975–5985 (2008). https://doi.org/10.1128/aem.01275-08

    Article  CAS  Google Scholar 

  123. Kimura, M., Jia, Z.-J., Nakayama, N., Asakawa, S.: Ecology of viruses in soils: past, present and future perspectives (Review). J. Plant Nutr. Soil Sci. 4, 1–32 (2008). https://doi.org/10.1111/j.747-0765.2007.00197.x

    Article  Google Scholar 

  124. Kits, K.D., Jung, M., Vierheilig, J., Pjevac, P., Sedlacek, C.J., Liu, S., Herbold, C., Stein, L.Y., Richter, A., Wissel, H., Brüggemann, N., Wagner, M., Holger, D.: Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata. Nat. Commun. 10, 1836 (2019). https://doi.org/10.1038/s41467-019-09790-x

  125. De Klein, C.A.M., Monaghan, R.M.: The effect of farmland catchment management on nitrogen transformations and N2O losses from pastoral systems—can we offset the effects of future intensification? Curr. Opin. Environ. Sustain. 3, 396–406 (2011). https://doi.org/10.1016/j.cosust.2011.08.002

    Article  Google Scholar 

  126. Klein, D.A.: Diversity of chytrids in biodiversity. In: Benckiser, G., Schnell, S. (eds.) Biodiv. Agricult. Product. Syst. Taylor and Francis, Boca Raton (2007)

    Google Scholar 

  127. Koch, H., Lücker, S., Albertsen, M., Kitzinger, K., Herbold, C., Spieck, E., Nielsen, P.H., Wagner, M., Daims, H.: Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. PNAS 112, 11371–11376 (2015). https://doi.org/10.1073/pnas.1506533112

    Article  CAS  Google Scholar 

  128. Koonin, E.V., Dolja, V.V., Krupovic, M.: Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology 479–480, 2–25 (2015). https://doi.org/10.1016/j.virol.2015.02.039

    Article  CAS  Google Scholar 

  129. Kristiansen, J., Škaloud, P.: Chrysophyta. In: Archibald, J., Simpson, A., Slamovits, C. (eds) Handbook of the Protists. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-28149-0_43

  130. Krupp, F., Said, N., Huang, Y.-H., Loll, B., Bürger, J., Mielke, T., Spahn, C.M.T., Wahl, M.C.: Structural basis for the action of an all-purpose transcription anti-termination factor. Mol. Cell 74, 143–157.e5 (2019). https://doi.org/10.1016/j.molcel.2019.01.016

    Article  CAS  Google Scholar 

  131. Kuzyakov, Y., Mason-Jones, K.: Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemic turnover and ecosystem functions. Soil Biol. Biochem 127, 305–317 (2018). https://doi.org/10.1016/j.soilbio.2018.09.032

  132. Lander, E.S.: (International Human Genome Sequencing Consortium, 2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001). https://doi.org/10.1038/35057062

    Article  CAS  Google Scholar 

  133. Lane, D.J.R., Bae, D.-H., Siafakas, A.R., Rahmanto, Y.S., Al-Akra, L., Jansson, P., Casero, Jr, R.A., Richardson, D.R.: Coupling of the polyamine and iron metabolism pathways in the regulation of proliferation: Mechanistic links to alterations in key polyamine biosynthetic and catabolic enzymes. Biochim. Biophys. Acta (BBA) Mol. Basis Dis. 1864, 2793–2813 (2018). https://doi.org/10.1016/j.bbadis.2018.05.007

  134. Lavelle, P., Decaëns, T., Aubert, M., Barot, S., Blouin, M., Bureau, F., Margerie, P., Mora, P., Rossi, J.-P.: Soil invertebrates and ecosystem services. Eur. J. Soil Biol. 42(supplement 1), S3–S15 (2006). https://doi.org/10.1016/j.ejsobi.2006.10.002

    Article  Google Scholar 

  135. Lee, B.Y., Wiringa, A.E., Bailey, R.R., Goyal, V., Tsui, B., Lewis, G.J., Muder, R.R., Harrison, L.M.: The economic effect of screening orthopedic surgery patients preoperatively for methicillin‐resistant Staphylococcus aureus. Infect. Control Hosp. Epidemiol. 30, 130–1138 (2010). https://doi.org/10.1086/657969

  136. Lefeuvre, P., Martin, D.P., Elena, S.F., Shepherd, D.N., Roumagnac, P., Varsani, A.: Evolution and ecology of plant viruses. Nat. Rev. Microbiol. 17, 632–644 (2019). https://doi.org/10.1038/s41579-019-0232-3

    Article  CAS  Google Scholar 

  137. Li, Y., Wu, J., Shen, J., Liu, S., Wang, C., Chen, D., Huang, T., Zhang, J.: Soil microbial C: N ratio is a robust indicator of soil productivity for paddy fields. Sci. Rep. 6, 35266 (2016). https://doi.org/10.1038/srep35266

    Article  CAS  Google Scholar 

  138. Li, P., Lin, H., Mi, Z.: Screening of polyvalent phage-resistant Escherichia coli strains based on phage receptor analysis. Front. Microbiol. (2019). https://doi.org/10.3389/fmicb.2019.00850

  139. Liang, X., Radosevich, M.: Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Front. Microbiol. 10, 1201 (2019). https://doi.org/10.3389/fmicb.2019.01201

    Article  Google Scholar 

  140. Liang, X., Zhuang, J., Löffler, F.E., Zhang, Y., DeBruyn, J.M., Wilhelm, S.W., et al.: Viral and bacterial community responses to stimulated Fe(III)-bioreduction during simulated subsurface bioremediation. Environ. Microbiol. 2019, 14566 (2019). https://doi.org/10.1111/1462-2920.14566

    Article  CAS  Google Scholar 

  141. Liao, J.B.: Viruses and human cancer. Yale J. Biol. Med. 79, 115–122 (2006) published online 2007

    Google Scholar 

  142. Lindow, S.E., Brandl, M.T.: Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875–1883 (2003). https://doi.org/10.1128/aem.69.4.1875-1883.2003

    Article  CAS  Google Scholar 

  143. Liu, M., Deora, R., Doulatov, S.R., et al.: Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295, 2091–2094 (2002). https://doi.org/10.1126/science.1067467

    Article  CAS  Google Scholar 

  144. Liu, B., Zhang, X., Bakken, L., Snipen, L.-G., Frostegård, Å.: Rapid succession of actively transcribing denitrifier populations in agricultural soil during an anoxic spell. Front. Microbiol. (2019). https://doi.org/10.3389/fmicb.2018.03208)

  145. Lovley, D.R., Walker, D.J.F.: Geobacter Protein Nanowires. Front. Microbiol. (2010). https://doi.org/10.3389/fmicb.2019.02078

  146. Lozano, R., Naghavi, M., Foreman, K., Lim, S., Shibuya, K., Aboyans, V., Abraham, J., Adair, T., Aggarwal, R., Ahn, S.Y., Alvarado, M., Anderson, H.R., Anderson, L.M., Andrews, K.G., Atkinson, C., Baddour, L.M., Barker-Collo, S., Bartels, D.H., Bell, M.L., Benjamin, E.J., Bennett, D., Bhalla, K., Bikbov, B., Bin Abdulhak, A., Birbeck, G., Blyth, F., Bolliger, I., Boufous, S., Bucello, C., Burch, M., Burney, P., Carapetis, J., Chen, H., Chou, D., Chugh, S.S., Coffeng, L.E., Colan, S.D., Colquhoun, S., Colson, K.E., Condon, J., Connor, M.D., Cooper, L.T., Corriere, M., Cortinovis, M., de Vaccaro, K.C., Couser, W., Cowie, B.C., Criqui, M.H., Cross, M., Dabhadkar, K.C., Dahodwala, N., De Leo, D., Degenhardt, L., Delossantos, A., Denenberg, J., Des Jarlais, D.C., Dharmaratne, S.D., Dorsey, E.R., Driscoll, T., Duber, H., Ebel, B., Erwin, P.J., Espindola, P., Ezzati, M., Feigin, V., Flaxman, A.D., Forouzanfar, M.H., Fowkes, F.G., Franklin, R., Fransen, M., Freeman, M.K., Gabriel, S.E., Gakidou, E., Gaspari, F., Gillum, R.F., Gonzalez-Medina, D., Halasa, Y.A., Haring, D., Harrison, J.E., Havmoeller, R., Hay, R.J., Hoen, B., Hotez, P.J., Hoy, D., Jacobsen, K.H., James, S.L., Jasrasaria, R., Jayaraman, S., Johns, N., Karthikeyan, G., Kassebaum, N., Keren, A., Khoo, J.P., Knowlton, L.M., Kobusingye, O., Koranteng, A., Krishnamurthi, R., Lipnick, M., Lipshultz, S.E., Ohno, S.L., Mabweijano, J., MacIntyre, M.F., Mallinger, L., March, L., Marks, G.B., Marks, R., Matsumori, A., Matzopoulos, R., Mayosi, B.M., McAnulty, J.H., McDermott, M.M., McGrath, J., Mensah, G.A., Merriman, T.R., Michaud, C., Miller, M., Miller, T.R., Mock, C., Mocumbi, A.O., Mokdad, A.A., Moran, A., Mulholland, K., Nair, M.N., Naldi, L., Narayan, K.M., Nasseri, K., Norman, P., O’Donnell, M., Omer, S.B., Ortblad, K., Osborne, R., Ozgediz, D., Pahari, B., Pandian, J.D., Rivero, A.P., Padilla, R.P., Perez-Ruiz, F., Perico, N., Phillips, D., Pierce, K., Pope 3rd, C.A., Porrini, E., Pourmalek, F., Raju, M., Ranganathan, D., Rehm, J.T., Rein, D.B., Remuzzi, G., Rivara, F.P., Roberts, T., De León, F.R., Rosenfeld, L.C., Rushton, L., Sacco, R.L., Salomon, J.A., Sampson, U., Sanman, E., Schwebel, D.C., Segui-Gomez, M., Shepard, D.S., Singh, D., Singleton, J., Sliwa, K., Smith, E., Steer, A., Taylor, J.A., Thomas, B., Tleyjeh, I.M., Towbin, J.A., Truelsen, T., Undurraga, E.A., Venketasubramanian, N., Vijayakumar, L., Vos, T., Wagner, G.R., Wang, M., Wang, W., Watt, K., Weinstock, M.A., Weintraub, R., Wilkinson, J.D., Woolf, A.D., Wulf, S., Yeh, P.H., Yip, P., Zabetian, A., Zheng, Z.J., Lopez, A.D., Murray, C.J., AlMazroa, M.A., Memish, Z.A.: Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 380, 2095–2128 (2012). https://doi.org/10.1016/s0140-6736(12)61728-0.ErratuminLancet2013381,628

    Article  Google Scholar 

  147. Ludescher, J., Bunde, A., Schellnhuber, H.J.: Statistical significance of seasonal warming/cooling trends. PNAS 114, E2998–E3003 (2017). https://doi.org/10.1073/pnas.1700838114

  148. Madawala, H.M.S.P.: Soil-plant microbiome: a promising frontier for research. Ceylon J. Sci. 48, 195–196 (2019). https://doi.org/10.4038/cjs.v48i3.7642

    Article  Google Scholar 

  149. Marsh, M., Helenius, A.: Virus entry: open sesame. Cell 124, 729–740 (2006). https://doi.org/10.1016/j.cell.2006.02.0074

    Article  CAS  Google Scholar 

  150. Martiny, A.C.: High proportions of bacteria are culturable across major biomes. ISME J. 4, 2125–8 (2019). https://doi.org/10.1038/s41396-019-0410-3

    Article  Google Scholar 

  151. Martínez-García, M., Santos, F., Moreno-Paz, M., Parro, V., Antón, J.: Unveiling viral–host interactions within the ‘microbial dark matter’. Nat. Commun. 5, 4542 (2014). https://doi.org/10.1038/ncomms5542

  152. Maruyama, F., Ueki. S.: Evolution and phylogeny of large DNA viruses, Mimiviridae and Phycodnaviridae including newly characterized Heterosigma akashiwo virus. Front. Microbiol. 7, 1942 (2016). https://doi.org/10.3389/fmicb.2016.01942

  153. Mateo-Sagasta, J., Raschid-Sally, L., Thebo, A.: Global wastewater and sludge production, treatment and use. In: Drechse, l.P., et al. (eds.) Wastewater (2015). Springer Science + Business Media, Dordrecht. https://doi.org/10.1007/978-94-017-9545-6_2

  154. Mateo-Sagasta, J., Zadeh, S.M., Turral, H.: Water Pollution from Agriculture: A Global Review. FAO, Rome (2017). www.fao.org/land-water/overview/globalframework/global-framework, and IWMI, Colombo, www.iwmi.cgiar.org

  155. McCaig, A.E., Griffiths, B.S., Prosser, J.I.: Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl. Environ. Microbiol. 68, 6094–6105 (2002). https://doi.org/10.1128/aem.68.12.6094-6105.2002

    Article  Google Scholar 

  156. McLellan, E.L., Cassman, K.G., Eagle, A.J., Woodbury, P.B., Sela, S., Tonitto, C., Marjerison, R.D., van Es H.M.: The nitrogen balancing act: Tracking the environmental performance of food production. BioScience 68, 194–203 (2018). https://doi.org/10.1093/biosci/bix164

  157. Medina, G.N., Díaz-San Segundo, F., Stenfeldt, C., et al.: The different tactics of foot-and-mouth disease virus to evade innate immunity. Front. Microbiol. (2018). https://doi.org/10.3389/fmicb.2018.02644

  158. Meng, Z., Li, X., Wang, H., Deng, F., Li, X., Mi, X.: Effects of converting natural grasslands into planted grasslands on ecosystem respiration: a case study in Inner Mongolia. China J. Arid Land 9, 38–50 (2017). https://doi.org/10.1007/s40333-016-0059-y

    Article  Google Scholar 

  159. Middelboe, M., Brussaard, C.P.D.: Marine viruses: key players in marine ecosystems. Viruses 9, 302 (2017). https://doi.org/10.3390/v9100302

    Article  Google Scholar 

  160. Middelboe, M., Jørgensen, N.O.G.: Viral lysis of bacteria: an important source of dissolved amino acids and cell wall compounds. J. Mar. Biol. Ass. UK, 86, 605–661 (2006). http://dx.doi.org/0.1017/S0025315406013518

  161. Millen, S., Gross, C., Donhauser, N., Mann, M.C., Péloponèse, Jr., J.-M., Thoma-Kress, A.K.: Collagen IV (COL4A1, COL4A2), a component of the viral biofilm, is induced by the HTLV-1 Oncoprotein Tax and impacts virus transmission. Front. Microbiol. 23 (2019). https://doi.org/10.3389/fmicb.2019.02439

  162. Mosier, A., Parkin, T.: Gaseous emissions (CO2, CH4, N2O and NO) from diverse agricultural soils. In: Benckiser, G., Schnell, S. (eds.) Biodiversity in Agricultural Production Systems, pp. 317–348. Taylor and Francis, Boca Raton pp (2007)

    Google Scholar 

  163. Mougari, S., Bekliz, M., Abrahao, J., et al.: Guarani Virophage, a new sputnik-like isolate from a Brazilian lake. Front. Microbiol. (2019). https://doi.org/10.3389/fmicb.2019.01003

  164. Mundepi, A., Cabrera, M., Norton, J., Habteselassie, M.: Ammonia oxidizers as biological health indicators of elevated Zn and Cu in poultry litter amended soil. Water Air Soil Pollut. 230, 239 (2019). https://doi.org/10.1007/s11270-019-4283-x

  165. Nacry, P., Bouguyon, E., Gojon, A.: Nitrogen acquisition by roots: physiological and developmental mechanisms ensuring plant adaptation to a fluctuating resource. Plant Soil 370, 1–29 (2013). https://doi.org/10.1007/s11104-013-1645-9

  166. Nakatsukasa-Akune, M., Yamashita, K., Shimoda, Y., et al.: Suppression of root nodule formation by artificial expression of the TrEnodDR1 (coat protein of White clover cryptic virus 1) gene in Lotus japonicus. Mol. Plant Microbe Interact. 18, 1069–1080 (2005). https://doi.org/10.1094/mpmi-18-1069

    Article  CAS  Google Scholar 

  167. Naumov, A.: New relationship in carbon cycle. Low Carbon Econ. 3, 111–114 (2012). https://doi.org/10.4236/lce.2012.323015

    Article  Google Scholar 

  168. Newbold, C.J., de la Fuente, G., Belanche, A., Ramos-Morales, E., McEwan, N.R.: The role of ciliate protozoa in the rumen. Front Microbiol. 6, 1313 (2015). https://doi.org/10.3389/fmicb.2015.01313

    Article  Google Scholar 

  169. Ni, T., Zeng, Q.: Diel Infection of Cyanobacteria by Cyanophages. Front. Mar. Sci. 2, 123 (2016). https://doi.org/10.3389/fmars.2015.0012311

    Article  Google Scholar 

  170. Opitz v. Boberfeld, W. Grünlandlehre - biologische und ökologische Grundlagen, Ulmer, Germany (1994)

    Google Scholar 

  171. Osiander, C.N., Tafel, G.L.F., Schwab, G. (Hrsg.): First edition of Xenophon’s von Athen Werke, Band 40, Von der Haushaltskunst und Hiero oder Herrscherleben. Publisher Metzler JB, Stuttgart, – In: Griechische Prosaiker in neuen Uebersetzungen (1831). https://www.booklooker.de›Bücher›Angebote›titel=Griechische+Prosai

    Google Scholar 

  172. De Paepe, M., Taddei, F.: Viruses’ life history: towards a mechanistic basis of a trade-off between survival and reproduction among phages. PLoS Biol. 4, e273 (2006). https://doi.org/10.1371/journal.pbio.0040193

    Article  CAS  Google Scholar 

  173. Paez-Espino, D., Chen, I.A., Palaniappan, K., et al.: IMG/VR: a database of cultured and uncultured DNA viruses and retroviruses. Nucl. Acids Res. 45, D457–D465 (2017). https://doi.org/10.1093/nar/gkw1030

    Article  CAS  Google Scholar 

  174. Paez-Espino, D., Eloe-Fadrosh, E.A., Pavlopoulos, G.A., Thomas, A.D., Huntemann, M., Mikhailova, N., Rubin, E., Ivanova, N.N., Kyrpides, N.C.: Uncovering Earth’s virome Nature 536, 425–430 (2016). https://doi.org/10.1038/nature19094

    Article  CAS  Google Scholar 

  175. Palatinszky, M., Herbold, C., Jehmlich, N., Pogoda, M., Han, P., von Bergen, M., Lagkouvardos, I., Karst, S.M., Galushko, A., Koch, H., Berry, D., Daims, H., Wagner, M.: Cyanate as an energy source for nitrifiers. Nature 524, 105–108 (2015). https://doi.org/10.1038/nature14856

  176. Parker, M.T.: An ecological framework of the human virome provides classification of current knowledge and identifies areas of forthcoming discovery. Yale J. Biol. Med. 89, 339–351 PMC5045143 (2016)

    Google Scholar 

  177. Parton, W.J., Scurlock, J.M.O., Ojima, D.S., Schimel, D.S., Hall, D.O., Scopegram Group Members: impact of climate change on grassland production and soil carbon worldwide. Global Change Biol. 1, 13–22 (1995). https://doi.org/10.1111/j.1365-2486.1995.tb00002.x

  178. Parvathi, A., Jasna, V., Aparna, S., Ram, A.S.P., Aswathy, V.K., Balachandran, K.K., Muraleedharan, K.R., Mathew, D., Sime-Ngando, T.: High incidence of lysogeny in the oxygen minimum zones of the Arabian Sea (Southwest Coast of India). Viruses 10, 588 (2018). https://doi.org/10.3390/v10110588

  179. Pavlopoulos, G.A., Thomas, A.D., Huntemann, M., et al.: Uncovering Earth’s virome. Nature 536, 425–430 (2016). https://doi.org/10.1038/nature19094

    Article  CAS  Google Scholar 

  180. Personnic, S., Domaizon, I., Sime-Ngando, T., Jacquet, Stéphan: Seasonal variations of microbial abundances and virus- versus flagellate-induced mortality of picoplankton in three peri-alpine lakes. J. Plankton Res. 31, 1161–1177 (2009). https://doi.org/10.1093/plankt/fbp057

    Article  Google Scholar 

  181. Petersen, J.M.: Microbiomes In Natura: Importance of Invertebrates in understanding the natural variety of animal-microbe interactions-host-microbe biology. mSystems 3, e00179–1713 (2018). https://doi.org/10.1128/msystems.00179-17

    Article  Google Scholar 

  182. Powel, J.M., Barros, T., Danes, M., et al.: Nitrogen use efficiencies to grow, feed, and recycle manure from the major diet components fed to dairy cows in the USA. Agri. Ecosyst. Environ. 239, 274–282 (2017). https://doi.org/10.1016/j.agee.2017.01.023

    Article  Google Scholar 

  183. Quipot, L.M.G.: ANMI fights off a vampire insect. Rice Today 11, 16–17 (2012)

    Google Scholar 

  184. Ramirez, K.S., Leff, J.W., Barberán, A.., Bates, S.T., Betley, J., Crowther, T.W., Kelly, E.R., Oldfield, E.E., Shaw, E.A., Steenbock, C., Bradford, M.A., Wall, D.H., Fierer, N.: Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc. R. Soc. B 281 (2014). https://doi.org/10.1098/rspb.2014.1988

  185. Raynaud, X., Nunan, N.: Spatial ecology of bacteria at the microscale in soil. Plos 9, e87217 (2014). https://doi.org/10.1371/journal.pone.0087217

    Article  CAS  Google Scholar 

  186. Reavy, B., Swanson, M.M., Cock, P.J.A., Dawson, L., Freitag, T.E., Singh, B.K., Torrance, L., Mushegian, A.R., Taliansky, M.: Distinct circular single-stranded DNA viruses exist in different soil types. Appl. Environm. Microbiol. 81, 3934–3945 (2015). https://doi.org/10.1128/aem.03878-14

  187. Renou-Wilson, F., Barry, C., Müller, C., Wilson, D.: The impacts of drainage, nutrient status and management practice on the full carbon balance of grasslands on organic soils in a maritime temperate zone. Biogeoscience 11, 4361–4379 (2014). https://doi.org/10.5194/bg-11-4361-2014

    Article  CAS  Google Scholar 

  188. Reynolds, D., Bowman, B.T., Drury, C.F., Tan, C.S., Lu, X.: Indicators of good soil physical quality: density and storage parameters. Geoderma 110, 131–146 (2002). https://doi.org/10.1016/s0016-7061(02)00228-8

    Article  CAS  Google Scholar 

  189. Reynolds, D., Drury, C.F., Tan, C.S., Fox, C.A., Yang, X.: Use of indicators of pore volume-function characteristics to quantify soil physical quality. Geoderma 152, 252–263 (2009). https://doi.org/10.1016/j.geoderma.2009.06.009

    Article  Google Scholar 

  190. Richert-Pöggeler, K.R., Franzke, K., Hipp, K., Kleespies, R.G.: Electron microscopy methods for virus diagnosis and hgh resolution analysis of viruses. Front. Microbiol. 9, 3255 (2019). https://doi.org/10.3389/fmicb.2018.03255

    Article  Google Scholar 

  191. Rodrigues, R.A.L., Andrade, A.C.S.P., Boratto, P.V.M., Trindade, G.S., Kroon, Erna G., Abrahão, J.S.: An anthropocentric view of the Virosphere-Host Relationship. Front. Microbiol. (2017). https://doi.org/10.3389/fmicb.2017.01673

    Article  Google Scholar 

  192. Rohwer, F., Thurber, R.V.: Viruses manipulate the marine environment. Nature 459, 207–212 (2009). https://doi.org/10.1038/nature08060

    Article  CAS  Google Scholar 

  193. Rollins, M.C.F., Chowdhury, S., Carter, J., Golden, S.M., Miettinen, H.M., Santiago-Frangos, A., Faith, D., Lawrence, C.M., Lander, G.C., Wiedenheft, B.: Structure reveals a mechanism of CRISPR-RNA-guided nuclease recruitment and Anti-CRISPR viral mimicry. Mol. Cell 132–142, e5 (2019). https://doi.org/10.1016/j.molcel.2019.02.001

    Article  CAS  Google Scholar 

  194. Roossinck, M.J.: Move over, bacteria! Viruses make their mark as mutualistic microbial symbionts. J. Virol. 89, 6532–6535 (2015). https://doi.org/10.1128/jvi.02974-14

    Article  CAS  Google Scholar 

  195. Roossinck, M.J.: Plants, viruses and the environment: ecology and mutualism. Virology 479–480, 271–277 (2015). https://doi.org/10.1016/j.virol.2015.03.041

    Article  CAS  Google Scholar 

  196. Rosario, K., Nilsson, C., Lim, Y.W., Ruan, Y., Breitbart, M.: Metagenomic analysis of viruses in reclaimed water. Environ. Microbiol. 11, 2806–2820 (2009). https://doi.org/10.1111/j.1462-2920.2009.01964.x

    Article  CAS  Google Scholar 

  197. Roux, S., Enault, F., Robin, A., Ravet, V., Personnic, S., Theil, S., Colombet, J., Sime-Ngando, T., Debroas, D.: Assessing the diversity and specificity of two freshwater viral communities through metagenomics. Plos (2012). https://doi.org/10.1371/journal.pone.0033641

  198. Roux, S., Adriaenssens, E.M., Dutilh, B.E., Koonin, E.V., Kropinski, A.M., Krupovic, M., Kuhn, J.H., Lavigne, R.J., Brister, R., Varsani, R.: Minimum information about an uncultivated Virus Genome (MIUViG). Nat. Biotech. 37, 29–37 (2019). https://doi.org/10.1038/nbt.4306.pasteur-01977322

  199. Russell, J.B., Rychlik, J.L.: Factors that alter rumen microbial ecology. Science 292, 1119–1122 (2001). https://doi.org/10.1126/science.1058830

    Article  CAS  Google Scholar 

  200. Röder, J., Dickmeis, C., Commandeur, U.: Small, smaller, nano: new applications for potato virus X in nanotechnology. Front. Plant. Sci. 10, 158 (2019). https://doi.org/10.3389/fpls.2019.00158

  201. Saleem, M., Fetzer, I., Harms, H., Chatzinotas, A.: Diversity of protists and bacteria determines predation performance and stability. ISME J. 7, 1912–1921 (2013). https://doi.org/10.1038/ismej.2013.95)

    Article  Google Scholar 

  202. Sanjuán, R.: Collective infectious units in viruses. Trends Microbiol. 25, 402–412 (2017). https://doi.org/10.1038/ismej.2017.16

    Article  Google Scholar 

  203. Scheer, C., Rowlings, D., Firrell, M., Deuter, P., Morris, S., Riches, D., Porter, I., Grace, P.: Nitrification inhibitors can increase post-harvest nitrous oxide emissions in an intensive vegetable production system. Sci. Rep. 7, 43677 (2017). https://doi.org/10.1038/srep43677

    Article  Google Scholar 

  204. Schiemann, J., Paape, M., Kellmann, J.W.: Erreger auf Wanderschaft: Transportproteine verraten pflanzenpathogenen Viren den Weg von Zelle zu Zelle. Bioforum 30, 22–25 (2007)

    CAS  Google Scholar 

  205. Schils, R., Velthof, G., Mucher, S., Hazeu, G., Oenema, O., de Wit, A., Smit, A.: Current methods to estimate grassland production and biological fixation. Alterra Final Report Task 2 March 2014.docx Alterra, info.alterra@wur.nl (2013)

    Google Scholar 

  206. Schlüter, S., Henjes, S., Zawallich, J., Bergaust, L., Horn, M., Ippisch, O., Vogel, H.-J., Dörsch, P.: Denitrification in soil aggregate analogues-effect of aggregate size and oxygen diffusion. Front. Environ. Sci. (2018). https://doi.org/10.3389/fenvs.2018.00017)

  207. Schmid, M., Speiseder, T., Dobner, T., Gonzalez, R.A.: Virus-cell interactions DNA virus replication compartments. J. Int. Virol. 88, 1404–1420 (2014). https://doi.org/10.1128/jvi.02046-13

    Article  Google Scholar 

  208. Schroeck, A.M., GaubeV, Haas E., Winiwarter, W.: Estimating nitrogen flows of agricultural soils at a landscape level—a modelling study of the Upper Enns Valley, a long-term socio-ecological research region in Austria. Sci. Total Environ. 665, 275–289 (2019). https://doi.org/10.1016/j.scitotenv.2019.02.071

    Article  CAS  Google Scholar 

  209. Schulze-Makuch, D., Wagner, D., Kounaves, S.P., Mangelsdorf, K., Devine, K.G., de Vera, J.P., Schmitt-Kopplin, P., Grossart, H.P., Parro, V., Kaupenjohann, M., Galy, A., Schneider, B., Airo, A., Frösler, J., Davila, A.F., Arens, F.L., Cáceres, L., Cornejo, F.S., Carrizo, D., Dartnell, L., DiRuggiero, J., Flury, M., Ganzert, L., Gessner, M.O., Grathwohl, P., Guan, L., Heinz, J., Hess, M., Keppler, F., Maus, K.D., McKay, C.P., Meckenstock, R.U., Montgomery, W., Oberlin, E.A., Probst, A.J., Sáenz, J.S., Sattler, T., Schirmack, J., Sephton, M.A., Schloter, M., Uhl, J., Valenzuela, B., Vestergaard, G., Wörmer, L., Zamorano, P.: Transitory microbial habitat in the hyperarid Atacama Desert. PNAS 115, 2670–2675 (2018). https://doi.org/10.1073/pnas.1714341115)

    Article  CAS  Google Scholar 

  210. Seligmann, H., Raoult, D.: Stem-loop RNA hairpins in giant viruses: invading rRNA-like repeats and a template free RNA. Front. Microbiol. 9, 101 (2018). https://doi.org/10.3389/fmicb.2018.00101b

    Article  Google Scholar 

  211. Sharma, D., Misba, L., Khan, A.U.: Antibiotics versus biofilm: an emerging battleground in microbial communities. Antimicrob. Resist. Infect. Control. 8, 76 (2019). https://doi.org/10.1186/s13756-019-0533-3

    Article  Google Scholar 

  212. Shestakov, S.V., Karbysheva, E.A.: The role of viruses in the evolution of cyanobacteria. Biol. Bull. Rev. 5, 527–537 (2015). https://doi.org/10.1134/s2079086415060079

  213. Sikorski, J.: The prokaryotic biology of soil. Soil Organ. 87, 1–28 (2015)

    Google Scholar 

  214. Silpe, J.E., Bassler, B.L.: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell 176, 268–280 (2019). https://doi.org/10.1016/j.cell.2018.10.059

    Article  CAS  Google Scholar 

  215. Sime-Ngando, T.: Environmental bacteriophages: viruses of microbes in aquatic ecosystems. Front. Microbiol. (2014). https://doi.org/10.3389/fmicb.2014.00355

  216. Simpson, A., Slamovits, C., Archibald, J.M.: Protist diversity and eukaryote phylogeny. In: Archibald, J., Simpson, A., Slamovits, C. (eds.) Handbook of the Protists. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-28149-0_45

  217. Sochorec, M., Jandák, J., Raus, J., Kvasnovský, M., Hejduk, S., Knot, P.: Influence of different grassland management on water infiltration and soil physical properties Bulgarian. J. Agricult. Sci. 21, 573–578 (2015)

    Google Scholar 

  218. Song, W., Xiaojuan, T., Jinsong, Z., Meng, P., Jun, L.: Autotrophic and heterotrophic components of soil respiration caused by rhizosphere priming effects in a plantation. Plant. Soil. Environ. 63, 295–299 (2017). https://doi.org/10.17221/233/2017-PSE

  219. Srinivasiah, S., Lovett, J., Polson, S., Bhavsar, S., Ghosh, D., Roy, K., Fuhrmann, J.J., Radosevich, M., Wommack, K.: Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA. Appl. Environ. Microbiol. 79, 5450–5457 (2013). https://doi.org/10.1128/AEM.00268-13

  220. Staege, M.S., Emmer, A.: Endogenous viral elements—links between autoimmunity and cancer? Front. Microbiol. (2018). https://doi.org/10 3389/fmicb.201801371

    Google Scholar 

  221. Stahl, A., Vollrath, P., Samans, B., Frisch, M., Wittkop, B., Snowdon, R.J.: Effect of breeding on nitrogen use efficiency-associated traits in oilseed rape. J. Exp. Bot. 70, 1969–1986 (2019). https://doi.org/10.1093/jxb/erz044 https://doi.org/10.1080/1343943X.2019.1617638

  222. Steen, A.D., Crits-Christoph, A., Carini, P., DeAngelis, K.M., Fierer, N., Lloyd, K.G., Cameron Thrash, J.: High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. (2019). https://doi.org/10.1038/s41396-019-0484-y

  223. Steidinger, B.S., Crowther, T.W., Liang, J., Van Nuland, M.E., Werner, G.D.A.., Reich, P.B., Nabuurs, G., de-Miguel, S., Zhou, M., Picard, N., Herault, B., Zhao, X., Zhang, C., Routh, D., Peay, K.G.: Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature 569, 404–408 (2019). https://doi.org/10.1038/s41586-019-1128-0

  224. Stewart, F.M., Levin, B.R.: The population biology of bacterial viruses: why be temperate. Theor. Popul. Biol. 26, 93–117 (1984)

    Article  CAS  Google Scholar 

  225. Stewart, P.S., Franklin, M.J.: Physiological heterogeneity in biofilms. Nat. Rev. Microbiol. 6, 99–210 (2008). https://doi.org/10.1038/nrmicro1838

  226. Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M., Horn, M., Daims, H., Bartol-Mavel, D., Wincker, P., Barbe, V., Fonknechten, N., Vallenet, D., Segurens, B., Schenowitz-Truong, C., Médigue, C., Collingro, A., Snel, B., Dutilh, B.E., Op den Camp, H.J.M., van der Drift, C., Cirpus, I., van de Pas-Schoonen, K.T., Harhangi, H.R., van Niftrik, L., Schmid, M., Keltjens, J., van de Vossenberg, J., Kartal, B., Meier, H., Dj, Frishman, Huynen, M.A., Mewes, H.-W., Weissenbach, J., Jetten, M.S.M., Wagner, M., Le Paslier, D.: Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440, 790–794 (2006). https://doi.org/10.1038/nature04647

    Article  Google Scholar 

  227. Tebbe, C.C., Schloter, M.: Discerning the diversity of soil prokaryotes (bacteriaand archaea) and their impact on agriculture. In: Benckiser, G., Schnell, S. (eds.) Biodiversity in Agricultural Production Systems, pp. 81–100. Taylor and Francis, Boca Raton pp (2007)

    Google Scholar 

  228. Tennant, P., Fermin, G., Foster, J.E. (eds.): Viruses: Molecular Biology, Host Interactions, and Applications to Biotechnology, p. 224. Academic Press, London (2018)

    Google Scholar 

  229. Thomas, R., Berdjeb, L., Sime-Ngando, T., Jacquet, S.: Viral abundance, production, decay rates and life strategies (lysogeny versus lysis) in Lake Bourget (France). Envron. Microbiol. 13, 616–630 (2011). https://doi.org/10.1111/j.1462-2920.2010.02364.x

    Article  CAS  Google Scholar 

  230. Thompson, L.R., Zeng, Q., Kelly, L., et al.: Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. PNAS 108, 757–764 (2011). https://doi.org/10.1073/pnas.110216410810

    Article  Google Scholar 

  231. Thomson, B.C., Ostle, N.J., McNamara, N.P., Oakley, S., Whiteley, A.S., Bailey, M.J., Griffiths, R.I.: Plant soil interactions alter carbon cycling in an upland grassland soil. Front. Microbiol. (2013). https://doi.org/10.3389/fmicb.2013.00253

  232. Thézé, J., Bézier, A., Periquet, G., Drezen, J.-M., Herniou, E.A.: Paleozoic origin of insect large dsDNA viruses. PNAS 108, 15931–15935 (2011). https://doi.org/10.1073/pnas.1105580108

    Article  Google Scholar 

  233. Torsvik, V., Daae, F.L., Sandaa, R.-A., Øvreås, L.: Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64, 53–62 (1998). https://doi.org/10.1016/s0168-1656(98)00103-5

    Article  CAS  Google Scholar 

  234. Tsujimoto, Y., Rakotoson, T., Tanaka, A., Saito, K.: Challenges and opportunities for improving N use efficiency for rice production in sub-Saharan Africa. Plant Prod. Sci. 22, 413–427 (2019). https://doi.org/10.1080/1343943x.2019.1617638

  235. Turkington, C.J.R., Morozov, A., Clokie, M.R.J., Bayliss, C.D.: phage-resistant phase-variant subpopulations mediate herd immunity against bacteriophage invasion of bacterial meta-populations. Fron Microbiol. (2019). https://doi.org/10.3389/micb.2019.01473

  236. Villamar, C.-A., Vera-Puerto, I., Rivera, D., De la Hoz, F.: Reuse and recycling of livestock and municipal wastewater in Chilean agriculture: a preliminary assessment. Water 10, 817 (2018). https://doi.org/10.3390/w10060817

    Article  Google Scholar 

  237. Vincent, S.J., Coutts, B.A., Jones, R.A.C.: Effects of introduced and indigenous viruses on native plants: exploring their disease causing potential at the agro-ecological interface. PLoS ONE 9, e91224 (2014). https://doi.org/10.1371/journal.pone.0091224

    Article  CAS  Google Scholar 

  238. Vinoth Kumar, R.: Plant antiviral immunity against geminiviruses and viral counter-defense for survival. Front. Microbiol. (2019). https://doi.org/10.3389/fmicb.2019.01460

  239. Vogel, H.J., Babel, U.: Soil space diversity and its dynamics: qualitative and quantitative considerations. In: Benckiser, G., Schnell, S. (eds.) Biodiversity in agricultural production systems. Taylor & Francis, Boca Raton (2007)

    Google Scholar 

  240. Volle, R., Razafindratsimandresy, R., Joffret, M.-L., Bessaud, M., Rabemanantsoa, S., Andriamamonjy, S., Raharinantoanina, J., Blondel, B., Heraud, J.-M., Bailly, J.-L., Francis, Delpeyroux: High permissiveness for genetic exchanges between enteroviruses of species A, including enterovirus 71, favours evolution through intertypic recombination in Madagascar. J Virol. (2019). https://doi.org/10.1128/jvi.01667-18

    Article  Google Scholar 

  241. Vrede, K., Heldal, M., Norland, S., Bratbak, G.: Elemental composition (C, N, P) and cell volume of exponentially growing and nutrient-limited bacterioplankton. Appl. Environ. Microbiol. 68, 965–2971 (2002). https://doi.org/10.1128/aem.68.6.2965-2971.2002

    Article  Google Scholar 

  242. Wagner, M.: Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Ann. Rev. Microbiol. 63: 411–429 (2009). https://doi.org/10.1146/annurev.micro.091208.073233

  243. Wang, P., Xu, J., Wang, Y., Cao, X.: An interferon-independent lncRNA promotes viral replication by modulating cellular metabolism. Science 358, 1051–1055 (2017). https://doi.org/10.1126/science.aao0409

    Article  CAS  Google Scholar 

  244. Weinbauer, W.G.: Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28, 127–181 (2004). https://doi.org/10.1016/j.femsre.2003.08.001

    Article  CAS  Google Scholar 

  245. Weitz, J.S., Dushoff, J.: Alternative stable states in host-phage dynamics. Theor. Ecol 1, 13–19 (2008). https://doi.org/10.1007/s12080-007-0001-1

    Article  Google Scholar 

  246. Weitz, J.S., Wilhelm Steven, W.: Ocean viruses and their effects on microbial communities and biogeochemical cycles. F1000 Biol. Rep. 4, 17 (2012). https://doi.org/10.3410/b4-17

  247. Whipps, J.M., Lewis, K., Cooke, R.C.: Mycoparasitism and plant disease control, pp. 161–187. In: Burge, M.N. (ed.) Fungi and Biological Control Systems. Manchester University Press, Manchester (1988)

    Google Scholar 

  248. Whitaker, B.K., Rua, M.A., Mitchel, C.E.: Viral pathogen production in a wild grass host driven by host growth and soil nitrogen. New Phytol. 207, 768 (2015). https://doi.org/10.1111/nph.13369

    Article  CAS  Google Scholar 

  249. White, R.R.: Increasing energy and protein use efficiency improves opportunities to decrease land use, water use, and greenhouse gas emissions from dairy production. Agric. Syst. 146, 20–29 (2016). https://doi.org/10.1016/j.agsy.2016.03.013

    Article  Google Scholar 

  250. Whitfield, A.E., Falk, B.W., Rotenberg, D.: Insect vector-mediated transmission of plant viruses. Virology 479–480, 278–289 (2015). https://doi.org/10.1016/j.virol.2015.03.026

    Article  CAS  Google Scholar 

  251. Wilhelm, S.W., Suttle, C.A.: Viruses and nutrient cycles in the sea. Bioscience 49, 781–788 (1999)

    Article  Google Scholar 

  252. Williamson, K.E., Fuhrmann, J.J., Wommack, K.E., Radosevich, M.: Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annu. Rev. Virol. 29, 201–219 (2017). https://doi.org/10.1146/annurev-virology-101416-041639

    Article  CAS  Google Scholar 

  253. Williamson, K.E.: Soil phage ecology: abundance, distribution, and interactions with bacterial hosts. In: Wiltzany, G. (ed.) Bio-Communication in Soil Microorganisms. Soil Biology, vol. 23, pp 113–136. Springer, Berlin (2011)

    Google Scholar 

  254. Wilpiszeski, R.L., Aufrecht, J.A., Retterer, S.T., Sullivan, M.B., Graham, D.E., Pierce, E.M., Zablocki, O.D., Palumbo, A.V., Elias, D.A.: Soil aggregate microbial communities: towards understanding microbiome interactions at biologically relevant scales. Appl. Environ. Microbiol. 85, e00324–19 (2019). https://doi.org/10.1128/aem.00324-19

    Article  CAS  Google Scholar 

  255. Wu, G.A., Jun, S.-R., Sims, G.E., Kim, S.-H.: Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. PNAS 106, 12826–2831 (2009). https://doi.org/10.1073/pnas.0905115106

    Article  Google Scholar 

  256. Xiao, X., Melillo, M., Kicklighter, D.W., McGuire, A.D., Prinn, R.G., Wang, C., Stone, P.H., Sokolov, A.: Transient climate change and net ecosystem production of the terrestrial biosphere. Global Biochem. Cycl. 12, 345–360 (1998). https://doi.org/10.1029/98GB01035

    Article  CAS  Google Scholar 

  257. Xu, P., Liu Y, Graham, R.I., et al.: Densovirus is a mutualistic symbiont of a global crop pest (Helicoverpa armigera) and protects against a baculovirus and Bt biopesticide. PLoS Pathog. 10, e1004490 (2014). https://doi.org/10.1371/journal.ppat.1004490

  258. Yaeger, R.G.: Protozoa: structure, classification, growth, and development. In: Baron, S. (ed.) Medical Microbiology, 4th edn. (Chap. 77) (1996). University of Texas Medical Branch at Galveston, Galveston (TX). Available from: https://www.ncbi.nlm.nih.gov/books/NBK8325/

  259. Yang, X., Chen, B., Zhang, T., et al.: Geographic distribution and genetic diversity of rice stripe mosaic virus in Southern China. Front. Microbiol. (2018). https://doi.org/10.3389/fmicb.2018.03068

  260. Ye, J., Perez, P.G., Zhang, R., Nielsen, S., Huang, D., Thomas, T.: Effects of different C/N ratios on bacterial compositions and processes in an organically managed soil. Biol. Fertil. Soils 54, 137–147 (2018). https://doi.org/10.1007/s00374-017-1246-5

    Article  CAS  Google Scholar 

  261. Yeates, G.W.: Diversity of nematodes. In: Benckiser, G., Schnell, S. (eds.) Biodiversity in Agricultural Production Systems, pp. 215–235. Taylor and Francis, Boca Raton (2007)

    Google Scholar 

  262. Young, R.F., White, R.L.: Lysis of the host by bacteriophage. In: Mahy, B.J.W., van Regenmortel, M.H.V.: (eds.) Encyclopedia of Virology, 3rd edn. Elsevier Ltd., Oxford, pp. 144–158 (2008)

    Google Scholar 

  263. Yu, H., Ling, N., Wang, T., Zhu, C., Wang, Y., Wang, S., Gao, Q.: Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types. Soil Tillage Res. 185, 61–69 (2019). https://doi.org/10.1016/j.still.2018.08.017

    Article  Google Scholar 

  264. Zhang, X., Hu, H.-Y., Men, Y., Yang, Y., Christoffersen, K.S.: Feeding characteristics of a golden alga (Poterioochromonas sp.) grazing on toxic cyanobacterium Microcystis aeruginosa. Water Res. 43, 2953–2960 (2009). https://doi.org/10.1016/j.watres.2009.04.003

    Article  CAS  Google Scholar 

  265. Zhang, Y.Z., Shi, M., Holmes, E.C.: Using metagenomics to characterize an expanding virosphere. Cell 172, 1168–1172 (2018). https://doi.org/10.1016/j.cell.2018.02.043

    Article  CAS  Google Scholar 

  266. Zhang, J., Elser, J.J.: Carbon:Nitrogen:Phosphorus stoichiometry in fungi: a meta-analysis. Front. Microbiol. 8, 1281 (2017). https://doi.org/10.3389/fmicb.2017.01281

  267. Zhivich, A.: Fighting bacterial resistance: approaches, challenges, and opportunities in the search for new antibiotics. In: Part 1. Antibiotics used in clinical practice: mechanisms of action and the development of bacterial resistance MIR J 4 (2017). https://doi.org/10.18527/2500-2236-2017-4-1-31-51

  268. Zhou, L., Zhao, B., Zhang, L., Wang, S., Dong, D., Lv, H., Shang, P.: Alterations in cellular iron metabolism provide more therapeutic opportunities for cancer. Int. J. Mol. Sci. 19, 1545 (2018). https://doi.org/10.3390/ijms19051545

  269. Zhu, D., Palatinszky, M., Schintlmeister, A., Schmid, M.C., Hanson, B.T., Shterzer, N., Mizrahi, I., Rauch, I., Decker, T., Bocklitz, T., Popp, J., Gibson, C.M., Fowler, P.W., Huang, W.E., Wagner, M.: Tracking heavy water (D2O) incorporation for identifying and sorting active microbial l cells. PNAS 112, E194-E203 (2015). https://doi.org/10.1073/pnas.1420406112

  270. Zunke, U., Perry, R.N.: Nematodes: harmful and beneficial organisms. In: Benckiser, G. (ed.) Fauna in Soil Ecosystems—Recycling Processes, Nutrient Fluxes, and Agricultural Production, pp. 85–133. Marcel Dekker, New York, USA) (1997)

    Google Scholar 

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Acknowledgements

I thank my former Department Head, the microbiologist Sylvia Schnell, for her great support in publishing this book, the ecologist Stuart Bamforth, Emeritus Tualane University, Department Ecology, Evolution, and Organismal Biology, NewOrleans, Lousiana, USA, and the virologist Prof Dr. Hans-Dieter Klenk, Emeritus Marburg University, Germany for their inputs.

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    Gero Benckiser

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Benckiser, G. (2021). Soil Microbiological Recycling and the Virome Role in a Hectare Grassland. In: Benckiser, G. (eds) Soil and Recycling Management in the Anthropocene Era. Environmental Science and Engineering(). Springer, Cham. https://doi.org/10.1007/978-3-030-51886-8_2

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