Breitbart M, Rohwer F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 2005;13:278–84.
Hatfull GF. Dark matter of the biosphere: the amazing world of bacteriophage diversity. J Virol. 2015;89:8107–10.
Bouvier T, Del Giorgio PA. Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol. 2007;9:287–97.
Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brüssow H. Phage as agents of lateral gene transfer. Curr Opin Microbiol. 2003;6:417–24.
Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA, Brewer HM, et al. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. ISME J. 2018;12:1605–18.
Weinbauer MG, Rassoulzadegan F. Are viruses driving microbial diversification and diversity? Environ Microbiol. 2004;6:1–11.
Thurber RV. Current insights into phage biodiversity and biogeography. Curr Opin Microbiol. 2009;12:582–7.
Chow C-ET, Suttle CA. Biogeography of viruses in the sea. Annu Rev Virol. 2015;2:41–66.
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 2016;537:689–93.
Shkoporov AN, Khokhlova EV, Fitzgerald CB, Stockdale SR, Draper LA, Ross RP, et al. ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis. Nat Commun. 2018;9:4781.
Breitbart M, Miyake JH, Rohwer F. Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett. 2004;236:249–56.
Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498.
Jameson E, Mann NH, Joint I, Sambles C, Mühling M. The diversity of cyanomyovirus populations along a North-South Atlantic Ocean transect. ISME J. 2011;5:1713–21.
Delong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N, et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311:496–503.
Finke JF, Suttle CA. The environment and cyanophage diversity: insights from environmental sequencing of DNA polymerase. Front Microbiol. 2019;10:167.
Hanson CA, Marston MF, Martiny JB. Biogeographic variation in host range phenotypes and taxonomic composition of marine cyanophage isolates. Front Microbiol. 2016;7:983.
Huang S, Zhang S, Jiao N, Chen F. Marine cyanophages demonstrate biogeographic patterns throughout the global ocean. Appl Environ Microbiol. 2015;81:441–52.
Marston MF, Taylor S, Sme N, Parsons RJ, Noyes TJE, Martiny JBH. Marine cyanophages exhibit local and regional biogeography. Environ Microbiol. 2013;15:1452–63.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. Uncovering Earth’s virome. Nature. 2016;536:425–30.
Winter C, Matthews B, Suttle CA. Effects of environmental variation and spatial distance on bacteria, archaea and viruses in sub-polar and arctic waters. ISME J. 2013;7:1507–18.
Luo E, Aylward FO, Mende DR, Delong EF. Bacteriophage distributions and temporal variability in the ocean’s interior. mBio 2017;8:e01903–17.
Brum JR, Ignacio-espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, et al. Patterns and ecological drivers of ocean viral communities. Science. 2015;348:1261498.
Dennehy JJ. What ecologists can tell virologists. Annu Rev Microbiol. 2014;68:117–35.
Held NL, Whitaker RJ. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ Microbiol. 2009;11:457–66.
Ashby B, Boots M. Multi-mode fluctuating selection in host–parasite coevolution. Ecol Lett. 2017;20:357–65.
Koskella B, Brockhurst MA. Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev. 2014;38:916–31.
Vos M, Birkett PJ, Birch E, Griffiths RI, Buckling A. Local adaptation of bacteriophages to their bacterial hosts in soil. Science 2009;325:833.
Gomez P, Buckling A. Coevolution with phages does not influence the evolution of bacterial mutation rates in soil. ISME J. 2013;7:2242–4.
Kraemer SA, Boynton PJ. Evidence for microbial local adaptation in nature. Mol Ecol. 2017;26:1860–76.
Kawecki T, Ebert D. Conceptual issues in local adaptation. Ecol Lett. 2004;7:1225–41.
Lenormand T. Gene flow and the limits to natural selection. Trends Ecol Evol. 2002;17:183–9.
Nosil P, Egan SP, Funk DJ. Heterogeneous genomic differentiation between walking-stick ecotypes: “isolation by adaptation” and multiple roles for divergent selection. Evolution. 2008;62:316–36.
Orsini L, Vanoverbeke J, Swillen I, Mergeay J, De Meester L. Drivers of population genetic differentiation in the wild: Isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol Ecol. 2013;22:5983–99.
Zhang Q-G, Buckling A. Migration highways and migration barriers created by host–parasite interactions. Ecol Lett. 2016;19:1479–85.
Wang IJ, Bradburd GS. Isolation by environment. Mol Ecol. 2014;23:5649–62.
Buckling A, Rainey PB. Antagonistic coevolution between a bacterium and a bacteriophage. Proc Biol Sci. 2002;269:931–6.
Kunin V, He S, Warnecke F, Peterson SB, Garcia Martin H, Haynes M, et al. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res. 2008;18:293–7.
Lopez Pascua L, Gandon S, Buckling A. Abiotic heterogeneity drives parasite local adaptation in coevolving bacteria and phages. J Evol Biol. 2012;25:187–95.
Baumann P. Biology of endosymbionts of plant sap-sucking insects. Annu Rev Microbiol. 2005;59:155–89.
Levy A, Gonzalez IS, Mittelviefhaus M, Clingenpeel S, Paredes SH, Miao J, et al. Genomic features of bacterial adaptation to plants. Nat Genet. 2018;50:138–50.
Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005;307:1915–20.
Heath KD, Tiffin P. Context dependence in the coevolution of plant and rhizobial mutualists. Proc Biol Sci. 2007;274:1905–12.
Koch M, Delmotte N, Rehrauer H, Vorholt JA, Pessi G, Hennecke H. Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis. Mol Plant Microbe Interact. 2010;23:784–90.
Aguilar OM, Riva O, Peltzer E. Analysis of Rhizobium etli and of its symbiosis with wild Phaseolus vulgaris supports coevolution in centers of host diversification. Proc Natl Acad Sci. 2004;101:13548–53.
Bitocchi E, Bellucci E, Giardini A, Rau D, Rodriguez M, Biagetti E, et al. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. N Phytol. 2013;197:300–13.
Koenig R, Gepts P. Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of genetic diversity. Theor Appl Genet. 1989;78:809–17.
Melkonian R, Moulin L, Béna G, Tisseyre P, Chaintreuil C, Heulin K, et al. The geographical patterns of symbiont diversity in the invasive legume Mimosa pudica can be explained by the competitiveness of its symbionts and by the host genotype. Environ Microbiol. 2014;16:2099–111.
Tian CF, Young JPW, Wang ET, Tamimi SM, Chen WX. Population mixing of Rhizobium leguminosarum bv. viciae nodulating Vicia faba: the role of recombination and lateral gene transfer. FEMS Microbiol Ecol. 2010;73:563–76.
Burdon JJ, Thrall PH. Spatial and temporal patterns in coevolving plant and pathogen associations. Am Nat. 1999;153:S15–S33.
Van Cauwenberghe J, Visch W, Michiels J, Honnay O. Selection mosaics differentiate Rhizobium-host plant interactions across nitrogen environments. Oikos 2016;125:1755–61.
Guimarães PR, Pires MM, Jordano P, Bascompte J, Thompson JN. Indirect effects drive coevolution in mutualistic networks. Nature 2017;550:511–4.
Heath KD, Lau JA. Herbivores alter the fitness benefits of a plant–rhizobium mutualism. Acta Oecol. 2011;37:87–92.
Rogers HS, Buhle ER, HilleRisLambers J, Fricke EC, Miller RH, Tewksbury JJ. Effects of an invasive predator cascade to plants via mutualism disruption. Nat Commun. 2017;8:6–13.
Delmas E, Besson M, Brice MH, Burkle LA, Dalla Riva GV, Fortin MJ, et al. Analysing ecological networks of species interactions. Biol Rev. 2019;94:16–36.
Gaiarsa MP, Guimarães PR. Interaction strength promotes robustness against cascading effects in mutualistic networks. Sci Rep. 2019;9:1–7.
Sih A, Crowley P, McPeek M, Petranka J, Strohmeier K. Predation, competition, and prey communities: a review of field experiments. Annu Rev Ecol Syst. 1985;16:269–311.
Parratt SR, Barrès B, Penczykowski RM, Laine AL. Local adaptation at higher trophic levels: contrasting hyperparasite–pathogen infection dynamics in the field and laboratory. Mol Ecol. 2017;26:1964–79.
Hatcher MJ, Dick JTA, Dunn AM. How parasites affect interactions between competitors and predators. Ecol Lett. 2006;9:1253–71.
Hutchinson MC, Bramon Mora B, Pilosof S, Barner AK, Kéfi S, Thébault E, et al. Seeing the forest for the trees: putting multilayer networks to work for community ecology. Funct Ecol. 2019;33:206–17.
Koskella B, Taylor TB. Multifaceted impacts of bacteriophages in the plant microbiome. Annu Rev Phytopathol. 2018;56:361–80.
Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol. 2010;8:317–27.
Evans TJ, Ind A, Komitopoulou E, Salmond GPC. Phage-selected lipopolysaccharide mutants of Pectobacterium atrosepticum exhibit different impacts on virulence. J Appl Microbiol. 2010;109:505–14.
Perez Carrascal OM, Vaninsberghe D, Juárez S, Polz MF. Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris. Environ Microbiol. 2016;18:2660–76.
Santamaría RI, Bustos P, Sepúlveda-Robles O, Lozano L, Rodríguez C, Fernández JL, et al. Narrow-host-range bacteriophages that infect Rhizobium etli associate with distinct genomic types. Appl Environ Microbiol. 2014;80:446–54.
Carlson K. Working with bacteriophages: common techniques and methodological approaches. In: Kutter E, Sulakvelidze A (eds). Bacteriophages: biology and applications. Boca Raton, FL: CRC Press; 2005). p. 437–94.
Werle E, Schneider C, Renner M, Völker M, Fiehn W. Convenient single-step, one tube purification of PCR products for direct sequencing. Nucleic Acids Res. 1994;22:4354–5.
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–20.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-Cell sequencing. J Comput Biol. 2012;19:455–77.
Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.
Gordon D, Green P. Consed: a graphical editor for next-generation sequencing. Bioinformatics 2013;29:2936–7.
Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep. 2016;6:24373.
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3 — new capabilities and interfaces. Nucleic Acids Res. 2012;40:e115.
Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci. 2009;106:19126–31.
Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods. 2016;8:12–14.
Lopes A, Tavares P, Petit M, Guérois R, Zinn-justin S. Automated classification of tailed bacteriophages according to their neck organization. BMC Genom. 2014;15:1027.
Hyman P, Abedon ST. Phage host range and efficiency of plating. In: Clokie MRJ, Kropinski AM (eds). Bacteriophages, methods and protocols. Vol. I: Isolation, characterization, and interactions. Totowa, NJ: Humana Press; 2009. p. 175–202.
Hyman P, Abedon ST. Bacteriophage host range and bacterial resistance. Adv Appl Microbiol. 2010;70:217–48.
Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom RR, Blow MJ, et al. Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol. 2016;18:3949–61.
Ishizawa H, Kuroda M, Morikawa M, Ike M. Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor. Biotechnol Biofuels. 2017;10:1–10.
Cenens W, Makumi A, Mebrhatu MT, Lavigne R, Aertsen A. Phage–host interactions during pseudolysogeny. Bacteriophage 2013;3:e25029.
Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, et al. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature. 2018;554:118–22.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, Glinn D, et al. Community Ecology Package. https://cran.r-project.org, https://github.com/vegandevs/vegan. 2019.
Flores CO, Poisot T, Valverde S, Weitz JS. BiMat: a MATLAB package to facilitate the analysis of bipartite networks. Methods Ecol Evol. 2016;7:127–32.
Consul PC. A simple urn model dependent on predetermined strategy. Sankhyā Indian J Stat Ser B. 1974;36:391–9.
Borcard D, Legendre P. All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol Modell. 2002;153:51–68.
Flores CO, Valverde S, Weitz JS. Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages. ISME J. 2013;7:520–32.
Porter SS, Chang PL, Conow CA, Dunham JP, Friesen ML. Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. ISME J. 2016;11:248–62.
Greenlon A, Chang PL, Damtew ZM, Muleta A, Carrasquilla-Garcia N, Kim D, et al. Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proc Natl Acad Sci. 2019;116:15200–9.
Scola V, Ramond JB, Frossard A, Zablocki O, Adriaenssens EM, Johnson RM, et al. Namib desert soil microbial community diversity, assembly, and function along a natural xeric gradient. Micro Ecol. 2018;75:193–203.
Short CM, Suttle CA. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol. 2005;71:480–6.
Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, et al. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol. 2019;4:1727–36.
Culley AI, Steward GF. New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences. Appl Environ Microbiol. 2007;73:5937–44.
Miranda-Sánchez F, Rivera J, Vinuesa P. Diversity patterns of Rhizobiaceae communities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes. Environ Microbiol. 2016;18:2375–91.
Bontemps C, Rogel MA, Wiechmann A, Mussabekova A, Moody S, Simon MF, et al. Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts. N Phytol. 2016;209:319–33.
Van Cauwenberghe J, Lemaire B, Stefan A, Efrose R, Michiels J, Honnay O. Symbiont abundance is more important than pre-infection partner choice in a Rhizobium – legume mutualism. Syst Appl Microbiol. 2016;39:345–9.
Van Cauwenberghe J, Michiels J, Honnay O. Effects of local environmental variables and geographical location on the genetic diversity and composition of Rhizobium leguminosarum nodulating Vicia cracca populations. Soil Biol Biochem. 2015;90:71–9.
Van Cauwenberghe J, Verstraete B, Lemaire B, Lievens B, Michiels J, Honnay O. Population structure of root nodulating Rhizobium leguminosarum in Vicia cracca populations at local to regional geographic scales. Syst Appl Microbiol. 2014;37:613–21.
Hurwitz BL, Brum JR, Sullivan MB. Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. ISME J. 2015;9:472–84.
Mühling M, Fuller NJ, Millard A, Somerfield PJ, Marie D, Wilson WH, et al. Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton. Environ Microbiol. 2005;7:499–508.
Sun Y, Zhang S, Long L, Dong J, Chen F, Huang S. Genetic diversity and cooccurrence patterns of marine cyanopodoviruses and picocyanobacteria. Appl Environ Microbiol. 2018;84:e00591–18.
Chase AB, Arevalo P, Brodie EL, Polz MF, Karaoz U, Martiny JBH. Maintenance of sympatric and allopatric populations in free-living terrestrial bacteria. mBio. 2019;10:e02361–19.
Flores CO, Meyer JR, Valverde S, Farr L, Weitz JS. Statistical structure of host – phage interactions. Proc Natl Acad Sci. 2011;108:E288.
Koskella B, Thompson JN, Preston GM, Buckling A. Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria. Am Nat. 2011;177:440–51.
Koskella B, Parr N. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philos Trans R Soc B Biol Sci. 2015;370:20140297.
Morgan AD, Gandon S, Buckling A. The effect of migration on local adaptation in a coevolving host-parasite system. Nature 2005;437:253–6.
Gómez P, Paterson S, De Meester L, Liu X, Lenzi L, Sharma MD, et al. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community. Nat Commun. 2016;7:12453.
Zhang Q-G, Buckling A. Resource-dependent antagonistic coevolution leads to a new paradox of enrichment. Ecology 2016;97:1319–28.
Lopez-Pascua LDC, Buckling A. Increasing productivity accelerates host-parasite coevolution. J Evol Biol. 2008;21:853–60.
Gurney J, Aldakak L, Betts A, Gougat-Barbera C, Poisot T, Kaltz O, et al. Network structure and local adaptation in co-evolving bacteria–phage interactions. Mol Ecol. 2017;26:1764–77.
Thompson JN. The geographic mosaic of coevolution. Chicago, IL: Uni. Chicago Press; 2005.
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