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Abstract

Mobilization of DNA by horizontal gene transfer (HGT) is an important process in the evolution of many organisms because it allows the recipient lineage to rapidly acquire metabolic innovations and adapt to new ecological niches. However, the significance of HGT in specific ecosystems remains poorly understood. In this review, we present major findings that illustrate how HGT affects managed ecosystems, such as farmlands, orchards, pastures, and managed grasslands. First, acquisition of functions via HGT can lead to the emergence of novel or more virulent pathogens and parasites of crops by allowing them to circumvent host defenses and currently used pest management approaches. Second, HGT of antibiotic resistance genes from the application of wastewater effluent for irrigation or manure as fertilizer can facilitate the emergence of highly resistant microbial lineages. Lastly, HGT can enhance the functional diversity of microbial communities and potentially influence biogeochemical processes. Characterization of lineages possessing horizontally acquired genetic material and their ecology will aid in enhancing the productivity and sustainability of managed ecosystems. We conclude with recommendations for key research directions that will advance our understanding of the causes and consequences of HGT in managed ecosystems.

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2015-12-04
2024-03-28
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Literature Cited

  1. Acuña R, Padilla BE, Flórez-Ramos CP, Rubio JD, Herrera JC. et al. 2012. Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. PNAS 109:114197–202 [Google Scholar]
  2. Ahn S-J, Dermauw W, Wybouw N, Heckel DG, Van Leeuwen T. 2014. Bacterial origin of a diverse family of UDP-glycosyltransferase genes in the Tetranychus urticae genome. Insect Biochem. Mol. Biol. 50:43–57 [Google Scholar]
  3. Akiyama T, Asfahl KL, Savin MC. 2010. Broad-host-range plasmids in treated wastewater effluent and receiving streams. J. Environ. Qual. 39:62211–15 [Google Scholar]
  4. Alexander TW, Yanke JL, Reuter T, Topp E, Read RR. et al. 2011. Longitudinal characterization of antimicrobial resistance genes in feces shed from cattle fed different subtherapeutic antibiotics. BMC Microbiol. 11:119 [Google Scholar]
  5. Althabegoiti MJ, Ormeño-Orrillo E, Lozano L, Torres Tejerizo G, Rogel MA. et al. 2014. Characterization of Rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia. BMC Microbiol. 14:6 [Google Scholar]
  6. Alves JMP, Klein CC, da Silva FM, Costa-Martins AG, Serrano MG. et al. 2013. Endosymbiosis in trypanosomatids: The genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. BMC Evol. Biol. 13:190 [Google Scholar]
  7. Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Mukhtar MS. et al. 2011. Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLOS Pathog. 7:7e1002132 [Google Scholar]
  8. Battistone A, Buttinelli G, Bonomo P, Fiore S, Amato C. et al. 2014. Detection of enteroviruses in influent and effluent flow samples from wastewater treatment plants in Italy. Food Environ. Virol. 6:113–22 [Google Scholar]
  9. Berge O, Monteil CL, Bartoli C, Chandeysson C, Guilbaud C. et al. 2014. A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. PLOS ONE 9:9e105547 [Google Scholar]
  10. Berthrong ST, Buckley DH, Drinkwater LE. 2013. Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling. Microb. Ecol. 66:1158–70 [Google Scholar]
  11. Beukes CW, Venter SN, Law IJ, Phalane FL, Steenkamp ET. 2013. South African papilionoid legumes are nodulated by diverse Burkholderia with unique nodulation and nitrogen-fixation loci. PLOS ONE 8:7e68406 [Google Scholar]
  12. Blaxter M, Koutsovoulos G. 2015. The evolution of parasitism in Nematoda. Parasitology 142:S26–39 [Google Scholar]
  13. Bolhuis H, Severin I, Confurius-Guns V, Wollenzien UIA, Stal LJ. 2010. Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes. ISME J. 4:1121–30 [Google Scholar]
  14. Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT. et al. 2003. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. PNAS 100:1810181–86 [Google Scholar]
  15. Caillaud M-C, Dubreuil G, Quentin M, Perfus-Barbeoch L, Lecomte P. et al. 2008. Root-knot nematodes manipulate plant cell functions during a compatible interaction. J. Plant Physiol. 165:1104–13 [Google Scholar]
  16. Carrión VJ, Gutiérrez-Barranquero JA, Arrebola E, Bardaji L, Codina JC. et al. 2013. The mangotoxin biosynthetic operon (mbo) is specifically distributed within Pseudomonas syringae genomospecies 1 and was acquired only once during evolution. Appl. Environ. Microbiol. 79:3756–67 [Google Scholar]
  17. Carvalho FM, Souza RC, Barcellos FG, Hungria M, Vasconcelos ATR. 2010. Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. BMC Microbiol. 10:37 [Google Scholar]
  18. Che D, Hasan MS, Chen B. 2014. Identifying pathogenicity islands in bacterial pathogenomics using computational approaches. Pathogens 3:136–56 [Google Scholar]
  19. Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P. et al. 2014. Dense genomic sampling identifies highways of pneumococcal recombination. Nat. Genet. 46:3305–9 [Google Scholar]
  20. Clark IM, Buchkina N, Jhurreea D, Goulding KWT, Hirsch PR. 2012. Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment. Philos. Trans. R. Soc. B 367:15931235–44 [Google Scholar]
  21. Clerissi C, Grimsley N, Desdevises Y. 2013. Genetic exchanges of inteins between prasinoviruses (Phycodnaviridae). Evolution 67:118–33 [Google Scholar]
  22. Cox GW. 1984. The linkage of inputs to outputs in agroecosystems. Ecosystems: Unifying Concepts R Lowrance, BR Stinner, GJ House 187–208 New York: Wiley [Google Scholar]
  23. Czekalski N, Berthold T, Caucci S, Egli A, Bürgmann H. 2012. Increased levels of multiresistant bacteria and resistance genes after wastewater treatment and their dissemination into Lake Geneva, Switzerland. Front. Microbiol. 3:106 [Google Scholar]
  24. Danchin EGJ, Rosso M-N, Vieira P, de Almeida-Engler J, Coutinho PM. et al. 2010. Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. PNAS 107:4117651–56 [Google Scholar]
  25. Delihas N. 2011. Impact of small repeat sequences on bacterial genome evolution. Genome Biol. Evol. 3:959–73 [Google Scholar]
  26. DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JAE. et al. 2013. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. PNAS 110:4216939–44 [Google Scholar]
  27. Demba Diallo M, Monteil CL, Vinatzer BA, Clarke CR, Glaux C. et al. 2012. Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in nonagricultural habitats, are phylogenetically diverse and can be pathogenic. ISME J. 6:71325–35 [Google Scholar]
  28. Dinh PTY, Knoblauch M, Elling AA. 2014. Nondestructive imaging of plant-parasitic nematode development and host response to nematode pathogenesis. Phytopathology 104:5497–506 [Google Scholar]
  29. Donato JJ, Moe LA, Converse BJ, Smart KD, Berklein FC. et al. 2010. Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Appl. Environ. Microbiol. 76:134396–401 [Google Scholar]
  30. Dudnik A, Dudler R. 2014. Genomics-based exploration of virulence determinants and host-specific adaptations of Pseudomonas syringae strains isolated from grasses. Pathology 3:1121–48 [Google Scholar]
  31. Encinas D, Garcillán-Barcia MP, Santos-Merino M, Delaye L, Moya A, de la Cruz F. 2014. Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria. J. Bacteriol. 196:81551–59 [Google Scholar]
  32. Fahrenfeld N, Knowlton K, Krometis LA, Hession WC, Xia K. et al. 2014. Effect of manure application on abundance of antibiotic resistance genes and their attenuation rates in soil: field-scale mass balance approach. Environ. Sci. Technol. 48:52643–50 [Google Scholar]
  33. Fournier GP, Andam CP, Alm EJ, Gogarten JP. 2011. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig. Life Evol. Biosph. 41:6621–32 [Google Scholar]
  34. Frimmel FH. 2003. Water technology for specific water usage. Environ. Sci. Pollut. Res. 10:6408–13 [Google Scholar]
  35. Gaby JC, Buckley DH. 2011. A global census of nitrogenase diversity. Environ. Microbiol. 13:71790–99 [Google Scholar]
  36. Gaby JC, Buckley DH. 2014. A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria. Database 2014:bau001 [Google Scholar]
  37. Gardiner DM, McDonald MC, Covarelli L, Solomon PS, Rusu AG. et al. 2012. Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts. PLOS Pathog. 8:9e1002952 [Google Scholar]
  38. Gazi AD, Sarris PF, Fadouloglou VE, Charova SN, Mathioudakis N. et al. 2012. Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains. BMC Microbiol. 12:188 [Google Scholar]
  39. Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P. et al. 2011. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479:7374487–92 [Google Scholar]
  40. Gregersen LH, Bryant DA, Frigaard N-U. 2011. Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria. Front. Microbiol. 2:116 [Google Scholar]
  41. Hachich EM, Galvani AT, Padula JA, Stoppe NC, Garcia SC. et al. 2013. Pathogenic parasites and enteroviruses in wastewater: support for a regulation on water reuse. Water Sci. Technol. 67:71512–18 [Google Scholar]
  42. Haegeman A, Jones JT, Danchin EGJ. 2011. Horizontal gene transfer in nematodes: a catalyst for plant parasitism?. Mol. Plant Microbe Interact. 24:8879–87 [Google Scholar]
  43. Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K. et al. 2006. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLOS Biol. 4:4e95 [Google Scholar]
  44. Hartmann M, Frey B, Mayer J, Mäder P, Widmer F. 2015. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J. 9:1177–94 [Google Scholar]
  45. Heuer H, Solehati Q, Zimmerling U, Kleineidam K, Schloter M. et al. 2011. Accumulation of sulfonamide resistance genes in arable soils due to repeated application of manure containing sulfadiazine. Appl. Environ. Microbiol. 77:72527–30 [Google Scholar]
  46. Hewezi T, Howe P, Maier TR, Hussey RS, Mitchum MG. et al. 2008. Cellulose binding protein from the parasitic nematode Heterodera schachtii interacts with Arabidopsis pectin methylesterase: cooperative cell wall modification during parasitism. Plant Cell 20:113080–93 [Google Scholar]
  47. Holkenbrink C, Barbas SO, Mellerup A, Otaki H, Frigaard N-U. 2011. Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system. Microbiology 157:Pt 41229–39 [Google Scholar]
  48. Hollowell AC, Gano KA, Lopez G, Shahin K, Regus JU. et al. 2015. Native California soils are selective reservoirs for multidrug resistant bacteria. Environ. Microbiol. Rep. 7:3442–49 [Google Scholar]
  49. Hsu S-F, Buckley DH. 2009. Evidence for the functional significance of diazotroph community structure in soil. ISME J. 3:1124–36 [Google Scholar]
  50. Hu J, Chen C, Peever T, Dang H, Lawrence C, Mitchell T. 2012. Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genomics 13:171 [Google Scholar]
  51. Huang J, Gogarten JP. 2009. Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol. Biol. 532:127–39 [Google Scholar]
  52. Hwang MSH, Morgan RL, Sarkar SF, Wang PW, Guttman DS. 2005. Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae. Appl. Environ. Microbiol. 71:95182–91 [Google Scholar]
  53. Islas-Espinoza M, Reid BJ, Wexler M, Bond PL. 2012. Soil bacterial consortia and previous exposure enhance the biodegradation of sulfonamides from pig manure. Microb. Ecol. 64:1140–51 [Google Scholar]
  54. Ivancevic AM, Walsh AM, Kortschak RD, Adelson DL. 2013. Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution. BioEssays 35:121071–82 [Google Scholar]
  55. Jechalke S, Kopmann C, Rosendahl I, Groeneweg J, Weichelt V. et al. 2013. Increased abundance and transferability of resistance genes after field application of manure from sulfadiazine-treated pigs. Appl. Environ. Microbiol. 79:51704–11 [Google Scholar]
  56. Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R. et al. 2005. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J. Bacteriol. 187:186488–98 [Google Scholar]
  57. Jones CM, Stres B, Rosenquist M, Hallin S. 2008. Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol. Biol. Evol. 25:91955–66 [Google Scholar]
  58. Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N. et al. 2011. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLOS Pathog. 7:9e1002219 [Google Scholar]
  59. Kim K-R, Owens G, Ok YS, Park W-K, Lee DB, Kwon S-I. 2012. Decline in extractable antibiotics in manure-based composts during composting. Waste Manag. 32:1110–16 [Google Scholar]
  60. Kirsch R, Gramzow L, Theißen G, Siegfried BD, Ffrench-Constant RH. et al. 2014. Horizontal gene transfer and functional diversification of plant cell wall degrading polygalacturonases: key events in the evolution of herbivory in beetles. Insect Biochem. Mol. Biol. 52:33–50 [Google Scholar]
  61. Kotlarska E, Luczkiewicz A, Pisowacka M, Burzyński A. 2015. Antibiotic resistance and prevalence of class 1 and 2 integrons in Escherichia coli isolated from two wastewater treatment plants, and their receiving waters (Gulf of Gdansk, Baltic Sea, Poland). Environ. Sci. Pollut. Res. Int. 22:32018–30 [Google Scholar]
  62. Labbate M, Boucher Y, Luu I, Chowdhury PR, Stokes HW. 2012. Integron associated mobile genes: just a collection of plug in apps or essential components of cell network hardware?. Mob. Genet. Elem. 2:113–18 [Google Scholar]
  63. Lang AS, Zhaxybayeva O, Beatty JT. 2012. Gene transfer agents: phage-like elements of genetic exchange. Nat. Rev. Microbiol. 10:7472–82 [Google Scholar]
  64. Laranjo M, Alexandre A, Oliveira S. 2014. Legume growth-promoting rhizobia: an overview on the Mesorhizobium genus. Microbiol. Res. 169:12–17 [Google Scholar]
  65. Lauber CL, Ramirez KS, Aanderud Z, Lennon J, Fierer N. 2013. Temporal variability in soil microbial communities across land-use types. ISME J. 7:81641–50 [Google Scholar]
  66. Le Fourn C, Brasseur G, Brochier-Armanet C, Pieulle L, Brioukhanov A. et al. 2011. An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales. Environ. Microbiol. 13:82132–45 [Google Scholar]
  67. Leclercq S, Giraud I, Cordaux R. 2011. Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbionts. Mol. Biol. Evol. 28:1685–97 [Google Scholar]
  68. Lee J, Teitzel GM, Munkvold K, del Pozo O, Martin GB. et al. 2012. Type III secretion and effectors shape the survival and growth pattern of Pseudomonas syringae on leaf surfaces. Plant Physiol. 158:41803–18 [Google Scholar]
  69. Leininger S, Urich T, Schloter M, Schwark L, Qi J. et al. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:7104806–9 [Google Scholar]
  70. Lucas JA, García-Villaraco A, Ramos B, García-Cristobal J, Algar E, Gutierrez-Mañero J. 2013. Structural and functional study in the rhizosphere of Oryza sativa L. plants growing under biotic and abiotic stress. J. Appl. Microbiol. 115:1218–35 [Google Scholar]
  71. Luk AWS, Williams TJ, Erdmann S, Papke RT, Cavicchioli R. 2014. Viruses of haloarchaea. Life 4:4681–715 [Google Scholar]
  72. Ma Y, Allen LZ, Palenik B. 2014. Diversity and genome dynamics of marine cyanophages using metagenomic analyses. Environ. Microbiol. Rep. 6:6583–94 [Google Scholar]
  73. Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M. et al. 2012. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol. Plant Pathol. 13:6614–29 [Google Scholar]
  74. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E. et al. 2014. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42:D1D560–67 [Google Scholar]
  75. Marcelletti S, Scortichini M. 2014. Definition of plant-pathogenic Pseudomonas genomospecies of the Pseudomonas syringae complex through multiple comparative approaches. Phytopathology 104:121274–82 [Google Scholar]
  76. Marti R, Tien Y-C, Murray R, Scott A, Sabourin L, Topp E. 2014. Safely coupling livestock and crop production systems: How rapidly do antibiotic resistance genes dissipate in soil following a commercial application of swine or dairy manure?. Appl. Environ. Microbiol. 80:103258–65 [Google Scholar]
  77. Mazel D. 2006. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4:8608–20 [Google Scholar]
  78. McCann HC, Rikkerink EHA, Bertels F, Fiers M, Lu A. et al. 2013. Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease. PLOS Pathog. 9:7e1003503 [Google Scholar]
  79. McCarthy AJ, Loeffler A, Witney AA, Gould KA, Lloyd DH, Lindsay JA. 2014. Extensive horizontal gene transfer during Staphylococcus aureus co-colonization in vivo. Genome Biol. Evol. 6:102697–708 [Google Scholar]
  80. McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH. 2010. High frequency of horizontal gene transfer in the oceans. Science 330:600050 [Google Scholar]
  81. Menna P, Hungria M. 2011. Phylogeny of nodulation and nitrogen-fixation genes in Bradyrhizobium: supporting evidence for the theory of monophyletic origin, and spread and maintenance by both horizontal and vertical transfer. Int. J. Syst. Evol. Microbiol. 61:Pt 123052–67 [Google Scholar]
  82. Monteil CL, Cai R, Liu H, Llontop MEM, Leman S. et al. 2013. Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens. New Phytol. 199:3800–11 [Google Scholar]
  83. Murillo J, Bardaji L, Navarro de la Fuente L, Führer ME, Aguilera S, Alvarez-Morales A. 2011. Variation in conservation of the cluster for biosynthesis of the phytotoxin phaseolotoxin in Pseudomonas syringae suggests at least two events of horizontal acquisition. Res. Microbiol. 162:3253–61 [Google Scholar]
  84. Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M. et al. 2012. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. PNAS 109:5020537–42 [Google Scholar]
  85. Nowell RW, Green S, Laue BE, Sharp PM. 2014. The extent of genome flux and its role in the differentiation of bacterial lineages. Genome Biol. Evol. 6:61514–29 [Google Scholar]
  86. Obeng AS, Rickard H, Ndi O, Sexton M, Barton M. 2012. Antibiotic resistance, phylogenetic grouping and virulence potential of Escherichia coli isolated from the faeces of intensively farmed and free range poultry. Vet. Microbiol. 154:3–4305–15 [Google Scholar]
  87. Owen JG, Reddy BVB, Ternei MA, Charlop-Powers Z, Calle PY. et al. 2013. Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products. PNAS 110:2911797–802 [Google Scholar]
  88. Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P. et al. 2012. Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. PLOS ONE 7:11e50875 [Google Scholar]
  89. Palomares-Rius JE, Hirooka Y, Tsai IJ, Masuya H, Hino A. et al. 2014. Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi. BMC Evol. Biol. 14:69 [Google Scholar]
  90. Pauchet Y, Heckel DG. 2013. The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer. Proc. R. Soc. B. 280:176320131021 [Google Scholar]
  91. Poly F, Ranjard L, Nazaret S, Gourbière F, Monrozier LJ. 2001. Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Appl. Environ. Microbiol. 67:52255–62 [Google Scholar]
  92. Pourcher A-M, Jadas-Hécart A, Cotinet P, Dabert P, Ziebal C. et al. 2014. Effect of land application of manure from enrofloxacin-treated chickens on ciprofloxacin resistance of Enterobacteriaceae in soil. Sci. Total Environ. 482–483:269–75 [Google Scholar]
  93. Price DC, Chan CX, Yoon HS, Yang EC, Qiu H. et al. 2012. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335:6070843–47 [Google Scholar]
  94. Rahube TO, Viana LS, Koraimann G, Yost CK. 2014. Characterization and comparative analysis of antibiotic resistance plasmids isolated from a wastewater treatment plant. Front. Microbiol. 5:558 [Google Scholar]
  95. Raz Y, Tannenbaum E. 2010. The influence of horizontal gene transfer on the mean fitness of unicellular populations in static environments. Genetics 185:1327–37 [Google Scholar]
  96. Reed SC, Townsend AR, Cleveland CC, Nemergut DR. 2010. Microbial community shifts influence patterns in tropical forest nitrogen fixation. Oecologia 164:2521–31 [Google Scholar]
  97. Riber L, Poulsen PHB, Al-Soud WA, Skov Hansen LB, Bergmark L. et al. 2014. Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance. FEMS Microbiol. Ecol. 90:1206–24 [Google Scholar]
  98. Richards TA, Soanes DM, Jones MDM, Vasieva O, Leonard G. et al. 2011. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. PNAS 108:3715258–63 [Google Scholar]
  99. Romanchuk A, Jones CD, Karkare K, Moore A, Smith BA. et al. 2014. Bigger is not always better: transmission and fitness burden of ∼1 MB Pseudomonas syringae megaplasmid pMPPla107. Plasmid 73:16–25 [Google Scholar]
  100. Rosenberg Goldstein RE, Micallef SA, Gibbs SG, Davis JA, He X. et al. 2012. Methicillin-resistant Staphylococcus aureus (MRSA) detected at four U.S. wastewater treatment plants. Environ. Health Perspect. 120:111551–58 [Google Scholar]
  101. Rosenberg Goldstein RE, Micallef SA, Gibbs SG, George A, Claye E. et al. 2014. Detection of vancomycin-resistant enterococci (VRE) at four U.S. wastewater treatment plants that provide effluent for reuse. Sci. Total Environ. 466–467:404–11 [Google Scholar]
  102. Rothman DH, Fournier GP, French KL, Alm EJ, Boyle EA. et al. 2014. Methanogenic burst in the end-Permian carbon cycle. PNAS 111:155462–67 [Google Scholar]
  103. Shintani M, Matsui K, Inoue J-I, Hosoyama A, Ohji S. et al. 2014. Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community. Appl. Environ. Microbiol. 80:1138–45 [Google Scholar]
  104. Shinya R, Morisaka H, Kikuchi T, Takeuchi Y, Ueda M, Futai K. 2013. Secretome analysis of the pine wood nematode Bursaphelenchus xylophilus reveals the tangled roots of parasitism and its potential for molecular mimicry. PLOS ONE 8:6e67377 [Google Scholar]
  105. Siefert JL. 2009. Defining the mobilome. Methods Mol. Biol. 532:13–27 [Google Scholar]
  106. Siguier P, Gourbeyre E, Chandler M. 2014. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol. Rev. 38:5865–91 [Google Scholar]
  107. Silby MW, Winstanley C, Godfrey SAC, Levy SB, Jackson RW. 2011. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol. Rev. 35:4652–80 [Google Scholar]
  108. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:7376241–44 [Google Scholar]
  109. Smith MCM, Hendrix RW, Dedrick R, Mitchell K, Ko C-C. et al. 2013. Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp. J. Bacteriol. 195:214924–35 [Google Scholar]
  110. Sorokin DY, Lücker S, Vejmelkova D, Kostrikina NA, Kleerebezem R. et al. 2012. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J. 6:122245–56 [Google Scholar]
  111. Soucy SM, Fullmer MS, Papke RT, Gogarten JP. 2014. Inteins as indicators of gene flow in the halobacteria. Front. Microbiol. 5:299 [Google Scholar]
  112. Spoor LE, McAdam PR, Weinert LA, Rambaut A, Hasman H. et al. 2013. Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus. mBio 4:4e00356–13 [Google Scholar]
  113. Stavrinides J, Kirzinger MWB, Beasley FC, Guttman DS. 2012. E622, a miniature, virulence-associated mobile element. J. Bacteriol. 194:2509–17 [Google Scholar]
  114. Swithers KS, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP. 2013. Distribution and evolution of the mobile vma-1b intein. Mol. Biol. Evol. 30:122676–87 [Google Scholar]
  115. Szöllosi GJ, Tannier E, Lartillot N, Daubin V. 2013. Lateral gene transfer from the dead. Syst. Biol. 62:3386–97 [Google Scholar]
  116. Thoma L, Muth G. 2015. The conjugative DNA-transfer apparatus of Streptomyces. Int. J. Med. Microbiol. 305:2224–29 [Google Scholar]
  117. Thomas CM, Nielsen KM. 2005. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3:9711–21 [Google Scholar]
  118. Thomas J, Schaack S, Pritham EJ. 2010. Pervasive horizontal transfer of rolling-circle transposons among animals. Genome Biol. Evol. 2:656–64 [Google Scholar]
  119. Tian CF, Zhou YJ, Zhang YM, Li QQ, Zhang YZ. et al. 2012. Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. PNAS 109:228629–34 [Google Scholar]
  120. Tiburcio RA, Costa GGL, Carazzolle MF, Mondego JMC, Schuster SC. et al. 2010. Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao. J. Mol. Evol. 70:185–97 [Google Scholar]
  121. Udikovic-Kolic N, Wichmann F, Broderick NA, Handelsman J. 2014. Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. PNAS 111:4215202–7 [Google Scholar]
  122. Valentin L, Sharp H, Hille K, Seibt U, Fischer J. et al. 2014. Subgrouping of ESBL-producing Escherichia coli from animal and human sources: an approach to quantify the distribution of ESBL types between different reservoirs. Int. J. Med. Microbiol. 304:7805–16 [Google Scholar]
  123. van der Does HC, Rep M. 2012. Horizontal transfer of supernumerary chromosomes in fungi. Methods Mol. Biol. 835:427–37 [Google Scholar]
  124. Vinatzer BA, Teitzel GM, Lee M-W, Jelenska J, Hotton S. et al. 2006. The type III effector repertoire of Pseudomonas syringae pv. syringae B728a and its role in survival and disease on host and non-host plants. Mol. Microbiol. 62:126–44 [Google Scholar]
  125. Wertz S, Leigh AKK, Grayston SJ. 2012. Effects of long-term fertilization of forest soils on potential nitrification and on the abundance and community structure of ammonia oxidizers and nitrite oxidizers. FEMS Microbiol. Ecol. 79:1142–54 [Google Scholar]
  126. Wichmann F, Udikovic-Kolic N, Andrew S, Handelsman J. 2014. Diverse antibiotic resistance genes in dairy cow manure. mBio 5:2e01017 [Google Scholar]
  127. Wirsenius S, Azar C, Berndes G. 2010. How much land is needed for global food production under scenarios of dietary changes and livestock productivity increases in 2030?. Agric. Syst. 103:9621–38 [Google Scholar]
  128. Worobey M, Han G-Z, Rambaut A. 2014. Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus. PNAS 111:228107–12 [Google Scholar]
  129. Wybouw N, Balabanidou V, Ballhorn DJ, Dermauw W, Grbić M. et al. 2012. A horizontally transferred cyanase gene in the spider mite Tetranychus urticae is involved in cyanate metabolism and is differentially expressed upon host plant change. Insect Biochem. Mol. Biol. 42:12881–89 [Google Scholar]
  130. Zhao C, Doucet D, Mittapalli O. 2014. Characterization of horizontally transferred β-fructofuranosidase (ScrB) genes in Agrilus planipennis. Insect Mol. Biol. 23:6821–32 [Google Scholar]
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