Horizontal Gene Flow in Managed Ecosystems

Annual Review of Ecology, Evolution, and Systematics

Volumn 46, Issue , 2015, Pages 121-143

  Andam, Cheryl P ^a   Carver, Sarah M ^b   Berthrong, Sean T ^c  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b Central Research   (United States)

^c BUTLER UNIVERSITY   (United States)

Author keywords

Antibiotic resistance; Horizontal gene transfer; Managed ecosystem; Nutrient cycling; Pathogen

Indexed keywords

ANTIBIOTIC RESISTANCE; ECOSYSTEM FUNCTION; ECOSYSTEM MANAGEMENT; FERTILIZER APPLICATION; GENE FLOW; GENE TRANSFER; IRRIGATION SYSTEM; MICROBIAL COMMUNITY; NUTRIENT CYCLING; PARASITE; PATHOGEN; PEST CONTROL;

EID: 84948992144     PISSN: 1543592X     EISSN: 15452069     Source Type: Book Series    
DOI: 10.1146/annurev-ecolsys-112414-054126     Document Type: Article

References (130)

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(11): 4197-202
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
3. Akiyama T, Asfahl KL, Savin MC. 2010. Broad-host-range plasmids in treated wastewater effluent and receiving streams. J. Environ. Qual. 39(6): 2211-15
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(1): 19
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
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
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(7): e1002132
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(1): 13-22
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(9): e105547
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(1): 158-70
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(7): e68406
12. Blaxter M, Koutsovoulos G. 2015. The evolution of parasitism in Nematoda. Parasitology 142: S26-39
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(1): 121-30
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(18): 10181-86
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(1): 104-13
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(3): 756-67
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
18. Che D, Hasan MS, Chen B. 2014. Identifying pathogenicity islands in bacterial pathogenomics using computational approaches. Pathogens 3(1): 36-56
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(3): 305-9
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(1593): 1235-44
21. Clerissi C, Grimsley N, Desdevises Y. 2013. Genetic exchanges of inteins between prasinoviruses (Phycodnaviridae). Evolution 67(1): 18-33
22. Cox GW. 1984. The linkage of inputs to outputs in agroecosystems. In Ecosystems: Unifying Concepts, ed. R Lowrance, BR Stinner, GJ House, pp. 187-208. New York: Wiley
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
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(41): 17651-56
25. Delihas N. 2011. Impact of small repeat sequences on bacterial genome evolution. Genome Biol. Evol. 3: 959-73
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(42): 16939-44
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(7): 1325-35
28. Dinh PTY,Knoblauch M, Elling AA. 2014. Nondestructive imaging of plant-parasitic nematode development and host response to nematode pathogenesis. Phytopathology 104(5): 497-506
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(13): 4396-401
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(1): 121-48
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(8): 1551-59
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(5): 2643-50
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(6): 621-32
34. Frimmel FH. 2003. Water technology for specific water usage. Environ. Sci. Pollut. Res. 10(6): 408-13
35. Gaby JC, Buckley DH. 2011. A global census of nitrogenase diversity. Environ. Microbiol. 13(7): 1790-99
36. Gaby JC, Buckley DH. 2014. A comprehensive aligned nifH gene database: A multipurpose tool for studies of nitrogen-fixing bacteria. Database 2014: bau001
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(9): e1002952
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
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(7374): 487-92
40. Gregersen LH, Bryant DA, Frigaard N-U. 2011. Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria. Front. Microbiol. 2: 116
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(7): 1512-18
42. Haegeman A, Jones JT, Danchin EGJ. 2011. Horizontal gene transfer in nematodes: A catalyst for plant parasitism? Mol. Plant Microbe Interact. 24(8): 879-87
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(4): e95
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
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(7): 2527-30
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(11): 3080-93
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 4): 1229-39
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(3): 442-49
49. Hsu S-F, Buckley DH. 2009. Evidence for the functional significance of diazotroph community structure in soil. ISME J. 3(1): 124-36
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
51. Huang J, Gogarten JP. 2009. Ancient gene transfer as a tool in phylogenetic reconstruction. MethodsMol. Biol. 532: 127-39
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(9): 5182-91
53. Islas-EspinozaM, Reid BJ, WexlerM, Bond PL. 2012. Soil bacterial consortia and previous exposure enhance the biodegradation of sulfonamides from pig manure. Microb. Ecol. 64(1): 140-51
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(12): 1071-82
55. Jechalke S,KopmannC,Rosendahl I, Groeneweg J,WeicheltV, et al. 2013. Increased abundance and transferability of resistance genes after field application of manure from sulfadiazine-treated pigs. Appl. Environ. Microbiol. 79(5): 1704-11
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(18): 6488-98
57. JonesCM, StresB,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(9): 1955-66
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(9): e1002219
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(1): 110-16
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
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(3): 2018-30
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(1): 13-18
63. Lang AS, Zhaxybayeva O, Beatty JT. 2012. Gene transfer agents: phage-like elements of genetic exchange. Nat. Rev. Microbiol. 10(7): 472-82
64. Laranjo M, Alexandre A, Oliveira S. 2014. Legume growth-promoting rhizobia: an overview on the Mesorhizobium genus. Microbiol. Res. 169(1): 2-17
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(8): 1641-50
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(8): 2132-45
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(1): 685-97
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(4): 1803-18
69. Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. 2006. Archaea predominate among ammoniaoxidizing prokaryotes in soils. Nature 442(7104): 806-9
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(1): 218-35
71. Luk AWS, WilliamsTJ, Erdmann S, Papke RT,Cavicchioli R. 2014. Viruses of haloarchaea. Life 4(4): 681-715
72. Ma Y, Allen LZ, Palenik B. 2014. Diversity and genome dynamics of marine cyanophages using metagenomic analyses. Environ. Microbiol. Rep. 6(6): 583-94
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(6): 614-29
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(D1): D560-67
75. Marcelletti S, Scortichini M. 2014. Definition of plant-pathogenic Pseudomonas genomospecies of the Pseudomonas syringae complex through multiple comparative approaches. Phytopathology 104(12): 1274-82
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(10): 3258-65
77. Mazel D. 2006. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4(8): 608-20
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(7): e1003503
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(10): 2697-708
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(6000): 50
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 12): 3052-67
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(3): 800-11
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(3): 253-61
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(50): 20537-42
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(6): 1514-29
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(3-4): 305-15
87. Owen JG, Reddy BVB, Ternei MA, Charlop-Powers Z, Calle PY, et al. 2013. Mapping gene clusters within arrayedmetagenomic libraries to expand the structural diversity of biomedically relevant natural products. PNAS 110(29): 11797-802
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(11): e50875
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
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(1763): 20131021
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(5): 2255-62
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
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(6070): 843-47
94. Rahube TO, Viana LS, KoraimannG, Yost CK. 2014. Characterization and comparative analysis of antibiotic resistance plasmids isolated from a wastewater treatment plant. Front. Microbiol. 5: 558
95. Raz Y, Tannenbaum E. 2010. The influence of horizontal gene transfer on the mean fitness of unicellular populations in static environments. Genetics 185(1): 327-37
96. Reed SC, Townsend AR, Cleveland CC, Nemergut DR. 2010. Microbial community shifts influence patterns in tropical forest nitrogen fixation. Oecologia 164(2): 521-31
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(1): 206-24
98. Richards TA, SoanesDM, JonesMDM, Vasieva O, LeonardG, et al. 2011. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. PNAS 108(37): 15258-63
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
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(11): 1551-58
101. Rosenberg Goldstein RE, Micallef SA, Gibbs SG, George A, Claye E, et al. 2014. Detection of vancomycinresistant enterococci (VRE) at four U.S. wastewater treatment plants that provide effluent for reuse. Sci. Total Environ. 466-467: 404-11
102. Rothman DH, Fournier GP, French KL, Alm EJ, Boyle EA, et al. 2014. Methanogenic burst in the end-Permian carbon cycle. PNAS 111(15): 5462-67
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(1): 138-45
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(6): e67377
105. Siefert JL. 2009. Defining the mobilome. Methods Mol. Biol. 532: 13-27
106. Siguier P, Gourbeyre E, ChandlerM. 2014. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol. Rev. 38(5): 865-91
107. Silby MW, Winstanley C, Godfrey SAC, Levy SB, Jackson RW. 2011. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol. Rev. 35(4): 652-80
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(7376): 241-44
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(21): 4924-35
110. Sorokin DY, Lucker 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(12): 2245-56
111. Soucy SM, Fullmer MS, Papke RT, Gogarten JP. 2014. Inteins as indicators of gene flow in the halobacteria. Front. Microbiol. 5: 299
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(4): e0035613
113. Stavrinides J,KirzingerMWB,Beasley FC, Guttman DS. 2012. E622, aminiature, virulence-associated mobile element. J. Bacteriol. 194(2): 509-17
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(12): 2676-87
115. Szollosi GJ, Tannier E, LartillotN,Daubin V. 2013. Lateral gene transfer from the dead. Syst. Biol. 62(3): 386-97
116. Thoma L, Muth G. 2015. The conjugative DNA-transfer apparatus of Streptomyces. Int. J. Med. Microbiol. 305(2): 224-29
117. Thomas CM, Nielsen KM. 2005. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3(9): 711-21
118. Thomas J, Schaack S, Pritham EJ. 2010. Pervasive horizontal transfer of rolling-circle transposons among animals. Genome Biol. Evol. 2: 656-64
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(22): 8629-34
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(1): 85-97
121. Udikovic-Kolic N, Wichmann F, Broderick NA, Handelsman J. 2014. Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. PNAS 111(42): 15202-7
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(7): 805-16
123. van der Does HC, Rep M. 2012. Horizontal transfer of supernumerary chromosomes in fungi. Methods Mol. Biol. 835: 427-37
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(1): 26-44
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(1): 142-54
126. Wichmann F, Udikovic-Kolic N, Andrew S, Handelsman J. 2014. Diverse antibiotic resistance genes in dairy cow manure. mBio 5(2): e01017
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(9): 621-38
128. Worobey M, Han G-Z, Rambaut A. 2014. Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus. PNAS 111(22): 8107-12
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(12): 881-89
130. Zhao C, Doucet D, Mittapalli O. 2014. Characterization of horizontally transferred β-fructofuranosidase (ScrB) genes in Agrilus planipennis. Insect Mol. Biol. 23(6): 821-32