Microbial invasions: The process, patterns, and mechanisms

Trends in Microbiology

Volumn 23, Issue 11, 2015, Pages 719-729

  Mallon, Cyrus Alexander ^a   Van Elsas, Jan Dirk ^a   Salles, Joana Falcão ^a  

^a Groningen Institute for Evolutionary Life Sciences   (Netherlands)

Author keywords

Diversity; Microbial invasion; Resource availability; Species evenness; Species richness

Indexed keywords

ABIOTIC STRESS; ANTIBIOTIC RESISTANCE; BACTERIAL ENDOSPORE; BACTERIAL FLAGELLUM; BACTERIAL TRANSMISSION; BIOFILM; COMMUNITY STRUCTURE; ECOLOGICAL NICHE; ECOLOGY; ECOSYSTEM; HIGH THROUGHPUT SEQUENCING; INTERSPECIFIC COMPETITION; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL GROWTH; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; MICROBIOSTASIS; NONHUMAN; PLANT PATHOGEN INTERACTION; PRIORITY JOURNAL; QUORUM SENSING; RESOURCE ALLOCATION; REVIEW; SPECIES EVENNESS; SPECIES INVASION; SPECIES RICHNESS; BACTERIUM; BIODIVERSITY; BIOLOGICAL MODEL; ENVIRONMENTAL PROTECTION; EVOLUTION; FUNGUS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; POPULATION GROWTH; VIRUS;

BACTERIA; BIODIVERSITY; BIOLOGICAL EVOLUTION; CONSERVATION OF NATURAL RESOURCES; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; FUNGI; MODELS, BIOLOGICAL; POPULATION GROWTH; VIRUSES;

EID: 84960388975     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2015.07.013     Document Type: Review

References (96)

1. Litchman E. Invisible invaders: non-pathogenic invasive microbes in aquatic and terrestrial ecosystems. Ecol. Lett. 2010, 13:1560-1572.
2. Acea M.J., et al. Survival and growth of bacteria introduced into soil. Soil Biol. Biochem. 1988, 20:509-515.
3. Acea M., Alexander M. Growth and survival of bacteria introduced into carbon-amended soil. Soil Biol. Biochem. 1988, 20:703-709.
4. O'Malley M.A. The nineteenth century roots of 'everything is everywhere'. Nat. Rev. Microbiol. 2007, 5:647-651.
5. Martiny J.B.H., et al. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 2006, 4:102-112.
6. Beijerinck M.W. De infusies en de ontdekking der bakterien. Jaarboek van de Koninklijke Akademie van Wetenschappen 1913, 1-28. Koninklijke Akademie van Wetenschappen. J. Muller (Ed.).
7. Fierer N., Jackson R. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:626-631.
8. Horner-Devine M.C., et al. A taxa-area relationship for bacteria. Nature 2004, 432:750-753.
9. Gibbons S.M., et al. Evidence for a persistent microbial seed bank throughout the global ocean. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:4651-4655.
10. Boto L. Horizontal gene transfer in evolution: facts and challenges. Proc. Biol. Sci. 2010, 277:819-827.
11. Cohan F.M. Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2006, 361:1985-1996.
12. Cohan F.M., Perry E.B. A systematics for discovering the fundamental units of bacterial diversity. Curr. Biol. 2007, 17:R373-R386.
13. Fierer N. Microbial biogeography: patterns in microbial diversity across space and time. Accessing Uncultivated Microorganisms: from the Environment to Organisms and Genomes and Back 2008, 95. ASM Press. K. Zengler (Ed.).
14. Whitaker R.J., et al. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 2003, 301:976-978.
15. van Elsas J.D., et al. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:1159-1164.
16. Jousset A., et al. Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. ISME J. 2011, 5:1108-1114.
17. Hornak K., Corno G. Every coin has a back side: invasion by Limnohabitans planktonicus promotes the maintenance of species diversity in bacterial communities. PLoS ONE 2012, 7:e51576.
18. De Roy K., et al. Environmental conditions and community evenness determine the outcome of biological invasion. Nat. Commun. 2013, 4:1383.
19. Li W., Stevens M.H.H. Fluctuating resource availability increases invasibility in microbial microcosms. Oikos 2012, 121:435-441.
20. Stecher B., et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 2010, 6:e1000711.
21. Van Nevel S., et al. Bacterial invasion potential in water is determined by nutrient availability and the indigenous community. FEMS Microbiol. Ecol. 2013, 85:593-603.
22. Amalfitano S., et al. A microbial perspective on biological invasions in aquatic ecosystems. Hydrobiologia 2015, 746:13-22.
23. Eisenhauer N., et al. Niche dimensionality links biodiversity and invasibility of microbial communities. Funct. Ecol. 2013, 27:282-288.
24. Vivant A., et al. Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil. PLoS ONE 2013, 8:e76911.
25. Van der Putten, Wim H., et al. Microbial ecology of biological invasions. ISME J. 2007, 1:28-37.
26. Mallon C.A., et al. Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities. Ecology 2015, 96:915.
27. Liu M., et al. Disturbance promotes non-indigenous bacterial invasion in soil microcosms: analysis of the roles of resource availability and community structure. PLoS ONE 2012, 7:e45306.
28. Catford J.A., et al. Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework. Divers. Distrib. 2009, 15:22-40.
29. Levine J., et al. A meta-analysis of biotic resistance to exotic plant invasions. Ecol. Lett. 2004, 7:975-989.
30. Mueller A.L., et al. Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents. ISME J. 2014, 8:1153-1165.
31. Hellweger F.L., et al. Biogeographic patterns in ocean microbes emerge in a neutral agent-based model. Science 2014, 345:1346-1349.
32. Smith D.J., et al. Free tropospheric transport of microorganisms from Asia to North America. Microb. Ecol. 2012, 64:973-985.
33. Smith D.J., et al. Intercontinental dispersal of bacteria and archaea by transpacific winds. Appl. Environ. Microbiol. 2013, 79:1134-1139.
34. Hammer B.K., Bassler B.L. Quorum sensing controls biofilm formation in Vibrio cholerae. Mol. Microbiol. 2003, 50:101-104.
35. Kierek K., Watnick P.I. Environmental determinants of Vibrio cholerae biofilm development. Appl. Environ. Microbiol. 2003, 69:5079-5088.
36. Rice S.A., et al. Biofilm formation and sloughing in Serratia marcescens are controlled by quorum sensing and nutrient cues. J. Bacteriol. 2005, 187:3477-3485.
37. Nadell C.D., Bassler B.L. A fitness trade-off between local competition and dispersal in Vibrio cholerae biofilms. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:14181-14185.
38. Nadell C.D., et al. Extracellular matrix structure governs invasion resistance in bacterial biofilms. ISME J. 2015, 9:1700-1709.
39. Ames P., Bergman K. Competitive advantage provided by bacterial motility in the formation of nodules by Rhizobium meliloti. J. Bacteriol. 1981, 148:728-908.
40. Scher F., et al. Chemotaxis of fluorescent Pseudomonas spp. to soybean seed exudates in vitro and in soil. Can. J. Microbiol. 1985, 31:570-574.
41. Stocker R., Seymour J.R. Ecology and physics of bacterial chemotaxis in the ocean. Microbiol. Mol. Biol. Rev. 2012, 76:792-812.
42. Butler S.M., Camilli A. Going against the grain: chemotaxis and infection in Vibrio cholerae. Nat. Rev. Microbiol. 2005, 3:611-620.
43. Yawata Y., et al. Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:5622-5627.
44. Winfield M., Groisman E. Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli. Appl. Environ. Microbiol. 2003, 69:3687-3694.
45. Ferenci T. Maintaining a healthy SPANC balance through regulatory and mutational adaptation. Mol. Microbiol. 2005, 57:1-8.
46. Malik-Kale P., et al. The bimodal lifestyle of intracellular Salmonella in epithelial cells: replication in the cytosol obscures defects in vacuolar replication. PLoS ONE 2012, 7:e38732.
47. Nicholson W., et al. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol. Mol. Biol. Rev. 2000, 64:548-572.
48. Thiennimitr P., et al. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:17480-17485.
49. Stecher B., et al. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:1269-1274.
50. Lawley T.D., et al. Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota. Infect. Immun. 2008, 76:403-416.
51. Lang J., et al. Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host. PLoS Pathog. 2014, 10:e1004444.
52. Sukenik A., et al. Invasion of Nostocales (cyanobacteria) to subtropical and temperate freshwater lakes - physiological, regional, and global driving forces. Front. Microbiol. 2012, 3:86.
53. Mehnert G., et al. Competitiveness of invasive and native cyanobacteria from temperate freshwaters under various light and temperature conditions. J. Plankton Res. 2010, 32:1009-1021.
54. Grad Y.H., et al. Comparative genomics of recent shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. mBio 2013, 4:e00452-e512.
55. Gillings M., Fahy P. Genetic diversity of Pseudomonas solanacearum biovar-2 and biovar-N2 assessed using restriction-endonuclease analysis of total genomic DNA. Plant Pathol. 1993, 42:744-753.
56. Wicker E., et al. Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA. ISME J. 2012, 6:961-974.
57. Milling A., et al. Interactions with hosts at cool temperatures, not cold tolerance, explain the unique epidemiology of Ralstonia solanacearum race 3 biovar 2. Phytopathology 2009, 99:1127-1134.
58. Hayward A.C., Hartman G.L. Bacterial Wilt: The Disease and Its Causative Agent, Pseudomonas Solanacearum 1994, CAB International.
59. Whitney K.D., Gabler C.A. Rapid evolution in introduced species, 'invasive traits' and recipient communities: challenges for predicting invasive potential. Divers. Distrib. 2008, 14:569-580.
60. Barberán A., et al. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 2012, 6:343-351.
61. Padron B., et al. Impact of alien plant invaders on pollination networks in two archipelagos. PLoS ONE 2009, 4:e6275.
62. Albrecht M., et al. Consequences of plant invasions on compartmentalization and species' roles in plant-pollinator networks. Proc. Biol. Sci. 2014, 281:20140773.
63. O'Dowd D., et al. Invasional 'meltdown' on an oceanic island. Ecol. Lett. 2003, 6:812-817.
64. Ho W., Ko W. Characteristics of soil microbiostasis. Soil Biol. Biochem. 1982, 14:589-593.
65. Naeem S., et al. Plant diversity increases resistance to invasion in the absence of covarying extrinsic factors. Oikos 2000, 91:97-108.
66. Kennedy T., et al. Biodiversity as a barrier to ecological invasion. Nature 2002, 417:636-638.
67. Russel E.J., Hutchinson H.B. The effect of paetial stabilisation of soil on the production of plant food. J. Agric. Sci. 1909, 3:111-144.
68. Lingappa B., Lockwood J. Nature of widespread soil fungistasis. J. Gen. Microbiol. 1961, 26:473-485.
69. Ko W., Chow F. Characteristics of bacteriostasis in natural soils. J. Gen. Microbiol. 1977, 102:295-298.
70. van Elsas J.D., et al. Survival of genetically marked Escherichia coli O157:H7 in soil as affected by soil microbial community shifts. ISME J. 2007, 1:204-214.
71. Rossello-Mora R., Amann R. The species concept for prokaryotes. FEMS Microbiol. Rev. 2001, 25:39-67.
72. Hardin G. Competitive exclusion principle. Science 1960, 131:1292-1297.
73. Davis M., et al. Fluctuating resources in plant communities: a general theory of invasibility. J. Ecol. 2000, 88:528-534.
74. Tilman D. Niche tradeoffs, neutrality, and community structure: A stochastic theory of resource competition, invasion, and community assembly. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:10854-10861.
75. Davis M., Pelsor M. Experimental support for a resource-based mechanistic model of invasibility. Ecol. Lett. 2001, 4:421-428.
76. Fargione J., Tilman D. Diversity decreases invasion via both sampling and complementarity effects. Ecol. Lett. 2005, 8:604-611.
77. O'Toole G., et al. Biofilm formation as microbial development. Annu. Rev. Microbiol. 2000, 54:49-79.
78. Salles J.F., et al. Community niche predicts the functioning of denitrifying bacterial assemblages. Ecology 2009, 90:3324-3332.
79. Levins R., Culver D. Regional coexistence of species and competition between rare species. Proc. Natl. Acad. Sci. U.S.A. 1971, 68:1246-1248.
80. Miller M.B., Bassler B.L. Quorum sensing in bacteria. Annu. Rev. Microbiol. 2001, 55:165-199.
81. Smith B., Wilson J.B. A consumer's guide to evenness indices. Oikos 1996, 76:70-82.
82. Savageau M.A. Escherichia coli habitats, cell-types, and molecular mechanisms of gene-control. Am. Nat. 1983, 122:732-744.
83. Franz E., et al. Variability of Escherichia coli O157 strain survival in manure-amended soil in relation to strain origin, virulence profile, and carbon nutrition profile. Appl. Environ. Microbiol. 2011, 77:8088-8096.
84. Semenov A.V., et al. Influence of temperature fluctuations on Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium in cow manure. FEMS Microbiol. Ecol. 2007, 60:419-428.
85. Zhang T., et al. Survival of Escherichia coli O157:H7 in soils from Jiangsu Province, China. PLoS ONE 2013, 8:e81178.
86. Ishii S., et al. Presence and growth of naturalized Escherichia coli in temperate soils from lake superior watersheds. Appl. Environ. Microbiol. 2006, 72:612-621.
87. Yao Z., et al. Interaction between the microbial community and invading Escherichia coli O157:H7 in soils from vegetable fields. Appl. Environ. Microbiol. 2014, 80:70-76.
88. Cardoza Y.J., et al. Bacteria in oral secretions of an endophytic insect inhibit antagonistic fungi. Ecol. Entomol. 2006, 31:636-645.
89. Matsui T., et al. Antibiotics production by an actinomycete isolated from the termite gut. J. Basic Microbiol. 2012, 52:731-735.
90. Marsh P., Wellington E. Phage-host interactions in soil. FEMS Microbiol. Ecol. 1994, 15:99-107.
91. Vos M., et al. Local adaptation of bacteriophages to their bacterial hosts in soil. Science 2009, 325:833.
92. Duerkop B.A., et al. A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:17621-17626.
93. Pukatzki S., Provenzano D. Vibrio cholerae as a predator: lessons from evolutionary principles. Front. Microbiol. 2013, 4:384.
94. Ravva S.V., et al. Altered protozoan and bacterial communities and survival of Escherichia coli O157:H7 in monensin-treated wastewater from a dairy lagoon. PLoS ONE 2013, 8:e54782.
95. Vargas R., Hattori T. Protozoan predation of bacterial-cells in soil aggregates. FEMS Microbiol. Ecol. 1986, 38:233-242.
96. Postma J., Van Veen J. Habitable pore-space and survival of Rhizobium leguminosarum biovar trifolii introduced into soil. Microb. Ecol. 1990, 19:149-161.