soil microbial invasions v2 - rijksuniversiteit groningenoutbreak of gastroenteritis in a nursery...

23
University of Groningen Soil microbial invasions Mallon, Cyrus Alexander IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2015 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Mallon, C. A. (2015). Soil microbial invasions: Patterns, mechanisms, and impacts garnered from Escherichia coli invasions into soil. [Groningen]: University of Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 17-04-2020

Upload: others

Post on 15-Apr-2020

4 views

Category:

Documents


0 download

TRANSCRIPT

Page 1: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

University of Groningen

Soil microbial invasionsMallon, Cyrus Alexander

IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.

Document VersionPublisher's PDF, also known as Version of record

Publication date:2015

Link to publication in University of Groningen/UMCG research database

Citation for published version (APA):Mallon, C. A. (2015). Soil microbial invasions: Patterns, mechanisms, and impacts garnered fromEscherichia coli invasions into soil. [Groningen]: University of Groningen.

CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).

Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.

Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.

Download date: 17-04-2020

Page 2: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

REFERENCES

Page 3: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 7 6 | S O I L M I C RO B I A L I N VA S I O N S

AAanderud, Z., S. Jones, N. Fierer, and J. T. Lennon. 2015. Resuscitation of the rare

biosphere contributes to pulses of ecosystem activity. Name: Frontiers in Microbiology 6:24.

Acea, M. J., C. R. Moore, and M. Alexander. 1988. Survival and growth of bacteria introduced into soil. Soil Biology and Biochemistry 20:509-515.

Acea, M., and M. Alexander. 1988. Growth and Survival of Bacteria Introduced into Carbon-Amended Soil. Soil Biology & Biochemistry 20:703-709.

Ahmer, B. M. 2004. Cell‐to‐cell signalling in Escherichia coli and Salmonella enterica. Molecular microbiology 52:933-945.

Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological reviews 59:143-169.

Ampe, F., and E. Miambi. 2000. Cluster analysis, richness and biodiversity indexes derived from denaturing gradient gel electrophoresis fingerprints of bacterial communities demonstrate that traditional maize fermentations are driven by the transformation process. International journal of food microbiology 60:91-97.

Anderson, M. J., T. O. Crist, J. M. Chase, M. Vellend, B. D. Inouye, A. L. Freestone, N. J. Sanders, H. V. Cornell, L. S. Comita, and K. F. Davies. 2011. Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. Ecology Letters 14:19-28.

Andersson, A. F., M. Lindberg, H. Jakobsson, F. Bäckhed, P. Nyrén, and L. Engstrand. 2008. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PloS one 3:e2836.

BBach, H., Tomanova, J., Schloter, M. & Munch, J. (2002). Enumeration of total

bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification. J.Microbiol.Methods, 49, 235-245.

Bances, M., A. Herrero, Y. Gonzalez, M. Rosario Rodicio, and M. Angeles Gonzalez-Hevia. 2007. Outbreak of gastroenteritis in a nursery school caused by a strain of Salmonella enterica serovar Typhimurium carrying the hybrid virulence-resistance plasmid pUO-StVR2. Enfermedades infecciosas y microbiologia clinica 25:376-381.

Bassler, B. L., and R. Losick. 2006. Bacterially speaking. Cell 125:237-246.Bathe, S., W. Achouak, A. Hartmann, T. Heulin, M. Schloter, and M. Lebuhn.

2006. Genetic and phenotypic microdiversity of Ochrobactrum spp. FEMS microbiology ecology 56:272-280.

Page 4: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 7 7

Beals, E. W. 1984. Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. Advances in Ecological Research 14:1-55.

Beijerinck, M. W. 1913. De infusies en de ontdekking der bakterien. Jaarboek van de Koninklijke Akademie van Wetenschappen :1-28.

Bell, T., A. K. Lilley, A. Hector, B. Schmid, L. King, and J. A. Newman. 2009. A Linear Model Method for Biodiversity-Ecosystem Functioning Experiments. American Naturalist 174:836-849.

Bell, T., J. Newman, B. Silverman, S. Turner, and A. Lilley. 2005. The contribution of species richness and composition to bacterial services. Nature 436:1157-1160.

Benlloch, S., A. López‐López, E. O. Casamayor, L. Øvreås, V. Goddard, F. L. Daae, G. Smerdon, R. Massana, I. Joint, and F. Thingstad. 2002. Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environmental microbiology 4:349-360.

Blagodatskaya, E., and Y. Kuzyakov. 2013. Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biology and Biochemistry 67:192-211.

Brito, P. H., E. P. Rocha, K. B. Xavier, and I. Gordo. 2013. Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception. Genome biology and evolution 5:16-30.

Brockhurst, M. A., A. Buckling, D. Racey, and A. Gardner. 2008. Resource supply and the evolution of public-goods cooperation in bacteria. Bmc Biology 6:20.

Burmølle, M., D. Ren, T. Bjarnsholt, and S. J. Sørensen. 2014. Interactions in multispecies biofilms: do they actually matter? Trends in microbiology 22:84-91.

Burmolle, M., J. Webb, D. Rao, L. Hansen, S. Sorensen, and S. Kjelleberg. 2006. Enhanced biofilm formation and increased resistance to antimicrobial agents and bacterial invasion are caused by synergistic interactions in multispecies biofilms. Applied and Environmental Microbiology 72:3916-3923.

Bush, G. L. 1969. Sympatric host race formation and speciation in frugivorous flies of the genus Rhagoletis (Diptera, Tephritidae). Evolution :237-251.

CCallaway, R. M., and E. T. Aschehoug. 2000. Invasive plants versus their new and old

neighbors: a mechanism for exotic invasion. Science (New York, N.Y.) 290:521-523.Camargo, J. 1993. Must dominance increase with the number of subordinate species in

competitive interactions? Journal of theoretical biology 161:537-542.Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello,

N. Fierer, A. G. Pena, J. K. Goodrich, J. I. Gordon, G. A. Huttley, S. T. Kelley, D. Knights, J. E. Koenig, R. E. Ley, C. A. Lozupone, D. McDonald, B. D. Muegge, M. Pirrung, J. Reeder, J. R. Sevinsky, P. J. Tumbaugh, W. A. Walters, J. Widmann, T. Yatsunenko, J. Zaneveld, and R. Knight. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7:335-336.

Page 5: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 7 8 | S O I L M I C RO B I A L I N VA S I O N S

Cardoza, Y. J., K. D. Klepzig, and K. F. Raffa. 2006. Bacteria in oral secretions of an endophytic insect inhibit antagonistic fungi. Ecological Entomology 31:636-645.

Carrero-Colon, M., C. Nakatsu, and A. Konopka. 2006. Microbial community dynamics in nutrient-pulsed chemostats. FEMS microbiology ecology 57:1-8.

Case, T. 1990. Invasion Resistance Arises in Strongly Interacting Species-Rich Model Competition Communities. Proceedings of the National Academy of Sciences of the United States of America 87:9610-9614.

Catford, J. A., R. Jansson, and C. Nilsson. 2009. Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework. Diversity and Distributions 15:22-40.

Chao, L., and B. Levin. 1981. Structured Habitats and the Evolution of Anticompetitor Toxins in Bacteria. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 78:6324-6328.

Clarke, K., and G. R. PRIMER. 2006. V6: user manual/tutorial. Primer-E Ltd.Plymouth.

Comte, J., and P. A. Del Giorgio. 2010. Linking the patterns of change in composition and function in bacterioplankton successions along environmental gradients. Ecology 91:1466-1476.

Cook, K., J. Garland, A. Layton, H. Dionisi, L. Levine, and G. Sayler. 2006. Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system. Microbial ecology 52:725-737.

Costa, A. L., S. M. Paixão, I. Caçador, and M. Carolino. 2007. CLPP and EEA profiles of microbial communities in salt marsh sediments. Journal of Soils and Sediments 7:418-425.

Costello, E. K., K. Stagaman, L. Dethlefsen, B. J. M. Bohannan, and D. A. Relman. 2012. The Application of Ecological Theory Toward an Understanding of the Human Microbiome. Science 336:1255-1262.

DDarbyshire, J., R. Wheatley, M. Greaves, and R. Inkson. 1974. A rapid micromethod

for estimating bacterial and protozoan populations in soil. Revue d’Ecologie et de Biologie du Sol (France).

Darwin, Charles. 1859. On the origin of species by means of natural selection. London: Murray

Davis, M., and M. Pelsor. 2001. Experimental support for a resource-based mechanistic model of invasibility. Ecology Letters 4:421-428.

Davis, M., J. Grime, and K. Thompson. 2000. Fluctuating resources in plant communities: a general theory of invasibility. Journal of Ecology 88:528-534.

Page 6: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 7 9

De Roy, K., M. Marzorati, A. Negroni, O. Thas, A. Balloi, F. Fava, W. Verstraete, D. Daffonchio, and N. Boon. 2013. Environmental conditions and community evenness determine the outcome of biological invasion. Nature Communications 4:1383.

De Schryver, P., and O. Vadstein. 2014. Ecological theory as a foundation to control pathogenic invasion in aquaculture. The ISME journal 8:2360-2368.

Dicksved, J., P. Ellstrom, L. Engstrand, and H. Rautelin. 2014. Susceptibility of Campylobacter Infection Is Associated with the Species Composition of the Human Fecal Microbiota Species Composition of the Human Fecal Microbiota. Mbio 5.5, e01212-14:.

Drake, L. A., M. A. Doblin, and F. C. Dobbs. 2007. Potential microbial bioinvasions via ships’ ballast water, sediment, and biofilm. Marine pollution bulletin 55:333-341.

Duerkop, B. A., C. V. Clements, D. Rollins, J. L. M. Rodrigues, and L. V. Hooper. 2012. A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proceedings of the National Academy of Sciences of the United States of America 109:17621-17626.

Dukes, J. S. 2001. Biodiversity and invasibility in grassland microcosms. Oecologia 126:563-568.

Dykhuizen, D. E. 1998. Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73:25-33.

Ee Silva, Michele C Pereira, A. V. Semenov, J. D. van Elsas, and J. F. Salles. 2011.

Seasonal variations in the diversity and abundance of diazotrophic communities across soils. FEMS microbiology ecology 77:57-68.

Edgar, R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461.

Eisenhauer, N., W. Schulz, S. Scheu, and A. Jousset. 2013. Niche dimensionality links biodiversity and invasibility of microbial communities. Functional Ecology 27:282-288.

Elton, Charles S. 1958. The ecology of invasions by plants and animals. London: Methuen

FFaith, D. P. 1992. Conservation evaluation and phylogenetic diversity. Biological

Conservation 61:1-10.Faith, D. P. 1992. Conservation evaluation and phylogenetic diversity. Biological

Conservation 61:1-10.Fargione, J., and D. Tilman. 2005. Diversity decreases invasion via both sampling and

complementarity effects. Ecology Letters 8:604-611.

Page 7: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 8 0 | S O I L M I C RO B I A L I N VA S I O N S

Ferenci, T. 2005. Maintaining a healthy SPANC balance through regulatory and mutational adaptation. Molecular microbiology 57:1-8.

Fierer, N. 2008. Microbial biogeography: patterns in microbial diversity across space and time . Pages 95 In Zengler, K., editor. Accessing Uncultivated Microorganisms: from the Environment to Organisms and Genomes and Back, ASM Press, Washington DC.

Fierer, N., and R. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 103:626-631.

Fierer, N., J. W. Leff, B. J. Adams, U. N. Nielsen, S. T. Bates, C. L. Lauber, S. Owens, J. A. Gilbert, D. H. Wall, and J. G. Caporaso. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America 109:21390-21395.

Flory, S. L., and K. Clay. 2010. Non-native grass invasion alters native plant composition in experimental communities. Biological Invasions 12:1285-1294.

Franklin, R. B., and A. L. Mills. 2006. Structural and functional responses of a sewage microbial community to dilution-induced reductions in diversity. Microbial ecology 52:280-288.

Franz, E., A. D. van Diepeningen, O. J. de Vos, and A. H. van Bruggen. 2005. Effects of cattle feeding regimen and soil management type on the fate of Escherichia coli O157:H7 and salmonella enterica serovar typhimurium in manure, manure-amended soil, and lettuce. Applied and Environmental Microbiology 71:6165-6174.

Franz, E., A. H. A. M. van Hoek, E. Bouw, and H. J. M. Aarts. 2011. Variability of Escherichia coli O157 Strain Survival in Manure-Amended Soil in Relation to Strain Origin, Virulence Profile, and Carbon Nutrition Profile. Applied and Environmental Microbiology 77:8088-8096.

Franz, E., A. V. Semenov, A. J. Termorshuizen, O. De Vos, J. G. Bokhorst, and A. H. Van Bruggen. 2008. Manure‐amended soil characteristics affecting the survival of E. coli O157: H7 in 36 Dutch soils. Environmental microbiology 10:313-327.

Franz, E., M. M. Klerks, O. J. De Vos, A. J. Termorshuizen, and A. H. van Bruggen. 2007. Prevalence of Shiga toxin-producing Escherichia coli stx1, stx2, eaeA, and rfbE genes and survival of E. coli O157:H7 in manure from organic and low-input conventional dairy farms. Applied and Environmental Microbiology 73:2180-2190.

Fridley, J., J. Stachowicz, S. Naeem, D. Sax, E. Seabloom, M. Smith, T. Stohlgren, D. Tilman, and B. V. Holle. 2007. The invasion paradox: reconciling pattern and process in species invasions. Ecology 88:3-17.

Page 8: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 8 1

Frostegård, Å, A. Tunlid, and E. Bååth. 2011. Use and misuse of PLFA measurements in soils. Soil Biology and Biochemistry 43:1621-1625.

Funk, J. L., and P. M. Vitousek. 2007. Resource-use efficiency and plant invasion in low-resource systems. Nature 446:1079-1081.

GGans, J., M. Wolinsky, and J. Dunbar. 2005. Computational improvements reveal great

bacterial diversity and high metal toxicity in soil. Science (New York, N.Y.) 309:1387-1390.

Garbeva, P. 2005. The significance of microbial diversity in agricultural soil for disease suppressiveness. PhD thesis.

Garbeva, P., J. A. van Veen, and J. D. van Elsas. 2004. Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes. FEMS microbiology ecology 47:51-64.

Garland, J. L., and A. L. Mills. 1991. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Applied and Environmental Microbiology 57:2351-2359.

Gillings, M., and P. Fahy. 1993. Genetic Diversity of Pseudomonas-Solanacearum Biovar-2 and Biovar-N2 Assessed using Restriction-Endonuclease Analysis of Total Genomic DNA. Plant Pathology 42:744-753.

Ginolhac, A., C. Jarrin, B. Gillet, P. Robe, P. Pujic, K. Tuphile, H. Bertrand, T. M. Vogel, G. Perriere, P. Simonet, and R. Nalin. 2004. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Applied and Environmental Microbiology 70:5522-5527.

Gonzalez, J. M., M. C. Portillo, P. Belda-Ferre, and A. Mira. 2012. Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities. PLoS One 7:e29973.

Gopinath, S., S. Carden, and D. Monack. 2012. Shedding light on Salmonella carriers. Trends in microbiology 20:320-327.

Grad, Y. H., P. Godfrey, G. C. Cerquiera, P. Mariani-Kurkdjian, M. Gouali, E. Bingen, T. P. Shea, B. J. Haas, A. Griggs, S. Young, Q. Zeng, M. Lipsitch, M. K. Waldor, F. Weill, J. R. Wortman, and W. P. Hanage. 2013. Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen. Mbio 4:e00452-12.

Grayston, S. J., and C. E. Prescott. 2005. Microbial communities in forest floors under four tree species in coastal British Columbia. Soil Biology and Biochemistry 37:1157-1167.

Griffin, A., S. West, and A. Buckling. 2004. Cooperation and competition in pathogenic bacteria. Nature 430:1024-1027.

Page 9: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 8 2 | S O I L M I C RO B I A L I N VA S I O N S

Griffiths, B., K. Ritz, N. Ebblewhite, and G. Dobson. 1998. Soil microbial community structure: effects of substrate loading rates. Soil Biology and Biochemistry 31:145-153.

Griffiths, B., K. Ritz, R. D. Bardgett, R. Cook, S. Christensen, F. Ekelund, S. J. Sørensen, E. Bååth, J. Bloem, and P. De Ruiter. 2000. Ecosystem response of pasture soil communities to fumigation‐induced microbial diversity reductions: an examination of the biodiversity–ecosystem function relationship. Oikos 90:279-294.

HHaas, B. J., D. Gevers, A. M. Earl, M. Feldgarden, D. V. Ward, G. Giannoukos,

D. Ciulla, D. Tabbaa, S. K. Highlander, E. Sodergren, B. Methe, T. Z. DeSantis, J. F. Petrosino, R. Knight, B. W. Birren, and Human Microbiome Consortium. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome research 21:494-504.

Hardin, G. 1960. Competitive Exclusion Principle. Science 131:1292-1297.Hayward, A. C., and G. L. Hartman. 1994. Bacterial Wilt: The Disease and Its

Causative Agent, Pseudomonas Solanacearum. CAB International, .Hector, A., K. Dobson, A. Minns, E. Bazeley-White, and J. H. Lawton. 2001.

Community diversity and invasion resistance: An experimental test in a grassland ecosystem and a review of comparable studies. Ecological Research 16:819-831.

Hejda, M., P. Pysek, and V. Jarosik. 2009. Impact of invasive plants on the species richness, diversity and composition of invaded communities. Journal of Ecology 97:393-403.

Heylen, K., D. Gevers, B. Vanparys, L. Wittebolle, J. Geets, N. Boon, and P. De Vos. 2006. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environmental microbiology 8:2012-2021.

Ho, W., and W. Ko. 1982. Characteristics of soil microbiostasis. Soil Biology and Biochemistry 14:589-593.

Hodgson, D. J., P. B. Rainey, and A. Buckling. 2002. Mechanisms linking diversity, productivity and invasibility in experimental bacterial communities. Proceedings of the Royal Society of London Series B-Biological Sciences 269:2277-2283.

Holle, B. V., and D. Simberloff. 2005. Ecological resistance to biological invasion overwhelmed by propagule pressure. Ecology 86:3212-3218.

Hong, Y., A. Steinman, B. Biddanda, R. Rediske, and G. Fahnenstiel. 2006. Occurrence of the toxin-producing cyanobacterium Cylindrospermopsis raciborskii in Mona and Muskegon Lakes, Michigan. Journal of Great Lakes Research 32:645-652.

Page 10: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 8 3

Hooper, D., F. Chapin, J. Ewel, A. Hector, P. Inchausti, S. Lavorel, J. Lawton, D. Lodge, M. Loreau, S. Naeem, B. Schmid, H. Setala, A. Symstad, J. Vandermeer, and D. Wardle. 2005. Effects of biodiversity on ecosystem functioning: A consensus of current knowledge. Ecological Monographs 75:3-35.

Hornak, K., and G. Corno. 2012. Every Coin Has a Back Side: Invasion by Limnohabitans planktonicus Promotes the Maintenance of Species Diversity in Bacterial Communities. Plos One 7:e51576.

Horner-Devine, M. C., M. Lage, J. B. Hughes, and B. J. Bohannan. 2004. A taxa–area relationship for bacteria. Nature 432:750-753.

Horton, R. A., L. P. Randall, E. L. Snary, H. Cockrem, S. Lotz, H. Wearing, D. Duncan, A. Rabie, I. McLaren, E. Watson, R. M. La Ragione, and N. G. Coldham. 2011. Fecal Carriage and Shedding Density of CTX-M Extended-Spectrum beta-Lactamase-Producing Escherichia coli in Cattle, Chickens, and Pigs: Implications for Environmental Contamination and Food Production. Applied and Environmental Microbiology 77:3715-3719.

Hoskins, L., M. Agustines, W. Mckee, E. Boulding, M. Kriaris, and G. Niedermeyer. 1985. Mucin Degradation in Human-Colon Ecosystems - Isolation and Properties of Fecal Strains that Degrade Abh Blood-Group Antigens and Oligosaccharides from Mucin Glycoproteins. Journal of Clinical Investigation 75:944-953.

IIrikiin, Y., M. Nishiyama, S. Otsuka, and K. Senoo. 2006. Rhizobacterial community-

level, sole carbon source utilization pattern affects the delay in the bacterial wilt of tomato grown in rhizobacterial community model system. Applied Soil Ecology 34:27-32.

Ishii, S., W. B. Ksoll, R. E. Hicks, and M. J. Sadowsky. 2006. Presence and growth of naturalized Escherichia coli in temperate soils from lake superior watersheds. Applied and Environmental Microbiology 72:612-621.

JJensen, S., L. Øvreås, F. L. Daae, and V. Torsvik. 1998. Diversity in methane

enrichments from agricultural soil revealed by DGGE separation of PCR amplified 16S rDNA fragments. FEMS microbiology ecology 26:17-26.

Jiang, X., J. Morgan, and M. P. Doyle. 2002. Fate of Escherichia coli O157:H7 in manure-amended soil. Applied and Environmental Microbiology 68:2605-2609.

Jousset, A., N. Eisenhauer, E. Materne, and S. Scheu. 2013. Evolutionary history predicts the stability of cooperation in microbial communities. Nature Communications 4:2573.

Page 11: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 8 4 | S O I L M I C RO B I A L I N VA S I O N S

Jousset, A., W. Schulz, S. Scheu, and N. Eisenhauer. 2011. Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. Isme Journal 5:1108-1114.

KKaur, A., A. Chaudhary, A. Kaur, R. Choudhary, and R. Kaushik. 2005. Phospholipid

fatty acid-A bioindicator of environment monitoring and assessment in soil ecosystem. Current Science-Bangalore- 89:1103.

Keijser, B. J., E. Zaura, S. M. Huse, J. M. van der Vossen, F. H. Schuren, R. C. Montijn, J. M. ten Cate, and W. Crielaard. 2008. Pyrosequencing analysis of the oral microflora of healthy adults. Journal of dental research 87:1016-1020.

Kennedy, T., S. Naeem, K. Howe, J. Knops, D. Tilman, and P. Reich. 2002. Biodiversity as a barrier to ecological invasion. Nature 417:636-638.

Klitgord, N., and D. Segre. 2010. Environments that Induce Synthetic Microbial Ecosystems. Plos Computational Biology 6:e1001002.

Klitgord, N., and D. Segre. 2011. Ecosystems biology of microbial metabolism. Current opinion in biotechnology 22:541-546.

Ko, W., and F. Chow. 1977. Characteristics of Bacteriostasis in Natural Soils. Journal of general microbiology 102:295-298.

Koh, K. S., C. Matz, C. H. Tan, H. L. Le, S. A. Rice, D. J. Marshall, P. D. Steinberg, and S. Kjelleberg. 2012. Minimal increase in genetic diversity enhances predation resistance. Molecular ecology 21:1741-1753.

Koh, K. S., C. Matz, C. H. Tan, H. L. Le, S. A. Rice, D. J. Marshall, P. D. Steinberg, and S. Kjelleberg. 2012. Minimal increase in genetic diversity enhances predation resistance. Molecular ecology 21:1741-1753.

Krause, S., X. Le Roux, P. A. Niklaus, P. M. Van Bodegom, J. T. Lennon, S. Bertilsson, H. Grossart, L. Philippot, and P. L. E. Bodelier. 2014. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Frontiers in Microbiology 5:251.

LLangenheder, S., M. T. Bulling, M. Solan, and J. I. Prosser. 2010. Bacterial Biodiversity-

Ecosystem Functioning Relations Are Modified by Environmental Complexity. Plos One 5:e10834.

Lawley, T. D., D. A. Bouley, Y. E. Hoy, C. Gerke, D. A. Relman, and D. M. Monack. 2008. Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota. Infection and immunity 76:403-416.

Page 12: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 8 5

Lee, K. W. K., S. Periasamy, M. Mukherjee, C. Xie, S. Kjelleberg, and S. A. Rice. 2014. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. Isme Journal 8:894-907.

Lejeune, J. T., and M. D. Kauffman. 2005. Effect of sand and sawdust bedding materials on the fecal prevalence of Escherichia coli O157:H7 in dairy cows. Applied and Environmental Microbiology 71:326-330.

Levine, J. M. 2000. Species diversity and biological invasions: relating local process to community pattern. Science (New York, N.Y.) 288:852-854.

Levine, J. M., and C. M. D’Antonio. 1999. Elton revisited: a review of evidence linking diversity and invasibility. Oikos :15-26.

Levine, J., M. Vila, C. D’Antonio, J. Dukes, K. Grigulis, and S. Lavorel. 2003. Mechanisms underlying the impacts of exotic plant invasions. Proceedings of the Royal Society B-Biological Sciences 270:775-781.

Levine, J., P. Adler, and S. Yelenik. 2004. A meta-analysis of biotic resistance to exotic plant invasions. Ecology Letters 7:975-989.

Li, W., and M. H. H. Stevens. 2012. Fluctuating resource availability increases invasibility in microbial microcosms. Oikos 121:435-441.

Lingappa, B., and J. Lockwood. 1961. Nature of Widespread Soil Fungistasis. Journal of general microbiology 26:473-485.

Lingappa, B., and J. Lockwood. 1961. Nature of Widespread Soil Fungistasis. Journal of general microbiology 26:473-&.

Litchman, E. 2010. Invisible invaders: non-pathogenic invasive microbes in aquatic and terrestrial ecosystems. Ecology Letters 13:1560-1572.

Liu, M., L. Bjornlund, R. Ronn, S. Christensen, and F. Ekelund. 2012. Disturbance Promotes Non-Indigenous Bacterial Invasion in Soil Microcosms: Analysis of the Roles of Resource Availability and Community Structure. Plos One 7:e45306.

Lockwood, J. L., M. F. Hoopes, and M. P. Marchetti. 2007. Invasion Ecology. Blackwell Publishing, .

Lozupone, C. A., and R. Knight. 2008. Species divergence and the measurement of microbial diversity. FEMS microbiology reviews 32:557-578.

Lozupone, C. A., M. Hamady, S. T. Kelley, and R. Knight. 2007. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Applied and Environmental Microbiology 73:1576-1585.

Lozupone, C., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71:8228-8235.

Lyautey, E., B. Lacoste, L. Ten-Hage, J. Rols, and F. Garabetian. 2005. Analysis of bacterial diversity in river biofilms using 16S rDNA PCR-DGGE: methodological settings and fingerprints interpretation. Water research 39:380-388.

Page 13: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 8 6 | S O I L M I C RO B I A L I N VA S I O N S

MMa, C., M. Liu, H. Wang, C. Chen, W. Fan, B. Griffiths, and H. Li. 2015. Resource

utilization capability of bacteria predicts their invasion potential in soil. Soil Biology and Biochemistry 81:287-290.

Ma, J., A. M. Ibekwe, C. Yang, and D. E. Crowley. 2013. Influence of bacterial communities based on 454-pyrosequencing on the survival of Escherichia coli O157: H7 in soils. FEMS microbiology ecology 84:542-554.

Malik-Kale, P., S. Winfree, and O. Steele-Mortimer. 2012. The Bimodal Lifestyle of Intracellular Salmonella in Epithelial Cells: Replication in the Cytosol Obscures Defects in Vacuolar Replication. Plos One 7:e38732.

Mallon, C. A., F. Poly, X. Le Roux, I. Marring, J. D. van Elsas, and J. F. Salles. 2015. Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities. Ecology 96:915-926.

Mallon, C.A., F. Poly, X. Le Roux, I. Marring, J.D. van Elsas, J.F. Salles. 2015. Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities. Ecology 96: 915-926.

Maron, J. L., and M. Marler. 2008. Effects of native species diversity and resource additions on invader impact. American Naturalist 172:S18-S33.

Maron, J., and M. Marler. 2007. Native plant diversity resists invasion at both low and high resource levels. Ecology 88:2651-2661.

Marsh, P., and E. Wellington. 1994. Phage-Host Interactions in Soil. FEMS microbiology ecology 15:99-107.

Martin, A. P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Applied and Environmental Microbiology 68:3673-3682.

Martiny, J. B. H., B. J. Bohannan, J. H. Brown, R. K. Colwell, J. A. Fuhrman, J. L. Green, M. C. Horner-Devine, M. Kane, J. A. Krumins, and C. R. Kuske. 2006. Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4:102-112.

Matos, A., L. Kerkhof, and J. Garland. 2005. Effects of microbial community diversity on the survival of Pseudomonas aeruginosa in the wheat rhizosphere. Microbial ecology 49:257-264.

Matsui, T., J. Tanaka, T. Namihira, and N. Shinzato. 2012. Antibiotics production by an actinomycete isolated from the termite gut. Journal of Basic Microbiology 52:731-735.

McGrady-Steed, J., P. M. Harris, and P. J. Morin. 1997. Biodiversity regulates ecosystem predictability. Nature 390:162-165.

Messiha, N. A., A. H. van Bruggen, A. D. van Diepeningen, O. J. de Vos, A. J. Termorshuizen, N. Tjou-Tam-Sin, and J. Janse. 2007. Potato brown rot incidence and severity under different management and amendment regimes in different soil types. European Journal of Plant Pathology 119:367-381.

Page 14: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 8 7

Messiha, N., A. Van Bruggen, E. Franz, J. Janse, M. Schoeman-Weerdesteijn, A. Termorshuizen, and A. Van Diepeningen. 2009. Effects of soil type, management type and soil amendments on the survival of the potato brown rot bacterium Ralstonia solanacearum. Applied soil ecology 43:206-215.

Miller, M. B., and B. L. Bassler. 2001. Quorum sensing in bacteria. Annual Reviews in Microbiology 55:165-199.

Milling, A., F. Meng, T. P. Denny, and C. Allen. 2009. Interactions with Hosts at Cool Temperatures, Not Cold Tolerance, Explain the Unique Epidemiology of Ralstonia solanacearum Race 3 Biovar 2. Phytopathology 99:1127-1134.

Monod, J. 1949. The Growth of Bacterial Cultures. Annual Review of Microbiology 3:371-394.

Morris, J. J., R. E. Lenski, and E. R. Zinser. 2012. The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss. Mbio 3:e00036.

Mueller, A. L., J. R. de Rezende, C. R. J. Hubert, K. U. Kjeldsen, I. Lagkouvardos, D. Berry, B. B. Jorgensen, and A. Loy. 2014. Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents. Isme Journal 8:1153-1165.

Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59:695-700.

NNaeem, S., J. M. H. Knops, D. Tilman, K. M. Howe, T. Kennedy, and S. Gale. 2000.

Plant diversity increases resistance to invasion in the absence of covarying extrinsic factors. Oikos 91:97-108.

Nicholson, W., N. Munakata, G. Horneck, H. Melosh, and P. Setlow. 2000. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiology and Molecular Biology Reviews 64:548.

Nowakowska, J., and J. D. Oliver. 2013. Resistance to environmental stresses by Vibrio vulnificus in the viable but nonculturable state. FEMS microbiology ecology 84:213-222.

OO’Malley, M. A. 2007. The nineteenth century roots of ‘everything is everywhere’.

Nature Reviews Microbiology 5:647-651.Oelschlaeger, T. A. 2010. Mechanisms of probiotic actions–a review. International

Journal of Medical Microbiology 300:57-62.Oksanen, J., R. Kindt, P. Legendre, B. O’Hara, M. H. H. Stevens, M. J. Oksanen, and

M. Suggests. 2007. The vegan package. Community ecology package.

Page 15: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 8 8 | S O I L M I C RO B I A L I N VA S I O N S

PPatten, C., M. Kirchhof, M. Schertzberg, R. Morton, and H. Schellhorn. 2004.

Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Molecular Genetics and Genomics 272:580-591.

Pereira e Silva, M. C., B. Schloter-Hai, M. Schloter, J. D. van Elsas, and J. F. Salles. 2013. Temporal Dynamics of Abundance and Composition of Nitrogen-Fixing Communities across Agricultural Soils. Plos One 8:e74500.

Perez-Cobas, A. E., A. Artacho, S. J. Ott, A. Moya, M. J. Gosalbes, and A. Latorre. 2014. Structural and functional changes in the gut microbiota associated to Clostridium difficile infection. Frontiers in Microbiology 5:335.

Postma, J., and J. Van Veen. 1990. Habitable Pore-Space and Survival of Rhizobium-Leguminosarum Biovar Trifolii Introduced into Soil. Microbial ecology 19:149-161.

Price, M. N., P. S. Dehal, and A. P. Arkin. 2009. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. Molecular biology and evolution 26:1641-1650.

Puentes-Teliez, P. E., M. A. Hansen, S. J. Sorensen, and J. D. van Elsas. 2013. Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments. Applied and Environmental Microbiology 79:1008-1017.

Pukatzki, S., and D. Provenzano. 2013. Vibrio cholerae as a predator: lessons from evolutionary principles. Frontiers in Microbiology 4:384.

RRainey, P., and M. Travisano. 1998. Adaptive radiation in a heterogeneous environment.

Nature 394:69-72.Ravva, S. V., C. Z. Sarreal, and R. E. Mandrell. 2013. Altered Protozoan and Bacterial

Communities and Survival of Escherichia coli O157:H7 in Monensin-Treated Wastewater from a Dairy Lagoon. Plos One 8:e54782.

Reeder, J., and R. Knight. 2010. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nature Methods 7:668-669.

Ren, D., J. Madsen, S. Sorensen, and M. Burmolle. 2014. Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. Isme Journal :.

Renne, I. J., B. F. Tracy, and I. A. Colonna. 2006. Shifts in grassland invasibility: Effects of soil resources, disturbance, composition, and invader size. Ecology 87:2264-2277.

Ritchie, J., G. Campbell, J. Shepherd, Y. Beaton, D. Jones, K. Killham, and R. Artz. 2003. A stable bioluminescent construct of Escherichia coli O157 : H7 for hazard assessments of long-term survival in the environment. Applied and Environmental Microbiology 69:3359-3367.

Page 16: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 8 9

Rodríguez‐Echeverría, S. 2010. Rhizobial hitchhikers from Down Under: invasional meltdown in a plant–bacteria mutualism? Journal of Biogeography 37:1611-1622.

Rokka, S., and P. Rantamäki. 2010. Protecting probiotic bacteria by microencapsulation: challenges for industrial applications. European Food Research and Technology 231:1-12.

Romanuk, T. N., and J. Kolasa. 2005. Resource limitation, biodiversity, and competitive effects interact to determine the invasibility of rock pool microcosms. Biological Invasions 7:711-722.

Ronn, R., A. E. McCaig, B. S. Griffiths, and J. I. Prosser. 2002. Impact of protozoan grazing on bacterial community structure in soil microcosms. Applied and Environmental Microbiology 68:6094-6105.

Roscher, C., H. Bessler, Y. Oelmann, C. Engels, W. Wilcke, and E. Schulze. 2009. Resources, recruitment limitation and invader species identity determine pattern of spontaneous invasion in experimental grasslands. Journal of Ecology 97:32-47.

Rossello-Mora, R., and R. Amann. 2001. The species concept for prokaryotes. FEMS microbiology reviews 25:39-67.

Rothrock, M. J., and F. Garcia‐Pichel. 2005. Microbial diversity of benthic mats along a tidal desiccation gradient. Environmental microbiology 7:593-601.

Rousk, J., E. Bååth, P. C. Brookes, C. L. Lauber, C. Lozupone, J. G. Caporaso, R. Knight, and N. Fierer. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME journal 4:1340-1351.

Russel, E. J., and H. B. Hutchinson. 1909. The Effect of Paetial Stabilisation of Soil on the Production of Plant Food. Journal of Agricultural Science III:111-144.

Ryan, R. P., and J. M. Dow. 2008. Diffusible signals and interspecies communication in bacteria. Microbiology (Reading, England) 154:1845-1858.

SSalles, J. F., F. Poly, B. Schmid, and X. Le Roux. 2009. Community niche predicts the

functioning of denitrifying bacterial assemblages. Ecology 90:3324-3332.Salles, J. F., X. Le Roux, and F. Poly. 2012. Relating phylogenetic and functional

diversity among denitrifiers and quantifying their capacity to predict community functioning. Frontiers in Microbiology 3:209.

Savageau, M. A. 1983. Escherichia-Coli Habitats, Cell-Types, and Molecular Mechanisms of Gene-Control. American Naturalist 122:732-744.

Schikora, A., A. Carreri, E. Charpentier, and H. Hirt. 2008. The Dark Side of the Salad: Salmonella typhimurium Overcomes the Innate Immune Response of Arabidopsis thaliana and Shows an Endopathogenic Lifestyle. Plos One 3:e2279.

Page 17: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 9 0 | S O I L M I C RO B I A L I N VA S I O N S

Schrezenmeir, J., and M. de Vrese. 2001. Probiotics, prebiotics, and synbiotics--approaching a definition. The American Journal of Clinical Nutrition 73:361S-364S.

Sekiguchi, H., M. Watanabe, T. Nakahara, B. Xu, and H. Uchiyama. 2002. Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Applied and Environmental Microbiology 68:5142-5150.

Semenov, A. V., A. H. C. van Bruggen, L. van Overbeek, A. J. Termorshuizen, and A. M. Semenov. 2007. Influence of temperature fluctuations on Escherichia coli O157 : H7 and Salmonella enterica serovar Typhimurium in cow manure. FEMS microbiology ecology 60:419-428.

Semenov, A. V., E. Franz, L. van Overbeek, A. J. Termorshuizen, and A. H. C. van Bruggen. 2008. Estimating the stability of Escherichia coli O157 : H7 survival in manure-amended soils with different management histories. Environmental microbiology 10:1450-1459.

Semenov, A. V., E. Franz, L. van Overbeek, A. J. Termorshuizen, and A. H. C. van Bruggen. 2008. Estimating the stability of Escherichia coli O157 : H7 survival in manure-amended soils with different management histories. Environmental microbiology 10:1450-1459.

Shafquat, A., R. Joice, S. L. Simmons, and C. Huttenhower. 2014. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends in microbiology 22:261-266.

Sieber, J. R., M. J. McInerney, and R. P. Gunsalus. 2012. Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation. Annual Review of Microbiology 66:429-452.

Smalla, K., U. Wachtendorf, H. Heuer, W. T. Liu, and L. Forney. 1998. Analysis of BIOLOG GN Substrate Utilization Patterns by Microbial Communities. Applied and Environmental Microbiology 64:1220-1225.

Smith, D. J., D. A. Jaffe, M. N. Birmele, D. W. Griffin, A. C. Schuerger, J. Hee, and M. S. Roberts. 2012. Free Tropospheric Transport of Microorganisms from Asia to North America. Microbial ecology 64:973-985.

Smith, D. J., H. J. Timonen, D. A. Jaffe, D. W. Griffin, M. N. Birmele, K. D. Perry, P. D. Ward, and M. S. Roberts. 2013. Intercontinental Dispersal of Bacteria and Archaea by Transpacific Winds. Applied and Environmental Microbiology 79:1134-1139.

Söderberg, K., A. Probanza, A. Jumpponen, and E. Bååth. 2004. The microbial community in the rhizosphere determined by community-level physiological profiles (CLPP) and direct soil–and cfu–PLFA techniques. Applied Soil Ecology 25:135-145.

Stachowicz, J., R. Whitlatch, and R. Osman. 1999. Species diversity and invasion resistance in a marine ecosystem. Science 286:1577-1579.

Page 18: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 9 1

Stecher, B., R. Denzler, L. Maier, F. Bernet, M. J. Sanders, D. J. Pickard, M. Barthel, A. M. Westendorf, K. A. Krogfelt, A. W. Walker, M. Ackermann, U. Dobrindt, N. R. Thomson, and W. Hardt. 2012. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proceedings of the National Academy of Sciences of the United States of America 109:1269-1274.

Stecher, B., S. Chaffron, R. Kaeppeli, S. Hapfelmeier, S. Freedrich, T. C. Weber, J. Kirundi, M. Suar, K. D. McCoy, C. von Mering, A. J. Macpherson, and W. Hardt. 2010. Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria. Plos Pathogens 6:e1000711.

Stevens, M. P., T. J. Humphrey, and D. J. Maskell. 2009. Molecular insights into farm animal and zoonotic Salmonella infections. Philosophical Transactions of the Royal Society B-Biological Sciences 364:2709-2723.

Stevens, P., and J. D. van Elsas. 2010. A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 98:359-377.

Stüken, A., J. Rücker, T. Endrulat, K. Preussel, M. Hemm, B. Nixdorf, U. Karsten, and C. Wiedner. 2006. Distribution of three alien cyanobacterial species (Nostocales) in northeast Germany: Cylindrospermopsis raciborskii, Anabaena bergii and Aphanizomenon aphanizomenoides. Phycologia 45:696-703.

Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology 62:625-630.

TTeam, R. C. 2014. R: a language and environment for statistical computing. Vienna,

Austria: R Foundation for Statistical Computing; 2012. Open access available at: http://cran.r-project.org :.

Thiennimitr, P., S. E. Winter, M. G. Winter, M. N. Xavier, V. Tolstikov, D. L. Huseby, T. Sterzenbach, R. M. Tsolis, J. R. Roth, and A. J. Baeumler. 2011. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proceedings of the National Academy of Sciences of the United States of America 108:17480-17485.

Tilman, D. 1977. Resource Competition between Planktonic Algae - Experimental and Theoretical Approach. Ecology 58:338-348.

Tilman, D. 1982. Resource Competition and Community Structure. (Mpb-17). Princeton University Press.

Tilman, D. 1985. The Resource-Ratio Hypothesis of Plant Succession. American Naturalist 125:827-852.

Page 19: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 9 2 | S O I L M I C RO B I A L I N VA S I O N S

Tilman, D. 1999. The ecological consequences of changes in biodiversity: A search for general principles 101. Ecology 80:1455-1474.

Tilman, D. 2004. Niche tradeoffs, neutrality, and community structure: A stochastic theory of resource competition, invasion, and community assembly. Proceedings of the National Academy of Sciences of the United States of America 101:10854-10861.

Timmusk, S., I. A. Abd El-Daim, L. Copolovici, T. Tanilas, A. Kannaste, L. Behers, E. Nevo, G. Seisenbaeva, E. Stenstrom, and U. Niinemets. 2014. Drought-Tolerance of Wheat Improved by Rhizosphere Bacteria from Harsh Environments: Enhanced Biomass Production and Reduced Emissions of Stress Volatiles. Plos One 9:e96086.

Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Applied and Environmental Microbiology 56:782-787.

UUl Haq, I., M. Zhang, P. Yang, and J. D. van Elsas. 2014. The Interactions of Bacteria

with Fungi in Soil: Emerging Concepts. Advances in Applied Microbiology, Vol 89 89:185-215.

Vvan Elsas, J. D., M. Chiurazzi, C. A. Mallon, D. Elhottova, V. Kristufek, and J. F.

Salles. 2012. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences of the United States of America 109:1159-1164.

van Elsas, J. D., P. Hill, A. Chronakova, M. Grekova, Y. Topalova, D. Elhottova, and V. Kristufek. 2007. Survival of genetically marked Escherichia coli O157 : H7 in soil as affected by soil microbial community shifts. Isme Journal 1:204-214.

van Elsas, J.D., and J. Jansson. 2007. Modern soil microbiology. CRc Press.Van Nevel, S., K. De Roy, and N. Boon. 2013. Bacterial invasion potential in water is

determined by nutrient availability and the indigenous community. FEMS microbiology ecology 85:593-603.

vanVeen, J. A., L. S. vanOverbeek, and J. D. vanElsas. 1997. Fate and activity of microorganisms introduced into soil. Microbiology and Molecular Biology Reviews 61:121-135.

Vargas, R., and T. Hattori. 1986. Protozoan Predation of Bacterial-Cells in Soil Aggregates. FEMS microbiology ecology 38:233-242.

Vendeville, A., K. Winzer, K. Heurlier, C. M. Tang, and K. R. Hardie. 2005. Making’sense’of metabolism: autoinducer-2, LuxS and pathogenic bacteria. Nature Reviews Microbiology 3:383-396.

Page 20: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 9 3

Vessey, J. K. 2003. Plant growth promoting rhizobacteria as biofertilizers. Plant and Soil 255:571-586.

Vitousek, P. M., C. M. D’Antonio, L. L. Loope, and R. Westbrooks. 1996. Biological invasions as global environmental change. American Scientist 84:468-478.

Vitousek, P. M., L. R. Walker, L. D. Whiteaker, D. Mueller-Dombois, and P. A. Matson. 1987. Biological Invasion by Myrica faya Alters Ecosystem Development in Hawaii. Science (New York, N.Y.) 238:802-804.

Vivant, A., D. Garmyn, P. Maron, V. Nowak, and P. Piveteau. 2013. Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil. Plos One 8 (10), e76911.

Vos, M., P. J. Birkett, E. Birch, R. I. Griffiths, and A. Buckling. 2009. Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil. Science 325:833-833.

WWallace, R. 1985. Synergism between Different Species of Proteolytic Rumen Bacteria.

Current microbiology 12:59-63.Wang, H., A. M. Ibekwe, J. Ma, L. Wu, J. Lou, Z. Wu, R. Liu, J. Xu, and S. R. Yates.

2014. A glimpse of Escherichia coli O157:H7 survival in soils from eastern China. Science of the Total Environment 476:49-56.

Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73:5261-5267.

Warnes, G. R., B. Bolker, L. Bonebakker, R. Gentleman, W. Huber, A. Liaw, T. Lumley, M. Maechler, A. Magnusson, and S. Moeller. 2009. gplots: Various R programming tools for plotting data. R package version 2:.

Weekers, P. H., P. L. Bodelier, J. P. Wijen, and G. D. Vogels. 1993. Effects of Grazing by the Free-Living Soil Amoebae Acanthamoeba castellanii, Acanthamoeba polyphaga, and Hartmannella vermiformis on Various Bacteria. Applied and Environmental Microbiology 59:2317-2319.

Weller, D. M. 1988. Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annual Review of Phytopathology 26:379-407.

Wertz, S., V. Degrange, J. I. Prosser, F. Poly, C. Commeaux, N. Guillaumaud, and X. Le Roux. 2007. Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance. Environmental microbiology 9:2211-2219.

Wertz, S., V. Degrange, J. I. Prosser, F. Poly, C. Commeaux, T. Freitag, N. Guillaumaud, and X. L. Roux. 2006. Maintenance of soil functioning following erosion of microbial diversity. Environmental microbiology 8:2162-2169.

Page 21: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

1 9 4 | S O I L M I C RO B I A L I N VA S I O N S

West, S. A., A. S. Griffin, A. Gardner, and S. P. Diggle. 2006. Social evolution theory for microorganisms. Nature Reviews Microbiology 4:597-607.

West, S. A., A. S. Griffin, and A. Gardner. 2007. Evolutionary explanations for cooperation. Current Biology 17:R661-R672.

Westphal, A., M. L. Williams, F. Baysal-Gurel, J. T. LeJeune, and B. B. McSpadden Gardener. 2011. General suppression of Escherichia coli O157:H7 in sand-based dairy livestock bedding. Applied and Environmental Microbiology 77:2113-2121.

White, D., J. Stair, and D. Ringelberg. 1996. Quantitative comparisons ofin situ microbial biodiversity by signature biomarker analysis. Journal of industrial microbiology 17:185-196.

Whitney, K. D., and C. A. Gabler. 2008. Rapid evolution in introduced species,’invasive traits’ and recipient communities: challenges for predicting invasive potential. Diversity and Distributions 14:569-580.

Whittaker, R. H. 1960. Vegetation of the Siskiyou mountains, Oregon and California. Ecological Monographs 30:279-338.

Wicker, E., P. Lefeuvre, J. de Cambiaire, C. Lemaire, S. Poussier, and P. Prior. 2012. Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA. Isme Journal 6:961-974.

Winding, A., K. Hund-Rinke, and M. Rutgers. 2005. The use of microorganisms in ecological soil classification and assessment concepts. Ecotoxicology and environmental safety 62:230-248.

Winfield, M., and E. Groisman. 2003. Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli. Applied and Environmental Microbiology 69:3687-3694.

Woese, C. R., and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America 74:5088-5090.

Wohlgemuth, S., G. Loh, and M. Blaut. 2010. Recent developments and perspectives in the investigation of probiotic effects. International Journal of Medical Microbiology 300:3-10.

YYang, Y., C. Campbell, L. Clark, C. Cameron, and E. Paterson. 2006. Microbial

indicators of heavy metal contamination in urban and rural soils. Chemosphere 63:1942-1952.

Yao, Z., H. Wang, L. Wu, J. Wu, P. C. Brookes, and J. Xu. 2014. Interaction between the Microbial Community and Invading Escherichia coli O157:H7 in Soils from Vegetable Fields. Applied and Environmental Microbiology 80:70-76.

Page 22: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical

R E F E R E N C E S | 1 9 5

ZZavaleta, E., and K. Hulvey. 2004. Realistic species losses disproportionately reduce

grassland resistance to biological invaders. Science 306:1175-1177.Zelles, L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the

characterisation of microbial communities in soil: a review. Biology and Fertility of Soils 29:111-129.

Zhang, T., H. Wang, L. Wu, J. Lou, J. Wu, P. C. Brookes, and J. Xu. 2013. Survival of Escherichia coli O157:H7 in Soils from Jiangsu Province, China. Plos One 8:e81178.

Zoetendal, E. G., A. D. Akkermans, W. M. Akkermans-van Vliet, de Visser, J Arjan GM, and W. M. de Vos. 2001. The host genotype affects the bacterial community in the human gastronintestinal tract. Microbial Ecology in Health and Disease 13:129-134.

Page 23: Soil microbial invasions V2 - Rijksuniversiteit GroningenOutbreak of gastroenteritis in a nursery school caused by a strain ... ecology by integrating hypotheses into a single theoretical