Evolutionary instability of symbiotic function in Bradyrhizobium japonicum

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Sachs, Joel L ^a   Russell, James E ^a,b   Hollowell, Amanda C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b GEORGIA GWINNETT COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BRADYRHIZOBIUM JAPONICUM; CONTROLLED STUDY; GENE LOCUS; GENOTYPE; IN VITRO STUDY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NODULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; SYMBIONT; SYMBIOSIS; BRADYRHIZOBIUM; CLASSIFICATION; EVOLUTION; GENETICS; POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM; BRADYRHIZOBIUM JAPONICUM; EUKARYOTA;

BIOLOGICAL EVOLUTION; BRADYRHIZOBIUM; PHYLOGENY; POLYMERASE CHAIN REACTION; SYMBIOSIS;

EID: 80355129320     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026370     Document Type: Article

References (51)

1. Sachs JL, Essenberg CJ, Turcotte MM, (2011) New paradigms for the evolution of beneficial infections. Trends Ecol Evol 26: 202-209.
2. Sachs JL, Skophammer RG, Regus JU, (2011) Evolutionary transitions in bacterial symbiosis. Proc Natl Acad Sci USA 108: 10800-10807.
3. Bright M, Bulgheresi S, (2010) A complex journey: transmission of microbial symbionts. Nat Rev Microbiol 8: 218-230.
4. Savage DC, (1977) Microbial Ecology of Gastrointestinal-Tract. Ann Rev Microbiol 31: 107-133.
5. Sachs JL, Kembel SW, Lau AH, Simms EL, (2009) In Situ Phylogenetic Structure and Diversity of Wild Bradyrhizobium Communities. Appl Environ Microbiol 75: 4727-4735.
6. Huss-Danell K, Frej AK, (1986) Distribution of Frankia in Soils from Forest and Afforestation Sites in Northern Sweden. Plant Soil 90: 407-417.
7. Mueller UG, Dash D, Rabeling C, Rodrigues A, (2008) Coevolution between Attine Ants and Actinomycete Bacteria: A Reevaluation. Evolution 62: 2894-2912.
8. Mueller UG, Ishak H, Lee JC, Sen R, Gutell RR, (2010) Placement of attine ant-associated Pseudonocardia in a global Pseudonocardia phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models. Antonie Van Leeuwenhoek 98: 195-212.
9. Nussbaumer AD, Fisher CR, Bright M, (2006) Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 441: 345-348.
10. Kikuchi Y, Hosokawa T, Fukatsu T, (2007) Insect-microbe mutualism without vertical transmission: a stinkbug acquires a beneficial gut symbiont from the environment every generation. Appl Environ Microbiol 73: 4308-4316.
11. Kikuchi Y, Hosokawa T, Fukatsu T, (2011) An ancient but promiscuous host-symbiont association between Burkholderia gut symbionts and their heteropteran hosts. ISME Journal 5: 446-460.
12. Visick KL, Ruby EG, (2006) Vibrio fischeri and its host: it takes two to tango. Curr Opin Micobiol 9: 632-638.
13. O'Brien H, Miadlikowska J, Lutzoni F, (2005) Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen Peltigera. Eur J of Phycol 40: 363-378.
14. Keeler KH, (1985) Cost:benefit models of mutualism. The Biology of Mutualism, Ecology and Evolution Boucher DH Oxford University Press pp. 100-127.
15. Bull JJ, Rice WR, (1991) Distinguishing Mechanisms for the Evolution of Cooperation. J Theor Biol 149: 63-74.
16. Sachs JL, (2006) Cooperation within and among species. J Evol Biol 19: 1415-1418.
17. Sachs JL, Simms EL, (2006) Pathways to mutualism breakdown. Trends Ecol Evol 21: 585-592.
18. Sachs JL, Simms EL, (2008) The origins of uncooperative rhizobia. Oikos 7: 961-966.
19. Holland JN, DeAngelis DL, (2009) Consumer-resource theory predicts dynamic transitions between outcomes of interspecific interactions. Ecol Lett 12: 1357-1366.
20. Denison RF, Kiers ET, (2004) Lifestyle alternatives for rhizobia: mutualism, parastitism, and forgoing symbiosis. FEMS Microbiol Lett 237: 187-193.
21. Nishiguchi MK, Nair VS, (2003) Evolution of symbiosis in the Vibroonaceae: a combined approach using molecules and physiology. Int J Syst Evol Microbiol 53: 2019-2026.
22. Sachs JL, Ehinger MO, Simms EL, (2010) Origins of cheating and loss of symbiosis in wild Bradyrhizobium. J Evol Biol 23: 1075-1089.
23. Sawada H, Kuykendall LD, Young JM, (2003) Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J Gen Appl Microbiol 49: 155-179.
24. Sprent JI, Sutherland JM, Faria SM, (1987) Some aspects of the biology of nitrogen-fixing organisms. Philos Trans Roy Soc Lond B Biol Sci 317: 111-129.
25. Lodwig EM, et al. (2003) Amino-acid cycling drives nitrogen fixation in the legume- Rhizobium symbiosis. Nature 422: 722-726.
26. Wernegreen JJ, Riley MA, (1999) Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages. Mol Biol Evol 16: 98-113.
27. Moulin L, Bena G, Boivin-Masson C, Stepkowski T, (2004) Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus. Mol Phylogenet Evol 30: 720-732.
28. Sachs JL, et al. (2010) Host control over infection and proliferation of a cheater symbiont. J Evol Biol 23: 1075-1089.
29. Somasegaran P, Hoben J, (1994) New York Springer-Verlag.
30. Vinuesa P, Silva C, Werner D, Martinez Romero E, (2005) Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34: 29-54.
31. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuc Acid Res 25: 3389-3402.
32. Thompson JD, Higgins DG, Gibson TJ, (1994) Clustal-W- Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nuc Acid Res 22: 4673-4680.
33. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL, (2004) Bayesian phylogenetic analysis of combined data. Syst Biol 53: 47-67.
34. Akaike H, (1973) Information theory and an extension of the maximum likelihood principle. Second International Symposium on Information Theory, Budapest, Hungary.
35. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
36. Maddison WP, Maddison DR, (2011) Mesquite: a modular system for evolutionary analysis. Version 2.75http://mesquiteproject.org.
37. Huelsenbeck JP, Nielsen R, Bollback JP, (2003) Stochastic mapping of morphological characters. Syst Biol 52: 131-158.
38. Bollback JP, (2006) SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics pp. 7.
39. Pagel M, Meade A, Barker D, (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53: 673-684.
40. Parker MA, (2000) Divergent Bradyrhizobium symbionts on Tachigali versicolor from Barro Colorado Island, Panama. Syst Appl Microbiol 23: 585-590.
41. Kaneko T, et al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9: 189-197.
42. Segovia L, Pinero D, Palacios R, Martinez Romero E, (1991) Genetic-Structure of a Soil Population of Nonsymbiotic Rhizobium-Leguminosarum. Appl Environ Microbiol 57: 426-433.
43. Pongsilp N, Teaumroong N, Nuntagij A, Boonkerd N, Sadowski MJ, (2002) Genetic structure of indigenous non-nodulating and nodulating populations of Bradyrhizobium in soils from Thailand. Symbiosis 33: 39-58.
44. Laguerre G, Bardin M, Amarger N, (1993) Isolation from Soil of Symbiotic and Nonsymbiotic Rhizobium-Leguminosarum by DNA Hybridization. Can J Microbiol 39: 1142-1149.
45. Rao JR, Fenton M, Jarvis BDW, (1994) Symbiotic Plasmid Transfer in Rhizobium-Leguminosarum Biovar Trifolii and Competition between the Inoculant Strain Icmp2163 and Transconjugant Soil Bacteria. Soil Biol Biochem 26: 339-351.
46. Sullivan JT, Ronson CW, (1998) Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci USA 95: 5145-5149.
47. Velicer GJ, et al. (2006) Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc Natl Acad Sci USA 103: 8107-8112.
48. Lee DH, Palsson BO, (2010) Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol. Appl Environ Microbiol 76: 6327-6327.
49. Zurkowski W, Lorkiewicz Z, (1979) Plasmid-Mediated Control of Nodulation in Rhizobium-Trifolii. Arch Micriobiol 123: 195-201.
50. Djordjevic MA, Zurkowski W, Rolfe BG, (1982) Plasmids and Stability of Symbiotic Properties of Rhizobium-Trifolii. J Bacteriol 151: 560-568.
51. Uchiumi T, et al. (2004) Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J Bacteriol 186: 2439-2448.