A Genomic Encyclopedia of the root nodule bacteria: Assessing genetic diversity through a systematic biogeographic survey

Standards in Genomic Sciences

Volumn 10, Issue FEBRUARY2015, 2015, Pages

  Reeve, Wayne ^a   Ardley, Julie ^a   Tian, Rui ^a   Eshragi, Leila ^a   Yoon, Je Won ^a   Ngamwisetkun, Pinyaruk ^a   Seshadri, Rekha ^b   Ivanova, Natalia N ^b   Kyrpides, Nikos C ^b,c  

^a MURDOCH UNIVERSITY   (Australia)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Diversity; GEBA RNB; Nitrogen fixation; Root nodule bacteria; Symbiosis

Indexed keywords

NUCLEIC ACID;

ALPHAPROTEOBACTERIA; BACTERIAL GROWTH; BETAPROTEOBACTERIA; BIOGEOGRAPHY; GENE SEQUENCE; GENETIC VARIABILITY; GENOMICS; MICROBIAL GENOME; MOLECULAR GENETICS; MULTILOCUS SEQUENCE TYPING; NITROGEN FIXATION; NODULATION; NONHUMAN; NOTE; PHYLOGENY; RHIZOBIACEAE; SAMPLING; SYMBIOSIS;

EID: 84940529532     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.1186/1944-3277-10-14     Document Type: Note

References (35)

1. Lewis G, Schrire B, Mackinder B, Lock M. Legumes of the World. Richmond, Surrey: Royal Botanic Gardens, Kew; 2005
2. Graham PH, Vance CP. Legumes: importance and constraints to greater use. Plant Physiol. 2003;131:872-7
3. Sprent JI, James EK. Legume evolution: where do nodules and mycorrhizas fit in? Plant Physiol. 2007;144:575-81
4. Sprent JI, Ardley JK, James EK. From North to South: a latitudinal look at legume nodulation processes. S Afr J Bot. 2013;89:31-41
5. Socolow RH. Nitrogen management and the future of food: Lessons from the management of energy and carbon. Proc Natl Acad Sci U S A. 1999;96:6001-8
6. Galloway JN, Schlesinger WH, Levy H, Michaels A, Schnoor JL. Nitrogen fixation: anthropogenic enhancement-environmental response. Global Biogeochem Cy. 1995;9:235-52
7. Tauer L. Economic impact of future biological nitrogen fixation technologies on United States agriculture. Plant Soil. 1989;119:261-70
8. Vance CP. Symbiotic nitrogen fixation and phosphorus acquisition: plant nutrition in a world of declining renewable resources. Plant Physiol. 2001;127:390-7
9. Gregorich EG, Rochette P, VandenBygaart AJ, Angers DA. Greenhouse gas contributions of agricultural soils and potential mitigation practices in Eastern Canada. Soil Till Res. 2005;83:53-72
10. Robertson GP, Vitousek PM. Nitrogen in agriculture: balancing the cost of an essential resource. Annu Rev Env Resour. 2009;34:97-125
11. Ray DK, Mueller ND, West PC, Foley JA. Yield trends are insufficient to double global crop production by 2050. Plos One. 2013;8:e66428
12. Howieson JG, O’Hara GW, Carr SJ. Changing roles for legumes in Mediterranean agriculture: developments from an Australian perspective. Field Crop Res. 2000;65:107-22
13. Zohary M, Heller D. The Genus Trifolium. Jerusalem: The Israel Academy of Sciences and Humanities Ahva Printing Press; 1984
14. Gladstones JS, Atkins CA, Hamblin J. Lupins as Crop Plants: Biology, Production, and Utilization. Wallingford, Oxon, UK: New York, NY, USA: CAB International; 1998
15. Howieson J, Yates R, O'Hara G, Ryder M, Real D. The interactions of Rhizobium leguminosarum biovar trifolii in nodulation of annual and perennial Trifolium spp from diverse centres of origin. Aust J Exp Agric. 2005;45:199-207
16. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, et al. A phylogenydriven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009;462:1056-60
17. Reeve W, Chain P, O'Hara G, Ardley J, Nandesena K, Brau L, et al. Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genom Sci. 2010;2:77-86
18. Reeve W, O'Hara G, Chain P, Ardley J, Brau L, Nandesena K, et al. Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers. Stand Genom Sci. 2010;2:347-56
19. Reeve W, O'Hara G, Chain P, Ardley J, Brau L, Nandesena K, et al. Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum. Stand Genom Sci. 2010;2:66-76
20. Reeve WG, Nandasena K, Yates R, Tiwari R, O'Hara G, Ninawi M, et al. Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075T. Stand Genom Sci. 2013;9:294-303
21. Reeve W, Nandasena K, Yates R, Tiwari R, O'Hara G, Ninawi M, et al. Complete genome sequence of Mesorhizobium australicum type strain (WSM2073T). Stand Genom Sci. 2013;9:410-9
22. Nanadasena K, Yates R, Tiwari R, O'Hara G, Howieson J, Ninawi M, et al. Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271T). Stand Genom Sci. 2013;9:462-72
23. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI standard operating procedure for the annotations of microbial genomes. Stand Genom Sci. 2009;1:63-7
24. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, et al. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010;7:455-7
25. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25:2271-8
26. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone S-A, Angiuoli S, et al. Toward a standards-compliant genomic and metagenomic publication record. Omics. 2008;12:157-60
27. Garrity GM. The state of standards in genomic sciences. Stand Genom Sci. 2011;5:262-8
28. Poole PS, Hynes MF, Johnston AWB, Tiwari RP, Reeve WG, Downie JA. Physiology of root nodule bacteria. In: Dilworth MJ, James EK, Sprent JI, Newton WE, editors. Nitrogen-Fixing Legume Symbioses, vol 7 Dordrecht, The Netherlands: Springer; 2008. p. 241-92
29. Farrell AE, Plevin RJ, Turner BT, Jones AD, O'Hare M, Kammen DM. Ethanol can contribute to energy and environmental goals. Science. 2006;311:506-8
30. Hill J, Nelson E, Tilman D, Polasky S, Tiffany D. Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc Natl Acad Sci U S A. 2006;103:11206-10
31. Samuel S, Scott PT, Gresshoff PM. Nodulation in the legume biofuel feedstock tree Pongamia pinnata. Agric Res. 2013;2:207-14
32. Parniske M. Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Micro. 2008;6:763-75
33. Deakin WJ, Broughton WJ. Symbiotic use of pathogenic strategies: rhizobial protein secretion systems. Nat Rev Micro. 2009;7:312-20
34. Toft C, Andersson SGE. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet. 2010;11:465-75
35. Charpentier M, Oldroyd G. How close are we to nitrogen-fixing cereals? Curr Opin Plant Biol. 2010;13:556-64