Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice

Microbiological Research

Volumn 190, Issue , 2016, Pages 12-18

  Wang, Wenfeng ^a   Zhai, Yanyan ^a   Cao, Lixiang ^a   Tan, Hongming ^a   Zhang, Renduo ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

Actinobacteriome; Dietzia; Endophyte; Plant microbiome; Pseudonocardia; Rice

Indexed keywords

BACTERIA;

ACTINOBACTERIOME; DIETZIA; ENDOPHYTE; MICROBIOME; PSEUDONOCARDIA; RICE;

GRAIN (AGRICULTURAL PRODUCT);

ABUNDANCE ESTIMATION; BACTERIUM; DISEASE RESISTANCE; ENDOPHYTE; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MUTUALISM; NUTRIENT USE EFFICIENCY; RICE; ROOT; STEM; TAXONOMY;

ACTINOBACTERIA; AGROCOCCUS; CITRICOCCUS; CORYNEBACTERIUM; DIETZIA; MAGNAPORTHE GRISEA; MYCOBACTERIUM; NOCARDIOIDES; OTUS; PSEUDONOCARDIA; SALINIBACTERIUM; STREPTOMYCES;

ACTINOBACTERIA; BIODIVERSITY; CLASSIFICATION; ENDOPHYTE; GENETICS; HIGH THROUGHPUT SEQUENCING; MICROBIOLOGY; ORYZA; PLANT ROOT; PLANT SEED; PLANT STEM;

ACTINOBACTERIA; BIODIVERSITY; ENDOPHYTES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; ORYZA; PLANT ROOTS; PLANT STEMS; SEEDS;

EID: 84969142704     PISSN: 09445013     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micres.2016.05.003     Document Type: Article

References (33)

1. Aly A.H., Debbab A., Proksch P. Fungal endophytes: unique plant inhabitants with great promises. Appl. Environ. Microbiol. 2011, 90:1829-1845.
2. Becerril-Espinosa A., Freel K.C., Jensen P.R., Soria-Mercado I.E. Marine actinobacteria from the gulf of California: diversity, abundance and secondary metabolite biosynthetic potential. Anton Leeuw 2013, 103:809-819.
3. Bokulich N.A., Subramanian S., Faith J.J., Gevers D., Gordon J.I., Knight R., Mills D.A., Caporaso J.G. Quality-filtering vastly improves diversity estimates from illumine amplicon sequencing. Nat. Methods 2013, 10:57-59.
4. Cao L., Qiu Z., You J., Tan H., Zhou S. Isolation and characterization of endophytic streptomycete antagonists of fusarium wilt pathogen from surface-sterilized banana roots. FEMS Microbiol. Lett. 2005, 247:147-152.
5. Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Huntley J., Fierer N., Owens S.M., Betley J., Fraser L., Bauer M., Gormley N., Gilbert J.A., Smith G., Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012, 6:1621-1624.
6. Duncan K.R., Haltli B., Gill K.A., Correa H., Berrué F., Kerr R.G. Exploring the diversity and metabolic potential of actinomycetes from temperate marine sediments from Newfoundland Canada. J. Ind. Microbiol. Biotechnol. 2015, 42:57-72.
7. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
8. Edgar R.C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 2013, 10:996-998.
9. Edwards J., Johnson C., Santos-Medellin C., Lurie E., Podishetty N.K., Bhatnagar S., Eisen J.A., Sundaresan V. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. U. S. A. 2015, 10.1073/pnas.1414592112.
10. Getha K., Vikineswary S. Antagonistic effects of Streptomyces violaceusniger strain G10 on Fusarium oxysporum f.sp. cubense race 4: Indirect evidence for the role of antibiosis in the antagonistic process. J. Ind. Microbiol. Biotechnol. 2002, 28:303-310.
11. Gundel P.E., Rudgers J.A., Ghersa C.M. Incorporating the process of vertical transmission into understanding of host-symbiont dynamics. Oikos 2011, 120:1121-1128.
12. Haas B.J., Gevers D., Earl A.M., Feldgarden M., Ward D.V., Giannoukos G., Ciulla D., Tabbaa D., Highlander S.K., Sodergren E., Methé B., DeSantis T.Z., Petrosino J.F., Knight R., Birren B.W. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011, 21:494-504.
13. Hardoim P.R., Hardoim C.C.P., van Overbeek L.S., van Elsas J.D. Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS One 2012, 7:e30438. 10.1371/journal.pone.0030438.
14. Hirsch P.R., Mauchline T.H. Who's who in the plant root microbiome. Nat. Biotechnol. 2012, 30:961-962.
15. Kõljalg U., Nilsson R.H., Abarenkov K., Tedersoo L., Taylor A.F.S., Bahram M., Bates S.T., Bruns T.D., Bengtsson-palme J., Callaghan T.M., Douglas B., Drenkhan T., Eberhardt U., Dueñas M., Grebenc T., Griffith G.W., Hartmann M., Kirk P.M., Kohout P., Larsson E., Lindahl B., Lücking R., Martín M.P., Matheny P.B., Nguyen N.H., Niskanen T., Oja J., Peay K.G., Peintner U., Peterson M., Põldmaa K., Saag L., Saar I., Schüßler A., Scott J.A., Senés C., Smith M.E., Suija A., Taylor D.L., Telleria M.T., Weiss M. Larsson K-H. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 2013, 22:5271-5277.
16. Kemp P.F., Aller J.Y. Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol. Ecol. 2004, 47:161-177.
17. Li Q., Jiang Y., Ning P., Zheng L., Huang J., Li G., Jiang D., Hsiang T. Suppression of Magnaporthe oryzae by culture filtrates of Streptomyces globisporus JK-1. Biol. Control 2011, 58:139-148.
18. Lindahl B.D., Nilsson R.H., Tedersoo L., Abarenkov K., Carlsen T., Kjøller R., Kõljalg U., Pennanen T., Rosendahl S., Stenlid J., Kauserud H. Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide. New Phytol. 2013, 199:288-299.
19. Lundberg D.S., Lebeis S.L., Paredes S.H., Yourstone S., Gehring J., Malfatti S., Tremblay J., Engelbrektson A., Kunin V., del Rio T.G., Edgar R.C., Eickhorst T., Ley R.E., Hugenholtz P., Tringe S.G., Dangl J.L. Defining the core Arabidopsis thaliana root microbiome. Nature 2012, 488:86-90.
20. Magoč T., Salzberg S.L.F.L.A.S.H. fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011, 27:2957-2963.
21. Mendes R., Garbeva P., Raaijmakers J.M. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 2013, 37:634-663.
22. Ofek M., Hadar Y., Minz D. Colonization of cucumber seeds by bacteria during germination. Environ. Microbiol. 2011, 13:2794-2807.
23. Okubo T., Ikeda S., Sasaki K., Ohshima K., Hattori M., Sato T., Minamisawa K. Phylogeny and functions of bacterial communities associated with field-grown rice shoots. Microbes Environ. 2014, 29:329-332.
24. Ondov B.D., Bergman N.H., Phillippy A.M. Interactive metagenomic visualization in a web browser. BMC Bioinf. 2011, 12:385.
25. Prabavathy V.R., Mathivanan N., Murugesan K. Control of blast and sheath blight diseases of rice using antifungal metabolites produced by Streptomyces sp. PM5. Biol. Control 2006, 39:313-319.
26. Priya H., Prasanna R., Ramakrishnan B., Bidyarani N., Babu S., Thapa S., Renuka N. Influence of cyanobacterial inoculation on the culturable microbiome and growth of rice. Microbiol. Res. 2015, 171:78-89.
27. Shi Y., Yang H., Zhang T., Sun J., Lou K. Illumina-based analysis of endophytic bacterial diversity and space-time dynamics in sugar beet on the north slope of Tianshan mountain. Appl. Microbiol. Biotechnol. 2014, 98:6375-6385.
28. Tian X., Cao L., Tan H., Han W., Chen M., Liu Y., Zhou S. Diversity of cultivated and uncultivated actinobacterial endophytes in the stems and roots of rice. Microb. Ecol. 2007, 53:700-707.
29. Turner T.R., James E.K., Poole P.S. The plant microbiome. Genome Biol. 2013, 14:209. http://genomebiology.com/2013/14/6/209.
30. Ventura M., Canchaya C., Tauch A., Chantra G., Fitzgerald G.F., Chater K.F., van Sinderen D. Genomics of actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. Rev. 2007, 71:495-548.
31. Vivas M., Kemler M., Slippers B. Maternal effects on tree phenotypes: considering the microbiome. Trends Plant Sci. 2015, 20:541-544.
32. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
33. Zhao K., Penttinen P., Chen Q., Guan T., Lindström K., Ao X.L., Zhang L., Zhang X. The rhizosphere of traditional medicinal plants in Panxi China, host a diverse selection of actinobacteria with antimicrobial properties. Appl. Microbiol. Biotechnol. 2012, 94:1321-1335.