Abstract
Plants are complex biological systems under constant and dynamic interaction with diverse microbial communities which influence their development. The microbial communities associated to plants could possess specific functions on basis on colonized tissue. In crop plants, microbial diversity and their beneficial effects can be affected by plant genotype and farming activities. In this context, we explored biodiversity of Pseudomonas strains isolated from leaves of pepper and lettuce crops, through phylogenetic analysis and physiological profile coupled with specific biochemical tests for plant-microorganism interaction. Bacterial isolates showed genetic and phenotypic diversity despite to be isolated from domestic plant crops. The importance of biodiversity at taxonomic and functional level found in phyllosphere of plant crops and its relationship to achieving sustainability is discussed.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- 16S rRNA:
-
(16S ribosomal RNA)
- PGPB:
-
(Plant Growth Promoting Bacteria)
- LOPAT:
-
(Levan production; Oxidase presence; Pectinolytic activity in potatoes; Arginine hydrolase presence; Hypersensitive response in Tobacco)
- BK:
-
(King B medium)
- BLASTn:
-
(Basic Local Alignment Search Tool)
- NCBI:
-
(National Center for Biotechnology Information)
- SINA:
-
(SILVA Incremental Aligner tool)
- MUSCLE:
-
(Multiple Sequence Comparison by Log-Expectation)
- ML:
-
(Maximum likelihood)
- NBRIP:
-
(National Botanical Research Institute’s Phosphate growth medium)
- CAS:
-
(Chrome azurol S)
- IAA:
-
(Indole acetic acid)
- Cmm:
-
(Clavibacter michiganensis subsp. michiganensis)
- TN93 + G:
-
(Tamura-Nei model with a discrete Gamma distribution)
- HR:
-
(Reaction of hypersensitivity)
- BIC:
-
(Bayesian Information Criterion).
References
Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. J King Saud Univ Sci 26:1–20. https://doi.org/10.1016/j.jksus.2013.05.001
Ahmad F, Ahmad I, Khan MS (2008) Screenig of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res 163:173–181. https://doi.org/10.1016/j.micres.2006.04.001
Ahmed E, Holmström SJ (2014) Siderophores in environmental research: roles and applications. Microb Biotechnol 7:196–208. https://doi.org/10.1111/1751-7915.12117
Alexander DB, Zuberer DA (1991) Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biol Fertil Soils 12:39–45. https://doi.org/10.1007/BF00369386
Amkraz N, Boudyach EH, Boubaker H et al (2010) Screening for fluorescent pseudomonades, isolated from the rizhosphere of tomato, for antagonistic activity toward Clavibacter michiganensis subsp. michiganensis. World J Microbiol Biotechnol 26:1059–1065. https://doi.org/10.1007/s11274-009-0270-5
Bal HB, Das S, Dangar TK, Adhya TK (2013) ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants. J Basic Microbiol 53:972–984. https://doi.org/10.1002/jobm.201200445
Berg G, Rybakova D, Grube M, Köberl M (2016) The plant microbiome explored: implications for experimental botany. J Exp Bot 67:995–1002. https://doi.org/10.1093/jxb/erv466
Brenner DJ, Farmer J (2015). Enterobacteriaceae. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P, Hedlund B, Dedysh S (eds) Bergey's Manual of Systematics of Archaea and Bacteria, pp1–24 https://doi.org/10.1002/9781118960608.fbm00222
Compant S, Samad A, Faist H, Sessitsch A (2019) A review on the plant microbiome: ecology, functions, and emerging trends in microbial application. J Adv Res 19:29–37. https://doi.org/10.1016/j.jare.2019.03.004
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Etesami H, Alikhani HA, Hosseini HM (2015) Indole-3-acetic acid (IAA) production trait, a useful screening to select endophytic and rhizosphere competent bacteria for rice growth promoting agents. MethodsX 2:72–78. https://doi.org/10.1016/j.mex.2015.02.008
Evtushenko LI, Takeuchi M (2006) The family Microbacteriaceae. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, 3rd edn. NY pp, Springer, New York, pp 1020–1098
Felestrino ÉB, Santiago IF, Freitas LD et al (2017) Plant growth promoting bacteria associated with Langsdorffia hypogaea-rhizosphere-host biological interface: a neglected model of bacterial prospection. Front Microbiol 8:172. https://doi.org/10.3389/fmicb.2017.00172
Galperin MY (2013) Genome diversity of spore-forming Firmicutes. Microbiol Spectr. https://doi.org/10.1128/microbiolspectrum.TBS-0015-2012
Garrido-Sanz D, Meier-Kolthoff JP, Göker M et al (2016) Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One 11:e0150183. https://doi.org/10.1371/journal.pone.0150183
Garrity GM, Bell JA, Lilburn T (2015) Pseudomonadaceae. In: In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P, Hedlund B, Dedysh S (eds). Manual of Systematics of Archaea and Bacteria, Bergey's. https://doi.org/10.1002/9781118960608.fbm00232
Gomila M, Peña A, Mulet M et al (2015) Phylogenomics and systematics in Pseudomonas. Front Microbiol 6:214. https://doi.org/10.3389/fmicb.2015.00214
Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224. https://doi.org/10.1093/molbev/msp259
van Groenigen J, Huygens D, Boeckx P et al (2015) The soil N cycle: new insights and key challenges. Soil 1:235–256. https://doi.org/10.5194/soil-1-235-2015
Heuer H, Krsek M, Baker P et al (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241
Hirsch PR, Mauchline TH (2015) The importance of the microbial N cycle in soil for crop plant nutrition. Adv Appl Microbiol 93:45–71. https://doi.org/10.1016/bs.aambs.2015.09.001
Hulin MT, Armitage AD, Vicente JG et al (2018) Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium). New Phytol 219:672–696. https://doi.org/10.1111/nph.15182
Jaspers E, Overmann J (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 70:4831–4839. https://doi.org/10.1128/AEM.70.8.4831-4839.2004
Kaluzna M, Janse J, Young JM (2012) Detection and identification methods and new tests as used and developed in the framework of cost 873 for bacteria pathogenic to stone fruits and nuts Pseudomonas syringae pathovars. J Plant Pathol 94:S1.117–S1.126. https://doi.org/10.4454/jpp.v94i1sup.019
Kembel SW, O’Connor TK, Arnold HK et al (2014) Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc Natl Acad Sci U S A 111:13715–13720. https://doi.org/10.1073/pnas.1216057111
Kiani T, Khan SA, Noureen N et al (2019) Isolation and characterization of culturable endophytic bacterial community of stripe rust-resistant and stripe rust-susceptible Pakistani wheat cultivars. Int Microbiol 22:191–201. https://doi.org/10.1007/s10123-018-00039-z
Klockgether J, Cramer N, Wiehlmann L et al (2011) Pseudomonas aeruginosa genomic structure and diversity. Front Microbiol 2:150. https://doi.org/10.3389/fmicb.2011.00150
Krapp A (2015) Plant nitrogen assimilation and its regulation: a complex puzzle with missing pieces. Curr Opin Plant Biol 25:115–122. https://doi.org/10.1016/j.pbi.2015.05.010
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Lanteigne C, Gadkar VJ, Wallon T et al (2012) Production of DAPG and HCN by Pseudomonas sp. LBUM300 contributes to the biological control of bacterial canker of tomato. Phytopathology 102:967–973. https://doi.org/10.1094/PHYTO-11-11-0312
Lelliott RA, Billing E, Hayward AC (1966) A determinative scheme for the fluorescent plant pathogenic Pseudomonas. J Appl Bacteriol 29:470–448. https://doi.org/10.1111/j.1365-2672.1966.tb03499.x
Loper JE, Hassan KA, Mavrodi DV et al (2012) Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS genet 8(7): e1002784. https://doi.org/10.1371/journal.pgen.1002784
Louden BC, Haarmann D, Lynne AM (2011) Use of blue agar CAS assay for siderophore detection. J Microbiol Biol Educ 12:51–53. https://doi.org/10.1128/jmbe.v12i1.249
Macfaddin JF (2000) Biochemical tests for identification of medical bacteria, 3rd edn. Lippincott Williams & Wilkins, Philadelphia, PA
Martínez-Castro E, Jarquín-Galvez R, Alpuche-Solís ÁG et al (2018) Bacterial wilt and canker of tomato: fundamentals of a complex biological system. Euphytica 214:72. https://doi.org/10.1007/s10681-018-2140-4
Matsutani M, Fukushima K, Kayama C et al (2014) Replacement of a terminal cytochrome c oxidase by ubiquinol oxidase during the evolution of acetic acid bacteria. Biochim Biophys Acta 1837:1810–1820. https://doi.org/10.1016/j.bbabio.2014.05.355
Mendes R, Kruijt M, de Bruijn I et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100. https://doi.org/10.1126/science.1203980
Mulet M, Bennasar A, Lalucat J, García-Valdés E (2009) An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cell Probes 23:140–147. https://doi.org/10.1016/j.mcp.2009.02.001
Nautiyal CS (1999) An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 170:265–270. https://doi.org/10.1111/j.1574-6968.1999.tb13383.x
Octavia S, Lan R (2014) The family Enterobacteriaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes, 4th edn. Springer, Berlin, Heidelberg, pp225–286. https://doi.org/10.1007/978-3-642-38922-1_167
Orem JC, Silva WMC, Raiol T et al (2019) Phylogenetic diversity of aerobic spore-forming Bacillalles isolated from Brazilian soils. Int Microbiol. https://doi.org/10.1007/s10123-019-00080-6
Oteino N, Lally RD, Kiwanuka S et al (2015) Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Front Microbiol 6:745. https://doi.org/10.3389/fmicb.2015.00745
Paulin MM, Novinscak A, Lanteigne C et al (2017) Interaction between 2,4-diacetylphloroglucinol- and hydrogen cyanide-producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the tomato rhizosphere. Appl Environ Microbiol 83:e00073–e00017. https://doi.org/10.1128/AEM.00073-17
Pei AY, Oberdorf WE, Nossa CW et al (2010) Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76:3886–3897. https://doi.org/10.1128/AEM.02953-09
Pérez-Jaramillo JE, Carrión VJ, de Hollander M, Raaijmakers JM (2018) The wild side of plant microbiomes. Microbiome 6:143. https://doi.org/10.1186/s40168-018-0519-z
Pruesse E, Peplies J, Glöckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829. https://doi.org/10.1093/bioinformatics/bts252
Quast C, Pruesse E, Yilmaz P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res 41:D590–D596. https://doi.org/10.1093/nar/gks1219
Radzki W, Gutierrez Mañero FJ, Algar E et al (2013) Bacterial siderophores efifciently provide iron to iron-starved tomato plants in hydroponics culture. Antonie Van Leeuwenhoek 104:321–330. https://doi.org/10.1007/s10482-013-9954-9
Rajwar A, Sahgal M (2016) Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas-specific and rpoD genes. 3 biotech 6:80. https://doi.org/10.1007/s13205-016-0386-x
Rastogi G, Sbodio A, Tech JJ et al (2012) Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field grown lettuce. ISME J 6:1812–1822. https://doi.org/10.1038/ismej.2012.32
Rastogi G, Coaker GL, Leveau JH (2013) New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett 348:1–10. https://doi.org/10.1111/1574-6968.12225
Rijavec T, Lapanje A (2016) Hydrogen cyanide in the rhizosphere: not suppressing plant pathogens, but rather regulating availability of phosphate. Front Microbiol 7:1785. https://doi.org/10.3389/fmicb.2016.01785
Saeid A, Prochownik E, Dobrowolska-Iwanek J (2018) Phosphorus solubilization by Bacillus species. Molecules 23:2897. https://doi.org/10.3390/molecules23112897
Saha M, Sarkar S, Sarkar B et al (2016) Microbial siderophores and their potential applications: a review. Environ Sci Pollut Res Int 23:3984–3999. https://doi.org/10.1007/s11356-015-4294-0
Silby MW, Winstanley C, Godfrey SA et al (2011) Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 35:652–680. https://doi.org/10.1111/j.1574-6976.2011.00269.x
Soni R, Kapoor RA, Kaur M (2017) Evaluation of siderophore production and antimicrobial activity by fluorescent Pseudomonas diversity associated with rhizosphere of apple and pear. Int J Agric Environ Biotechnol 9:1109–1115. https://doi.org/10.5958/2230-732X.2016.00140.6
Sridevi M, Mallaiah KV (2009) Phosphate solubilization by Rhizobium strains. Indian J Microbiol 49:98–102. https://doi.org/10.1007/s12088-009-0005-1
Tayeb L, Ageron E, Grimont F, Grimont PAD (2005) Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156:763–773. https://doi.org/10.1016/j.resmic.2005.02.009
Vacheron J, Desbrosses G, Bouffaud M-L et al (2013) Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci 4:356. https://doi.org/10.3389/fpls.2013.00356
Valot B, Guyeux C, Rolland JY et al (2015) What it takes to be a Pseudomonas aeruginosa? The core genome of the opportunistic pathogen updated. PLoS One 10:e0126468. https://doi.org/10.1371/journal.pone.0126468
Vásquez-Ponce F, Higuera-Llantén S, Pavlov MS et al (2018) Phylogenetic MLSA and phenotypic analysis identification of three probable novel Pseudomonas species isolated on King George Island, south Shetland. Antarctica Braz J Microbiol 49:695–702. https://doi.org/10.1016/j.bjm.2018.02.005
Verma VC, Singh SK, Prakash S (2011) Bio-control and plant growth promotion potential of siderophore producing endophytic Streptomyces from Azadirachta indica a. Juss J Basic Microbiol 51:550–556. https://doi.org/10.1002/jobm.201000155
Xin XF, Kvitko B, He SY (2018) Pseudomonas syringae: what it takes to be a pathogen. Nat Rev Microbiol 16:316–328. https://doi.org/10.1038/nrmicro.2018.17
Yu X, Ai C, Xin L, Zhou G (2011) The siderophore producing bacterium, Bacillus subtilis CAS15, has a biocontrol effect on Fusarium wilt and promotes the growth of pepper. Eur J Soil Biol 47:138–145. https://doi.org/10.1016/j.ejsobi.2010.11.001
Acknowledgments
This work was funded by Consejo Nacional de Ciencia y Tecnología-Secretaría de Educación Pública (CONACyT-SEP Project 236066), Fondo de Apoyo a la Investigación-UASLP (Project C14-FAI-04-05.05) and Programa de Mejoramiento del Profesorado-Secretaría de Educación Pública (PRODEP-SEP Project DSA/103.5/14/7437). We thank anonymous reviewers for their highly constructive and detailed feedback that helped us improve our manuscript substantially.
Author Contribution Statement
JPLA conceived and designed research. SAMS conducted experiments. SAMS, JMS, GAB, JPLA analyzed data. MRA, RFR, RJG contributed new reagents or analytical tools. SAMS, MRVP, JPLA wrote the paper. All authors read and approved the manuscript.
Conflict of interest
The authors declare that they have no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(DOCX 1201 kb)
Rights and permissions
About this article
Cite this article
Medina-Salazar, S.A., Rodríguez-Aguilar, M., Vallejo-Pérez, M.R. et al. Biodiversity of epiphytic Pseudomonas strains isolated from leaves of pepper and lettuce. Biologia 75, 773–784 (2020). https://doi.org/10.2478/s11756-019-00392-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.2478/s11756-019-00392-y