Functional Microbiome for Crop Improvement Under a Changing Environment
Abbaci Hocine
Laboratoire de Maitrise des Énergies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
Search for more papers by this authorBensidhoum Leila
Laboratoire de Maitrise des Énergies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
Search for more papers by this authorHouali Karim
Department of Microbiology and Biochemistry, Université Mouloud Mammeri de Tizi Ouzou, Tizi Ouzou, Algeria
Search for more papers by this authorNabti Elhafid
Laboratoire de Maitrise des Énergies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
Search for more papers by this authorAbbaci Hocine
Laboratoire de Maitrise des Énergies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
Search for more papers by this authorBensidhoum Leila
Laboratoire de Maitrise des Énergies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
Search for more papers by this authorHouali Karim
Department of Microbiology and Biochemistry, Université Mouloud Mammeri de Tizi Ouzou, Tizi Ouzou, Algeria
Search for more papers by this authorNabti Elhafid
Laboratoire de Maitrise des Énergies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
Search for more papers by this authorAlok Kumar Srivastava
ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, India
Search for more papers by this authorPrem Lal Kashyap
ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, Haryana, India
Search for more papers by this authorMadhumita Srivastava
Sunbeam College for Women, Varanasi, Uttar Pradesh, India
Search for more papers by this authorSummary
In a context of a changing environment, it is crucial to maximize our knowledge on all the mechanisms involved in plant microbiome interactions at the genetic, physiological, and ecological levels. This chapter reviews some recent advances in plant microbiome investigations and describes potential applications of such associations for the mitigation of both abiotic and biotic stresses to improve crop health and productivity. Understanding the full potential of microbes in the ecosystem functioning in general and their complex beneficial interactions in improving agriculture productivity in particular requires the development and improvement of compatible tools that can be verified in biological assays, always bearing in mind their reproducibility in situ on different scales. Progress in the engineering microbiome have made it possible to show how meta-omics (metataxonomic, metagenomics, metatranscriptomics, and metaproteomics) can be potentially powerful tools to gain deeper knowledge of the functional capabilities of the microbiome and how they can shape ecosystems.
References
- Adam, A. 2008. Elicitation de la résistance systémique induite chez la tomate et le concombre et activation de la voie de la lipoxygénase par des rhizobactéries non-pathogènes. [Elicitation of induced systemic resistance in tomato and cucumber and activation of the lipoxygenase pathway by non-pathogenic rhizobacteria]. Doctoral thesis, Université de Liege.
- Ahmad, F., Ahmad, I., and Khan, M.S. (2008). Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiological Research 163 (2): 173–181.
- Ahmad, M., Zahir, Z.A., Nazli, F. et al. (2013). Effectiveness of halo-tolerant, auxin producing Pseudomonas and Rhizobium strains to improve osmotic stress tolerance in mung bean (Vigna radiata L.). Brazilian Journal of Microbiology 44 (4): 1341–1348.
- Ajouz, S. 2009. December. Estimation du potentiel de résistance de Botrytis cinerea à des biofongicides . Avignon. Ciences Agricoles, Université d'Avignon, Français. NNT: 2009AVIG0622.
- Alabouvette, C., Olivain, C., and Steinberg, C. (2006). Biological control of plant diseases: the European situation. European Journal of Plant Pathology 114 (3): 329–341.
- Al-Amin, A.Q., Rasiah, R., and Chenayah, S. (2015). Prioritizing climate change mitigation: an assessment using Malaysia to reduce carbon emissions in future. Environmental Science & Policy 50: 24–33.
- Ali, S.Z., Sandhya, V., Grover, M. et al. (2011). Effect of inoculation with a thermotolerant plant growth promoting Pseudomonas putida strain AKMP7 on growth of wheat (Triticum spp.) under heat stress. Journal of Plant Interactions 6 (4): 239–246.
- Ambrose, K.V., Koppenhöfer, A.M., and Belanger, F.C. (2014). Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses. Scientific Reports 4: 5562.
- Andrew, D.R., Fitak, R.R., Munguia-Vega, A. et al. (2012). Abiotic factors shape microbial diversity in Sonoran Desert soils. Applied and Environmental Microbiology 78 (21): 7527–7537.
- Antoun, H. and Prévost, D. (2005). Ecology of plant growth promoting rhizobacteria. In: PGPR: Biocontrol and Biofertilization (ed. Z.A. Siddiqui), 1–38. Dordrecht: Springer.
- Arndt, C., Chinowsky, P., Robinson, S. et al. (2012). Economic development under climate change rode. Review of Development Economics 16: 369–377.
- Austin, A.T. and Ballaré, C.L. (2014). Plant interactions with other organisms: molecules, ecology and evolution. New Phytologist 204 (2): 257–260.
- Bakker, P.A., Pieterse, C.M., and Van Loon, L.C. (2007). Induced systemic resistance by fluorescent Pseudomonas spp. Phytopathology 97 (2): 239–243.
- Barea, J.M. (2015). Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions. Journal of Soil Science and Plant Nutrition 15 (2): 261–282.
- Benítez, T., Rincón, A.M., Limón, M.C., and Codon, A.C. (2004). Biocontrol mechanisms of Trichoderma strains. International Microbiology 7 (4): 249–260.
- Bensidhoum, L., Nabti, E., Tabli, N. et al. (2016). Heavy metal tolerant Pseudomonas protegens isolates from agricultural well water in northeastern Algeria with plant growth promoting, insecticidal and antifungal activities. European Journal of Soil Biology 75: 38–46.
-
Bent, E. (2006). Induced systemic resistance mediated by plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF). In: (eds. S. Tuzun and E. Bent) Multigenic and Induced Systemic Resistance in Plants, 225–258. Boston, MA: Springer.
10.1007/0-387-23266-4_10 Google Scholar
- Berg, G., Grube, M., Schloter, M., and Smalla, K. (2014). The plant microbiome and its importance for plant and human health. Frontiers in Microbiology 5: Article 491. https://doi.org/10.3389/fmicb.2014.00491.
- Birgander, J., Rousk, J., and Olsson, P.A. (2014). Comparison of fertility and seasonal effects on grassland microbial communities. Soil Biology and Biochemistry 76: 80–89.
- Biswas, K.K. and Sen, C. (2000). Management of stem rot of groundnut caused by Sclerotium rolfsii through Trichoderma harzianum . Indian Phytopathology 53 (3): 290–295.
- Blaha, D., Prigent-Combaret, C., Mirza, M.S., and Moënne-Loccoz, Y. (2006). Phylogeny of the 1-aminocyclopropane-1-carboxylic acid deaminase-encoding gene acdS in phytobeneficial and pathogenic Proteobacteria and relation with strain biogeography. FEMS Microbiology Ecology 56 (3): 455–470.
- Boddey, R.M., Baldani, V.L., Baldani, J.I., and Döbereiner, J. (1986). Effect of inoculation of Azospirillum spp. on nitrogen accumulation by field-grown wheat. Plant and Soil 95 (1): 109–121.
- Bojanowski, A. 2011. Molécules antifongiques et activité antagoniste de deux souches de Pseudomonas envers Helminthosporium solani, agent responsable de la tache argentée de la pomme de terre . Thesis, Université Laval.
- Bonfils, C., Duffy, P.B., Santer, B.D. et al. (2008). Identification of external influences on temperatures in California. Climatic Change 87 (1): 43–55.
- Borriss, R. (2011). Use of plant-associated Bacillus strains as biofertilizers and biocontrol agents in agriculture. In: Bacteria in Agrobiology: Plant Growth Responses, 41–76. Berlin, Heidelberg: Springer.
- Bulgarelli, D., Garrido-Oter, R., Münch, P.C. et al. (2015). Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host & Microbe 17 (3): 392–403.
- Calvo, P., Ormeño-Orrillo, E., Martínez-Romero, E., and Zúñiga, D. (2010). Characterization of Bacillus isolates of potato rhizosphere from Andean soils of Peru and their potential PGPR characteristics. Brazilian Journal of Microbiology 41 (4): 899–906.
- Carson, J.K., Gonzalez-Quiñones, V., Murphy, D.V. et al. (2010). Low pore connectivity increases bacterial diversity in soil. Applied and Environmental Microbiology 76 (12): 3936–3942.
- Carvalho, T.L.G., Balsemão-Pires, E., Saraiva, R.M. et al. (2014). Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria. Journal of Experimental Botany 65 (19): 5631–5642.
- Castro, H.F., Classen, A.T., Austin, E.E. et al. (2010). Soil microbial community responses to multiple experimental climate change drivers. Applied and Environmental Microbiology 76 (4): 999–1007.
- Charest, M.H., Beauchamp, C.J., and Antoun, H. (2005). Effects of the humic substances of de-inking paper sludge on the antagonism between two compost bacteria and Pythium ultimum . FEMS Microbiology Ecology 52 (2): 219–227.
- Cherif, H., Marasco, R., Rolli, E. et al. (2015). Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought. Environmental Microbiology Reports 7 (4): 668–678.
- Chet, I. (1987). Trichoderma: application, mode of action, and potential as biocontrol agent of soilborne plant pathogenic fungi. In: Innovative Approaches to Plant Disease Control (ed. I. Chet), 137–160. Wiley.
- Crickmore, N., Zeigler, D.R., Feitelson, J. et al. (1998). Revision of the nomenclature for the Bacillus thuringiensis pesticidal crystal proteins. Microbiology and Molecular Biology Reviews 62 (3): 807–813.
- D'Annibale, A., Ricci, M., Leonardi, V. et al. (2005). Degradation of aromatic hydrocarbons by white-rot fungi in a historically contaminated soil. Biotechnology and Bioengineering 90 (6): 723–731.
- D'Annibale, A., Rosetto, F., Leonardi, V. et al. (2006). Role of autochthonous filamentous fungi in bioremediation of a soil historically contaminated with aromatic hydrocarbons. Applied and Environmental Microbiology 72 (1): 28–36.
-
Das, S., Raj, R., Mangwani, N. et al. (2014). Heavy metals and hydrocarbons: adverse effects and mechanism of toxicity. In: Microbial Biodegradation and Bioremediation (ed. S. Das), 23–54. Elsevier.
10.1016/B978-0-12-800021-2.00002-9 Google Scholar
- Dell'Amico, E., Cavalca, L., and Andreoni, V. (2008). Improvement of Brassica napus growth under cadmium stress by cadmium-resistant rhizobacteria. Soil Biology and Biochemistry 40 (1): 74–84.
- Duffy, B.K. and Défago, G. (1999). Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Applied and Environmental Microbiology 65 (6): 2429–2438.
-
Elad, Y. and Stewart, A. (2007). Microbial control of Botrytis spp. In: Botrytis: Biology, Pathology and Control (eds. Y. Elad et al.), 223–241. Dordrecht: Springer.
10.1007/978-1-4020-2626-3_13 Google Scholar
- Elad, Y., Chet, I., and Katan, J. (1980). Trichoderma harzianum: a biocontrol agent effective against Sclerotium rolfsii and Rhizoctonia solani . Phytopathology 70 (2): 119–121.
- El-Hamshary, O.I.M., Abo-Aba, S.E.M., Awad, N., and Gomaa, A.M. (2008). Genetic profile of Bacillus cereus and Bacillus subtilis indigenous isolates and their performance as bio-control agent against the plant pathogen Fusarium oxysporum . Research Journal of Cell and Molecular Biology 2 (2): 30–38.
- de Escudero, I.R., Estela, A., Porcar, M. et al. (2006). Molecular and insecticidal characterization of a Cry1I protein toxic to insects of the families Noctuidae, Tortricidae, Plutellidae, and Chrysomelidae. Applied and Environmental Microbiology 72 (7): 4796–4804.
- Federici, E., Leonardi, V., Giubilei, M.A. et al. (2007). Addition of allochthonous fungi to a historically contaminated soil affects both remediation efficiency and bacterial diversity. Applied Microbiology and Biotechnology 77 (1): 203–211.
- Fernando, W.D., Nakkeeran, S., and Zhang, Y. (2005). Biosynthesis of antibiotics by PGPR and its relation in biocontrol of plant diseases. In: PGPR: Biocontrol and Biofertilization (ed. Z.A. Siddiqui), 67–109. Dordrecht: Springer.
- Fierer, N. and Jackson, R.B. (2006). The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 103 (3): 626–631.
-
Fritsche, W. and Hofrichter, M. (2005). Aerobic degradation of recalcitrant organic compounds by microorganisms. In: Environmental Biotechnology: Concepts and Applications (eds. H.-J. Jördening and J. Winter). Wiley-VCH.
10.1002/3527604286.ch7 Google Scholar
- Gamalero, E. and Glick, B.R. (2015). Bacterial modulation of plant ethylene levels. Plant Physiology 169 (1): 13–22.
- Garrido-Sanz, D., Meier-Kolthoff, J.P., Göker, M. et al. (2016). Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One 11 (2): e0150183.
- Glick, B.R. (2005). Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase. FEMS Microbiology Letters 251 (1): 1–7.
- Glick, B.R., Penrose, D.M., and Li, J. (1998). A model for the lowering of plant ethylene concentrations by plant growth-promoting bacteria. Journal of Theoretical Biology 190 (1): 63–68.
-
Glick, B.R., Cheng, Z., Czarny, J., and Duan, J. (2007). Promotion of plant growth by ACC deaminase-producing soil bacteria. In: New Perspectives and Approaches in Plant Growth-Promoting Rhizobacteria Research (ed. J.C. Shuttle), 329–339. Dordrecht: Springer.
10.1007/978-1-4020-6776-1_8 Google Scholar
- Gopalakrishnan, S., Sathya, A., Vijayabharathi, R. et al. (2015). Plant growth promoting rhizobia: challenges and opportunities. 3 Biotech 5 (4): 355–377.
- Grimes, H.D. and Mount, M.S. (1984). Influence of Pseudomonas putida on nodulation of Phaseolus vulgaris . Soil Biology and Biochemistry 16 (1): 27–30.
- Grover, M., Ali, S.Z., Sandhya, V. et al. (2011). Role of microorganisms in adaptation of agriculture crops to abiotic stresses. World Journal of Microbiology and Biotechnology 27 (5): 1231–1240.
-
Gusain, Y.S., Singh, U.S., and Sharma, A.K. (2015). Bacterial mediated amelioration of drought stress in drought tolerant and susceptible cultivars of rice (Oryza sativa L.). African Journal of Biotechnology
14 (9): 764–773.
10.5897/AJB2015.14405 Google Scholar
- Haas, D. and Keel, C. (2003). Regulation of antibiotic production in root-colonizing Pseudomonas spp. and relevance for biological control of plant disease. Annual Review of Phytopathology 41 (1): 117–153.
- Haines, A., Kovats, R.S., Campbell-Lendrum, D., and Corvalán, C. (2006). Climate change and human health: impacts, vulnerability and public health. Public Health 120 (7): 585–596.
- Han, H.S. and Lee, K.D. (2005). Plant growth promoting rhizobacteria effect on antioxidant status, photosynthesis, mineral uptake and growth of lettuce under soil salinity. Research Journal of Agriculture and Biological Sciences 1 (3): 210–215.
- Handelsman, J. and Stabb, E.V. (1996). Biocontrol of soilborne plant pathogens. The Plant Cell 8 (10): 1855.
- Hardoim, P.R., van Overbeek, L.S., and van Elsas, J.D. (2008). Properties of bacterial endophytes and their proposed role in plant growth. Trends in Microbiology 16 (10): 463–471.
- Hartmann, A., Schmid, M., Van Tuinen, D., and Berg, G. (2009). Plant-driven selection of microbes. Plant and Soil 321 (1–2): 235–257.
- Hartmann, A., Rothballer, M., Hense, B.A., and Schröder, P. (2014). Bacterial quorum sensing compounds are important modulators of microbe-plant interactions. Frontiers in Plant Science 5: 131.
- Hirsch, P.R. and Mauchline, T.H. (2012). Who's who in the plant root microbiome? Nature Biotechnology 30 (10): 961.
- Iavicoli, A., Boutet, E., Buchala, A., and Métraux, J.P. (2003). Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. Molecular Plant-Microbe Interactions 16 (10): 851–858.
- Inglis, G.D., Goettel, M.S., Butt, T.M., and Strasser, H.E. (2001). Use of hyphomycetous fungi for managing insect pests. In: Fungi as Biocontrol Agents (eds. T.M. Butt et al.), 23–69.
- Jamali, F., Sharifi-Tehrani, A., Lutz, M.P., and Maurhofer, M. (2009). Influence of host plant genotype, presence of a pathogen, and coinoculation with Pseudomonas fluorescens strains on the rhizosphere expression of hydrogen cyanide-and 2, 4-diacetylphloroglucinol biosynthetic genes in P. fluorescens biocontrol strain CHA0. Microbial Ecology 57 (2): 267–275.
- Jha, Y., Subramanian, R.B., and Patel, S. (2011). Combination of endophytic and rhizospheric plant growth promoting rhizobacteria in Oryza sativa shows higher accumulation of osmoprotectant against saline stress. Acta Physiologiae Plantarum 33 (3): 797–802.
- Johansson, P.M., 2003. Biocontrol of Fusarium in wheat-introducing bacteria to a system of complex interactions . Doctoral thesis, Swedish University of Agricultural Sciences Uppsala, 2003.
- Jourdan, E., Ongena, M. and Thonart, P. 2008. Caractéristiques moléculaires de l'immunité des plantes induite par les rhizobactéries non pathogènes. BASE.
- Kanwal, S., Ilyas, N., Batool, N., and Arshad, M. (2017). Amelioration of drought stress in wheat by combined application of PGPR, compost, and mineral fertilizer. Journal of Plant Nutrition 40 (9): 1250–1260.
-
Kaymak, H.C. (2010). Potential of PGPR in agricultural innovations. In: Plant Growth and Health Promoting Bacteria (ed. K.D. Maheshwari), 45–79. Berlin, Heidelberg: Springer.
10.1007/978-3-642-13612-2_3 Google Scholar
- Kempster, V.N., Scott, E.S., and Davies, K.A. (2002). Evidence for systemic, cross-resistance in white clover (Trifolium repens) and annual medic (Medicago truncatula var truncatula) induced by biological and chemical agents. Biocontrol Science and Technology 12 (5): 615–623.
-
Kerry, B.R. (2001). Exploitation of the nematophagous fungal Verticillium chlamydosporium Goddard for the biological control of root-knot nematodes (Meloidogyne spp.). In: Fungi as Biocontrol Agents: Progress, Problems and Potential, 155–167. Wallingford, UK: CAB International.
10.1079/9780851993560.0155 Google Scholar
- Kieber, J.J. (1997). The ethylene signal transduction pathway in Arabidopsis . Journal of Experimental Botany 48 (2): 211–218.
- Knight, R., Vrbanac, A., Taylor, B.C. et al. (2018). Best practices for analysing microbiomes. Nature Reviews Microbiology 16 (7): 410.
- Kunert, K.J., Vorster, B.J., Fenta, B.A. et al. (2016). Drought stress responses in soybean roots and nodules. Frontiers in Plant Science 7: 1015.
- Lareen, A., Burton, F., and Schäfer, P. (2016). Plant root-microbe communication in shaping root microbiomes. Plant Molecular Biology 90 (6): 575–587.
- Lavelle, P., Blouin, M., Boyer, J. et al. (2004). Plant parasite control and soil fauna diversity. Comptes Rendus Biologies 327 (7): 629–638.
- van Lenteren, J.C., Bolckmans, K., Köhl, J. et al. (2018). Biological control using invertebrates and microorganisms: plenty of new opportunities. BioControl 63 (1): 39–59.
- Leonardi, V., Giubilei, M.A., Federici, E. et al. (2008). Mobilizing agents enhance fungal degradation of polycyclic aromatic hydrocarbons and affect diversity of indigenous bacteria in soil. Biotechnology and Bioengineering 101 (2): 273–285.
- Lim, H.S., Kim, Y.S., and Kim, S.D. (1991). Pseudomonas stutzeri YPL-1 genetic transformation and antifungal mechanism against Fusarium solani, an agent of plant root rot. Applied and Environmental Microbiology 57 (2): 510–516.
-
Malik, K.A., Bilal, R., Mehnaz, S. et al. (1997). Association of nitrogen-fixing, plant-growth-promoting rhizobacteria (PGPR) with kallar grass and rice. In: Opportunities for Biological Nitrogen Fixation in Rice and Other Non-Legumes, 37–44. Dordrecht: Springer.
10.1007/978-94-011-5744-5_5 Google Scholar
- Manteau, S., Abouna, S., Lambert, B., and Legendre, L. (2003). Differential regulation by ambient pH of putative virulence factor secretion by the phytopathogenic fungus Botrytis cinerea . FEMS Microbiology Ecology 43 (3): 359–366.
- Mantelin, S. and Touraine, B. (2004). Plant growth-promoting bacteria and nitrate availability: impacts on root development and nitrate uptake. Journal of Experimental Botany 55 (394): 27–34.
- Marasco, R., Rolli, E., Ettoumi, B. et al. (2012). A drought resistance-promoting microbiome is selected by root system under desert farming. PLoS One 7 (10): e48479.
- Marschner, P., Crowley, D., and Rengel, Z. (2011). Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis–model and research methods. Soil Biology and Biochemistry 43 (5): 883–894.
- Mayak, S., Tirosh, T., and Glick, B.R. (2004). Plant growth-promoting bacteria that confer resistance to water stress in tomatoes and peppers. Plant Science 166 (2): 525–530.
- Meena, H., Ahmed, M.A., and Prakash, P. (2015). Amelioration of heat stress in wheat, Triticum aestivum by PGPR (Pseudomonas aeruginosa strain 2CpS1). Bioscience Biotechnology Research Communications 8 (2): 171–174.
- Meena, K.K., Sorty, A.M., Bitla, U.M. et al. (2017). Abiotic stress responses and microbe-mediated mitigation in plants: the omics strategies. Frontiers in Plant Science 8: 172.
- Miliute, I., Buzaite, O., Baniulis, D., and Stanys, V. (2015). Bacterial endophytes in agricultural crops and their role in stress tolerance: a review. Zemdirbyste-Agriculture 102 (4): 465–478.
- Mommer, L., Kirkegaard, J., and van Ruijven, J. (2016). Root–root interactions: towards a rhizosphere framework. Trends in Plant Science 21 (3): 209–217.
- Nabti, E., Sahnoune, M., Adjrad, S. et al. (2007). A halophilic and osmotolerant Azospirillum brasilense strain from Algerian soil restores wheat growth under saline conditions. Engineering in Life Sciences 7 (4): 354–360.
- Nabti, E., Sahnoune, M., Ghoul, M. et al. (2010). Restoration of growth of durum wheat (Triticum durum var. waha) under saline conditions due to inoculation with the rhizosphere bacterium Azospirillum brasilense NH and extracts of the marine alga Ulva lactuca . Journal of Plant Growth Regulation 29 (1): 6–22.
-
Nabti, E.H., Mokrane, N., Ghoul, M. et al. (2013). Isolation and characterization of two halophilic Bacillus (B. licheniformis and Bacillus sp.) with antifungal activity. Journal of Ecology of Health & Environment
1 (1): 13–17.
10.12785/jehe/010102 Google Scholar
- Nadeem, S.M., Hussain, I., Naveed, M. et al. (2006). Performance of plant growth promoting rhizobacteria containing ACC-deaminase activity for improving growth of maize under salt-stressed conditions. Pakistan Journal of Agricultural Sciences 43 (3–4): 114–121.
- Nandakumar, R., Babu, S., Viswanathan, R. et al. (2001). Induction of systemic resistance in rice against sheath blight disease by Pseudomonas fluorescens . Soil Biology and Biochemistry 33 (4–5): 603–612.
- Nies, D.H. (1999). Microbial heavy-metal resistance. Applied Microbiology and Biotechnology 51 (6): 730–750.
- Olcott, M.H., Henkels, M.D., Rosen, K.L. et al. (2010). Lethality and developmental delay in Drosophila melanogaster larvae after ingestion of selected Pseudomonas fluorescens strains. PLoS One 5 (9): e12504.
- Pal, K.K. and Gardener, B.M. 2006. Biological control of plant pathogens. The Plant Health Instructor [electronic resource].
- Péchy-Tarr, M., Bruck, D.J., Maurhofer, M. et al. (2008). Molecular analysis of a novel gene cluster encoding an insect toxin in plant-associated strains of Pseudomonas fluorescens . Environmental Microbiology 10 (9): 2368–2386.
-
Quan, C.S., Wang, X., and Fan, S.D. (2010). Antifungal compounds of plant growth promoting rhizobacteria and its action mode. In: Plant Growth and Health Promoting Bacteria (ed. K.D. Maheshwari), 117–156. Berlin, Heidelberg: Springer.
10.1007/978-3-642-13612-2_6 Google Scholar
- Raaijmakers, J.M., Vlami, M., and De Souza, J.T. (2002). Antibiotic production by bacterial biocontrol agents. Antonie van Leeuwenhoek 81 (1–4): 537.
- Ramamoorthy, V., Viswanathan, R., Raguchander, T. et al. (2001). Induction of systemic resistance by plant growth promoting rhizobacteria in crop plants against pests and diseases. Crop Protection 20 (1): 1–11.
- Reich, P.B. and Oleksyn, J. (2004). Global patterns of plant leaf N and P in relation to temperature and latitude. Proceedings of the National Academy of Sciences of the United States of America 101 (30): 11001–11006.
- Rolli, E., Marasco, R., Vigani, G. et al. (2015). Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environmental Microbiology 17 (2): 316–331.
-
Ronseaux, S., Clément, C., and Barka, E. (2013). Interaction of Ulocladium atrum, a potential biological control agent, with Botrytis cinerea and grapevine plantlets. Agronomy
3 (4): 632–647.
10.3390/agronomy3040632 Google Scholar
- Rousk, J., Brookes, P.C., and Bååth, E. (2009). Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization. Applied and Environmental Microbiology 75 (6): 1589–1596.
- Rudrappa, T., Biedrzycki, M.L., Kunjeti, S.G. et al. (2010). The rhizobacterial elicitor acetoin induces systemic resistance in Arabidopsis thaliana . Communicative & Integrative Biology 3 (2): 130–138.
- Ryu, C.M., Farag, M.A., Hu, C.H. et al. (2003). Bacterial volatiles promote growth in Arabidopsis . Proceedings of the National Academy of Sciences of the United States of America 100 (8): 4927–4932.
- Ryu, C.M., Farag, M.A., Hu, C.H. et al. (2004). Bacterial volatiles induce systemic resistance in Arabidopsis . Plant Physiology 134 (3): 1017–1026.
- de Salamone, I.G., Döbereiner, J., Urquiaga, S., and Boddey, R.M. (1996). Biological nitrogen fixation in Azospirillum strain-maize genotype associations as evaluated by the 15 N isotope dilution technique. Biology and Fertility of Soils 23 (3): 249–256.
- Santoyo, G., Pacheco, C.H., Salmerón, J.H., and León, R.H. (2017). The role of abiotic factors modulating the plant-microbe-soil interactions: toward sustainable agriculture. A review. Spanish Journal of Agricultural Research 15 (1): 13.
- Schardl, C.L., Young, C.A., Faulkner, J.R. et al. (2012). Chemotypic diversity of epichloae, fungal symbionts of grasses. Fungal Ecology 5 (3): 331–344.
- Segata, N., Boernigen, D., Tickle, T.L. et al. (2013). Computational meta'omics for microbial community studies. Molecular Systems Biology 9 (1): 666.
- Sergaki, C., Lagunas, B., Lidbury, L. et al. (2018). Challenges and approaches in microbiome research: from fundamental to applied. Frontiers in Plant Science https://doi.org/10.3389/fpls.2018.01205.
- Shaharoona, B., Arshad, M., Zahir, Z.A., and Khalid, A. (2006). Performance of Pseudomonas spp. containing ACC-deaminase for improving growth and yield of maize (Zea mays L.) in the presence of nitrogenous fertilizer. Soil Biology and Biochemistry 38 (9): 2971–2975.
- Shams-Ghahfarokhi, M., Kalantari, S., and Razzaghi-Abyaneh, M. (2013). Terrestrial bacteria from agricultural soils: versatile weapons against aflatoxigenic fungi. In: Aflatoxins: Recent Advances and Future Prospects (ed. M. Razzaghi-Abyaneh), 23–40. https://doi.org/10.5772/45918.
- Shoresh, M., Harman, G.E., and Mastouri, F. (2010). Induced systemic resistance and plant responses to fungal biocontrol agents. Annual Review of Phytopathology 48: 21–43.
- Shrivastava, P. and Kumar, R. (2015). Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi Journal of Biological Sciences 22 (2): 123–131.
- Siddiqui, I.A. and Shaukat, S.S. (2003). Suppression of root-knot disease by Pseudomonas fluorescens CHA0 in tomato: importance of bacterial secondary metabolite, 2, 4-diacetylpholoroglucinol. Soil Biology and Biochemistry 35 (12): 1615–1623.
- Singh, R. (2014). Microorganism as a tool of bioremediation technology for cleaning environment: a review. Proceedings of the International Academy of Ecology and Environmental Sciences 4 (1): 1.
- Siwar, C., Alam, M., Murad, M., and Al-Amin, A.Q. (2009). A review of the linkages between climate change, agricultural sustainability and poverty in Malaysia. International Review of Business Research Papers (ISSN 1832-9543) 5 (6): 309–321.
- Song, H., Nan, Z., Song, Q. et al. (2016). Advances in research on Epichloë endophytes in Chinese native grasses. Frontiers in Microbiology 7: 1399.
- Su, F., Jacquard, C., Villaume, S. et al. (2015). Burkholderia phytofirmans PsJN reduces impact of freezing temperatures on photosynthesis in Arabidopsis thaliana . Frontiers in Plant Science 6: 810.
-
Szilagyi-Zecchin, V.J., Mógor, Á.F., and Figueiredo, G.G.O. (2016). Strategies for characterization of agriculturally important bacteria. In: Microbial Inoculants in Sustainable Agricultural Productivity (ed. D.P. Singh), 1–21. New Delhi: Springer.
10.1007/978-81-322-2647-5_1 Google Scholar
- Tabli, N., Rai, A., Bensidhoum, L. et al. (2018). Plant growth promoting and inducible antifungal activities of irrigation well water-bacteria. Biological Control 117: 78–86.
- Tang, C. and Thomson, B.D. (1996). Effects of solution pH and bicarbonate on the growth and nodulation of a range of grain legume species. Plant and Soil 186 (2): 321–330.
- Thornton, P.K., Ericksen, P.J., Herrero, M., and Challinor, A.J. (2014). Climate variability and vulnerability to climate change: a review. Global Change Biology 20 (11): 3313–3328.
- Tilman, D., Balzer, C., Hill, J., and Befort, B.L. (2011). Global food demand and the sustainable intensification of agriculture. Proceedings of the National Academy of Sciences of the United States of America 108 (50): 20260–20264.
- Tripathi, P., Rabara, R.C., Reese, R.N. et al. (2016). A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes. BMC Genomics 17 (1): 102.
- Trivedi, P., Schenk, P.M., Wallenstein, M.D., and Singh, B.K. (2017). Tiny Microbes, Big Yields: enhancing food crop production with biological solutions. Microbial Biotechnology 10 (5): 999–1003.
- Vallad, G.E. and Goodman, R.M. (2004). Systemic acquired resistance and induced systemic resistance in conventional agriculture. Crop Science 44 (6): 1920–1934.
- Vandenkoornhuyse, P., Quaiser, A., Duhamel, M. et al. (2015). The importance of the microbiome of the plant holobiont. New Phytologist 206 (4): 1196–1206.
- Vardharajula, S., Zulfikar Ali, S., Grover, M. et al. (2011). Drought-tolerant plant growth promoting Bacillus spp.: effect on growth, osmolytes, and antioxidant status of maize under drought stress. Journal of Plant Interactions 6 (1): 1–14.
-
Viswanathan, R. and Samiyappan, R. (2004). Secondary metabolites production by Pseudomonas spp. strains antagonistic to Colletotrichum falcatum causing red rot disease in sugarcane. Acta Phytopathologica Entomologica et Hungarica
39: 28–37.
10.1556/APhyt.39.2004.1-3.4 Google Scholar
- Voisard, C., Keel, C., Haas, D., and Dèfago, G. (1989). Cyanide production by Pseudomonas fluorescens helps suppress black root rot of tobacco under gnotobiotic conditions. The EMBO Journal 8 (2): 351–358.
- Wang, M., Li, E., Liu, C. et al. (2017). Functionality of root-associated bacteria along a salt marsh primary succession. Frontiers in Microbiology 8: 2102.
- Wani, P.A., Khan, M.S., and Zaidi, A. (2007). Synergistic effects of the inoculation with nitrogen-fixing and phosphate-solubilizing rhizobacteria on the performance of field-grown chickpea. Journal of Plant Nutrition and Soil Science 170 (2): 283–287.
- Weller, D.M. (2007). Pseudomonas biocontrol agents of soilborne pathogens: looking back over 30 years. Phytopathology 97 (2): 250–256.
- Weller, D.M., Mavrodi, D.V., van Pelt, J.A. et al. (2012). Induced systemic resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato by 2, 4-diacetylphloroglucinol-producing Pseudomonas fluorescens . Phytopathology 102 (4): 403–412.
- Whipps, J.M. (2001). Microbial interactions and biocontrol in the rhizosphere. Journal of Experimental Botany 52: 487–511.
- Zhalnina, K., Dias, R., de Quadros, P.D. et al. (2015). Soil pH determines microbial diversity and composition in the park grass experiment. Microbial Ecology 69 (2): 395–406.
- Zhang, W., Li, F., and Nie, L. (2010). Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology 156 (2): 287–301.