Skip to main content
SpringerLink
Log in

Friends and Foes: Phyto-Microbial Interactions in Molecular Perspective

  • Chapter
  • First Online:
Phyto-Microbiome in Stress Regulation

Part of the book series: Environmental and Microbial Biotechnology ((EMB))

Abstract

Soil acts as an natural abode for plants as well as for diverse micro/macroflora and fauna, and thus provides the rhizosphere environment, the fraction of soil surrounding the root system, where plants interact with their root microbiomes. Plants maintain a continuum of interactions with associated microbes that have effects on their cellular physiology resulting in changes in development and function, which can have both positive and negative outcomes. Plant-microbial or microbial-microbial interactions that occur at the plant root-soil interface can also have dynamic effects on the rhizosphere microbiome that greatly affects the overall health and vigor of plants, a key metric in agricultural productivity. This chapter reviews the current understanding of the range of interactions happening in the rhizosphere and the recent advancements that next generation sequencing technologies have had on the ability to identify and classify the rhizosphere microbiome.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186:2629–2635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Agrios G (2005) Plant pathology, 5th edn. Academic Press, San Diego, CA

    Google Scholar 

  • Akter Z, Pageni B, Lupwayi N, Balasubramanian P (2013) Biological nitrogen fixation and nif H gene expression in dry beans (Phaseolus vulgaris L.). Can J Plant Sci 94:203–212

    Article  Google Scholar 

  • Alexopoulos CJ, Mims C, Blackwell M (1996) Introductory mycology. John Wiley and Sons, New York, NY

    Google Scholar 

  • Badri DV, Chaparro JM, Manter DK, Martinoia E, Vivanco JM (2012) Influence of ATP-binding cassette transporters in root exudation of Phytoalexins, signals, and in disease resistance. Front Plant Sci 3:149

    Article  PubMed  PubMed Central  Google Scholar 

  • Bangera MG, Thomashow LS (1999) Identification and characterization of a gene cluster for synthesis of the polyketide antibiotic 2,4-diacetylphloroglucinol from Pseudomonas fluorescens Q2–87. J Bacteriol 181:3155–3163

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beckman, C. (1987). The nature of wilt diseases of plants (APS press)

    Google Scholar 

  • Benítez T, Rincón AM, Limón MC, Codón AC (2004) Biocontrol mechanisms of Trichoderma strains. Int Microbiol 7:249–260

    PubMed  Google Scholar 

  • Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13

    Article  CAS  PubMed  Google Scholar 

  • Bohlool BB, Schmidt EL (1974) Lectins: a possible basis for specificity in the rhizobium–legume root nodule symbiosis. Science 185:269–271

    Article  CAS  PubMed  Google Scholar 

  • Brodie EL, DeSantis TZ, Parker JPM, Zubietta IX, Piceno YM, Andersen GL (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci U S A 104:299–304

    Article  CAS  PubMed  Google Scholar 

  • Bruehl, G. (1987). Soilborne plant pathogens (Macmillan publishing company)

    Google Scholar 

  • Buée M, De Boer W, Martin F, van Overbeek L, Jurkevitch E (2009) The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant Soil 321:189–212

    Article  CAS  Google Scholar 

  • Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren van Themaat E, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17:392–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bürgmann H, Widmer F, Sigler WV, Zeyer J (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69:1928–1935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bürgmann H, Widmer F, Von Sigler W, Zeyer J (2004) New molecular screening tools for analysis of free-living diazotrophs in soil. Appl Environ Microbiol 70:240–247

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burns R, Hardy R (2012) Nitrogen fixation in bacteria and higher plants. Springer, Berlin

    Google Scholar 

  • Caetano-Anollés G, Wrobel-Boerner E, Bauer WD (1992) Growth and movement of spot inoculated rhizobium meliloti on the root surface of alfalfa. Plant Physiol 98:1181–1189

    Article  PubMed  PubMed Central  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Castañeda LE, Barbosa O (2017) Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests. Peer J 5:e3098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chakravorty S, Helb D, Burday M, Connell N, Alland D (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69:330–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chelius M, Lepo J (1999) Restriction fragment length polymorphism analysis of PCR-amplified nifH sequences from wetland plant rhizosphere communities. Environ Technol 20:883–889

    Article  CAS  Google Scholar 

  • Chen W, Zhang CK, Cheng Y, Zhang S, Zhao H (2013) A comparison of methods for clustering 16S rRNA sequences into OTUs. PLoS One 8:e70837

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chowdhury SP, Hartmann A, Gao X, Borriss R (2015) Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42 - a review. Front Microbiol 6:780

    Article  PubMed  PubMed Central  Google Scholar 

  • Clooney AG, Fouhy F, Sleator RD, O’ Driscoll A, Stanton C, Cotter PD, Claesson MJ (2016) Comparing apples and oranges?: next generation sequencing and its impact on microbiome analysis. PLoS One e0148028:11

    Google Scholar 

  • Costa R, Gomes NCM, Krögerrecklenfort E, Opelt K, Berg G, Smalla K (2007) Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses. Environ Microbiol 9:2260–2273

    Article  CAS  PubMed  Google Scholar 

  • Dakora FD, Phillips DA (2002) Root exudates as mediators of mineral acquisition in low-nutrient environments. Plant Soil 245:35–47

    Article  CAS  Google Scholar 

  • De Lajudie P, Willems A, Nick G, Moreira F, Molouba F, Hoste B, Torck U, Neyra M, Collins MD, Lindström K et al (1998) Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Int J Syst Bacteriol 48(Pt 2):369–382

    Article  PubMed  Google Scholar 

  • De-la-Peña C, Loyola-Vargas VM (2014) Biotic interactions in the rhizosphere: a diverse cooperative enterprise for plant productivity. Plant Physiol 166:701–719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA et al (2012) Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6:1677–1687

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fierer N, Strickland MS, Liptzin D, Bradford MA, Cleveland CC (2009) Global patterns in belowground communities. Ecol Lett 12:1238–1249

    Article  PubMed  Google Scholar 

  • Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017

    Article  CAS  PubMed  Google Scholar 

  • Freitag TE, Prosser JI (2003) Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl Environ Microbiol 69:1359–1371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gaby JC, Buckley DH (2017) The use of degenerate primers in qPCR analysis of functional genes can cause dramatic quantification bias as revealed by investigation of nifH primer performance. Microb Ecol 74:701

    Article  CAS  PubMed  Google Scholar 

  • Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390

    Article  CAS  PubMed  Google Scholar 

  • Gilbert JA, Jansson JK, Knight R (2014) The earth microbiome project: successes and aspirations. BMC Biol 12:69

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamelin J, Fromin N, Tarnawski S, Teyssier-Cuvelle S, Aragno M (2002) nifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass. Environ Microbiol 4:477–481

    Article  CAS  PubMed  Google Scholar 

  • Han Y, Liu X, Benny U, Kistler HC, VanEtten HD (2001) Genes determining pathogenicity to pea are clustered on a supernumerary chromosome in the fungal plant pathogen Nectria haematococca. Plant J 25:305–314

    Article  CAS  PubMed  Google Scholar 

  • Haukka K, Lindström K, Young JP (1998) Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Appl Environ Microbiol 64:419–426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL et al (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330:204–208

    Article  CAS  PubMed  Google Scholar 

  • Hennecke H, Kaluza K, Thöny B, Fuhrmann M, Ludwig W, Stackebrandt E (1985) Concurrent evolution of nitrogenase genes and 16S rRNA in rhizobium species and other nitrogen fixing bacteria. Arch Microbiol 142:342–348

    Article  CAS  Google Scholar 

  • Hinsinger P, Marschner P (2006) Rhizosphere—perspectives and challenges—a tribute to lorenz hiltner 12–17 September 2004—Munich, Germany. Plant Soil 283:vii–viii

    Article  CAS  Google Scholar 

  • Hong S, Bunge J, Leslin C, Jeon S, Epstein SS (2009) Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J 3:1365–1373

    Article  CAS  PubMed  Google Scholar 

  • Hong Y, Ma Y, Wu L, Maki M, Qin W, Chen S (2012) Characterization and analysis of nifH genes from Paenibacillus sabinae T27. Microbiol Res 167:596–601

    Article  CAS  PubMed  Google Scholar 

  • Hsu S-F, Buckley DH (2009) Evidence for the functional significance of diazotroph community structure in soil. ISME J 3:124–136

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Chaparro J, Reardon K, Zhang R, Shen Q, Vivanco J (2014) Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267–275

    Article  Google Scholar 

  • Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh H-J, Tappu R (2016) MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol 12:e1004957

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Izquierdo JA, Nüsslein K (2006) Distribution of extensive nifH gene diversity across physical soil microenvironments. Microb Ecol 51:441–452

    Article  PubMed  Google Scholar 

  • Kamilova F, Kravchenko LV, Shaposhnikov AI, Azarova T, Makarova N, Lugtenberg B (2006) Organic acids, sugars, and L-tryptophane in exudates of vegetables growing on stonewool and their effects on activities of rhizosphere bacteria. Mol Plant-Microbe Interact 19:250–256

    Article  CAS  PubMed  Google Scholar 

  • Kim J, Rees DC (1994) Nitrogenase and biological nitrogen fixation. Biochemistry 33:389–397

    Article  CAS  PubMed  Google Scholar 

  • Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 72:557–578, Table of Contents

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • KuzdraliÅ„ski A, Szczerba H, Tofil K, Filipiak A, Garbarczyk E, Dziadko P, MuszyÅ„ska M, Solarska E (2014) Early PCR-based detection of Fusarium culmorum, F. graminearum, F. sporotrichioides and F. poae on stem bases of winter wheat throughout Poland. Eur J Plant Pathol 140:491–502

    Article  CAS  Google Scholar 

  • Long SR (2001) Genes and signals in the rhizobium-legume symbiosis. Plant Physiol 125:69–72

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480:368–371

    Article  CAS  PubMed  Google Scholar 

  • McMullen M, Bergstrom G, Wolf E, Dill-Macky R, Hershman D, Shaner G, Sanford D (2012) A unified effort to fight an enemy of wheat and barley: Fusarium head blight. Plant Dis 96:1712–1728

    Article  PubMed  Google Scholar 

  • Mehta MP, Butterfield DA, Baross JA (2003) Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca ridge. Appl Environ Microbiol 69:960–970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100

    Article  CAS  PubMed  Google Scholar 

  • Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663

    Article  CAS  PubMed  Google Scholar 

  • Mitchell A, Bucchini F, Cochrane G, Denise H, ten Hoopen P, Fraser M, Pesseat S, Potter S, Scheremetjew M, Sterk P et al (2016) EBI metagenomics in 2016—an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Res 44:D595–D603

    Article  CAS  PubMed  Google Scholar 

  • Neufeld JD, Driscoll BT, Knowles R, Archibald FS (2001) Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation in pulp and paper mill effluent treatment systems. Can J Microbiol 47:925–934

    Article  CAS  PubMed  Google Scholar 

  • Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E (2009) The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett 296:97–101

    Article  CAS  PubMed  Google Scholar 

  • O’Donnell K, Ward TJ, Aberra D, Kistler HC, Aoki T, Orwig N, Kimura M, Bjørnstad S, Klemsdal SS (2008) Multilocus genotyping and molecular phylogenetics resolve a novel head blight pathogen within the Fusarium graminearum species complex from Ethiopia. Fungal Genet Biol 45:1514–1522

    Article  CAS  PubMed  Google Scholar 

  • Op De Beeck M, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV (2014) Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. PLoS One 9:e97629

    Article  Google Scholar 

  • Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I (2015) Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights 9:75–88

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by ribosomal RNA sequences. In: Marshall KC (ed) Advances in microbial ecology. Springer, Boston, MA, pp 1–55

    Google Scholar 

  • Peters JW, Fisher K, Dean DR (1995) Nitrogenase structure and function: a biochemical-genetic perspective. Annu Rev Microbiol 49:335–366

    Article  CAS  PubMed  Google Scholar 

  • Phillips D (1980) Efficiency of symbiotic nitrogen fixation in legumes. Annu Rev Plant Physiol 31:29–49

    Article  CAS  Google Scholar 

  • Piceno YM, Lovell CR (2000) Stability in natural bacterial communities: I. nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb Ecol 39:32–40

    Article  CAS  PubMed  Google Scholar 

  • Poly F, Ranjard L, Nazaret S, Gourbière F, Monrozier LJ (2001) Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Appl Environ Microbiol 67:2255–2262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quince C, Walker AW, Simpson JT, Loman NJ, Segata N (2017) Shotgun metagenomics, from sampling to analysis. Nat Biotechnol 35:833–844

    Article  CAS  PubMed  Google Scholar 

  • Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361

    Article  CAS  Google Scholar 

  • Ree HK, Cao KM, Thurlow DL, Zimmermann RA (1989) The structure and organization of the 16S ribosomal RNA gene from the archaebacterium Thermoplasma acidophilum. Can J Microbiol 35:124–133

    Article  CAS  PubMed  Google Scholar 

  • Reed SC, Townsend AR, Cleveland CC, Nemergut DR (2010) Microbial community shifts influence patterns in tropical forest nitrogen fixation. Oecologia 164:521–531

    Article  PubMed  Google Scholar 

  • Sanyal D, Solanki S, Ameen G, Brueggeman RS, Chatterjee A (2020) Understanding the expression dynamics of symbiont rhizobial nifH and nitrogen assimilatory NR and GS genes in dry bean (Phaseolus vulgaris L.) genotypes at various growth stages. Legum Sci. https://doi.org/10.1002/leg3.26

  • Schloss PD, Westcott SL (2011) Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219–3226

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium, and Fungal Barcoding Consortium Author List (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 109:6241–6246

    Article  PubMed  PubMed Central  Google Scholar 

  • Sharpton TJ (2014) An introduction to the analysis of shotgun metagenomic data. Front Plant Sci 5:209

    Article  PubMed  PubMed Central  Google Scholar 

  • Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF et al (2012) FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 40:D675–D681

    Article  CAS  PubMed  Google Scholar 

  • Stielow JB, Lévesque CA, Seifert KA, Meyer W, Iriny L, Smits D, Renfurm R, Verkley GJM, Groenewald M, Chaduli D et al (2015) One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia 35:242–263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stres B, Mahne I, Avgustin G, Tiedje JM (2004) Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils. Appl Environ Microbiol 70:301–309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Szoboszlay M, White-Monsant A, Moe LA (2016) The effect of root exudate 7,4′-dihydroxyflavone and Naringenin on soil bacterial community structure. PLoS One 11:e0146555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2:3

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Rhijn P, Vanderleyden J (1995) The rhizobium-plant symbiosis. Microbiol Rev 59:124–142

    Article  PubMed  PubMed Central  Google Scholar 

  • Vandermeer JH (1972) Niche theory. Annu Rev Ecol Syst 3:107–132

    Article  Google Scholar 

  • Vogel T, Simonet P, Nalin R, Philippot L (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252

    Article  CAS  Google Scholar 

  • Wagg C, Bender SF, Widmer F, van der Heijden MGA (2014) Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc Natl Acad Sci U S A 111:5266–5270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang C-L, Cheng Y-H (2017) Identification and trichothecene genotypes of Fusarium graminearum species complex from wheat in Taiwan. Bot Stud (Taipei, Taiwan) 58:4

    Article  CAS  Google Scholar 

  • Wartiainen I, Eriksson T, Zheng W, Rasmussen U (2008) Variation in the active diazotrophic community in rice paddy—nifH PCR-DGGE analysis of rhizosphere and bulk soil. Appl Soil Ecol 39:65–75

    Article  Google Scholar 

  • Wasmann C, VanEtten H (1996) Transformation-mediated chromosome loss and disruption of a gene for pisatin demethylase decrease the virulence of Nectria haematococca on pea. Molecular Plant-microbe Interactions: MPMI (USA)

    Google Scholar 

  • Weinert N, Piceno Y, Ding G-C, Meincke R, Heuer H, Berg G, Schloter M, Andersen G, Smalla K (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75:497–506

    Article  CAS  PubMed  Google Scholar 

  • Weller DM (2007) Pseudomonas biocontrol agents of soilborne pathogens: looking back over 30 years. Phytopathology 97:250–256

    Article  PubMed  Google Scholar 

  • Wetterstrand K (2016) DNA sequencing costs: data from the NHGRI genome sequencing program (GSP)

    Google Scholar 

  • Wood S, Newcomb W (1989) Nodule morphogenesis: the early infection of alfalfa (Medicago sativa) root hairs by rhizobium meliloti. Can J Bot 67:3108–3122

    Article  Google Scholar 

  • Wu H, Liu D, Ning-Ling, Bao W, Ying R, Ou Y, Huo Z, Li Y, Shen Q (2008a) Effects of vanillic acid on the growth and development of Fusarium oxysporum f. sp. niveum. Allelopath J 22:111–121

    Google Scholar 

  • Wu H-S, Raza W, Fan J-Q, Sun Y-G, Bao W, Liu D-Y, Huang Q-W, Mao Z-S, Shen Q-R, Miao W-G (2008b) Antibiotic effect of exogenously applied salicylic acid on in vitro soilborne pathogen, Fusarium oxysporum f.sp.niveum. Chemosphere 74:45–50

    Article  CAS  PubMed  Google Scholar 

  • Yates M, Stacey G, Burris R, Evans H (1992) Biological nitrogen fixation. 685–735

    Google Scholar 

  • Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yuan Z, Zhang Z, Wang X, Li L, Cai K, Han H (2017) Novel impacts of functionalized multi-walled carbon nanotubes in plants: promotion of nodulation and nitrogenase activity in the rhizobium-legume system. Nanoscale 9:9921–9937

    Article  CAS  PubMed  Google Scholar 

  • Zehr JP, McReynolds LA (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55:2522–2526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zehr JP, Mellon M, Braun S, Litaker W, Steppe T, Paerl HW (1995) Diversity of heterotrophic nitrogen fixation genes in a marine cyanobacterial mat. Appl Environ Microbiol 61:2527–2532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, DC, USA

    Shyam Solanki, Gazala Ameen, Leah Brueggeman & Robert Brueggeman

  2. Department of Soil Science, North Dakota State University, Fargo, ND, USA

    Debankur Sanyal

  3. Department of Plant Pathology, North Dakota State University, Fargo, USA

    Shalu Jain & Kishore Chittem

  4. Institute of Plant Genetic Resources, Kyushu University, Fukuoka, Japan

    Ammar Elakhdar

  5. ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India

    Shwetank Lall

  6. Department of Plant Sciences, North Dakota State University, Fargo, ND, USA

    Ajay Kumar

Authors
  1. Shyam Solanki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gazala Ameen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Debankur Sanyal
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shalu Jain
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ammar Elakhdar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shwetank Lall
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kishore Chittem
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Leah Brueggeman
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Ajay Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Robert Brueggeman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shyam Solanki .

Editor information

Editors and Affiliations

  1. Department of Life Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India

    Manoj Kumar

  2. Swami Rama Himalayan University, Himalayan School of Biosciences, Dehradun, Uttarakhand, India

    Vivek Kumar

  3. Department of Botany, Mahatma Gandhi Central University, Motihari, Bihar, India

    Ram Prasad

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Solanki, S. et al. (2020). Friends and Foes: Phyto-Microbial Interactions in Molecular Perspective. In: Kumar, M., Kumar, V., Prasad, R. (eds) Phyto-Microbiome in Stress Regulation. Environmental and Microbial Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-15-2576-6_5

Download citation

Publish with us

Policies and ethics

Search

Navigation