Abstract
The collective genomes of the holobiont plant comprising diverse microbiota encode a number of functions required for the host as well as for supporting the interaction between the plant and its associated microbiome. This chapter reviews various plant habitats for microorganisms, microbiome functions, and functional as well as sequence-based metagenomics screening approaches, which can be used to elucidate holobiont functioning.
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References
Abbà S, Galetto L, Carle P et al (2014) RNA-Seq profile of flavescence dorée phytoplasma in grapevine. BMC Genomics 15:1088
Adams IP, Glover RH, Monger WA et al (2009) Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol 104:5375–5345
Alvarez TM, Goldbeck R, Santos CR et al (2013a) Development and biotechnological application of a novel endoxylanase family GH10 identified from sugarcane soil metagenome. PLoS One 8:e70014
Alvarez TM, Paiva JH, Ruiz DM et al (2013b) Structure and function of a novel cellulase 5 from sugarcane soil metagenome. PLoS One 8:e83635
Bag S, Al Rwahnih M, Li A et al (2015) Detection of a new luteovirus in imported nectarine trees: a case study to propose adoption of metagenomics in post-entry quarantine. Phytopathology 105:840–846
Bai Y, Liang J, Liu R et al (2014) Metagenomic analysis reveals microbial diversity and function in the rhizosphere soil of a constructed wetland. Environ Technol 35:2521–2527
Bai Y, Müller DB, Srinivas G et al (2015) Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528:364–369
Barry SM, Challis GL (2009) Recent advances in siderophore biosynthesis. Curr Opin Chem Biol 13:205–215
Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486
Bertaccini A, Duduk B, Paltrinieri S, Contaldo N (2014) Phytoplasmas and Phytoplasma diseases: a severe threat to agriculture. Am J Plant Sci 5:1763–1788
Besserer A, Puech-Pages V, Kiefer P et al (2006) Strigolactones stimulate arbuscular mycorrhizal fungi by activating mitochondria. PLoS Biol 4:e226
Blainey PC (2013) The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev 37:407
Bordenstein SR, Theis KR (2015) Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biol 13:e1002226
Bragina A, Maier S, Berg C et al (2012) Similar diversity of alphaproteobacteria and nitrogenase gene amplicons on two related Sphagnum mosses. Front Microbiol 2:275
Bragina A, Berg C, Müller H (2013) Insights into functional bacterial diversity and its effect on Alpine bog ecosystem functioning. Sci Rep 3:1955
Bragina A, Oberauner-Wappis L, Zachow C et al (2014) The Sphagnum microbiome supports ecosystem functioning under extreme conditions. Mol Ecol 23:4498–4510
Bragina A, Berg C, Berg G (2015) The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity. Mol Ecol 24:4795–4807
Buee 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
Bulgarelli D, Rott M, Schlaeppi K et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95
Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838
Bulgarelli D, Garrido-Oter R, Münch PC et al (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17:392–403
Bush LP, Wilkinson HH, Schardl CL (1997) Bioprotective alkaloids of grass-fungal endophyte symbioses. Plant Physiol 114:1–7
Calheiros CSC, Duque AF, Moura A et al (2009) Substrate effect on bacterial communities from constructed wetlands planted with Typha latifolia treating industrial wastewater. Ecol Eng 35:744–753
Camerota C, Raddadi N, Pizzinat A et al (2012) Incidence of ‘Candidatus Liberibacter europaeus’ and phytoplasmas in Cacopsylla species (Hemiptera: Psyllidae) and their host/shelter plants. Phytoparasitica 40:213–221
Caporaso JG, Lauber CL, Walters WA et al (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624
Carlier AL, Eberl L (2012) The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host. Environ Microbiol 14:2757–2769
Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803
Charlop-Powers Z, Owen J, Reddy B et al (2015) Global biogeographic sampling of bacterial secondary metabolism. elife 4:e05048
Cheng J, Pinnell L, Engel K, Neufeld JD, Charles TC (2014) Versatile broad-host-range cosmids for construction of high quality metagenomic libraries. J Microbiol Method 99:27–34
Chhabra S, Brazil D, Morrissey J et al (2013) Characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome. Microbiol Open 2:717–724
Cobo-Díaz JF, Fernández-González AJ, Villadas PJ et al (2015) Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a Mediterranean forest after a wildfire. Microb Ecol 69:895–904
Compant S, Cement C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678
Cretiou MS, Kielak AM, Abu Al-Soud W et al (2012) Mining of unexplored habitats for novel chitinases – chiA as a helper gene proxy in metagenomics. Appl Microbiol Biotechnol 94(5):1347–1358
Duan YP, Zhou LJ, Hall DG et al (2009) Complete genome sequence of citrus Huanglongbing bacterium, ‘Candidatus Liberibacter asiaticus’ obtained through metagenomics. Mol Plant-Microbe Interact 22:1011–1020
Engel K, Pinnell L, Cheng J, Charles TC, Neufeld JD (2012) Nonlinear electrophoresis for purification of soil DNA for metagenomics. J Microbiol Method 88:35–40
Engel K, Ashby D, Brady SF et al (2013) Meeting report: 1st international functional metagenomics workshop May 7-8, 2012, St Jacobs, Ontario, Canada. Stand Genom Sci 8(1):106–111
Erlacher A, Cernava T, Cardinale M et al (2015) Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. Front Microbiol 6:53
Escobar MA, Dandekar AM (2003) Agrobacterium tumefaciens as an agent of disease. Trends Plant Sci 8:380–386
Fibach-Baldi S, Burdman S, Okon Y (2012) Key physiological properties contributing to rhizosphere adaptation and plant growth promotion abilities of Azospirillum brasilense. FEMS Microbiol Lett 326:99–108
Fuqua C, Parsek MR, Greenberg EP (2001) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet 35:439–468
Gilbert J, Li LL, Taghavi S et al (2012) Bioprospecting metagenomics for new glycoside hydrolases. Methods Mol Biol 908:141–151
Grube M, Cernava T, Soh J et al (2015) Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative genomics. ISME J 9:412–424
Guerriero G, Hausman JF, Strauss J et al (2015) Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases. Plant Sci 234:180–193
Hardoim PR, van Overbeek LS, Berg G et al (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320
Hoshi A, Oshima K, Kakizawa S et al (2009) A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium. Proc Natl Acad Sci U S A 106:6416–6421
Imfeld G, Aragones CE, Fetzer I et al (2010) Characterization of microbial communities in the aqueous phase of a constructed model wetland treating 1,2-dichloroethene-contaminated groundwater. FEMS Microbiol Ecol 72:74–88
Junker R, Loewel C, Gross R et al (2011) Composition of epiphytic bacterial communities differs on petals and leaves. Plant Biol 13:918
Kakizawa S, Makino A, Ishii Y et al (2014) Draft genome sequence of “Candidatus Phytoplasma asteris” strain OY-V, an unculturable plant-pathogenic bacterium. Genome Announc 18:2
Lebeis SL (2015) Greater than the sum of their parts: characterizing plant microbiomes at the community level. Curr Opin Plant Biol 24:82–86
Lee SW, Kim HK, Lim HK et al (2004) Searching antimicrobial activities from plant rhizosphere metagenomics library. Phytopathology 94:S59
Lee MH, Hong KS, Malhotra S et al (2010) A new esterase EstD2 isolated from plant rhizosphere soil metagenome. Appl Microbiol Biotechnol 88:1125–1134
Lee S, Ishiga Y, Clermont K, Mysore KS (2013) Coronatine inhibits stomatal closure and delays hypersensitive response cell death induced by non-host bacterial pathogens. PeerJ 1:e34
Leininger S, Urich T, Schloter M et al (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809
Lin H, Lou B, Glynn JM et al (2011) The complete genome sequence of ‘Candidatus Liberibacter solanacearum’, the bacterium associated with potato zebra chip disease. PLoS One 6(4):e19135
Lugtenberg BJJ, Dekkers L, Bloemberg GV (2001) Molecular determinants of rhizosphere colonization by Pseudomonas. Annu Rev Phytopathol 39:461–490
Lundberg DS, Lebeis SL, Paredes SH (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90
Martin M, Biver S, Barbeyron T et al (2014) identification and characterization of a halotolerant, cold-active marine endo-ß-1,4-glucanase by using functional metagenomics of seaweed-associated microbiota. Appl Environ Microbiol 80:4958–4967
Mason CJ, Couture JJ, Raffa KF (2014) Plant-associated bacteria degrade defense chemicals and reduce their adverse effects on an insect defoliator. Oecologia 175:901–910
McCormick SP (2013) Microbial detoxification of mycotoxins. J Chem Ecol 39:907–918
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
Mitrovic J, Siewert C, Duduk B et al (2014) Generation and analysis of draft sequences of ‘Stolbur’ Phytoplasma from multiple displacement amplification templates. J Mol Microbiol Biotechnol 24:1–11
Mitter B, Petric A, Shin MW et al (2013a) Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front Plant Sci 4:120
Mitter B, Brader G, Afzal M et al (2013b) Advances in elucidating plant-soil-microbe (bacteria) interactions. Adv Agronomy 121:381–445
Morohoshi T, Oikawa M, Sato S et al (2011) Isolation and characterization of novel lipases from a metagenomic library of the microbial community in the pitcher fluid of the carnivorous plant Nepenthes hybrida. J Biosci Bioeng 112:315–320
Moubayidin L, Di Mambro R, Sabatini S (2009) Cytokinin-auxin crosstalk. Trends Plant Sci 14:557–562
Neufeld J, Engel K, Cheng J et al (2011) Open resource metagenomics: a model for sharing metagenomic libraries. Stand Genom Sci 5(2):203–210
Nikolic B, Schwab H, Sessitsch A (2011) Metagenomic analysis of the 1-aminocyclopropane-1-carboxylate deaminase gene (acdS) operon of an uncultured bacterial endophyte colonizing Solanum tuberosum L. Arch Microbiol 193:665–676
Ofek-Lalzar M, Sela N, Goldman-Voronov M et al (2014) Niche and host-associated functional signatures of the root surface microbiome. Nat Commun 5:4950
Osbourn AE, Qi X, Townsend B, Qin B (2003) Dissecting plant secondary metabolism - constitutive chemical defenses in cereals. New Phytol 159:101–108
Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Microbiol 6:763–775
Peiffer JA, Spor A, Koren O et al (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A 110:6548–6553
Porazinska DL, Morgan MJ, Gaspar JM et al (2014) Discrimination of plant-parasitic nematodes from complex soil communities using ecometagenetics. Phytopathology 104:749–761
Puspita ID, Kamagata Y, Tanaka M, Asano K, Nakatsu CH (2012) Are uncultivated bacteria really uncultivable? Microbes Environ 27:356–366
Raaijmakers JM, Mazzola M (2012) Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu Rev Phytopathol 50:403–424
Raaijmakers JM, De Bruijn I, Nybroe O, Ongena M (2010) Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics. FEMS Microbiol Rev 34:1037
Ramirez-Puebla ST, Servin-Garciduenas LE, Jimenez-Marin B et al (2013) Gut and root microbiota commonalities. Appl Environ Microbiol 79:2–9
Rasche F, Hödl V, Poll C et al (2006a) Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities in comparison to effects of soil, wildtype potatoes, vegetation stage and pathogen exposure. FEMS Microbiol Ecol 56:219–235
Rasche F, Velvis H, Zachow C et al (2006b) Impact of transgenic potatoes expressing antibacterial agents on bacterial endophytes is comparable to effects of wildtype potatoes and changing environmental conditions. J Appl Ecol 43:555–566
Rastogi G, Coaker GL, Leveau JHJ (2013) New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett 348:1–10
Roossinck MJ, Martin DP, Roumagnac P (2015) Plant virus metagenomics: advances in virus discovery. Phytopathology 105:716–727
Rosenberg E, Sharon G, Zilber-Rosenberg I (2009) The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework. Environ Microbiol 11:2959–2962
Ryan RP, Monchy S, Cardinale M et al (2009) The versatility and adaptation of bacteria from the genus Stenotrophomonas. Nat Rev Microbiol 7:514–525
Schardl CL, Leuchtmann A, Spiering MJ (2004) Symbioses of grasses with seedborne fungal endophytes. Annu Rev Plant Biol 55:315–340
Sessitsch A, Hardoim P, Döring J et al (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microb Interact 25:28–36
Siewert C, Luge T, Duduk B et al (2014) Analysis of expressed genes of the bacterium Candidatus Phytoplasma Mali: highlights key features of virulence and metabolism. PLoS One 9:e94391
Singh S (2014) A review on possible elicitor molecules of cyanobacteria: their role in improving plant growth and providing tolerance against biotic or abiotic stress. J Appl Microbiol 117:1221–1244
Singh A, Sarma BK, Harikesh B, Upadhyay RS (2014) Trichoderma: a silent worker of plant rhizosphere. In: Gupta VK, Schmoll M, Herrera-Estrella A, Upadhyay RS, Druzhinina I, Ruohy MG (eds) Biotechnology and biology of Trichoderma. Elsevier, The Netherlands, pp 533–542
Singh RP, Kumari P, Reddy CRK (2015) Antimicrobial compounds from seaweeds-associated bacteria and fungi. Appl Microbiol Biotechnol 99:1571–1586
Souza RC, Cantão ME, Ribeiro Vasconcelos AT et al (2013) Soil metagenomics reveals differences under conventional and no-tillage with crop rotation or succession. Appl Soil Ecol 72:49–61
Stottmeister U, Wissner A, Kuschk P et al (2003) Effects of plants and microorganisms in constructed wetlands for wastewater treatment. Biotechnol Adv 22:93–117
Suzaki T, Ito M, Kawaguchi M (2013) Genetic basis of cytokinin and auxin functions during root nodule development. Front Plant Science 4:42
Swain SM, Singh DP (2005) Tall tales from sly dwarves: novel functions of gibberellins in plant development. Trends Plant Sci 10:123–129
Toth IK, Bell KS, Holeva MC, Birch PR (2003) Soft rot Erwiniae: from genes to genomes. Mol Plant Pathol 4:17–30
Tsurumaru H, Okubo T, Okazaki K et al (2015) Metagenomic analysis of the bacterial community associated with the taproot of sugar beet. Microbes Environ 30:63–69
Turner TR, Ramakrishnan K, Walshaw J et al (2013) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J 7:2248–2258
Vacheron J, Desbrosses G, Bouffaud M-L et al (2013) Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci 4:356
Vadassery J, Ritter C, Venus Y et al (2008) The role of auxins and cytokinins in the mutualistic interaction between Arabidopsis and Piriformospora indica. Mol Plant-Microbe Interact 21:1371–1383
Verastegui Y, Cheng J, Engel K et al (2014) Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities. MBio 5:e01157-14
Vey G, Charles TC (2014). MetaProx: the database of metagenomic proximons. Database 2014:ID bau097
Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840
Vorwerk S, Somerville S, Somerville C (2004) The role of plant cell wall polysaccharide composition in disease resistance. Trends Plant Sci 9:203–209
Weinert N, Piceno Y, Ding GC et al (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
Yang CH, Crowley DE, Borneman J, Keen NT (2001) Microbial phyllosphere populations are more complex than previously realized. Proc Natl Acad Sci U S A 98:3889–3894
Yilmaz S, Singh AK (2012) Single cell genome sequencing. Curr Opin Biotechnol 23:437–443
Zarraonaindia I, Owens SM, Weisenhorn P et al (2015) The soil microbiome influences grapevine-associated microbiota. MBio 6:e02527-14
Zuccaro A, Schoch CL, Spatafora JW et al (2008) Detection and identification of fungi intimately associated with the brown seaweed Fucus serratus. Appl Environ Microbiol 74:931–941
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Brader, G., Corretto, E., Sessitsch, A. (2017). Metagenomics of Plant Microbiomes. In: Charles, T., Liles, M., Sessitsch, A. (eds) Functional Metagenomics: Tools and Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-61510-3_11
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