Abstract
The mycorrhizosphere is an active and dynamic region with various types of organisms inhabiting this zone. While the most important player in the mycorrhizosphere may be the mycorrhizae, past research has indicated an equally important role for the bacterial community within this biosphere. The bacterial community interacts with the mycorrhizae and also with other communities and these interactions can either be direct or indirect and beneficial or non-beneficial. Exploring the immense diversity within this biosphere will require techniques that will best represent the microbial diversity and structure. This is especially important when a large number of these organisms are non-culturable or difficult to culture, therefore making the entire process of isolation, identification and characterization more difficult. Molecular microbial diversity assessment is a way forward for us to analyze the soil diversity in the mycorrhizosphere. This chapter will address the various PCR based and non PCR based molecular techniques that may be utilized to study the microbial diversity and structure within the mycorrhizosphere.
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References
Agrawal, P. K., & Shrivastava, R. (2013). Molecular markers. In J. Saxena, I. Ravi, & M. Bhaunthiyal (Eds.), Advance in biotechnology (pp. 25–39). New Delhi: Springer.
Amann, R. I., Ludwig, W., & Schleifer, K.-H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 59, 143–169.
Atkins, S. D., & Clark, I. M. (2004). Fungal molecular diagnostics: A mini review. Journal of Applied Genetics, 45, 3–15.
Avise, J. C. (1994). Molecular tools. In Molecular markers, natural history and evolution (pp. 44–91). Boston: Springer. https://doi.org/10.1007/978-1-4615-2381-9.
Banfield, J. F., Verberkmoes, N. C., Hettich, R. L., & Thelen, M. P. (2005). Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS: A Journal of Integrative Biology, 9, 301–333. https://doi.org/10.1089/omi.2005.9.301.
Bashiardes, S., Zilberman-Schapira, G., & Elinav, E. (2016). Use of metatranscriptomics in microbiome research. Bioinformatics and Biology Insights, 10, BBI. S34610.
Benndorf, D., Balcke, G. U., Harms, H., & Von Bergen, M. (2007). Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. The ISME Journal, 1, 224. https://doi.org/10.1038/ismej.2007.39.
Bianciotto, V., Minerdi, D., Perotto, S., & Bonfante, P. (1996). Cellular interactions between arbuscular mycorrhizal fungi and rhizosphere bacteria. Protoplasma, 193, 123–131. https://doi.org/10.1007/BF01276640.
Bianciotto, V., Lumini, E., Lanfranco, L., Minerdi, D., Bonfante, P., & Perotto, S. (2000). Detection and identification of bacterial endosymbionts in arbuscular mycorrhizal fungi belonging to the family Gigasporaceae. Applied and Environmental Microbiology, 66, 4503–4509. https://doi.org/10.1128/AEM.66.10.4503-4509.2000.
Caracciolo, A. B., Bottoni, P., & Grenni, P. (2010). Fluorescence in situ hybridization in soil and water ecosystems: A useful method for studying the effect of xenobiotics on bacterial community structure. Toxicological & Environmental Chemistry, 92, 567–579. https://doi.org/10.1080/02772241003620244.
Cardinale, M., et al. (2004). Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Applied and Environmental Microbiology, 70, 6147–6156. https://doi.org/10.1128/AEM.70.10.6147-6156.2004.
Case, R. J., Boucher, Y., Dahllöf, I., Holmström, C., Doolittle, W. F., & Kjelleberg, S. (2007). Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Applied and Environmental Microbiology, 73, 278–288. https://doi.org/10.1128/AEM.01177-06.
Cetecioglu, Z., Ince, O., & Ince, B. (2012). Gel electrophoresis based genetic fingerprinting techniques on environmental ecology. In Gel electrophoresis-advanced techniques. Rijeka: InTech.
Ciardo, D. E., Schär, G., Altwegg, M., Böttger, E. C., & Bosshard, P. P. (2007). Identification of moulds in the diagnostic laboratory—An algorithm implementing molecular and phenotypic methods. Diagnostic Microbiology and Infectious Disease, 59, 49–60.
Ciardo, D. E., Lucke, K., Imhof, A., Bloemberg, G. V., & Böttger, E. C. (2010). Systematic internal transcribed spacer sequence analysis for identification of clinical mold isolates in diagnostic mycology: A 5-year study. Journal of Clinical Microbiology, 48, 2809–2813.
Costa, R., Gomes, N., 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 analyzes. Environmental Microbiology, 9, 2260–2273. https://doi.org/10.1111/j.1462-2920.2007.01340.x.
Coutinho, M., et al. (2013). Microbial communities on deteriorated artistic tiles from Pena National Palace (Sintra, Portugal). International Biodeterioration & Biodegradation, 84, 322–332. https://doi.org/10.1016/j.ibiod.2012.05.028.
Dakal, T. C., & Arora, P. K. (2012). Evaluation of potential of molecular and physical techniques in studying biodeterioration. Reviews in Environmental Science and Bio/Technology, 11, 71–104. https://doi.org/10.1007/s11157-012-9264-0.
De Ley, J. (1970). Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. Journal of Bacteriology, 101, 738–754.
Deja-Sikora, E., Sikora, M., Golebiewski, M., & Tretyn, A. (2007). Metagenomic libraries as sources of genes useful for biotechnology. Biotechnologia, 4, 125–139.
Delmotte, N., et al. (2009). Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proceedings of the National Academy of Sciences, 106, 16428–16433. https://doi.org/10.1073/pnas.0905240106.
DeSantis, T. Z., Brodie, E. L., Moberg, J. P., Zubieta, I. X., Piceno, Y. M., & Andersen, G. L. (2007). High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial Ecology, 53, 371–383. https://doi.org/10.1007/s00248-006-9134-9.
Elshahed, M. S., et al. (2008). Novelty and uniqueness patterns of rare members of the soil biosphere. Applied and Environmental Microbiology, 74, 5422–5428. https://doi.org/10.1128/AEM.00410-08.
Fakruddin, M., & Mannan, K. (2013). Methods for analyzing diversity of microbial communities in natural environments. Ceylon Journal of Science (Biological Sciences), 42. https://doi.org/10.4038/cjsbs.v42i1.5896.
Finlay, B. B., & Medzhitov, R. (2007). Host-microbe interactions: Fulfilling a niche. Cell Host & Microbe, 1, 3–4.
Fisher, M. M., & Triplett, E. W. (1999). Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Applied and Environmental Microbiology, 65, 4630–4636.
Gaylarde, C. C., Rodríguez, C. H., Navarro-Noya, Y. E., & Ortega-Morales, B. O. (2012). Microbial biofilms on the sandstone monuments of the Angkor Wat complex, Cambodia. Current Microbiology, 64, 85–92. https://doi.org/10.1007/s00284-011-0034-y.
Giacomucci, L., et al. (2011). Microbial deterioration of artistic tiles from the façade of the Grande Albergo Ausonia & Hungaria (Venice, Italy). Microbial Ecology, 62, 287–298. https://doi.org/10.1007/s00248-011-9812-0.
Gich, F. B., Amer, E., Figueras, J. B., Charles, A., Abella, C. A. A., Balaguer, M. D., & Poch, M. (2000). Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA). International Microbiology, 3, 103–106.
González, J. M., & Saiz-Jiménez, C. (2005). Application of molecular nucleic acid-based techniques for the study of microbial communities in monuments and artworks. International Microbiology, 8, 189.
Gonzalez, J., Ortiz-Martinez, A., Gonzalez-delValle, M., Laiz, L., & Saiz-Jimenez, C. (2003). An efficient strategy for screening large cloned libraries of amplified 16S rDNA sequences from complex environmental communities. Journal of Microbiological Methods, 55, 459–463.
Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P., & Tiedje, J. M. (2007). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology, 57, 81–91. https://doi.org/10.1099/ijs.0.64483-0.
Greene, E. A., & Voordouw, G. (2003). Analysis of environmental microbial communities by reverse sample genome probing. Journal of Microbiological Methods, 53, 211–219.
He, L., et al. (2007). A microRNA component of the p53 tumour suppressor network. Nature, 447, 1130. https://doi.org/10.1038/nature05939.
Hugenholtz, P., Goebel, B. M., & Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 180, 4765–4774.
Hugenholtz, P., Tyson, G. W., Webb, R. I., Wagner, A. M., & Blackall, L. L. (2001). Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Applied and Environmental Microbiology, 67, 411–419. https://doi.org/10.1128/AEM.67.1.411-419.2001.
Jacobi, S. K., Xi, L., Maltecca, C., Borst, L., Smith, A., & Odle, J. (2017). Dietary prebiotics and arachidonic acid (ARA) modulate intestinal injury and microbial taxa following acute dextran sodium sulfate induced colitis in formula-fed piglets. The FASEB Journal, 31, lb324–lb324.
Karp, A., Seberg, O., & Buiatti, M. (1996). Molecular techniques in the assessment of botanical diversity. Annals of Botany, 78, 143–149.
Keller, M., & Hettich, R. (2009). Environmental proteomics: A paradigm shift in characterizing microbial activities at the molecular level. Microbiology and Molecular Biology Reviews, 73, 62–70. https://doi.org/10.1128/MMBR.00028-08.
Kolb, S., Knief, C., Stubner, S., & Conrad, R. (2003). Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Applied and Environmental Microbiology, 69, 2423–2429. https://doi.org/10.1128/AEM.69.5.2423-2429.2003.
Krieg, N., & Holt, J. (1984). Bergey’s manual of systemic bacteriology (Vol. 1). The William & Wilkins Co: Baltimore. https://doi.org/10.1007/978-0-387-21609-6.
Lauber, C. L., Strickland, M. S., Bradford, M. A., & Fierer, N. (2008). The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology and Biochemistry, 40, 2407–2415.
Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology, 75, 5111–5120. https://doi.org/10.1128/AEM.00335-09.
Li, T., Wu, T. D., Mazéas, L., Toffin, L., Guerquin-Kern, J. L., Leblon, G., & Bouchez, T. (2008). Simultaneous analysis of microbial identity and function using NanoSIMS. Environmental Microbiology, 10, 580–588. https://doi.org/10.1111/j.1462-2920.2007.01478.x.
Liu, W.-T., Marsh, T. L., Cheng, H., & Forney, L. J. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology, 63, 4516–4522.
Liu, Z., Lozupone, C., Hamady, M., Bushman, F. D., & Knight, R. (2007). Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Research, 35, e120. https://doi.org/10.1093/nar/gkm541.
Mandel, M., & Marmur, J. (1968). [109] Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods in enzymology, 12, 195–206. Elsevier. https://doi.org/10.1016/0076-6879(67)12133-2.
Margulies, M., et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376. https://doi.org/10.1038/nature03959.
McNamara, C. J., Perry, T. D., Bearce, K. A., Hernandez-Duque, G., & Mitchell, R. (2006). Epilithic and endolithic bacterial communities in limestone from a Maya archaeological site. Microbiology. Ecology, 51, 51–64. https://doi.org/10.1007/s00248-005-0200-5.
Mecler, I., & Nawrot, U. (2007). Molecular methods applied in microbiological diagnosis. Mikologia Lekarska, 14, 280.
Mesbah, M., Premachandran, U., & Whitman, W. B. (1989). Precise measurement of the G+ C content of deoxyribonucleic acid by high-performance liquid chromatography. International Journal of Systematic and Evolutionary Microbiology, 39, 159–167. https://doi.org/10.1099/00207713-39-2-159.
Mocali, S., & Benedetti, A. (2010). Exploring research frontiers in microbiology: The challenge of metagenomics in soil microbiology. Research in Microbiology, 161, 497–505. https://doi.org/10.1016/j.resmic.2010.04.010.
Moran, M. A. (2009). Metatranscriptomics: Eavesdropping on Complex Microbial Communities-Large-scale sequencing of mRNAs retrieved from natural communities provides insights into microbial activities and how they are regulated. Microbe, 4, 329.
Muller, M. P., et al. (2016). Antimicrobial surfaces to prevent healthcare-associated infections: A systematic review. Journal of Hospital Infection, 92, 7–13.
Muyzer, G. (1999). DGGE/TGGE a method for identifying genes from natural ecosystems. Current Opinion in Microbiology, 2, 317–322. https://doi.org/10.1016/S1369-5274(99)80055-1.
Muyzer, G., & Smalla, K. (1998). Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek, 73, 127–141.
Muyzer, G., De Waal, E. C., & Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 59, 695–700.
Nadarajah, K. (2017). Rhizosphere interactions: Life below ground. In Plant-microbe interaction: An approach to sustainable agriculture (pp. 3–23). Singapore: Springer. https://doi.org/10.1007/978-981-10-2854-0_1.
Neelakanta, G., & Sultana, H. (2013). The use of metagenomic approaches to analyze changes in microbial communities. Microbiology Insights, 6, MBI. S10819. https://doi.org/10.4137/MBI.S10819.
Nüsslein, K., & Tiedje, J. M. (1999). Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil. Applied and Environmental Microbiology, 65, 3622–3626.
Orita, M., Suzuki, Y., Sekiya, T., & Hayashi, K. (1989). Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics, 5, 874–879.
Piñar, G., Ramos, C., Rölleke, S., Schabereiter-Gurtner, C., Vybiral, D., Lubitz, W., & Denner, E. B. (2001a). Detection of indigenous Halobacillus populations in damaged ancient wall paintings and building materials: Molecular monitoring and cultivation. Applied and Environmental Microbiology, 67, 4891–4895.
Piñar, G., Saiz-Jimenez, C., Schabereiter-Gurtner, C., Blanco-Varela, M. T., Lubitz, W., & Rölleke, S. (2001b). Archaeal communities in two disparate deteriorated ancient wall paintings: Detection, identification and temporal monitoring by denaturing gradient gel electrophoresis. FEMS Microbiology Ecology, 37, 45–54. https://doi.org/10.1111/j.1574-6941.2001.tb00852.x.
Piñar, G., Ripka, K., Weber, J., & Sterflinger, K. (2009). The micro-biota of a sub-surface monument: The medieval chapel of St. Virgil (Vienna, Austria). International Biodeterioration & Biodegradation, 63, 851–859.
Piñar, G., Piombino-Mascali, D., Maixner, F., Zink, A., & Sterflinger, K. (2013). Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: Biodeterioration risk and contamination of the indoor air. FEMS Microbiology Ecology, 86, 341–356. https://doi.org/10.1111/1574-6941.12165.
Popa, R., Popa, R., Mashall, M. J., Nguyen, H., Tebo, B. M., & Brauer, S. (2009). Limitations and benefits of ARISA intra-genomic diversity fingerprinting. Journal of Microbiological Methods, 78, 111–118. https://doi.org/10.1016/j.mimet.2009.06.005.
Poretsky, R. S., et al. (2005). Analysis of microbial gene transcripts in environmental samples. Applied and Environmental Microbiology, 71, 4121–4126. https://doi.org/10.1128/AEM.71.7.4121-4126.2005.
Puppi, G., Azcón, R., & Höflich, G. (1994). Management of positive interactions of arbuscular mycorrhizal fungi with essential groups of soil microorganisms. In Impact of arbuscular mycorrhizas on sustainable agriculture and natural ecosystems (pp. 201–215). Springer. https://doi.org/10.1007/978-3-0348-8504-1_16.
Quince, C., et al. (2009). Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6, 639. https://doi.org/10.1038/nmeth.1361.
Rastogi, G., & Sani, R. K. (2011). Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In Microbes and microbial technology (pp. 29–57). Springer.
Roesch, L. F., et al. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME Journal, 1, 283. https://doi.org/10.1038/ismej.2007.53.
Rogers, S. W., Moorman, T. B., & Ong, S. K. (2007). Fluorescent in situ hybridization and micro-autoradiography applied to ecophysiology in soil. Soil Science Society of America Journal, 71, 620–631. https://doi.org/10.2136/sssaj2006.0105.
Ross, J. (1980). Effect of nontreated field soil on sporulation of vesicular-arbuscular mycorrhizal fungi associated with soybean. Phytopathology, 70, 1200–1205.
Rothberg, J. M., & Leamon, J. H. (2008). The development and impact of 454 sequencing. Nature Biotechnology, 26, 1117. https://doi.org/10.1038/nbt1485.
Santos-González, J. C., Finlay, R. D., & Tehler, A. (2007). Seasonal dynamics of arbuscular mycorrhizal fungal communities in roots in a seminatural grassland. Applied and Environmental Microbiology, 73, 5613–5623. https://doi.org/10.1128/AEM.00262-07.
Sehgal, A. K., & Sagar, A. (2017). Ectomycorrhiza and fungal diversity in the mycorrhizosphere of Pinus gerardiana. International Journal of Pure Applied Bioscience, 5, 475–483.
Simon, L., Lalonde, M., & Bruns, T. (1992). Specific amplification of 18S fungal ribosomal genes from vesicular-arbuscular endomycorrhizal fungi colonizing roots. Applied and Environmental Microbiology, 58, 291–295.
Singh, S., Khawale, R., Singh, R., & Vimala, Y. (2005). Use of random amplified polymorphic DNA (RAPD) analysis to confirm genetic stability of in vitro regenerated grape plantlets. Indian Journal of Horticulture, 62, 12–15.
Streit, W. R., & Schmitz, R. A. (2004). Metagenomics–the key to the uncultured microbes. Current Opinion in Microbiology, 7, 492–498. https://doi.org/10.1016/j.mib.2004.08.002.
Tacão, M., Moura, A., Alves, A., Henriques, I., Saavedra, M. J., & Correia, A. (2005). Evaluation of 16S rDNA-and gyrB-DGGE for typing members of the genus Aeromonas. FEMS Microbiology Letters, 246, 11–18. https://doi.org/10.1016/j.femsle.2005.03.033.
Tatusova, T. A., & Madden, T. L. (1999). BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiology Letters, 174, 247–250.
Tiedje, J. M., Asuming-Brempong, S., Nüsslein, K., Marsh, T. L., & Flynn, S. J. (1999). Opening the black box of soil microbial diversity. Applied Soil Ecology, 13, 109–122. https://doi.org/10.1016/S0929-1393(99)00026-8.
Tommerup, I. (1985). Inhibition of spore germination of vesicular-arbuscular mycorrhizal fungi in soil. Transactions of the British Mycological Society, 85, 267–278. https://doi.org/10.1016/S0007-1536(85)80188-1.
Urich, T., Lanzén, A., Qi, J., Huson, D. H., Schleper, C., & Schuster, S. C. (2008). Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One, 3, e2527. https://doi.org/10.1371/journal.pone.0002527.
Van Elsas, J., & Boersma, F. (2011). A review of molecular methods to study the microbiota of soil and the mycosphere European Journal of Soil Biology, 47, 77–87.
van Elsas, J. D., Trevors, J. T., Jansson, J. K., & Nannipieri, P. (2006). Modern soil microbiology. CRC Press.
Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K., & Swings, J. (1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiological Reviews, 60, 407–438.
Waleron, M., Waleron, K., Geider, K., & Lojkowska, E. (2008). Application of RFLP analysis of recA, gyrA and rpoS gene fragments for rapid differentiation of Erwinia amylovora from Erwinia strains isolated in Korea and Japan. European Journal of Plant Pathology, 121, 161–172. https://doi.org/10.1007/s10658-007-9260-3.
Więckowicz, M. (2009). Molekularne metody identyfikacji mikroorganizmów w złożonych ekosystemach. Post Mikrobiol, 48, 67–73. (in Polish).
Wilmes, P., & Bond, P. L. (2006). Metaproteomics: Studying functional gene expression in microbial ecosystems. Trends in Microbiology, 14, 92–97. https://doi.org/10.1016/j.tim.2005.12.006.
Wilson, G., Hetrick, B. D., & Kitt, D. G. (1988). Suppression of mycorrhizal growth response of big bluestem by non-sterile soil. Mycologia, 338–343. https://doi.org/10.2307/3807630.
Yergeau, E., Kang, S., He, Z., Zhou, J., & Kowalchuk, G. A. (2007). Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal, 1, 163. https://doi.org/10.1038/ismej.2007.24.
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Nadarajah, K., Kumar, I.S. (2019). Molecular Microbial Biodiversity Assessment in the Mycorrhizosphere. In: Varma, A., Choudhary, D. (eds) Mycorrhizosphere and Pedogenesis. Springer, Singapore. https://doi.org/10.1007/978-981-13-6480-8_23
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