Tool and techniques study to plant microbiome current understanding and future needs: an overview

References

• Zhai Y, Li X, Wang T, et al. A review on airborne microorganisms in particulate matters: composition, characteristics and influence factors. Environ Int. 2018;113:74–90.
   PubMed Web of Science ®Google Scholar
• Zhou Q, Li K, Jun X, et al. Role and functions of beneficial microorganisms in sustainable aquaculture. Bioresour Technol. 2009;100(16):3780–3786.
   PubMed Web of Science ®Google Scholar
• Jacoby R, Peukert M, Succurro A, et al. The role of soil microorganisms in plant mineral nutrition—current knowledge and future directions. Front Plant Sci. 2017;8:1617.
   PubMed Web of Science ®Google Scholar
• Pronk LJ, Bakker PA, Keel C, et al. The secret life of plant‐beneficial rhizosphere bacteria: insects as alternative hosts. Environ Microbiol. 2022;24:1–17.
   PubMed Web of Science ®Google Scholar
• Xu J. Invited review: microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Molecul Ecol. 2006;15:1713–1731.
   PubMed Web of Science ®Google Scholar
• Ferone M, Gowen A, Fanning S, et al. Microbial detection and identification methods: bench top assays to omics approaches. Comprehen Rev Food Sci Food Safe. 2020;19(6):3106–3129.
   PubMed Web of Science ®Google Scholar
• Lagier JC, Edouard S, Pagnier I, et al. Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev. 2015;28(1):208–236.
   PubMed Web of Science ®Google Scholar
• Pace NR. A molecular view of microbial diversity and the biosphere. Science. 1997;276(5313):734–740.
   PubMed Web of Science ®Google Scholar
• Compant S, Cambon MC, Vacher C, et al. The plant endosphere world–bacterial life within plants. Environ Microbiol. 2021;23(4):1812–1829.
   PubMed Web of Science ®Google Scholar
• Bodor A, Bounedjoum N, Vincze GE, et al. Challenges of unculturable bacteria: environmental perspectives. Rev Environ Sci Bio/Technol. 2020;19(1):1–22.
   Web of Science ®Google Scholar
• Li L, Mendis N, Trigui H, et al. The importance of the viable but non-culturable state in human bacterial pathogens. Front Microbiol. 2014;5:258.
   PubMed Web of Science ®Google Scholar
• Hibbing ME, Fuqua C, Parsek MR, et al. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol. 2010;8(1):15–25.
   PubMed Web of Science ®Google Scholar
• Palková Z. Multicellular microorganisms: laboratory versus nature. EMBO Rep. 2004;5(5):470–476.
   PubMed Web of Science ®Google Scholar
• Rantsiou K, Urso R, Iacumin L, et al. Culture-dependent and-independent methods to investigate the microbial ecology of Italian fermented sausages. Appl Environ Microbiol. 2005;71(4):1977–1986.
   PubMed Web of Science ®Google Scholar
• Su C, Lei L, Duan Y, et al. Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol. 2012;93(3):993–1003.
   PubMed Web of Science ®Google Scholar
• Frank DN, Spiegelman GB, Davis W, et al. Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J Clinical Microbiol. 2003;41(1):295–303.
   PubMed Web of Science ®Google Scholar
• Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clinical Microbiol. 2007;45(9):2761–2764.
   PubMed Web of Science ®Google Scholar
• Rosselló‐Móra R. Towards taxonomy of bacteria and archaea based on interactive and cumulative data repositories. Environ Microbiol. 2012;14(2):318–334.
   PubMed Web of Science ®Google Scholar
• Cao Y, Fanning S, Proos S, et al. A review on the applications of next generation sequencing technologies as applied to food-related microbiome studies. Front Microbiol. 2017;8:182.
   PubMed Web of Science ®Google Scholar
• Schoch CL, Seifert KA, Huhndorf S, et al. Fungal barcoding consortium, fungal barcoding consortium author list nuclear ribosomal internal transcribed spacer (its) region as a universal dna barcode marker for fungi. Precede National Acad Sci. 2012;109(16):6241–6246.
   PubMed Web of Science ®Google Scholar
• Gu X, Cheng X, Zhang J, et al. Identification of fungal community in otomycosis by internal transcribed spacer sequencing. Front Microbiol. 2022;13:820423.
   PubMed Web of Science ®Google Scholar
• Clarridge IIIJE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004;17:840–862.
   PubMed Web of Science ®Google Scholar
• Winand R, Bogaerts B, Hoffman S, et al. Targeting the 16s rRNA gene for bacterial identification in complex mixed samples: comparative evaluation of second (illumina) and third (Oxford nanopore technologies) generation sequencing technologies. Int J Mol Sci. 2019;21(1):298.
   PubMed Web of Science ®Google Scholar
• Jenkins C, Chapman TA, Micallef JL, et al. Molecular techniques for the detection and differentiation of host and parasitoid species and the implications for fruit fly management. Insects. 2012;3(3):763–788.
   PubMedGoogle Scholar
• Topalović O, Hussain M, Heuer H. Plants and associated soil microbiota cooperatively suppress plant-parasitic nematodes. Front Microbiol. 2020;11:313.
   PubMed Web of Science ®Google Scholar
• Bez C, Esposito A, Thuy HD, et al. The rice foot rot pathogen dickeya zeae alters the in‐field plant microbiome. Environ Microbiol. 2021;23:7671–7687.
   PubMed Web of Science ®Google Scholar
• Saeed Q, Xiukang W, Haider FU, et al. Rhizosphere bacteria in plant growth promotion, biocontrol, and bioremediation of contaminated sites: a comprehensive review of effects and mechanisms. Int J Molecul Sci. 2021;22(19):10529.
   PubMed Web of Science ®Google Scholar
• Elshaghabee FM, Bockelmann W, Meske D, et al. Ethanol production by selected intestinal microorganisms and lactic acid bacteria growing under different nutritional conditions. Front Microbiol. 2016;7:47.
   PubMed Web of Science ®Google Scholar
• Aguiar-Pulido V, Huang W, Suarez-Ulloa V, et al. Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis: supplementary issue: bioinformatics methods and applications for big metagenomics data. Evol Bioinform. 2016;12:EBO–S36436.
   Google Scholar
• Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Molecul Bio Rev. 2004;68:669–685.
   PubMed Web of Science ®Google Scholar
• Zhang L, Chen F, Zeng Z, et al. Advances in metagenomics and its application in environmental microorganisms. Front Microbiol. 2021;12:766364.
   PubMed Web of Science ®Google Scholar
• Hamady M, Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 2009;19:1141–1152.
   PubMed Web of Science ®Google Scholar
• Rout ME.2014. The plant microbiome. InAdvances in botanical research. Academic Press. Vol. 69. p. 279–309.
   Google Scholar
• Turner TR, James EK, Poole PS. The plant microbiome. Genome Biol. 2013;14(6):1–10.
   Web of Science ®Google Scholar
• Babalola OO, Fadiji AE, Enagbonma BJ, et al. The nexus between plant and plant microbiome: revelation of the networking strategies. Front Microbiol. 2020;11:2128.
   Web of Science ®Google Scholar
• Mercado-Blanco J, Abrantes I, Barra Caracciolo A, et al. Belowground microbiota and the health of tree crops. Front Microbiol. 2018;9:1006.
   PubMed Web of Science ®Google Scholar
• Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev. 2013;37(5):634–663.
   PubMed Web of Science ®Google Scholar
• Ortíz-Castro R, Contreras-Cornejo HA, Macías-Rodríguez L, et al. The role of microbial signals in plant growth and development. Plant Signal Behav. 2009;4(8):701–712.
   PubMedGoogle Scholar
• Chandra P, Singh E Applications and mechanisms of plant growth-stimulating rhizobacteria. In Plant-microbe interaction: an approach to sustainable agriculture. Springer, Singapore. (Ed.), 2016; (pp. 37–62).
   Google Scholar
• Mhlongo MI, Piater LA, Madala NE, et al. The chemistry of plant–microbe interactions in the rhizosphere and the potential for metabolomics to reveal signaling related to defense priming and induced systemic resistance. Front Plant Sci. 2018;9:112.
   PubMed Web of Science ®Google Scholar
• Santos LF, Olivares FL. Plant microbiome structure and benefits for sustainable agriculture. Curr Plant Biol. 2021;26:100198.
   Web of Science ®Google Scholar
• Cirvilleri G, Spina S, Iacona C, et al. Study of rhizosphere and phyllosphere bacterial community and resistance to bacterial canker in genetically engineered phytochrome A cherry plants. J Plant Physiol. 2008;165(10):1107–1119.
   PubMed Web of Science ®Google Scholar
• Bakker PA, Berendsen RL, Doornbos RF, et al. The rhizosphere revisited: root microbiomics. Front Plant Sci. 2013;4:165.
   PubMed Web of Science ®Google Scholar
• Hu J, Wei Z, Kowalchuk GA, et al. Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development. Environ Microbiol. 2020;22(12):5005–5018.
   PubMed Web of Science ®Google Scholar
• Barea JM, Pozo MJ, Azcon R, et al. Microbial co-operation in the rhizosphere. J Exp Bot. 2005;56(417):1761–1778.
   PubMed Web of Science ®Google Scholar
• Mahmud K, Missaoui A, Lee K, et al. Rhizosphere microbiome manipulation for sustainable crop production. Curr Plant Biol. 2021;27:100210.
   Web of Science ®Google Scholar
• Chandra P, Enespa. Soil–microbes–plants: interactions and ecological diversity. In Varma, A., Tripathi, S., Prasad, R. (eds). Plant microbe interface. Cham: Springer; 2019. p. 145–176.
   Google Scholar
• Enespa CP.2017. Microbial Volatiles as Chemical Weapons Against Pathogenic Fungi. In Choudhary, D., Sharma, A., Agarwal, P., Varma, A., Tuteja, N. (eds.). Volatiles and Food Security. Singapore: Springer. p. 227–254.
   Google Scholar
• Miranda‐Sánchez F, Rivera J, Vinuesa P. Diversity patterns of rhizobiaceae communities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes. Environ Microbiol. 2016;18(8):2375–2391.
   PubMed Web of Science ®Google Scholar
• Kudoyarova G, Arkhipova T, Korshunova T, et al. Phytohormone mediation of interactions between plants and non-symbiotic growth promoting bacteria under edaphic stresses. Front Plant Sci. 2019;10 (1368):1–11.
   Web of Science ®Google Scholar
• Starr MP. Bacteria as plant pathogens. Annual Rev Microbiol. 1959;13:211–238.
   Web of Science ®Google Scholar
• Lindow SE, Brandl MT. Microbiology of the phyllosphere. Appl Environ Microbiol. 2003;69(4):1875–1883.
   PubMed Web of Science ®Google Scholar
• Bringel F, Couée I. Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. Front Microbiol. 2015;6:486.
   PubMed Web of Science ®Google Scholar
• Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30(6):492–506.
   PubMed Web of Science ®Google Scholar
• Braga RM, Dourado MN, Araújo WL. Microbial interactions: ecology in a molecular perspective. Brazilian J Microbiol. 2016;47:86–98.
   PubMed Web of Science ®Google Scholar
• Gottel NR, Castro HF, Kerley M, et al. Distinct microbial communities within the endosphere and rhizosphere of populus deltoides roots across contrasting soil types. Appl Environ Microbiol. 2011;77(17):5934–5944.
   PubMed Web of Science ®Google Scholar
• Nongkhlaw FM, Joshi SR. Distribution pattern analysis of epiphytic bacteria on ethno medicinal plant surfaces: a micrographical and molecular approach. J Microscopy Ultrastruct. 2014;2(1):34–40.
   Google Scholar
• Der Wal A V, Tecon R, Kreft JU, et al. Explaining bacterial dispersion on leaf surfaces with an individual-based model (PHYLLOSIM). PloS one. 2013;8(10):e75633.
   PubMed Web of Science ®Google Scholar
• Carvalho SD, Castillo JA. Influence of light on plant–phyllosphere interaction. Front Plant Sci. 2018;9:1482.
   PubMed Web of Science ®Google Scholar
• Afzal I, Shinwari ZK, Sikandar S, et al. Plant beneficial endophytic bacteria: mechanisms, diversity, host range and genetic determinants. Microbiol Res. 2019;221:36–49.
   PubMed Web of Science ®Google Scholar
• Partida-Martínez LP, Heil M. The microbe-free plant: fact or artifact? Front Plant Sci. 2011;2:100.
   PubMed Web of Science ®Google Scholar
• Vishwakarma K, Kumar N, Shandilya C, et al. Revisiting plant–microbe interactions and microbial consortia application for enhancing sustainable agriculture: a review. Front Microbiol. 2020;11:560406.
   PubMed Web of Science ®Google Scholar
• Baldrian P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol Rev. 2017;41(2):109–130.
   PubMed Web of Science ®Google Scholar
• Grilli J. Macroecological laws describe variation and diversity in microbial communities. Nat Commun. 2020;11(1):1.
   PubMed Web of Science ®Google Scholar
• Franco-Duarte R, Černáková L, Kadam S, et al. Advances in chemical and biological methods to identify microorganisms—from past to present. Microorganism. 2019;7(5):130.
   PubMed Web of Science ®Google Scholar
• Ritchie NJ, Schutter ME, Dick RP, et al. Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Appl Environ Microbiol. 2000;66(4):1668–1675.
   PubMed Web of Science ®Google Scholar
• Portillo MC, Villahermosa D, Corzo A. Microbial community fingerprinting by differential display-denaturing gradient gel electrophoresis. Appl Environ Microbiol. 2011;77(1):351–354.
   PubMed Web of Science ®Google Scholar
• Keyser M, Witthuhn RC, Lamprecht C, et al. PCR-based DGGE fingerprinting and identification of methanogens detected in three different types of UASB granules. Syst Appl Microbiol. 2006;29(1):77–84.
   PubMed Web of Science ®Google Scholar
• Wertz S, Degrange V, Prosser JI, et al. Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance. Environ Microbiol. 2007;9(9):2211–2219.
   PubMed Web of Science ®Google Scholar
• Berg G, Smalla K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol. 2009;68(1):1–3.
   PubMed Web of Science ®Google Scholar
• Chen X, Zheng B, Liu H. Optical and digital microscopic imaging techniques and applications in pathology. Anal Cell Pathol. 2011;34(1–2):5–18.
   Web of Science ®Google Scholar
• Wisse E, Braet F, Duimel H, et al. Fixation methods for electron microscopy of human and other liver. World J Gastroenterol. 2010;16(23):2851.
   PubMed Web of Science ®Google Scholar
• Goldsmith CS, Miller SE. Modern uses of electron microscopy for detection of viruses. Clin Microbiol Rev. 2009;22(4):552–563.
   PubMed Web of Science ®Google Scholar
• Berg G, Rybakova D, Fischer D, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiom. 2020;8(1):1–22.
   PubMed Web of Science ®Google Scholar
• Romano I, Ventorino V, Pepe O. Effectiveness of plant beneficial microbes: overview of the methodological approaches for the assessment of root colonization and persistence. Front Plant Sci. 2020;11:6.
   PubMed Web of Science ®Google Scholar
• Wu CH, Bernard SM, Andersen GL, et al. Developing microbe–plant interactions for applications in plant‐growth promotion and disease control, production of useful compounds, remediation and carbon sequestration. Microbial Biotechnol. 2009;2(4):428–440.
   PubMed Web of Science ®Google Scholar
• Hannig C, Follo M, Hellwig E, et al. Visualization of adherent micro-organisms using different techniques. J Medical Microbiol. 2010;59(1):1–7.
   PubMed Web of Science ®Google Scholar
• Scott TM, Rose JB, Jenkins TM, et al. Microbial source tracking: current methodology and future directions. Appl Environ Microbiol. 2002;68(12):5796–5803.
   PubMed Web of Science ®Google Scholar
• Ali N, Rampazzo RD, Costa AD, et al. Current nucleic acid extraction methods and their implications to point-of-care diagnostics. BioMed Res Int. 2017;1–17.
   Web of Science ®Google Scholar
• Sirakov IN. Nucleic acid isolation and downstream applications. Nucleic Acids-From Basic Aspects to Laboratory Tools. 2016;1–26.
   Google Scholar
• Collins ML, Zayati C, Detmer JJ, et al. Preparation and characterization of RNA standards for use in quantitative branched DNA hybridization assays. Analyt Biochem. 1995;226(1):120–129.
   PubMed Web of Science ®Google Scholar
• Olson ND, Morrow JB. DNA extract characterization process for microbial detection methods development and validation. BMC Res Note. 2012;5(1):1–4.
   PubMedGoogle Scholar
• Hafner M, Katsantoni M, Köster T, et al. CLIP and complementary methods. Nat Rev Met Primers. 2021;1(1):1–23.
   Google Scholar
• Wintzingerode F, Göbel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev. 1997;21(3):213–229.
   PubMed Web of Science ®Google Scholar
• Li Q, Luan G, Guo Q, et al. A new class of homogeneous nucleic acid probes based on specific displacement hybridization. Nucleic Acids Res. 2002;30(2):e5.
   PubMed Web of Science ®Google Scholar
• Pagano JM, Clingman CC, Ryder SP. Quantitative approaches to monitor protein–nucleic acid interactions using fluorescent probes. Rna. 2011;17(1):14–20.
   PubMed Web of Science ®Google Scholar
• Volpi EV, Bridger JM. FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques. 2008;45(4):385–409.
   PubMed Web of Science ®Google Scholar
• Ratan ZA, Zaman SB, Mehta V, et al. Application of fluorescence in situ hybridization (FISH) technique for the detection of genetic aberration in medical science. Cureus. 2017;9(6):e1325.
   PubMed Web of Science ®Google Scholar
• Ramette A, Tiedje JM. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proceed National Acad Sci. 2007;104(8):2761–2766.
   PubMed Web of Science ®Google Scholar
• Gabor EM, de Vries Ej, Janssen DB. Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. FEMS Microbiol Ecol. 2003;44(2):153–163.
   PubMed Web of Science ®Google Scholar
• Huber D, von Voithenberg Lv, Kaigala GV. Fluorescence in situ hybridization (FISH): history, limitations and what to expect from micro-scale FISH? Micro Nano Engineer. 2018;1:15–24.
   Google Scholar
• Wang T, Chen C, Larcher LM, et al. Three decades of nucleic acid aptamer technologies: lessons learned, progress and opportunities on aptamer development. Biotechnol Adv. 2019;37(1):28–50.
   PubMed Web of Science ®Google Scholar
• Garibyan L, Avashia N. Research techniques made simple: polymerase chain reaction (PCR). J Investigat Dermatol. 2013;133(3):e6.
   PubMedGoogle Scholar
• Mirmajlessi SM, Destefanis M, Gottsberger RA, et al. PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review. Systemat Rev. 2015;4(1):1–11.
   PubMedGoogle Scholar
• Chen L, Cai Y, Zhou G, et al. Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens. PloS one. 2014;9(2):e88886.
   PubMed Web of Science ®Google Scholar
• Barghouthi SA. A universal method for the identification of bacteria based on general PCR primers. Indian J Microbiol. 2011;51:430–444.
   PubMed Web of Science ®Google Scholar
• Giglio S, Monis PT, Saint CP. Demonstration of preferential binding of SYBR green I to specific DNA fragments in real‐time multiplex PCR. Nucleic Acid Res. 2003;31(22):e136.
   PubMed Web of Science ®Google Scholar
• Espy MJ, Uhl JR, Sloan LM, et al. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev. 2006;19(1):165–256.
   PubMed Web of Science ®Google Scholar
• Kralik P, Ricchi M. A basic guide to real time PCR in microbial diagnostics: definitions, parameters, and everything. Front Microbiol. 2017;8:108.
   PubMed Web of Science ®Google Scholar
• Overbergh L, Giulietti A, Valckx D, et al. The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression. J Biomol Tech. 2003;14(1):33.
   PubMedGoogle Scholar
• Del Mar Lleò M, Pierobon S, Tafi MC, et al. mRNA detection by reverse transcription-PCR for monitoring viability over time in an Enterococcus faecalis viable but nonculturable population maintained in a laboratory microcosm. Appl Environ Microbiol. 2000;66(10):4564–4567.
   PubMed Web of Science ®Google Scholar
• Yang S, Rothman RE. PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. Lancet Infect Dis. 2004;4(6):337–348.
   PubMed Web of Science ®Google Scholar
• Sharkey FH, Banat IM, Marchant R. Detection and quantification of gene expression in environmental bacteriology. Appl Environ Microbiol. 2004;70(7):3795–3806.
   PubMed Web of Science ®Google Scholar
• Khan S, Ullah MW, Siddique R, et al. Role of recombinant DNA technology to improve life. Int J Genom. 2016;1–15.
   Web of Science ®Google Scholar
• Rasmussen HB. Restriction fragment length polymorphism analysis of PCR-amplified fragments (PCR-RFLP) and gel electrophoresis-valuable tool for genotyping and genetic fingerprinting. Techopen. 2012;1–22.
   Google Scholar
• Johnston‐Monje D, Lopez Mejia J. Botanical microbiomes on the cheap: inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi. Appl Plant Sci. 2020;8(4):e11334.
   PubMed Web of Science ®Google Scholar
• Osborn AM, Moore ER, Timmis KN. An evaluation of terminal‐restriction fragment length polymorphism (T‐RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol. 2000;2(1):39–50.
   PubMed Web of Science ®Google Scholar
• DeAngelis KM, Wu CH, Beller HR, et al. PCR amplification-independent methods for detection of microbial communities by the high-density microarray phyloChip. Appl Environ Microbiol. 2011;77(18):6313–6322.
   PubMed Web of Science ®Google Scholar
• Weinstock GM. Genomic approaches to studying the human microbiota. Nature. 2012;489(7415):250–256.
   PubMed Web of Science ®Google Scholar
• Al‐Mailem DM, Kansour MK, Radwan SS. Capabilities and limitations of DGGE for the analysis of hydrocarbonoclastic prokaryotic communities directly in environmental samples. Microbiol Open. 2017;6(5):e00495.
   Google Scholar
• Urashima Y, Sonoda T, Fujita Y, et al. Application of PCR-denaturing-gradient gel electrophoresis (DGGE) method to examine microbial community structure in asparagus fields with growth inhibition due to continuous cropping. Microbe Environ. 2009;27:43–48.
   Google Scholar
• Douterelo I, Boxall JB, Deines P, et al. Methodological approaches for studying the microbial ecology of drinking water distribution systems. Water Res. 2014;65:134–156.
   PubMed Web of Science ®Google Scholar
• Rastogi G, Sani RK.2011. Molecular tTechniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment. In Ahmad, I., Ahmad, F., Pichtel, J. (eds). Microbes and Microbial Technology. New York NY: Springer. p. 29–57.
   Google Scholar
• Das S, Dash HR, Mangwani N, et al. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods. 2014;103:80–100.
   PubMed Web of Science ®Google Scholar
• Schabereiter‐Gurtner C, Saiz‐Jimenez C, Piñar G, et al. Phylogenetic 16S rRNA analysis reveals the presence of complex and partly unknown bacterial communities in tito bustillo cave, Spain, and on its palaeolithic paintings. Environ Microbiol. 2002;4(7):392–400.
   PubMed Web of Science ®Google Scholar
• Dı́ez B, Pedrós-Alió C, Marsh TL, et al. Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl Environ Microbiol. 2001;67(7):2942–2951.
   PubMed Web of Science ®Google Scholar
• Muyzer G, De Waal EC, Uitterlinden A. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59(3):695–700.
   PubMed Web of Science ®Google Scholar
• Morales SE, Cosart TF, Johnson JV, et al. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters. Appl Environ Microbiol. 2009;75(3):668–675.
   PubMed Web of Science ®Google Scholar
• Schloter M, Nannipieri P, Sørensen SJ, et al. Microbial indicators for soil quality. Biol Fertil Soil. 2018;54(1):1–10.
   Web of Science ®Google Scholar
• Hoekstra HE, Coyne JA. The locus of evolution: evo devo and the genetics of adaptation. Evol Int J Organic Evol. 2007;61(5):995–1016.
   PubMed Web of Science ®Google Scholar
• Goldfarb KC, Karaoz U, Hanson CA, et al. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol. 2011;2:94.
   PubMed Web of Science ®Google Scholar
• Tan B, Ng CM, Nshimyimana JP, et al. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front Microbiol. 2015;6:1027.
   PubMed Web of Science ®Google Scholar
• Priemé A, Braker G, Tiedje JM. Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol. 2002;68(4):1893–1900.
   PubMed Web of Science ®Google Scholar
• Braker G, Zhou J, Wu L, et al. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl Environ Microbiol. 2000;66(5):2096–2104.
   PubMed Web of Science ®Google Scholar
• Raman R. The impact of Genetically Modified (GM) crops in modern agriculture: a review. GM Crops Food. 2017;8(4):195–208.
   PubMed Web of Science ®Google Scholar
• Frapolli M, Moënne-Loccoz Y, Meyer J, et al. A new DGGE protocol targeting 2, 4-diacetylphloroglucinol biosynthetic gene phlD from phylogenetically contrasted biocontrol pseudomonads for assessment of disease-suppressive soils. FEMS Microbiol Ecol. 2008;64(3):468–481.
   PubMed Web of Science ®Google Scholar
• Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.
   PubMed Web of Science ®Google Scholar
• Lu F, Jiang H, Ding J, et al. cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics. 2007;8(1):1.
   PubMedGoogle Scholar
• Smalla K, Jechalke S, Top EM. Plasmid detection, characterization, and ecology. Microbiol Spectr. 2015;3(1):3–21.
   Google Scholar
• Shintani M, Sanchez ZK, Kimbara K. Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy. Front Microbiol. 2015;6:242.
   PubMed Web of Science ®Google Scholar
• Blainey PC. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev. 2013;37:407–427.
   PubMed Web of Science ®Google Scholar
• Hayat R, Ali S, Amara U, et al. Soil beneficial bacteria and their role in plant growth promotion: a review. Annal Microbiol. 2010;60(4):579–598.
   Web of Science ®Google Scholar
• Trevino V, Falciani F, Barrera-Saldaña HA. DNA microarrays: a powerful genomic tool for biomedical and clinical research. Mol Med. 2007;13(9):527–541.
   PubMed Web of Science ®Google Scholar
• Bumgarner R. Overview of DNA microarrays: types, applications, and their future. Curr Protoc Mol Biol. 2013;101:1–22.
   Google Scholar
• Lucito R, Healy J, Alexander J, et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 2003;13(10):2291–2305.
   PubMed Web of Science ®Google Scholar
• Miller MB, Tang YW. Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev. 2009;22(4):611–633.
   PubMed Web of Science ®Google Scholar
• Thomsen PF, Willerslev E. Environmental DNA–an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv. 2015;183:4–18.
   Web of Science ®Google Scholar
• Li Q, Birkbak NJ, Gyorffy B, et al. Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics. 2011;12(1):1–7.
   PubMedGoogle Scholar
• Koltai H, Weingarten-Baror C. Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction. Nucleic Acid Res. 2008;36(7):2395–2405.
   PubMed Web of Science ®Google Scholar
• Butte A. The use and analysis of microarray data. Nat Rev Drug Discov. 2002;1:951–960.
   PubMed Web of Science ®Google Scholar
• Tu Q, Yu H, He Z, et al. GeoChip 4: a functional gene‐array‐based high‐throughput environmental technology for microbial community analysis. Mol Ecol Resour. 2014;14(5):914–928.
   PubMed Web of Science ®Google Scholar
• Xie J, He Z, Liu X, et al. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Appl Environ Microbiol. 2011;77(3):991–999.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Lu Z, Liu S, et al. Geochip-based analysis of microbial communities in alpine meadow soils in the qinghai-tibetan plateau. BMC Microbiol. 2013;13(1):1–9.
   PubMedGoogle Scholar
• Escobar-Zepeda A, Vera-Ponce de Leon A, Sanchez-Flores A. The road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics. Front Genet. 2015;6:348.
   PubMed Web of Science ®Google Scholar
• Ronaghi M, Uhlén M, Nyrén P. A sequencing method based on real-time pyrophosphate. Science. 1998;281(5375):363–365.
   PubMed Web of Science ®Google Scholar
• Van Nieuwerburgh F, Thompson RC, Ledesma J, et al. Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acid Res. 2012;40(3):e24.
   PubMed Web of Science ®Google Scholar
• Van Elsas JD, Boersma FG. A review of molecular methods to study the microbiota of soil and the mycosphere. European J Soil Biol. 2011;47(2):77–87.
   Web of Science ®Google Scholar
• Head SR, Komori HK, LaMere SA, et al. Library construction for next-generation sequencing: overviews and challenges. Biotechniques. 2014;56(2):61–77.
   PubMed Web of Science ®Google Scholar
• Martin-Laurent F, Philippot L, Hallet S, et al. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol. 2001;67(5):2354–2359.
   PubMed Web of Science ®Google Scholar
• Bashir A, Klammer AA, Robins WP, et al. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol. 2012;30(7):701–707.
   PubMed Web of Science ®Google Scholar
• Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Molecul Cell. 2015;58(4):586–597.
   PubMed Web of Science ®Google Scholar
• Marchev AS, Vasileva LV, Amirova KM, et al. Metabolomics and health: from nutritional crops and plant-based pharmaceuticals to profiling of human biofluids. Cell Mol Life Sci. 2021;78:6487–6503.
   PubMed Web of Science ®Google Scholar
• Razzaq A, Sadia B, Raza A, et al. Metabolomics: a way forward for crop improvement. Metabolites. 2019;9(12):303.
   PubMed Web of Science ®Google Scholar
• Salem MA, Perez de Souza L, Serag A, et al. Metabolomics in the context of plant natural products research: from sample preparation to metabolite analysis. Metabolites. 2020;10(1):37.
   PubMed Web of Science ®Google Scholar
• Lucaciu R, Pelikan C, Gerner S, et al. A bioinformatics guide to plant microbiome analysis. Front Plant Sci. 2019;10:1313.
   PubMed Web of Science ®Google Scholar
• Emwas AH, Roy R, McKay RT, et al. NMR spectroscopy for metabolomics research. Metabolites. 2019;9(7):123.
   PubMed Web of Science ®Google Scholar
• Xiao JF, Zhou B, Ressom HW. Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trends Anal Chem. 2012;32:1–14.
   PubMed Web of Science ®Google Scholar
• Scalbert A, Brennan L, Fiehn O, et al. Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics. 2009;5(4):435–458.
   PubMed Web of Science ®Google Scholar
• Dona Anthony C, Michael K, Flora S, et al. A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments. Comput Struct Biotechnol J. 2016;14:135–153.
   PubMed Web of Science ®Google Scholar
• Vladimir V, Schriemer David C. Supporting metabolomics with adaptable software: design architectures for the end-user. Curr Opin Biotechnol. 2017;43:110–117.
   PubMed Web of Science ®Google Scholar
• Martin M, Legat B, Leenders J, et al. PepsNMR for 1H NMR metabolomic data pre-processing. Anal Chim Acta. 2018;1019:1–13.
   PubMed Web of Science ®Google Scholar
• Sumner LW, Amberg A, Barrett D, et al. Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics. 2007;3(3):211–221.
   PubMed Web of Science ®Google Scholar
• Emwas AH, Roy R, McKay RT, et al. NMR spectroscopy for metabolomics research. Metabolites. 2019;9(7):123.
   PubMed Web of Science ®Google Scholar
• Reck M, Tomasch J, Deng Z, et al. Stool metatranscriptomics: a technical guideline for mRNA stabilisation and isolation. BMC Genomics. 2015;16:494.
   PubMed Web of Science ®Google Scholar
• Song L, Sabunciyan S, Yang G, et al. A multi-sample approach increases the accuracy of transcript assembly. Nat Commun. 2019;10(1):5000.
   PubMedGoogle Scholar
• Hettich RL, Pan C, Chourey K, et al. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem. 2013;85(9):4203–4214.
   PubMed Web of Science ®Google Scholar
• Wang DZ, Kong LF, Li YY, et al. Environmental microbial community proteomics: status, challenges and perspectives. Int J Mol Sci. 2016;17(8):1275.
   PubMed Web of Science ®Google Scholar
• Benndorf D, Reichl U. Proteomics in environmental and technical microbiology. Eng Life Sci. 2014;14(1):27–46.
   Web of Science ®Google Scholar
• Lambais MR, Barrera SE, Santos EC, et al. Phyllosphere metaproteomics of trees from the Brazilian Atlantic forest show high levels of functional redundancy. Microb Ecol. 2017;73(1):123–134.
   PubMed Web of Science ®Google Scholar
• Levy A, Conway JM, Dangl JL, et al. Elucidating bacterial gene functions in the plant microbiome. Cell Host Microbe. 2018;24(4):475–485.
   PubMed Web of Science ®Google Scholar
• Turner TR, James EK, Poole PS. The plant microbiome. Genome Biol. 2013;14(6):1-10.
   Web of Science ®Google Scholar
• Maron PA, Ranjard L, Mougel C, et al. Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol. 2007;53(3):486–493.
   PubMed Web of Science ®Google Scholar
• Kleiner M. Metaproteomics: much more than measuring gene expression in microbial communities. mSystems. 2019;4(3):e00115–19.
   PubMed Web of Science ®Google Scholar
• Blakeley-Ruiz JA, Kleiner M. Considerations for constructing a protein sequence database for metaproteomics. Comput Struct Biotechnol J. 2022;20:937–952.
   PubMed Web of Science ®Google Scholar
• Timmins-Schiffman E, May DH, Mikan M, et al. Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. ISME J. 2017;11(2):309–314.
   PubMed Web of Science ®Google Scholar
• Bastida F, Hernández T, García C. Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods. J Proteomics. 2014;101:31–42.
   PubMed Web of Science ®Google Scholar
• Hettich RL, Pan C, Chourey K, et al. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem. 2013;85(9):4203–4214.
   PubMed Web of Science ®Google Scholar
• Gavrilaș S, Ursachi CȘ, Perța-Crișan S, et al. recent trends in biosensors for environmental quality monitoring. Sensors. 2022;22(4):1513. (Basel, Switzerland).
   PubMed Web of Science ®Google Scholar
• Mokhtarzadeh A, Eivazzadeh-Keihan R, Pashazadeh P, et al. Nanomaterial-based biosensors for detection of pathogenic virus. Trends Anal Chem. 2017;97:445–457.
   PubMed Web of Science ®Google Scholar
• Mohajerani A, Burnett L, Smith JV, et al. Nanoparticles in construction materials and other applications, and implications of nanoparticle use. Materials (Basel). 2019;12(19):3052.
   PubMed Web of Science ®Google Scholar
• Liu L, Song B, Ma J, et al. Bioinformatics approaches for deciphering the epitranscriptome: recent progress and emerging topics. Comput Struct Biotechnol J. 2020;18:1587–1604.
   PubMed Web of Science ®Google Scholar
• Boon E, Meehan CJ, Whidden C, et al. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev. 2014;38(1):90–118.
   PubMed Web of Science ®Google Scholar
• Hasin Y, Seldin M, Lusis A. Multi-omics approaches to disease. Genome Biol. 2017;18(1):1–5.
   PubMedGoogle Scholar
• Bisanz JE, Soto-Perez P, Noecker C, et al. A genomic toolkit for the mechanistic dissection of intractable human gut bacteria. Cell Host Microb. 2020;27(6):1001–1013.
   PubMed Web of Science ®Google Scholar
• Thomas T, Gilbert J, Meyer F. Metagenomics-a guide from sampling to data analysis. Microb Inform Exp. 2012;2(1):1–2.
   PubMedGoogle Scholar
• Pinu FR, Villas-Boas SG, Aggio R. Analysis of intracellular metabolites from microorganisms: quenching and extraction protocols. Metabol. 2017;7(4):53.
   Google Scholar
• Hartmann M, Frey B, Mayer J, et al. Distinct soil microbial diversity under long-term organic and conventional farming. Isme J. 2015;9(5):1177–1194.
   PubMed Web of Science ®Google Scholar
• Rakoff-Nahoum S, Foster KR, Comstock LE. The evolution of cooperation within the gut microbiota. Nature. 2016;533(7602):255–259.
   PubMed Web of Science ®Google Scholar
• Bharti R, Grimm DG. Current challenges and best-practice protocols for microbiome analysis. Briefing Bioinform. 2021;22:178–193.
   PubMed Web of Science ®Google Scholar
• Buermans HPJ, Den Dunnen JT. Next generation sequencing technology: advances and applications. Biochim Biophysica Acta. 2014;1842:1932–1941.
   PubMed Web of Science ®Google Scholar