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Analytical Techniques/Technologies for Studying Ecological Microbial Samples

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Advances in the Domain of Environmental Biotechnology

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

Abstract

It is known that most of the microorganisms in the environment are unculturable and using the culture-dependent methods in isolating these organisms may be time consuming among other disadvantages. As a result, methods used in studying microbes have evolved from the traditional culture-dependent methods to culture-independent molecular-based approaches. This chapter discusses the classical culture-independent molecular techniques with an emphasis on the latest information on novel methods in microbial ecological research including the use of “omics” approaches such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics for identifying total microbial community structure and their functions in the environment. It also covers the recent use of a combination of “omics” (multi-omics) approach and the use of improved bioinformatics pipeline for big data analysis and interpretation.

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Abbreviations

ARDRA:

Amplified ribosomal DNA restriction analysis

cRNAs:

coding RNAs

DGGE:

Denaturing gradient gel electrophoresis

DNA:

Deoxyribonucleic acid

HTS:

High-throughput sequencing

ISR:

Intergenic spacer region

MS:

Mass spectroscopy

ncRNAs:

Noncoding RNAs

NMR:

Nuclear magnetic resonance

OUT:

Operational taxonomic unit

PCA:

Principle component analysis

PCR:

Polymerase chain reaction

qPCR:

Quantitative polymerase chain reaction

rRNA:

Ribosomal ribonucleic acid

RFLP:

Restriction fragment length polymorphism

RISA:

Ribosomal intergenic spacer analysis

RNA:

Ribonucleic acid

SCSU:

Sole carbon-source utilization

SIP:

Stable-isotope probing

SPE:

Solid-phase extraction

SSCP:

Single-stranded conformation polymorphism

ssDNA:

Single-stranded DNA

T-RFLP:

Terminal restriction fragment length polymorphism

References

  • Akasaka K (2015) High pressure NMR spectroscopy. Subcell Biochem 72:707–721

    Article  CAS  PubMed  Google Scholar 

  • Alguacil M, Díaz-Pereira E, Caravaca F, Fernández DA, Roldán A (2009) Increased diversity of arbuscular mycorrhizal fungi in a long-term field experiment via application of organic amendments to a semiarid degraded soil. Appl Environ Microbiol 75:4254–4263

    Article  CAS  Google Scholar 

  • Angel R, Panhölzl C, Gabriel R, Herbold C, Wanek W, Richter A, Eichorst SA, Woebken D (2018) Application of stable-isotope labelling techniques for the detection of active diazotrophs. Environ Microbiol 20:44–61

    Article  CAS  PubMed  Google Scholar 

  • Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–2168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH (2017) Proteomics: technologies and their applications. J Chromatogr Sci 55:182–196

    Article  CAS  PubMed  Google Scholar 

  • Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134

    Article  PubMed  PubMed Central  Google Scholar 

  • Austin B (2017) The value of cultures to modern microbiology. Antonie Van Leeuwenhoek 110:1247–1256

    Article  CAS  PubMed  Google Scholar 

  • Barua S, Hait A, Barua S (2017) Metatranscriptomic study of microbes in environment: a community function based approach. J Bacteriol Mycol 4:12–15

    Google Scholar 

  • Beale DJ, Crosswell J, Karpe AV, Metcalfe SS, Morrison PD, Staley C, Ahmed W, Sadowsky MJ, Palombo EA, Steven ADL (2018) Seasonal metabolic analysis of marine sediments collected from Moreton Bay in south East Queensland, Australia, using a multi-omics-based approach. Sci Total Environ 631–632:1328–1341

    Article  PubMed  CAS  Google Scholar 

  • Beale DJ, Karpe AV, Ahmed W, Cook S, Morrison PD, Staley C, Sadowsky MJ, Palombo EA (2017) A community multi-omics approach towards the assessment of surface water quality in an urban river system. Int J Environ Res Public Health 14(303):1–24

    Google Scholar 

  • Beale DJ, Karpe AV, McLeod JD, Gondalia SV, Muster TH, Othman MZ, Palombo EA, Joshi D (2016) An ‘omics’ approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge. Water Res 88:346–357

    Article  CAS  PubMed  Google Scholar 

  • Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child Educ Pract Ed 98:236–238

    Article  PubMed  PubMed Central  Google Scholar 

  • Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) GenBank. Nucleic Acids Res 41:D36–D42

    Article  CAS  PubMed  Google Scholar 

  • Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM (2015) Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 33:623–630

    Article  CAS  PubMed  Google Scholar 

  • Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E (2018) Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clin Microbiol Infect 24:335–341

    Article  CAS  PubMed  Google Scholar 

  • Bhadange Y, Sharma S, Das S, Sahu SK (2013) Role of liquid culture media in the laboratory diagnosis of microbial keratitis. Am J Ophthalmol 156:745–751

    Article  PubMed  Google Scholar 

  • Bingol K (2018) Recent advances in targeted and untargeted metabolomics by NMR and MS/NMR methods. High Throughput 7:9

    Article  CAS  PubMed Central  Google Scholar 

  • Bingol K, Brüschweiler R (2015) Two elephants in the room: new hybrid nuclear magnetic resonance and mass spectrometry approaches for metabolomics. Curr Opin Clin Nutr Metab Care 18:471–477

    Google Scholar 

  • Bonnet M, Lagier JC, Raoult D, Khelaifia S (2019) Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology. New Microb New infect 34:100622

    Article  Google Scholar 

  • Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Breindel L, Burz DS, Shekhtman A (2019) Interaction proteomics by using in-cell NMR spectroscopy. J Proteome 191:202–211

    Article  CAS  Google Scholar 

  • Broadhurst DI, Kell DB (2006) Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics 2:171–196

    Article  CAS  Google Scholar 

  • Calderón-Celis F, Encinar JR, Sanz-Medel A (2018) Standardization approaches in absolute quantitative proteomics with mass spectrometry. Mass Spectrom Rev 37:715–737

    Article  PubMed  CAS  Google Scholar 

  • Campillo JA, Sevilla A, Gonza’lez-Ferna’ndez C, Bellas J, Bernal C, Ca’novas M, Albentosa M (2019) Metabolomic responses of mussel Mytilus galloprovincialis to fluoranthene exposure under different nutritive conditions. Mar Environ Res 144:194–202

    Article  CAS  PubMed  Google Scholar 

  • Cardullo RA, Agrawal S, Flores C, Zamecnik PC, Wolf DE (1988) Detection of nucleic acid hybridization by nonradioactive fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 85:8790–8794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carvalho M, Tondella ML, McCaustland K, Weidlich L, McGee L, Mayer LW, Steigerwalt A, Whaley M, Facklam RR, Fields B, Carlone G, Ades EW, Dagan R, Sampson JS (2007) Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol 45:2460–2466

    Article  CAS  PubMed Central  Google Scholar 

  • Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38:D473–D479. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808959/

  • Çelen I, Doh JH, Sabanayagam CR (2018) Effects of liquid cultivation on gene expression and phenotype of C. elegans. BMC Genomics 19:562

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen L-H, Huang XQ, Zhang FG, Zhao DK, Yang XM, Shen QR (2012) Application of Trichoderma harzianum SQR-T037 bio-organic fertiliser significantly controls Fusarium wilt and affects the microbial communities of continuously cropped soil of cucumber. J Sci Food Agric 92(12):2465–2470

    Google Scholar 

  • Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC (2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13:1050–1054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chong J, Soufan O, Li C, Caraus I, Li S, Bourque G, Wishart DS, Xia J (2018) MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Res 46:W486–W494

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christensen H, Bojesen AM, Bisgaard M (2011) Mannheimiacaviae sp. nov., isolated from epidemic conjunctivitis and otitis media in guinea pigs. Int J Syst Evol Microbiol 61:1699–1704

    Google Scholar 

  • Cid FP, Inostroza NG, Graether SP, Bravo LA, Jorquera MA (2017) Bacterial community structures and ice recrystallization inhibition activity of bacteria isolated from the phyllosphere of the Antarctic vascular plant Deschampsia antarctica. Polar Biol 40:1319–1331

    Article  Google Scholar 

  • Coscia F, Lengyel E, Duraiswamy J, Ashcroft B, Bassani-Sternberg M, Wierer M, Johnson A, Wroblewski K, Montag A, Yamada SD, Lopez-Mendez B, Nilsson J, Mund A, Mann M, Curtis M (2018) Multi-level proteomics identifies CT45 as a chemosensitivity mediator and immunotherapy target in ovarian cancer. Cell 175:159–170.e116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Costa A, Franco OL (2017) Impact and influence of “omics” technology on hypertension studies. Int J Cardiol 228:1022–1034

    Article  PubMed  Google Scholar 

  • Cubaka KA, Cornu BM, van Vliet F, Meyer C, Mergeay M, Simbi JL, Droogmans L, Wauven CV, Verbruggen N (2010) Diversity of endophytic bacteria from the cuprophytes Haumaniastrum katangense and Crepidorhopalon tenuis. Plant Soil 334:461–474

    Article  CAS  Google Scholar 

  • Davis JM, Ekman DR, Teng Q, Ankley GT, Berninger JP, Cavallin JE, Jensen KM, Kahl MD, Schroeder AL, Villeneuve DL, Jorgenson ZG, Lee KE, Collette TW (2016) Linking field-based metabolomics and chemical analyses to prioritize contaminants of emerging concern in the Great Lakes basin. Environ Toxicol Chem 35:2493–2502

    Article  CAS  PubMed  Google Scholar 

  • De Meutter J, Vandenameele J, Matagne A, Goormaghtigh E (2017) Infrared imaging of high density protein arrays. Analyst 142:1371–1380

    Article  PubMed  CAS  Google Scholar 

  • DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Andersen GL (2011) PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol 77:6313–6322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dec M, Puchalski A, Urban-Chmiel R, Wernicki A (2016) 16S-ARDRA and MALDITOF mass spectrometry as tools for identification of Lactobacillus bacteria isolated from poultry. BMC Microbiol 16:105

    Google Scholar 

  • van Dekken H, Bauman JOJ (1988) A new application of in situ hybridization: detection of numerical and structural chromosome aberrations with a combination centromeric- telomeric DNA probe. Cytogenet Cell Genet 48:188–189

    Article  PubMed  Google Scholar 

  • Dihazi H, Asif AR, Beißbarth T, Bohrer R, Feussner K, Feussner I, Jahn O, Lenz C, Majcherczyk A, Schmidt B, Schmitt K, Urlaub H, Valerius O (2018) Integrative omics - from data to biology. Expert Rev Proteom 15:463–466

    Article  CAS  Google Scholar 

  • van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30:418–426

    Article  PubMed  CAS  Google Scholar 

  • Dubinsky EA, Butkus SR, Andersen GL (2016) Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification. Water Res 105:56–64

    Article  CAS  PubMed  Google Scholar 

  • Dunford EA, Neufeld JD (2010) DNA stable-isotope probing (DNA-SIP). JoVE (J Vis Exp) 42:e2027–e2027

    Google Scholar 

  • Emwas AHM (2015) The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research. In: Bjerrum J (ed) Metabonomics. Methods in molecular biology. Humana Press, New York, pp 161–193

    Google Scholar 

  • Engskog MKR, Haglöf J, Arvidsson T, Pettersson C (2016) LC–MS based global metabolite profiling: the necessity of high data quality. Metabolomics 12(7)

    Google Scholar 

  • Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorsor S, Varusai T, Viteri G, Weiser J, Wu G et al (2018) The reactome pathway knowledgebase. Nucleic Acids Res 46:D649–D655

    Article  CAS  PubMed  Google Scholar 

  • Fierer N, Jackson JA, Vilgalys R, Jackson RB (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71:4117–4120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Foti M, Sorokin DY, Lomans B, Mussman M, Zacharova EE, Pimenov NV, Kuenen JG, Muyzer G (2007) Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Appl Environ Microbiol 73:2093–3000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fraher MH, O’Toole PW, Quigley EM (2012) Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol 9:312–322

    Article  CAS  PubMed  Google Scholar 

  • Gao G, Yin D, Chen S, Xia F, Yang J, Li Q, Wang W (2012) Effect of biocontrol agent Pseudomonas fluorescens 2P24 on soil fungal community in cucumber rhizosphere using T-RFLP and DGGE. PLoS One 7:e31806

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level-sole-carbon-source utilization. Appl Environ Microbiol 57:2351–2359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geoghegan JL, Holmes EC (2018) Evolutionary virology at 40. Genetics 210:1151–1162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghaste M, Mistrik R, Shulaev V (2016) Applications of Fourier transform ion cyclotron resonance (FT-ICR) and Orbitrap based high resolution mass spectrometry in metabolomics and lipidomics. Int J Mol Sci 17:816

    Article  PubMed Central  CAS  Google Scholar 

  • Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG (2019) Tracking virus outbreaks in the twenty-first century. Nat Microbiol 4:10–19

    Article  CAS  PubMed  Google Scholar 

  • Handy SM, Hutchins DA, Cary SC, Coyne KJ (2006) Simultaneous enumeration of multiple raphidophyte species by quantitative real-time PCR, capabilities and limitations. Limnol Oceanogr Methods 4:193–204

    Article  Google Scholar 

  • Hashimoto Y, Greco TM, Cristea IM (2019) Contribution of mass spectrometry-based proteomics to discoveries in developmental biology. Adv Exp Med Biol 1140:143–154

    Article  CAS  PubMed  Google Scholar 

  • Hinchliffe TE, Lin ZT, Wu T (2016) Protein arrays for biomarker discovery in lupus. Proteomics Clin Appl 10:625–634

    Article  CAS  PubMed  Google Scholar 

  • Hou S, Wentzell PD (2014) Regularized projection pursuit for data with a small sample-to-variable ratio. Metabolomics 10:589–606

    Article  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hultman J, Waldrop MP, Mackelprang R, David MM, Mcfarland J, Blazewicz SJ, Harden J, Turetsky MR, Mcguire AD, Shah MB, Verberkmoes NC, Lee LH, Mavrommatis K, Jansson JK (2015) Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521:208–212

    Article  CAS  PubMed  Google Scholar 

  • Jaing C, Gardner S, McLoughlin K, Mulakken N, Michelle Alegria-Hartman M, Banda P, Williams P, Gu P, Wagner M, Manohar C, Slezak T (2008) A functional gene array for detection of bacterial virulence elements. PLoS One 3:e2163

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jeewon R, Yeung QSY, Wannasinghe DN, Rampadarath S, Puchooa D, Wang HK, Hyde KD (2018) Hidden mycota of pine needles: molecular signatures from PCR-DGGE and ribosomal DNA phylogenetic characterization of novel phylotypes. Sci Rep 8:18053

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jian C, Luukkonen P, Yki-Ja¨rvinen H, Salonen A, Korpela K (2020) Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling. PLoS One 15:e0227285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnston-Monje D, Loewen S, Lazarovits G (2017) Mycobiomes of tomato plants with vine decline. Can J Plant Pathol 39:184–200

    Article  Google Scholar 

  • Johnston-Monje D, Lopez Mejia J (2020) Botanical microbiomes on the cheap: inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi. Appl Plant Sci 8:e11334

    Article  PubMed  PubMed Central  Google Scholar 

  • Jordan KW, Nordenstam J, Lauwers GY, Rothenberger DA, Alavi K, Garwood M, Cheng LL (2009) Metabolomic characterization of human rectal adenocarcinoma with intact tissue magnetic resonance spectroscopy. Dis Colon Rectum 52:520–525

    Article  PubMed  PubMed Central  Google Scholar 

  • Junier P, Junier T, Witzel KP (2008) TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets. Appl Environ Microbiol 74:6452–6456

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaczanowski R, Trzeciak L, Kucharczyk K (2001) Multitemperature single-strand conformation polymorphism. Electrophoresis 22:3539–3545

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M (2002) The KEGG database. Novartis Found Symp 247:91–101

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2016) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Karczewski K, Wolfgang RH, Meyer EI (2017) Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems. Limnologica 67:1–9

    Article  Google Scholar 

  • Ke R, Mignardi M, Hauling T, Nilsson M (2016) Fourth generation of next-generation sequencing technologies: promise and consequences. Hum Mutat 37:1363–1367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Key KC, Sublette KL, Duncan K, Mackay DM, Scow KM, Ogles D (2013) Using DNA-stable isotope probing to identify MTBE- and TBA-degrading microorganisms in contaminated groundwater. Ground Water Monit Remediat 33:57–68

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khan AL, Asaf S, Al-Rawahi A, Lee I-J, Al-Harrasi A (2017) Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree. PLoS One 12:e0186939

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kim HJ, Koedrith P, Seo YR (2015) Ecotoxicogenomic approaches for understanding molecular mechanisms of environmental chemical toxicity using aquatic invertebrate, Daphnia model organism. Int J Mol Sci 16:12261–12287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kimes NE, Callaghan AV, Aktas DF, Smith WL, Sunner J, Golding BT, Drozdowska M, Hazen TC, Suflita JM, Morris PJ (2013) Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Front Microbiol 4:50

    Article  PubMed  PubMed Central  Google Scholar 

  • Kingston JJ, Radhika M, Roshini PT, Raksha MA, Murali HS, Batra HV (2010) Molecular characterization of lactic acid bacteria recovered from natural fermentation of beet root and carrot Kanji. Indian J Microbiol 50:292–298

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kjellin J, Pränting M, Bach F, Vaid R, Edelbroek B, Li Z, Hoeppner MP, Grabherr M, Isberg RR, Hagedorn M, Söderbom F (2019) Investigation of the host transcriptional response to intracellular bacterial infection using Dictyostelium discoideum as a host model. BMC Genomics 20:961

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kovacevic V, Simpson JM (2020) Fundamentals of environmental metabolomics. Environ Metabol 2020:1–33

    Google Scholar 

  • Kubo KS, Stuart RM, Freitas-Astúa J, Antonioli-Luizon R, Locali-Fabris EC, Coletta-Filho HD, Machado MA, Kitajima EW (2009) Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and nucleotide sequencing of a fragment from the nucleocapsid gene. Arch Virol 154:1009–1014

    Article  CAS  PubMed  Google Scholar 

  • Kuo TC, Tian TF, Tseng YJ (2013) Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. BMC Syst Biol 7:64

    Google Scholar 

  • Kwan AH, Mobli M, Gooley PR, King GF, Mackay JP (2011) Macromolecular NMR spectroscopy for the non-spectroscopist. FEBS J 278:687–703

    Article  CAS  PubMed  Google Scholar 

  • Lamizadeh E, Enayatizamir N, Motamedi M (2019) Difference in some biological properties of saline and non-saline soil under sugarcane cultivation. Eurasian Soil Sci 52:690–695

    Article  Google Scholar 

  • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959

    Google Scholar 

  • Lee Y, van Nostrand J, Tu Q, Lu Z, Cheng L, Yuan T, Deng Y, Carter MQ, He Z, Wu L, Yang F, Xu J, Zhou J (2013) The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J 7:1974–1984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levy SE, Myers RM (2016) Advancements in next-generation sequencing. Annu Rev Genomics Hum Genet 17:95–115

    Article  CAS  PubMed  Google Scholar 

  • Liou JS-C, DeRito CM, Madsen EL (2008) Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment. Environ Microbiol 10:1964–1977

    Article  CAS  PubMed  Google Scholar 

  • Liswara N, Rudy AN, Yukio K, Naru T, Koji K (2020) Water quality measurements with a simple molecular analysis (PCR-RFLP) of the microbiome in a metropolitan river system in Japan. Walailak J Sci Tech 17(3):257–268

    Google Scholar 

  • Loy A, Pester M, Steger D (2011) Phylogenetic microarrays for cultivation-independent identification and metabolic characterization of microorganisms in complex samples. Methods Molecul Biol (Clifton, NJ) 688:187–206

    CAS  Google Scholar 

  • Loy A, Schulz C, Lücker S, Schöpfer-Wendels A, Stoecker K, Baranyi C, Lehner A, Wagner M (2005) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order “Rhodocyclales”. Appl Environ Microbiol 71:1373–1386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu Y, Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309:1088–1090

    Article  CAS  PubMed  Google Scholar 

  • Lucio, M., 2009. Datamining metabolomics: the convergence point of non-target approach and statistical investigation. Thesis, Technical University of Munchen, 189p

    Google Scholar 

  • Malik S, Beer M, Megharaj M, Naidu R (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34:265–276

    Article  CAS  PubMed  Google Scholar 

  • Manaia CM, Rocha J, Scaccia N, Marano R, Radu E, Biancullo F, Cerqueira F, Fortunato G, Iakovides IC, Zammit I, Kampouris I, Vaz-Moreira I, Nunes OC (2018) Antibiotic resistance in wastewater treatment plants: tackling the black box. Environ Int 115:312–324

    Article  CAS  PubMed  Google Scholar 

  • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68:5367–e5373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matthiesen R, Bunkenborg J (2013) Introduction to mass spectrometry-based proteomics. Methods Molecul Biol (Clifton, N.J.) 1007:1–45

    CAS  Google Scholar 

  • Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang K, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyo D, Ellis MJ, Carr SA, NCI CPTAC (2016) Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 534:55–62

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mignardi M, Nilsson M (2014) Fourth-generation sequencing in the cell and the clinic. Genome Med 6:31

    Article  PubMed  PubMed Central  Google Scholar 

  • Mullard G, Allwood JW, Weber R, Brown M, Begley P, Hollywood KA, Jones M, Unwin RD, Bishop PN, Cooper GJS, Dunn WB (2015) A new strategy for MS/MS data acquisition applying multiple data dependent experiments on Orbitrap mass spectrometers in non-targeted metabolomic applications. Metabolomics 11:1068–1080

    Article  CAS  Google Scholar 

  • Murros-Kontiainen A, Fredriksson-Ahomaa M, Korkeala H, Johansson P, Rahkila R, Björkroth J (2011) Yersinianurmii sp. nov. Int J Syst Evol Microbiol 61:2368–2372

    Article  PubMed  Google Scholar 

  • Mushtag MY, Choi YH, Verpoorte R, Wilson EG (2013) Extraction for metabolomics: access to the metabolome. Phytochem Anal 25:291–306

    Article  CAS  Google Scholar 

  • Nayfach S, Pollard KS (2016) Toward accurate and quantitative comparative metagenomics. Cell 166:1103–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Neufeld JD, Chen Y, Dumont MG, Murrell JC (2008) Marine methylotrophs revealed by stable isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol 10:1526–1535

    Article  CAS  PubMed  Google Scholar 

  • Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, Murrell JC (2007) DNA stable-isotope probing. Nat Protoc 2:860–866

    Article  CAS  PubMed  Google Scholar 

  • Nikolaki S, Tsiamis G (2013) Microbial diversity in the era of omic technologies. Biomed Res Int 2013:958719

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Niu L, Shoukui Hu S, Shan Lu S, Xin-He Lai X-H, Jing Yang J, Jin D, Langyu Rao L, Gang Lu G, Xu J (2018) Isolation and characterization of Streptococcus respiraculi sp. nov. from Marmota himalayana (Himalayan marmot) respiratory tract. Int J Syst Evol Microbiol 68:2082–2087

    Article  CAS  PubMed  Google Scholar 

  • Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E (2016) Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation. mSystems 2016:1

    Google Scholar 

  • O’Rourke MB, Padula MP (2016) Analysis of formalin-fixed, para_n-embedded (FFPE) tissue via proteomic techniques and misconceptions of antigen retrieval. BioTechniques 60:229–238

    Article  PubMed  Google Scholar 

  • Orita M, Iwahana H, Knazawa H, Hayashi K, Sekiya T (1989) Detection of the polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci U S A 86:2766–2770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paes F, Liu X, Mattes TE, Cupples AM (2015) Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing. Appl Microbiol Biotechnol 99:7735–7743

    Article  CAS  PubMed  Google Scholar 

  • Penuelas J, Rico L, Ogaya R, Jump A, Terradas J (2012) Summer season and long-term drought increase the richness of bacteria and fungi in the foliar phyllosphere of Quercus ilex in a mixed Mediterranean forest. Plant Biol 14:565–575

    Article  CAS  PubMed  Google Scholar 

  • Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, del Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jimenez RC, Nesvizhskii AI, Sansone S, Steinbeck C, Lopez R, Vizcaino JA, Ping P, Hermjakob H (2017) Discovering and linking public omics data sets using the Omics discovery index. Nat Biotechnol 35:406–409

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pinu FR, Baele DJ, Paten AM, Kouremenos K, Swarup S, Schirra H, Wishart D (2019) Systems biology and multi-omics integration: viewpoints from the metabolomics research community. Metabolites 9:1–31

    Google Scholar 

  • Posada-Cespedes S, Seifert D, Niko B (2017) Recent advances in inferring viral diversity from high-throughput sequencing data. Virus Res 239:17–32

    Article  CAS  PubMed  Google Scholar 

  • Preston-Mafham J, Boddy L, Randerson PF (2002) Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles- a critique. FEMS Microbiol Ecol 42:1–14

    CAS  PubMed  Google Scholar 

  • Qing-Lei S, Zhang J, Wang M-X, Cao L, Zeng-Feng D, Sun Y-Y, Liu S-Q, Li C-L, Sun L (2020) High-throughput sequencing reveals a potentially novel Sulfurovum species dominating the microbial communities of the seawater–sediment Interface of a Deep-Sea cold seep in South China Sea. Microorganisms 8:1–18

    Google Scholar 

  • Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI, Murrell JC (2002) Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology 148:2331–2342

    Article  CAS  PubMed  Google Scholar 

  • Ralli E, Amargianitaki M, Manolopoulou E, Misiak M, Markakis G, Tachtalidou S, Kolesnikova A, Dais P, Spyros A (2018) NMR spectroscopy protocols for food metabolomics applications. Methods Molecul Biol (Clifton, NJ) 1738:203–211

    CAS  Google Scholar 

  • Ramirez-Gaona M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Feunang Y, Arndt D, Wishart DS (2017) YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res 45:D440–D445

    Article  CAS  PubMed  Google Scholar 

  • Ramisse V, Balandreau J, Thibault F, Vidal D, Vergnaud G, Normand P (2003) DNA-DNA hybridization study of Burkholderia species using genomic DNA macro-array analysis coupled to reverse genome probing. Int J Syst Evol Microbiol 53:739–746

    Article  CAS  PubMed  Google Scholar 

  • Rangel-Castro JI, Killham K, Ostle N, Nicol GW, Anderson IC, Scrimgeour CM, Ineson P, Meharg AA, Prosser JI (2005) Stable isotope probing analysis of the influence of liming on root exudates utilization by soil microorganisms. Environ Microbiol 7:828–838

    Article  CAS  PubMed  Google Scholar 

  • Ravi RK, Walton K, Khosroheidari M (2018) MiSeq: a next generation sequencing platform for genomic analysis. Methods Molecul Biol (Clifton, N.J.) 1706:223–232

    CAS  Google Scholar 

  • Redenšek S, Dolžan V, Kunej T (2018) From genomics to Omics landscapes of Parkinson’s disease: revealing the molecular mechanisms. Omics 22:1–16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reed LK, Baer CF, Edison AS (2017) Considerations when choosing a genetic model organism for metabolomics studies. Curr Opin Chem Biol 36:7–14

    Article  CAS  PubMed  Google Scholar 

  • Ren S, Hinzman AA, Kang EL, Szczesniak RD, Lu LJ (2015) Computational and statistical analysis of metabolomics data. Metabolomics 11:1492–1513

    Article  CAS  Google Scholar 

  • Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13:278–289

    Article  PubMed  PubMed Central  Google Scholar 

  • Rickwood D (1992) Centrifugal methods for characterizing macromolecules and their interactions. In: Rickwood D (ed) Preparative centrifugation: a practical approach. Oxford University Press, Oxford, pp 143–186

    Google Scholar 

  • Rinttila T, Kassinen A, Malinen E, Krogius L, Palva A (2004) Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J Appl Microbiol 97:1166–1177

    Article  CAS  PubMed  Google Scholar 

  • Rocha J, Manaia CM (2020) Cell-based internal standard for q PCR determination of antibiotic resistance indicators in environmental water samples. Ecol Indic 113:106194

    Article  CAS  Google Scholar 

  • Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS (2016) ECMDB 2.0: a richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res 44:D495–D501

    Article  CAS  PubMed  Google Scholar 

  • Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilic-Stojanovic M, Kekkonen RA, Palva A, de Vos WM (2010) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 81:127–134

    Article  CAS  PubMed  Google Scholar 

  • Sánchez J, Vegas C, Zavaleta AI, Esteve-Zarzoso B (2019) Predominance of Lactobacillus plantarum strains in Peruvia Amazonian fruits. Pol J Microbiol 68:127–137

    Article  PubMed  PubMed Central  Google Scholar 

  • Sasaki K, Sagawa H, Suzuki M, Yamamoto H, Tomita M, Soga T, Ohashi Y (2018) Metabolomics platform with capillary electrophoresis coupled with high-resolution mass spectrometry for plasma analysis. Anal Chem 91:1295–1301

    Article  PubMed  CAS  Google Scholar 

  • Saunders NA (2004) Introduction to real-time PCR. In: Edwards K, Logan J, Saunders N (eds) Real-Time PCR: An Essential Guide. Horizon Biosci, Norfolk, pp 1–11

    Google Scholar 

  • Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Appl Environ Microbiol 76:5636–5638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schloss PD (2018) Identifying and overcoming threats to reproducibility, replicability, robustness, and generalizability in microbiome research. MBio 9:00525–00518

    Article  Google Scholar 

  • Schmalenberger A, Tebbe CC (2014) Profiling the diversity of microbial communities with single-strand conformation polymorphism (SSCP). In: Paulsen IT, Holmes AJ (eds) Environmental microbiology: methods and protocols. Springer, Berlin, pp 71–83

    Chapter  Google Scholar 

  • Shi Z, Yin H, Van Nostrand JD, Voordeckers JW, Tu Q, Deng Y, Yuan M, Zhou A, Zhang P, Xiao N, Ning D, He Z, Wu L, Zhou J (2019) Functional gene Array-based ultrasensitive and quantitative detection of microbial populations in complex communities. mSystems 4:e00296–e00219

    Article  PubMed  PubMed Central  Google Scholar 

  • Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ (2007) MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb Ecol 53:562–570

    Article  CAS  PubMed  Google Scholar 

  • Sigler WV, Zeyer J (2002) Microbial diversity and activity along the forefields of two receding glaciers. Microb Ecol 43:397–407

    Article  CAS  PubMed  Google Scholar 

  • Simmons DBD, Benskin JP, Cosgrove JR, Duncker BP, Ekman DR, Martyniuk CJ, Sherry JP (2015) Omics for aquatic ecotoxicology: control of extraneous variability to enhance the analysis of environmental effects. Environ Toxicol Chem 34:1693e1704

    Article  CAS  Google Scholar 

  • Southam AD, Weber RJM, Engel J, Jones MR, Viant MR (2017) A complete workflow for high resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics. Nat Protoc 12:310–328

    Article  CAS  Google Scholar 

  • Srinivasan S, Morgan MT, Fiedler TL, Djukovic D, Homan NG, Raftery D, Marrazzo JM, Fredricks DN (2015) Metabolic signatures of bacterial vaginosis. MBio 6:e00204–e00215

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Srivastava S (2016) Protein arrays: promises and potential for the translational research. Proteomics 16:1191–1192

    Article  CAS  PubMed  Google Scholar 

  • Strom SP (2019) Fundamentals of RNA analysis on biobanked specimens. In: Yong WH (ed) Biobanking: methods and protocols. Springer, New York, pp 345–357

    Chapter  Google Scholar 

  • Subhash Y, Lee SS (2018) Roseomonas deserti sp. nov., isolated from crude oil contaminated desert sand. Int J Syst Evol Microbiol 68:675–680

    Google Scholar 

  • Tabacchioni S, Chiarini L, Bevivino A, Cantale C, Dalmastri C (2000) Bias caused by using different isolation media for assessing the genetic diversity of a natural microbial population. Microb Ecol 40:169–176

    Article  CAS  PubMed  Google Scholar 

  • Tabb DL, Vega-Montoto L, Rudnick PA, Variyath AM, Ham AJ, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling B, Tegeler TJ, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Fisher SJ, Gibson BW, Kinsinger CR, Mesri M, Rodriguez H, Stein SE, Tempst P, Paulovich AG, Liebler DC, Spiegelman C (2010) Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res 9:761–776

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang Y, Qiu J, Machner M, LaBaer J (2017) Discovering protein-protein interactions using nucleic acid programmable protein arrays. Curr Protoc Cell Biol 74:1–15

    Article  Google Scholar 

  • Taubert M, Baumann S, von Bergen M, Seifert J (2011) Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein- SIP). Anal Bioanal Chem 401:1975–1982

    Article  CAS  PubMed  Google Scholar 

  • Taylor NS, Kirwan JA, Yan ND, Viant MR, Gunn JM, McGeer JC (2016) Metabolomics confirms that dissolved organic carbon mitigates copper toxicity. Environ Toxicol Chem 35:635–644

    Article  CAS  PubMed  Google Scholar 

  • Tian Z, Faure A, Mori H, Matsuno H (2013) Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional petri net model. BMC Syst Biol 7:S1

    Article  PubMed  PubMed Central  Google Scholar 

  • Tiedje JM, Asuming-Brempong S, Nusslein K, Marsh TL, Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13:109–122

    Article  Google Scholar 

  • Tingli F, Yongxue S, Wu JPQ, Yi M (2018) Xiaohui Zhou combination of amplified rDNA restriction analysis and high-throughput sequencing revealed the negative effect of colistin sulfate on the diversity of soil microorganisms. Microbiol Res 206:9–15

    Article  CAS  Google Scholar 

  • Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459:950–956

    Article  CAS  PubMed  Google Scholar 

  • Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee Y-J, Qin Y, Hemme CL, Shi Z, Xue K, Yuan T, Wang A, Zhou J (2014) GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 14:914–928

    CAS  PubMed  Google Scholar 

  • Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T (2013) Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 31:154–165

    Article  CAS  PubMed  Google Scholar 

  • Van Nostrand JD, He Z, Zhou J (2012) Use of functional gene arrays for elucidating in situ biodegradation. Front Microbiol 3:339

    Article  PubMed  PubMed Central  Google Scholar 

  • Vogt C, Lueders T, Richnow HH, Krüger M, von Bergen M, Seifert J (2016) Stable isotope probing approaches to study anaerobic hydrocarbon degradation and degraders. J Mol Microbiol Biotechnol 26:195–210

    CAS  PubMed  Google Scholar 

  • Wald J, Hroudova M, Jansa J, Vrchotova B, Macek T, Uhlik O (2015) Pseudomonads rule degradation of polyaromatic hydrocarbons in aerated sediment. Front Microbiol 6:1268

    Article  PubMed  PubMed Central  Google Scholar 

  • Walitang DI, Kim CG, Kim K, Kang Y, Kim YK, Sa T (2018) The influence of host genotype and salt stress on the seed endophytic community of salt-sensitive and salt-tolerant rice cultivars. BMC Plant Biol 18:51

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wall DH, Virginia RA (1999) Controls on soil biodiversity: insights from extreme environments. Appl Soil Ecol 13:137–150

    Article  Google Scholar 

  • Wan T, Zhao H, Wang W (2018) Effects of the biocontrol agent Bacillus amyloliquefaciens SN16-1 on the rhizosphere bacterial community and growth of tomato. J Phytopathol 166:324–332

    Article  CAS  Google Scholar 

  • Whiteley AS, Thomson B, Lueders T, Manefield M (2007) RNA stable-isotope probing. Nat Protoc 2:838–844

    Article  CAS  PubMed  Google Scholar 

  • Wilhelm BT, Landry J-R (2009) RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48:249–257

    Article  CAS  PubMed  Google Scholar 

  • Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltra A et al (2016) The FAIR guiding principles for scientific data management and stewardship. Sci Data 3:160018

    Article  PubMed  PubMed Central  Google Scholar 

  • Wu L, Liu X, Fields M, Thompson D, Bagwell C, Tiedje J, Hazen T, Zhou J (2008) Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness. ISME J 2:642–655

    Article  CAS  PubMed  Google Scholar 

  • Yang J-L, Jia RY, Cheng AC, Wang MS (2010) A simple equipment for casting denature gradient gel in DGGE analysis. J Food Agric Environ 8:710–712

    Google Scholar 

  • Yao H, He Z, Wilson MJ, Campbell CD (2000) Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use. Microb Ecol 40:223–237

    Article  CAS  PubMed  Google Scholar 

  • Yao L, Lai Y, Xue F, Sun L, Wang J (2019) Paracandidimonas caeni sp. nov., isolated from sludge. Int J Syst Evol Microbiol 69:3332–3337

    Article  CAS  PubMed  Google Scholar 

  • Youngblut ND, Barnett SE, Buckley DH (2018) SIPSim: a modeling toolkit to predict accuracy and aid design of DNA-SIP experiments. Front Microbiol 9:570

    Article  PubMed  PubMed Central  Google Scholar 

  • Zak JC, Willig MR, Moorhead DL, Wildman HG (1994) Functional diversity of microbial communities: a quantitative approach. Soil Biol Biochem 26:1101–1108

    Article  Google Scholar 

  • Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, Weinberger A, Ben-Yacov O, Lador D, Avnit-Sagi T, Lotan-Pompan M, Suez J, Mahdi JA, Matot E, Malka G, Kosower N, Rein M, Zilberman-Schapira M, Dohnalova L, Pevsner-Fischer M, Bikovsky R, Halpern Z, Elinav E, Segal E (2015) Personalized nutrition by prediction of glycemic responses. Cell 163:1079–1094

    Article  CAS  PubMed  Google Scholar 

  • Zelena E, Dunn WB, Broadhurst D, Francis-McIntyre S, Carroll KM, Begley P, O’Hagan S, Knowles JD, Halsall A, HUSERMET Consortium, Wilson ID, Kell DB (2009) Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. Anal Chem 81:1357–1364

    Google Scholar 

  • Zhang X, Ding X, Ji Y, Wang S, Chen Y, Luo J, Shen Y, Peng L (2018) Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice (Glycyrrhiza uralensis) plants under UV-B irradiation. Sci Rep 8:6144

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang Y, Deng W, Xie X, Jiao N (2016) Differential incorporation of carbon substrates among microbial populations identified by field-based, DNA stable-isotope probing in South China Sea. PLoS One 11:e0157178

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang Z, Wu S, Stenoien DL, Paša-Tolić L (2014) High-throughput proteomics. Ann Rev Anal Chem (Palo Alto, Calif) 7:427–454

    Article  CAS  Google Scholar 

  • Ziels RM, Sousa DZ, Stensel HD, Beck DAC (2018) DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid degrading populations in anaerobic digesters with different feeding frequencies. ISME J 12:112–123

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Microbiology, University of Nigeria, Nsukka, Nigeria

    Chidinma Lynda Akaihe, Emeka Innocent Nweze & Paul Ekene Chidebelu

  2. Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria

    Ebubechukwu Nnamdi Dim

  3. Department of Chemical Engineering, University of Alcala, Alcala de Henares, Madrid, Spain

    Chizoba I. Ezugwu

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  1. Facultad de Ciencias de la Salud y Instituto de Investigación, Universidad Técnica de Manabí, Portoviejo, Ecuador

    Naga Raju Maddela

  2. Ingeniería Agronómica y Instituto de Investigación, Universidad Técnica de Manabí, Portoviejo, Ecuador

    Luz C García Cruzatty

  3. School of Environmental Science and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, China

    Sagnik Chakraborty

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Akaihe, C.L., Dim, E.N., Ezugwu, C.I., Nweze, E.I., Chidebelu, P.E. (2021). Analytical Techniques/Technologies for Studying Ecological Microbial Samples. In: Maddela, N.R., García Cruzatty, L.C., Chakraborty, S. (eds) Advances in the Domain of Environmental Biotechnology. Environmental and Microbial Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-15-8999-7_18

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