Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi

The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to genera...

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Vydané v:	Sensors (Basel, Switzerland) Ročník 20; číslo 11; s. 3292
Hlavní autori:	Gryta, Agata, Frąc, Magdalena
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Switzerland MDPI AG 09.06.2020 MDPI
Predmet:	Archaea - classification Bacteria Bacteria - classification Biodiversity Biosensors capillary electrophoresis Climate change Deoxyribonucleic acid DNA Fungi Fungi - classification Genetic diversity genetic fingerprinting Genetic testing Information sources Land use planning Methods microbial genetic diversity multiplex t-RFLP Polymerase Chain Reaction Polymorphism Polymorphism, Restriction Fragment Length Research methodology Soil Microbiology soil microbiome Soil microorganisms Taxonomy United States > US microbial genetic diversity multiplex t-RFLP genetic fingerprinting capillary electrophoresis soil microbiome
ISSN:	1424-8220, 1424-8220
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Abstract	The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.
AbstractList	The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness. The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.
Author	Gryta, Agata Frąc, Magdalena
AuthorAffiliation	Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; m.frac@ipan.lublin.pl
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Cites_doi	10.1093/nar/gkn182 10.1016/j.tree.2010.06.016 10.1016/B978-0-12-374513-2.00006-3 10.1111/j.1574-6941.2007.00386.x 10.1128/aem.63.11.4516-4522.1997 10.1111/j.1365-2257.2005.00671.x 10.1128/AEM.72.2.1346-1354.2006 10.1371/journal.pone.0029380 10.1128/AEM.71.2.1004-1011.2005 10.1038/s41598-019-55063-4 10.1111/j.1461-0248.2006.00963.x 10.1099/00207713-47-2-328 10.1128/AEM.71.3.1671-1673.2005 10.1111/j.1462-2920.2005.00904.x 10.1007/s00248-001-1062-0 10.1111/j.1462-2920.2004.00634.x 10.1007/s13353-020-00549-5 10.1371/journal.pone.0101435 10.1007/s00248-003-2000-0 10.3389/fmicb.2013.00291 10.1128/AEM.69.1.320-326.2003 10.1128/aem.63.2.803-805.1997 10.1038/nrmicro3109 10.1016/j.femsle.2005.05.043 10.1111/j.1461-0248.2007.01139.x 10.1371/journal.pone.0043672 10.1046/j.1351-0754.2003.0556.x 10.1128/AEM.01394-08 10.1016/S0006-3207(03)00291-X 10.1128/AEM.72.1.713-722.2006 10.3390/s120303253 10.1111/j.1365-294X.1993.tb00005.x 10.1111/1574-6941.12308 10.1017/S0953756200002835 10.1093/nar/26.11.2797 10.1128/AEM.64.2.795-799.1998 10.1016/j.agee.2004.01.008 10.1002/(SICI)1522-2683(19990601)20:7<1492::AID-ELPS1492>3.0.CO;2-V 10.1111/j.1574-6941.2005.00047.x 10.1007/s00253-018-9102-6 10.3121/cmr.2.1.37 10.3390/f11030262 10.1111/j.1469-8137.2006.01669.x 10.1128/AEM.02738-17 10.1111/j.1462-2920.2004.00675.x 10.1128/AEM.00510-06 10.1007/s00248-006-9106-0 10.1016/j.funeco.2009.04.001 10.7717/peerj.2915 10.3390/d5030581 10.1128/AEM.69.5.2555-2562.2003
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References	Carvalhais (ref_6) 2013; 5 Wu (ref_37) 2006; 8 Singh (ref_14) 2006; 72 Dorst (ref_21) 2014; 89 Hoshino (ref_48) 2006; 55 Jurgens (ref_25) 1997; 63 Mohanty (ref_39) 2006; 72 Buchan (ref_41) 2002; 43 Gardes (ref_28) 1993; 2 ref_55 ref_52 ref_51 Sar (ref_49) 2018; 102 Dimitrov (ref_40) 2017; 5 ref_18 ref_15 Oszust (ref_56) 2012; 12 Shyu (ref_53) 2007; 53 Bardgett (ref_5) 2008; 11 Nkongolo (ref_12) 2020; 61 Balvanera (ref_9) 2006; 9 Tu (ref_45) 1998; 26 Philippot (ref_2) 2013; 11 Viaud (ref_34) 2000; 104 ref_20 Kerkhof (ref_38) 2005; 71 Jurgens (ref_24) 1999; 29 ref_29 Magurran (ref_30) 2010; 10 Song (ref_16) 2000; 187 Gillison (ref_11) 2004; 104 Anderson (ref_13) 2004; 6 Marchesi (ref_26) 1998; 64 Egert (ref_43) 2003; 69 Christensen (ref_50) 2004; 2 Ricke (ref_54) 2005; 71 Matz (ref_42) 2003; 45 Nannipieri (ref_1) 2003; 54 Sauberer (ref_10) 2004; 117 Hauben (ref_27) 1997; 47 ref_31 Maron (ref_7) 2018; 84 Liu (ref_33) 1997; 63 Reed (ref_8) 2007; 62 Sui (ref_3) 2019; 9 Lueders (ref_44) 2003; 69 Hullar (ref_32) 2006; 72 Junier (ref_23) 2008; 74 Fish (ref_22) 2013; 4 Genney (ref_35) 2006; 170 Gillevet (ref_19) 2009; 2 Osborne (ref_47) 2005; 248 Kotsyurbenko (ref_36) 2004; 6 Stankovic (ref_17) 2005; 27 Behr (ref_46) 1999; 20 ref_4
References_xml	– ident: ref_52 doi: 10.1093/nar/gkn182 – volume: 10 start-page: 574 year: 2010 ident: ref_30 article-title: Long-term datasets in biodiversity research and monitoring: Assessing change in ecological communities through time publication-title: Trends Ecol. Evol. doi: 10.1016/j.tree.2010.06.016 – ident: ref_51 doi: 10.1016/B978-0-12-374513-2.00006-3 – ident: ref_55 – volume: 62 start-page: 161 year: 2007 ident: ref_8 article-title: Testing the functional significance of microbial composition in natural communities publication-title: FEMS Microbiol. Ecol. doi: 10.1111/j.1574-6941.2007.00386.x – volume: 63 start-page: 4516 year: 1997 ident: ref_33 article-title: Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA publication-title: Appl. Environ. Microbiol. doi: 10.1128/aem.63.11.4516-4522.1997 – volume: 27 start-page: 145 year: 2005 ident: ref_17 article-title: Indirect diagnosis of haemophilia B by multiplex PCR/RFLP publication-title: Clin. Lab. Haematol. doi: 10.1111/j.1365-2257.2005.00671.x – volume: 187 start-page: 167 year: 2000 ident: ref_16 article-title: Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA publication-title: FEMS Microbiol. Lett. – volume: 72 start-page: 1346 year: 2006 ident: ref_39 article-title: Differential effects of nitrogenous fertilizers onmethane-consuming microbes in rice field and forest soils publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.72.2.1346-1354.2006 – ident: ref_20 doi: 10.1371/journal.pone.0029380 – volume: 71 start-page: 1004 year: 2005 ident: ref_38 article-title: Phylogeography of sulfatereducing bacteria among disturbed sediments, disclosed analysis of the dissimilatory sulfite reductase genes (dsrAB) publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.71.2.1004-1011.2005 – volume: 9 start-page: 18535 year: 2019 ident: ref_3 article-title: Land use change effects on diversity of soil bacterial, Acidobacterial and fungal communities in wetlands of the Sanjiang Plain, northeastern China publication-title: Sci. Rep. doi: 10.1038/s41598-019-55063-4 – volume: 9 start-page: 1146 year: 2006 ident: ref_9 article-title: Quantifying the evidence for biodiversity effects on ecosystem functioning and services publication-title: Ecol. Lett. doi: 10.1111/j.1461-0248.2006.00963.x – volume: 47 start-page: 328 year: 1997 ident: ref_27 article-title: Comparison of 16S ribosomal DNA sequence of all Xanthomonas species publication-title: Int. J. Syst. Bacteriol. doi: 10.1099/00207713-47-2-328 – volume: 71 start-page: 1671 year: 2005 ident: ref_54 article-title: Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.71.3.1671-1673.2005 – volume: 8 start-page: 394 year: 2006 ident: ref_37 article-title: Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils publication-title: Environ. Microbiol. doi: 10.1111/j.1462-2920.2005.00904.x – volume: 43 start-page: 329 year: 2002 ident: ref_41 article-title: Analysis of internal transcribed spacer (ITS) regions of rRNA genes in fungal communities in a southeastern U.S. salt marsh publication-title: Microb. Ecol. doi: 10.1007/s00248-001-1062-0 – volume: 6 start-page: 1159 year: 2004 ident: ref_36 article-title: Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian peat bog publication-title: Environ. Microbiol. doi: 10.1111/j.1462-2920.2004.00634.x – volume: 61 start-page: 249 year: 2020 ident: ref_12 article-title: Advances in monitoring soil microbial community dynamic and function publication-title: J. Appl. Genetics doi: 10.1007/s13353-020-00549-5 – ident: ref_31 – ident: ref_18 doi: 10.1371/journal.pone.0101435 – volume: 45 start-page: 384 year: 2003 ident: ref_42 article-title: Interaction of nutrient limitation and protozoan grazing determines the phenotypic structure of a bacterial community publication-title: Microb. Ecol. doi: 10.1007/s00248-003-2000-0 – volume: 4 start-page: 1 year: 2013 ident: ref_22 article-title: FunGene: The functional gene pipeline and repository publication-title: Front. Microbiol. doi: 10.3389/fmicb.2013.00291 – volume: 69 start-page: 320 year: 2003 ident: ref_44 article-title: Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.69.1.320-326.2003 – volume: 63 start-page: 803 year: 1997 ident: ref_25 article-title: Novel group within the kingdom Crenarchaeota from boreal forest soil publication-title: Appl. Environ. Microbiol. doi: 10.1128/aem.63.2.803-805.1997 – volume: 11 start-page: 789 year: 2013 ident: ref_2 article-title: Going back to the roots: The microbial ecology of the rhizosphere publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro3109 – volume: 248 start-page: 183 year: 2005 ident: ref_47 article-title: PCR-generated artifact from 16S rRNA gene-specific primers publication-title: FEMS Microbiol. Lett. doi: 10.1016/j.femsle.2005.05.043 – volume: 11 start-page: 296 year: 2008 ident: ref_5 article-title: The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems publication-title: Ecol. Lett. doi: 10.1111/j.1461-0248.2007.01139.x – ident: ref_15 doi: 10.1371/journal.pone.0043672 – volume: 54 start-page: 655 year: 2003 ident: ref_1 article-title: Microbial diversity and soil functions publication-title: Eur. J. Soil Sci. doi: 10.1046/j.1351-0754.2003.0556.x – volume: 29 start-page: 205 year: 1999 ident: ref_24 article-title: Diversity of soil Archaea in boreal forest before, and after clean-cutting and prescribed burning publication-title: FEMS Microbiol. Ecol. – volume: 74 start-page: 6452 year: 2008 ident: ref_23 article-title: TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.01394-08 – volume: 117 start-page: 181 year: 2004 ident: ref_10 article-title: Surrogate taxa for biodiversity in agricultural landscape of eastern Austria publication-title: Biol. Conser. doi: 10.1016/S0006-3207(03)00291-X – volume: 72 start-page: 713 year: 2006 ident: ref_32 article-title: Recurring seasonal dynamics of microbial communities in stream habits publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.72.1.713-722.2006 – volume: 12 start-page: 3253 year: 2012 ident: ref_56 article-title: Community level physiological profiles (CLPP), characterization and microbial activity of soil amended with dairy sewage sludge publication-title: Sensors doi: 10.3390/s120303253 – volume: 2 start-page: 113 year: 1993 ident: ref_28 article-title: ITS primers with enhanced specificity for basidiomycetes: Application to the identification of mycorrhiza and rusts publication-title: Mol. Ecol. doi: 10.1111/j.1365-294X.1993.tb00005.x – volume: 89 start-page: 316 year: 2014 ident: ref_21 article-title: Community fingerprinting in a sequencing world. Community fingerprinting in a sequencing world publication-title: FEMS Microbiol. Ecol. doi: 10.1111/1574-6941.12308 – volume: 104 start-page: 1027 year: 2000 ident: ref_34 article-title: Diversity of soil fungi studied by PCR-RFLP of ITS publication-title: Mycol. Res. doi: 10.1017/S0953756200002835 – volume: 26 start-page: 2797 year: 1998 ident: ref_45 article-title: The influence of fluorescent dye structure on the electrophoretic mobility of end-labeled DNA publication-title: Nucleic Acid Res doi: 10.1093/nar/26.11.2797 – volume: 64 start-page: 795 year: 1998 ident: ref_26 article-title: Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.64.2.795-799.1998 – volume: 104 start-page: 75 year: 2004 ident: ref_11 article-title: Assessing biodiversity at landscape level in northern Thailand and Sumatra (Indonesia): The importance of environmental context publication-title: Agr. Ecosyst. Environ. doi: 10.1016/j.agee.2004.01.008 – volume: 20 start-page: 1492 year: 1999 ident: ref_46 article-title: A fully automated multicapillary electrophoresis device for DNA analysis publication-title: Electrophoresis doi: 10.1002/(SICI)1522-2683(19990601)20:7<1492::AID-ELPS1492>3.0.CO;2-V – volume: 55 start-page: 459 year: 2006 ident: ref_48 article-title: Long-term monitoring of the succession of a microbial community in activated sludge from a circulation flush toilet as a closed system publication-title: FEMS Microbiol. Ecol. doi: 10.1111/j.1574-6941.2005.00047.x – volume: 102 start-page: 6207 year: 2018 ident: ref_49 article-title: Isolation of high molecular weight and humic acid-free metagenomic DNA from lignocellulose-rich samples compatible for direct fosmid cloning publication-title: Appl. Microbiol. Biotechnol. doi: 10.1007/s00253-018-9102-6 – volume: 2 start-page: 37 year: 2004 ident: ref_50 article-title: Rapid molecular diagnosis of lactobacillus bacteremia by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene publication-title: Clin. Med. Res. doi: 10.3121/cmr.2.1.37 – ident: ref_4 doi: 10.3390/f11030262 – ident: ref_29 – volume: 170 start-page: 381 year: 2006 ident: ref_35 article-title: Fine-scale distribution of pine ectomycorrhizas and their extramatrical mycelium publication-title: New Phytol. doi: 10.1111/j.1469-8137.2006.01669.x – volume: 84 start-page: e02738-17 year: 2018 ident: ref_7 article-title: High microbial diversity promotes soil ecosystem functioning publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.02738-17 – volume: 6 start-page: 769 year: 2004 ident: ref_13 article-title: Diversity and ecology of soil fungal communities: Increased understanding through the application of molecular techniques publication-title: Environ. Microbiol. doi: 10.1111/j.1462-2920.2004.00675.x – volume: 72 start-page: 7278 year: 2006 ident: ref_14 article-title: Use of multiplex terminal restriction fragment length polymorphism for rapid and simultaneous analysis of different components of the soil microbial community publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.00510-06 – volume: 53 start-page: 562 year: 2007 ident: ref_53 article-title: MiCA: A webbased tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes publication-title: Microb. Ecol. doi: 10.1007/s00248-006-9106-0 – volume: 2 start-page: 160 year: 2009 ident: ref_19 article-title: Analyzing salt-marsh fungal diversity: Comparing ARISA fingerprinting with clone sequencing and pyrosequencing publication-title: Fungal. Ecol. doi: 10.1016/j.funeco.2009.04.001 – volume: 5 start-page: e2915 year: 2017 ident: ref_40 article-title: Successive DNA extractions improve characterization of soil microbial communities publication-title: Peer J. doi: 10.7717/peerj.2915 – volume: 5 start-page: 581 year: 2013 ident: ref_6 article-title: Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology publication-title: Diversity doi: 10.3390/d5030581 – volume: 69 start-page: 2555 year: 2003 ident: ref_43 article-title: Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.69.5.2555-2562.2003
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SubjectTerms	Archaea - classification Bacteria Bacteria - classification Biodiversity Biosensors capillary electrophoresis Climate change Deoxyribonucleic acid DNA Fungi Fungi - classification Genetic diversity genetic fingerprinting Genetic testing Information sources Land use planning Methods microbial genetic diversity multiplex t-RFLP Polymerase Chain Reaction Polymorphism Polymorphism, Restriction Fragment Length Research methodology Soil Microbiology soil microbiome Soil microorganisms Taxonomy
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Title	Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi
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