Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors
— Owing to the high resolving power and efficiency of DNA sequencing, researchers have discovered the extremely high diversity of bacterial, fungal, protist, and microinvertebrate communities in the soil, wood, phyllosphere, and other natural media. Studies on the properties of these communities req...
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| Veröffentlicht in: | Russian journal of ecology 2021-05, Vol.52 (3), p.188-200 |
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| container_title | Russian journal of ecology |
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| creator | Mikryukov, V. S. Dulya, O. V. Likhodeevskii, G. A Vorobeichik, E. L. |
| description | —
Owing to the high resolving power and efficiency of DNA sequencing, researchers have discovered the extremely high diversity of bacterial, fungal, protist, and microinvertebrate communities in the soil, wood, phyllosphere, and other natural media. Studies on the properties of these communities require powerful tools for analyzing multicomponent systems. One of them is the analysis of ecological networks, which makes it possible to solve a broad range of problems. This review briefly describes the possibilities of network analysis, its concepts, and metrics of network topology.It also indicates limitations related to specific features of DNA sequencing (compositionality and data sparsity) and potential sources of errors in the interpretation of results (relic DNA, artifactual DNA sequences and spurious connections in a network). The focus is on the communities of microorganisms, but the discussed issues are relevant for most other groups of the biota. |
| doi_str_mv | 10.1134/S1067413621030085 |
| format | Article |
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Owing to the high resolving power and efficiency of DNA sequencing, researchers have discovered the extremely high diversity of bacterial, fungal, protist, and microinvertebrate communities in the soil, wood, phyllosphere, and other natural media. Studies on the properties of these communities require powerful tools for analyzing multicomponent systems. One of them is the analysis of ecological networks, which makes it possible to solve a broad range of problems. This review briefly describes the possibilities of network analysis, its concepts, and metrics of network topology.It also indicates limitations related to specific features of DNA sequencing (compositionality and data sparsity) and potential sources of errors in the interpretation of results (relic DNA, artifactual DNA sequences and spurious connections in a network). The focus is on the communities of microorganisms, but the discussed issues are relevant for most other groups of the biota.</description><identifier>ISSN: 1067-4136</identifier><identifier>EISSN: 1608-3334</identifier><identifier>DOI: 10.1134/S1067413621030085</identifier><language>eng</language><publisher>Moscow: Pleiades Publishing</publisher><subject>Biomedical and Life Sciences ; Biota ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Ecology ; Environment ; Life Sciences ; Microorganisms ; Network analysis ; Network topologies ; Nucleotide sequence ; Phyllosphere ; Resolution ; Topology</subject><ispartof>Russian journal of ecology, 2021-05, Vol.52 (3), p.188-200</ispartof><rights>Pleiades Publishing, Ltd. 2021. ISSN 1067-4136, Russian Journal of Ecology, 2021, Vol. 52, No. 3, pp. 188–200. © Pleiades Publishing, Ltd., 2021. Russian Text © The Author(s), 2021, published in Ekologiya, 2021, No. 3, pp. 179–192.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c316t-7232ed7c2a2130d56fdd0a84954f55b5b2420abe434a6e88f2b5c4bd723b0c3e3</citedby><cites>FETCH-LOGICAL-c316t-7232ed7c2a2130d56fdd0a84954f55b5b2420abe434a6e88f2b5c4bd723b0c3e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1134/S1067413621030085$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1134/S1067413621030085$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Mikryukov, V. S.</creatorcontrib><creatorcontrib>Dulya, O. V.</creatorcontrib><creatorcontrib>Likhodeevskii, G. A</creatorcontrib><creatorcontrib>Vorobeichik, E. L.</creatorcontrib><title>Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors</title><title>Russian journal of ecology</title><addtitle>Russ J Ecol</addtitle><description>—
Owing to the high resolving power and efficiency of DNA sequencing, researchers have discovered the extremely high diversity of bacterial, fungal, protist, and microinvertebrate communities in the soil, wood, phyllosphere, and other natural media. Studies on the properties of these communities require powerful tools for analyzing multicomponent systems. One of them is the analysis of ecological networks, which makes it possible to solve a broad range of problems. This review briefly describes the possibilities of network analysis, its concepts, and metrics of network topology.It also indicates limitations related to specific features of DNA sequencing (compositionality and data sparsity) and potential sources of errors in the interpretation of results (relic DNA, artifactual DNA sequences and spurious connections in a network). The focus is on the communities of microorganisms, but the discussed issues are relevant for most other groups of the biota.</description><subject>Biomedical and Life Sciences</subject><subject>Biota</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Ecology</subject><subject>Environment</subject><subject>Life Sciences</subject><subject>Microorganisms</subject><subject>Network analysis</subject><subject>Network topologies</subject><subject>Nucleotide sequence</subject><subject>Phyllosphere</subject><subject>Resolution</subject><subject>Topology</subject><issn>1067-4136</issn><issn>1608-3334</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp1kE1LAzEQhhdRsFZ_gLeAV1cnX9vVWyn1A-oHqOclm82W1N2kZlKkR_-5aSt4EE8zw_s-7zCTZacULijl4vKFQjESlBeMAgco5V42oAWUOedc7Kc-yflGP8yOEBcAFKCgg-xr7FS3RovEt2SqfefnVquOPJr46cM7EuvIw6qLVvt-6Z1xkUx836-cjdZsoQerg_dhrpzFHq_Js0e0te22hnMys72NKlrv0qBck_SYUmzaMQ3BBzzODlrVoTn5qcPs7Wb6OrnLZ0-395PxLNecFjEfMc5MM9JMMcqhkUXbNKBKcSVFK2UtayYYqNoILlRhyrJltdSibhJXg-aGD7OzXe4y-I-VwVgt_Cqk67FiUgClsuQsuejOlY5CDKatlsH2KqwrCtXm09WfTyeG7RhMXjc34Tf5f-gb3dCB6Q</recordid><startdate>20210501</startdate><enddate>20210501</enddate><creator>Mikryukov, V. S.</creator><creator>Dulya, O. V.</creator><creator>Likhodeevskii, G. A</creator><creator>Vorobeichik, E. L.</creator><general>Pleiades Publishing</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7SN</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20210501</creationdate><title>Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors</title><author>Mikryukov, V. S. ; Dulya, O. V. ; Likhodeevskii, G. A ; Vorobeichik, E. L.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c316t-7232ed7c2a2130d56fdd0a84954f55b5b2420abe434a6e88f2b5c4bd723b0c3e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Biomedical and Life Sciences</topic><topic>Biota</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Ecology</topic><topic>Environment</topic><topic>Life Sciences</topic><topic>Microorganisms</topic><topic>Network analysis</topic><topic>Network topologies</topic><topic>Nucleotide sequence</topic><topic>Phyllosphere</topic><topic>Resolution</topic><topic>Topology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mikryukov, V. S.</creatorcontrib><creatorcontrib>Dulya, O. V.</creatorcontrib><creatorcontrib>Likhodeevskii, G. A</creatorcontrib><creatorcontrib>Vorobeichik, E. L.</creatorcontrib><collection>CrossRef</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Russian journal of ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mikryukov, V. S.</au><au>Dulya, O. V.</au><au>Likhodeevskii, G. A</au><au>Vorobeichik, E. L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors</atitle><jtitle>Russian journal of ecology</jtitle><stitle>Russ J Ecol</stitle><date>2021-05-01</date><risdate>2021</risdate><volume>52</volume><issue>3</issue><spage>188</spage><epage>200</epage><pages>188-200</pages><issn>1067-4136</issn><eissn>1608-3334</eissn><abstract>—
Owing to the high resolving power and efficiency of DNA sequencing, researchers have discovered the extremely high diversity of bacterial, fungal, protist, and microinvertebrate communities in the soil, wood, phyllosphere, and other natural media. Studies on the properties of these communities require powerful tools for analyzing multicomponent systems. One of them is the analysis of ecological networks, which makes it possible to solve a broad range of problems. This review briefly describes the possibilities of network analysis, its concepts, and metrics of network topology.It also indicates limitations related to specific features of DNA sequencing (compositionality and data sparsity) and potential sources of errors in the interpretation of results (relic DNA, artifactual DNA sequences and spurious connections in a network). The focus is on the communities of microorganisms, but the discussed issues are relevant for most other groups of the biota.</abstract><cop>Moscow</cop><pub>Pleiades Publishing</pub><doi>10.1134/S1067413621030085</doi><tpages>13</tpages></addata></record> |
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| ispartof | Russian journal of ecology, 2021-05, Vol.52 (3), p.188-200 |
| issn | 1067-4136 1608-3334 |
| language | eng |
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| source | SpringerLink Journals |
| subjects | Biomedical and Life Sciences Biota Deoxyribonucleic acid DNA DNA sequencing Ecology Environment Life Sciences Microorganisms Network analysis Network topologies Nucleotide sequence Phyllosphere Resolution Topology |
| title | Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors |
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