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Assembly of the amphibian microbiome is influenced by the effects of land‐use change on environmental reservoirs
Summary A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphi...
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| Published in: | Environmental microbiology 2021-08, Vol.23 (8), p.4595-4611 |
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| Main Authors: | , , , , , |
| Format: | Article |
| Language: | English |
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| cited_by | cdi_FETCH-LOGICAL-c3893-32952bd81d1990746e4992d825eed1233dc8b2d092971ab76ff30f03af1a64323 |
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| cites | cdi_FETCH-LOGICAL-c3893-32952bd81d1990746e4992d825eed1233dc8b2d092971ab76ff30f03af1a64323 |
| container_end_page | 4611 |
| container_issue | 8 |
| container_start_page | 4595 |
| container_title | Environmental microbiology |
| container_volume | 23 |
| creator | Barnes, Elle M. Kutos, Steve Naghshineh, Nina Mesko, Marissa You, Qing Lewis, J. D. |
| description | Summary
A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land‐use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land‐use associated factors creating site‐specific compositions. By employing a quantitative, null‐based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function. |
| doi_str_mv | 10.1111/1462-2920.15653 |
| format | article |
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A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land‐use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land‐use associated factors creating site‐specific compositions. By employing a quantitative, null‐based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.</description><identifier>ISSN: 1462-2912</identifier><identifier>EISSN: 1462-2920</identifier><identifier>DOI: 10.1111/1462-2920.15653</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Amphibians ; Aquatic reptiles ; Assembly ; Community composition ; Composition ; Cores ; Dispersal ; Fungi ; Metropolitan areas ; Microbial activity ; Microbiomes ; Microorganisms ; Pathogens ; Skin ; Soil ; Soils ; Symbionts</subject><ispartof>Environmental microbiology, 2021-08, Vol.23 (8), p.4595-4611</ispartof><rights>2021 Society for Applied Microbiology and John Wiley & Sons Ltd.</rights><rights>2021 Society for Applied Microbiology and John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3893-32952bd81d1990746e4992d825eed1233dc8b2d092971ab76ff30f03af1a64323</citedby><cites>FETCH-LOGICAL-c3893-32952bd81d1990746e4992d825eed1233dc8b2d092971ab76ff30f03af1a64323</cites><orcidid>0000-0001-8003-7169</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2F1462-2920.15653$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1462-2920.15653$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,786,790,27957,27958,50923,51032</link.rule.ids></links><search><creatorcontrib>Barnes, Elle M.</creatorcontrib><creatorcontrib>Kutos, Steve</creatorcontrib><creatorcontrib>Naghshineh, Nina</creatorcontrib><creatorcontrib>Mesko, Marissa</creatorcontrib><creatorcontrib>You, Qing</creatorcontrib><creatorcontrib>Lewis, J. D.</creatorcontrib><title>Assembly of the amphibian microbiome is influenced by the effects of land‐use change on environmental reservoirs</title><title>Environmental microbiology</title><description>Summary
A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land‐use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land‐use associated factors creating site‐specific compositions. By employing a quantitative, null‐based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.</description><subject>Amphibians</subject><subject>Aquatic reptiles</subject><subject>Assembly</subject><subject>Community composition</subject><subject>Composition</subject><subject>Cores</subject><subject>Dispersal</subject><subject>Fungi</subject><subject>Metropolitan areas</subject><subject>Microbial activity</subject><subject>Microbiomes</subject><subject>Microorganisms</subject><subject>Pathogens</subject><subject>Skin</subject><subject>Soil</subject><subject>Soils</subject><subject>Symbionts</subject><issn>1462-2912</issn><issn>1462-2920</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNqFkb1OwzAUhSMEEqUws1piYQn1T_48VlWBSkUsMFtOck1dJXaxk6JsPALPyJPgtqgDC16uffWd66Nzo-ia4DsSzoQkGY0pp-GZZik7iUbHzunxTuh5dOH9GmOSsxyPIjf1HtqyGZBVqFsBku1mpUstDWp15WypbQtIe6SNanowFdSoHPYkKAVV53fCRpr6-_Or94CqlTRvgKxBYLbaWdOC6WSDHHhwW6udv4zOlGw8XP3WcfR6P3-ZPcbL54fFbLqMK1ZwFjPKU1rWBakJ5zhPMkg4p3VBU4CaUMbqqihpjTnlOZFlninFsMJMKiKzhFE2jm4PczfOvvfgO9FqX0ETzILtvaBpkvE8JZwE9OYPura9M8FdoLKU0PBLEqjJgQq5eO9AiY3TrXSDIFjsdiB2KYtd4mK_g6BID4oP3cDwHy7mT4uD7gcMLIlE</recordid><startdate>202108</startdate><enddate>202108</enddate><creator>Barnes, Elle M.</creator><creator>Kutos, Steve</creator><creator>Naghshineh, Nina</creator><creator>Mesko, Marissa</creator><creator>You, Qing</creator><creator>Lewis, J. D.</creator><general>John Wiley & Sons, Inc</general><general>Wiley Subscription Services, Inc</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QH</scope><scope>7QL</scope><scope>7ST</scope><scope>7T7</scope><scope>7TN</scope><scope>7U9</scope><scope>7UA</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H94</scope><scope>H95</scope><scope>H97</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>SOI</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-8003-7169</orcidid></search><sort><creationdate>202108</creationdate><title>Assembly of the amphibian microbiome is influenced by the effects of land‐use change on environmental reservoirs</title><author>Barnes, Elle M. ; Kutos, Steve ; Naghshineh, Nina ; Mesko, Marissa ; You, Qing ; Lewis, J. D.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3893-32952bd81d1990746e4992d825eed1233dc8b2d092971ab76ff30f03af1a64323</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Amphibians</topic><topic>Aquatic reptiles</topic><topic>Assembly</topic><topic>Community composition</topic><topic>Composition</topic><topic>Cores</topic><topic>Dispersal</topic><topic>Fungi</topic><topic>Metropolitan areas</topic><topic>Microbial activity</topic><topic>Microbiomes</topic><topic>Microorganisms</topic><topic>Pathogens</topic><topic>Skin</topic><topic>Soil</topic><topic>Soils</topic><topic>Symbionts</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Barnes, Elle M.</creatorcontrib><creatorcontrib>Kutos, Steve</creatorcontrib><creatorcontrib>Naghshineh, Nina</creatorcontrib><creatorcontrib>Mesko, Marissa</creatorcontrib><creatorcontrib>You, Qing</creatorcontrib><creatorcontrib>Lewis, J. D.</creatorcontrib><collection>CrossRef</collection><collection>Aqualine</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Oceanic Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Water Resources Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 3: Aquatic Pollution & Environmental Quality</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Environmental microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Barnes, Elle M.</au><au>Kutos, Steve</au><au>Naghshineh, Nina</au><au>Mesko, Marissa</au><au>You, Qing</au><au>Lewis, J. D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Assembly of the amphibian microbiome is influenced by the effects of land‐use change on environmental reservoirs</atitle><jtitle>Environmental microbiology</jtitle><date>2021-08</date><risdate>2021</risdate><volume>23</volume><issue>8</issue><spage>4595</spage><epage>4611</epage><pages>4595-4611</pages><issn>1462-2912</issn><eissn>1462-2920</eissn><notes>Barnes and Kutos are joint first authors.</notes><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>Summary
A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land‐use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land‐use associated factors creating site‐specific compositions. By employing a quantitative, null‐based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.</abstract><cop>Hoboken, USA</cop><pub>John Wiley & Sons, Inc</pub><doi>10.1111/1462-2920.15653</doi><tpages>17</tpages><orcidid>https://orcid.org/0000-0001-8003-7169</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Environmental microbiology, 2021-08, Vol.23 (8), p.4595-4611 |
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| language | eng |
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| source | Wiley-Blackwell Journals |
| subjects | Amphibians Aquatic reptiles Assembly Community composition Composition Cores Dispersal Fungi Metropolitan areas Microbial activity Microbiomes Microorganisms Pathogens Skin Soil Soils Symbionts |
| title | Assembly of the amphibian microbiome is influenced by the effects of land‐use change on environmental reservoirs |
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