Impact of land-use and fecal contamination on Escherichia populations in environmental samples
Abstract Understanding the composition of complex Escherichia coli populations from the environment is necessary for identifying strategies to reduce the impacts of fecal contamination and protect public health. Metabarcoding targeting the hypervariable gene gnd was used to reveal the complex popula...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-12-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-83594-y |
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| author | Adrian L. Cookson Jonathan C. Marshall Patrick J. Biggs Lynn E. Rogers Rose M. Collis Megan Devane Rebecca Stott Gale Brightwell |
| author_facet | Adrian L. Cookson Jonathan C. Marshall Patrick J. Biggs Lynn E. Rogers Rose M. Collis Megan Devane Rebecca Stott Gale Brightwell |
| author_sort | Adrian L. Cookson |
| collection | DOAJ |
| description | Abstract Understanding the composition of complex Escherichia coli populations from the environment is necessary for identifying strategies to reduce the impacts of fecal contamination and protect public health. Metabarcoding targeting the hypervariable gene gnd was used to reveal the complex population diversity of E. coli and phenotypically indistinct Escherichia species in water, soil, sediment, aquatic biofilm, and fecal samples from native forest and pastoral sites. The resulting amplicons were cross-referenced against a database containing over 700 different partial gnd sequences from E. coli/non-E. coli Escherichia species. Alpha and beta measures of diversity of Escherichia populations were lowest in feces, soil and sediment compared to water and aquatic biofilm samples. Escherichia populations recovered from extensive freshwater catchments dominated by sheep, beef and dairy farming were extremely diverse but well-separated from a wetland dairy site. In contrast, Escherichia populations from the low-impact native forest site with fewer fecal sources were less diverse. Metabarcoding distinguished E. coli populations important to fecal contamination monitoring from non-E. coli Escherichia environmental populations. These data represent in-depth analysis and geographic stability of Escherichia populations from environmental samples with extensive heterogeneity, and reveal links with diverse fecal sources, land-use and the overall burden of fecal contamination at sample sites. |
| format | Article |
| id | doaj-art-d247c83be6e0442699e14c6f88005957 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-d247c83be6e0442699e14c6f880059572025-01-05T12:23:35ZengNature PortfolioScientific Reports2045-23222024-12-0114111410.1038/s41598-024-83594-yImpact of land-use and fecal contamination on Escherichia populations in environmental samplesAdrian L. Cookson0Jonathan C. Marshall1Patrick J. Biggs2Lynn E. Rogers3Rose M. Collis4Megan Devane5Rebecca Stott6Gale Brightwell7Food System Integrity, AgResearch Limited, Hopkirk Research Institute, Massey UniversitymEpiLab, School of Veterinary Science, Massey UniversitymEpiLab, School of Veterinary Science, Massey UniversityFood System Integrity, AgResearch Limited, Hopkirk Research Institute, Massey UniversityFood System Integrity, AgResearch Limited, Hopkirk Research Institute, Massey UniversityEnvironmental Science and Research LimitedNational Institute of Water and Atmospheric ResearchFood System Integrity, AgResearch Limited, Hopkirk Research Institute, Massey UniversityAbstract Understanding the composition of complex Escherichia coli populations from the environment is necessary for identifying strategies to reduce the impacts of fecal contamination and protect public health. Metabarcoding targeting the hypervariable gene gnd was used to reveal the complex population diversity of E. coli and phenotypically indistinct Escherichia species in water, soil, sediment, aquatic biofilm, and fecal samples from native forest and pastoral sites. The resulting amplicons were cross-referenced against a database containing over 700 different partial gnd sequences from E. coli/non-E. coli Escherichia species. Alpha and beta measures of diversity of Escherichia populations were lowest in feces, soil and sediment compared to water and aquatic biofilm samples. Escherichia populations recovered from extensive freshwater catchments dominated by sheep, beef and dairy farming were extremely diverse but well-separated from a wetland dairy site. In contrast, Escherichia populations from the low-impact native forest site with fewer fecal sources were less diverse. Metabarcoding distinguished E. coli populations important to fecal contamination monitoring from non-E. coli Escherichia environmental populations. These data represent in-depth analysis and geographic stability of Escherichia populations from environmental samples with extensive heterogeneity, and reveal links with diverse fecal sources, land-use and the overall burden of fecal contamination at sample sites.https://doi.org/10.1038/s41598-024-83594-yFecal indicator bacteriaFreshwaterSource trackingMicrobial community profilingZoonotic pathogensLand-use |
| spellingShingle | Adrian L. Cookson Jonathan C. Marshall Patrick J. Biggs Lynn E. Rogers Rose M. Collis Megan Devane Rebecca Stott Gale Brightwell Impact of land-use and fecal contamination on Escherichia populations in environmental samples Scientific Reports Fecal indicator bacteria Freshwater Source tracking Microbial community profiling Zoonotic pathogens Land-use |
| title | Impact of land-use and fecal contamination on Escherichia populations in environmental samples |
| title_full | Impact of land-use and fecal contamination on Escherichia populations in environmental samples |
| title_fullStr | Impact of land-use and fecal contamination on Escherichia populations in environmental samples |
| title_full_unstemmed | Impact of land-use and fecal contamination on Escherichia populations in environmental samples |
| title_short | Impact of land-use and fecal contamination on Escherichia populations in environmental samples |
| title_sort | impact of land use and fecal contamination on escherichia populations in environmental samples |
| topic | Fecal indicator bacteria Freshwater Source tracking Microbial community profiling Zoonotic pathogens Land-use |
| url | https://doi.org/10.1038/s41598-024-83594-y |
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