Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches
AbstractCoastal environments, crucial and intricate ecosystems, face threats from human activities like pollution, eutrophication, and climate change. Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comp...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-01-01
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| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.504 |
| _version_ | 1797277050993639424 |
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| author | Ion L. Abad‐Recio Laura Alonso‐Sáez Anders Lanzén |
| author_facet | Ion L. Abad‐Recio Laura Alonso‐Sáez Anders Lanzén |
| author_sort | Ion L. Abad‐Recio |
| collection | DOAJ |
| description | AbstractCoastal environments, crucial and intricate ecosystems, face threats from human activities like pollution, eutrophication, and climate change. Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics. Results revealed significant functional diversity across all sampling sites, irrespective of their environmental status. Most predicted KEGG Orthologs (KOs) showed consistency between metagenomics and Tax4Fun datasets, with correlated abundances. However, abundances derived from GeoChip did not correlate with either dataset. When comparing estuaries based on environmental status, Tax4Fun and metagenomics identified over 24% of KOs with significantly different abundances. KOs overrepresented in estuaries with a poor ecological status displayed an abundance of pathways associated with anaerobic metabolism, such as methanogenesis. |
| first_indexed | 2024-03-07T15:38:05Z |
| format | Article |
| id | doaj.art-dde449a8661b4eb2896c089683324a2d |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-03-07T15:38:05Z |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-dde449a8661b4eb2896c089683324a2d2024-03-05T09:32:37ZengWileyEnvironmental DNA2637-49432024-01-0161n/an/a10.1002/edn3.504Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approachesIon L. Abad‐Recio0Laura Alonso‐Sáez1Anders Lanzén2AZTI, Marine Research, Basque Research and Technology Alliance (BRTA)PasaiaSpainAZTI, Marine Research, Basque Research and Technology Alliance (BRTA)PasaiaSpainAZTI, Marine Research, Basque Research and Technology Alliance (BRTA)PasaiaSpainAbstractCoastal environments, crucial and intricate ecosystems, face threats from human activities like pollution, eutrophication, and climate change. Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics. Results revealed significant functional diversity across all sampling sites, irrespective of their environmental status. Most predicted KEGG Orthologs (KOs) showed consistency between metagenomics and Tax4Fun datasets, with correlated abundances. However, abundances derived from GeoChip did not correlate with either dataset. When comparing estuaries based on environmental status, Tax4Fun and metagenomics identified over 24% of KOs with significantly different abundances. KOs overrepresented in estuaries with a poor ecological status displayed an abundance of pathways associated with anaerobic metabolism, such as methanogenesis.https://doi.org/10.1002/edn3.504eDNAfunctional profilingmetabarcodingmetagenomicsmicrobiomics |
| spellingShingle | Ion L. Abad‐Recio Laura Alonso‐Sáez Anders Lanzén Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches Environmental DNA eDNA functional profiling metabarcoding metagenomics microbiomics |
| title | Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches |
| title_full | Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches |
| title_fullStr | Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches |
| title_full_unstemmed | Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches |
| title_short | Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches |
| title_sort | toward functional profiling for edna based monitoring in coastal environments a comparison of three approaches |
| topic | eDNA functional profiling metabarcoding metagenomics microbiomics |
| url | https://doi.org/10.1002/edn3.504 |
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