Decrypting soil microbial communities using metagenomic approaches
Microbial ecology is beginning to interact with metagenomics and many microbiologists are attracted to metagenomics in the hope of discovering novel relationships between microorganisms and/or confirming that work done on isolates applies to the remaining uncultured members of the different ecosyste...
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ftunivlyon1:oai:HAL:tel-01090720v1 2023-11-12T04:06:13+01:00 Decrypting soil microbial communities using metagenomic approaches Description des communautés microbiennes du sol par une approche métagénomique Delmont, Tom Ampère (AMPERE) École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Ecole Centrale de Lyon Timothy Vogel 2011-12-19 https://theses.hal.science/tel-01090720 https://theses.hal.science/tel-01090720/document https://theses.hal.science/tel-01090720/file/TH_T2265_tdelmont_pdfcreator.pdf en eng HAL CCSD NNT: 2011ECDL0048 tel-01090720 https://theses.hal.science/tel-01090720 https://theses.hal.science/tel-01090720/document https://theses.hal.science/tel-01090720/file/TH_T2265_tdelmont_pdfcreator.pdf info:eu-repo/semantics/OpenAccess https://theses.hal.science/tel-01090720 Other. Ecole Centrale de Lyon, 2011. English. ⟨NNT : 2011ECDL0048⟩ Microbial communities Metagenomics Soil Métagénomique Sol Communautés microbiennes [SPI.OTHER]Engineering Sciences [physics]/Other info:eu-repo/semantics/doctoralThesis Theses 2011 ftunivlyon1 2023-10-31T23:49:13Z Microbial ecology is beginning to interact with metagenomics and many microbiologists are attracted to metagenomics in the hope of discovering novel relationships between microorganisms and/or confirming that work done on isolates applies to the remaining uncultured members of the different ecosystems. With a growing number of available metagenomic datasets, metagenomes can be intensively mined by microbial ecologists in search of previously undetected correlations (both structural and functional). Here, we provide a preliminary exploration of 77 publically available metagenomes corresponding to DNA samples extracted from oceans, atoll corals, deep oceans, Antarctic aquatic environments, Arctic snows, terrestrial environments (sediments, soils, sludges, microbial fuel cell anode biofilms, acid mine drainage biofilms), polluted air, and animal and human microbiomes (human feces, mouse and chicken cecum, and cow rumen). Results show well-defined environmental specificities that emphasize microbial adaptation and evolution capabilities. Unexpected observations were also made for several ecosystems, thus providing new hypotheses about the life style of their microbial communities. Available metagenomes are a gold mine of underexploited information that could be used to explore specific microbial structural and functional relationships. The statistical analysis provided here depends in part on replicates from the different ecosystems. With the continued emphasis on metagenomic sequencing, future analyses should support rigorous statistical treatment. This preliminary metagenomic decryption could represent a pilot-scale test for a future Earth microbiome global comparison Les données présentées dans ce manuscrit de thèse sont principalement basées sur l'analyse de séquences d'ADN extraites directement de l'environnement (et en particulier du sol) en les comparant aux données cumulées au fil des siècles sur les microorganismes cultivés en laboratoire. Les objectifs, difficultés, résultats et perspectives de cette ... Doctoral or Postdoctoral Thesis Antarc* Antarctic Arctic HAL Lyon 1 (University Claude Bernard Lyon 1) Antarctic Arctic |
institution |
Open Polar |
collection |
HAL Lyon 1 (University Claude Bernard Lyon 1) |
op_collection_id |
ftunivlyon1 |
language |
English |
topic |
Microbial communities Metagenomics Soil Métagénomique Sol Communautés microbiennes [SPI.OTHER]Engineering Sciences [physics]/Other |
spellingShingle |
Microbial communities Metagenomics Soil Métagénomique Sol Communautés microbiennes [SPI.OTHER]Engineering Sciences [physics]/Other Delmont, Tom Decrypting soil microbial communities using metagenomic approaches |
topic_facet |
Microbial communities Metagenomics Soil Métagénomique Sol Communautés microbiennes [SPI.OTHER]Engineering Sciences [physics]/Other |
description |
Microbial ecology is beginning to interact with metagenomics and many microbiologists are attracted to metagenomics in the hope of discovering novel relationships between microorganisms and/or confirming that work done on isolates applies to the remaining uncultured members of the different ecosystems. With a growing number of available metagenomic datasets, metagenomes can be intensively mined by microbial ecologists in search of previously undetected correlations (both structural and functional). Here, we provide a preliminary exploration of 77 publically available metagenomes corresponding to DNA samples extracted from oceans, atoll corals, deep oceans, Antarctic aquatic environments, Arctic snows, terrestrial environments (sediments, soils, sludges, microbial fuel cell anode biofilms, acid mine drainage biofilms), polluted air, and animal and human microbiomes (human feces, mouse and chicken cecum, and cow rumen). Results show well-defined environmental specificities that emphasize microbial adaptation and evolution capabilities. Unexpected observations were also made for several ecosystems, thus providing new hypotheses about the life style of their microbial communities. Available metagenomes are a gold mine of underexploited information that could be used to explore specific microbial structural and functional relationships. The statistical analysis provided here depends in part on replicates from the different ecosystems. With the continued emphasis on metagenomic sequencing, future analyses should support rigorous statistical treatment. This preliminary metagenomic decryption could represent a pilot-scale test for a future Earth microbiome global comparison Les données présentées dans ce manuscrit de thèse sont principalement basées sur l'analyse de séquences d'ADN extraites directement de l'environnement (et en particulier du sol) en les comparant aux données cumulées au fil des siècles sur les microorganismes cultivés en laboratoire. Les objectifs, difficultés, résultats et perspectives de cette ... |
author2 |
Ampère (AMPERE) École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Ecole Centrale de Lyon Timothy Vogel |
format |
Doctoral or Postdoctoral Thesis |
author |
Delmont, Tom |
author_facet |
Delmont, Tom |
author_sort |
Delmont, Tom |
title |
Decrypting soil microbial communities using metagenomic approaches |
title_short |
Decrypting soil microbial communities using metagenomic approaches |
title_full |
Decrypting soil microbial communities using metagenomic approaches |
title_fullStr |
Decrypting soil microbial communities using metagenomic approaches |
title_full_unstemmed |
Decrypting soil microbial communities using metagenomic approaches |
title_sort |
decrypting soil microbial communities using metagenomic approaches |
publisher |
HAL CCSD |
publishDate |
2011 |
url |
https://theses.hal.science/tel-01090720 https://theses.hal.science/tel-01090720/document https://theses.hal.science/tel-01090720/file/TH_T2265_tdelmont_pdfcreator.pdf |
geographic |
Antarctic Arctic |
geographic_facet |
Antarctic Arctic |
genre |
Antarc* Antarctic Arctic |
genre_facet |
Antarc* Antarctic Arctic |
op_source |
https://theses.hal.science/tel-01090720 Other. Ecole Centrale de Lyon, 2011. English. ⟨NNT : 2011ECDL0048⟩ |
op_relation |
NNT: 2011ECDL0048 tel-01090720 https://theses.hal.science/tel-01090720 https://theses.hal.science/tel-01090720/document https://theses.hal.science/tel-01090720/file/TH_T2265_tdelmont_pdfcreator.pdf |
op_rights |
info:eu-repo/semantics/OpenAccess |
_version_ |
1782327321912410112 |