Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics
Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00358/full |
| _version_ | 1818957605219860480 |
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| author | Tom O Delmont Tom O Delmont A Murat Eren Lorrie eMaccario Emmanuel ePrestat Özcan eEsen Eric ePelletier Eric ePelletier Eric ePelletier Denis eLePaslier Denis eLePaslier Denis eLePaslier Pascal eSIMONET Timothy eVogel |
| author_facet | Tom O Delmont Tom O Delmont A Murat Eren Lorrie eMaccario Emmanuel ePrestat Özcan eEsen Eric ePelletier Eric ePelletier Eric ePelletier Denis eLePaslier Denis eLePaslier Denis eLePaslier Pascal eSIMONET Timothy eVogel |
| author_sort | Tom O Delmont |
| collection | DOAJ |
| description | Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for four months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n=2), Rhodanobacter (n=5), Acidobacteria (n=2), Sporolactobacillus (n=2, novel nitrogen fixing taxon), Ktedonobacter (n=1, second representative of the family Ktedonobacteraceae), Streptomyces (n=3, novel polyketide synthase modules) and Burkholderia (n=2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment. |
| first_indexed | 2024-12-20T11:12:30Z |
| format | Article |
| id | doaj.art-9320f099b47142328b2cf2305f14004f |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-20T11:12:30Z |
| publishDate | 2015-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-9320f099b47142328b2cf2305f14004f2022-12-21T19:42:43ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-04-01610.3389/fmicb.2015.00358140100Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and MetagenomicsTom O Delmont0Tom O Delmont1A Murat Eren2Lorrie eMaccario3Emmanuel ePrestat4Özcan eEsen5Eric ePelletier6Eric ePelletier7Eric ePelletier8Denis eLePaslier9Denis eLePaslier10Denis eLePaslier11Pascal eSIMONET12Timothy eVogel13Marine Biological LaboratoryEcole centrale de Lyon, Université de Lyon, CNRSMarine Biological LaboratoryEcole centrale de Lyon, Université de Lyon, CNRSEcole centrale de Lyon, Université de Lyon, CNRSMarine Biological LaboratoryCommissariat a l'énergie atomiqueCentre national de la recherche scientifiqueUniversité d'Evry Val d'EssonneCommissariat a l'énergie atomiqueCentre national de la recherche scientifiqueUniversité d'Evry Val d'EssonneEcole centrale de Lyon, Université de Lyon, CNRSEcole centrale de Lyon, Université de Lyon, CNRSDespite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for four months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n=2), Rhodanobacter (n=5), Acidobacteria (n=2), Sporolactobacillus (n=2, novel nitrogen fixing taxon), Ktedonobacter (n=1, second representative of the family Ktedonobacteraceae), Streptomyces (n=3, novel polyketide synthase modules) and Burkholderia (n=2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00358/fullGenomicsMetagenomicsPlasmidsSoil MicrobiologyEnrichmentFunctional Networks |
| spellingShingle | Tom O Delmont Tom O Delmont A Murat Eren Lorrie eMaccario Emmanuel ePrestat Özcan eEsen Eric ePelletier Eric ePelletier Eric ePelletier Denis eLePaslier Denis eLePaslier Denis eLePaslier Pascal eSIMONET Timothy eVogel Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics Frontiers in Microbiology Genomics Metagenomics Plasmids Soil Microbiology Enrichment Functional Networks |
| title | Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics |
| title_full | Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics |
| title_fullStr | Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics |
| title_full_unstemmed | Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics |
| title_short | Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics |
| title_sort | reconstructing rare soil microbial genomes using in situ enrichments and metagenomics |
| topic | Genomics Metagenomics Plasmids Soil Microbiology Enrichment Functional Networks |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00358/full |
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