Ohne Titel

Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydroge...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Khdhiri, Mondher [verfasserIn] Piché-Choquette, Sarah [verfasserIn] Tremblay, Julien [verfasserIn] Tringe, Susannah G. [verfasserIn] Constant, Philippe [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2018

Schlagwörter:	Metagenomic Metatranscriptomics Biogeochemistry Microbial ecology H

Übergeordnetes Werk:	Enthalten in: Soil biology & biochemistry - Amsterdam [u.a.] : Elsevier Science, 1969, 125, Seite 239-243
Übergeordnetes Werk:	volume:125 ; pages:239-243

DOI / URN:	10.1016/j.soilbio.2018.07.020

Katalog-ID:	ELV000314102

Internformat


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520			\|a Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil.
650		4	\|a Metagenomic
650		4	\|a Metatranscriptomics
650		4	\|a Biogeochemistry
650		4	\|a Microbial ecology
650		4	\|a H
700	1		\|a Piché-Choquette, Sarah \|e verfasserin \|0 (orcid)0000-0002-7447-1177 \|4 aut
700	1		\|a Tremblay, Julien \|e verfasserin \|4 aut
700	1		\|a Tringe, Susannah G. \|e verfasserin \|4 aut
700	1		\|a Constant, Philippe \|e verfasserin \|4 aut
773	0	8	\|i Enthalten in \|t Soil biology & biochemistry \|d Amsterdam [u.a.] : Elsevier Science, 1969 \|g 125, Seite 239-243 \|h Online-Ressource \|w (DE-627)306591596 \|w (DE-600)1498740-5 \|w (DE-576)100704522 \|7 nnns
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Indexfelder

author_variant	m k mk s p c spc j t jt s g t sg sgt p c pc
matchkey_str	ELV000314102
hierarchy_sort_str	2018
bklnumber	38.60 48.32
publishDate	2018
allfields	10.1016/j.soilbio.2018.07.020 doi (DE-627)ELV000314102 (ELSEVIER)S0038-0717(18)30248-7 DE-627 ger DE-627 rda eng 570 540 DE-600 BIODIV DE-30 fid 38.60 bkl 48.32 bkl Khdhiri, Mondher verfasserin aut 2018 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil. Metagenomic Metatranscriptomics Biogeochemistry Microbial ecology H Piché-Choquette, Sarah verfasserin (orcid)0000-0002-7447-1177 aut Tremblay, Julien verfasserin aut Tringe, Susannah G. verfasserin aut Constant, Philippe verfasserin aut Enthalten in Soil biology & biochemistry Amsterdam [u.a.] : Elsevier Science, 1969 125, Seite 239-243 Online-Ressource (DE-627)306591596 (DE-600)1498740-5 (DE-576)100704522 nnns volume:125 pages:239-243 GBV_USEFLAG_U SYSFLAG_U GBV_ELV FID-BIODIV SSG-OLC-PHA SSG-OPC-GGO SSG-OPC-FOR GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 38.60 Bodenkunde: Allgemeines Geowissenschaften 48.32 Bodenkunde Bodenbewertung Land- und Forstwirtschaft AR 125 239-243
spelling	10.1016/j.soilbio.2018.07.020 doi (DE-627)ELV000314102 (ELSEVIER)S0038-0717(18)30248-7 DE-627 ger DE-627 rda eng 570 540 DE-600 BIODIV DE-30 fid 38.60 bkl 48.32 bkl Khdhiri, Mondher verfasserin aut 2018 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil. Metagenomic Metatranscriptomics Biogeochemistry Microbial ecology H Piché-Choquette, Sarah verfasserin (orcid)0000-0002-7447-1177 aut Tremblay, Julien verfasserin aut Tringe, Susannah G. verfasserin aut Constant, Philippe verfasserin aut Enthalten in Soil biology & biochemistry Amsterdam [u.a.] : Elsevier Science, 1969 125, Seite 239-243 Online-Ressource (DE-627)306591596 (DE-600)1498740-5 (DE-576)100704522 nnns volume:125 pages:239-243 GBV_USEFLAG_U SYSFLAG_U GBV_ELV FID-BIODIV SSG-OLC-PHA SSG-OPC-GGO SSG-OPC-FOR GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 38.60 Bodenkunde: Allgemeines Geowissenschaften 48.32 Bodenkunde Bodenbewertung Land- und Forstwirtschaft AR 125 239-243
allfields_unstemmed	10.1016/j.soilbio.2018.07.020 doi (DE-627)ELV000314102 (ELSEVIER)S0038-0717(18)30248-7 DE-627 ger DE-627 rda eng 570 540 DE-600 BIODIV DE-30 fid 38.60 bkl 48.32 bkl Khdhiri, Mondher verfasserin aut 2018 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil. Metagenomic Metatranscriptomics Biogeochemistry Microbial ecology H Piché-Choquette, Sarah verfasserin (orcid)0000-0002-7447-1177 aut Tremblay, Julien verfasserin aut Tringe, Susannah G. verfasserin aut Constant, Philippe verfasserin aut Enthalten in Soil biology & biochemistry Amsterdam [u.a.] : Elsevier Science, 1969 125, Seite 239-243 Online-Ressource (DE-627)306591596 (DE-600)1498740-5 (DE-576)100704522 nnns volume:125 pages:239-243 GBV_USEFLAG_U SYSFLAG_U GBV_ELV FID-BIODIV SSG-OLC-PHA SSG-OPC-GGO SSG-OPC-FOR GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 38.60 Bodenkunde: Allgemeines Geowissenschaften 48.32 Bodenkunde Bodenbewertung Land- und Forstwirtschaft AR 125 239-243
allfieldsGer	10.1016/j.soilbio.2018.07.020 doi (DE-627)ELV000314102 (ELSEVIER)S0038-0717(18)30248-7 DE-627 ger DE-627 rda eng 570 540 DE-600 BIODIV DE-30 fid 38.60 bkl 48.32 bkl Khdhiri, Mondher verfasserin aut 2018 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil. Metagenomic Metatranscriptomics Biogeochemistry Microbial ecology H Piché-Choquette, Sarah verfasserin (orcid)0000-0002-7447-1177 aut Tremblay, Julien verfasserin aut Tringe, Susannah G. verfasserin aut Constant, Philippe verfasserin aut Enthalten in Soil biology & biochemistry Amsterdam [u.a.] : Elsevier Science, 1969 125, Seite 239-243 Online-Ressource (DE-627)306591596 (DE-600)1498740-5 (DE-576)100704522 nnns volume:125 pages:239-243 GBV_USEFLAG_U SYSFLAG_U GBV_ELV FID-BIODIV SSG-OLC-PHA SSG-OPC-GGO SSG-OPC-FOR GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 38.60 Bodenkunde: Allgemeines Geowissenschaften 48.32 Bodenkunde Bodenbewertung Land- und Forstwirtschaft AR 125 239-243
allfieldsSound	10.1016/j.soilbio.2018.07.020 doi (DE-627)ELV000314102 (ELSEVIER)S0038-0717(18)30248-7 DE-627 ger DE-627 rda eng 570 540 DE-600 BIODIV DE-30 fid 38.60 bkl 48.32 bkl Khdhiri, Mondher verfasserin aut 2018 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil. Metagenomic Metatranscriptomics Biogeochemistry Microbial ecology H Piché-Choquette, Sarah verfasserin (orcid)0000-0002-7447-1177 aut Tremblay, Julien verfasserin aut Tringe, Susannah G. verfasserin aut Constant, Philippe verfasserin aut Enthalten in Soil biology & biochemistry Amsterdam [u.a.] : Elsevier Science, 1969 125, Seite 239-243 Online-Ressource (DE-627)306591596 (DE-600)1498740-5 (DE-576)100704522 nnns volume:125 pages:239-243 GBV_USEFLAG_U SYSFLAG_U GBV_ELV FID-BIODIV SSG-OLC-PHA SSG-OPC-GGO SSG-OPC-FOR GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 38.60 Bodenkunde: Allgemeines Geowissenschaften 48.32 Bodenkunde Bodenbewertung Land- und Forstwirtschaft AR 125 239-243
language	English
source	Enthalten in Soil biology & biochemistry 125, Seite 239-243 volume:125 pages:239-243
sourceStr	Enthalten in Soil biology & biochemistry 125, Seite 239-243 volume:125 pages:239-243
format_phy_str_mv	Article
bklname	Bodenkunde: Allgemeines Bodenkunde Bodenbewertung
institution	findex.gbv.de
topic_facet	Metagenomic Metatranscriptomics Biogeochemistry Microbial ecology H
dewey-raw	570
isfreeaccess_bool	false
container_title	Soil biology & biochemistry
authorswithroles_txt_mv	Khdhiri, Mondher @@aut@@ Piché-Choquette, Sarah @@aut@@ Tremblay, Julien @@aut@@ Tringe, Susannah G. @@aut@@ Constant, Philippe @@aut@@
publishDateDaySort_date	2018-01-01T00:00:00Z
hierarchy_top_id	306591596
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id	ELV000314102
language_de	englisch
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author	Khdhiri, Mondher
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abstract	Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil.
abstractGer	Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil.
abstract_unstemmed	Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil.
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author2	Piché-Choquette, Sarah Tremblay, Julien Tringe, Susannah G. Constant, Philippe
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up_date	2024-07-06T17:32:50.008Z
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score	7.401143

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