Changes in abundance and composition of nitrifying communities in barley (Hordeum vulgare L.) rhizosphere and bulk soils over the growth period following combined biochar and urea amendment
To understand the effects of biochar and urea on soil N availability and plant growth, we conducted a pot experiment growing barley ( Hordeum vulgare L.) under six treatments: control (N0), soil with 30 g kg −1 biochar (N0B), soil with 0.23 g kg −1 urea (N1), soil with 0.23 g kg −1 urea and 30 g kg...
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| Veröffentlicht in: | Biology and fertility of soils 2020-02, Vol.56 (2), p.169-183 |
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| creator | Yu, Lu Homyak, Peter M. Kang, Xiaoxi Brookes, Philip C. Ye, Yikai Lin, Yeneng Muhammad, Afzal Xu, Jianming |
| description | To understand the effects of biochar and urea on soil N availability and plant growth, we conducted a pot experiment growing barley (
Hordeum vulgare
L.) under six treatments: control (N0), soil with 30 g kg
−1
biochar (N0B), soil with 0.23 g kg
−1
urea (N1), soil with 0.23 g kg
−1
urea and 30 g kg
−1
biochar (N1B), soil with 0.46 g kg
−1
urea (N2), and soil with 0.46 g kg
−1
urea and 30 g kg
−1
biochar (N2B). The nitrifying community abundance and compositions in rhizosphere and bulk soils were analyzed using quantitative polymerase chain reaction (qPCR) and amplicon-based Illumina Hiseq sequencing. Adding urea with biochar (N1B) produced the greatest increase in above- and belowground plant biomass, followed by doubling the amount of urea with biochar (N2B); both treatments raised pH (
p
|
| doi_str_mv | 10.1007/s00374-019-01410-6 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2400446414</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2400446414</sourcerecordid><originalsourceid>FETCH-LOGICAL-c352t-ba39cd3e8dfd623e91ec439073e125740b4a9712527bee38446aff90ea561ab73</originalsourceid><addsrcrecordid>eNp9kc1u1DAUhS0EEsPAC7CyxKYsUvyXOF6iEaVII3UDa8tJbiYujh3suNX03Xg33KYSEgsWV7Z1z3eudQ9C7ym5pITIT4kQLkVFqColKKmaF2hHBWcVka16iXaEyrZismGv0ZuUbgmhdUvVDv0-TMafIGHrsemyH4zvARs_4D7MS0h2tcHjMGJv12jHs_Wnx86cy9tuWGeigzO-uA5xgDzju-xOJgI-Xn7EcbIPIS0TxM20y-4nTsG6hMMdRLxOgE8x3K8TXiDaMOAxOBfun8d01kOBbOgnE58McgSDzQx-KLW-Ra9G4xK8ez736MfVl--H6-p48_Xb4fOx6nnN1qozXPUDh3YYh4ZxUBR6wRWRHCirpSCdMEqWK5MdAG-FaMw4KgKmbqjpJN-ji813ieFXhrTq2aYenDMeQk6aCUIKJMrG9-jDP9LbkKMvv9OMC1FLJRUpKrap-hhSijDqJdrZxLOmRD8mqrdEdUlUPyWqmwLxDUpFXEKLf63_Q_0BNjynZA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2344579790</pqid></control><display><type>article</type><title>Changes in abundance and composition of nitrifying communities in barley (Hordeum vulgare L.) rhizosphere and bulk soils over the growth period following combined biochar and urea amendment</title><source>SpringerLink Journals - AutoHoldings</source><creator>Yu, Lu ; Homyak, Peter M. ; Kang, Xiaoxi ; Brookes, Philip C. ; Ye, Yikai ; Lin, Yeneng ; Muhammad, Afzal ; Xu, Jianming</creator><creatorcontrib>Yu, Lu ; Homyak, Peter M. ; Kang, Xiaoxi ; Brookes, Philip C. ; Ye, Yikai ; Lin, Yeneng ; Muhammad, Afzal ; Xu, Jianming</creatorcontrib><description>To understand the effects of biochar and urea on soil N availability and plant growth, we conducted a pot experiment growing barley (
Hordeum vulgare
L.) under six treatments: control (N0), soil with 30 g kg
−1
biochar (N0B), soil with 0.23 g kg
−1
urea (N1), soil with 0.23 g kg
−1
urea and 30 g kg
−1
biochar (N1B), soil with 0.46 g kg
−1
urea (N2), and soil with 0.46 g kg
−1
urea and 30 g kg
−1
biochar (N2B). The nitrifying community abundance and compositions in rhizosphere and bulk soils were analyzed using quantitative polymerase chain reaction (qPCR) and amplicon-based Illumina Hiseq sequencing. Adding urea with biochar (N1B) produced the greatest increase in above- and belowground plant biomass, followed by doubling the amount of urea with biochar (N2B); both treatments raised pH (
p
< 0.001) and lowered extractable N in the rhizosphere (
p
< 0.05). N1B treatment produced the greatest increase in ammonia-oxidizing bacteria (AOB)
amoA
gene copies, presumably because the combined amendment raised soil pH, which favored AOB access to NH
4
+
. Nitrifier sequences were selected after blasting with reported nitrifiers in NCBI (similarity ≥ 97%).
Nitrosospira
dominated AOB communities during the plant seedling stage; however, during the mature stage,
Nitrosomonas
dominated over
Nitrosospira
and the nitrite-oxidizing bacteria (NOB) community became diverse. Redundancy analysis indicated that nitrifying community composition was affected by multiple soil properties, including N availability (i.e., exchangeable NH
4
+
and NO
3
−
) and soil chemistry (i.e., pH, dissolved organic C, and exchangeable base cations). Our research suggests a positive application of combining biochar with urea in improving N bioavailability and promoting plant growth in the acidic soil.</description><identifier>ISSN: 0178-2762</identifier><identifier>EISSN: 1432-0789</identifier><identifier>DOI: 10.1007/s00374-019-01410-6</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Abundance ; acid soils ; Acidic soils ; Agriculture ; Ammonia ; Ammonia-oxidizing bacteria ; ammonium ; AmoA gene ; Availability ; Bacteria ; Barley ; Bioavailability ; biochar ; Biomedical and Life Sciences ; Blasting ; Cation exchanging ; Cations ; Charcoal ; chemical bases ; Community composition ; community structure ; Composition ; dissolved organic carbon ; genes ; Hordeum vulgare ; Life Sciences ; nitrates ; Nitrification ; nitrifying bacteria ; nitrogen-fixing bacteria ; Nitrosomonas ; Nitrosospira ; Nucleotide sequence ; Organic chemistry ; Original Paper ; Oxidation ; PCR ; pH effects ; phytomass ; Plant biomass ; Plant communities ; Plant growth ; Polymerase chain reaction ; quantitative polymerase chain reaction ; Redundancy ; Rhizosphere ; Seedlings ; Soil analysis ; Soil chemistry ; Soil pH ; Soil properties ; Soil Science & Conservation ; Soils ; Urea</subject><ispartof>Biology and fertility of soils, 2020-02, Vol.56 (2), p.169-183</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2019</rights><rights>Biology and Fertility of Soils is a copyright of Springer, (2019). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c352t-ba39cd3e8dfd623e91ec439073e125740b4a9712527bee38446aff90ea561ab73</citedby><cites>FETCH-LOGICAL-c352t-ba39cd3e8dfd623e91ec439073e125740b4a9712527bee38446aff90ea561ab73</cites><orcidid>0000-0002-2954-9764</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00374-019-01410-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00374-019-01410-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids></links><search><creatorcontrib>Yu, Lu</creatorcontrib><creatorcontrib>Homyak, Peter M.</creatorcontrib><creatorcontrib>Kang, Xiaoxi</creatorcontrib><creatorcontrib>Brookes, Philip C.</creatorcontrib><creatorcontrib>Ye, Yikai</creatorcontrib><creatorcontrib>Lin, Yeneng</creatorcontrib><creatorcontrib>Muhammad, Afzal</creatorcontrib><creatorcontrib>Xu, Jianming</creatorcontrib><title>Changes in abundance and composition of nitrifying communities in barley (Hordeum vulgare L.) rhizosphere and bulk soils over the growth period following combined biochar and urea amendment</title><title>Biology and fertility of soils</title><addtitle>Biol Fertil Soils</addtitle><description>To understand the effects of biochar and urea on soil N availability and plant growth, we conducted a pot experiment growing barley (
Hordeum vulgare
L.) under six treatments: control (N0), soil with 30 g kg
−1
biochar (N0B), soil with 0.23 g kg
−1
urea (N1), soil with 0.23 g kg
−1
urea and 30 g kg
−1
biochar (N1B), soil with 0.46 g kg
−1
urea (N2), and soil with 0.46 g kg
−1
urea and 30 g kg
−1
biochar (N2B). The nitrifying community abundance and compositions in rhizosphere and bulk soils were analyzed using quantitative polymerase chain reaction (qPCR) and amplicon-based Illumina Hiseq sequencing. Adding urea with biochar (N1B) produced the greatest increase in above- and belowground plant biomass, followed by doubling the amount of urea with biochar (N2B); both treatments raised pH (
p
< 0.001) and lowered extractable N in the rhizosphere (
p
< 0.05). N1B treatment produced the greatest increase in ammonia-oxidizing bacteria (AOB)
amoA
gene copies, presumably because the combined amendment raised soil pH, which favored AOB access to NH
4
+
. Nitrifier sequences were selected after blasting with reported nitrifiers in NCBI (similarity ≥ 97%).
Nitrosospira
dominated AOB communities during the plant seedling stage; however, during the mature stage,
Nitrosomonas
dominated over
Nitrosospira
and the nitrite-oxidizing bacteria (NOB) community became diverse. Redundancy analysis indicated that nitrifying community composition was affected by multiple soil properties, including N availability (i.e., exchangeable NH
4
+
and NO
3
−
) and soil chemistry (i.e., pH, dissolved organic C, and exchangeable base cations). Our research suggests a positive application of combining biochar with urea in improving N bioavailability and promoting plant growth in the acidic soil.</description><subject>Abundance</subject><subject>acid soils</subject><subject>Acidic soils</subject><subject>Agriculture</subject><subject>Ammonia</subject><subject>Ammonia-oxidizing bacteria</subject><subject>ammonium</subject><subject>AmoA gene</subject><subject>Availability</subject><subject>Bacteria</subject><subject>Barley</subject><subject>Bioavailability</subject><subject>biochar</subject><subject>Biomedical and Life Sciences</subject><subject>Blasting</subject><subject>Cation exchanging</subject><subject>Cations</subject><subject>Charcoal</subject><subject>chemical bases</subject><subject>Community composition</subject><subject>community structure</subject><subject>Composition</subject><subject>dissolved organic carbon</subject><subject>genes</subject><subject>Hordeum vulgare</subject><subject>Life Sciences</subject><subject>nitrates</subject><subject>Nitrification</subject><subject>nitrifying bacteria</subject><subject>nitrogen-fixing bacteria</subject><subject>Nitrosomonas</subject><subject>Nitrosospira</subject><subject>Nucleotide sequence</subject><subject>Organic chemistry</subject><subject>Original Paper</subject><subject>Oxidation</subject><subject>PCR</subject><subject>pH effects</subject><subject>phytomass</subject><subject>Plant biomass</subject><subject>Plant communities</subject><subject>Plant growth</subject><subject>Polymerase chain reaction</subject><subject>quantitative polymerase chain reaction</subject><subject>Redundancy</subject><subject>Rhizosphere</subject><subject>Seedlings</subject><subject>Soil analysis</subject><subject>Soil chemistry</subject><subject>Soil pH</subject><subject>Soil properties</subject><subject>Soil Science & Conservation</subject><subject>Soils</subject><subject>Urea</subject><issn>0178-2762</issn><issn>1432-0789</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kc1u1DAUhS0EEsPAC7CyxKYsUvyXOF6iEaVII3UDa8tJbiYujh3suNX03Xg33KYSEgsWV7Z1z3eudQ9C7ym5pITIT4kQLkVFqColKKmaF2hHBWcVka16iXaEyrZismGv0ZuUbgmhdUvVDv0-TMafIGHrsemyH4zvARs_4D7MS0h2tcHjMGJv12jHs_Wnx86cy9tuWGeigzO-uA5xgDzju-xOJgI-Xn7EcbIPIS0TxM20y-4nTsG6hMMdRLxOgE8x3K8TXiDaMOAxOBfun8d01kOBbOgnE58McgSDzQx-KLW-Ra9G4xK8ez736MfVl--H6-p48_Xb4fOx6nnN1qozXPUDh3YYh4ZxUBR6wRWRHCirpSCdMEqWK5MdAG-FaMw4KgKmbqjpJN-ji813ieFXhrTq2aYenDMeQk6aCUIKJMrG9-jDP9LbkKMvv9OMC1FLJRUpKrap-hhSijDqJdrZxLOmRD8mqrdEdUlUPyWqmwLxDUpFXEKLf63_Q_0BNjynZA</recordid><startdate>20200201</startdate><enddate>20200201</enddate><creator>Yu, Lu</creator><creator>Homyak, Peter M.</creator><creator>Kang, Xiaoxi</creator><creator>Brookes, Philip C.</creator><creator>Ye, Yikai</creator><creator>Lin, Yeneng</creator><creator>Muhammad, Afzal</creator><creator>Xu, Jianming</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7T7</scope><scope>7UA</scope><scope>7X2</scope><scope>7XB</scope><scope>88I</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>F1W</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>H95</scope><scope>HCIFZ</scope><scope>L.G</scope><scope>LK8</scope><scope>M0K</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0002-2954-9764</orcidid></search><sort><creationdate>20200201</creationdate><title>Changes in abundance and composition of nitrifying communities in barley (Hordeum vulgare L.) rhizosphere and bulk soils over the growth period following combined biochar and urea amendment</title><author>Yu, Lu ; Homyak, Peter M. ; Kang, Xiaoxi ; Brookes, Philip C. ; Ye, Yikai ; Lin, Yeneng ; Muhammad, Afzal ; Xu, Jianming</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c352t-ba39cd3e8dfd623e91ec439073e125740b4a9712527bee38446aff90ea561ab73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Abundance</topic><topic>acid soils</topic><topic>Acidic soils</topic><topic>Agriculture</topic><topic>Ammonia</topic><topic>Ammonia-oxidizing bacteria</topic><topic>ammonium</topic><topic>AmoA gene</topic><topic>Availability</topic><topic>Bacteria</topic><topic>Barley</topic><topic>Bioavailability</topic><topic>biochar</topic><topic>Biomedical and Life Sciences</topic><topic>Blasting</topic><topic>Cation exchanging</topic><topic>Cations</topic><topic>Charcoal</topic><topic>chemical bases</topic><topic>Community composition</topic><topic>community structure</topic><topic>Composition</topic><topic>dissolved organic carbon</topic><topic>genes</topic><topic>Hordeum vulgare</topic><topic>Life Sciences</topic><topic>nitrates</topic><topic>Nitrification</topic><topic>nitrifying bacteria</topic><topic>nitrogen-fixing bacteria</topic><topic>Nitrosomonas</topic><topic>Nitrosospira</topic><topic>Nucleotide sequence</topic><topic>Organic chemistry</topic><topic>Original Paper</topic><topic>Oxidation</topic><topic>PCR</topic><topic>pH effects</topic><topic>phytomass</topic><topic>Plant biomass</topic><topic>Plant communities</topic><topic>Plant growth</topic><topic>Polymerase chain reaction</topic><topic>quantitative polymerase chain reaction</topic><topic>Redundancy</topic><topic>Rhizosphere</topic><topic>Seedlings</topic><topic>Soil analysis</topic><topic>Soil chemistry</topic><topic>Soil pH</topic><topic>Soil properties</topic><topic>Soil Science & Conservation</topic><topic>Soils</topic><topic>Urea</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Lu</creatorcontrib><creatorcontrib>Homyak, Peter M.</creatorcontrib><creatorcontrib>Kang, Xiaoxi</creatorcontrib><creatorcontrib>Brookes, Philip C.</creatorcontrib><creatorcontrib>Ye, Yikai</creatorcontrib><creatorcontrib>Lin, Yeneng</creatorcontrib><creatorcontrib>Muhammad, Afzal</creatorcontrib><creatorcontrib>Xu, Jianming</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Water Resources Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni 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Database</collection><collection>ProQuest Central Student</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>SciTech Premium Collection</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Biology and fertility of soils</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yu, Lu</au><au>Homyak, Peter M.</au><au>Kang, Xiaoxi</au><au>Brookes, Philip C.</au><au>Ye, Yikai</au><au>Lin, Yeneng</au><au>Muhammad, Afzal</au><au>Xu, Jianming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Changes in abundance and composition of nitrifying communities in barley (Hordeum vulgare L.) rhizosphere and bulk soils over the growth period following combined biochar and urea amendment</atitle><jtitle>Biology and fertility of soils</jtitle><stitle>Biol Fertil Soils</stitle><date>2020-02-01</date><risdate>2020</risdate><volume>56</volume><issue>2</issue><spage>169</spage><epage>183</epage><pages>169-183</pages><issn>0178-2762</issn><eissn>1432-0789</eissn><abstract>To understand the effects of biochar and urea on soil N availability and plant growth, we conducted a pot experiment growing barley (
Hordeum vulgare
L.) under six treatments: control (N0), soil with 30 g kg
−1
biochar (N0B), soil with 0.23 g kg
−1
urea (N1), soil with 0.23 g kg
−1
urea and 30 g kg
−1
biochar (N1B), soil with 0.46 g kg
−1
urea (N2), and soil with 0.46 g kg
−1
urea and 30 g kg
−1
biochar (N2B). The nitrifying community abundance and compositions in rhizosphere and bulk soils were analyzed using quantitative polymerase chain reaction (qPCR) and amplicon-based Illumina Hiseq sequencing. Adding urea with biochar (N1B) produced the greatest increase in above- and belowground plant biomass, followed by doubling the amount of urea with biochar (N2B); both treatments raised pH (
p
< 0.001) and lowered extractable N in the rhizosphere (
p
< 0.05). N1B treatment produced the greatest increase in ammonia-oxidizing bacteria (AOB)
amoA
gene copies, presumably because the combined amendment raised soil pH, which favored AOB access to NH
4
+
. Nitrifier sequences were selected after blasting with reported nitrifiers in NCBI (similarity ≥ 97%).
Nitrosospira
dominated AOB communities during the plant seedling stage; however, during the mature stage,
Nitrosomonas
dominated over
Nitrosospira
and the nitrite-oxidizing bacteria (NOB) community became diverse. Redundancy analysis indicated that nitrifying community composition was affected by multiple soil properties, including N availability (i.e., exchangeable NH
4
+
and NO
3
−
) and soil chemistry (i.e., pH, dissolved organic C, and exchangeable base cations). Our research suggests a positive application of combining biochar with urea in improving N bioavailability and promoting plant growth in the acidic soil.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s00374-019-01410-6</doi><tpages>15</tpages><orcidid>https://orcid.org/0000-0002-2954-9764</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0178-2762 |
| ispartof | Biology and fertility of soils, 2020-02, Vol.56 (2), p.169-183 |
| issn | 0178-2762 1432-0789 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2400446414 |
| source | SpringerLink Journals - AutoHoldings |
| subjects | Abundance acid soils Acidic soils Agriculture Ammonia Ammonia-oxidizing bacteria ammonium AmoA gene Availability Bacteria Barley Bioavailability biochar Biomedical and Life Sciences Blasting Cation exchanging Cations Charcoal chemical bases Community composition community structure Composition dissolved organic carbon genes Hordeum vulgare Life Sciences nitrates Nitrification nitrifying bacteria nitrogen-fixing bacteria Nitrosomonas Nitrosospira Nucleotide sequence Organic chemistry Original Paper Oxidation PCR pH effects phytomass Plant biomass Plant communities Plant growth Polymerase chain reaction quantitative polymerase chain reaction Redundancy Rhizosphere Seedlings Soil analysis Soil chemistry Soil pH Soil properties Soil Science & Conservation Soils Urea |
| title | Changes in abundance and composition of nitrifying communities in barley (Hordeum vulgare L.) rhizosphere and bulk soils over the growth period following combined biochar and urea amendment |
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