Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils
Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motili...
Saved in:
| Published in | The Science of the total environment Vol. 891; p. 164221 |
|---|---|
| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Netherlands
Elsevier B.V
15.09.2023
Elsevier |
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites.
[Display omitted]
•Motility and polymer utilization capacity were highly enriched in rhizosphere.•Motility was significantly correlated with the utilization of polymeric carbon.•These two genetic traits act as the key determinants for niche differentiation.•Motility-encoding rhizosphere MAGs were enriched in beneficial genetic traits.•Potential contribution of these MAGs to maize yield |
|---|---|
| AbstractList | Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites. Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites. [Display omitted] •Motility and polymer utilization capacity were highly enriched in rhizosphere.•Motility was significantly correlated with the utilization of polymeric carbon.•These two genetic traits act as the key determinants for niche differentiation.•Motility-encoding rhizosphere MAGs were enriched in beneficial genetic traits.•Potential contribution of these MAGs to maize yield Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites.Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites. |
| ArticleNumber | 164221 |
| Author | Liesack, Werner Luo, Yu Zhou, Xi Bei, Shuikuan Wu, Xingjie Pivato, Barbara He, Zhibin Peng, Jingjing Song, Chunxu Yuan, Huimin |
| Author_xml | – sequence: 1 givenname: Xingjie surname: Wu fullname: Wu, Xingjie organization: State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China – sequence: 2 givenname: Shuikuan surname: Bei fullname: Bei, Shuikuan organization: State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China – sequence: 3 givenname: Xi surname: Zhou fullname: Zhou, Xi organization: State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China – sequence: 4 givenname: Yu surname: Luo fullname: Luo, Yu organization: Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China – sequence: 5 givenname: Zhibin surname: He fullname: He, Zhibin organization: State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China – sequence: 6 givenname: Chunxu surname: Song fullname: Song, Chunxu organization: State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China – sequence: 7 givenname: Huimin surname: Yuan fullname: Yuan, Huimin email: hmyuan@cau.edu.cn organization: State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China – sequence: 8 givenname: Barbara surname: Pivato fullname: Pivato, Barbara organization: Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France – sequence: 9 givenname: Werner surname: Liesack fullname: Liesack, Werner organization: Research Group “Methanotrophic Bacteria and Environmental Genomics/Transcriptomics”, Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany – sequence: 10 givenname: Jingjing surname: Peng fullname: Peng, Jingjing email: jingjing.peng@cau.edu.cn organization: State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing 100193, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37263432$$D View this record in MEDLINE/PubMed https://hal.inrae.fr/hal-04208731$$DView record in HAL |
| BookMark | eNqNkTuPEzEUhS20iM0G_gJMCcUEP-ZhFxTRClikIBqoLY_nTuaGiR1sJyv49TjMkoKGdXPto-8cXfnckCvnHRDyitEVo6x5u1tFi8kncKcVp1ysWFNxzp6QBZOtKhnlzRVZUFrJUjWqvSY3Me5oPq1kz8i1aHkjKsEXJH2GZLbg_B5tgS7idkwxX5Ivsgopq4OxyYdY9AFP6LZFl98Q0EyFQztC0eMwQACX0CT0rugg3QPkeZy-F8b1RRjxl4-HMUNF9DjF5-TpYKYILx7mknz78P7r7V25-fLx0-16U9pKyFRywfq6rlUruanamioKAwxUSmlsB3UDfS_UUKvO1FaJVmQh_0EHYCpg0nCxJG_m3NFM-hBwb8JP7Q3qu_VGnzVacSpbwU4ss69n9hD8jyPEpPcYLUyTceCPUXNZKalqUdFHoJyLvHROXpKXD-ix20N_WeJvARloZ8AGH2OA4YIwqs9V652-VK3PVeu56ux8948zY38aSMHg9Aj_evZDbuCEEM4cOAs9BrBJ9x7_m_Eb2bXMDQ |
| CitedBy_id | crossref_primary_10_1038_s41545_024_00352_3 crossref_primary_10_1007_s11104_024_06847_9 crossref_primary_10_1016_j_ecoinf_2024_102817 crossref_primary_10_1016_j_isci_2024_110890 crossref_primary_10_1093_ismejo_wrae067 crossref_primary_10_1007_s00253_023_12977_4 crossref_primary_10_1016_j_jwpe_2023_104301 |
| Cites_doi | 10.1016/j.soilbio.2019.01.023 10.1007/s11103-016-0432-4 10.1111/nph.17057 10.1038/s41396-018-0234-6 10.1038/ismej.2014.17 10.1111/nph.16171 10.1111/1462-2920.13288 10.1038/nmeth.3176 10.1016/j.geoderma.2014.10.016 10.1016/S0378-1119(98)00160-7 10.1128/aem.58.4.1153-1158.1992 10.1007/s11104-021-05036-2 10.1186/s12864-022-08738-8 10.1016/j.scitotenv.2021.147329 10.1016/j.scitotenv.2020.139710 10.1111/j.1462-2920.2010.02291.x 10.1016/j.pbi.2021.102025 10.1038/s41579-021-00626-4 10.1093/bioinformatics/btz848 10.1038/s43705-022-00100-z 10.1186/s40168-019-0756-9 10.1038/s41467-021-24005-y 10.1038/s41396-021-01125-3 10.1186/s40168-018-0541-1 10.1093/bioinformatics/btu170 10.1111/j.2517-6161.1995.tb02031.x 10.1038/s41396-022-01277-w 10.1093/nar/gkw290 10.3390/microorganisms10081564 10.1016/j.scitotenv.2021.152896 10.1038/s43017-022-00366-w 10.1128/AEM.72.5.3429-3434.2006 10.1093/femsre/fux052 10.1038/nrmicro.2017.87 10.1128/msystems.01107-21 10.1094/MPMI-20-5-0526 10.1038/s41579-019-0182-9 10.1038/ncomms5950 10.1038/s41564-018-0129-3 10.1073/pnas.1414592112 10.3390/biology10060475 10.1186/s40168-018-0546-9 10.1038/ismej.2013.163 10.1093/bioinformatics/btv033 10.1016/j.soilbio.2018.05.006 10.1007/s11104-021-04851-x 10.1038/s41396-019-0567-9 10.1128/mBio.02527-14 10.1038/ismej.2013.254 10.1016/j.soilbio.2021.108364 10.1371/journal.pcbi.1004957 10.1186/1471-2105-11-119 10.1093/nar/gkab1045 10.1101/gr.186072.114 10.1111/nph.16890 10.1016/j.bcab.2019.101326 10.1093/nar/28.1.27 10.1111/gcb.15439 10.1111/j.1365-3040.2009.01926.x 10.1016/j.soilbio.2020.108071 10.1038/nbt.3893 10.1038/s41579-020-0412-1 10.3390/ijms22136655 |
| ContentType | Journal Article |
| Copyright | 2023 Elsevier B.V. Copyright © 2023 Elsevier B.V. All rights reserved. Distributed under a Creative Commons Attribution 4.0 International License |
| Copyright_xml | – notice: 2023 Elsevier B.V. – notice: Copyright © 2023 Elsevier B.V. All rights reserved. – notice: Distributed under a Creative Commons Attribution 4.0 International License |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 7S9 L.6 1XC |
| DOI | 10.1016/j.scitotenv.2023.164221 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic AGRICOLA AGRICOLA - Academic Hyper Article en Ligne (HAL) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic AGRICOLA AGRICOLA - Academic |
| DatabaseTitleList | AGRICOLA MEDLINE - Academic MEDLINE |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Public Health Biology Environmental Sciences |
| EISSN | 1879-1026 |
| ExternalDocumentID | oai_HAL_hal_04208731v1 37263432 10_1016_j_scitotenv_2023_164221 S0048969723028425 |
| Genre | Journal Article |
| GroupedDBID | --- --K --M .~1 0R~ 1B1 1RT 1~. 1~5 4.4 457 4G. 5VS 7-5 71M 8P~ 9JM AABNK AACTN AAEDT AAEDW AAHBH AAIKJ AAKOC AALRI AAOAW AAQFI AATTM AAXKI AAXUO ABFNM ABFYP ABJNI ABLST ABMAC ACDAQ ACGFS ACRLP ADBBV ADEZE AEBSH AEIPS AEKER AENEX AFJKZ AFTJW AFXIZ AGUBO AGYEJ AHEUO AHHHB AIEXJ AIKHN AITUG AKIFW AKRWK ALMA_UNASSIGNED_HOLDINGS AMRAJ ANKPU AXJTR BKOJK BLECG BLXMC BNPGV CS3 DU5 EBS EFJIC EO8 EO9 EP2 EP3 F5P FDB FIRID FNPLU FYGXN G-Q GBLVA IHE J1W K-O KCYFY KOM LY9 M41 MO0 N9A O-L O9- OAUVE OZT P-8 P-9 P2P PC. Q38 RNS ROL RPZ SCU SDF SDG SDP SES SPCBC SSH SSJ SSZ T5K ~02 ~G- ~KM 53G AAQXK AAYJJ AAYWO AAYXX ABEFU ABWVN ABXDB ACRPL ACVFH ADCNI ADMUD ADNMO ADXHL AEGFY AEUPX AFPUW AGCQF AGHFR AGQPQ AGRNS AIGII AIIUN AKBMS AKYEP APXCP ASPBG AVWKF AZFZN CITATION EJD FEDTE FGOYB G-2 HMC HVGLF HZ~ R2- RIG SEN SEW WUQ XPP ZXP ZY4 AFKWA AJOXV AMFUW CGR CUY CVF ECM EIF NPM 7X8 EFKBS 7S9 L.6 1XC UMC |
| ID | FETCH-LOGICAL-c438t-231d5559782a475090efef0888acbe56edd39f59ba5c93736ed221beea4e18a23 |
| IEDL.DBID | .~1 |
| ISSN | 0048-9697 1879-1026 |
| IngestDate | Fri May 09 12:05:53 EDT 2025 Fri Jul 11 11:07:54 EDT 2025 Tue Aug 05 10:37:04 EDT 2025 Wed Feb 19 02:23:41 EST 2025 Thu Apr 24 23:07:22 EDT 2025 Tue Jul 01 02:08:52 EDT 2025 Sun Apr 06 06:54:27 EDT 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Keywords | Rhizosphere Metagenomics Genomes Bacterial motility Microbiome |
| Language | English |
| License | Copyright © 2023 Elsevier B.V. All rights reserved. Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c438t-231d5559782a475090efef0888acbe56edd39f59ba5c93736ed221beea4e18a23 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ORCID | 0000-0003-4500-8834 |
| PMID | 37263432 |
| PQID | 2822378287 |
| PQPubID | 23479 |
| ParticipantIDs | hal_primary_oai_HAL_hal_04208731v1 proquest_miscellaneous_2849895340 proquest_miscellaneous_2822378287 pubmed_primary_37263432 crossref_primary_10_1016_j_scitotenv_2023_164221 crossref_citationtrail_10_1016_j_scitotenv_2023_164221 elsevier_sciencedirect_doi_10_1016_j_scitotenv_2023_164221 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2023-09-15 |
| PublicationDateYYYYMMDD | 2023-09-15 |
| PublicationDate_xml | – month: 09 year: 2023 text: 2023-09-15 day: 15 |
| PublicationDecade | 2020 |
| PublicationPlace | Netherlands |
| PublicationPlace_xml | – name: Netherlands |
| PublicationTitle | The Science of the total environment |
| PublicationTitleAlternate | Sci Total Environ |
| PublicationYear | 2023 |
| Publisher | Elsevier B.V Elsevier |
| Publisher_xml | – name: Elsevier B.V – name: Elsevier |
| References | Parks, Imelfort, Skennerton, Hugenholtz, Tyson (bb0215) 2015; 25 Martinez-Granero, Rivilla, Martin (bb0165) 2006; 72 Uritskiy, DiRuggiero, Taylor (bb0290) 2018; 6 Hyatt, Chen, Locascio, Land, Larimer, Hauser (bb0125) 2010; 11 Edwards, Johnson, Santos-Medellín, Lurie, Podishetty, Bhatnagar, Eisen, Sundaresan (bb0080) 2015; 112 Oksanen, Blanchet, Kindt, Legendre, Minchin, O’hara, Wagner (bb0205) 2013 Yergeau, Sanschagrin, Maynard, St-Arnaud, Greer (bb0330) 2014; 8 Ofek-Lalzar, Sela, Goldman-Voronov, Green, Hadar, Minz (bb0200) 2014; 5 Peng, Wegner, Bei, Liu, Liesack (bb0220) 2018; 6 Schmidt, Kent, Brisson, Gaudin (bb0250) 2019; 7 Archer (bb0010) 2013 Liu, Li, Carvalhais, Percy, Prakash, Schenk, Singh (bb0150) 2021; 229 Zarraonaindia, Owens, Weisenhorn, West, Hampton-Marcell, Lax, Bokulich, Mills, Martin, Taghavi, van der Lelie, Gilbert (bb0335) 2015; 6 Wu, Liu, Shang, Liu, Liesack, Cui, Peng, Zhang (bb0310) 2022; 470 Kanehisa, Goto (bb0130) 2000; 28 Naik, Mishra, Srichandan, Singh, Sarangi (bb0195) 2019; 21 Fierer (bb0100) 2017; 15 Wu, Peng, Liu, Bei, Rensing, Li, Yuan, Liesack, Zhang, Cui (bb0305) 2021; 785 Colin, Ni, Laganenka, Sourjik (bb0060) 2021; fuab038 Letunic, Bork (bb0135) 2016; 44 Li, de Jonge, Liu, Jiang, Friman, Pieterse, Bakker, Jousset (bb0145) 2021; 12 Wei, Hu, Cai, Yao, Ye, Sun, Veresoglou, Li, Zhu, Guggenberger, Chen, Su, Li, Wu, Ge (bb0300) 2021; 161 Pandey, Kumar, Kaviraj, Minick, Mishra, Singh (bb0210) 2020; 738 Sun, Xu, Xie, Hesselberg-Thomsen, Tan, Zheng, Strube, Dragos, Shen, Zhang, Kovacs (bb0275) 2022; 16 Huson, Beier, Flade, Górska, El-Hadidi, Mitra, Ruscheweyh, Tappu (bb0120) 2016; 12 Abdallah, Wegner, Liesack (bb0005) 2019; 132 Wu, Cui, Peng, Zhang, Liesack (bb0315) 2022; 2 Dharmatilake, Bauer (bb0070) 1992; 58 Song, Jin, Raaijmakers (bb0265) 2021; 62 Shen, Geng, Li, Lu (bb0255) 2022; 815 Emmett, Buckley, Drinkwater (bb0085) 2020; 225 Barahona, Navazo, Yousef-Coronado, Aguirre, Martinez-Granero, Espinosa-Urgel, Martin, Rivilla (bb0020) 2010; 12 Mendes, Mendes, Raaijmakers, Tsai (bb0185) 2018; 12 Bolger, Lohse, Usadel (bb0035) 2014; 30 Li, Liu, Luo, Sadakane, Lam (bb0140) 2015; 31 Dai, Liu, Chen, Chen, Wang, Ai, Wei, Li, Ma, Tang, Brookes, Xu (bb0065) 2020; 14 Mendes, Kuramae, Navarrete, van Veen, Tsai (bb0180) 2014; 8 Matilla, Krell (bb0175) 2018; 42 Raina, Fernandez, Lambert, Stocker, Seymour (bb0230) 2019; 17 Drula, Garron, Dogan, Lombard, Henrissat, Terrapon (bb0075) 2022; 50 Hartmann, Six (bb0115) 2023; 4 Xiong, Zhu, Wang, Singh, Han, Shen, Li, Wang, Wu, Ge, Zhang, He (bb0325) 2021; 229 Engelhardt, Patko, Liu, Mimault, de Las, George, MacDonald, Ptashnyk, Sukhodub, Stanley-Wall, Holden, Daniell, Dupuy (bb0090) 2022; 16 Sourjik, Sterr, Platzer, Bos, Haslbeck, Schmitt (bb0270) 1998; 223 Trivedi, Leach, Tringe, Sa, Singh (bb0285) 2021; 18 Scharf, Hynes, Alexandre (bb0245) 2016; 90 Wadhwa, Berg (bb0295) 2022; 20 Mushinski, Payne, Raff, Craig, Pusede, Rusch, White, Phillips (bb0190) 2020; 27 Makino, Nakai, Yoneda, Toyama, Tanaka, Meng, Mori, Ike, Morikawa, Kamagata, Tamaki (bb0160) 2022; 10 Mason, Scott, Gonzalez, Robbins-Pianka, Baelum, Kimbrel, Bouskill, Prestat, Borglin, Joyner, Fortney, Jurelevicius, Stringfellow, Alvarez-Cohen, Hazen, Knight, Gilbert, Jansson (bb0170) 2014; 8 Boehm, Hurek, Reinhold-Hurek (bb0030) 2007; 20 Hartman, van der Heijden, Wittwer, Banerjee, Walser, Schlaeppi (bb0110) 2018; 6 Chaumeil, Mussig, Hugenholtz, Parks (bb0055) 2019; 36 Song, Kidarsa, van de Mortel, Loper, Raaijmakers (bb0260) 2016; 18 Wu, Rensing, Han, Xiao, Dai, Tang, Liesack, Peng, Cui, Zhang (bb0320) 2022; 7 Feng, Fu, Hou, Lv, Zhang, Liu, Xu, Miao, Krell, Shen, Zhang (bb0095) 2021; 22 Putz, Schleusner, Rütting, Hallin (bb0225) 2018; 123 Badri, Vivanco (bb0015) 2009; 32 Santoyo, Urtis-Flores, Loeza-Lara, Orozco-Mosqueda, Glick (bb0240) 2021; 10 Liu, Ling, Luo, Guo, Zhu, Xu, Guo (bb0155) 2021; 152 Bowers, Kyrpides, Stepanauskas, Harmon-Smith, Doud, Reddy, Schulz, Jarett, Rivers, Eloe-Fadrosh, Tringe, Ivanova, Copeland, Clum, Becraft, Malmstrom, Birren, Podar, Bork, Weinstock, Garrity, Dodsworth, Yooseph, Sutton, Glockner, Gilbert, Nelson, Hallam, Jungbluth, Ettema, Tighe, Konstantinidis, Liu, Baker, Rattei, Eisen, Hedlund, McMahon, Fierer, Knight, Finn, Cochrane, Karsch-Mizrachi, Tyson, Rinke, Lapidus, Meyer, Yilmaz, Parks, Eren, Schriml, Banfield, Hugenholtz, Woyke (bb0045) 2017; 35 Zhalnina, Louie, Hao, Mansoori, Da Rocha, Shi, Cho, Karaoz, Loqué, Bowen, Firestone, Northen, Brodie (bb0340) 2018; 3 Fraser, Lynch, Entz, Dunfield (bb0105) 2015; 257 Sanchez, Trinchera, Russolillo (bb0235) 2014 Benjamini, Hochberg (bb0025) 1995; 57 Buchfink, Xie, Huson (bb0050) 2015; 12 Sun, Tian, Chang, Shi, Zhang, Xie, Cai, Chen, Kuramae, van Veen, Li, Tran, Tian (bb0280) 2021; 466 Boss, Wanees, Zaslow, Normile, Izquierdo (bb0040) 2022; 23 Boehm (10.1016/j.scitotenv.2023.164221_bb0030) 2007; 20 Shen (10.1016/j.scitotenv.2023.164221_bb0255) 2022; 815 Buchfink (10.1016/j.scitotenv.2023.164221_bb0050) 2015; 12 Mushinski (10.1016/j.scitotenv.2023.164221_bb0190) 2020; 27 Pandey (10.1016/j.scitotenv.2023.164221_bb0210) 2020; 738 Huson (10.1016/j.scitotenv.2023.164221_bb0120) 2016; 12 Raina (10.1016/j.scitotenv.2023.164221_bb0230) 2019; 17 Scharf (10.1016/j.scitotenv.2023.164221_bb0245) 2016; 90 Edwards (10.1016/j.scitotenv.2023.164221_bb0080) 2015; 112 Zarraonaindia (10.1016/j.scitotenv.2023.164221_bb0335) 2015; 6 Matilla (10.1016/j.scitotenv.2023.164221_bb0175) 2018; 42 Engelhardt (10.1016/j.scitotenv.2023.164221_bb0090) 2022; 16 Wadhwa (10.1016/j.scitotenv.2023.164221_bb0295) 2022; 20 Archer (10.1016/j.scitotenv.2023.164221_bb0010) 2013 Wu (10.1016/j.scitotenv.2023.164221_bb0320) 2022; 7 Martinez-Granero (10.1016/j.scitotenv.2023.164221_bb0165) 2006; 72 Li (10.1016/j.scitotenv.2023.164221_bb0140) 2015; 31 Hartman (10.1016/j.scitotenv.2023.164221_bb0110) 2018; 6 Hyatt (10.1016/j.scitotenv.2023.164221_bb0125) 2010; 11 Abdallah (10.1016/j.scitotenv.2023.164221_bb0005) 2019; 132 Zhalnina (10.1016/j.scitotenv.2023.164221_bb0340) 2018; 3 Sun (10.1016/j.scitotenv.2023.164221_bb0280) 2021; 466 Fierer (10.1016/j.scitotenv.2023.164221_bb0100) 2017; 15 Colin (10.1016/j.scitotenv.2023.164221_bb0060) 2021; fuab038 Uritskiy (10.1016/j.scitotenv.2023.164221_bb0290) 2018; 6 Drula (10.1016/j.scitotenv.2023.164221_bb0075) 2022; 50 Feng (10.1016/j.scitotenv.2023.164221_bb0095) 2021; 22 Putz (10.1016/j.scitotenv.2023.164221_bb0225) 2018; 123 Mendes (10.1016/j.scitotenv.2023.164221_bb0180) 2014; 8 Boss (10.1016/j.scitotenv.2023.164221_bb0040) 2022; 23 Wu (10.1016/j.scitotenv.2023.164221_bb0315) 2022; 2 Sourjik (10.1016/j.scitotenv.2023.164221_bb0270) 1998; 223 Fraser (10.1016/j.scitotenv.2023.164221_bb0105) 2015; 257 Santoyo (10.1016/j.scitotenv.2023.164221_bb0240) 2021; 10 Hartmann (10.1016/j.scitotenv.2023.164221_bb0115) 2023; 4 Sanchez (10.1016/j.scitotenv.2023.164221_bb0235) 2014 Liu (10.1016/j.scitotenv.2023.164221_bb0150) 2021; 229 Wu (10.1016/j.scitotenv.2023.164221_bb0310) 2022; 470 Dai (10.1016/j.scitotenv.2023.164221_bb0065) 2020; 14 Bowers (10.1016/j.scitotenv.2023.164221_bb0045) 2017; 35 Liu (10.1016/j.scitotenv.2023.164221_bb0155) 2021; 152 Emmett (10.1016/j.scitotenv.2023.164221_bb0085) 2020; 225 Ofek-Lalzar (10.1016/j.scitotenv.2023.164221_bb0200) 2014; 5 Xiong (10.1016/j.scitotenv.2023.164221_bb0325) 2021; 229 Benjamini (10.1016/j.scitotenv.2023.164221_bb0025) 1995; 57 Chaumeil (10.1016/j.scitotenv.2023.164221_bb0055) 2019; 36 Song (10.1016/j.scitotenv.2023.164221_bb0265) 2021; 62 Trivedi (10.1016/j.scitotenv.2023.164221_bb0285) 2021; 18 Naik (10.1016/j.scitotenv.2023.164221_bb0195) 2019; 21 Dharmatilake (10.1016/j.scitotenv.2023.164221_bb0070) 1992; 58 Song (10.1016/j.scitotenv.2023.164221_bb0260) 2016; 18 Kanehisa (10.1016/j.scitotenv.2023.164221_bb0130) 2000; 28 Badri (10.1016/j.scitotenv.2023.164221_bb0015) 2009; 32 Wu (10.1016/j.scitotenv.2023.164221_bb0305) 2021; 785 Letunic (10.1016/j.scitotenv.2023.164221_bb0135) 2016; 44 Schmidt (10.1016/j.scitotenv.2023.164221_bb0250) 2019; 7 Parks (10.1016/j.scitotenv.2023.164221_bb0215) 2015; 25 Bolger (10.1016/j.scitotenv.2023.164221_bb0035) 2014; 30 Yergeau (10.1016/j.scitotenv.2023.164221_bb0330) 2014; 8 Li (10.1016/j.scitotenv.2023.164221_bb0145) 2021; 12 Peng (10.1016/j.scitotenv.2023.164221_bb0220) 2018; 6 Mason (10.1016/j.scitotenv.2023.164221_bb0170) 2014; 8 Oksanen (10.1016/j.scitotenv.2023.164221_bb0205) 2013 Mendes (10.1016/j.scitotenv.2023.164221_bb0185) 2018; 12 Sun (10.1016/j.scitotenv.2023.164221_bb0275) 2022; 16 Wei (10.1016/j.scitotenv.2023.164221_bb0300) 2021; 161 Barahona (10.1016/j.scitotenv.2023.164221_bb0020) 2010; 12 Makino (10.1016/j.scitotenv.2023.164221_bb0160) 2022; 10 |
| References_xml | – volume: 257 start-page: 115 year: 2015 end-page: 122 ident: bb0105 article-title: Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial publication-title: Geoderma – volume: 223 start-page: 283 year: 1998 end-page: 290 ident: bb0270 article-title: Mapping of 41 chemotaxis, flagellar and motility genes to a single region of the Sinorhizobium meliloti chromosome publication-title: Gene – volume: 6 year: 2015 ident: bb0335 article-title: The soil microbiome influences grapevine-associated microbiota publication-title: mBio – volume: 11 start-page: 119 year: 2010 ident: bb0125 article-title: Prodigal: prokaryotic gene recognition and translation initiation site identification publication-title: BMC Bioinform. – volume: 229 start-page: 2873 year: 2021 end-page: 2885 ident: bb0150 article-title: Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogens publication-title: New Phytol. – volume: 10 start-page: 475 year: 2021 ident: bb0240 article-title: Rhizosphere colonization determinants by plant growth-promoting rhizobacteria (PGPR) publication-title: Biology – year: 2013 ident: bb0010 article-title: rfPermute: Estimate Permutation p-values for Random Forest Importance Metrics. R Package Version 1.5. 2 – volume: 4 start-page: 4 year: 2023 end-page: 18 ident: bb0115 article-title: Soil structure and microbiome functions in agroecosystems publication-title: Nat. Rev. Earth Environ. – volume: 57 start-page: 289 year: 1995 end-page: 300 ident: bb0025 article-title: Controlling the false discovery rate: a practical and powerful approach to multiple testing publication-title: J. R. Stat. Soc. – volume: 90 start-page: 549 year: 2016 end-page: 559 ident: bb0245 article-title: Chemotaxis signaling systems in model beneficial plant–bacteria associations publication-title: Plant Mol. Biol. – volume: 785 year: 2021 ident: bb0305 article-title: Metagenomic insights into nitrogen and phosphorus cycling at the soil aggregate scale driven by organic material amendments publication-title: Sci. Total Environ. – volume: 22 start-page: 6655 year: 2021 ident: bb0095 article-title: Chemotaxis of beneficial rhizobacteria to root exudates: the first step towards root–microbe rhizosphere interactions publication-title: Int. J. Mol. Sci. – volume: 58 start-page: 1153 year: 1992 end-page: 1158 ident: bb0070 article-title: Chemotaxis of rhizobium meliloti towards nodulation gene-inducing compounds from alfalfa roots publication-title: Appl. Environ. Microbiol. – volume: 30 start-page: 2114 year: 2014 end-page: 2120 ident: bb0035 article-title: Trimmomatic: a flexible trimmer for Illumina sequence data publication-title: Bioinformatics – start-page: 321 year: 2013 end-page: 326 ident: bb0205 article-title: Community Ecology Package. R Package Version 2 – volume: 12 start-page: 3185 year: 2010 end-page: 3195 ident: bb0020 article-title: Efficient rhizosphere colonization by Pseudomonas fluorescens f113 mutants unable to form biofilms on abiotic surfaces publication-title: Environ. Microbiol. – volume: 23 start-page: 508 year: 2022 ident: bb0040 article-title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata publication-title: BMC Genomics – volume: 28 start-page: 27 year: 2000 end-page: 30 ident: bb0130 article-title: KEGG: kyoto encyclopedia of genes and genomes publication-title: Nucleic Acids Res. – volume: 20 start-page: 526 year: 2007 end-page: 533 ident: bb0030 article-title: Twitching motility is essential for endophytic rice colonization by the N2-fixing endophyte Azoarcus sp. strain BH72 publication-title: Mol. Plant-Microbe Interact. – volume: 738 year: 2020 ident: bb0210 article-title: DNRA: a short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems publication-title: Sci. Total Environ. – volume: 14 start-page: 757 year: 2020 end-page: 770 ident: bb0065 article-title: Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems publication-title: ISME J. – volume: 225 start-page: 960 year: 2020 end-page: 973 ident: bb0085 article-title: Plant growth rate and nitrogen uptake shape rhizosphere bacterial community composition and activity in an agricultural field publication-title: New Phytol. – volume: 12 year: 2016 ident: bb0120 article-title: MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data publication-title: PLoS Comput. Biol. – volume: 27 start-page: 1068 year: 2020 end-page: 1082 ident: bb0190 article-title: Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests publication-title: Glob. Chang. Biol. – volume: 2 start-page: 1 year: 2022 end-page: 4 ident: bb0315 article-title: Genome-resolved metagenomics identifies the particular genetic traits of phosphate-solubilizing bacteria in agricultural soil publication-title: ISME Commun. – volume: 50 start-page: 571 year: 2022 end-page: 577 ident: bb0075 article-title: The carbohydrate-active enzyme database: functions and literature publication-title: Nucleic Acids Res. – volume: 21 year: 2019 ident: bb0195 article-title: Plant growth promoting microbes: potential link to sustainable agriculture and environment publication-title: Biocatal. Agric. Biotechnol. – volume: 123 start-page: 97 year: 2018 end-page: 104 ident: bb0225 article-title: Relative abundance of denitrifying and DNRA bacteria and their activity determine nitrogen retention or loss in agricultural soil publication-title: Soil Biol. Biochem. – volume: 3 start-page: 470 year: 2018 end-page: 480 ident: bb0340 article-title: Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly publication-title: Nat. Microbiol. – volume: fuab038 year: 2021 ident: bb0060 article-title: Multiple functions of flagellar motility and chemotaxis in bacterial physiology publication-title: FEMS Microbiol. Rev. – volume: 6 start-page: 1 year: 2018 end-page: 14 ident: bb0110 article-title: Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming publication-title: Microbiome – volume: 8 start-page: 344 year: 2014 end-page: 358 ident: bb0330 article-title: Microbial expression profiles in the rhizosphere of willows depend on soil contamination publication-title: ISME J. – volume: 132 start-page: 131 year: 2019 end-page: 142 ident: bb0005 article-title: Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life publication-title: Soil Biol. Biochem. – volume: 10 start-page: 1564 year: 2022 ident: bb0160 article-title: Isolation of aquatic plant growth-promoting bacteria for the floating plant duckweed (Lemna minor) publication-title: Microorganisms – volume: 25 start-page: 1043 year: 2015 end-page: 1055 ident: bb0215 article-title: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes publication-title: Genome Res. – volume: 20 start-page: 161 year: 2022 end-page: 173 ident: bb0295 article-title: Bacterial motility: machinery and mechanisms publication-title: Nat. Rev. Microbiol. – volume: 161 year: 2021 ident: bb0300 article-title: Organic phosphorus availability shapes the diversity of phoD-harboring bacteria in agricultural soil publication-title: Soil Biol. Biochem. – year: 2014 ident: bb0235 article-title: Introduction to the R Package plspm – volume: 44 start-page: 242 year: 2016 end-page: 245 ident: bb0135 article-title: Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees publication-title: Nucleic Acids Res. – volume: 36 start-page: 1925 year: 2019 end-page: 1927 ident: bb0055 article-title: GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database publication-title: Bioinformatics – volume: 112 start-page: 911 year: 2015 end-page: 920 ident: bb0080 article-title: Structure, variation, and assembly of the root-associated microbiomes of rice publication-title: Proc. Natl. Acad. Sci. – volume: 62 year: 2021 ident: bb0265 article-title: Designing a home for beneficial plant microbiomes publication-title: Curr. Opin. Plant Biol. – volume: 815 year: 2022 ident: bb0255 article-title: Evaluation of phosphorus removal in floating treatment wetlands: new insights in non-reactive phosphorus publication-title: Sci. Total Environ. – volume: 152 year: 2021 ident: bb0155 article-title: Active phoD-harboring bacteria are enriched by long-term organic fertilization publication-title: Soil Biol. Biochem. – volume: 229 start-page: 1091 year: 2021 end-page: 1104 ident: bb0325 article-title: Host selection shapes crop microbiome assembly and network complexity publication-title: New Phytol. – volume: 7 year: 2022 ident: bb0320 article-title: Genome-resolved metagenomics reveals distinct phosphorus acquisition strategies between soil microbiomes publication-title: mSystems – volume: 470 start-page: 21 year: 2022 end-page: 34 ident: bb0310 article-title: Peat-vermiculite alters microbiota composition towards increased soil fertility and crop productivity publication-title: Plant Soil – volume: 15 start-page: 579 year: 2017 end-page: 590 ident: bb0100 article-title: Embracing the unknown: disentangling the complexities of the soil microbiome publication-title: Nat. Rev. Microbiol. – volume: 8 start-page: 1464 year: 2014 end-page: 1475 ident: bb0170 article-title: Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill publication-title: ISME J. – volume: 5 start-page: 4950 year: 2014 ident: bb0200 article-title: Niche and host-associated functional signatures of the root surface microbiome publication-title: Nat. Commun. – volume: 466 start-page: 81 year: 2021 end-page: 99 ident: bb0280 article-title: Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems publication-title: Plant Soil – volume: 31 start-page: 1674 year: 2015 end-page: 1676 ident: bb0140 article-title: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph publication-title: Bioinformatics – volume: 18 start-page: 3453 year: 2016 end-page: 3465 ident: bb0260 article-title: Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility publication-title: Environ. Microbiol. – volume: 12 start-page: 3038 year: 2018 end-page: 3042 ident: bb0185 article-title: Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean publication-title: ISME J. – volume: 35 start-page: 725 year: 2017 end-page: 731 ident: bb0045 article-title: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea publication-title: Nat. Biotechnol. – volume: 12 start-page: 59 year: 2015 end-page: 60 ident: bb0050 article-title: Fast and sensitive protein alignment using DIAMOND publication-title: Nat. Methods – volume: 8 start-page: 1577 year: 2014 end-page: 1587 ident: bb0180 article-title: Taxonomical and functional microbial community selection in soybean rhizosphere publication-title: ISME J. – volume: 42 start-page: fux052 year: 2018 ident: bb0175 article-title: The effect of bacterial chemotaxis on host infection and pathogenicity publication-title: FEMS Microbiol. Rev. – volume: 18 start-page: 607 year: 2021 end-page: 621 ident: bb0285 article-title: Plant-microbiome interactions: from community assembly to plant health publication-title: Nat. Rev. Microbiol. – volume: 6 start-page: 1 year: 2018 end-page: 16 ident: bb0220 article-title: Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil publication-title: Microbiome – volume: 16 start-page: 2337 year: 2022 end-page: 2347 ident: bb0090 article-title: Novel form of collective movement by soil bacteria publication-title: ISME J. – volume: 32 start-page: 666 year: 2009 end-page: 681 ident: bb0015 article-title: Regulation and function of root exudates publication-title: Plant Cell Environ. – volume: 7 start-page: 1 year: 2019 end-page: 18 ident: bb0250 article-title: Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling publication-title: Microbiome – volume: 12 start-page: 3829 year: 2021 ident: bb0145 article-title: Rapid evolution of bacterial mutualism in the plant rhizosphere publication-title: Nat. Commun. – volume: 6 start-page: 1 year: 2018 end-page: 13 ident: bb0290 article-title: MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis publication-title: Microbiome – volume: 17 start-page: 284 year: 2019 end-page: 294 ident: bb0230 article-title: The role of microbial motility and chemotaxis in symbiosis publication-title: Nat. Rev. Microbiol. – volume: 72 start-page: 3429 year: 2006 end-page: 3434 ident: bb0165 article-title: Rhizosphere selection of highly motile phenotypic variants of Pseudomonas fluorescens with enhanced competitive colonization ability publication-title: Appl. Environ. Microbiol. – volume: 16 start-page: 774 year: 2022 end-page: 787 ident: bb0275 article-title: Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions publication-title: ISME J. – volume: 132 start-page: 131 year: 2019 ident: 10.1016/j.scitotenv.2023.164221_bb0005 article-title: Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life publication-title: Soil Biol. Biochem. doi: 10.1016/j.soilbio.2019.01.023 – volume: 90 start-page: 549 year: 2016 ident: 10.1016/j.scitotenv.2023.164221_bb0245 article-title: Chemotaxis signaling systems in model beneficial plant–bacteria associations publication-title: Plant Mol. Biol. doi: 10.1007/s11103-016-0432-4 – volume: 229 start-page: 2873 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0150 article-title: Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogens publication-title: New Phytol. doi: 10.1111/nph.17057 – volume: 12 start-page: 3038 year: 2018 ident: 10.1016/j.scitotenv.2023.164221_bb0185 article-title: Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean publication-title: ISME J. doi: 10.1038/s41396-018-0234-6 – volume: 8 start-page: 1577 year: 2014 ident: 10.1016/j.scitotenv.2023.164221_bb0180 article-title: Taxonomical and functional microbial community selection in soybean rhizosphere publication-title: ISME J. doi: 10.1038/ismej.2014.17 – volume: 225 start-page: 960 year: 2020 ident: 10.1016/j.scitotenv.2023.164221_bb0085 article-title: Plant growth rate and nitrogen uptake shape rhizosphere bacterial community composition and activity in an agricultural field publication-title: New Phytol. doi: 10.1111/nph.16171 – volume: 18 start-page: 3453 year: 2016 ident: 10.1016/j.scitotenv.2023.164221_bb0260 article-title: Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility publication-title: Environ. Microbiol. doi: 10.1111/1462-2920.13288 – volume: 12 start-page: 59 year: 2015 ident: 10.1016/j.scitotenv.2023.164221_bb0050 article-title: Fast and sensitive protein alignment using DIAMOND publication-title: Nat. Methods doi: 10.1038/nmeth.3176 – volume: 257 start-page: 115 year: 2015 ident: 10.1016/j.scitotenv.2023.164221_bb0105 article-title: Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial publication-title: Geoderma doi: 10.1016/j.geoderma.2014.10.016 – volume: 223 start-page: 283 year: 1998 ident: 10.1016/j.scitotenv.2023.164221_bb0270 article-title: Mapping of 41 chemotaxis, flagellar and motility genes to a single region of the Sinorhizobium meliloti chromosome publication-title: Gene doi: 10.1016/S0378-1119(98)00160-7 – volume: 58 start-page: 1153 year: 1992 ident: 10.1016/j.scitotenv.2023.164221_bb0070 article-title: Chemotaxis of rhizobium meliloti towards nodulation gene-inducing compounds from alfalfa roots publication-title: Appl. Environ. Microbiol. doi: 10.1128/aem.58.4.1153-1158.1992 – volume: 466 start-page: 81 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0280 article-title: Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems publication-title: Plant Soil doi: 10.1007/s11104-021-05036-2 – volume: 23 start-page: 508 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0040 article-title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata publication-title: BMC Genomics doi: 10.1186/s12864-022-08738-8 – volume: 785 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0305 article-title: Metagenomic insights into nitrogen and phosphorus cycling at the soil aggregate scale driven by organic material amendments publication-title: Sci. Total Environ. doi: 10.1016/j.scitotenv.2021.147329 – volume: 738 year: 2020 ident: 10.1016/j.scitotenv.2023.164221_bb0210 article-title: DNRA: a short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems publication-title: Sci. Total Environ. doi: 10.1016/j.scitotenv.2020.139710 – volume: 12 start-page: 3185 year: 2010 ident: 10.1016/j.scitotenv.2023.164221_bb0020 article-title: Efficient rhizosphere colonization by Pseudomonas fluorescens f113 mutants unable to form biofilms on abiotic surfaces publication-title: Environ. Microbiol. doi: 10.1111/j.1462-2920.2010.02291.x – volume: 62 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0265 article-title: Designing a home for beneficial plant microbiomes publication-title: Curr. Opin. Plant Biol. doi: 10.1016/j.pbi.2021.102025 – volume: 20 start-page: 161 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0295 article-title: Bacterial motility: machinery and mechanisms publication-title: Nat. Rev. Microbiol. doi: 10.1038/s41579-021-00626-4 – volume: 36 start-page: 1925 year: 2019 ident: 10.1016/j.scitotenv.2023.164221_bb0055 article-title: GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz848 – volume: 2 start-page: 1 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0315 article-title: Genome-resolved metagenomics identifies the particular genetic traits of phosphate-solubilizing bacteria in agricultural soil publication-title: ISME Commun. doi: 10.1038/s43705-022-00100-z – volume: 7 start-page: 1 year: 2019 ident: 10.1016/j.scitotenv.2023.164221_bb0250 article-title: Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling publication-title: Microbiome doi: 10.1186/s40168-019-0756-9 – volume: 6 start-page: 1 year: 2018 ident: 10.1016/j.scitotenv.2023.164221_bb0110 article-title: Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming publication-title: Microbiome – volume: 12 start-page: 3829 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0145 article-title: Rapid evolution of bacterial mutualism in the plant rhizosphere publication-title: Nat. Commun. doi: 10.1038/s41467-021-24005-y – volume: 16 start-page: 774 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0275 article-title: Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions publication-title: ISME J. doi: 10.1038/s41396-021-01125-3 – volume: 6 start-page: 1 year: 2018 ident: 10.1016/j.scitotenv.2023.164221_bb0290 article-title: MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis publication-title: Microbiome doi: 10.1186/s40168-018-0541-1 – volume: 30 start-page: 2114 year: 2014 ident: 10.1016/j.scitotenv.2023.164221_bb0035 article-title: Trimmomatic: a flexible trimmer for Illumina sequence data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu170 – volume: 57 start-page: 289 year: 1995 ident: 10.1016/j.scitotenv.2023.164221_bb0025 article-title: Controlling the false discovery rate: a practical and powerful approach to multiple testing publication-title: J. R. Stat. Soc. doi: 10.1111/j.2517-6161.1995.tb02031.x – volume: 16 start-page: 2337 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0090 article-title: Novel form of collective movement by soil bacteria publication-title: ISME J. doi: 10.1038/s41396-022-01277-w – volume: 44 start-page: 242 year: 2016 ident: 10.1016/j.scitotenv.2023.164221_bb0135 article-title: Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw290 – volume: 10 start-page: 1564 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0160 article-title: Isolation of aquatic plant growth-promoting bacteria for the floating plant duckweed (Lemna minor) publication-title: Microorganisms doi: 10.3390/microorganisms10081564 – volume: 815 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0255 article-title: Evaluation of phosphorus removal in floating treatment wetlands: new insights in non-reactive phosphorus publication-title: Sci. Total Environ. doi: 10.1016/j.scitotenv.2021.152896 – volume: 4 start-page: 4 year: 2023 ident: 10.1016/j.scitotenv.2023.164221_bb0115 article-title: Soil structure and microbiome functions in agroecosystems publication-title: Nat. Rev. Earth Environ. doi: 10.1038/s43017-022-00366-w – volume: 72 start-page: 3429 year: 2006 ident: 10.1016/j.scitotenv.2023.164221_bb0165 article-title: Rhizosphere selection of highly motile phenotypic variants of Pseudomonas fluorescens with enhanced competitive colonization ability publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.72.5.3429-3434.2006 – volume: 42 start-page: fux052 year: 2018 ident: 10.1016/j.scitotenv.2023.164221_bb0175 article-title: The effect of bacterial chemotaxis on host infection and pathogenicity publication-title: FEMS Microbiol. Rev. doi: 10.1093/femsre/fux052 – volume: 15 start-page: 579 year: 2017 ident: 10.1016/j.scitotenv.2023.164221_bb0100 article-title: Embracing the unknown: disentangling the complexities of the soil microbiome publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro.2017.87 – volume: 7 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0320 article-title: Genome-resolved metagenomics reveals distinct phosphorus acquisition strategies between soil microbiomes publication-title: mSystems doi: 10.1128/msystems.01107-21 – volume: 20 start-page: 526 year: 2007 ident: 10.1016/j.scitotenv.2023.164221_bb0030 article-title: Twitching motility is essential for endophytic rice colonization by the N2-fixing endophyte Azoarcus sp. strain BH72 publication-title: Mol. Plant-Microbe Interact. doi: 10.1094/MPMI-20-5-0526 – volume: 17 start-page: 284 year: 2019 ident: 10.1016/j.scitotenv.2023.164221_bb0230 article-title: The role of microbial motility and chemotaxis in symbiosis publication-title: Nat. Rev. Microbiol. doi: 10.1038/s41579-019-0182-9 – year: 2013 ident: 10.1016/j.scitotenv.2023.164221_bb0010 – volume: 5 start-page: 4950 year: 2014 ident: 10.1016/j.scitotenv.2023.164221_bb0200 article-title: Niche and host-associated functional signatures of the root surface microbiome publication-title: Nat. Commun. doi: 10.1038/ncomms5950 – volume: 3 start-page: 470 year: 2018 ident: 10.1016/j.scitotenv.2023.164221_bb0340 article-title: Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly publication-title: Nat. Microbiol. doi: 10.1038/s41564-018-0129-3 – volume: 112 start-page: 911 year: 2015 ident: 10.1016/j.scitotenv.2023.164221_bb0080 article-title: Structure, variation, and assembly of the root-associated microbiomes of rice publication-title: Proc. Natl. Acad. Sci. doi: 10.1073/pnas.1414592112 – year: 2014 ident: 10.1016/j.scitotenv.2023.164221_bb0235 – volume: 10 start-page: 475 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0240 article-title: Rhizosphere colonization determinants by plant growth-promoting rhizobacteria (PGPR) publication-title: Biology doi: 10.3390/biology10060475 – volume: 6 start-page: 1 year: 2018 ident: 10.1016/j.scitotenv.2023.164221_bb0220 article-title: Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil publication-title: Microbiome doi: 10.1186/s40168-018-0546-9 – volume: 8 start-page: 344 year: 2014 ident: 10.1016/j.scitotenv.2023.164221_bb0330 article-title: Microbial expression profiles in the rhizosphere of willows depend on soil contamination publication-title: ISME J. doi: 10.1038/ismej.2013.163 – volume: 31 start-page: 1674 year: 2015 ident: 10.1016/j.scitotenv.2023.164221_bb0140 article-title: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv033 – volume: 123 start-page: 97 year: 2018 ident: 10.1016/j.scitotenv.2023.164221_bb0225 article-title: Relative abundance of denitrifying and DNRA bacteria and their activity determine nitrogen retention or loss in agricultural soil publication-title: Soil Biol. Biochem. doi: 10.1016/j.soilbio.2018.05.006 – volume: 470 start-page: 21 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0310 article-title: Peat-vermiculite alters microbiota composition towards increased soil fertility and crop productivity publication-title: Plant Soil doi: 10.1007/s11104-021-04851-x – volume: 14 start-page: 757 year: 2020 ident: 10.1016/j.scitotenv.2023.164221_bb0065 article-title: Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems publication-title: ISME J. doi: 10.1038/s41396-019-0567-9 – volume: 6 year: 2015 ident: 10.1016/j.scitotenv.2023.164221_bb0335 article-title: The soil microbiome influences grapevine-associated microbiota publication-title: mBio doi: 10.1128/mBio.02527-14 – volume: 8 start-page: 1464 year: 2014 ident: 10.1016/j.scitotenv.2023.164221_bb0170 article-title: Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill publication-title: ISME J. doi: 10.1038/ismej.2013.254 – volume: 161 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0300 article-title: Organic phosphorus availability shapes the diversity of phoD-harboring bacteria in agricultural soil publication-title: Soil Biol. Biochem. doi: 10.1016/j.soilbio.2021.108364 – volume: 12 year: 2016 ident: 10.1016/j.scitotenv.2023.164221_bb0120 article-title: MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1004957 – volume: 11 start-page: 119 year: 2010 ident: 10.1016/j.scitotenv.2023.164221_bb0125 article-title: Prodigal: prokaryotic gene recognition and translation initiation site identification publication-title: BMC Bioinform. doi: 10.1186/1471-2105-11-119 – volume: 50 start-page: 571 year: 2022 ident: 10.1016/j.scitotenv.2023.164221_bb0075 article-title: The carbohydrate-active enzyme database: functions and literature publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkab1045 – volume: fuab038 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0060 article-title: Multiple functions of flagellar motility and chemotaxis in bacterial physiology publication-title: FEMS Microbiol. Rev. – volume: 25 start-page: 1043 year: 2015 ident: 10.1016/j.scitotenv.2023.164221_bb0215 article-title: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes publication-title: Genome Res. doi: 10.1101/gr.186072.114 – volume: 229 start-page: 1091 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0325 article-title: Host selection shapes crop microbiome assembly and network complexity publication-title: New Phytol. doi: 10.1111/nph.16890 – volume: 21 year: 2019 ident: 10.1016/j.scitotenv.2023.164221_bb0195 article-title: Plant growth promoting microbes: potential link to sustainable agriculture and environment publication-title: Biocatal. Agric. Biotechnol. doi: 10.1016/j.bcab.2019.101326 – volume: 28 start-page: 27 year: 2000 ident: 10.1016/j.scitotenv.2023.164221_bb0130 article-title: KEGG: kyoto encyclopedia of genes and genomes publication-title: Nucleic Acids Res. doi: 10.1093/nar/28.1.27 – volume: 27 start-page: 1068 year: 2020 ident: 10.1016/j.scitotenv.2023.164221_bb0190 article-title: Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests publication-title: Glob. Chang. Biol. doi: 10.1111/gcb.15439 – volume: 32 start-page: 666 year: 2009 ident: 10.1016/j.scitotenv.2023.164221_bb0015 article-title: Regulation and function of root exudates publication-title: Plant Cell Environ. doi: 10.1111/j.1365-3040.2009.01926.x – volume: 152 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0155 article-title: Active phoD-harboring bacteria are enriched by long-term organic fertilization publication-title: Soil Biol. Biochem. doi: 10.1016/j.soilbio.2020.108071 – volume: 35 start-page: 725 year: 2017 ident: 10.1016/j.scitotenv.2023.164221_bb0045 article-title: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea publication-title: Nat. Biotechnol. doi: 10.1038/nbt.3893 – volume: 18 start-page: 607 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0285 article-title: Plant-microbiome interactions: from community assembly to plant health publication-title: Nat. Rev. Microbiol. doi: 10.1038/s41579-020-0412-1 – start-page: 321 year: 2013 ident: 10.1016/j.scitotenv.2023.164221_bb0205 – volume: 22 start-page: 6655 year: 2021 ident: 10.1016/j.scitotenv.2023.164221_bb0095 article-title: Chemotaxis of beneficial rhizobacteria to root exudates: the first step towards root–microbe rhizosphere interactions publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms22136655 |
| SSID | ssj0000781 |
| Score | 2.481296 |
| Snippet | Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other... |
| SourceID | hal proquest pubmed crossref elsevier |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 164221 |
| SubjectTerms | Bacteria - metabolism Bacterial motility Burkholderiaceae Carbohydrates carbon chemotaxis corn cucumbers depolymerization ecological differentiation environment field experimentation genome Genomes Humans Life Sciences Metagenome Metagenomics Microbiome mineralization nitrate reduction phosphates polymers Rhizosphere Soil Soil Microbiology solubilization Sphingomonadaceae wheat |
| Title | Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils |
| URI | https://dx.doi.org/10.1016/j.scitotenv.2023.164221 https://www.ncbi.nlm.nih.gov/pubmed/37263432 https://www.proquest.com/docview/2822378287 https://www.proquest.com/docview/2849895340 https://hal.inrae.fr/hal-04208731 |
| Volume | 891 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3db9MwELfGEBLShEZhUNgmg3hN1_gjiXmrpk2Fwh4QE3uznNoWgZJMTTppL_zt3NVOpz1se-ApycmOE9_Zd7Z_d0fIB2W8Sg2sVKXlPBE-z5PSeptwI0zmnMxZiPZ5lk3PxecLebFFjntfGIRVxrk_zOnr2TpSjmJvHl1WFfr4ikJlmDULdCSIHnqwixylfPT3BuaBwWzCKTMMbCh9C-MF7-0asE2vRphFfARLB8bSuzTUo58IlbzLDl3ro9Nd8iwaknQSvvU52XL1gDwJqSWvB2Tv5MaDDYrFIdwOyE7YqKPB_-gF6b66zmCk1j9ArOoWF-st3HQNBSq6ONKYk4faZYXbD7QMEZ7htTUCSWmfZKULbKYR-0XL1eI3NbWlSwT2tRjAwNG2qRbtS3J-evL9eJrEVAzJXPCiS8AKtBIXHwUzAo2MsfPOwwxVmHnpZOas5cpLVRo5B4OHAwF6snTOCJcWhvE9sl03tXtNaJlLr5gTXvBceC5K65hV3lpmwLhM2ZBkfffreYxTjukyFroHpP3SG75p5JsOfBuS8abiZQjV8XCVjz1_9S2p06BQHq78HiRi0xTG6Z5OvmikjRG0kPP0Cgq96wVGw8DF0xhTu2bVasTv8hzzDdxXRqhCSS7GQ_IqSNumPZ6zDL2C3_zPP7wlT_EJATCp3Cfb3XLlDsDK6srD9TA6JI8nn2bTM7zOvv2Y_QNzpyti |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Lb9QwEB61RYhKqIKFloUCBnHNduNHHtyqqtUC255aqTfLWdsisCTVJluJC7-dmXWyVQ9tD71FEzsPz4w9Tr6ZD-BLbnweG9ypKitEJH2aRoX1NhJGmsQ5lfJQ7fMsmVzI75fqcgOO-lwYglV2c3-Y01ezdSc56Ebz4KosKcdXZnlCrFm4RqLpbcITie5LNAajfzc4D6pmE34zo2dj81sgL7xwW2Nwej0iGvER7h04j-9aojZ_ElbyrkB0tSCdvICdLpJkh-FhX8KGqwbwNHBL_h3A7vFNChs263y4GcDz8KWOhQSkV9CeutZQqdY_KCyrhnbrDR60NUMp5TiyjpSH2UVJ3x9YEUo842UrQpKynmWlDXpmHfiLFcv5b2YqyxaE7GuogoFjTV3Om9dwcXJ8fjSJOi6GaCZF1kYYBlpFu4-MG0lRxth553GKysyscCpx1orcq7wwaoYRj0ABjmThnJEuzgwXu7BV1ZV7A6xIlc-5k16KVHohC-u4zb213GB0GfMhJP3w61lXqJz4Mua6R6T90mu9adKbDnobwnjd8SrU6ni4y9dev_qW2WlcUR7u_BktYn0rKtQ9OZxqko0JtZCK-BobfeoNRqPn0u8YU7l62WgC8IqUCAfuayPzLFdCjoewF6xtfT-R8oTSgt8-5h0-wrPJ-elUT7-d_XgH23SG0DCx2oetdrF07zHkaosPK5f6D6gkK00 |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Metagenomic+insights+into+genetic+factors+driving+bacterial+niche+differentiation+between+bulk+and+rhizosphere+soils&rft.jtitle=The+Science+of+the+total+environment&rft.au=Wu%2C+Xingjie&rft.au=Bei%2C+Shuikuan&rft.au=Zhou%2C+Xi&rft.au=Luo%2C+Yu&rft.date=2023-09-15&rft.pub=Elsevier&rft.issn=0048-9697&rft.eissn=1879-1026&rft.volume=891&rft_id=info:doi/10.1016%2Fj.scitotenv.2023.164221&rft.externalDBID=HAS_PDF_LINK&rft.externalDocID=oai_HAL_hal_04208731v1 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0048-9697&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0048-9697&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0048-9697&client=summon |