{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T15:55:24Z","timestamp":1789487724930,"version":"build-2803163510"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100008789","name":"Department of Science & Technology","doi-asserted-by":"publisher","award":["SR\/WOS-A\/LS-463\/2017"],"award-info":[{"award-number":["SR\/WOS-A\/LS-463\/2017"]}],"id":[{"id":"10.13039\/501100008789","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008789","name":"Department of Science & Technology","doi-asserted-by":"publisher","award":["DST\/WISE-PDF\/LS-4\/2023"],"award-info":[{"award-number":["DST\/WISE-PDF\/LS-4\/2023"]}],"id":[{"id":"10.13039\/501100008789","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>The bioinoculant properties of a newly identified ammonium-releasing novel strain of Actinomycetota-Microbacterium bengalense sp. nov. GB16_1_BI (Accession number: SRX9280401) on the microbiome structure of rice rhizosphere were assessed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods and result<\/jats:title>\n                    <jats:p>GB16_1_BI may inhibit most bacteria present in the rice rhizosphere as well as encouraged the growth of rare bacteria specific to the waterlogged rice rhizosphere. The genome sequence as well as untargeted metabolome analyses of GB16_1_BI showed abundance of secondary metabolites with probable antimicrobial activity. Amplicon sequencing of the 16S rRNA V3-V4 region from the rhizosphere of the black rice showed inhibition of most bacteria by GB16_1_BI. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis showed increased abundance in the marker genes for nitrogen cycling (nifH, nrfA, and\u00a0nrt) but not for nifD or nifK, which was also reflected in the ANOSIM analysis in the OTUs of the N-fixing bacteria. Higher abundance of the nitrogen-fixing methanotrophs, Methylosinus and Methylocystis in inoculated plants also led to study of the marker genes for methane metabolism.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Microbes present in the rhizosphere contribute to the biogeochemical cycle by transforming unavailable minerals and by retaining nutrients for their growth, which get released after death for plant adsorption. However, not all microbes contribute positively to plant growth. Microbes compete with plants for nutrients, cause disease, or produce harmful greenhouse gases. Hence, GB16_1_BI could influence plant growth predominantly by suppressing microbes and encouraged niche-specific microbes specifically involved in nitrogen cycling.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jambio\/lxag221","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T13:11:42Z","timestamp":1788181902000},"source":"Crossref","is-referenced-by-count":0,"title":["Manipulation of rhizosphere microbiome by\n                    <i>Microbacterium<\/i>\n                    sp. GB16_1_BI to promote plant growth"],"prefix":"10.1093","volume":"137","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0283-1193","authenticated-orcid":false,"given":"Papri","family":"Nag","sequence":"first","affiliation":[{"name":"Present affiliation: Department of Soil Science, ICAR-Indian Institute of Rice Research , Rajendranagar, Telangana, 500030 ,","place":["India"]},{"name":"Division of Biological Sciences, Bose Institute , Kolkata, 700091 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajani","family":"Govindannagari","sequence":"additional","affiliation":[{"name":"Present affiliation: Department of Soil Science, ICAR-Indian Institute of Rice Research , Rajendranagar, Telangana, 500030 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kavuru","family":"Prasad","sequence":"additional","affiliation":[{"name":"Present affiliation: Department of Soil Science, ICAR-Indian Institute of Rice Research , Rajendranagar, Telangana, 500030 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tummala","family":"Mounika","sequence":"additional","affiliation":[{"name":"Present affiliation: Department of Soil Science, ICAR-Indian Institute of Rice Research , Rajendranagar, Telangana, 500030 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4235-5702","authenticated-orcid":false,"given":"Latha P","family":"Chandran","sequence":"additional","affiliation":[{"name":"Present affiliation: Department of Soil Science, ICAR-Indian Institute of Rice Research , Rajendranagar, Telangana, 500030 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2923-1668","authenticated-orcid":false,"given":"Sampa","family":"Das","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, Bose Institute , Kolkata, 700091 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M B B","family":"Prasad\u00a0Babu","sequence":"additional","affiliation":[{"name":"Present affiliation: Department of Soil Science, ICAR-Indian Institute of Rice Research , Rajendranagar, Telangana, 500030 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R M","family":"Sundaram","sequence":"additional","affiliation":[{"name":"Present affiliation: Department of Soil Science, ICAR-Indian Institute of Rice Research , Rajendranagar, Telangana, 500030 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"2026091510312513100_bib1","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1093\/bioinformatics\/btz859","article-title":"KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold","volume":"36","author":"Aramaki","year":"2020","journal-title":"Bioinformatics"},{"key":"2026091510312513100_bib2","doi-asserted-by":"publisher","first-page":"e00249","DOI":"10.1128\/JB00249-18","article-title":"Relationship between the viable but nonculturable state and antibiotic persister cells","volume":"200","author":"Ayrapetyan","year":"2018","journal-title":"J Bacteriol"},{"key":"2026091510312513100_bib3","doi-asserted-by":"publisher","first-page":"5043","DOI":"10.1128\/AEM00969-14","article-title":"Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants","volume":"80","author":"Bao","year":"2014","journal-title":"Appl Environ Microb"},{"key":"2026091510312513100_bib4","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1042\/ETLS20180031","article-title":"Methanogens: pushing the boundaries of biology","volume":"2","author":"Baun","year":"2018","journal-title":"Emerg Top Life Sci"},{"key":"2026091510312513100_bib5","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/jscitotenv201809141","article-title":"Mechanism of plant mediated methane emission in tropical lowland rice","volume":"651","author":"Bhattacharyya","year":"2019","journal-title":"Sci Total Environ"},{"key":"2026091510312513100_bib6","doi-asserted-by":"publisher","first-page":"W46","DOI":"10.1093\/nar\/gkad344","article-title":"antiSMASH 70: new and improved predictions for detection, regulation, chemical structures and visualisation","volume":"51","author":"Blin","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026091510312513100_bib7","doi-asserted-by":"publisher","first-page":"27964","DOI":"10.1021\/jacs4c11899","article-title":"Direct conversion of N2 and air to nitric acid in gas-water microbubbles","volume":"146","author":"Bose","year":"2024","journal-title":"J Am Chem Soc"},{"key":"2026091510312513100_bib8","doi-asserted-by":"publisher","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci Rep"},{"key":"2026091510312513100_bib9","doi-asserted-by":"publisher","first-page":"3196","DOI":"10.1128\/AEM02610-06","article-title":"Stable isotope probing with 15N2 reveals novel noncultivated diazotrophs in soil","volume":"73","author":"Buckley","year":"2007","journal-title":"Appl Environ Microb"},{"key":"2026091510312513100_bib10","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1146\/annurev-arplant-050312-120106","article-title":"Structure and functions of the bacterial microbiota of plants","volume":"64","author":"Bulgarelli","year":"2013","journal-title":"Annu Rev Plant Biol"},{"key":"2026091510312513100_bib11","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s40168-021-01049-2","article-title":"Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field","volume":"9","author":"Cadot","year":"2021","journal-title":"Microbiome"},{"key":"2026091510312513100_bib12","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/jmimet201903020","article-title":"Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification","volume":"160","author":"Cannon","year":"2019","journal-title":"J Microbiol Methods"},{"key":"2026091510312513100_bib13","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1038\/s41559-019-0994-z","article-title":"Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere","volume":"3","author":"Carlstr\u00f6m","year":"2019","journal-title":"Nat Ecol Evol"},{"key":"2026091510312513100_bib14","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2026091510312513100_bib15","doi-asserted-by":"publisher","first-page":"15164","DOI":"10.1038\/nplants2015164","article-title":"Three geographically separate domestications of Asian rice","volume":"1","author":"Civ\u00e1\u0148","year":"2015","journal-title":"Nat Plants"},{"key":"2026091510312513100_bib16","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/s41893-024-01496-3","article-title":"Data-driven strategies to improve nitrogen use efficiency of rice farming in South Asia","volume":"8","author":"Coggins","year":"2025","journal-title":"Nat Sustain"},{"key":"2026091510312513100_bib17","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"De\u00a0Coster","year":"2018","journal-title":"Bioinformatics"},{"key":"2026091510312513100_bib18","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1016\/jtim202002016","article-title":"Gaseous milieu: extending the boundaries of the rhizosphere","volume":"28","author":"de\u00a0la\u00a0Porte","year":"2020","journal-title":"Trends Microbiol"},{"key":"2026091510312513100_bib19","doi-asserted-by":"publisher","first-page":"fiz040","DOI":"10.1093\/femsec\/fiz040","article-title":"Microbiomes inhabiting rice roots and rhizosphere","volume":"95","author":"Ding","year":"2019","journal-title":"FEMS Microbiol Ecol"},{"key":"2026091510312513100_bib20","doi-asserted-by":"publisher","first-page":"2746","DOI":"10.1021\/acsaccounts4c00413","article-title":"Toward the use of methyl-coenzyme M reductase for methane bioconversion applications","volume":"57","author":"Dinh","year":"2024","journal-title":"Acc Chem Res"},{"key":"2026091510312513100_bib21","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2026091510312513100_bib22","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1007\/BF01636899","article-title":"Sources and sinks of atmospheric methane","volume":"116","author":"Ehhalt","year":"1978","journal-title":"Pure Appl Geophys"},{"key":"2026091510312513100_bib23","doi-asserted-by":"publisher","first-page":"20130116","DOI":"10.1098\/rstb20130116","article-title":"Consequences of human modification of the global nitrogen cycle","volume":"368","author":"Erisman","year":"2013","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"2026091510312513100_bib24","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nrmicro.2017.42","article-title":"Persistent bacterial infections and persister cells","volume":"15(8)","author":"Fisher","year":"2017","journal-title":"Nat Rev Microbiol"},{"key":"2026091510312513100_bib25","doi-asserted-by":"publisher","first-page":"E1157","DOI":"10.1073\/pnas1717617115","article-title":"Assembly and ecological function of the root microbiome across angiosperm plant species","volume":"115","author":"Fitzpatrick","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091510312513100_bib26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s11104-024-07001-1","article-title":"Science losing its way: examples from the realm of microbial N2-fixation in cereals and other non-legumes","volume":"511","author":"Giller","year":"2025","journal-title":"Plant Soil"},{"key":"2026091510312513100_bib27","doi-asserted-by":"publisher","first-page":"678057","DOI":"10.3389\/fmicb2021678057","article-title":"Methanotrophs: discoveries, environmental relevance, and a perspective on current and future applications","volume":"1","author":"Guerrero-Cruz","year":"2021","journal-title":"Front Microbiol"},{"key":"2026091510312513100_bib28","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1002\/0471142727mb1025s88","article-title":"Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow","volume":"Chapter 10","author":"Gundry","year":"2009","journal-title":"Curr Protoc Mol Biol"},{"key":"2026091510312513100_bib29","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1264\/jsme2me13110","article-title":"Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions","volume":"29","author":"Ikeda","year":"2014","journal-title":"Microbes Environ"},{"key":"2026091510312513100_bib30","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1002\/pro3711","article-title":"KEGG Mapper for inferring cellular functions from protein sequences","volume":"29","author":"Kanehisa","year":"2020","journal-title":"Protein Sci"},{"key":"2026091510312513100_bib31","doi-asserted-by":"publisher","first-page":"2073","DOI":"10.1016\/jcell202512051","article-title":"Planetary microbiome structure and generalist-driven gene flow across disparate habitats","volume":"189","author":"Kim","year":"2026","journal-title":"Cell"},{"key":"2026091510312513100_bib32","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1038\/ngeo1955","article-title":"Three decades of global methane sources and sinks","volume":"6","author":"Kirschke","year":"2013","journal-title":"Nature Geosci"},{"key":"2026091510312513100_bib33","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/417067a","article-title":"Feedback with soil biota contributes to plant rarity and invasiveness in communities","volume":"417","author":"Klironomos","year":"2002","journal-title":"Nature"},{"key":"2026091510312513100_bib34","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026091510312513100_bib35","doi-asserted-by":"publisher","first-page":"9720","DOI":"10.1073\/pnas1809276115","article-title":"High nitrous oxide fluxes from rice indicate the need to manage water for both long- and short-term climate impacts","volume":"115","author":"Kritee","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091510312513100_bib36","doi-asserted-by":"publisher","first-page":"10515","DOI":"10.1021\/acsanalchem4c00371","article-title":"Water microdroplets in air: a hitherto unnoticed natural source of nitrogen oxides","volume":"96","author":"Kumar","year":"2024","journal-title":"Anal Chem"},{"key":"2026091510312513100_bib37","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.soilbio.2015.10.016","article-title":"Past water management affected GHG production and microbial community pattern in Italian rice paddy soils","volume":"93","author":"Lagomarsino","year":"2016","journal-title":"Soil Biol Biochem"},{"key":"2026091510312513100_bib38","doi-asserted-by":"publisher","first-page":"e0097224","DOI":"10.1128\/mbio00972-24","article-title":"Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant","volume":"15","author":"Laurich","year":"2024","journal-title":"mBio"},{"key":"2026091510312513100_bib39","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1111\/1574-694112282","article-title":"Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem","volume":"88","author":"Lee","year":"2014","journal-title":"FEMS Microbiol Ecol"},{"key":"2026091510312513100_bib40","doi-asserted-by":"publisher","first-page":"D490","DOI":"10.1093\/nar\/gkt1178","article-title":"The carbohydrate-active enzymes database (CaZy) in 2013","volume":"42","author":"Lombard","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026091510312513100_bib41","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1038\/s41396-017-0003-y","article-title":"The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader\u2019s niche","volume":"12","author":"Mallon","year":"2018","journal-title":"ISME J"},{"key":"2026091510312513100_bib42","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1002\/ird2756","article-title":"Effect of infiltration rate on methane emission properties in pot-cultured rice under alternate wetting and drying irrigation","volume":"72","author":"Matsuda","year":"2023","journal-title":"Irrig Drain"},{"key":"2026091510312513100_bib43","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1093\/bbb\/zbac177","article-title":"Mitigation of greenhouse gas emission by nitrogen-fixing bacteria","volume":"87","author":"Minamisawa","year":"2023","journal-title":"Biosc Biotechnol Biochem"},{"key":"2026091510312513100_bib44","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database","volume":"249","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026091510312513100_bib45","doi-asserted-by":"publisher","first-page":"pdb.top17","DOI":"10.1101\/pdbtop17","article-title":"Using the basic local alignment search tool (BLAST)","author":"Mount","year":"2007","journal-title":"CSH Protoc"},{"key":"2026091510312513100_bib46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jobm70145","article-title":"Isolation of an ammonium excreting Actinomycetota, Microbacterium bengalense sp nov GB16_1_BIT, from rice rhizosphere","volume":"61","author":"Nag","year":"2026","journal-title":"J Basic Microbiol"},{"key":"2026091510312513100_bib47","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1038\/ismej2016100","article-title":"The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria","volume":"11","author":"Ney","year":"2017","journal-title":"ISME J"},{"key":"2026091510312513100_bib48","doi-asserted-by":"publisher","first-page":"3635","DOI":"10.1093\/bioinformatics\/btx445","article-title":"gVolante for standardizing completeness assessment of genome and transcriptome assemblies","volume":"33","author":"Nishimura","year":"2017","journal-title":"Bioinformatics"},{"key":"2026091510312513100_bib49","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1104\/pp94159","article-title":"Mechanism of methane transport from the rhizosphere to the atmosphere through rice plants","volume":"94","author":"Nouchi","year":"1990","journal-title":"Plant Physiol"},{"key":"2026091510312513100_bib50","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1104\/pp.020013","article-title":"Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration","volume":"129","author":"Oliveira","year":"2002","journal-title":"Plant Physiol"},{"key":"2026091510312513100_bib51","doi-asserted-by":"publisher","first-page":"126439","DOI":"10.1016\/j.micres.2020.126439","article-title":"ACC deaminase in plant growth-promoting bacteria (PGPB): an efficient mechanism to counter salt stress in crops","volume":"235","author":"Orozco-Mosqueda","year":"2020","journal-title":"Microbiol Res"},{"key":"2026091510312513100_bib52","doi-asserted-by":"publisher","first-page":"2253","DOI":"10.1890\/08-08511","article-title":"Contrasts between habitat generalists and specialists: an empirical extension to the basic metacommunity framework","volume":"90","author":"Pandit","year":"2009","journal-title":"Ecology"},{"key":"2026091510312513100_bib53","doi-asserted-by":"publisher","first-page":"6082","DOI":"10.1073\/pnas86166082","article-title":"Purification and characterization of the nifN and nifE gene products from Azotobacter vinelandii mutant UW45","volume":"86","author":"Paustian","year":"1989","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091510312513100_bib54","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1007\/s003740050568","article-title":"Microsensor analysis of oxygen and pH in the rice rhizosphere under field and laboratory conditions","volume":"29","author":"Revsbech","year":"1999","journal-title":"Biol Fertil Soils"},{"key":"2026091510312513100_bib55","doi-asserted-by":"publisher","first-page":"ME22052","DOI":"10.1264\/jsme2ME22052","article-title":"Mitigation of paddy field soil methane emissions by betaproteobacterium Azoarcus inoculation of rice seeds","volume":"37","author":"Sakoda","year":"2022","journal-title":"Microbes Environ"},{"key":"2026091510312513100_bib56","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2026091510312513100_bib57","doi-asserted-by":"publisher","first-page":"7611","DOI":"10.1128\/AEM.02379-14","article-title":"Evidence for the co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in a flooded paddy field","volume":"80","author":"Shen","year":"2014","journal-title":"Appl Environ Microb"},{"key":"2026091510312513100_bib58","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1186\/s40168-025-02120-y","article-title":"Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces","volume":"13","author":"Sun","year":"2025","journal-title":"Microbiome"},{"key":"2026091510312513100_bib59","doi-asserted-by":"publisher","first-page":"5173","DOI":"10.1128\/jcm41115173-51772003","article-title":"Rapid colorimetric method for testing susceptibility of Mycobacterium tuberculosis to isoniazid and rifampin in liquid cultures","volume":"41","author":"Syre","year":"2003","journal-title":"J Clinc Microbiol"},{"key":"2026091510312513100_bib60","doi-asserted-by":"publisher","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026091510312513100_bib61","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"'UniProt: a worldwide hub of protein knowledge'","volume":"47","author":"UniProt Consortium","year":"2025","journal-title":"Nucleic Acids Research, 47(D1), D506\u2013D515"},{"key":"2026091510312513100_bib62","doi-asserted-by":"publisher","first-page":"e00046","DOI":"10.1128\/AEM00046-21","article-title":"Succession of the resident soil microbial community in response to periodic inoculations","volume":"87","author":"Wang","year":"2021","journal-title":"Appl Environ Microb"},{"key":"2026091510312513100_bib63","doi-asserted-by":"publisher","first-page":"e000132","DOI":"10.1099\/mgen0000132","article-title":"Completing bacterial genome assemblies with multiplex MinION sequencing","volume":"3","author":"Wick","year":"2017","journal-title":"Microb Genom"},{"key":"2026091510312513100_bib64","doi-asserted-by":"publisher","first-page":"W443","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: faster than PHASTER, better than PHAST","volume":"51","author":"Wishart","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026091510312513100_bib65","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol"},{"key":"2026091510312513100_bib66","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1093\/jexbot\/53.370.917","article-title":"Genetic manipulation and quantitative-trait loci mapping for nitrogen recycling in rice","volume":"53","author":"Yamaya","year":"2002","journal-title":"J Exp Bot"},{"key":"2026091510312513100_bib67","doi-asserted-by":"publisher","first-page":"408","DOI":"10.3390\/plants8100408","article-title":"Molecular analyses of the distribution and function of diazotrophic rhizobia and methanotrophs in the tissues and rhizosphere of non-leguminous plants","volume":"8","author":"Yoneyama","year":"2019","journal-title":"Plants (Basel)"},{"key":"2026091510312513100_bib68","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/s41396-023-01399-9","article-title":"Plant latent defense response against compatibility","volume":"17","author":"Zhang","year":"2023","journal-title":"ISME J"},{"key":"2026091510312513100_bib69","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/nature15743","article-title":"Managing nitrogen for sustainable development","volume":"528","author":"Zhang","year":"2015","journal-title":"Nature"},{"key":"2026091510312513100_bib70","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","article-title":"PEAR: a fast and accurate Illumina Paired-End reAd merger","volume":"30","author":"Zhang","year":"2014","journal-title":"Bioinformatics"},{"key":"2026091510312513100_bib71","doi-asserted-by":"publisher","first-page":"W95","DOI":"10.1093\/nar\/gky418","article-title":"dbCAN2: a meta server for automated carbohydrate-active enzyme annotation","volume":"46","author":"Zhang","year":"2018","journal-title":"Nucleic Acids Res"}],"container-title":["Journal of Applied Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jambio\/advance-article-pdf\/doi\/10.1093\/jambio\/lxag221\/70881946\/lxag221.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jambio\/article-pdf\/137\/9\/lxag221\/70881946\/lxag221.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jambio\/article-pdf\/137\/9\/lxag221\/70881946\/lxag221.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T14:31:34Z","timestamp":1789482694000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jambio\/article\/doi\/10.1093\/jambio\/lxag221\/8776680"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,31]]},"references-count":71,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,2]]}},"URL":"https:\/\/doi.org\/10.1093\/jambio\/lxag221","relation":{},"ISSN":["1365-2672"],"issn-type":[{"value":"1365-2672","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,8,31]]},"article-number":"lxag221"}}