{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T09:56:32Z","timestamp":1790934992465,"version":"4.1.0"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["World J Microbiol Biotechnol"],"DOI":"10.1007\/s11274-026-05257-6","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T07:08:53Z","timestamp":1788937733000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Synergistic regulation of aquatic microbiome assembly and function by carbon resource availability and a bivalve bioengineer"],"prefix":"10.1007","volume":"42","author":[{"given":"Jinglun","family":"Xiao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huimin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiubao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junren","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liping","family":"Qiu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longxiang","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuping","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shunlong","family":"Meng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Limin","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"5257_CR17","doi-asserted-by":"publisher","first-page":"1193","DOI":"10.1111\/raq.12520","volume":"13","author":"G Abakari","year":"2021","unstructured":"Abakari G, Luo GZ, Kombat EO, Alhassan EH (2021) Supplemental carbon sources applied in biofloc technology aquaculture systems: types, effects and future research. Reviews Aquaculture 13:1193\u20131222","journal-title":"Reviews Aquaculture"},{"key":"5257_CR30","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41579-018-0024-1","volume":"16","author":"S Banerjee","year":"2018","unstructured":"Banerjee S, Schlaeppi K, van der Heijden MGA (2018) Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 16:567\u2013576","journal-title":"Nat Rev Microbiol"},{"key":"5257_CR9","doi-asserted-by":"crossref","unstructured":"Bi Z, Wang XL, Fu H, Huang Y (2025) Carbon source shaped microbial ecology, metabolism and performance in biofilm system for simultaneous phosphorus recovery and nitrogen removal. Environ Res 286:122800","DOI":"10.1016\/j.envres.2025.122800"},{"key":"5257_CR18","doi-asserted-by":"crossref","unstructured":"Bolger AM, Marc L, Bjoern U (2014)Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114\u20132120","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"5257_CR24","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1111\/oik.06866","volume":"129","author":"J Cordeiro","year":"2020","unstructured":"Cordeiro J, de Oliveira JHF, Schmitz HJ, Vizentin-Bugoni J (2020) High niche partitioning promotes highly specialized, modular and non-nested florivore-plant networks across spatial scales and reveals drivers of specialization. Oikos 129:619\u2013629","journal-title":"Oikos"},{"key":"5257_CR37","doi-asserted-by":"crossref","unstructured":"Cui L, Wang B, Luo K, Liu Y, Xie YM, Liu LZ, Chen JW, Fan GY, Liu SS, Tian XL (2025) The diversity, composition, network characteristics and community assembly of intestinal microbiome in sea cucumber reflect the differences in habitats and aquaculture practices. J Environ Manage 376:124487","DOI":"10.1016\/j.jenvman.2025.124487"},{"key":"5257_CR25","doi-asserted-by":"crossref","unstructured":"de Celis M, Duque J, Marquina D, Salvad\u00f3 H, Serrano S, Arregui L, Santos A, Belda I (2022) Niche differentiation drives microbial community assembly and succession in full-scale activated sludge bioreactors. Npj Biofilms Microbiomes 8(1):23","DOI":"10.1038\/s41522-022-00291-2"},{"key":"5257_CR31","doi-asserted-by":"crossref","unstructured":"Dasgupta D, Richardson AE, Camuy-V\u00e9lez LA, Kirkby C, Kirkegaard JA, Banerjee S (2024) Microbial dynamics during in-situ organic matter decomposition reveals the importance of keystone taxa in the core microbiome. Appl Soil Ecol 199:105396","DOI":"10.1016\/j.apsoil.2024.105396"},{"key":"5257_CR11","doi-asserted-by":"publisher","first-page":"E1326","DOI":"10.1073\/pnas.1414261112","volume":"112","author":"F Dini-Andreote","year":"2015","unstructured":"Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF (2015) Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci USA 112:E1326\u2013E1332","journal-title":"Proc Natl Acad Sci USA"},{"key":"5257_CR13","doi-asserted-by":"crossref","unstructured":"Emerenciano MGC, Khanjani MH, Sharifinia M, Miranda-Baeza A (2025) Could Biofloc Technology (BFT) Pave the Way Toward a More Sustainable Aquaculture in Line With the Circular Economy? Aquaculture Research 2025","DOI":"10.1155\/are\/1020045"},{"key":"5257_CR27","doi-asserted-by":"publisher","first-page":"1528","DOI":"10.1016\/j.cub.2019.03.047","volume":"29","author":"TN Enke","year":"2019","unstructured":"Enke TN, Datta MS, Schwartzman J, Cermak N, Schmitz D, Barrere J, Pascual-Garc\u00eda A, Cordero OX (2019) Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities. Curr Biol 29:1528\u2013","journal-title":"Curr Biol"},{"key":"5257_CR3","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1126\/science.1153213","volume":"320","author":"PG Falkowski","year":"2008","unstructured":"Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive Earth\u2019s biogeochemical cycles. Science 320:1034\u20131039","journal-title":"Science"},{"key":"5257_CR2","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1038\/nature08058","volume":"459","author":"JA Fuhrman","year":"2009","unstructured":"Fuhrman JA (2009) Microbial community structure and its functional implications. Nature 459:193\u2013199","journal-title":"Nature"},{"key":"5257_CR21","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1126\/science.aat1168","volume":"361","author":"JE Goldford","year":"2018","unstructured":"Goldford JE, Lu NX, Bajic D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A, Segr\u00e8 D, Mehta P, Sanchez A (2018) Emergent simplicity in microbial community assembly. Science 361:469\u2013474","journal-title":"Science"},{"key":"5257_CR38","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1034\/j.1600-0706.2003.12322.x","volume":"101","author":"JL Guti\u00e9rrez","year":"2003","unstructured":"Guti\u00e9rrez JL, Jones CG, Strayer DL, Iribarne OO (2003) Mollusks as ecosystem engineers:: the role of shell production in aquatic habitats. Oikos 101:79\u201390","journal-title":"Oikos"},{"key":"5257_CR4","doi-asserted-by":"crossref","unstructured":"Gweon HS, Bowes MJ, Moorhouse HL, Oliver AE, Bailey MJ, Acreman MC, Read DS (2021) Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum. Environ Microbiol 23(1): 484\u2013498","DOI":"10.1111\/1462-2920.15337"},{"key":"5257_CR23","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/nrmicro2795","volume":"10","author":"CA Hanson","year":"2012","unstructured":"Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH (2012) Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10:497\u2013506","journal-title":"Nat Rev Microbiol"},{"key":"5257_CR22","doi-asserted-by":"crossref","unstructured":"Hou DD, Hong M, Wang K, Yan HZ, Wang YT, Dong PS, Li DJ, Liu K, Zhou ZC, Zhang DM (2021) Prokaryotic community succession and assembly on different types of microplastics in a mariculture cage. Environ Pollut 268:115756","DOI":"10.1016\/j.envpol.2020.115756"},{"key":"5257_CR20","doi-asserted-by":"publisher","first-page":"5013","DOI":"10.1007\/s00253-021-11378-9","volume":"105","author":"DW Hou","year":"2021","unstructured":"Hou DW, Zhou RJ, Zeng SZ, Wei DD, Deng XS, Xing CG, Weng SP, He JG, Huang ZJ (2021) Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments. Appl Microbiol Biotechnol 105:5013\u20135022","journal-title":"Appl Microbiol Biotechnol"},{"key":"5257_CR6","doi-asserted-by":"crossref","unstructured":"Kong S, Chen Z, Ghonimy A, Li J, Zhao FZ (2023) Bivalves Improved Water Quality by Changing Bacterial Composition in Sediment and Water in an IMTA System. Aquaculture Research 2023","DOI":"10.1155\/2023\/1930201"},{"key":"5257_CR35","doi-asserted-by":"crossref","unstructured":"Krohn C, Khudur L, Dias DA, van den Akker B, Rees CA, Crosbie ND, Surapaneni A, O\u2019Carroll DM, Stuetz RM, Batstone DJ, Ball AS (2022) The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge. Front Microbiol 13:1079136","DOI":"10.3389\/fmicb.2022.1079136"},{"key":"5257_CR33","doi-asserted-by":"publisher","first-page":"133459","DOI":"10.1016\/j.biortech.2025.133459","volume":"440","author":"N Liu","year":"2026","unstructured":"Liu N, Zhang Y, Zhang Y, Yang Y, Long H, Huang A, Zeng Y, Xie Z (2026) Quorum sensing mediates spatiotemporal microbial community dynamics and nitrogen metabolism in biofloc-based Litopenaeus vannamei aquaculture systems. Bioresour Technol 440:133459","journal-title":"Bioresour Technol"},{"key":"5257_CR29","doi-asserted-by":"crossref","unstructured":"Liu X, Hu S, Sun R, Wu Y, Qiao Z, Wang S, Zhang Z, Cui C (2021) Dissolved oxygen disturbs nitrate transformation by modifying microbial community, co-occurrence networks, and functional genes during aerobic-anoxic transition. Sci Total Environ, 790:148245","DOI":"10.1016\/j.scitotenv.2021.148245"},{"key":"5257_CR15","doi-asserted-by":"crossref","unstructured":"Mao CZ, Li XH, Xiong XP, Kong QY, Wang YF, Han J, Cao XY, Xiong X, Yuan J, Wang QD, Huang J (2025) Differential community assembly mechanisms of shared and unique bacterioplankton in diverse aquaculture ponds. Aquaculture 598:741999","DOI":"10.1016\/j.aquaculture.2024.741999"},{"key":"5257_CR19","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1016\/S0044-8486(96)01487-1","volume":"151","author":"DJW Moriarty","year":"1997","unstructured":"Moriarty DJW (1997) The role of microorganisms in aquaculture ponds. Aquaculture 151:333\u2013349","journal-title":"Aquaculture"},{"key":"5257_CR1","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1128\/MMBR.00051-12","volume":"77","author":"DR Nemergut","year":"2013","unstructured":"Nemergut DR, Schmidt SK, Fukami T, O\u2019Neill SP, Bilinski TM, Stanish LF, Knelman JE, Darcy JL, Lynch RC, Wickey P, Ferrenberg S (2013) Patterns and Processes of Microbial Community Assembly. Microbiol Mol Biol Rev 77:342\u2013356","journal-title":"Microbiol Mol Biol Rev"},{"key":"5257_CR16","doi-asserted-by":"crossref","unstructured":"Niu SH, Xie J, Wang GJ, Li ZF, Zhang K, Li HY, Xia Y, Tian JJ, Yu EM, Xie WP, Gong WB (2024) Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system. Sci Total Environ 907:167913","DOI":"10.1016\/j.scitotenv.2023.167913"},{"key":"5257_CR26","doi-asserted-by":"crossref","unstructured":"Puente-S\u00e1nchez F, Pascual-Garc\u00eda A, Bastolla U, Pedr\u00f3s-Ali\u00f3 C, Tamames J (2024) Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity. Commun Biology 7(1):1046","DOI":"10.1038\/s42003-024-06616-5"},{"key":"5257_CR7","doi-asserted-by":"publisher","first-page":"4079","DOI":"10.1111\/1462-2920.15922","volume":"24","author":"M Qin","year":"2022","unstructured":"Qin M, Xu H, Zhao D, Zeng J, Wu QL (2022) Aquaculture drives distinct patterns of planktonic and sedimentary bacterial communities: insights into co-occurrence pattern and assembly processes. Environ Microbiol 24:4079\u20134093","journal-title":"Environ Microbiol"},{"key":"5257_CR5","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1046\/j.1365-2427.2001.00771.x","volume":"46","author":"CC Vaughn","year":"2001","unstructured":"Vaughn CC, Hakenkamp CC (2001) The functional role of burrowing bivalves in freshwater ecosystems. Freshw Biol 46:1431\u20131446","journal-title":"Freshw Biol"},{"key":"5257_CR34","doi-asserted-by":"crossref","unstructured":"Wang YT, Wang K, Huang L, Dong PS, Wang SP, Chen HP, Lu Z, Hou DD, Zhang DM (2020) Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle. Microbiome 8(1):106","DOI":"10.1186\/s40168-020-00879-w"},{"key":"5257_CR28","doi-asserted-by":"crossref","unstructured":"Xu HM, Zhang Y, Fan DY, Meng SL, Fan LM, Song C, Qiu LP, Li DD, Fang LX, Liu ZP, Bing XW (2024) Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns. Microb Ecol 87(1):145","DOI":"10.1007\/s00248-024-02461-5"},{"key":"5257_CR14","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.aquaculture.2022.738953","volume":"563","author":"LZ Wu","year":"2023","unstructured":"Wu LZ, Yang P, Zhang LH, Luo LJ, Hong Y, Zhu WY, Zheng LD, Zhao GH, Tong C, Pe\u00f1uelas J (2023) Sediment sulfate content determines assembly processes and network stability of bacteria communities of coastal land-based shrimp aquaculture ponds. Aquaculture 563:11","journal-title":"Aquaculture"},{"key":"5257_CR36","doi-asserted-by":"crossref","unstructured":"Yang SZ, Wen X, Shi YL, Liebner S, Jin HJ, Perfumo A (2016) Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments. Sci Rep 6:37473","DOI":"10.1038\/srep37473"},{"key":"5257_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jwpe.2025.108991","volume":"79","author":"Y Yang","year":"2025","unstructured":"Yang Y, Fan LM, Wang XC, Chen X, Qiu LP, Xu HM, Li DD, Song C, Meng SL, Chen JZ (2025) In-situ pretreatment of aquaculture tail water by molasses addition and the responses of bacterioplankton communities (56, 104526, 2023). J Water Process Eng 79:1","journal-title":"J Water Process Eng"},{"key":"5257_CR8","doi-asserted-by":"publisher","first-page":"738907","DOI":"10.1016\/j.aquaculture.2022.738907","volume":"563","author":"SY Yuan","year":"2023","unstructured":"Yuan SY, Zhu WJ, Neori A, Zhang Y, Li M, Li J, Chang ZQ (2023) Benthic suspension-feeding clams affect sedimentary microbial communities and nitrogen cycling in seawater pond IMTA. Aquaculture 563:738907","journal-title":"Aquaculture"},{"key":"5257_CR32","first-page":"18","volume":"13","author":"Q Zhao","year":"2025","unstructured":"Zhao Q, Zhou K, Zhang FF, Wang Y, Hao J, Xie FX, Yang Q (2025) Relations Between Core Taxa and Metabolic Characteristics of Bacterial Communities in Litopenaeus vannamei Ponds and Their Probiotic Potential. Microorganisms 13:18","journal-title":"Microorganisms"},{"key":"5257_CR10","doi-asserted-by":"crossref","unstructured":"Zhou JZ, Ning DL (2017) Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol Rev 81(4):e00002-17","DOI":"10.1128\/MMBR.00002-17"}],"container-title":["World Journal of Microbiology and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11274-026-05257-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11274-026-05257-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11274-026-05257-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T09:13:32Z","timestamp":1790932412000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11274-026-05257-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":38,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["5257"],"URL":"https:\/\/doi.org\/10.1007\/s11274-026-05257-6","relation":{},"ISSN":["1573-0972"],"issn-type":[{"value":"1573-0972","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,9]]},"assertion":[{"value":"15 April 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 September 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no conflicts of interest.","order":1,"name":"Ethics","label":"Conflicts of interest","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"526"}}