Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., & Nielsen, P. H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31, 533–538.
Article CAS PubMed Google Scholar
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019). Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857.
Article CAS PubMed PubMed Central Google Scholar
Bossier, P., & Ekasari, J. (2017). Biofloc technology application in aquaculture to support sustainable development goals. Microbial Biotechnology, 10, 1012–1016.
Article PubMed PubMed Central Google Scholar
Bovio-Winkler, P., Cabezas, A., & Etchebehere, C. (2024). Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses. ISME Communications, 4, ycae050.
Cardona, E., Gueguen, Y., Magré, K., Lorgeoux, B., Piquemal, D., Pierrat, F., Noguier, F., & Saulnier, D. (2016). Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system. BMC Microbiology, 16, 1–9.
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2022). GTDB-Tk v2: Memory friendly classification with the genome taxonomy database. Bioinformatics, 38, 5315–5316.
Article CAS PubMed PubMed Central Google Scholar
Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: A rapid, scalable, and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20, 1203–1212.
Article CAS PubMed Google Scholar
Crab, R., Defoirdt, T., Bossier, P., & Verstraete, W. (2012). Biofloc technology in aquaculture: Beneficial effects and future challenges. Aquaculture, 356, 351–356.
Cytryn, E., van Rijn, J., Schramm, A., Gieseke, A., de Beer, D., & Minz, D. (2005). Identification of bacteria potentially responsible for oxic and anoxic sulfide oxidation in biofilters of a recirculating mariculture system. Applied and Environmental Microbiology, 71, 6134–6141.
Article CAS PubMed PubMed Central Google Scholar
Dang, H., & Lovell, C. R. (2016). Microbial surface colonization and biofilm development in marine environments. Microbiology and Molecular Biology Reviews, 80, 91–138.
Article CAS PubMed Google Scholar
Dashtbin, R., Mahmoudi, N., Besharati, H., & Lalevic, B. (2023). Identification of sulfur-oxidizing bacteria from fishponds and their performance to remove hydrogen sulfide under aquarium conditions. Brazilian Journal of Microbiology, 54, 3163–3172.
Article CAS PubMed PubMed Central Google Scholar
Deng, C., Zhao, R., Qiu, Z., Li, B., Zhang, T., Guo, F., Mu, R., Wu, Y., Qiao, X., Zhang, L., et al. (2022). Genome-centric metagenomics provides new insights into the microbial community and metabolic potential of landfill leachate microbiota. Science of the Total Environment, 816, 151635.
Article CAS PubMed Google Scholar
Deng, M., Chen, J., Gou, J., Hou, J., Li, D., & He, X. (2018). The effect of different carbon sources on water quality, microbial community, and structure of biofloc systems. Aquaculture, 482, 103–110.
Deng, M., Dai, Z., Senbati, Y., Li, L., Song, K., & He, X. (2020). Aerobic denitrification microbial community and function in zero-discharge recirculating aquaculture system using a single biofloc-based suspended growth reactor: Influence of the carbon-to-nitrogen ratio. Frontiers in Microbiology, 11, 1760.
Article PubMed PubMed Central Google Scholar
Ding, W., Wang, S., Qin, P., Fan, S., Su, X., Cai, P., Lu, J., Cui, H., Wang, M., Shu, Y., et al. (2023). Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms. Nature Communications, 14, 2033.
Article CAS PubMed PubMed Central Google Scholar
Dogs, M., Wemheuer, B., Wolter, L., Bergen, N., Daniel, R., Simon, M., & Brinkhoff, T. (2017). Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Systematic and Applied Microbiology, 40, 370–382.
Article CAS PubMed Google Scholar
Dong, P., Guo, H., Huang, L., Zhang, D., & Wang, K. (2023). Glucose addition improves the culture performance of Pacific white shrimp by regulating the assembly of Rhodobacteraceae taxa in the gut bacterial community. Aquaculture, 567, 739254.
Durazzi, F., Sala, C., Castellani, G., Manfreda, G., Remondini, D., & De Cesare, A. (2021). Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota. Scientific Reports, 11, 3030.
Article CAS PubMed PubMed Central Google Scholar
Elifantz, H., Horn, G., Ayon, M., Cohen, Y., & Minz, D. (2013). Rhodobacteraceae are the key members of the microbial community of the initial biofilm formed in Eastern Mediterranean coastal seawater. FEMS Microbiology Ecology, 85, 348–357.
Article CAS PubMed Google Scholar
Guo, H., Fu, X., He, J., Wang, R., Yan, M., Wang, J., Dong, P., Huang, L., & Zhang, D. (2023a). Gut bacterial consortium enriched in a biofloc system protects shrimp against Vibrio parahaemolyticus infection. Microbiome, 11, 230.
Article CAS PubMed PubMed Central Google Scholar
Guo, H., Huang, L., Hu, S., Chen, C., Huang, X., Liu, W., Wang, S., Zhu, Y., Zhao, Y., & Zhang, D. (2020). Effects of carbon/nitrogen ratio on growth, intestinal microbiota, and metabolome of shrimp (Litopenaeus vannamei). Frontiers in Microbiology, 11, 652.
Article PubMed PubMed Central Google Scholar
Guo, X., Lai, C. Y., Hartmann, E. M., & Zhao, H. P. (2023b). Heterotrophic denitrification: An overlooked factor that contributes to nitrogen removal in n-DAMO mixed culture. Environmental Research, 216, 114802.
Article CAS PubMed Google Scholar
Hao, Z. L., Ali, A., Ren, Y., Su, J. F., & Wang, Z. (2022). A mechanistic review on aerobic denitrification for nitrogen removal in water treatment. Science of the Total Environment, 847, 157452.
Article CAS PubMed Google Scholar
Huang, L., Guo, H., Chen, C., Huang, X., Chen, W., Bao, F., Liu, W., Wang, S., & Zhang, D. (2020). The bacteria from large-sized bioflocs are more associated with the shrimp gut microbiota in culture system. Aquaculture, 523, 735159.
Jeong, S.-W., Han, J. E., Lee, J.-Y., Yoo, J.-H., Kim, D.-Y., Jeong, I. C., Choi, J. W., Jeong, Y. S., Lee, J. Y., Lee, S. Y., et al. (2022). Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish. Journal of Microbiology, 60, 576–584.
Article CAS PubMed Google Scholar
Kang, S., Lee, J.-Y., Han, J. E., Jeong, Y.-S., Gim, D.-H., & Bae, J.-W. (2022). Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead). Journal of Microbiology, 60, 890–898.
Article CAS PubMed Google Scholar
Khanjani, M. H., Mohammadi, A., & Emerenciano, M. G. C. (2022). Microorganisms in biofloc aquaculture system. Aquaculture Reports, 26, 101300.
Kim, S.-J., Kim, Y.-S., Kim, S.-E., Jung, H.-K., Park, J., Yu, M.-J., & Kim, K.-H. (2022a). Rasiella rasia gen. nov. sp. nov. within the family Flavobacteriaceae isolated from seawater recirculating aquaculture system. Journal of Microbiology, 60, 1070–1076.
Kim, S. K., Song, J., Rajeev, M., Kim, S. K., Kang, I., Jang, I. K., & Cho, J. C. (2022b). Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp (Litopenaeus vannamei) aquaculture system. Frontiers in Microbiology, 13, 995699.
Article PubMed PubMed Central Google Scholar
Lapébie, P., Lombard, V., Drula, E., Terrapon, N., & Henrissat, B. (2019). Bacteroidetes use thousands of enzyme combinations to break down glycans. Nature Communications, 10, 2043.
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