{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"Research Square"}],"indexed":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T16:03:35Z","timestamp":1764605015119,"version":"3.46.0"},"posted":{"date-parts":[[2025,2,19]]},"group-title":"In Review","reference-count":72,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,10,17]]},"abstract":"<title>Abstract<\/title>\n                <p>\n                  Background\n Biological chitin degradation is a major process in the ocean, governed primarily by the action of microorganisms. It is now known that the structure and taxonomic profile of chitin-degrading microbial communities change across marine biotopes, but efforts to harness the chitin turnover potential within these communities in the laboratory have seldom been attempted. In this study, we characterized the prokaryotic communities associated with the marine sponge\n                  <italic>Sarcotragus spinosulus<\/italic>\n                  , the octocoral\n                  <italic>Eunicella labiata<\/italic>\n                  , and their surrounding sediment and seawater and applied an artificial selection procedure to enrich bacterial consortia capable of degrading chitin from the abovementioned biotopes. Throughout the procedure, chitin degradation was monitored, and the taxonomic composition of four successive enrichment cultures from each biotope were followed.\nResults\n The naturally occurring prokaryotic communities of the two host species were distinct from each other with specific taxa associated with each animal even though they were co-inhabiting the same geographic area. We found that members of the microbial rare biosphere were recruited in the enrichment cultures from all biotopes, while dominant bacterial symbionts likely to play a role in chitin degradation within marine sponges and octocorals remained \u201cunculturable\u201d under the conditions used in this study. Well-known chitin degraders such as\n                  <italic>Vibrio<\/italic>\n                  ,\n                  <italic>Pseudoalteromonas<\/italic>\n                  and\n                  <italic>Aquimarina<\/italic>\n                  , as well as other taxa not known or yet poorly known for their role(s) in chitin degradation such as\n                  <italic>Aureivirga<\/italic>\n                  ,\n                  <italic>Halodesulfovibrio<\/italic>\n                  ,\n                  <italic>Motilimonas<\/italic>\n                  ,\n                  <italic>Muricauda<\/italic>\n                  ,\n                  <italic>Psychromonas<\/italic>\n                  ,\n                  <italic>Poseidonibacter<\/italic>\n                  ,\n                  <italic>Reichenbachiella<\/italic>\n                  , and\n                  <italic>Thalassotalea<\/italic>\n                  , among others, were enriched using our artificial selection approach. Distinct chitin-degrading consortia were enriched from each marine biotope, highlighting the feasibility of this approach in fostering the discovery of novel microorganisms and enzymes involved in chitin degradation pathways of relevance in applied biotechnology.\nConclusion\n In this study, distinct bacterial consortia possessing moderate to high efficiencies at degrading chitin were unveiled. They were composed of a mix of known chitin degraders, known chitin utilizers and many taxa poorly or not yet known for their role(s) in chitin degradation such as\n                  <italic>Aureivirga<\/italic>\n                  ,\n                  <italic>Psychromonas, Motilimonas, Reichenbachiella, or Halodesulfovibrio<\/italic>\n                  . The latter taxa are potential key players in marine chitin degradation whose study could lead to the discovery of novel enzyme variants able to degrade chitin and its derivatives.\n                <\/p>","DOI":"10.21203\/rs.3.rs-3456333\/v1","type":"posted-content","created":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T01:34:16Z","timestamp":1739928856000},"source":"Crossref","is-referenced-by-count":0,"title":["An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes"],"prefix":"10.21203","author":[{"given":"Laurence","family":"Meunier","sequence":"first","affiliation":[{"name":"Universit\u00e9 Libre de Bruxelles"}]},{"given":"Tina","family":"Keller-Costa","sequence":"additional","affiliation":[{"name":"University of Lisbon"}]},{"given":"David","family":"Cannella","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Libre de Bruxelles"}]},{"given":"Jorge","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Universidade do Algarve (UALG)"}]},{"given":"Etienne","family":"Dechamps","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Libre de Bruxelles"}]},{"given":"Matilde","family":"Marques","sequence":"additional","affiliation":[{"name":"University of Lisbon"}]},{"given":"Rodrigo","family":"Costa","sequence":"additional","affiliation":[{"name":"University of Lisbon"}]},{"given":"Isabelle F.","family":"George","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Libre de Bruxelles"}]}],"member":"297","reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1007\/978-1-4684-7612-5_10","volume-title":"Advances in Microbial Ecology","author":"Gooday GW","year":"1990","unstructured":"Gooday GW. The Ecology of Chitin Degradation. In: Marshall KC, editor. Advances in Microbial Ecology. Boston, MA: Springer US; 1990. pp. 387\u2013430."},{"key":"ref2","doi-asserted-by":"crossref","DOI":"10.5962\/bhl.title.10734","volume-title":"Conditions of life in the sea: a short account of quantitative marine biological research","author":"Johnston J","year":"1908","unstructured":"Johnston J. Conditions of life in the sea: a short account of quantitative marine biological research. University; 1908."},{"key":"ref3","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1007\/s10126-011-9388-1","article-title":"The Importance of Chitin in the Marine Environment","volume":"13","author":"Souza CP","year":"2011","unstructured":"Souza CP, Almeida BC, Colwell RR, Rivera ING. The Importance of Chitin in the Marine Environment. Mar Biotechnol. 2011;13:823\u201330.","journal-title":"Mar Biotechnol"},{"key":"ref4","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2013.00149","article-title":"Bacterial chitin degradation\u2014mechanisms and ecophysiological strategies","volume":"4","author":"Beier S","year":"2013","unstructured":"Beier S, Bertilsson S. Bacterial chitin degradation\u2014mechanisms and ecophysiological strategies. Front Microbiol. 2013;4.","journal-title":"Front Microbiol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"5498","DOI":"10.1128\/AEM.68.11.5498-5507.2002","article-title":"Bacteria of the \u03b3-Subclass Proteobacteria Associated with Zooplankton in Chesapeake Bay","volume":"68","author":"Heidelberg JF","year":"2002","unstructured":"Heidelberg JF, Heidelberg KB, Colwell RR. Bacteria of the \u03b3-Subclass Proteobacteria Associated with Zooplankton in Chesapeake Bay. Appl Environ Microbiol. 2002;68:5498\u2013507.","journal-title":"Appl Environ Microbiol"},{"key":"ref6","first-page":"151","article-title":"Chitin and chitosan","author":"Poulicek M","year":"1989","unstructured":"Poulicek M, Jeauniaux C. Chitin and chitosan. Elsevier Appl Sci. 1989;:151\u20135.","journal-title":"Elsevier Appl Sci"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s40168-020-00970-2","article-title":"Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes","volume":"9","author":"Raimundo I","year":"2021","unstructured":"Raimundo I, Silva R, Meunier L, Valente SM, Lago-Lest\u00f3n A, Keller-Costa T, et al. Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes. Microbiome. 2021;9:43.","journal-title":"Microbiome"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/s40168-022-01343-7","article-title":"Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome","volume":"10","author":"Keller-Costa T","year":"2022","unstructured":"Keller-Costa T, Kozma L, Silva SG, Toscan R, Gon\u00e7alves J, Lago-Lest\u00f3n A, et al. Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome. Microbiome. 2022;10:151.","journal-title":"Microbiome"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"2771","DOI":"10.1128\/AEM.71.5.2771-2776.2005","article-title":"Investigation of the Microbial Ecology of Intertidal Hot Springs by Using Diversity Analysis of 16S rRNA and Chitinase Genes","volume":"71","author":"Hobel CFV","year":"2005","unstructured":"Hobel CFV, Marteinsson VT, Hreggvidsson G\u00d3, Kristj\u00e1nsson JK. Investigation of the Microbial Ecology of Intertidal Hot Springs by Using Diversity Analysis of 16S rRNA and Chitinase Genes. Appl Environ Microbiol. 2005;71:2771\u20136.","journal-title":"Appl Environ Microbiol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1007\/s00253-012-4057-5","article-title":"Mining of unexplored habitats for novel chitinases\u2014chiA as a helper gene proxy in metagenomics","volume":"94","author":"Cretoiu MS","year":"2012","unstructured":"Cretoiu MS, Kielak AM, Al-Soud WA, S\u00f8rensen SJ, van Elsas JD. Mining of unexplored habitats for novel chitinases\u2014chiA as a helper gene proxy in metagenomics. Appl Microbiol Biotechnol. 2012;94:1347\u201358.","journal-title":"Appl Microbiol Biotechnol"},{"year":"2023","author":"Silva R","key":"ref11","unstructured":"Silva R. Uncovering the chitin degradation potential of the microbiomes of marine sponges and octocorals (unpublished doctoral dissertation). Universidade de Lisboa, Instituto Superior T\u00e9cnico, Lisbon. Universidade de Lisboa, Instituto Superior T\u00e9cnico; 2023."},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2079","DOI":"10.1007\/s11274-009-0098-z","article-title":"Culture medium for isolating chitinolytic bacteria from seawater and plankton","volume":"25","author":"Souza CP","year":"2009","unstructured":"Souza CP, Burbano-Rosero EM, Almeida BC, Martins GG, Albertini LS, Rivera ING. Culture medium for isolating chitinolytic bacteria from seawater and plankton. World J Microbiol Biotechnol. 2009;25:2079\u201382.","journal-title":"World J Microbiol Biotechnol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1186\/s40168-019-0702-x","article-title":"Understanding microbial community dynamics to improve optimal microbiome selection","volume":"7","author":"Wright RJ","year":"2019","unstructured":"Wright RJ, Gibson MI, Christie-Oleza JA. Understanding microbial community dynamics to improve optimal microbiome selection. Microbiome. 2019;7:85.","journal-title":"Microbiome"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1128\/aem.59.6.1717-1724.1993","article-title":"Selection of Xenobiotic-Degrading Microorganisms in a Biphasic Aqueous-Organic System","volume":"59","author":"Ascon-Cabrera M","year":"1993","unstructured":"Ascon-Cabrera M, Lebeault J-M. Selection of Xenobiotic-Degrading Microorganisms in a Biphasic Aqueous-Organic System. Appl Environ Microbiol. 1993;59:1717\u201324.","journal-title":"Appl Environ Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1046\/j.1462-2920.2000.00140.x","article-title":"Artificial selection of microbial ecosystems for 3-chloroaniline biodegradation","volume":"2","author":"Swenson W","year":"2000","unstructured":"Swenson W, Arendt J, Wilson DS. Artificial selection of microbial ecosystems for 3-chloroaniline biodegradation. Environ Microbiol. 2000;2:564\u201371.","journal-title":"Environ Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1016\/j.tim.2021.03.002","article-title":"Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology","volume":"29","author":"Borchert E","year":"2021","unstructured":"Borchert E, Hammerschmidt K, Hentschel U, Deines P. Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology. Trends Microbiol. 2021;29:908\u201318.","journal-title":"Trends Microbiol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.jgeb.2013.03.001","article-title":"Isolation of novel chitinolytic bacteria and production optimization of extracellular chitinase","volume":"11","author":"Saima KM","year":"2013","unstructured":"Saima KM, Roohi, Ahmad IZ. Isolation of novel chitinolytic bacteria and production optimization of extracellular chitinase. J Genetic Eng Biotechnol. 2013;11:39\u201346.","journal-title":"J Genetic Eng Biotechnol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1007\/s10311-019-00904-x","article-title":"Applications of chitosan in food, pharmaceuticals, medicine, cosmetics, agriculture, textiles, pulp and paper, biotechnology, and environmental chemistry","volume":"17","author":"Morin-Crini N","year":"2019","unstructured":"Morin-Crini N, Lichtfouse E, Torri G, Crini G. Applications of chitosan in food, pharmaceuticals, medicine, cosmetics, agriculture, textiles, pulp and paper, biotechnology, and environmental chemistry. Environ Chem Lett. 2019;17:1667\u201392.","journal-title":"Environ Chem Lett"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"230","DOI":"10.3390\/md14120230","article-title":"Biological Potential of Chitinolytic Marine Bacteria","volume":"14","author":"Paulsen SS","year":"2016","unstructured":"Paulsen SS, Andersen B, Gram L, Machado H. Biological Potential of Chitinolytic Marine Bacteria. Mar Drugs. 2016;14:230.","journal-title":"Mar Drugs"},{"key":"ref20","first-page":"108","article-title":"Extraction and characterisation of chitin and chitosan from mussel shell","volume":"3","author":"Abdulkarim A","year":"2013","unstructured":"Abdulkarim A, Isa MT, Abdulsalam S, Muhammad AJ, Ameh AO. Extraction and characterisation of chitin and chitosan from mussel shell. Civil Environ Res. 2013;3:108\u201314.","journal-title":"Civil Environ Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"7482","DOI":"10.1128\/AEM.02483-13","article-title":"Cooperative Degradation of Chitin by Extracellular and Cell Surface-Expressed Chitinases from Paenibacillus sp. Strain FPU-7","volume":"79","author":"Itoh T","year":"2013","unstructured":"Itoh T, Hibi T, Fujii Y, Sugimoto I, Fujiwara A, Suzuki F, et al. Cooperative Degradation of Chitin by Extracellular and Cell Surface-Expressed Chitinases from Paenibacillus sp. Strain FPU-7. Appl Environ Microbiol. 2013;79:7482\u201390.","journal-title":"Appl Environ Microbiol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.tifs.2015.11.007","article-title":"Industrial applications of crustacean by-products (chitin, chitosan, and chitooligosaccharides): A review","volume":"48","author":"Hamed I","year":"2016","unstructured":"Hamed I, \u00d6zogul F, Regenstein JM. Industrial applications of crustacean by-products (chitin, chitosan, and chitooligosaccharides): A review. Trends Food Sci Technol. 2016;48:40\u201350.","journal-title":"Trends Food Sci Technol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1016\/j.ijbiomac.2018.08.139","article-title":"Extraction, chemical modification and characterization of chitin and chitosan","volume":"120","author":"Knidri H","year":"2018","unstructured":"El Knidri H, Belaabed R, Addaou A, Laajeb A, Lahsini A. Extraction, chemical modification and characterization of chitin and chitosan. Int J Biol Macromol. 2018;120:1181\u20139.","journal-title":"Int J Biol Macromol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"fix143","DOI":"10.1093\/femsec\/fix143","article-title":"The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation","volume":"93","author":"Keller-Costa T","year":"2017","unstructured":"Keller-Costa T, Eriksson D, Gon\u00e7alves JMS, Gomes NCM, Lago-Lest\u00f3n A, Costa R. The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation. FEMS Microbiol Ecol. 2017;93:fix143.","journal-title":"FEMS Microbiol Ecol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3865","DOI":"10.1039\/c0jm03075a","article-title":"Novel hydrogels prepared via direct dissolution of chitin at low temperature: structure and biocompatibility","volume":"21","author":"Chang C","year":"2011","unstructured":"Chang C, Chen S, Zhang L. Novel hydrogels prepared via direct dissolution of chitin at low temperature: structure and biocompatibility. J Mater Chem. 2011;21:3865.","journal-title":"J Mater Chem"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/B978-0-323-39500-7.00002-2","volume-title":"Introduction to Plastics Engineering","author":"Shrivastava A","year":"2018","unstructured":"Shrivastava A. Polymerization. Introduction to Plastics Engineering. Elsevier; 2018. pp. 17\u201348."},{"year":"2023","author":"Kassambara A","key":"ref27","unstructured":"Kassambara A, ggpubr. \u2018ggplot2\u2019 Based Publication Ready Plots. GitHub. 2023. https:\/\/github.com\/cran\/ggpubr. Accessed 14 Apr 2023."},{"key":"ref28","doi-asserted-by":"crossref","first-page":"129","DOI":"10.3354\/ame01753","article-title":"Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton","volume":"75","author":"Apprill A","year":"2015","unstructured":"Apprill A, McNally S, Parsons R, Weber L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Microb Ecol. 2015;75:129\u201337.","journal-title":"Aquat Microb Ecol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1111\/1462-2920.13023","article-title":"Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples","volume":"18","author":"Parada AE","year":"2016","unstructured":"Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403\u201314.","journal-title":"Environ Microbiol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan BJ","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581\u20133.","journal-title":"Nat Methods"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1944-3277-10-18","article-title":"Large-scale contamination of microbial isolate genomes by Illumina PhiX control","volume":"10","author":"Mukherjee S","year":"2015","unstructured":"Mukherjee S, Huntemann M, Ivanova N, Kyrpides NC, Pati A. Large-scale contamination of microbial isolate genomes by Illumina PhiX control. Stand Genomic Sci. 2015;10:18.","journal-title":"Stand Genomic Sci"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast C","year":"2012","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590\u20136.","journal-title":"Nucleic Acids Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"D643","DOI":"10.1093\/nar\/gkt1209","article-title":"The SILVA and All-species Living Tree Project (LTP) taxonomic frameworks","volume":"42","author":"Yilmaz P","year":"2014","unstructured":"Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and All-species Living Tree Project (LTP) taxonomic frameworks. Nucl Acids Res. 2014;42:D643\u20138.","journal-title":"Nucl Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data","volume":"8","author":"McMurdie PJ","year":"2013","unstructured":"McMurdie PJ, Holmes S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE. 2013;8:1\u201311.","journal-title":"PLoS ONE"},{"year":"2023","author":"Wickham H","key":"ref35","unstructured":"Wickham H, Fran\u00e7ois R, Henry L, M\u00fcller K, Vaughan D, Software P et al. dplyr: A Grammar of Data Manipulation. 2023. https:\/\/CRAN.R-project.org\/package=dplyr. Accessed 15 Apr 2023."},{"key":"ref36","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham H","year":"2016","unstructured":"Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer International Publishing; 2016."},{"year":"2013","author":"Oksanen J","key":"ref37","unstructured":"Oksanen J, Blanchet F, Kindt R, Legendre P, Minchin P. vegan: R package for community ecologists: popular ordination methods, ecological null models & diversity analysis. GitHub. 2013. https:\/\/github.com\/vegandevs\/vegan. Accessed 14 Apr 2023."},{"key":"ref38","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s40168-019-0659-9","article-title":"Wd*-test: robust distance-based multivariate analysis of variance","volume":"7","author":"Hamidi B","year":"2019","unstructured":"Hamidi B, Wallace K, Vasu C, Alekseyenko AV. Wd*-test: robust distance-based multivariate analysis of variance. Microbiome. 2019;7:51.","journal-title":"Microbiome"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"D666","DOI":"10.1093\/nar\/gky901","article-title":"IMG\/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes","volume":"47","author":"Chen I-MA","year":"2019","unstructured":"Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, et al. IMG\/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 2019;47:D666\u201377.","journal-title":"Nucleic Acids Res"},{"key":"ref40","article-title":"Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges","volume":"5","author":"Hardoim CCP","year":"2014","unstructured":"Hardoim CCP, Cardinale M, C\u00f9cio ACB, Esteves AIS, Berg G, Xavier JR et al. Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges. Front Microbiol. 2014;5.","journal-title":"Front Microbiol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/s41579-021-00604-w","article-title":"Priority effects in microbiome assembly","volume":"20","author":"Debray R","year":"2022","unstructured":"Debray R, Herbert RA, Jaffe AL, Crits-Christoph A, Power ME, Koskella B. Priority effects in microbiome assembly. Nat Rev Microbiol. 2022;20:109\u201321.","journal-title":"Nat Rev Microbiol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/ismej.2010.164","article-title":"Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis","volume":"5","author":"Burke C","year":"2011","unstructured":"Burke C, Thomas T, Lewis M, Steinberg P, Kjelleberg S. Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis. ISME J. 2011;5:590\u2013600.","journal-title":"ISME J"},{"key":"ref43","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2017.00204","article-title":"Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery","volume":"8","author":"Califano G","year":"2017","unstructured":"Califano G, Castanho S, Soares F, Ribeiro L, Cox CJ, Mata L et al. Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery. Front Microbiol. 2017;8.","journal-title":"Front Microbiol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1111\/are.15648","article-title":"Effects of live feed manipulation with algal-derived antimicrobial metabolites on fish larvae microbiome assembly: A molecular-based assessment","volume":"53","author":"Sanches-Fernandes GMM","year":"2022","unstructured":"Sanches-Fernandes GMM, Califano G, Castanho S, Soares F, Ribeiro L, Pous\u00e3o-Ferreira P, et al. Effects of live feed manipulation with algal-derived antimicrobial metabolites on fish larvae microbiome assembly: A molecular-based assessment. Aquac Res. 2022;53:1062\u201383.","journal-title":"Aquac Res"},{"key":"ref45","first-page":"318","article-title":"A tentative direct microscopic method for counting living marine bacteria","volume":"26","author":"Kogure K","year":"1979","unstructured":"Kogure K, Shimizu U, Taga N. A tentative direct microscopic method for counting living marine bacteria. Can J Microbiol. 1979;26:318\u201323.","journal-title":"Can J Microbiol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1146\/annurev.mi.39.100185.001541","article-title":"Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats","volume":"39","author":"Staley JT","year":"1985","unstructured":"Staley JT, Konopka A. Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats. Annu Rev Microbiol. 1985;39:321\u201346.","journal-title":"Annu Rev Microbiol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1128\/mr.59.1.143-169.1995","article-title":"Phylogenetic identification and in situ detection of individual microbial cells without cultivation","volume":"59","author":"Amann RI","year":"1995","unstructured":"Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143\u201369.","journal-title":"Microbiol Rev"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1111\/j.1574-6941.2001.tb00888.x","article-title":"Temporal variation of the microbial community associated with the mediterranean sponge Aplysina aerophoba","volume":"38","author":"Friedrich AB","year":"2001","unstructured":"Friedrich AB, Fischer I, Proksch P, Hacker J, Hentschel U. Temporal variation of the microbial community associated with the mediterranean sponge Aplysina aerophoba. FEMS Microbiol Ecol. 2001;38:105\u201313.","journal-title":"FEMS Microbiol Ecol"},{"key":"ref49","first-page":"843","article-title":"The culturable microbial community of the Great Barrier Reef sponge Rhopaloeides odorabile is dominated by an alpha-proteobacterium","volume":"138","author":"Webster NS","year":"2001","unstructured":"Webster NS, Hill RT. The culturable microbial community of the Great Barrier Reef sponge Rhopaloeides odorabile is dominated by an alpha-proteobacterium. 2001;138:843\u201351."},{"key":"ref50","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/ismej.2012.111","article-title":"Sponge-specific\u2019 bacteria are widespread (but rare) in diverse marine environments","volume":"7","author":"Taylor MW","year":"2013","unstructured":"Taylor MW, Tsai P, Simister RL, Deines P, Botte E, Ericson G, et al. Sponge-specific\u2019 bacteria are widespread (but rare) in diverse marine environments. ISME J. 2013;7:438\u201343.","journal-title":"ISME J"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"5422","DOI":"10.1128\/AEM.00410-08","article-title":"Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere","volume":"74","author":"Elshahed MS","year":"2008","unstructured":"Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, et al. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere. Appl Environ Microbiol. 2008;74:5422\u20138.","journal-title":"Appl Environ Microbiol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nrmicro3400","article-title":"Ecology and exploration of the rare biosphere","volume":"13","author":"Lynch MDJ","year":"2015","unstructured":"Lynch MDJ, Neufeld JD. Ecology and exploration of the rare biosphere. Nat Rev Microbiol. 2015;13:217\u201329.","journal-title":"Nat Rev Microbiol"},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01371-14","article-title":"Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity","volume":"5","author":"Shade A","year":"2014","unstructured":"Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, et al. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity. mBio. 2014;5. 10.1128\/mbio.01371-14.","journal-title":"mBio"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.envpol.2014.07.024","article-title":"Rare biosphere\u2019 bacteria as key phenanthrene degraders in coastal seawaters","volume":"194","author":"Sauret C","year":"2014","unstructured":"Sauret C, S\u00e9verin T, V\u00e9tion G, Guigue C, Goutx M, Pujo-Pay M, et al. Rare biosphere\u2019 bacteria as key phenanthrene degraders in coastal seawaters. Environ Pollut. 2014;194:246\u201353.","journal-title":"Environ Pollut"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1128\/AEM.02625-15","article-title":"From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation","volume":"82","author":"Fuentes S","year":"2016","unstructured":"Fuentes S, Barra B, Caporaso JG, Seeger M. From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation. Appl Environ Microbiol. 2016;82:888\u201396.","journal-title":"Appl Environ Microbiol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"e03321","DOI":"10.1128\/AEM.03321-16","article-title":"Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem","volume":"83","author":"Wang Y","year":"2017","unstructured":"Wang Y, Hatt JK, Tsementzi D, Rodriguez -RLM, Ruiz-P\u00e9rez CA, Weigand MR, et al. Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem. Appl Environ Microbiol. 2017;83:e03321\u201316.","journal-title":"Appl Environ Microbiol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"423","DOI":"10.3390\/md20070423","article-title":"Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere","volume":"20","author":"Silva SG","year":"2022","unstructured":"Silva SG, Paula P, Da Silva JP, Mil-Homens D, Teixeira MC, Fialho AM, et al. Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere. Mar Drugs. 2022;20:423.","journal-title":"Mar Drugs"},{"key":"ref58","first-page":"21","article-title":"Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals","author":"Keller-Costa T","year":"2021","unstructured":"Keller-Costa T. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. 2021;:21."},{"key":"ref59","doi-asserted-by":"crossref","first-page":"573588","DOI":"10.3389\/fmicb.2020.573588","article-title":"Aquimarina sp. Associated With a Cuticular Disease of Cultured Larval Palinurid and Scyllarid Lobsters","volume":"11","author":"Ooi MC","year":"2020","unstructured":"Ooi MC, Goulden EF, Trotter AJ, Smith GG, Bridle AR. Aquimarina sp. Associated With a Cuticular Disease of Cultured Larval Palinurid and Scyllarid Lobsters. Front Microbiol. 2020;11:573588.","journal-title":"Front Microbiol"},{"key":"ref60","first-page":"422","article-title":"Cloning and expression analysis of a chitinase gene Crchi1 from the mycoparasitic fungus Clonostachys rosea (syn. Gliocladium roseum)","volume":"45","author":"Gan Z","year":"2007","unstructured":"Gan Z, Yang J, Tao N, Yu Z, Zhang K-Q. Cloning and expression analysis of a chitinase gene Crchi1 from the mycoparasitic fungus Clonostachys rosea (syn. Gliocladium roseum). J Microbiol. 2007;45:422\u201330.","journal-title":"J Microbiol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"e20210663","DOI":"10.1590\/0103-8478cr20210663","article-title":"Cloning, expression and antifungal effect of the recombinant chitinase from Streptomyces sampsonii KJ40","volume":"53","author":"Wang S","year":"2023","unstructured":"Wang S, Fang X, Liang K, Li S, Han S, Zhu T. Cloning, expression and antifungal effect of the recombinant chitinase from Streptomyces sampsonii KJ40. Cienc Rural. 2023;53:e20210663.","journal-title":"Cienc Rural"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1128\/aem.63.2.408-413.1997","article-title":"Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin","volume":"63","author":"Svitil AL","year":"1997","unstructured":"Svitil AL, Chadhain S, Moore JA, Kirchman DL. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin. Appl Environ Microbiol. 1997;63:408\u201313.","journal-title":"Appl Environ Microbiol"},{"year":"2020","author":"Laribi-Habchi H","key":"ref63","unstructured":"Laribi-Habchi H, Bouacem K, Allala F, Jabeur F, Selama O, Mechri S et al. Characterization of chitinase from Shewanella inventionis HE3 with bio-insecticidal effect against granary weevil, Sitophilus granarius Linnaeus (Coleoptera: Curculionidae). Process Biochemistry. 2020;97:222\u201333."},{"key":"ref64","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1099\/13500872-145-4-925","article-title":"Multiple genes involved in chitin degradation from the marine bacterium Pseudoalteromonas sp. strain S91","volume":"145","author":"Techkarnjanaruk S","year":"1999","unstructured":"Techkarnjanaruk S, Goodman AE. Multiple genes involved in chitin degradation from the marine bacterium Pseudoalteromonas sp. strain S91. Microbiology. 1999;145:925\u201334.","journal-title":"Microbiology"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"7044","DOI":"10.1128\/JB.183.24.7044-7052.2001","article-title":"Characterization of Pseudomonas aeruginosa Chitinase, a Gradually Secreted Protein","volume":"183","author":"Folders J","year":"2001","unstructured":"Folders J, Algra J, Roelofs MS, van Loon LC, Tommassen J, Bitter W. Characterization of Pseudomonas aeruginosa Chitinase, a Gradually Secreted Protein. J Bacteriol. 2001;183:7044\u201352.","journal-title":"J Bacteriol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"14395","DOI":"10.1038\/srep14395","article-title":"Enhanced nematicidal potential of the chitinase pachi from Pseudomonas aeruginosa in association with Cry21Aa","volume":"5","author":"Chen L","year":"2015","unstructured":"Chen L, Jiang H, Cheng Q, Chen J, Wu G, Kumar A, et al. Enhanced nematicidal potential of the chitinase pachi from Pseudomonas aeruginosa in association with Cry21Aa. Sci Rep. 2015;5:14395.","journal-title":"Sci Rep"},{"key":"ref67","article-title":"Aquimarina algiphila sp. nov., a chitin degrading bacterium isolated from the red alga Tichocarpus crinitus","volume":"68","author":"Nedashkovskaya O","year":"2018","unstructured":"Nedashkovskaya O, Kim S-G, Stenkova A, Kukhlevskiy A, Zhukova N, Mikhailov V. Aquimarina algiphila sp. nov., a chitin degrading bacterium isolated from the red alga Tichocarpus crinitus. Int J Syst Evol MicroBiol. 2018;68.","journal-title":"Int J Syst Evol MicroBiol"},{"key":"ref68","first-page":"1135","article-title":"Purification and characterization of beta-N-acetylglucosaminidase from Alteromonas sp. strain O-7. Bioscience, biotechnology, and biochemistry","volume":"59","author":"Tsujibo H","year":"1995","unstructured":"Tsujibo H, Fujimoto K, Kimura Y, Miyamoto K, Imada C, Okami Y et al. Purification and characterization of beta-N-acetylglucosaminidase from Alteromonas sp. strain O-7. Bioscience, biotechnology, and biochemistry. 1995;59:1135\u20136."},{"year":"2022","author":"Daniels M","key":"ref69","unstructured":"Daniels M, Stubbusch AKM, Held NA, Schubert OT, Ackermann M. Effects of interspecies interactions on marine community ecosystem function. preprint. Microbiology; 2022."},{"key":"ref70","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/s41396-022-01312-w","article-title":"Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community","volume":"17","author":"Daniels M","year":"2023","unstructured":"Daniels M, van Vliet S, Ackermann M. Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community. ISME J. 2023;17:406\u201316.","journal-title":"ISME J"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"eabk3076","DOI":"10.1126\/sciadv.abk3076","article-title":"Metabolic cross-feeding structures the assembly of polysaccharide degrading communities","volume":"8","author":"Pontrelli S","year":"2022","unstructured":"Pontrelli S, Szabo R, Pollak S, Schwartzman J, Ledezma-Tejeida D, Cordero OX, et al. Metabolic cross-feeding structures the assembly of polysaccharide degrading communities. Sci Adv. 2022;8:eabk3076.","journal-title":"Sci Adv"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"108786","DOI":"10.1016\/j.soilbio.2022.108786","article-title":"Microbial utilization of simple and complex carbon compounds in a temperate forest soil","volume":"173","author":"Martinovi\u0107 T","year":"2022","unstructured":"Martinovi\u0107 T, Ma\u0161\u00ednov\u00e1 T, L\u00f3pez-Mond\u00e9jar R, Jansa J, \u0160tursov\u00e1 M, Starke R, et al. Microbial utilization of simple and complex carbon compounds in a temperate forest soil. Soil Biol Biochem. 2022;173:108786.","journal-title":"Soil Biol Biochem"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/www.researchsquare.com\/article\/rs-3456333\/v1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.researchsquare.com\/article\/rs-3456333\/v1.html","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T16:00:09Z","timestamp":1764604809000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.researchsquare.com\/article\/rs-3456333\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,19]]},"references-count":72,"URL":"https:\/\/doi.org\/10.21203\/rs.3.rs-3456333\/v1","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1186\/s12866-025-04218-7","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2025,2,19]]},"subtype":"preprint"}}