{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T02:29:48Z","timestamp":1793327388659,"version":"4.5.0"},"reference-count":89,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,7,26]],"date-time":"2025-07-26T00:00:00Z","timestamp":1753488000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,7,26]],"date-time":"2025-07-26T00:00:00Z","timestamp":1753488000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100019559","name":"Carl von Ossietzky Universit\u00e4t Oldenburg","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100019559","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:p>Salt marshes are ecologically important ecosystems with dynamic nutrient exchange between land and sea. Their zonation along an elevation gradient supports specific communities exhibiting successional patterns. Previous studies have mainly focused on individual domains, with limited attempts to explore interdependencies of community assemblies across domains. Here, we investigated the co-occurrence of prokaryotes and microeukaryotes in natural salt marsh sediments and experimental islands placed in the adjacent tidal flat. The islands contained originally bare and transplanted plots at three different elevations, corresponding to the typical salt marsh zonation. After initial disturbance by the artificial setting, microbial metacommunities re-assembled along the elevation gradient, showing distinct community compositions comparable to those of the natural salt marsh zones. Interkingdom co-occurrence network analysis revealed sub-communities linked to the natural and artificial settings, with <jats:italic>Woeseiaceae<\/jats:italic>, <jats:italic>Flavobacteriaceae<\/jats:italic>, and <jats:italic>Rhodobacteraceae<\/jats:italic> playing important roles as keystone species. The community assembly was primarily driven by habitat filtering. In conclusion, this study provides insights into the assembly, co-occurrence patterns and recovery of microbial communities in salt marsh sediments. The research highlights the importance of elevation in shaping microbial communities. Understanding these ecological mechanisms is crucial for effective salt marsh protection and conservation facing potential threats like strong disturbances by enhanced storm surges.<\/jats:p>","DOI":"10.1038\/s41598-025-12995-4","type":"journal-article","created":{"date-parts":[[2025,7,26]],"date-time":"2025-07-26T02:09:29Z","timestamp":1753495769000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Microbial metacommunity of salt marshes rebuilds along an elevational gradient after initial disturbance"],"prefix":"10.1038","volume":"15","author":[{"given":"Dennis Alexander","family":"Tebbe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne","family":"Yong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Smykala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucie","family":"Kuczynski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel Lanza","family":"Gued\u00e1n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kertu","family":"L\u00f5hmus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Pieck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"Poehlein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendrik","family":"Sch\u00e4fer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"K\u00f6nneke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie D.","family":"Moorthi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bert","family":"Engelen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,7,26]]},"reference":[{"key":"12995_CR1","doi-asserted-by":"publisher","DOI":"10.3390\/jmse8100767","author":"DM Alongi","year":"2020","unstructured":"Alongi, D. M. Carbon balance in salt marsh and mangrove ecosystems: A global synthesis. J. Mar. Sci. Eng. https:\/\/doi.org\/10.3390\/jmse8100767 (2020).","journal-title":"J. Mar. Sci. Eng."},{"key":"12995_CR2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10050859","author":"DA Tebbe","year":"2022","unstructured":"Tebbe, D. A. et al. Seasonal and zonal succession of bacterial communities in North Sea salt marsh sediments. Microorganisms https:\/\/doi.org\/10.3390\/microorganisms10050859 (2022).","journal-title":"Microorganisms"},{"key":"12995_CR3","doi-asserted-by":"publisher","first-page":"1984","DOI":"10.1038\/ismej.2015.254","volume":"10","author":"F Dini-Andreote","year":"2016","unstructured":"Dini-Andreote, F., Pylro, V. S., Baldrian, P., van Elsas, J. D. & Salles, J. F. Ecological succession reveals potential signatures of marine-terrestrial transition in salt marsh fungal communities. ISME J. 10, 1984\u20131997. https:\/\/doi.org\/10.1038\/ismej.2015.254 (2016).","journal-title":"ISME J."},{"key":"12995_CR4","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1111\/jpy.12031","volume":"49","author":"L Ribeiro","year":"2013","unstructured":"Ribeiro, L., Brotas, V., Rince, Y. & Jesus, B. Structure and diversity of intertidal benthic diatom assemblages in contrasting shores: A case study from the Tagus estuary. J. Phycol. 49, 258\u2013270. https:\/\/doi.org\/10.1111\/jpy.12031 (2013).","journal-title":"J. Phycol."},{"key":"12995_CR5","doi-asserted-by":"publisher","first-page":"98","DOI":"10.3389\/fpls.2018.00098","volume":"9","author":"R Redelstein","year":"2018","unstructured":"Redelstein, R., Dinter, T., Hertel, D. & Leuschner, C. Effects of inundation, nutrient availability and plant species diversity on fine root mass and morphology across a saltmarsh flooding gradient. Front. Plant Sci. 9, 98. https:\/\/doi.org\/10.3389\/fpls.2018.00098 (2018).","journal-title":"Front. Plant Sci."},{"key":"12995_CR6","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/s12237-018-0420-9","volume":"42","author":"CN Janousek","year":"2019","unstructured":"Janousek, C. N., Thorne, K. M. & Takekawa, J. Y. Vertical zonation and niche breadth of tidal marsh plants along the northeast Pacific coast. Estuaries Coasts 42, 85\u201398. https:\/\/doi.org\/10.1007\/s12237-018-0420-9 (2019).","journal-title":"Estuaries Coasts"},{"key":"12995_CR7","doi-asserted-by":"publisher","first-page":"2869","DOI":"10.1890\/0012-9658(2002)083[2869:Rocwtr]2.0.Co;2","volume":"83","author":"JT Morris","year":"2002","unstructured":"Morris, J. T., Sundareshwar, P. V., Nietch, C. T., Kjerfve, B. & Cahoon, D. R. Responses of coastal wetlands to rising sea level. Ecology 83, 2869\u20132877. https:\/\/doi.org\/10.1890\/0012-9658(2002)083[2869:Rocwtr]2.0.Co;2 (2002).","journal-title":"Ecology"},{"key":"12995_CR8","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1007\/BF00572685","volume":"44","author":"JB Zedler","year":"1980","unstructured":"Zedler, J. B., Winfield, T. & Williams, P. Salt marsh productivity with natural and altered tidal circulation. Oecologia 44, 236\u2013240. https:\/\/doi.org\/10.1007\/BF00572685 (1980).","journal-title":"Oecologia"},{"key":"12995_CR9","doi-asserted-by":"publisher","DOI":"10.1071\/mf07164","author":"BM Spears","year":"2008","unstructured":"Spears, B. M., Saunders, J. E., Davidson, I. & Paterson, D. M. Microalgal sediment biostabilisation along a salinity gradient in the Eden Estuary, Scotland: Unravelling a paradox. Mar. Freshw. Res. https:\/\/doi.org\/10.1071\/mf07164 (2008).","journal-title":"Mar. Freshw. Res."},{"key":"12995_CR10","doi-asserted-by":"publisher","first-page":"223","DOI":"10.4319\/lo.1989.34.1.0223","volume":"34","author":"DM Paterson","year":"1989","unstructured":"Paterson, D. M. Short-term changes in the erodibility of intertidal cohesive sediments related to the migratory behavior of epipelic diatoms. Limnol. Oceanogr. 34, 223\u2013234. https:\/\/doi.org\/10.4319\/lo.1989.34.1.0223 (1989).","journal-title":"Limnol. Oceanogr."},{"key":"12995_CR11","doi-asserted-by":"publisher","first-page":"781","DOI":"10.2307\/1313569","volume":"49","author":"SW Wilhelm","year":"1999","unstructured":"Wilhelm, S. W. & Suttle, C. A. Viruses and nutrient cycles in the sea-Viruses play critical roles in the structure and function of aquatic food webs. Bioscience 49, 781\u2013788. https:\/\/doi.org\/10.2307\/1313569 (1999).","journal-title":"Bioscience"},{"key":"12995_CR12","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.protis.2016.01.001","volume":"167","author":"K Dumack","year":"2016","unstructured":"Dumack, K., Muller, M. E. & Bonkowski, M. Description of Lecythium terrestris sp nov (Chlamydophryidae, Cercozoa), a soil dwelling protist feeding on fungi and algae. Protist 167, 93\u2013105. https:\/\/doi.org\/10.1016\/j.protis.2016.01.001 (2016).","journal-title":"Protist"},{"key":"12995_CR13","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.3389\/fmicb.2015.01214","volume":"6","author":"H Montanie","year":"2015","unstructured":"Montanie, H., De Crignis, M. G. & Lavaud, J. Viral impact on prokaryotic and microalgal activities in the microphytobenthic biofilm of an intertidal mudflat (French Atlantic coast). Front. Microbiol. 6, 1214. https:\/\/doi.org\/10.3389\/fmicb.2015.01214 (2015).","journal-title":"Front. Microbiol."},{"key":"12995_CR14","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1126\/science.1218344","volume":"336","author":"H Teeling","year":"2012","unstructured":"Teeling, H. et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336, 608\u2013611. https:\/\/doi.org\/10.1126\/science.1218344 (2012).","journal-title":"Science"},{"key":"12995_CR15","doi-asserted-by":"publisher","first-page":"S69","DOI":"10.1016\/s0959-3780(99)00019-9","volume":"9","author":"R Nicholls","year":"1999","unstructured":"Nicholls, R., Hoozemans, F. & Marchand, M. Increasing flood risk and wetland losses due to global sea-level rise: Regional and global analyses. Glob. Environ. Change 9, S69\u2013S87. https:\/\/doi.org\/10.1016\/s0959-3780(99)00019-9 (1999).","journal-title":"Glob. Environ. Change"},{"key":"12995_CR16","doi-asserted-by":"publisher","DOI":"10.1007\/s13157-022-01628-5","author":"D de Paula","year":"2022","unstructured":"de Paula, D., Costa, M. & Macreadie, P. I. The evolution of blue carbon science. Wetlands https:\/\/doi.org\/10.1007\/s13157-022-01628-5 (2022).","journal-title":"Wetlands"},{"key":"12995_CR17","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1146\/annurev.marine.010908.163930","volume":"1","author":"KB Gedan","year":"2009","unstructured":"Gedan, K. B., Silliman, B. R. & Bertness, M. D. Centuries of human-driven change in salt marsh ecosystems. Ann. Rev. Mar. Sci. 1, 117\u2013141. https:\/\/doi.org\/10.1146\/annurev.marine.010908.163930 (2009).","journal-title":"Ann. Rev. Mar. Sci."},{"key":"12995_CR18","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/s40793-021-00377-y","volume":"16","author":"W Chen","year":"2021","unstructured":"Chen, W. & Wen, D. Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion. Environ. Microbiome 16, 10. https:\/\/doi.org\/10.1186\/s40793-021-00377-y (2021).","journal-title":"Environ. Microbiome"},{"key":"12995_CR19","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1007\/s12237-020-00719-y","volume":"43","author":"CA Lynum","year":"2020","unstructured":"Lynum, C. A. et al. Microbial community response to a passive salt marsh restoration. Estuaries Coasts 43, 1439\u20131455. https:\/\/doi.org\/10.1007\/s12237-020-00719-y (2020).","journal-title":"Estuaries Coasts"},{"key":"12995_CR20","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2021.151673","volume":"818","author":"J Li","year":"2022","unstructured":"Li, J. et al. Fungi drive soil multifunctionality in the coastal salt marsh ecosystem. Sci. Total Environ. 818, 151673. https:\/\/doi.org\/10.1016\/j.scitotenv.2021.151673 (2022).","journal-title":"Sci. Total Environ."},{"key":"12995_CR21","doi-asserted-by":"publisher","first-page":"14397","DOI":"10.1038\/s41598-018-32529-5","volume":"8","author":"MK Cheung","year":"2018","unstructured":"Cheung, M. K., Wong, C. K., Chu, K. H. & Kwan, H. S. Community structure, dynamics and interactions of bacteria, archaea and fungi in subtropical coastal wetland sediments. Sci. Rep. 8, 14397. https:\/\/doi.org\/10.1038\/s41598-018-32529-5 (2018).","journal-title":"Sci. Rep."},{"key":"12995_CR22","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1111\/j.1461-0248.2004.00608.x","volume":"7","author":"MA Leibold","year":"2004","unstructured":"Leibold, M. A. et al. The metacommunity concept: A framework for multi-scale community ecology. Ecol. Lett. 7, 601\u2013613. https:\/\/doi.org\/10.1111\/j.1461-0248.2004.00608.x (2004).","journal-title":"Ecol. Lett."},{"key":"12995_CR23","doi-asserted-by":"publisher","first-page":"3111","DOI":"10.1038\/s41396-021-01027-4","volume":"15","author":"K Faust","year":"2021","unstructured":"Faust, K. Open challenges for microbial network construction and analysis. ISME J. 15, 3111\u20133118. https:\/\/doi.org\/10.1038\/s41396-021-01027-4 (2021).","journal-title":"ISME J."},{"key":"12995_CR24","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecolind.2021.108484","author":"ZL Zhao","year":"2022","unstructured":"Zhao, Z. L. et al. Bacteria versus fungi for predicting anthropogenic pollution in subtropical coastal sediments: Assembly process and environmental response. Ecol. Indic. https:\/\/doi.org\/10.1016\/j.ecolind.2021.108484 (2022).","journal-title":"Ecol. Indic."},{"key":"12995_CR25","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1093\/femsre\/fuy030","volume":"42","author":"L Rottjers","year":"2018","unstructured":"Rottjers, L. & Faust, K. From hairballs to hypotheses-biological insights from microbial networks. FEMS Microbiol. Rev. 42, 761\u2013780. https:\/\/doi.org\/10.1093\/femsre\/fuy030 (2018).","journal-title":"FEMS Microbiol. Rev."},{"key":"12995_CR26","doi-asserted-by":"publisher","DOI":"10.2307\/3033543","author":"LC Freeman","year":"1977","unstructured":"Freeman, L. C. A set of measures of centrality based on betweenness. Sociometry https:\/\/doi.org\/10.2307\/3033543 (1977).","journal-title":"Sociometry"},{"key":"12995_CR27","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.socnet.2004.11.009","volume":"27","author":"MEJ Newman","year":"2005","unstructured":"Newman, M. E. J. A measure of betweenness centrality based on random walks. Soc. Netw. 27, 39\u201354. https:\/\/doi.org\/10.1016\/j.socnet.2004.11.009 (2005).","journal-title":"Soc. Netw."},{"key":"12995_CR28","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1038\/nature03288","volume":"433","author":"R Guimer\u00e0","year":"2005","unstructured":"Guimer\u00e0, R. & Nunes Amaral, L. A. Functional cartography of complex metabolic networks. Nature 433, 895\u2013900. https:\/\/doi.org\/10.1038\/nature03288 (2005).","journal-title":"Nature"},{"key":"12995_CR29","doi-asserted-by":"publisher","DOI":"10.3389\/fmars.2021.754905","author":"O Zielinski","year":"2022","unstructured":"Zielinski, O. et al. The Spiekeroog Coastal Observatory: A Scientific Infrastructure at the Land-Sea Transition Zone (Southern North Sea). Front. Mar. Sci. https:\/\/doi.org\/10.3389\/fmars.2021.754905 (2022).","journal-title":"Front. Mar. Sci."},{"key":"12995_CR30","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1016\/j.ecss.2017.09.021","volume":"198","author":"T Balke","year":"2017","unstructured":"Balke, T. et al. Experimental salt marsh islands: A model system for novel metacommunity experiments. Estuar. Coast. Shelf S. 198, 288\u2013298. https:\/\/doi.org\/10.1016\/j.ecss.2017.09.021 (2017).","journal-title":"Estuar. Coast. Shelf S."},{"key":"12995_CR31","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1111\/jvs.12915","volume":"31","author":"K L\u00f5hmus","year":"2020","unstructured":"L\u00f5hmus, K., Balke, T., Kleyer, M. & T\u00f6r\u00f6k, P. Spatial and temporal patterns of initial plant establishment in salt marsh communities. J. Veg. Sci. 31, 1122\u20131132. https:\/\/doi.org\/10.1111\/jvs.12915 (2020).","journal-title":"J. Veg. Sci."},{"key":"12995_CR32","doi-asserted-by":"publisher","first-page":"57","DOI":"10.3354\/meps14245","volume":"706","author":"M Rinke","year":"2023","unstructured":"Rinke, M., Lohmus, K., Pieck, D., Maraun, M. & Scheu, S. Channelling of basal resources and use of allochthonous marine carbon by soil arthropods of the Wadden Sea salt marsh. Mar. Ecol. Prog. Ser. 706, 57\u201371. https:\/\/doi.org\/10.3354\/meps14245 (2023).","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"12995_CR33","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.seares.2017.10.002","volume":"131","author":"G Lange","year":"2018","unstructured":"Lange, G., Haynert, K., Dinter, T., Scheu, S. & Kr\u00f6ncke, I. Adaptation of benthic invertebrates to food sources along marine-terrestrial boundaries as indicated by carbon and nitrogen stable isotopes. J. Sea. Res. 131, 12\u201321. https:\/\/doi.org\/10.1016\/j.seares.2017.10.002 (2018).","journal-title":"J. Sea. Res."},{"key":"12995_CR34","doi-asserted-by":"publisher","DOI":"10.1016\/j.jembe.2019.151268","author":"G Lange","year":"2020","unstructured":"Lange, G. et al. Elevation gradient affects the development of macrozoobenthic communities in the Wadden Sea: A field experiment with artificial islands. J. Exp. Mar. Biol. Ecol. https:\/\/doi.org\/10.1016\/j.jembe.2019.151268 (2020).","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"12995_CR35","doi-asserted-by":"publisher","DOI":"10.1101\/2022.03.09.483717","author":"DR Gon\u00e7alves","year":"2022","unstructured":"Gon\u00e7alves, D. R., Pena, R. & Albach, D. C. Polyploidy and plant-fungus symbiosis: Evidence of cytotype-specific microbiomes in the halophyte Salicornia (Amaranthaceae). BioRxiv https:\/\/doi.org\/10.1101\/2022.03.09.483717 (2022).","journal-title":"BioRxiv"},{"key":"12995_CR36","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2022.956092","author":"J Yong","year":"2022","unstructured":"Yong, J. et al. Spatial and temporal patterns of microphytobenthos communities along the marine-terrestrial boundary in the German Wadden Sea. Front. Ecol. Evol. https:\/\/doi.org\/10.3389\/fevo.2022.956092 (2022).","journal-title":"Front. Ecol. Evol."},{"key":"12995_CR37","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02602-18","author":"Z Yao","year":"2019","unstructured":"Yao, Z. et al. Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients. Appl. Environ. Microbiol. https:\/\/doi.org\/10.1128\/AEM.02602-18 (2019).","journal-title":"Appl. Environ. Microbiol."},{"key":"12995_CR38","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms8101619","author":"EG Hernandez","year":"2020","unstructured":"Hernandez, E. G., Baraza, E., Smit, C., Berg, M. P. & Falcao Salles, J. Salt marsh elevation drives root microbial composition of the native invasive grass Elytrigia atherica. Microorganisms https:\/\/doi.org\/10.3390\/microorganisms8101619 (2020).","journal-title":"Microorganisms"},{"key":"12995_CR39","doi-asserted-by":"publisher","first-page":"1414","DOI":"10.1038\/ismej.2011.24","volume":"5","author":"JA Steele","year":"2011","unstructured":"Steele, J. A. et al. Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J. 5, 1414\u20131425. https:\/\/doi.org\/10.1038\/ismej.2011.24 (2011).","journal-title":"ISME J."},{"key":"12995_CR40","doi-asserted-by":"publisher","first-page":"1918","DOI":"10.1038\/s41396-018-0104-2","volume":"12","author":"AM Oliverio","year":"2018","unstructured":"Oliverio, A. M. et al. The ecology and diversity of microbial eukaryotes in geothermal springs. ISME J. 12, 1918\u20131928. https:\/\/doi.org\/10.1038\/s41396-018-0104-2 (2018).","journal-title":"ISME J."},{"key":"12995_CR41","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s40168-020-00972-0","volume":"9","author":"S Hilton","year":"2021","unstructured":"Hilton, S. et al. Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale. Microbiome 9, 19. https:\/\/doi.org\/10.1186\/s40168-020-00972-0 (2021).","journal-title":"Microbiome"},{"key":"12995_CR42","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiz129","author":"T Dinter","year":"2019","unstructured":"Dinter, T., Geihser, S., Gube, M., Daniel, R. & Kuzyakov, Y. Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly. FEMS Microbiol. Ecol. https:\/\/doi.org\/10.1093\/femsec\/fiz129 (2019).","journal-title":"FEMS Microbiol. Ecol."},{"key":"12995_CR43","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.580024","volume":"11","author":"S Kalam","year":"2020","unstructured":"Kalam, S. et al. Recent understanding of soil Acidobacteria and their ecological significance: A critical review. Front. Microbiol. 11, 580024. https:\/\/doi.org\/10.3389\/fmicb.2020.580024 (2020).","journal-title":"Front. Microbiol."},{"key":"12995_CR44","doi-asserted-by":"publisher","first-page":"1626","DOI":"10.1099\/ijs.0.015644-0","volume":"60","author":"A Gittel","year":"2010","unstructured":"Gittel, A. et al. Desulfopila inferna sp. nov., a sulfate-reducing bacterium isolated from the subsurface of a tidal sand-flat. Int. J. Syst. Evol. Microbiol. 60, 1626\u20131630. https:\/\/doi.org\/10.1099\/ijs.0.015644-0 (2010).","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"12995_CR45","doi-asserted-by":"publisher","first-page":"1483","DOI":"10.1038\/ismej.2016.198","volume":"11","author":"M Simon","year":"2017","unstructured":"Simon, M. et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J. 11, 1483\u20131499. https:\/\/doi.org\/10.1038\/ismej.2016.198 (2017).","journal-title":"ISME J."},{"key":"12995_CR46","doi-asserted-by":"publisher","DOI":"10.1016\/j.csr.2020.104327","author":"E De Borger","year":"2021","unstructured":"De Borger, E., Braeckman, U. & Soetaert, K. Rapid organic matter cycling in North Sea sediments. Cont. Shelf. Res. https:\/\/doi.org\/10.1016\/j.csr.2020.104327 (2021).","journal-title":"Cont. Shelf. Res."},{"key":"12995_CR47","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/0022-0981(92)90292-i","volume":"165","author":"SS Epstein","year":"1992","unstructured":"Epstein, S. S., Burkovsky, I. V. & Shiaris, M. P. Ciliate grazing on bacteria, flagellates, and microalgae in a temperate zone sandy tidal flat: Ingestion rates and food niche partitioning. J. Exp. Mar. Biol. Ecol. 165, 103\u2013123. https:\/\/doi.org\/10.1016\/0022-0981(92)90292-i (1992).","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"12995_CR48","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiac057","author":"N Amacker","year":"2022","unstructured":"Amacker, N. et al. Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities. FEMS Microbiol. Ecol. https:\/\/doi.org\/10.1093\/femsec\/fiac057 (2022).","journal-title":"FEMS Microbiol. Ecol."},{"key":"12995_CR49","doi-asserted-by":"publisher","first-page":"61","DOI":"10.4490\/algae.2020.35.2.28","volume":"35","author":"JH You","year":"2020","unstructured":"You, J. H. et al. Feeding by common heterotrophic protist predators on seven Prorocentrum species. Algae 35, 61\u201378. https:\/\/doi.org\/10.4490\/algae.2020.35.2.28 (2020).","journal-title":"Algae"},{"key":"12995_CR50","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/j.pt.2007.11.005","volume":"24","author":"BS Leander","year":"2008","unstructured":"Leander, B. S. Marine gregarines: Evolutionary prelude to the apicomplexan radiation?. Trends Parasitol 24, 60\u201367. https:\/\/doi.org\/10.1016\/j.pt.2007.11.005 (2008).","journal-title":"Trends Parasitol"},{"key":"12995_CR51","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/bf00029115","volume":"295","author":"GB Bremer","year":"1995","unstructured":"Bremer, G. B. Lower marine fungi (labyrinthulomycetes) and the decay of mangrove leaf litter. Hydrobiologia 295, 89\u201395. https:\/\/doi.org\/10.1007\/bf00029115 (1995).","journal-title":"Hydrobiologia"},{"key":"12995_CR52","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0062169","volume":"8","author":"AC Bockelmann","year":"2013","unstructured":"Bockelmann, A. C., Tams, V., Ploog, J., Schubert, P. R. & Reusch, T. B. Quantitative PCR reveals strong spatial and temporal variation of the wasting disease pathogen, Labyrinthula zosterae in northern European eelgrass (Zostera marina) beds. PLoS ONE 8, e62169. https:\/\/doi.org\/10.1371\/journal.pone.0062169 (2013).","journal-title":"PLoS ONE"},{"key":"12995_CR53","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/s11104-022-05320-9","volume":"474","author":"H Liu","year":"2022","unstructured":"Liu, H. et al. The relative importance of intraspecific variation in above- and belowground plant traits in shaping salt marsh soil bacterial diversity and composition. Plant Soil 474, 125\u2013140. https:\/\/doi.org\/10.1007\/s11104-022-05320-9 (2022).","journal-title":"Plant Soil"},{"key":"12995_CR54","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/Bf02700169","volume":"30","author":"CN Janousek","year":"2007","unstructured":"Janousek, C. N., Currin, C. A. & Levin, L. A. Succession of microphytobenthos in a restored coastal wetland. Estuaries Coasts 30, 265\u2013276. https:\/\/doi.org\/10.1007\/Bf02700169 (2007).","journal-title":"Estuaries Coasts"},{"key":"12995_CR55","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1146\/annurev-arplant-050312-120106","volume":"64","author":"D Bulgarelli","year":"2013","unstructured":"Bulgarelli, D. et al. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant. Biol. 64, 807\u2013838. https:\/\/doi.org\/10.1146\/annurev-arplant-050312-120106 (2013).","journal-title":"Annu. Rev. Plant. Biol."},{"key":"12995_CR56","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1038\/nature11237","volume":"488","author":"DS Lundberg","year":"2012","unstructured":"Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86\u201390. https:\/\/doi.org\/10.1038\/nature11237 (2012).","journal-title":"Nature"},{"key":"12995_CR57","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1890\/05-2074","volume":"88","author":"CR Whitcraft","year":"2007","unstructured":"Whitcraft, C. R. & Levin, L. A. Regulation of benthic algal and animal communities by salt marsh plants: Impact of shading. Ecology 88, 904\u2013917. https:\/\/doi.org\/10.1890\/05-2074 (2007).","journal-title":"Ecology"},{"key":"12995_CR58","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiaa026","author":"M Kolton","year":"2020","unstructured":"Kolton, M., Rolando, J. L. & Kostka, J. E. Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA. FEMS Microbiol. Ecol. https:\/\/doi.org\/10.1093\/femsec\/fiaa026 (2020).","journal-title":"FEMS Microbiol. Ecol."},{"key":"12995_CR59","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1007\/s00248-019-01430-7","volume":"79","author":"G Zhang","year":"2020","unstructured":"Zhang, G. et al. Bacterial succession in salt marsh soils along a short-term invasion chronosequence of Spartina alterniflora in the Yellow River Estuary, China. Microb. Ecol. 79, 644\u2013661. https:\/\/doi.org\/10.1007\/s00248-019-01430-7 (2020).","journal-title":"Microb. Ecol."},{"key":"12995_CR60","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2020.143667","volume":"758","author":"G Zhang","year":"2021","unstructured":"Zhang, G. et al. Spartina alterniflora invasions reduce soil fungal diversity and simplify co-occurrence networks in a salt marsh ecosystem. Sci. Total Environ. 758, 143667. https:\/\/doi.org\/10.1016\/j.scitotenv.2020.143667 (2021).","journal-title":"Sci. Total Environ."},{"key":"12995_CR61","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.geomorph.2017.11.001","volume":"301","author":"N Leonardi","year":"2018","unstructured":"Leonardi, N. et al. Dynamic interactions between coastal storms and salt marshes: A review. Geomorphology 301, 92\u2013107. https:\/\/doi.org\/10.1016\/j.geomorph.2017.11.001 (2018).","journal-title":"Geomorphology"},{"key":"12995_CR62","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4735","volume":"6","author":"A Angermeyer","year":"2018","unstructured":"Angermeyer, A., Crosby, S. C. & Huber, J. A. Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient. PeerJ 6, e4735. https:\/\/doi.org\/10.7717\/peerj.4735 (2018).","journal-title":"PeerJ"},{"key":"12995_CR63","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1007\/s11306-012-0453-1","volume":"9","author":"C Paul","year":"2012","unstructured":"Paul, C., Mausz, M. A. & Pohnert, G. A co-culturing\/metabolomics approach to investigate chemically mediated interactions of planktonic organisms reveals influence of bacteria on diatom metabolism. Metabolomics 9, 349\u2013359. https:\/\/doi.org\/10.1007\/s11306-012-0453-1 (2012).","journal-title":"Metabolomics"},{"key":"12995_CR64","unstructured":"Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography (MPB-32). (2001)."},{"key":"12995_CR65","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1111\/j.1462-2920.2005.00956.x","volume":"8","author":"WT Sloan","year":"2006","unstructured":"Sloan, W. T. et al. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environ. Microbiol. 8, 732\u2013740. https:\/\/doi.org\/10.1111\/j.1462-2920.2005.00956.x (2006).","journal-title":"Environ. Microbiol."},{"key":"12995_CR66","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1038\/ismej.2015.164","volume":"10","author":"M Bahram","year":"2016","unstructured":"Bahram, M. et al. Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment. ISME J. 10, 885\u2013896. https:\/\/doi.org\/10.1038\/ismej.2015.164 (2016).","journal-title":"ISME J."},{"key":"12995_CR67","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1038\/ismej.2012.22","volume":"6","author":"JC Stegen","year":"2012","unstructured":"Stegen, J. C., Lin, X., Konopka, A. E. & Fredrickson, J. K. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 6, 1653\u20131664. https:\/\/doi.org\/10.1038\/ismej.2012.22 (2012).","journal-title":"ISME J."},{"key":"12995_CR68","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.1111\/oik.01493","volume":"123","author":"M Vellend","year":"2014","unstructured":"Vellend, M. et al. Assessing the relative importance of neutral stochasticity in ecological communities. Oikos 123, 1420\u20131430. https:\/\/doi.org\/10.1111\/oik.01493 (2014).","journal-title":"Oikos"},{"key":"12995_CR69","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.5194\/essd-10-1843-2018","volume":"10","author":"O Zielinski","year":"2018","unstructured":"Zielinski, O. et al. Environmental conditions of a salt-marsh biodiversity experiment on the island of Spiekeroog (Germany). ESSD 10, 1843\u20131858. https:\/\/doi.org\/10.5194\/essd-10-1843-2018 (2018).","journal-title":"ESSD"},{"key":"12995_CR70","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1111\/1462-2920.13023","volume":"18","author":"AE Parada","year":"2016","unstructured":"Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403\u20131414. https:\/\/doi.org\/10.1111\/1462-2920.13023 (2016).","journal-title":"Environ. Microbiol."},{"key":"12995_CR71","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00023-18","author":"YC Yeh","year":"2018","unstructured":"Yeh, Y. C., Needham, D. M., Sieradzki, E. T. & Fuhrman, J. A. Taxon disappearance from microbiome analysis reinforces the value of mock communities as a standard in every sequencing run. mSystems https:\/\/doi.org\/10.1128\/mSystems.00023-18 (2018).","journal-title":"mSystems"},{"key":"12995_CR72","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiw200","author":"R Piredda","year":"2017","unstructured":"Piredda, R. et al. Diversity and temporal patterns of planktonic protist assemblages at a mediterranean long therm ecological research site. FEMS Microbiol. Ecol. https:\/\/doi.org\/10.1093\/femsec\/fiw200 (2017).","journal-title":"FEMS Microbiol. Ecol."},{"key":"12995_CR73","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852\u2013857. https:\/\/doi.org\/10.1038\/s41587-019-0209-9 (2019).","journal-title":"Nat. Biotechnol."},{"key":"12995_CR74","doi-asserted-by":"publisher","first-page":"3240","DOI":"10.1111\/1462-2920.15553","volume":"23","author":"YC Yeh","year":"2021","unstructured":"Yeh, Y. C. et al. Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S. Environ. Microbiol. 23, 3240\u20133250. https:\/\/doi.org\/10.1111\/1462-2920.15553 (2021).","journal-title":"Environ. Microbiol."},{"key":"12995_CR75","doi-asserted-by":"publisher","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal (2011). https:\/\/doi.org\/10.14806\/ej.17.1.200","DOI":"10.14806\/ej.17.1.200"},{"key":"12995_CR76","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids. Res. 41, D590-596. https:\/\/doi.org\/10.1093\/nar\/gks1219 (2013).","journal-title":"Nucleic Acids. Res."},{"key":"12995_CR77","doi-asserted-by":"publisher","first-page":"D597","DOI":"10.1093\/nar\/gks1160","volume":"41","author":"L Guillou","year":"2013","unstructured":"Guillou, L. et al. The protist ribosomal reference database (PR2): A catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids. Res. 41, D597-604. https:\/\/doi.org\/10.1093\/nar\/gks1160 (2013).","journal-title":"Nucleic Acids. Res."},{"key":"12995_CR78","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581\u2013583. https:\/\/doi.org\/10.1038\/nmeth.3869 (2016).","journal-title":"Nat. Methods"},{"key":"12995_CR79","unstructured":"R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (R Foundation for Statistical Computing, 2020)."},{"key":"12995_CR80","unstructured":"vegan: Community ecology package. R package version 2.6-4. 2022 (2022)."},{"key":"12995_CR81","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/1471-2105-12-35","volume":"12","author":"H Chen","year":"2011","unstructured":"Chen, H. & Boutros, P. C. VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform. 12, 35. https:\/\/doi.org\/10.1186\/1471-2105-12-35 (2011).","journal-title":"BMC Bioinform."},{"key":"12995_CR82","unstructured":"agricolae: Statistical procedures for agricultural research. R package version 1.3-5. 2021 (2021)."},{"key":"12995_CR83","unstructured":"pairwiseAdonis: Pairwise multilevel comparison using adonis v. R package version 0.4 (2020)."},{"key":"12995_CR84","unstructured":"psych: Procedures for personality and psychological research, Northwestern University, Evanston, Illinois, USA v. 2.2.9 (2022)."},{"key":"12995_CR85","unstructured":"The igraph software package for complex network research (InterJournal, Complex Systems, 2006)."},{"key":"12995_CR86","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1038\/nphys489","volume":"3","author":"R Guimera","year":"2007","unstructured":"Guimera, R., Sales-Pardo, M. & Amaral, L. A. Classes of complex networks defined by role-to-role connectivity profiles. Nat. Phys. 3, 63\u201369. https:\/\/doi.org\/10.1038\/nphys489 (2007).","journal-title":"Nat. Phys."},{"key":"12995_CR87","doi-asserted-by":"publisher","first-page":"8890","DOI":"10.1038\/s41598-018-27172-z","volume":"8","author":"X Cao","year":"2018","unstructured":"Cao, X. et al. Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis. Sci. Rep. 8, 8890. https:\/\/doi.org\/10.1038\/s41598-018-27172-z (2018).","journal-title":"Sci. Rep."},{"key":"12995_CR88","doi-asserted-by":"publisher","first-page":"19891","DOI":"10.1073\/pnas.0706375104","volume":"104","author":"JM Olesen","year":"2007","unstructured":"Olesen, J. M., Bascompte, J., Dupont, Y. L. & Jordano, P. The modularity of pollination networks. PNAS 104, 19891\u201319896. https:\/\/doi.org\/10.1073\/pnas.0706375104 (2007).","journal-title":"PNAS"},{"key":"12995_CR89","doi-asserted-by":"publisher","unstructured":"B\u00fcrkner, P.-C. brms: An R package for Bayesian multilevel models using Stan. J. Stat. Softw. 80(1), 1\u201328. https:\/\/doi.org\/10.18637\/jss.v080.i01 (2017).","DOI":"10.18637\/jss.v080.i01"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-12995-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-12995-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-12995-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:02:46Z","timestamp":1753887766000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-12995-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,26]]},"references-count":89,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["12995"],"URL":"https:\/\/doi.org\/10.1038\/s41598-025-12995-4","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,26]]},"assertion":[{"value":"10 October 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 July 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 July 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"27178"}}