{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T10:45:37Z","timestamp":1791369937399,"version":"4.3.1"},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T00:00:00Z","timestamp":1764979200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000},"content-version":"vor","delay-in-days":37,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100013390","name":"Texas A&M University at Galveston","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100013390","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microb Ecol"],"DOI":"10.1007\/s00248-025-02661-7","type":"journal-article","created":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T12:53:30Z","timestamp":1765025610000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes"],"prefix":"10.1007","volume":"89","author":[{"given":"Kathryn L.","family":"Campbell","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna R.","family":"Armitage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica M.","family":"Labont\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,6]]},"reference":[{"key":"2661_CR1","doi-asserted-by":"publisher","first-page":"2665","DOI":"10.1111\/gcb.13176","volume":"22","author":"JE Hewitt","year":"2016","unstructured":"Hewitt JE, Ellis JI, Thrush SF (2016) Multiple stressors, nonlinear effects and the implications of climate change impacts on marine coastal ecosystems. Glob Change Biol 22:2665\u20132675. https:\/\/doi.org\/10.1111\/gcb.13176","journal-title":"Glob Change Biol"},{"key":"2661_CR2","doi-asserted-by":"publisher","unstructured":"Intergovernmental Panel on Climate Change (IPCC), editor. Oceans and Coastal Ecosystems and Their Services. Climate Change 2022 \u2013 Impacts, Adaptation and Vulnerability: Working Group II Contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge: Cambridge University Press; 2023. pp. 379\u2013550. https:\/\/doi.org\/10.1017\/9781009325844.005","DOI":"10.1017\/9781009325844.005"},{"key":"2661_CR3","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aaz5512","volume":"6","author":"TE T\u00f6rnqvist","year":"2020","unstructured":"T\u00f6rnqvist TE, Jankowski KL, Li Y-X, Gonz\u00e1lez JL (2020) Tipping points of Mississippi Delta marshes due to accelerated sea-level rise. Sci Adv 6:eaaz5512","journal-title":"Sci Adv"},{"key":"2661_CR4","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecoleng.2020.105815","volume":"151","author":"G Cagle","year":"2020","unstructured":"Cagle G, Lin Q, Graham SA, Mendelssohn I, Fleeger JW, Deis D et al (2020) Planting Spartina alterniflora in a salt marsh denuded of vegetation by an oil spill induces a rapid response in the soil microbial community. Ecol Eng 151:105815. https:\/\/doi.org\/10.1016\/j.ecoleng.2020.105815","journal-title":"Ecol Eng"},{"key":"2661_CR5","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1007\/s12237-020-00719-y","volume":"43","author":"CA Lynum","year":"2020","unstructured":"Lynum CA, Bulseco AN, Dunphy CM, Osborne SM, Vineis JH, Bowen JL (2020) Microbial community response to a passive salt marsh restoration. Estuaries Coasts 43:1439\u20131455. https:\/\/doi.org\/10.1007\/s12237-020-00719-y","journal-title":"Estuaries Coasts"},{"key":"2661_CR6","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1890\/10-1510.1","volume":"81","author":"EB Barbier","year":"2011","unstructured":"Barbier EB, Hacker SD, Kennedy C, Koch EW, Stier AC, Silliman BR (2011) The value of estuarine and coastal ecosystem services. Ecol Monogr 81:169\u2013193. https:\/\/doi.org\/10.1890\/10-1510.1","journal-title":"Ecol Monogr"},{"key":"2661_CR7","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.03049","author":"OV Mavrodi","year":"2018","unstructured":"Mavrodi OV, Jung CM, Eberly JO, Hendry SV, Namjilsuren S, Biber PD et al (2018) Rhizosphere microbial communities of Spartina alterniflora and Juncus roemerianus from restored and natural tidal marshes on Deer Island, Mississippi. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2018.03049","journal-title":"Front Microbiol"},{"key":"2661_CR8","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1007\/s00267-007-9002-5","volume":"41","author":"JW Matthews","year":"2008","unstructured":"Matthews JW, Endress AG (2008) Performance criteria, compliance success, and vegetation development in compensatory mitigation wetlands. Environ Manage 41:130\u2013141. https:\/\/doi.org\/10.1007\/s00267-007-9002-5","journal-title":"Environ Manage"},{"key":"2661_CR9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0215767","volume":"14","author":"F Thomas","year":"2019","unstructured":"Thomas F, Morris JT, Wigand C, Sievert SM (2019) Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities. PLOS ONE 14:e0215767. https:\/\/doi.org\/10.1371\/journal.pone.0215767","journal-title":"PLOS ONE"},{"key":"2661_CR10","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1007\/s12237-012-9502-2","volume":"35","author":"AE Bernhard","year":"2012","unstructured":"Bernhard AE, Marshall D, Yiannos L (2012) Increased variability of microbial communities in restored salt marshes nearly 30 years after tidal flow restoration. Estuaries Coasts 35:1049\u20131059. https:\/\/doi.org\/10.1007\/s12237-012-9502-2","journal-title":"Estuaries Coasts"},{"key":"2661_CR11","doi-asserted-by":"publisher","unstructured":"Bernhard AE, Dwyer C, Idrizi A, Bender G, Zwick R. Long-term impacts of disturbance on nitrogen-cycling bacteria in a New England salt marsh. Frontiers in Microbiology. 2015;6. https:\/\/doi.org\/10.3389\/fmicb.2015.00046","DOI":"10.3389\/fmicb.2015.00046"},{"key":"2661_CR12","doi-asserted-by":"publisher","first-page":"508","DOI":"10.4319\/lo.2007.52.2.0508","volume":"52","author":"C Corinaldesi","year":"2007","unstructured":"Corinaldesi C, Dell\u2019Anno A, Danovaro R (2007) Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems. Limnol Oceanogr 52:508\u2013516. https:\/\/doi.org\/10.4319\/lo.2007.52.2.0508","journal-title":"Limnol Oceanogr"},{"key":"2661_CR13","doi-asserted-by":"publisher","first-page":"1447","DOI":"10.4319\/lo.2003.48.4.1447","volume":"48","author":"M Middelboe","year":"2003","unstructured":"Middelboe M, Glud RN, Finster K (2003) Distribution of viruses and bacteria in relation to diagenetic activity in an estuarine sediment. Limnol Oceanogr 48:1447\u20131456. https:\/\/doi.org\/10.4319\/lo.2003.48.4.1447","journal-title":"Limnol Oceanogr"},{"key":"2661_CR14","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.1111\/j.1365-2427.2007.01929.x","volume":"53","author":"EF Jackson","year":"2008","unstructured":"Jackson EF, Jackson CR (2008) Viruses in wetland ecosystems. Freshw Biol 53:1214\u20131227. https:\/\/doi.org\/10.1111\/j.1365-2427.2007.01929.x","journal-title":"Freshw Biol"},{"key":"2661_CR15","doi-asserted-by":"crossref","unstructured":"Bonetti G, Trevathan-Tackett SM, Carnell PE, Macreadie PI. Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives. Frontiers in Microbiology. 2019;Volume 10-2019. Available: https:\/\/www.frontiersin.org\/journals\/microbiology\/articles\/10.3389\/fmicb.2019.01962","DOI":"10.3389\/fmicb.2019.01962"},{"key":"2661_CR16","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0522-4","volume":"6","author":"P Dalcin Martins","year":"2018","unstructured":"Dalcin Martins P, Danczak RE, Roux S, Frank J, Borton MA, Wolfe RA et al (2018) Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems. Microbiome 6:138. https:\/\/doi.org\/10.1186\/s40168-018-0522-4","journal-title":"Microbiome"},{"key":"2661_CR17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2202261119","volume":"119","author":"LPP Braga","year":"2022","unstructured":"Braga LPP, Orland C, Emilson EJS, Fitch AA, Osterholz H, Dittmar T et al (2022) Viruses direct carbon cycling in lake sediments under global change. Proc Natl Acad Sci U S A 119:e2202261119. https:\/\/doi.org\/10.1073\/pnas.2202261119","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2661_CR18","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2022.153359","volume":"821","author":"KM Abbott","year":"2022","unstructured":"Abbott KM, Quirk T, Fultz LM (2022) Soil microbial community development across a 32-year coastal wetland restoration time series and the relative importance of environmental factors. Sci Total Environ 821:153359. https:\/\/doi.org\/10.1016\/j.scitotenv.2022.153359","journal-title":"Sci Total Environ"},{"key":"2661_CR19","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-32529-5","volume":"8","author":"MK Cheung","year":"2018","unstructured":"Cheung MK, Wong CK, Chu KH, Kwan HS (2018) 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","journal-title":"Sci Rep"},{"key":"2661_CR20","doi-asserted-by":"publisher","first-page":"5361","DOI":"10.1111\/gcb.14376","volume":"24","author":"MJ Osland","year":"2018","unstructured":"Osland MJ, Gabler CA, Grace JB, Day RH, McCoy ML, McLeod JL et al (2018) Climate and plant controls on soil organic matter in coastal wetlands. Glob Change Biol 24:5361\u20135379. https:\/\/doi.org\/10.1111\/gcb.14376","journal-title":"Glob Change Biol"},{"key":"2661_CR21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0125404","volume":"10","author":"AR Armitage","year":"2015","unstructured":"Armitage AR, Highfield WE, Brody SD, Louchouarn P (2015) The contribution of mangrove expansion to salt marsh loss on the Texas Gulf Coast. PLoS One 10:e0125404. https:\/\/doi.org\/10.1371\/journal.pone.0125404","journal-title":"PLoS One"},{"key":"2661_CR22","doi-asserted-by":"publisher","unstructured":"McPherson R, Blackmar P, Heilman D. Restoring Estuarine Habitat in Galveston West Bay Through Placement of Dredged Sediments: Monitoring and Lessons Learned. 2015; 1\u20139. https:\/\/doi.org\/10.1142\/9789814689977_0090","DOI":"10.1142\/9789814689977_0090"},{"key":"2661_CR23","doi-asserted-by":"publisher","unstructured":"Augustin LN, J. HD, Rocha DD. Restoring Estuarine Habitat in Galveston West Bay Through Beneficial Use of Dredged Sediments. 2011; 2560\u20132570. https:\/\/doi.org\/10.1142\/9789814355537_0192","DOI":"10.1142\/9789814355537_0192"},{"key":"2661_CR24","unstructured":"Bushnell B, Rood J, Singer E. BBTools Software Package. In: PLOS ONE. 2017."},{"key":"2661_CR25","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.ymeth.2016.02.020","volume":"102","author":"D Li","year":"2016","unstructured":"Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K et al (2016) MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3\u201311. https:\/\/doi.org\/10.1016\/j.ymeth.2016.02.020","journal-title":"Methods"},{"key":"2661_CR26","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-119","author":"D Hyatt","year":"2010","unstructured":"Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. https:\/\/doi.org\/10.1186\/1471-2105-11-119","journal-title":"BMC Bioinformatics"},{"key":"2661_CR27","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink B, Reuter K, Drost H-G (2021) Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods 18:366\u2013368. https:\/\/doi.org\/10.1038\/s41592-021-01101-x","journal-title":"Nat Methods"},{"key":"2661_CR28","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403\u2013410. https:\/\/doi.org\/10.1016\/S0022-2836(05)80360-2","journal-title":"J Mol Biol"},{"key":"2661_CR29","doi-asserted-by":"publisher","unstructured":"Vasimuddin M, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). 2019. pp. 314\u2013324. https:\/\/doi.org\/10.1109\/IPDPS.2019.00041","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"2661_CR30","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7359","volume":"7","author":"DD Kang","year":"2019","unstructured":"Kang DD, Li F, Kirton E, Thomas A, Egan R, An H et al (2019) MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7:e7359. https:\/\/doi.org\/10.7717\/peerj.7359","journal-title":"PeerJ"},{"key":"2661_CR31","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043\u20131055. https:\/\/doi.org\/10.1101\/gr.186072.114","journal-title":"Genome Res"},{"key":"2661_CR32","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1319","author":"AM Eren","year":"2015","unstructured":"Eren AM, Esen OC, Quince C, Vineis JH, Morrison HG, Sogin ML et al (2015) Anvi\u2019o: an advanced analysis and visualization platformfor \u2019omics data. PeerJ. https:\/\/doi.org\/10.7717\/peerj.1319","journal-title":"PeerJ"},{"key":"2661_CR33","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01213-8","volume":"10","author":"Z Zhou","year":"2022","unstructured":"Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, Cowley ES et al (2022) METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 10:33. https:\/\/doi.org\/10.1186\/s40168-021-01213-8","journal-title":"Microbiome"},{"key":"2661_CR34","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00920-20","author":"HR Gruber-Vodicka","year":"2020","unstructured":"Gruber-Vodicka HR, Seah BKB, Pruesse E (2020) phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems. https:\/\/doi.org\/10.1128\/msystems.00920-20","journal-title":"mSystems"},{"key":"2661_CR35","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","volume":"39","author":"S Nayfach","year":"2021","unstructured":"Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC (2021) Checkv assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol 39:578\u2013585. https:\/\/doi.org\/10.1038\/s41587-020-00774-7","journal-title":"Nat Biotechnol"},{"key":"2661_CR36","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00867-0","volume":"8","author":"K Kieft","year":"2020","unstructured":"Kieft K, Zhou Z, Anantharaman K (2020) VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8:90. https:\/\/doi.org\/10.1186\/s40168-020-00867-0","journal-title":"Microbiome"},{"key":"2661_CR37","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00990-y","volume":"9","author":"J Guo","year":"2021","unstructured":"Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO et al (2021) Virsorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9:37. https:\/\/doi.org\/10.1186\/s40168-020-00990-y","journal-title":"Microbiome"},{"key":"2661_CR38","doi-asserted-by":"publisher","unstructured":"Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research. 2020;48: 8883\u20138900. https:\/\/doi.org\/10.1093\/nar\/gkaa621","DOI":"10.1093\/nar\/gkaa621"},{"key":"2661_CR39","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01953-y","author":"AP Camargo","year":"2023","unstructured":"Camargo AP, Roux S, Schulz F, Babinski M, Xu Y, Hu B et al (2023) Identification of mobile genetic elements with geNomad. Nat Biotechnol. https:\/\/doi.org\/10.1038\/s41587-023-01953-y","journal-title":"Nat Biotechnol"},{"key":"2661_CR40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002083","volume":"21","author":"S Roux","year":"2023","unstructured":"Roux S, Camargo AP, Coutinho FH, Dabdoub SM, Dutilh BE, Nayfach S et al (2023) IphoP: an integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria. PLoS Biol 21:e3002083","journal-title":"PLoS Biol"},{"key":"2661_CR41","unstructured":"RStudio Team. RStudio: Integrated Development for R. RStudio. PBC. Boston, MA; 2020. Available: http:\/\/www.rstudio.com\/"},{"key":"2661_CR42","unstructured":"Oksanen J, Simpson GL, Blanchet FG, Kindt R, Legendre P, Minchin PR, et al. vegan: Community Ecology Package. 2022. Available: https:\/\/cran.r-project.org\/package=vegan"},{"key":"2661_CR43","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-6-r60","volume":"12","author":"N Segata","year":"2011","unstructured":"Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS et al (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. https:\/\/doi.org\/10.1186\/gb-2011-12-6-r60","journal-title":"Genome Biol"},{"key":"2661_CR44","doi-asserted-by":"crossref","unstructured":"Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York; 2016. Available: https:\/\/ggplot2.tidyverse.org","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"2661_CR45","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/BF02181118","volume":"1","author":"RW Howarth","year":"1984","unstructured":"Howarth RW (1984) The ecological significance of sulfur in the energy dynamics of salt marsh and coastal marine sediments. Biogeochemistry 1:5\u201327. https:\/\/doi.org\/10.1007\/BF02181118","journal-title":"Biogeochemistry"},{"key":"2661_CR46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2019.00849","volume":"10","author":"BB J\u00f8rgensen","year":"2019","unstructured":"J\u00f8rgensen BB, Findlay AJ, Pellerin A (2019) The biogeochemical sulfur cycle of marine sediments. Front Microbiol 10:1\u201327. https:\/\/doi.org\/10.3389\/fmicb.2019.00849","journal-title":"Front Microbiol"},{"key":"2661_CR47","doi-asserted-by":"publisher","first-page":"2945","DOI":"10.1029\/2019JG005207","volume":"124","author":"N McTigue","year":"2019","unstructured":"McTigue N, Davis J, Rodriguez AB, McKee B, Atencio A, Currin C (2019) Sea level rise explains changing carbon accumulation rates in a salt marsh over the past two millennia. J Geophys Res Biogeosci 124:2945\u20132957. https:\/\/doi.org\/10.1029\/2019JG005207","journal-title":"J Geophys Res Biogeosci"},{"key":"2661_CR48","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/j.orggeochem.2006.06.006","volume":"38","author":"BJ Johnson","year":"2007","unstructured":"Johnson BJ, Moore KA, Lehmann C, Bohlen C, Brown TA (2007) Middle to late Holocene fluctuations of C3 and C4 vegetation in a Northern New England Salt Marsh, Sprague Marsh, Phippsburg Maine. Org Geochem 38:394\u2013403. https:\/\/doi.org\/10.1016\/j.orggeochem.2006.06.006","journal-title":"Org Geochem"},{"key":"2661_CR49","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1046\/j.1526-100X.2002.01054.x","volume":"10","author":"C Craft","year":"2002","unstructured":"Craft C, Eugene Turner R, Streever B (2002) Approaches to coastal wetland restoration: Northern Gulf of Mexico. Restor Ecol 10:731\u2013732. https:\/\/doi.org\/10.1046\/j.1526-100X.2002.01054.x","journal-title":"Restor Ecol"},{"key":"2661_CR50","doi-asserted-by":"publisher","first-page":"1352","DOI":"10.1038\/ismej.2014.220","volume":"9","author":"JS Weitz","year":"2015","unstructured":"Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A et al (2015) A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J 9:1352\u20131364. https:\/\/doi.org\/10.1038\/ismej.2014.220","journal-title":"ISME J"},{"key":"2661_CR51","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00234-25","volume":"0","author":"Isabelle Du Plessis","year":"2025","unstructured":"Du Plessis Isabelle, Snyder Hannah, Calder Rachel, Rolando Jos\u00e9 L., Kostka Joel E., Weitz Joshua S. et al (2025) Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora. mSphere 0:e00234-25. https:\/\/doi.org\/10.1128\/msphere.00234-25","journal-title":"mSphere"},{"key":"2661_CR52","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1038\/s41564-018-0166-y","volume":"3","author":"M Breitbart","year":"2018","unstructured":"Breitbart M, Bonnain C, Malki K, Sawaya NA (2018) Phage puppet masters of the marine microbial realm. Nat Microbiol 3:754\u2013766. https:\/\/doi.org\/10.1038\/s41564-018-0166-y","journal-title":"Nat Microbiol"},{"key":"2661_CR53","doi-asserted-by":"publisher","unstructured":"Stieglmeier M, Klingl A, Alves RJE, Rittmann SK-MR, Melcher M, Leisch N, et al. Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota. International Journal of Systematic and Evolutionary Microbiology,. 64: 2738\u20132752. https:\/\/doi.org\/10.1099\/ijs.0.063172-0","DOI":"10.1099\/ijs.0.063172-0"},{"key":"2661_CR54","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1016\/j.dsr.2007.02.003","volume":"54","author":"I Hewson","year":"2007","unstructured":"Hewson I, Fuhrman JA (2007) Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments. Deep Sea Res Part I Oceanogr Res Pap 54:811\u2013830. https:\/\/doi.org\/10.1016\/j.dsr.2007.02.003","journal-title":"Deep Sea Res Part I Oceanogr Res Pap"},{"key":"2661_CR55","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1128\/AEM.68.3.1157-1164.2002","volume":"68","author":"DJ Burke","year":"2002","unstructured":"Burke DJ, Hamerlynck EP, Hahn D (2002) Interactions among plant species and microorganisms in salt marsh sediments. Appl Environ Microbiol 68:1157\u20131164. https:\/\/doi.org\/10.1128\/AEM.68.3.1157-1164.2002","journal-title":"Appl Environ Microbiol"},{"key":"2661_CR56","doi-asserted-by":"publisher","first-page":"51","DOI":"10.2136\/sssaj1981.03615995004500010012x","volume":"45","author":"ME Casselman","year":"1981","unstructured":"Casselman ME, Patrick Jr. WH, DeLaune RD (1981) Nitrogen fixation in a Gulf Coast salt marsh. Soil Sci Soc Am J 45:51\u201356. https:\/\/doi.org\/10.2136\/sssaj1981.03615995004500010012x","journal-title":"Soil Sci Soc Am J"},{"key":"2661_CR57","doi-asserted-by":"publisher","first-page":"126","DOI":"10.4319\/lo.1979.24.1.0126","volume":"24","author":"JM Teal","year":"1979","unstructured":"Teal JM, Valiela I, Berlo D (1979) Nitrogen fixation by rhizosphere and free-living bacteria in salt marsh sediments1. Limnol Oceanogr 24:126\u2013132. https:\/\/doi.org\/10.4319\/lo.1979.24.1.0126","journal-title":"Limnol Oceanogr"},{"key":"2661_CR58","doi-asserted-by":"publisher","DOI":"10.1016\/j.catena.2022.106520","volume":"217","author":"S Zhao","year":"2022","unstructured":"Zhao S, Banerjee S, White JF, Liu J-J, Zhou N, Tian C-Y (2022) High salt stress increases archaeal abundance and network connectivity in saline agricultural soils. CATENA 217:106520. https:\/\/doi.org\/10.1016\/j.catena.2022.106520","journal-title":"CATENA"},{"key":"2661_CR59","doi-asserted-by":"publisher","first-page":"881","DOI":"10.2307\/2260404","volume":"74","author":"BL Howes","year":"1986","unstructured":"Howes BL, Dacey JWH, Goehringer DD (1986) Factors controlling the growth form of Spartina alterniflora: feedbacks between above-ground production, sediment oxidation, nitrogen and salinity. J Ecol 74:881\u2013898. https:\/\/doi.org\/10.2307\/2260404","journal-title":"J Ecol"},{"key":"2661_CR60","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1007\/s00442-010-1887-7","volume":"165","author":"RH Peng","year":"2011","unstructured":"Peng RH, Fang CM, Li B, Chen JK (2011) Spartina alterniflora invasion increases soil inorganic nitrogen pools through interactions with tidal subsidies in the Yangtze Estuary, China. Oecologia 165:797\u2013807. https:\/\/doi.org\/10.1007\/s00442-010-1887-7","journal-title":"Oecologia"},{"key":"2661_CR61","doi-asserted-by":"publisher","first-page":"3814","DOI":"10.1128\/AEM.66.9.3814-3822.2000","volume":"66","author":"CharlesR. Lovell","year":"2000","unstructured":"Lovell Charles R., Piceno Yvette M., Quattro Joseph M., Bagwell Christopher E. (2000) Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Appl Environ Microbiol 66:3814\u20133822. https:\/\/doi.org\/10.1128\/AEM.66.9.3814-3822.2000","journal-title":"Appl Environ Microbiol"},{"key":"2661_CR62","doi-asserted-by":"publisher","first-page":"70","DOI":"10.4319\/lo.1983.28.1.0070","volume":"28","author":"RW Howarth","year":"1983","unstructured":"Howarth RW, Giblin A (1983) Sulfate reduction in the salt marshes at Sapelo Island, Georgia1. Limnol Oceanogr 28:70\u201382. https:\/\/doi.org\/10.4319\/lo.1983.28.1.0070","journal-title":"Limnol Oceanogr"},{"key":"2661_CR63","doi-asserted-by":"publisher","first-page":"999","DOI":"10.4319\/lo.1979.24.6.0999","volume":"24","author":"RW Howarth","year":"1979","unstructured":"Howarth RW, Teal JM (1979) Sulfate reduction in a New England salt marsh1. Limnol Oceanogr 24:999\u20131013. https:\/\/doi.org\/10.4319\/lo.1979.24.6.0999","journal-title":"Limnol Oceanogr"},{"key":"2661_CR64","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1111\/1758-2229.12538","volume":"9","author":"K Wasmund","year":"2017","unstructured":"Wasmund K, Mu\u00dfmann M, Loy A (2017) The life sulfuric: microbial ecology of sulfur cycling in marine sediments. Environ Microbiol Rep 9:323\u2013344. https:\/\/doi.org\/10.1111\/1758-2229.12538","journal-title":"Environ Microbiol Rep"},{"key":"2661_CR65","doi-asserted-by":"publisher","DOI":"10.1016\/j.marenvres.2024.106497","volume":"198","author":"M Rubin-Blum","year":"2024","unstructured":"Rubin-Blum M, Makovsky Y, Rahav E, Belkin N, Antler G, Sisma-Ventura G et al (2024) Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea. Mar Environ Res 198:106497. https:\/\/doi.org\/10.1016\/j.marenvres.2024.106497","journal-title":"Mar Environ Res"},{"key":"2661_CR66","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2021.146016","volume":"777","author":"W Liu","year":"2021","unstructured":"Liu W, Rahaman MdH, M\u0105kinia J, Zhai J (2021) Coupling transformation of carbon, nitrogen and sulfur in a long-term operated full-scale constructed wetland. Sci Total Environ 777:146016. https:\/\/doi.org\/10.1016\/j.scitotenv.2021.146016","journal-title":"Sci Total Environ"},{"key":"2661_CR67","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1007\/s00248-002-1067-3","volume":"46","author":"I Hewson","year":"2003","unstructured":"Hewson I, Vargo GA, Fuhrman JA (2003) Bacterial Diversity in Shallow Oligotrophic Marine Benthos and Overlying Waters: effects of Virus Infection, Containment, and Nutrient Enrichment. Microb Ecol 46:322\u2013336. https:\/\/doi.org\/10.1007\/s00248-002-1067-3","journal-title":"Microb Ecol"},{"key":"2661_CR68","doi-asserted-by":"publisher","DOI":"10.1101\/2023.04.28.538735","author":"AM ter Horst","year":"2023","unstructured":"ter Horst AM, Fudyma JD, Sones JL, Emerson JB (2023) Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography. bioRxiv. https:\/\/doi.org\/10.1101\/2023.04.28.538735","journal-title":"bioRxiv"},{"key":"2661_CR69","doi-asserted-by":"publisher","unstructured":"Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Ho Bin Jang, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology. 2018;3: 870\u2013880. https:\/\/doi.org\/10.1038\/s41564-018-0190-y","DOI":"10.1038\/s41564-018-0190-y"},{"key":"2661_CR70","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1007\/s10533-021-00860-1","volume":"157","author":"Q Liu","year":"2022","unstructured":"Liu Q, Lu Y, Xu J, Zhu Z-Y, Yuan Y, Ma W-C et al (2022) Dissolved free amino acids and polyamines are two major dissolved organic nitrogen sources for marine bacterioplankton in the northern slope of the South China Sea. Biogeochemistry 157:109\u2013126. https:\/\/doi.org\/10.1007\/s10533-021-00860-1","journal-title":"Biogeochemistry"},{"key":"2661_CR71","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1038\/nsb1197-904","volume":"4","author":"Y Kakuta","year":"1997","unstructured":"Kakuta Y, Pedersen LG, Carter CW, Negishi M, Pedersen LC (1997) Crystal structure of estrogen sulphotransferase. Nat Struct Biol 4:904\u2013908. https:\/\/doi.org\/10.1038\/nsb1197-904","journal-title":"Nat Struct Biol"},{"key":"2661_CR72","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1099\/00221287-142-4-741","volume":"142","author":"A Pospiech","year":"1996","unstructured":"Pospiech A, Bietenhader J, Schupp T (1996) Two multifunctional peptide synthetases and an O-methyltransferase are involved in the biosynthesis of the DNA-binding antibiotic and antitumour agent saframycin Mx1 from Myxococcus xanthus. Microbiology, 142:741\u2013746. https:\/\/doi.org\/10.1099\/00221287-142-4-741","journal-title":"Microbiology,"},{"key":"2661_CR73","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1007\/s00248-023-02189-8","volume":"85","author":"C Kim","year":"2023","unstructured":"Kim C, Staver LW, Chen X, Bulseco A, Cornwell JC, Malkin SY (2023) Microbial community succession along a chronosequence in constructed salt marsh soils. Microb Ecol 85:931\u2013950. https:\/\/doi.org\/10.1007\/s00248-023-02189-8","journal-title":"Microb Ecol"}],"container-title":["Microbial Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00248-025-02661-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00248-025-02661-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00248-025-02661-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T10:52:23Z","timestamp":1768474343000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00248-025-02661-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,6]]},"references-count":73,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["2661"],"URL":"https:\/\/doi.org\/10.1007\/s00248-025-02661-7","relation":{},"ISSN":["1432-184X"],"issn-type":[{"value":"1432-184X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,6]]},"assertion":[{"value":"16 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"21"}}