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In soils, CO\n                      <jats:sub>2<\/jats:sub>\n                      -fixing microorganisms are preventing some of the CO\n                      <jats:sub>2<\/jats:sub>\n                      from entering the atmosphere. Yet, the controls of dark CO\n                      <jats:sub>2<\/jats:sub>\n                      fixation are rarely studied\n                      <jats:italic>in situ<\/jats:italic>\n                      . Here, we examined the gene and transcript abundance of key genes involved in microbial CO\n                      <jats:sub>2<\/jats:sub>\n                      fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO\n                      <jats:sub>2<\/jats:sub>\n                      fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood\u2013Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood\u2013Ljungdahl pathway was favored by reducing, O\n                      <jats:sub>2<\/jats:sub>\n                      -poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO\n                      <jats:sub>2<\/jats:sub>\n                      fixation was mainly linked to a few bacterial phyla, namely,\n                      <jats:italic>Desulfobacterota<\/jats:italic>\n                      ,\n                      <jats:italic>Methylomirabilota<\/jats:italic>\n                      ,\n                      <jats:italic>Nitrospirota<\/jats:italic>\n                      ,\n                      <jats:italic>Chloroflexota<\/jats:italic>\n                      , and\n                      <jats:italic>Pseudomonadota<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      The increasing concentration of atmospheric CO\n                      <jats:sub>2<\/jats:sub>\n                      has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO\n                      <jats:sub>2<\/jats:sub>\n                      fixation by soil microbes (a.k.a. dark CO\n                      <jats:sub>2<\/jats:sub>\n                      fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO\n                      <jats:sub>2<\/jats:sub>\n                      -fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO\n                      <jats:sub>2<\/jats:sub>\n                      fixation and its potential role in the global climate system.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/aem.02177-24","type":"journal-article","created":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T08:46:06Z","timestamp":1735634766000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":14,"title":["Assessing environmental gradients in relation to dark CO\n                    <sub>2<\/sub>\n                    fixation in estuarine wetland microbiomes"],"prefix":"10.1128","volume":"91","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6819-007X","authenticated-orcid":true,"given":"Luise","family":"Gr\u00fcterich","sequence":"first","affiliation":[{"name":"Department of Microbiology and Biotechnology, University of Hamburg","place":["Hamburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1129-5396","authenticated-orcid":false,"given":"Jason Nicholas","family":"Woodhouse","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Biotechnology, University of Hamburg","place":["Hamburg, Germany"]},{"name":"Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries","place":["Stechlin, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6974-5498","authenticated-orcid":false,"given":"Peter","family":"Mueller","sequence":"additional","affiliation":[{"name":"Institute of Landscape Ecology, University of M\u00fcnster","place":["M\u00fcnster, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-3951-4814","authenticated-orcid":false,"given":"Amos","family":"Tiemann","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Biotechnology, University of Hamburg","place":["Hamburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7473-6086","authenticated-orcid":false,"given":"Hans-Joachim","family":"Ruscheweyh","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich","place":["Zurich, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3065-0314","authenticated-orcid":false,"given":"Shinichi","family":"Sunagawa","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich","place":["Zurich, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9141-0325","authenticated-orcid":false,"given":"Hans-Peter","family":"Grossart","sequence":"additional","affiliation":[{"name":"Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries","place":["Stechlin, Germany"]},{"name":"Institute of Biochemistry and Biology, Potsdam University","place":["Potsdam, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7617-7396","authenticated-orcid":true,"given":"Wolfgang R.","family":"Streit","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Biotechnology, University of Hamburg","place":["Hamburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1244758"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2016.130"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00014586"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/nph.15283"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-47646-1"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00407-11"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.60.2.439-471.1996"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2011.03.003"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","unstructured":"Zimmermann M Mayr MJ Bouffard D Eugster W Steinsberger T Wehrli B Brand A B\u00fcrgmann H. 2019. 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