{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T06:51:05Z","timestamp":1791355865522,"version":"4.3.1"},"reference-count":49,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Small Methods"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Sediment microbiomes drive global biogeochemical cycling, but their functional heterogeneity and transcriptional activity are hardly resolved at single\u2010cell resolution. We optimized a scalable single\u2010microbe RNA sequencing workflow for environmental muddy sediment samples, achieving high\u2010throughput single cell sequencing across environmental gradients. The method integrates iohexol\u2010based microbial enrichment, optimized enzymatic digestion step, droplet\u2010based single\u2010cell barcoding, and RNA sequencing, then generating a transcriptomic atlas of 55\u00a0859 high\u2010quality microbial cells from 8 composite samples covering freshwater, estuarine and nearshore marine habitats. Comparison with metagenomic data showed a high consistency in species composition, supporting the reliability of single\u2010microbe RNA sequencing in community profiling. Taxonomic analysis revealed site\u2010specific microbial communities associated with methane oxidation, sulfur cycling and anaerobic nitrogen metabolism. 15 distinct functional clusters were identified transcriptionally, showing functional heterogeneity within sedimentary microbiome. Co\u2010expression network analysis further resolved coordinated gene modules, with module activities varying across samples. Overall, this work establishes a practical framework for single\u2010microbe transcriptomics in sediment systems and demonstrates the potential of single\u2010cell resolution to uncover functional heterogeneity within complex microbial communities.<\/jats:p>","DOI":"10.1002\/smtd.71082","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T06:07:35Z","timestamp":1791353255000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single\u2010Microbe Transcriptomics Reveal Functional Heterogeneity in Sediment Microbiomes"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6053-9508","authenticated-orcid":false,"given":"Lingxiao","family":"Zhu","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine of the First Affiliated Hospital &amp; Liangzhu Laboratory Zhejiang University School of Medicine  Hangzhou 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