Table_1_The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance.XLSX

Active sulfate-reducing microorganisms (SRM) in freshwater sediments are under-examined, despite the well-documented cryptic sulfur cycle occurring in these low-sulfate habitats. In Lake Constance sediment, sulfate reduction rates of up to 1,800 nmol cm-3 day-1 were previously measured. To characterize its SRM community, we used a tripartite amplicon sequencing approach based on 16S rRNA genes, 16S rRNA, and dsrB transcripts (encoding the beta subunit of dissimilatory sulfite reductase). We followed the respective amplicon dynamics in four anoxic microcosm setups supplemented either with (i) chitin and sulfate, (ii) sulfate only, (iii) chitin only, or (iv) no amendment. Chitin was used as a general substrate for the whole carbon degradation chain. Sulfate turnover in sulfate-supplemented microcosms ranged from 38 to 955 nmol day-1 (g sediment f. wt.)-1 and was paralleled by a decrease of 90–100% in methanogenesis as compared to the respective methanogenic controls. In the initial sediment, relative abundances of recognized SRM lineages accounted for 3.1 and 4.4% of all bacterial 16S rRNA gene and 16S rRNA sequences, respectively. When normalized against the 1.4 × 108 total prokaryotic 16S rRNA gene copies as determined by qPCR and taking multiple rrn operons per genome into account, this resulted in approximately 105–106 SRM cells (g sediment f. wt.)-1. The three amplicon approaches jointly identified Desulfobacteraceae and Syntrophobacteraceae as the numerically dominant and transcriptionally most active SRM in the initial sediment. This was corroborated in the time course analyses of sulfate-consuming sediment microcosms irrespective of chitin amendment. Uncultured dsrAB family-level lineages constituted in sum only 1.9% of all dsrB transcripts, with uncultured lineage 5 and 6 being transcriptionally most active. Our study is the first holistic molecular approach to quantify and characterize active SRM including uncultured dsrAB lineages not only in Lake Constance but for lake sediments in general.

尽管这类低硫酸盐生境中存在的隐秘硫循环已被充分记录，但淡水沉积物中的活性硫酸盐还原微生物（active sulfate-reducing microorganisms, SRM）仍未得到充分研究。此前在康斯坦茨湖沉积物中，已测得最高可达1800 nmol cm⁻³ d⁻¹的硫酸盐还原速率。为表征其SRM群落，我们采用了基于16S rRNA基因、16S rRNA以及dsrB转录本（编码异化亚硫酸盐还原酶β亚基）的三重扩增子测序策略。我们对四组厌氧微宇宙体系中的各类扩增子动态进行了追踪，这四组体系分别添加：(i) 几丁质与硫酸盐、(ii) 仅硫酸盐、(iii) 仅几丁质，以及(iv) 无添加物。几丁质被用作整个碳降解链的通用底物。添加硫酸盐的微宇宙体系中，硫酸盐周转速率介于38至955 nmol d⁻¹ (g sediment f. wt.)⁻¹之间，且与相应产甲烷对照相比，产甲烷作用降低了90%~100%。在初始沉积物中，已确认的SRM类群分别占所有细菌16S rRNA基因序列与16S rRNA序列的3.1%与4.4%。通过定量聚合酶链反应（quantitative PCR, qPCR）测定的1.4×10⁸个原核生物16S rRNA基因总拷贝数进行标准化，并考虑每个基因组内存在多个核糖体RNA操纵子（ribosomal RNA operon, rrn operon）的情况后，据此估算得到的SRM细胞数约为10⁵~10⁶个每克沉积物鲜重。三种扩增子测序策略共同鉴定出，初始沉积物中数量占优且转录活性最高的SRM为脱硫杆菌科（Desulfobacteraceae）与互营杆菌科（Syntrophobacteraceae）。这一结果在消耗硫酸盐的沉积物微宇宙的时间进程分析中得到了验证，且与是否添加几丁质无关。未培养的dsrAB科水平类群总计仅占所有dsrB转录本的1.9%，其中未培养类群5与6的转录活性最高。本研究不仅是康斯坦茨湖沉积物领域，更是针对全球湖泊沉积物首个量化并表征包括未培养dsrAB类群在内的活性SRM的整体性分子研究。