Mechanisms underlying growth inhibition of a denitrifier by reduced sulfur compounds

Competition among nitrate reducing bacteria (NRB) and sulfate reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater and sediment, and therefore may play important roles in competitive interactions. Here, using Intrasporangium calvum C5 as a model NRB, we performed comparative transcriptomic and metabolomic analyses to demonstrate that the reduced sulfur compounds cysteine and sulfide differentially inhibit respiratory growth on nitrate, and that inhibition by each can be selectively relieved by a specific carbon source. These findings provide mechanistic insights into the interplay and stratification of NRBs and SRBs in diverse environments. Overall design: Time series mRNA profiling of a bacterial strain subjected to reduced sulfur stress. Three conditions were tested, a reference (Regular) and four treatments. Each consists of measurements at four growth phases and were made in triplicate. Multiple sequencing runs were performed to obtain enough reads (e.g., L001, L002, L003, L004).

硝酸盐还原菌（nitrate reducing bacteria, NRB）与硫酸盐还原菌（sulfate reducing bacteria, SRB）在缺氧环境中对资源的竞争，此前普遍认为主要由热力学过程主导。如今已有研究证实，氮循环与硫循环的中间产物（如硫化氢、亚硝酸盐等）同样可直接影响淡水、废水及沉积物中的NRB与SRB活性，因此可能在二者的竞争互作中发挥关键作用。
本研究以裸孢囊菌C5（Intrasporangium calvum C5）作为模式NRB，开展比较转录组学与代谢组学分析，结果证实还原态硫化物半胱氨酸与硫化物可差异性抑制硝酸盐呼吸生长，且两种物质的抑制作用均可通过特定碳源选择性解除。上述研究结果为解析不同环境中NRB与SRB的互作关系与生态位分层机制提供了机制层面的新认知。
实验设计概述：对施加还原态硫胁迫的细菌菌株开展时间序列mRNA转录组分析。共测试了3组条件，包含1组对照组（常规组）与4组处理组；每组均在4个生长阶段进行取样，并设置3次生物学重复。通过多轮测序（如L001、L002、L003、L004）以获取足够的测序读段。