La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia.
Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia.
Environ Microbiol Rep. 2023 Aug;15(4):308-323. doi: 10.1111/1758-2229.13148. Epub 2023 Mar 29.
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
澳大利亚菲利普港湾的底栖渗流反硝化效率存在时空变异性。在此，我们评估了非靶向宏转录组学在解析底栖氮循环中微生物贡献的时空差异方面的能力。组装的最丰富的沉积物转录本与古菌硝化细菌 Nitrosopumilus 有关。在靠近有机氮外部输入的沉积物中，主要转录本与 Nitrosopumilus 一氧化二氮亚硝酸盐还原（nirK）有关。靠近有机氮输入的环境条件选择增加 Nitrosopumilus 的转录（amoCAB、nirK、nirS、nmo、hcp），还选择增加细菌亚硝酸盐还原（nxrB）和与厌氧氨氧化（hzo）相关的转录本，但不选择反硝化（细菌 nirS/nirk）。在远离有机氮外部输入的沉积物中，主要转录本与一氧化二氮还原（nosZ）有关，nosZ 转录物丰度的变化与与古菌硝化作用相关的转录特征无关。偶联的群落水平硝化-反硝化的协调转录没有得到宏转录组学的很好支持。相比之下，古菌 nirK 转录本的丰度具有特定地点和季节的特征。这项研究表明，古菌 nirK 对环境条件变化的转录可能是沿海沉积物氮循环的一个重要且被忽视的特征。
