Villemur Richard, Payette Geneviève, Geoffroy Valérie, Mauffrey Florian, Martineau Christine
INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, Québec, Canada.
Lallemand, Montréal, Québec, Canada.
PeerJ. 2019 Aug 13;7:e7467. doi: 10.7717/peerj.7467. eCollection 2019.
The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which and are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of strain NL23 and in the biofilm cultures. Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm.
The original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures. The OB was also cultivated in the commercial Instant Ocean seawater (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences. Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of strain NL23 and strain GP59.
High proportions of occurred in the biofilm cultures. strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl. It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0-1% NaCl and in the IO biofilm cultures. Denitrifying bacterial isolates affiliated to spp. and spp. were isolated. Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the spp. were metabolically active in the biofilm cultures.
These results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures. Up regulation of the denitrification genes of strain GP59 and strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm. Other denitrifying heterotrophic bacteria are present in low proportions, suggesting that the biofilm has the potential to adapt to heterotrophic, non-methylotrophic environments.
以甲醇为食源的海洋反硝化系统中的生物膜由多种微生物群落组成，其中[具体菌1]和[具体菌2]是参与反硝化活动的主要细菌。为评估其对环境变化的恢复力，该生物膜在缺氧条件下于人工海水（ASW）中培养，并暴露于一系列特定环境条件下。我们之前报道了这些变化对反硝化活性以及生物膜培养物中[菌株NL23]和[具体菌2]共存的影响。在此，我们报道这些变化对反硝化生物膜整体微生物群落动态的影响。
从反硝化系统获取的原始生物膜（OB）在缺氧条件下于不同NaCl浓度的ASW中培养，同时设置硝酸盐/甲醇浓度和温度的四种组合。原始生物膜也在市售的Instant Ocean海水（IO）中培养。通过16S核糖体RNA基因序列确定生物膜培养物和原始生物膜的细菌多样性。采用培养方法从生物膜培养物中分离其他反硝化细菌。获得选定生物膜培养物的宏转录组，以及[菌株NL23]和[菌株GP59]浮游纯培养物的转录组。
[具体菌1]在生物膜培养物中占比很高。在原始生物膜中发现[菌株NL23]占比很高，但在2.75% NaCl的ASW培养基中培养的生物膜培养物中不存在。然而，在0 - 1% NaCl的ASW培养基中培养的生物膜培养物和IO生物膜培养物中发现其占比很低。分离出了隶属于[具体菌属1]和[具体菌属2]的反硝化细菌分离株。与浮游纯培养物相比，生物膜培养物中[菌株GP59]和[菌株NL23]的反硝化基因上调。隶属于[具体菌属1]的反硝化细菌在生物膜培养物中具有代谢活性。
这些结果说明了反硝化生物膜培养物中微生物群落适应不同环境条件的动态变化。NaCl浓度是影响生物膜培养物中微生物群落的一个重要因素。生物膜培养物中[菌株GP59]和[菌株NL23]反硝化基因的上调表明生物膜中反硝化途径存在不同的调控机制。其他反硝化异养细菌占比很低，这表明生物膜有潜力适应异养、非甲基营养环境。
