Busigny Vincent, Mathon François P, Jézéquel Didier, Bidaud Cécile C, Viollier Eric, Bardoux Gérard, Bourrand Jean-Jacques, Benzerara Karim, Duprat Elodie, Menguy Nicolas, Monteil Caroline L, Lefevre Christopher T
Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.
Institut Universitaire de France, Paris, 75005, France.
Environ Microbiol. 2022 Feb;24(2):721-736. doi: 10.1111/1462-2920.15458. Epub 2021 Mar 23.
Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organism's recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behaviour allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.
对于那些研究难以在实验室条件下培养的生物体的科学家来说，获取用于非培养方法的特定微生物的高生物量产量是一项挑战。而在研究趋磁细菌（MTB）时，这一困难会大大降低，因为它们独特的行为使其能够从水生环境中存在的其他微生物中富集和纯化出来。在这里，我们将法国中央地块的一个永久分层湖泊——帕万湖作为天然实验室，以优化在水柱和沉积物中生长的MTB的收集和浓缩。本文介绍了一种从这个火山口湖沉积物中高度丰富的非生物磁性颗粒中分离MTB的方法。对于水柱，我们比较了不同的采样方法，如使用尼斯金采水器原位采集和在线抽水。通过监测水柱的几个物理化学参数，我们确定了MTB生存的生态位。然后，通过将采样集中在MTB丰度的峰值处，我们表明在线抽水系统对于以高空间分辨率快速回收大量水最为有效，考虑到水柱中观察到的急剧物理化学梯度，这是必要的。利用趋氧性和磁性MTB特性，我们提出了一种从大量水中浓缩MTB的有效方法。我们的方法代表了对帕万湖及其他地方MTB种群的多样性、宏基因组学和生态学进行进一步多学科研究以及对其磁小体进行化学和同位素分析的第一步。
