Active microorganisms thrive among extremely diverse communities in cloud water

Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active in situ remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~103−104 bacteria and archaea mL-1 and ~102−103 eukaryote cells mL-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.

云是地球系统运行的关键组分。云不仅可作为光辐射的阻隔体与云内化学反应的发生场景，还可能成为空气传播微生物的大气绿洲，为其提供水分、养分以及通往地面的通路。此前虽已在云体中检测到微生物活动，但原位活跃的微生物群落仍未被明确解析。本研究针对法国多姆山（Puy de Dôme Mountain）气象站（海拔1465米）采集的云水中的微生物群落进行采样固定，并通过对DNA与RNA提取物开展高通量测序（high-throughput sequencing），以鉴定群落内的活跃物种。该群落的细胞密度为每毫升约10³~10⁴个细菌与古菌，以及10²~10³个真核细胞。该群落物种丰富度极高，细菌类群中检测到逾28000个不同物种，真核生物类群中则检测到2600个不同物种。细菌群落主要由变形菌门（Proteobacteria）与拟杆菌门（Bacteroidetes）占据主导地位，而真核生物则主要分布于真菌界（Fungi）、不等鞭毛类（Stramenopiles）与囊泡虫类（Alveolata）类群中。在这些复杂的群落中，云微生物群的活跃成员被鉴定为α-变形菌纲（Alphaproteobacteria，包含鞘脂单胞菌目Sphingomonadales、红螺菌目Rhodospirillales与根瘤菌目Rhizobiales）、β-变形菌纲（Betaproteobacteria，包含伯克霍尔德菌目Burkholderiales）以及γ-变形菌纲（Gammaproteobacteria，包含假单胞菌目Pseudomonadales）。这些通常被归类为附生菌的细菌类群，极有可能是干扰云中非生物化学反应的最优候选类群，同时也是最易通过空气实现成功传播的类群。