Kaupper Thomas, Mendes Lucas W, Poehlein Anja, Frohloff Daria, Rohrbach Stephan, Horn Marcus A, Ho Adrian
Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
Center for Nuclear Energy in Agriculture, University of São Paulo CENA-USP, Piracicaba, SP, Brazil.
Environ Microbiome. 2022 Apr 5;17(1):15. doi: 10.1186/s40793-022-00409-1.
Biological interaction affects diverse facets of microbial life by modulating the activity, diversity, abundance, and composition of microbial communities. Aerobic methane oxidation is a community function, with emergent community traits arising from the interaction of the methane-oxidizers (methanotrophs) and non-methanotrophs. Yet little is known of the spatial and temporal organization of these interaction networks in naturally-occurring complex communities. We hypothesized that the assembled bacterial community of the interaction network in methane hotspots would converge, driven by high substrate availability that favors specific methanotrophs, and in turn influences the recruitment of non-methanotrophs. These environments would also share more co-occurring than site-specific taxa.
We applied stable isotope probing (SIP) using C-CH coupled to a co-occurrence network analysis to probe trophic interactions in widespread methane-emitting environments, and over time. Network analysis revealed predominantly unique co-occurring taxa from different environments, indicating distinctly co-evolved communities more strongly influenced by other parameters than high methane availability. Also, results showed a narrower network topology range over time than between environments. Co-occurrence pattern points to Chthoniobacter as a relevant yet-unrecognized interacting partner particularly of the gammaproteobacterial methanotrophs, deserving future attention. In almost all instances, the networks derived from the C-CH incubation exhibited a less connected and complex topology than the networks derived from the C-CH incubations, likely attributable to the exclusion of the inactive microbial population and spurious connections; DNA-based networks (without SIP) may thus overestimate the methane-dependent network complexity.
We demonstrated that site-specific environmental parameters more strongly shaped the co-occurrence of bacterial taxa than substrate availability. Given that members of the interactome without the capacity to oxidize methane can exert interaction-induced effects on community function, understanding the co-occurrence pattern of the methane-driven interaction network is key to elucidating community function, which goes beyond relating activity to community composition, abundances, and diversity. More generally, we provide a methodological strategy that substantiates the ecological linkages between potentially interacting microorganisms with broad applications to elucidate the role of microbial interaction in community function.
生物相互作用通过调节微生物群落的活性、多样性、丰度和组成，影响微生物生命的各个方面。好氧甲烷氧化是一种群落功能，甲烷氧化菌（甲烷营养菌）和非甲烷营养菌之间的相互作用产生了新的群落特征。然而，对于这些相互作用网络在自然存在的复杂群落中的时空组织，我们知之甚少。我们假设，在甲烷热点地区，相互作用网络中组装的细菌群落将趋同，这是由有利于特定甲烷营养菌的高底物可用性驱动的，进而影响非甲烷营养菌的招募。这些环境中共同出现的分类群也会比特定地点的分类群更多。
我们应用与共现网络分析相结合的¹³C-CH₄稳定同位素探测（SIP）来探究广泛的甲烷排放环境中以及随时间变化的营养相互作用。网络分析揭示了来自不同环境的主要是独特的共同出现的分类群，这表明明显共同进化的群落受其他参数的影响比高甲烷可用性更强。此外，结果显示随着时间推移，网络拓扑范围比不同环境之间的更窄。共现模式表明噬泥杆菌是一个相关但尚未被认识的相互作用伙伴，特别是与γ-变形菌纲甲烷营养菌的相互作用伙伴，值得未来关注。几乎在所有情况下，¹³C-CH₄培养产生的网络比¹²C-CH₄培养产生的网络具有更少的连接和更简单的拓扑结构，这可能归因于非活性微生物群体的排除和虚假连接；因此基于DNA的网络（无SIP）可能高估了甲烷依赖的网络复杂性。
我们证明，特定地点的环境参数比底物可用性更强烈地塑造了细菌分类群的共现。鉴于相互作用组中没有甲烷氧化能力的成员可以对群落功能产生相互作用诱导的影响，理解甲烷驱动的相互作用网络的共现模式是阐明群落功能的关键，这超越了将活性与群落组成、丰度和多样性联系起来。更一般地说，我们提供了一种方法策略，证实了潜在相互作用微生物之间的生态联系，具有广泛的应用，以阐明微生物相互作用在群落功能中的作用。
