Microbial active functional modules derived from network analysis and metabolic interactions decipher the complex microbiome assembly in mangrove sediments.
Microbial active functional modules derived from network analysis and metabolic interactions decipher the complex microbiome assembly in mangrove sediments.
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DOI：
10.1186/s40168-022-01421-w
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发表时间：
2022-12-13
期刊：
影响因子：
15.5
通讯作者：
中科院分区：
文献类型：
--
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微生物的代谢相互作用对微生物群落的组装有重要影响，微生物群落在生物地球化学过程中起着重要作用。然而，自然群落中微生物之间的大多数种间相互作用仍然未知，导致对群落组装机制的了解很差。在这里，我们使用了基于基因组规模代谢建模的方法来探索红树林沉积物中细菌和古菌之间的潜在相互作用。超过一半的组装微生物物种()结合了约3000个具有高潜力的成对代谢相互作用关系。预测相互作用的例子与基于微生物丰富/培养的研究的含义一致，表明我们从复杂的物种间网络中提取不同潜在相互作用的策略是可行的。此外，还预测了大量以前未知的微生物代谢相互作用。我们提出了微生物活性功能模块(MAFM)的概念，定义为一组具有较高代谢相互作用的微生物组成的联合体，它们可以通过这些联合体在元素转化中主动实现某些主导功能。根据微生物的代谢相互作用和转录物的分布，鉴定了分布在不同沉积物中的五个mAFM。整个功能模块覆盖了碳、氮和硫循环的大部分主要途径，而每个模块具有不同的主导功能。根据Thinctiis Diston的研究结果，我们推测MAFM通过其内部循环以及它们与沉积物之间的相互交换参与了元素循环。本研究结果极大地拓展了红树林沉积物中微生物的相互作用潜力，可为今后的共生体系建设和微生物富集培养提供支持。此外，mAFM可以帮助从整个群落中提取有价值的微生物代谢相互作用，并描述促进红树林沉积物中生物地球化学循环的微生物群落的功能。视频摘要在线版本包含可在10.1186/s40168022-022-w获得的补充材料。
The metabolic interactions of microbes significantly affect the assembly of microbial communities that play important roles in biogeochemical processes. However, most interspecies interactions between microorganisms in natural communities remain unknown, leading to a poor understanding of community assembly mechanisms. Here, we used a genome-scale metabolic modeling-based approach to explore the potential interactions among bacteria and archaea in mangrove sediments. More than half of the assembled microbial species () combined about 3000 pairwise metabolic interaction relationship with high potential. The examples of predicted interactions are consistent with the implications of studies based on microbial enrichment/culture, indicating the feasibility of our strategy for extracting diverse potential interactions from complex interspecies networks. Moreover, a substantial number of previously unknown microbial metabolic interactions were also predicted. We proposed a concept of microbial active functional module (mAFM), defined as a consortium constituted by a group of microbes possessing relatively high metabolic interactions via which they can actively realize certain dominant functions in element transformations. Based on the metabolic interactions and the transcript distribution of microorganisms, five mAFMs distributed in different layers of the sediments were identified. The whole group of mAFMs covered most of the principal pathways in the cycle of carbon, nitrogen, and sulfur, while each module possessed divergently dominant functions. According to thinctiis diston, we inferred that the mAFMs participated in the element cycles via their intra-cycle and the inter-exchange among them and the sediments. The results of this study greatly expanded interaction potential of microbes in mangrove sediments, which could provide supports for prospective mutualistic system construction and microbial enrichment culture. Furthermore, the mAFMs can help to extract valuable microbial metabolic interactions from the whole community and to profile the functioning of the microbial community that promote biogeochemical cycling in mangrove sediments. Video Abstract The online version contains supplementary material available at 10.1186/s40168-022-01421-w.
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影响因子：
16.6
作者：
Golyshina OV;Toshchakov SV;Makarova KS;Gavrilov SN;Korzhenkov AA;La Cono V;Arcadi E;Nechitaylo TY;Ferrer M;Kublanov IV;Wolf YI;Yakimov MM;Golyshin PN
通讯作者：
Golyshin PN
影响因子：
3.3
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影响因子：
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Dal Co, Alma;van Vliet, Simon;Ackermann, Martin
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Ackermann, Martin
影响因子：
12.3
作者：
Bernstein DB;Sulheim S;Almaas E;Segrè D
通讯作者：
Segrè D
影响因子：
9.2
作者：
Castelle, Cindy J.;Wrighton, Kelly C.;Banfield, Jillian F.
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Banfield, Jillian F.