Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA.
mSystems. 2024 Apr 16;9(4):e0000624. doi: 10.1128/msystems.00006-24. Epub 2024 Mar 12.
UNLABELLED: Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE: Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.
未加标签:理解微生物群落的组织原则对于解释生态系统稳定性至关重要。以前的研究已经在营养贫瘠的条件下或对强制性代谢相互依存关系下观察到不同物种之间的合作相互作用,研究了细菌群落的形成。然而,在没有强制性代谢相互依存关系的营养丰富的环境中,微生物如何形成稳定的群落,仍然没有得到充分揭示。在这项研究中,从根际分离出的三株细菌在复杂培养基中进行共培养,并跟踪其生长行为。这些菌株在混合培养中共同存在,并在多个生长稀释循环的连续传代中共存。基于它们的生长水平显著下降,提出了竞争是这三种细菌之间的一种新兴相互作用关系。研究了不同初始接种比例(高达三个数量级)对群落结构的影响,具有不同起始组成的混合群落的最终组成表明群落结构不依赖于初始接种比例。此外,不同初始接种比例不会改变群落内的竞争关系。通过广义 Lotka-Volterra 和动态通量平衡分析对群落结构进行模拟,为在营养丰富的环境下群落结构的出现提供了机制预测。代谢组学分析为计算模型预测的代谢物交换以及微生物在共培养中生长时高度改变的生理状态提供了支持。这些发现拓宽了我们对富营养环境下细菌群落动态和代谢多样性的理解,并且在根际细菌群落的管理中可能具有重要意义。
重要性:细菌自然地在多物种共生体中共存,而工程化这种系统的能力在生物技术中可能是有用的。尽管如此,很少有研究旨在了解细菌在营养丰富的条件下如何形成稳定的群落并相互作用。在这项研究中,我们使用复杂培养基研究了初始接种比例对细菌群落结构的影响,发现初始接种比例对最终群落结构或群落成员之间的相互作用模式没有显著影响。使用计算工具模拟微生物种群分布,以了解微生物之间的关系,并确定细菌群落稳定过程中发生的潜在代谢交换。研究微生物群落组装过程对于理解微生物生态系统中的基本生态原则至关重要,并且对于预测微生物群落结构和功能可能是关键的。
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