Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

Estrela, Sylvie; Sánchez-Gorostiaga, Alicia; Vila, Jean C. C.; Sánchez, Álvaro

doi:10.7554/elife.65948

Cited by 75 publications

(69 citation statements)

References 50 publications

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“…In contrast, the natural rhizosphere soil environments provide stages for cooperative interaction due to the local presence of diverse nutrients, root exudates, and heterogeneity. These findings are in accordance with previous studies, support the impact of spatial organization and nutrient condition on microbial interaction [ 68 , 69 ]. Our experimental setup involved co-cultivation of B. velezensis and P. stutzeri in liquid medium.…”

Section: Discussionsupporting

confidence: 93%

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

et al. 2021

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Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant ( Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.

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Section: Discussionsupporting

confidence: 93%

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

et al. 2021

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“…For the microbial growth in in silico experiment, not only resource availability but also resource quality should be considered in the mathematical model. It has been reported that the quality of resources, such as what metabolic by-products are produced from a resource and the combination of resources, influences the assembly of microbial communities [ 39 , 41 ]. For the mathematical model, the phenomenon was reproduced with many parameter sets in this study, but it is also important to identify the parameters of the mathematical model from in situ data by larger field sampling in the future.…”

Section: Discussionmentioning

confidence: 99%

Determinism of microbial community assembly by drastic environmental change

2021

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Microbial community assembly is shaped by deterministic and stochastic processes, but the relationship between these processes and the environment is not understood. Here we describe a rule for the determinism and stochasticity of microbial community assembly affected by the environment using in silico, in situ, and ex situ experiments. The in silico experiment with a simple mathematical model showed that the existence of essential symbiotic microorganisms caused stochastic microbial community assembly, unless the community was exposed to a non-adapted nutritional concentration. Then, a deterministic assembly occurred due to the low number of microorganisms adapted to the environment. In the in situ experiment in the middle of a river, the microbial community composition was relatively deterministic after the drastic environmental change caused by the treated wastewater contamination, as analyzed by 16S rRNA gene sequencing. Furthermore, by culturing microbial communities collected from the upstream natural area and downstream urban area of the river in test tubes with varying carbon source concentrations, the upstream community assembly became deterministic with high carbon concentrations while the downstream community assembly became deterministic with low carbon concentrations. These results suggest that large environmental changes, which are different from the original environment, result in a deterministic microbial community assembly.

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“…Patterns that deviate from the assumption arise from biological phenomena that are deemed non-additive. Much emphasis has been placed on predictions on the additive (or non-additive deviation) nature of growth outcomes in more complex environments (Foster and Bell, 2012;Pacheco et al, 2021;Estrela et al, 2021). Here, we evaluated non-additive responses (e.g.…”

Section: B Thailandensis-p Syringae Interspecies Networkmentioning

confidence: 99%

Bioactive exometabolites drive maintenance competition in simple bacterial communities

Chodkowski

Shade

2021

Preprint

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During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced by cells in stationary phase cultures, can, perhaps counterintuitively, include upregulation of cellular secondary metabolism and release of exometabolites into the local environment, at the cost of an energetic commitment to growth. As resource limitation is a characteristic feature of many habitats that harbor environmental microbial communities, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance, and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over stationary phase among three well-known environmental bacterial strains: Burkholderia thailandensis E264 (ATCC 700388), Chromobacterium violaceum ATCC 31532, and Pseudomonas syringae pv.tomato DC3000 (ATCC BAA-871). We assembled these stains into laboratory-scale synthetic communities that only permitted chemical interactions among them. We compared the responses (transcripts) and behaviors (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were altered in the presence of different neighbors, and that these changes could be attributed to the production of or response to bioactive exometabolites employed for competition during maintenance. B. thailandensis was especially influential and competitive within its communities, as it consistently upregulated additional biosynthetic gene clusters involved in the production of bioactive exometabolites for both exploitative and interference competition. Additionally, some of these bioactive exometabolites were upregulated and produced in a non-additive manner in the 3-member community. These results demonstrate that the active investment in competition during maintenance can contribute to both bacterial population fitness and community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be too narrow, and that maintenance competition could be an alternative measure

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Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

Cited by 75 publications

References 50 publications

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

Determinism of microbial community assembly by drastic environmental change

Bioactive exometabolites drive maintenance competition in simple bacterial communities

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