Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Apr 16;9(4):e0000624.
doi: 10.1128/msystems.00006-24. Epub 2024 Mar 12.

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition

Affiliations

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition

Jia Wang et al. mSystems. .

Abstract

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 Populus deltoides 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.

Keywords: dynamic flux balance analysis; initial inoculum ratio; metabolite exchange; metaproteomics; microbial community; rhizospheric bacteria.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig 1
Fig 1
Analysis of the bacterial community structure over assembly process and species growth behavior in passage 0 starting from the inoculum with three species in equal proportion in a nutrient-rich medium environment. The relative abundances of each species in the community are based on (a) plate counting and (b) qPCR method. (c) Comparison of the bacterial cell density values at the end of a growth period between mixed and pure culture modes analyzed by plate counting and qPCR methods. Asterisks show statistically significant decreases in cell abundance compared with monoculture using the same analytical method (P < 0.05). (d) Comparison of the maximum growth rate between mixed and pure culture modes determined by plate counting and qPCR methods. Asterisk shows statistically significant decrease in maximum growth rate compared with monoculture using the same analytical method (P < 0.05). Each column or data point represents the mean, and error bars are the standard error over three parallel experiments.
Fig 2
Fig 2
The final relative ratios (at the end of passage 5) of the three strains in the synthetic bacterial communities over a broad range of initial inoculum ratios analyzed by plate counting (PC) and qPCR methods. Each data column represents the mean, and error bars are the standard error over three parallel experiments. Different letters above each column indicate difference of community structure among groups at P < 0.05.
Fig 3
Fig 3
Dynamics of the composition of three-member communities with three representative initial inoculum ratios in a nutrient-rich medium environment. GM17-YR343-AP49 0.001-1-1 analyzed by (a) plate counting and (b) qPCR; GM17-YR343-AP49 1–0.001-0.001 analyzed by (c) plate counting and (d) qPCR; GM17-YR343-AP49 1–0.058-0.015 analyzed by (e) plate counting and (f) qPCR. Each data point represents the mean, and error bars are the standard error over three parallel experiments.
Fig 4
Fig 4
The dFBA model simulations for dynamics of three-member communities with representative initial inoculum ratios (a) 1-1-1, (b) 0.001-1-1, (c) 1–0.001-0.001, and (d) 1–0.126-0.013 of GM17-YR343-AP49.
Fig 5
Fig 5
Metabolic interaction network proposed by dFBA simulation in the co-culture with equal initial inoculum ratio. Metabolite abbreviation: HYXN, hypoxanthine.
Fig 6
Fig 6
Volcano plots showing the significant differentially abundant proteins for each bacterial species at 48 h in the three-member community with equal initial inoculum ratios (GM17-YR343-AP49 1-1-1) compared to their monocultures at the early stationary phase in R2A medium (a) Pseudomonas sp. GM17, (b) Pantoea sp. YR343, and (c) Sphingobium sp. AP49. Proteins involved in interspecies exchanges as predicted by dFBA analysis are highlighted in the upregulated proteins.

Similar articles

Cited by

References

    1. Liu F, Mao J, Kong W, Hua Q, Feng Y, Bashir R, Lu T. 2020. Interaction variability shapes succession of synthetic microbial ecosystems. Nat Commun 11:309. doi:10.1038/s41467-019-13986-6 - DOI - PMC - PubMed
    1. Niu B, Paulson JN, Zheng X, Kolter R. 2017. Simplified and representative bacterial community of maize roots. Proc Natl Acad Sci USA 114:E2450–E2459. doi:10.1073/pnas.1616148114 - DOI - PMC - PubMed
    1. Dennis PG, Miller AJ, Hirsch PR. 2010. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol Ecol 72:313–327. doi:10.1111/j.1574-6941.2010.00860.x - DOI - PubMed
    1. Prashar P, Kapoor N, Sachdeva S. 2014. Rhizosphere: its structure, bacterial diversity and significance. Rev Environ Sci Biotechnol 13:63–77. doi:10.1007/s11157-013-9317-z - DOI
    1. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. 2013. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799. doi:10.1038/nrmicro3109 - DOI - PubMed

LinkOut - more resources