Formation, characterization and modeling of emergent synthetic microbial communities

Wang, Jia; Carper, Dana L.; Burdick, Leah H.; Shrestha, Him K.; Appidi, Manasa R.; Abraham, Paul E.; Timm, Collin M.; Hettich, Robert L.; Pelletier, Dale A.; Doktycz, Mitchel J.

doi:10.1016/j.csbj.2021.03.034

Cited by 14 publications

(20 citation statements)

References 95 publications

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“…A recent study has shown Pseudomonas sp. GM17 to have negative interactions with majority of the microbial members in this 10-member DefCom [ 24 ]. In fact, notable changes in relative protein abundances were identified for a sensor histidine kinase GacS (WP_007927747.1), which plays a role in sensing environmental signals and GacA (WP_020295157.1), a response regulator activated by GacS (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…AP49, Paraburkholderia sp. BT03 also has a similar growth rate [ 24 ]. However, these microbes did not represent a significant portion of the stable community.…”

Section: Discussionmentioning

confidence: 99%

“…1 A). The growth rates (OD 600nm ) for these 10 microbial strains has been previously measured in R2A and MOPS+ 0.2 % glucose media [ 24 ]. Equal volumes of all 10 isolates with the same normalized OD 600 were mixed in 10 mL of R2A complex medium (Teknova, # R0005) [ 81 ] and 10 mL of MOPS minimal medium [ 82 ] supplemented with 0.2 % glucose at 30 °C with shaking at 200 rpm.…”

Section: Methodsmentioning

confidence: 99%

“…The remaining cultures were pelleted by centrifugation at 12,000 rpm for 15 min, and the spent culture supernatants were stored at -80 °C. Based on the 16 S rRNA gene amplicon sequencing results, 8-passages (0, 1, 2, 3, 4, 5, 10, 15, note: Passage 0 is after 48-hour growth in media) with three biological replicates for both R2A and MOPS+glucose were analyzed for proteomic analysis [ 24 ].…”

Section: Methodsmentioning

confidence: 99%

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Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

et al. 2021

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Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified.

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Section: Resultsmentioning

confidence: 99%

“…AP49, Paraburkholderia sp. BT03 also has a similar growth rate [ 24 ]. However, these microbes did not represent a significant portion of the stable community.…”

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

et al. 2021

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“…Synthetic microbial communities have been developed for both rhizosphere and phyllosphere communities in several species: most notably Arabidopsis , as well as maize, sorghum, and duckweed, among others, with varying levels of phylogenetic representation ( Table 1 ). Varied approaches have been taken for designing synthetic communities with the ultimate goal of developing a community representative of the function and interactions of a natural, complex microbiome (e.g., Timm et al, 2016 ; Wang et al, 2021 ). Co-occurrence network analyses are commonly used to identify core functional microbiomes – a reduced subset of microbial species that captures the main metabolic processes performed by a community ( Toju et al, 2020 ), but other methods recognize the inherent complexity of non-equilibrium microbe-environment interactions and incorporate time-series data with empirical methods ( Deyle et al, 2016 ; Suzuki et al, 2017 ).…”

Section: Overview Of Synthetic Communities In Plant Systemsmentioning

confidence: 99%

Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities

2022

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With a growing world population and increasing frequency of climate disturbance events, we are in dire need of methods to improve plant productivity, resilience, and resistance to both abiotic and biotic stressors, both for agriculture and conservation efforts. Microorganisms play an essential role in supporting plant growth, environmental response, and susceptibility to disease. However, understanding the specific mechanisms by which microbes interact with each other and with plants to influence plant phenotypes is a major challenge due to the complexity of natural communities, simultaneous competition and cooperation effects, signalling interactions, and environmental impacts. Synthetic communities are a major asset in reducing the complexity of these systems by simplifying to dominant components and isolating specific variables for controlled experiments, yet there still remains a large gap in our understanding of plant microbiome interactions. This perspectives article presents a brief review discussing ways in which metabolic modelling can be used in combination with synthetic communities to continue progress toward understanding the complexity of plant-microbe-environment interactions. We highlight the utility of metabolic models as applied to a community setting, identify different applications for both flux balance and elementary flux mode simulation approaches, emphasize the importance of ecological theory in guiding data interpretation, and provide ideas for how the integration of metabolic modelling techniques with big data may bridge the gap between simplified synthetic communities and the complexity of natural plant-microbe systems.

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Exploring the Potentials of Chitin and Chitosan‐Based Bioinks for 3D‐Printing of Flexible Electronics: The Future of Sustainable Bioelectronics

Kumi,

Wang,

Ejeromedoghene

et al. 2024

Small Methods

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Chitin and chitosan‐based bioink for 3D‐printed flexible electronics have tremendous potential for innovation in healthcare, agriculture, the environment, and industry. This biomaterial is suitable for 3D printing because it is highly stretchable, super‐flexible, affordable, ultrathin, and lightweight. Owing to its ease of use, on‐demand manufacturing, accurate and regulated deposition, and versatility with flexible and soft functional materials, 3D printing has revolutionized free‐form construction and end‐user customization. This study examined the potential of employing chitin and chitosan‐based bioinks to build 3D‐printed flexible electronic devices and optimize bioink formulation, printing parameters, and postprocessing processes to improve mechanical and electrical properties. The exploration of 3D‐printed chitin and chitosan‐based flexible bioelectronics will open new avenues for new flexible materials for numerous industrial applications.

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Formation, characterization and modeling of emergent synthetic microbial communities

Abstract: Graphical abstract

Cited by 14 publications

References 95 publications

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities

Exploring the Potentials of Chitin and Chitosan‐Based Bioinks for 3D‐Printing of Flexible Electronics: The Future of Sustainable Bioelectronics

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