Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry

Microbial communities drive many processes which affect human well-being directly, as in the human microbiome, or indirectly, as in natural environments or in biotechnological applications. Due to their complexity, their dynamics over time is difficult to monitor, and current sequence-based approaches are limited with respect to the temporal resolution. However, in order to eventually control microbial community dynamics, monitoring schemes of high temporal resolution are required. Flow cytometry provides single-cell-based data in the required temporal resolution, and we here use such data to compute stability properties as easy to interpret univariate indicators of microbial community dynamics. Such monitoring tools will allow for a fast, continuous, and cost-effective screening of stability states of microbiomes. Applicable to various environments, including bioreactors, surface water, and the human body, it will contribute to the development of control schemes to manipulate microbial community structures and performances.

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1618 - Monitor ecological stability properties of microbial community with high temporal resolution tools by using flow cytometric data

10.26226/morressier.5b5199c4b1b87b000eceefe0 ◽

2018 ◽

Author(s):

Zishu Liu ◽

Nicolas Cichocki ◽

Florian Centler

Keyword(s):

Microbial Community ◽

Temporal Resolution ◽

High Temporal Resolution ◽

Ecological Stability ◽

Stability Properties ◽

Flow Cytometric Data ◽

Flow Cytometric

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Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽

10.1128/msystems.00645-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 1

Author(s):

Arunima Bhattacharjee ◽

Dusan Velickovic ◽

Thomas W. Wietsma ◽

Sheryl L. Bell ◽

Janet K. Jansson ◽

...

Keyword(s):

Soil Moisture ◽

Microbial Community ◽

Microbial Communities ◽

Community Dynamics ◽

Soil Microbial Communities ◽

Soil Microbiome ◽

Soil Core ◽

Soil Microbial ◽

Functional Relationships ◽

Microbial Community Dynamics

ABSTRACT Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

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Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

Frontiers in Microbiology ◽

10.3389/fmicb.2018.02887 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 6

Author(s):

Christina J. Fiedler ◽

Christoph Schönher ◽

Philipp Proksch ◽

David Johannes Kerschbaumer ◽

Ernest Mayr ◽

...

Keyword(s):

Flow Cytometry ◽

Microbial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Community Dynamics ◽

River Bank ◽

Microbial Community Dynamics

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Flow cytometry for rapid characterisation of microbial community dynamics in waste stabilisation ponds

Water Research ◽

10.1016/j.watres.2019.115243 ◽

2020 ◽

Vol 169 ◽

pp. 115243 ◽

Cited By ~ 5

Author(s):

Liah X. Coggins ◽

Irma Larma ◽

Amy Hinchliffe ◽

Ruben Props ◽

Anas Ghadouani

Keyword(s):

Flow Cytometry ◽

Microbial Community ◽

Community Dynamics ◽

Waste Stabilisation Ponds ◽

Microbial Community Dynamics

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Constrained proteome allocation affects coexistence in models of competitive microbial communities

10.1101/2020.01.27.921478 ◽

2020 ◽

Cited By ~ 1

Author(s):

Leonardo Pacciani-Mori ◽

Samir Suweis ◽

Amos Maritan ◽

Andrea Giometto

Keyword(s):

Population Dynamics ◽

Microbial Community ◽

Microbial Communities ◽

Community Dynamics ◽

Bacterial Strains ◽

Theoretical Frameworks ◽

Microbial Community Dynamics ◽

Common Resource ◽

Multiple Species ◽

Consumer Resource

Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the metabolism of species in a community is intertwined with its composition, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how pro-teome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show experimentally that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. We then study the model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.

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Reproducible microbial community dynamics of two drinking water systems treating similar source waters

10.1101/678920 ◽

2019 ◽

Author(s):

Sarah C Potgieter ◽

Ameet J Pinto ◽

Minette Havenga ◽

Makhosazana Sigudu ◽

Stefanus N Venter

Keyword(s):

Drinking Water ◽

Microbial Community ◽

Microbial Communities ◽

Surface Waters ◽

Distribution Systems ◽

Community Dynamics ◽

Microbial Community Dynamics ◽

Two Systems ◽

The Impact ◽

Source Waters

AbstractIn addition to containing higher concentrations of organics and bacterial cells, surface waters are often more vulnerable to pollution and microbial contamination with intensive industrial and agricultural activities frequently occurring in areas surrounding the water source. Therefore, surface waters typically require additional treatment, where the choice of treatment strategy is critical for water quality. Using 16S rRNA gene profiling, this study provides a unique opportunity to simultaneously investigate and compare two drinking water treatment plants and their corresponding distribution systems. The two treatment plants treat similar surface waters, from the same river system, with the same sequential treatment strategies. Here, the impact of treatment and distribution on the microbial community within and between each system was compared over an eight-month sampling campaign. Overall, reproducible spatial and temporal dynamics within both DWTPs and their corresponding DWDSs were observed. Although source waters showed some dissimilarity in microbial community structure and composition, pre-disinfection treatments (i.e. coagulation, flocculation, sedimentation and filtration) resulted in highly similar microbial communities between the filter effluent samples. This indicated that the same treatments resulted in the development of similar microbial communities. Conversely, post-disinfection (i.e. chlorination and chloramination) resulted in increased dissimilarity between disinfected samples from the two systems, showing alternative responses of the microbial community to disinfection. Lastly, it was observed that within the distribution system the same dominant taxa were selected where samples increased in similarity with increased residence time. Although, differences were found between the two systems, overall treatment and distribution had a similar impact on the microbial community in each system. This study therefore provides valuable information on the impact of treatment and distribution on the drinking water microbiome.HighlightsSource waters show some dissimilarity in microbial community.Treatment processes increases similarity and selects for the same dominant taxa.Differential response to chlorination causing increased dissimilarity and variation.Stabilisation of DWDS microbial community through selection of same dominant taxa.Microbial community dynamics are reproducible between the two systems.

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Small subsets of highly connected taxa predict compositional change in microbial communities

10.1101/159087 ◽

2017 ◽

Cited By ~ 3

Author(s):

Cristina M. Herren ◽

Katherine D. McMahon

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Dynamics ◽

External Disturbance ◽

Biotic Interactions ◽

Microbial Community Dynamics ◽

Community Turnover ◽

Community Shifts ◽

Curtis Dissimilarity ◽

Community Connectivity

AbstractFor decades, ecological theory has predicted that the complexity of communities should be related to their stability. However, this prediction has rarely been tested empirically, because of both the difficulty of finding suitable systems where the question is tractable and the trouble of defining “stability” in real systems. Microbial communities provide the opportunity to investigate a related question: how does community connectivity relate to the rate of compositional turnover? We used a newly developed metric called community “cohesion” to test how microbial community connectivity relates to Bray-Curtis dissimilarity through time. In three long-term datasets, we found that stronger connectivity corresponded to lower rates of compositional turnover. Using two case studies of disturbed and reference communities, we found that the predictive power of community connectivity was diminished by external disturbance. Finally, we tested whether the highly connected taxa were disproportionately important in explaining compositional turnover. We found that subsets of highly connected “keystone” taxa, generally comprising 1-5% of community richness, explained community turnover better than using all taxa. Our results suggest that stronger biotic interactions within microbial community dynamics are stabilizing to community composition, and that highly connected taxa are good indicators of pending community shifts.

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A Long-Standing Complex Tropical Dipole Shapes Marine Microbial Biogeography

Applied and Environmental Microbiology ◽

10.1128/aem.00614-18 ◽

2018 ◽

Vol 84 (18) ◽

Cited By ~ 3

Author(s):

Wei Yan ◽

Rui Zhang ◽

Nianzhi Jiao

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Large Scale ◽

Community Dynamics ◽

Anticyclonic Eddy ◽

Cyclonic Eddy ◽

Content Type ◽

Microbial Community Dynamics ◽

Biogeographic Provinces

ABSTRACTMicrobial population size, production, diversity, and community structure are greatly influenced by the surrounding physicochemical conditions, such as large-scale biogeographic provinces and water masses. An oceanic mesoscale dipole consists of a cyclonic eddy and an anticyclonic eddy. Dipoles occur frequently in the ocean and usually last from a few days to several months; they have significant impacts on local and global oceanic biological, ecological, and geochemical processes. To better understand how dipoles shape microbial communities, we examined depth-resolved distributions of microbial communities across a dipole in the South China Sea. Our data demonstrated that the dipole had a substantial influence on microbial distributions, community structure, and functional groups both vertically and horizontally. Large alpha and beta diversity differences were observed between anticyclonic and cyclonic eddies in surface and subsurface layers, consistent with distribution changes of major bacterial groups in the dipole. The dipole created uplift, downward transport, enrichment, depletion, and horizontal transport effects. We also found that the edge of the dipole might induce strong subduction, indicated by the presence ofProchlorococcusandSynechococcusin deep waters. Our findings suggest that dipoles, with their unique characteristics, might act as a driver for microbial community dynamics.IMPORTANCEOceanic dipoles, which consist of a cyclonic eddy and an anticyclonic eddy together, are among the most contrasted phenomena in the ocean. Dipoles generate strong vertical mixing and horizontal advection, inducing biological responses. This study provides vertical profiles of microbial abundance, diversity, and community structure in a mesoscale dipole. We identify the links between the physical oceanography and microbial oceanography and demonstrate that the dipole, with its unique features, could act as a driver for microbial community dynamics, which may have large impacts on both the local and global marine biogeochemical cycles.

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