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Chen E, Shaffer MG, Bilodeau RE, West RE, Oberly PJ, Nolin TD, Culyba MJ. Clinical rel mutations in Staphylococcus aureus prime pathogen expansion under nutrient stress. mSphere 2023; 8:e0024923. [PMID: 37750686 PMCID: PMC10597345 DOI: 10.1128/msphere.00249-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 09/27/2023] Open
Abstract
Persistent infection by Staphylococcus aureus has been linked to the bacterial stringent response (SR), a conserved stress response pathway regulated by the Rel protein. Rel synthesizes (p)ppGpp "alarmones" in response to amino acid starvation, which enables adaptation to stress by modulating bacterial growth and virulence. We previously identified five novel protein-altering mutations in rel that arose in patients with persistent methicillin-resistant S. aureus bacteremia. The mutations mapped to both the enzymatic and regulatory protein domains of Rel. Here, we set out to characterize the phenotype of these mutations to understand how they may have been selected in vivo. After introducing each mutation into S. aureus strain JE2, we analyzed growth, fitness, and antibiotic profiles. Despite being located in different protein domains, we found that all of the mutations converged on the same phenotype. Each shortened the time of lag phase growth and imparted a fitness advantage in nutritionally depleted conditions. Through quantification of intracellular (p)ppGpp, we link this phenotype to increased SR activation, specifically during the stationary phase of growth. In contrast to two previously identified clinical rel mutations, we find that our rel mutations do not cause antibiotic tolerance. Instead, our findings suggest that in vivo selection was due to an augmented SR that primes cells for growth in nutrient-poor conditions, which may be a strategy for evading host-imposed nutritional immunity. Importance Host and pathogen compete for available nutrition during infection. For bacteria, the stringent response (SR) regulator Rel responds to amino acid deprivation by signaling the cell to modulate its growth rate, metabolism, and virulence. In this report, we characterize five rel mutations that arose during cases of persistent methicillin-resistant Staphylococcus aureus bacteremia. We find that all of the mutations augmented SR signaling specifically under nutrient-poor conditions, enabling the cell to more readily grow and survive. Our findings reveal a strategy used by bacterial pathogens to evade the nutritional immunity imposed by host tissues during infection.
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Affiliation(s)
- Edwin Chen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marla G. Shaffer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert E. Bilodeau
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Raymond E. West
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Patrick J. Oberly
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Thomas D. Nolin
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Matthew J. Culyba
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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2
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Liu YY. Controlling the human microbiome. Cell Syst 2023; 14:135-159. [PMID: 36796332 PMCID: PMC9942095 DOI: 10.1016/j.cels.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/18/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
We coexist with a vast number of microbes that live in and on our bodies. Those microbes and their genes are collectively known as the human microbiome, which plays important roles in human physiology and diseases. We have acquired extensive knowledge of the organismal compositions and metabolic functions of the human microbiome. However, the ultimate proof of our understanding of the human microbiome is reflected in our ability to manipulate it for health benefits. To facilitate the rational design of microbiome-based therapies, there are many fundamental questions to be addressed at the systems level. Indeed, we need a deep understanding of the ecological dynamics associated with such a complex ecosystem before we rationally design control strategies. In light of this, this review discusses progress from various fields, e.g., community ecology, network science, and control theory, that are helping us make progress toward the ultimate goal of controlling the human microbiome.
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Affiliation(s)
- Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
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3
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Zhang Z, Ge S, Fan LC, Guo S, Hu Q, Ahammed GJ, Yan P, Zhang LP, Li ZZ, Zhang JY, Fu J, Han W, Li X. Diversity in rhizospheric microbial communities in tea varieties at different locations and tapping potential beneficial microorganisms. Front Microbiol 2022; 13:1027444. [PMID: 36439826 PMCID: PMC9685800 DOI: 10.3389/fmicb.2022.1027444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/14/2022] [Indexed: 12/01/2023] Open
Abstract
Soil microenvironments and plant varieties could largely affect rhizosphere microbial community structure and functions. However, their specific effects on the tea rhizosphere microbial community are yet not clear. Beneficial microorganisms are important groups of microbial communities that hold ecological functionalities by playing critical roles in plant disease resistance, and environmental stress tolerance. Longjing43 and Zhongcha108 are two widely planted tea varieties in China. Although Zhongcha108 shows higher disease resistance than Longjing43, the potential role of beneficial tea rhizosphere microbes in disease resistance is largely unknown. In this study, the structure and function of rhizosphere microbial communities of these two tea varieties were compared by using the Illumina MiSeq sequencing (16S rRNA gene and ITS) technologies. Rhizosphere soil was collected from four independent tea gardens distributed at two locations in Hangzhou and Shengzhou cities in eastern China, Longjing43 and Zhongcha108 are planted at both locations in separate gardens. Significant differences in soil physicochemical properties as demonstrated by ANOVA and PCA, and distinct rhizosphere microbial communities by multiple-biotech analyses (PCoA, LEfSe, Co-occurrence network analyses) between both locations and tea varieties (p < 0.01) were found. Functions of bacteria were annotated by the FAPROTAX database, and a higher abundance of Nitrososphaeraceae relating to soil ecological function was found in rhizosphere soil in Hangzhou. LDA effect size showed that the abundance of arbuscular mycorrhizal fungi (AMF) was higher in Zhongcha108 than that in Longjing43. Field experiments further confirmed that the colonization rate of AMF was higher in Zhongcha108. This finding testified that AMF could be the major beneficial tea rhizosphere microbes that potentially function in enhanced disease resistance. Overall, our results confirmed that locations affected the microbial community greater than that of tea varieties, and fungi might be more sensitive to the change in microenvironments. Furthermore, we found several beneficial microorganisms, which are of great significance in improving the ecological environment of tea gardens and the disease resistance of tea plants. These beneficial microbial communities may also help to further reveal the mechanism of disease resistance in tea and potentially be useful for mitigating climate change-associated challenges to tea gardens in the future.
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Affiliation(s)
- Zheng Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - ShiBei Ge
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Li-Chao Fan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuai Guo
- Hangzhou Botanical Garden, Hangzhou West Lake Academy of Landscape Science, Hangzhou, China
| | - Qiang Hu
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Golam Jalal Ahammed
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Peng Yan
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Li-Ping Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zheng-Zhen Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jian-Yang Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianyu Fu
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Wenyan Han
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xin Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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4
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Ernakovich JG, Barbato RA, Rich VI, Schädel C, Hewitt RE, Doherty SJ, Whalen E, Abbott BW, Barta J, Biasi C, Chabot CL, Hultman J, Knoblauch C, Vetter M, Leewis M, Liebner S, Mackelprang R, Onstott TC, Richter A, Schütte U, Siljanen HMP, Taş N, Timling I, Vishnivetskaya TA, Waldrop MP, Winkel M. Microbiome assembly in thawing permafrost and its feedbacks to climate. GLOBAL CHANGE BIOLOGY 2022; 28:5007-5026. [PMID: 35722720 PMCID: PMC9541943 DOI: 10.1111/gcb.16231] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/24/2022] [Indexed: 05/15/2023]
Abstract
The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.
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Affiliation(s)
- Jessica G. Ernakovich
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
- Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
- EMergent Ecosystem Response to ChanGE (EMERGE) Biology Integration Institute
| | - Robyn A. Barbato
- U.S. Army Cold Regions Research and Engineering LaboratoryHanoverNew HampshireUSA
| | - Virginia I. Rich
- EMergent Ecosystem Response to ChanGE (EMERGE) Biology Integration Institute
- Microbiology DepartmentOhio State UniversityColumbusOhioUSA
- Byrd Polar and Climate Research CenterOhio State UniversityColombusOhioUSA
- Center of Microbiome ScienceOhio State UniversityColombusOhioUSA
| | - Christina Schädel
- Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Rebecca E. Hewitt
- Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
- Department of Environmental StudiesAmherst CollegeAmherstMassachusettsUSA
| | - Stacey J. Doherty
- Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
- U.S. Army Cold Regions Research and Engineering LaboratoryHanoverNew HampshireUSA
| | - Emily D. Whalen
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
| | - Benjamin W. Abbott
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtahUSA
| | - Jiri Barta
- Centre for Polar EcologyUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Christina Biasi
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandKuopioFinland
| | - Chris L. Chabot
- California State University NorthridgeNorthridgeCaliforniaUSA
| | | | - Christian Knoblauch
- Institute of Soil ScienceUniversität HamburgHamburgGermany
- Center for Earth System Research and SustainabilityUniversität HamburgHamburgGermany
| | - Maggie C. Y. Lau Vetter
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
- Laboratory of Extraterrestrial Ocean Systems (LEOS)Institute of Deep‐sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Mary‐Cathrine Leewis
- U.S. Geological Survey, GeologyMinerals, Energy and Geophysics Science CenterMenlo ParkCaliforniaUSA
- Agriculture and Agri‐Food CanadaQuebec Research and Development CentreQuebecQuebecCanada
| | - Susanne Liebner
- GFZ German Research Centre for GeosciencesSection GeomicrobiologyPotsdamGermany
| | | | | | - Andreas Richter
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | | | - Henri M. P. Siljanen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandKuopioFinland
| | - Neslihan Taş
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | | | - Tatiana A. Vishnivetskaya
- University of TennesseeKnoxvilleTennesseeUSA
- Institute of Physicochemical and Biological Problems of Soil SciencePushchinoRussia
| | - Mark P. Waldrop
- U.S. Geological Survey, GeologyMinerals, Energy and Geophysics Science CenterMenlo ParkCaliforniaUSA
| | - Matthias Winkel
- GFZ German Research Centre for GeosciencesInterface GeochemistryPotsdamGermany
- BfR Federal Institute for Risk AssessmentBerlinGermany
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5
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Wan K, Yu Y, Hu J, Liu X, Deng X, Yu J, Chi R, Xiao C. Recovery of anammox process performance after substrate inhibition: Reactor performance, sludge morphology, and microbial community. BIORESOURCE TECHNOLOGY 2022; 357:127351. [PMID: 35605779 DOI: 10.1016/j.biortech.2022.127351] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Most of the current studies have focused on the inhibition of anaerobic ammonium oxidation (anammox) by substrates, however, little attention has been paid to the recovery process of the reactor after inhibition. Therefore, we investigated the changes in reactor performance, granular sludge structure, and microbial community during the recovery phase after being inhibited by a high nitrogen load for 15 d. The nitrogen removal rate of the reactorwasrestored to pre-inhibition levels after 75 d of recovery, and the stoichiometric ratio converged to the theoretical value. The surface of the granular sludge developed into a broccoli-like structure, and the Ca and P contents of the granules increased from 6.88% and 4.39% to 24.42% and 13.88%, respectively. The abundance of the anammox bacterium Candidatus brocadia increased from 5.86% to 12.10%, and network analysis indicated that SMA102 and SBR1031 were positively correlated with the occurrence of Candidatus brocadia.
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Affiliation(s)
- Kai Wan
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Ye Yu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Jinggang Hu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Xuemei Liu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Xiangyi Deng
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Junxia Yu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Ruan Chi
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Chunqiao Xiao
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China.
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6
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Zhou W, Colpa DI, Geurkink B, Euverink GJW, Krooneman J. The impact of carbon to nitrogen ratios and pH on the microbial prevalence and polyhydroxybutyrate production levels using a mixed microbial starter culture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152341. [PMID: 34921889 DOI: 10.1016/j.scitotenv.2021.152341] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/16/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Growth conditions have been frequently studied in optimizing polyhydroxybutyrate (PHB) production, while few studies were performed to unravel the dynamic mixed microbial consortia (MMCs) in the process. In this study, the relationship between growth conditions (C/N ratios and pH) and the corresponding key-microbes were identified and monitored during PHB accumulation. The highest PHB level (70 wt% of dry cell mass) was obtained at pH 9, C/N 40, and acetic acid 10 g/L. Linking the dominant genera with the highest point of PHB accumulation, Thauera was the most prevalent species in all MMCs of pH 9, except when a C/N ratio of 1 was applied. Notably, dominant bacteria shifted at pH 7 (C/N 10) from Thauera (0 h) to Paracoccus, and subsequently to Alcaligenes following the process of PHB accumulation and consumption. Further understanding of the relationship between the structure of the microbial community and the performance will be beneficial for regulating and obtaining high PHB accumulation within an MMC. Our study illustrates the impact of C/N ratios and pH on microbial prevalence and PHB production levels using a mixed microbial starter culture. This knowledge will broaden industrial perspectives for regulating high PHB production and timely harvesting.
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Affiliation(s)
- Wen Zhou
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Dana Irene Colpa
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Bert Geurkink
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
| | - Gert-Jan Willem Euverink
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Janneke Krooneman
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands.
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7
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Abstract
Wastewater treatment plants are engineering technologies used worldwide to protect the environment and human health. Microbial communities sustain these plants, so it is crucial to know the key factors responsible for the community assembly. We show, in contrast to existing understanding, that microbial immigration largely controls the community structure in these plants and that the fate (growth or death) of immigrating species in the plants is controlled by local factors. The community structure was quantitatively predicted by the immigrating microbial community, highlighting the need to revise the way we today understand, design, and manage microbial communities in wastewater treatment plants. The assembly of bacterial communities in wastewater treatment plants (WWTPs) is affected by immigration via wastewater streams, but the impact and extent of bacterial immigrants are still unknown. Here, we quantify the effect of immigration at the species level in 11 Danish full-scale activated sludge (AS) plants. All plants have different source communities but have very similar process design, defining the same overall environmental growth conditions. The AS community composition in each plant was strongly reflected by the corresponding influent wastewater (IWW) microbial composition. Most species in AS across the plants were detected and quantified in the corresponding IWW, allowing us to identify their fate in the AS: growing, disappearing, or surviving. Most of the abundant species in IWW disappeared in AS, so their presence in the AS biomass was only due to continuous mass-immigration. In AS, most of the abundant growing species were present in the IWW at very low abundances. We predicted the AS species abundances from their abundance in IWW by using a partial least square regression model. Some species in AS were predicted by their own abundance in IWW, while others by multiple species abundances. Detailed analyses of functional guilds revealed different prediction patterns for different species. We show, in contrast to the present understanding, that the AS microbial communities were strongly controlled by the IWW source community and could be quantitatively predicted by taking into account immigration. This highlights a need to revise the way we understand, design, and manage the microbial communities in WWTPs.
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8
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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9
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Sörenson E, Capo E, Farnelid H, Lindehoff E, Legrand C. Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass. Front Microbiol 2021; 12:607601. [PMID: 33643237 PMCID: PMC7905023 DOI: 10.3389/fmicb.2021.607601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/12/2021] [Indexed: 12/17/2022] Open
Abstract
To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic interactions, functional adaptations, and community structure. Interactions between species are traditionally considered as, e.g., mutualistic, parasitic, or neutral but are here broadly defined as either coexistence or competition, while functions relate to their metabolism (e.g., autotrophy or heterotrophy) and roles in ecosystem functioning (e.g., oxygen production, organic matter degradation). The term structure here align with species richness and diversity, where a more diverse community is though to exhibit a broader functional capacity than a less diverse community. These concepts have here been combined with ecological theories commonly used in resilience studies, i.e., adaptive cycles, panarchy, and cross-scale resilience, that describe how the status and behavior at one trophic level impact that of surrounding levels. This allows us to explore the resilience of a marine microbial community, cultivated in an outdoor photobioreactor, when exposed to a naturally occurring seasonal stress. The culture was monitored for 6weeks during which it was exposed to two different temperature regimes (21 ± 2 and 11 ± 1°C). Samples were taken for metatranscriptomic analysis, in order to assess the regulation of carbon uptake and utilization, and for amplicon (18S and 16S rRNA gene) sequencing, to characterize the community structure of both autotrophs (dominated by the green microalgae Mychonastes) and heterotrophs (associated bacterioplankton). Differential gene expression analyses suggested that community function at warm temperatures was based on concomitant utilization of inorganic and organic carbon assigned to autotrophs and heterotrophs, while at colder temperatures, the uptake of organic carbon was performed primarily by autotrophs. Upon the shift from high to low temperature, community interactions shifted from coexistence to competition for organic carbon. Network analysis indicated that the community structure showed opposite trends for autotrophs and heterotrophs in having either high or low diversity. Despite an abrupt change of temperature, the microbial community as a whole responded in a way that maintained the overall level of diversity and function within and across autotrophic and heterotrophic levels. This is in line with cross-scale resilience theory describing how ecosystems may balance functional overlaps within and functional redundancy between levels in order to be resilient to environmental change (such as temperature).
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Affiliation(s)
- Eva Sörenson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eric Capo
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hanna Farnelid
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Elin Lindehoff
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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10
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Louca S, Rubin IN, Madilao LL, Bohlmann J, Doebeli M, Wegener Parfrey L. Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:514-524. [PMID: 32618124 DOI: 10.1111/1758-2229.12866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ilan N Rubin
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Lufiani L Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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11
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Gorochowski TE, Hauert S, Kreft JU, Marucci L, Stillman NR, Tang TYD, Bandiera L, Bartoli V, Dixon DOR, Fedorec AJH, Fellermann H, Fletcher AG, Foster T, Giuggioli L, Matyjaszkiewicz A, McCormick S, Montes Olivas S, Naylor J, Rubio Denniss A, Ward D. Toward Engineering Biosystems With Emergent Collective Functions. Front Bioeng Biotechnol 2020; 8:705. [PMID: 32671054 PMCID: PMC7332988 DOI: 10.3389/fbioe.2020.00705] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/05/2020] [Indexed: 12/31/2022] Open
Abstract
Many complex behaviors in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is difficult because they arise as a consequence of complex multi-level feedback, which often spans many length-scales. Here, we present a perspective on how some of these challenges could be overcome by using multi-agent modeling as a design framework within synthetic biology. Using case studies covering the construction of synthetic ecologies to biological computation and synthetic cellularity, we show how multi-agent modeling can capture the core features of complex multi-scale systems and provide novel insights into the underlying mechanisms which guide emergent functionalities across scales. The ability to unravel design rules underpinning these behaviors offers a means to take synthetic biology beyond single molecules or cells and toward the creation of systems with functions that can only emerge from collectives at multiple scales.
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Affiliation(s)
| | - Sabine Hauert
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Jan-Ulrich Kreft
- School of Biosciences and Institute of Microbiology and Infection and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Namid R. Stillman
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - T.-Y. Dora Tang
- Max Plank Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Physics of Life, Cluster of Excellence, Technische Universität Dresden, Dresden, Germany
| | - Lucia Bandiera
- School of Engineering, University of Edinburgh, Edinburgh, United Kingdom
| | - Vittorio Bartoli
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | | | - Alex J. H. Fedorec
- Division of Biosciences, University College London, London, United Kingdom
| | - Harold Fellermann
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alexander G. Fletcher
- Bateson Centre and School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
| | - Tim Foster
- School of Biosciences and Institute of Microbiology and Infection and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Luca Giuggioli
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | | | - Scott McCormick
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Sandra Montes Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Jonathan Naylor
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ana Rubio Denniss
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Daniel Ward
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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12
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Bacterial dominance is due to effective utilisation of secondary metabolites produced by competitors. Sci Rep 2020; 10:2316. [PMID: 32047185 PMCID: PMC7012823 DOI: 10.1038/s41598-020-59048-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/08/2020] [Indexed: 12/23/2022] Open
Abstract
Interactions between bacteria govern the progression of respiratory infections; however, the mechanisms underpinning these interactions are still unclear. Understanding how a bacterial species comes to dominate infectious communities associated with respiratory infections has direct relevance to treatment. In this study, Burkholderia, Pseudomonas, and Staphylococcus species were isolated from the sputum of an individual with Cystic Fibrosis and assembled in a fully factorial design to create simple microcosms. Measurements of growth and habitat modification were recorded over time, the later using proton Nuclear Magnetic Resonance spectra. The results showed interactions between the bacteria became increasingly neutral over time. Concurrently, the bacteria significantly altered their ability to modify the environment, with Pseudomonas able to utilise secondary metabolites produced by the other two isolates, whereas the reverse was not observed. This study indicates the importance of including data about the habitat modification of a community, to better elucidate the mechanisms of bacterial interactions.
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13
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Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol Ecol 2018; 94:5107865. [PMID: 30265315 PMCID: PMC6192502 DOI: 10.1093/femsec/fiy191] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.
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Affiliation(s)
- H J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A J Zelaya
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - K B De León
- Department of Biochemistry, University of Missouri, Columbia, MO
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - R Chakraborty
- Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - D A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - T C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Civil Engineering, Montana State University, Montana State University, Bozeman, MT
| | - M W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
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14
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Zepeda Mendoza ML, Roggenbuck M, Manzano Vargas K, Hansen LH, Brunak S, Gilbert MTP, Sicheritz-Pontén T. Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. Acta Vet Scand 2018; 60:61. [PMID: 30309375 PMCID: PMC6182802 DOI: 10.1186/s13028-018-0415-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut. Results We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut. Conclusions Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging. Electronic supplementary material The online version of this article (10.1186/s13028-018-0415-3) contains supplementary material, which is available to authorized users.
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15
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Bauer MA, Kainz K, Carmona-Gutierrez D, Madeo F. Microbial wars: Competition in ecological niches and within the microbiome. MICROBIAL CELL (GRAZ, AUSTRIA) 2018; 5:215-219. [PMID: 29796386 PMCID: PMC5961915 DOI: 10.15698/mic2018.05.628] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/03/2018] [Indexed: 12/22/2022]
Abstract
Many microbial communities live in highly competitive surroundings, in which the fight for resources determines their survival and genetic persistence. Humans live in a close relationship with microbial communities, which includes the health- and disease-determining interactions with our microbiome. Accordingly, the understanding of microbial competitive activities are essential at physiological and pathophysiological levels. Here we provide a brief overview on microbial competition and discuss some of its roles and consequences that directly affect humans.
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Affiliation(s)
- Maria A. Bauer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Frank Madeo
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
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16
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Huang L, Chen Z, Wen Q, Zhao L, Lee DJ, Yang L, Wang Y. Insights into Feast-Famine polyhydroxyalkanoate (PHA)-producer selection: Microbial community succession, relationships with system function and underlying driving forces. WATER RESEARCH 2018; 131:167-176. [PMID: 29281810 DOI: 10.1016/j.watres.2017.12.033] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
The Feast-Famine (FF) process has been frequently used to select polyhydroxyalkanoate (PHA)-accumulating mixed cultures (MCs), but there has been little insight into the ecophysiology of the microbial community during the selection process. In three FF systems with well-defined conditions, synchronized variations in higher-order properties of MCs and complicate microbial community succession mainly including enrichment and elimination of non-top competitors and unexpected turnover of top competitors, were observed. Quantification of PHA-accumulating function genes (phaC) revealed that the top competitors maintained the PHA synthesis by playing consecutive roles when the highly dynamic turnover occurred. Due to its specific physiological characteristics during the PHA-accumulating process, Thauera strain OTU 7 was found to be responsible for the fluctuating SVI, which threatened the robustness of the FF system. This trait was also responsible for its later competitive exclusion by the other PHA-producer, Paracoccus strain OTU 1. Deterministic processes dominated the entire FF system, resulting in the inevitable microbial community succession in the acclimation phase and maintenance of the stable PHA-accumulating function in the maturation phase. However, neutral processes, likely caused by predation from bacterial phages, also occurred, which led to the unpredictable temporal dynamics of the top competitors.
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Affiliation(s)
- Long Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Lizhi Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Lian Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yao Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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17
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18
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Feng K, Zhang Z, Cai W, Liu W, Xu M, Yin H, Wang A, He Z, Deng Y. Biodiversity and species competition regulate the resilience of microbial biofilm community. Mol Ecol 2017; 26:6170-6182. [DOI: 10.1111/mec.14356] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/30/2017] [Accepted: 09/05/2017] [Indexed: 01/30/2023]
Affiliation(s)
- Kai Feng
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- Department of Chemical and Biochemical Engineering Technical University of Denmark Lyngby Denmark
- Sino‐Danish Center for Education and Research Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Zhaojing Zhang
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China) School of Environmental Science and Technology Dalian University of Technology Dalian China
| | - Weiwei Cai
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology (SKLUWRE, HIT) Harbin China
| | - Wenzong Liu
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application Guangdong Institute of Microbiology Guangzhou China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering Central South University Changsha China
| | - Aijie Wang
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
| | - Zhili He
- School of Environmental Science and Engineering Sun Yat‐sen University Guangzhou China
- Department of Microbiology and Plant Biology Institute for Environmental Genomics University of Oklahoma Norman OK USA
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
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19
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Louca S, Doebeli M. Taxonomic variability and functional stability in microbial communities infected by phages. Environ Microbiol 2017; 19:3863-3878. [PMID: 28371143 DOI: 10.1111/1462-2920.13743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/16/2017] [Accepted: 03/24/2017] [Indexed: 11/28/2022]
Abstract
Microbial communities can display large variation in taxonomic composition, yet this variation can coincide with stable metabolic functional structure and performance. The mechanisms driving the taxonomic variation within functional groups remain largely unknown. Biotic interactions, such as predation by phages, have been suggested as potential cause of taxonomic turnover, but the conditions for this scenario have not been rigorously examined. Further, it is unknown how predation by phages affects community function, and how these effects are modulated by functional redundancy in the communities. Here, we address these questions using a model for a methanogenic microbial community that includes several interacting metabolic functional groups. Each functional group comprises multiple competing clades, and each clade is attacked by a specialist lytic phage. Our model predicts that phages induce intense taxonomic turnover, resembling the variability observed in previous experiments. The functional structure and performance of the community are also disturbed by phage predation, but they become more stable as the functional redundancy in the community increases. The extent of this stabilization depends on the particular functions considered. Our model suggests mechanisms by which functional redundancy stabilizes community function and supports the interpretation that biotic interactions promote taxonomic turnover within microbial functional groups.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Canada.,Department of Zoology, University of British Columbia, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Canada.,Department of Zoology, University of British Columbia, Canada.,Department of Mathematics, University of British Columbia, Canada
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20
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Ghoul M, Mitri S. The Ecology and Evolution of Microbial Competition. Trends Microbiol 2016; 24:833-845. [DOI: 10.1016/j.tim.2016.06.011] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/15/2016] [Accepted: 06/28/2016] [Indexed: 01/23/2023]
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21
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Günther S, Faust K, Schumann J, Harms H, Raes J, Müller S. Species-sorting and mass-transfer paradigms control managed natural metacommunities. Environ Microbiol 2016; 18:4862-4877. [DOI: 10.1111/1462-2920.13402] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/30/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Susanne Günther
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| | - Karoline Faust
- VIB Center for the Biology of Disease, KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
- Department of Microbiology and Immunology; KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
- Bioengineering Sciences; Vrije Universiteit Brussel; Pleinlaan 2 1050 Brussels Belgium
| | - Joachim Schumann
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| | - Hauke Harms
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| | - Jeroen Raes
- VIB Center for the Biology of Disease, KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
- Department of Microbiology and Immunology; KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
| | - Susann Müller
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
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22
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Louca S, Doebeli M. Calibration and analysis of genome-based models for microbial ecology. eLife 2015; 4:e08208. [PMID: 26473972 PMCID: PMC4608356 DOI: 10.7554/elife.08208] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 09/17/2015] [Indexed: 12/11/2022] Open
Abstract
Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.
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Affiliation(s)
- Stilianos Louca
- Institute of Applied Mathematics, University of British Columbia, Vancouver, Canada
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, Canada
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