1
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Vandermaesen J, Daly AJ, Mawarda PC, Baetens JM, De Baets B, Boon N, Springael D. Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship. Ecol Lett 2024; 27:e14433. [PMID: 38712704 DOI: 10.1111/ele.14433] [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: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024]
Abstract
The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.
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Affiliation(s)
| | - Aisling J Daly
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Panji Cahya Mawarda
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
- Research Center for Applied Microbiology, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, Indonesia
| | - Jan M Baetens
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Bernard De Baets
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
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2
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Čaušević S, Dubey M, Morales M, Salazar G, Sentchilo V, Carraro N, Ruscheweyh HJ, Sunagawa S, van der Meer JR. Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions. Nat Commun 2024; 15:2557. [PMID: 38519488 PMCID: PMC10959995 DOI: 10.1038/s41467-024-46933-1] [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: 10/17/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.
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Affiliation(s)
- Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Guillem Salazar
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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3
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Bongrand C, Foster JS. Modelled microgravity impacts Vibrio fischeri population structure in a mutualistic association with an animal host. Environ Microbiol 2023; 25:3269-3279. [PMID: 37828645 DOI: 10.1111/1462-2920.16522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Perturbations to host-microbe interactions, such as environmental stress, can alter and disrupt homeostasis. In this study, we examined the effects of a stressor, simulated microgravity, on beneficial bacteria behaviours when colonising their host. We studied the bacterium Vibrio fischeri, which establishes a mutualistic association in a symbiosis-specific organ within the bobtail squid, Euprymna scolopes. To elucidate how animal-microbe interactions are affected by the stress of microgravity, squid were inoculated with different bacterial strains exhibiting either a dominant- or sharing-colonisation behaviour in High Aspect Ratio Vessels, which simulate the low-shear environment of microgravity. The colonisation behaviours of the sharing and dominant strains under modelled microgravity conditions were determined by counting light-organ homogenate of squids as well as confocal microscopy to assess the partitioning of different strains within the light organ. The results indicated that although the colonisation behaviours of the strains did not change, the population levels of the sharing strains were at lower relative abundance in single-colonised animals exposed to modelled microgravity compared to unit gravity; in addition, there were shifts in the relative abundance of strains in co-colonised squids. Together these results suggest that the initiation of beneficial interactions between microbes and animals can be altered by environmental stress, such as simulated microgravity.
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Affiliation(s)
- Clotilde Bongrand
- Department of Microbiology and Cell Science, Space Life Sciences Lab, University of Florida, Merritt Island, Florida, USA
| | - Jamie S Foster
- Department of Microbiology and Cell Science, Space Life Sciences Lab, University of Florida, Merritt Island, Florida, USA
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4
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Woodhams DC, McCartney J, Walke JB, Whetstone R. The adaptive microbiome hypothesis and immune interactions in amphibian mucus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104690. [PMID: 37001710 DOI: 10.1016/j.dci.2023.104690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 05/20/2023]
Abstract
The microbiome is known to provide benefits to hosts, including extension of immune function. Amphibians are a powerful immunological model for examining mucosal defenses because of an accessible epithelial mucosome throughout their developmental trajectory, their responsiveness to experimental treatments, and direct interactions with emerging infectious pathogens. We review amphibian skin mucus components and describe the adaptive microbiome as a novel process of disease resilience where competitive microbial interactions couple with host immune responses to select for functions beneficial to the host. We demonstrate microbiome diversity, specificity of function, and mechanisms for memory characteristic of an adaptive immune response. At a time when industrialization has been linked to losses in microbiota important for host health, applications of microbial therapies such as probiotics may contribute to immunotherapeutics and to conservation efforts for species currently threatened by emerging diseases.
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Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Julia McCartney
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, 99004-2440, USA
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
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5
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Lear L, Padfield D, Inamine H, Shea K, Buckling A. Disturbance-mediated invasions are dependent on community resource abundance. Ecology 2022; 103:e3728. [PMID: 35412647 PMCID: PMC9542494 DOI: 10.1002/ecy.3728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/02/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022]
Abstract
Disturbances can facilitate biological invasions, with the associated increase in resource availability being a proposed cause. Here, we experimentally tested the interactive effects of disturbance regime (different frequencies of biomass removal at equal intensities) and resource abundance on invasion success using a factorial design containing five disturbance frequencies and three resource levels. We invaded populations of the bacterium Pseudomonas fluorescens with two ecologically different invader morphotypes: a fast‐growing “colonizer” type and a slower growing “competitor” type. As resident populations were altered by the treatments, we additionally tested their effect on invader success. Disturbance frequency and resource abundance interacted to affect the success of both invaders, but this interaction differed between the invader types. The success of the colonizer type was positively affected by disturbance under high resources but negatively under low. However, disturbance negatively affected the success of the competitor type under high resource abundance but not under low or medium. Resident population changes did not alter invader success beyond direct treatment effects. We therefore demonstrate that the same disturbance regime can either be beneficial or detrimental for an invader depending on both community resource abundance and its life history. These results may help to explain some of the inconsistencies found in the disturbance‐invasion literature.
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Affiliation(s)
- Luke Lear
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, UK
| | - Daniel Padfield
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, UK
| | - Hidetoshi Inamine
- Department of Biology and Center for Infectious Disease Dynamics, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Katriona Shea
- Department of Biology and Center for Infectious Disease Dynamics, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Angus Buckling
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, UK
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6
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Vandermaesen J, Du S, Daly AJ, Baetens JM, Horemans B, De Baets B, Boon N, Springael D. Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1352-1364. [PMID: 34982540 DOI: 10.1021/acs.est.1c06653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.
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Affiliation(s)
- Johanna Vandermaesen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Siyao Du
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Aisling J Daly
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Jan M Baetens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Benjamin Horemans
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
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7
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Hoogeveen AME, Moughan PJ, Henare SJ, Schulze P, McNabb WC, Montoya CA. Type of Dietary Fiber Is Associated with Changes in Ileal and Hindgut Microbial Communities in Growing Pigs and Influences In Vitro Ileal and Hindgut Fermentation. J Nutr 2021; 151:2976-2985. [PMID: 34320183 DOI: 10.1093/jn/nxab228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Accepted: 06/18/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The degree of ileal organic matter (OM) fermentation appears to be comparable to hindgut fermentation in growing pigs. OBJECTIVES This study aimed to determine if dietary fiber sources with known different total gastrointestinal tract (GIT) fermentability in humans affect ileal and hindgut microbial communities and ileal fermentation in growing pigs used as an animal model for human adults. METHODS Male pigs (21 kg bodyweight; 9 wk old; PIC Camborough 46 × PIC boar 356L; n = 8/diet) were fed for 42 d a diet containing cellulose (CEL, low fermentability) as the sole fiber source (4.5%) or diets in which half of the CEL was replaced by moderately fermentable fiber, psyllium (PSY), or kiwifruit (KF) fiber. For each diet, terminal jejunal (substrate) and ileal (inoculum) digesta were collected from euthanized animals for in vitro ileal fermentation (2 h). Terminal ileal (substrate) and cecal (inoculum) digesta were used for in vitro hindgut fermentation (24 h). After in vitro fermentations, OM fermentation and short-chain fatty acid (SCFA) production were determined. Ileal digesta and feces were collected for microbial analysis. Data were analyzed by 2-factor ANOVA (diet × GIT region). RESULTS In vitro ileal OM fermentation was on average 22% and comparable to hindgut OM fermentation. Ileal and hindgut OM fermentation, SCFA production, and microbial community composition changed (P < 0.05) when CEL was partially replaced by KF or PSY. For instance, pigs fed the PSY diet had 3-fold higher (P ≤ 0.05) number of ileal and fecal bacteria than pigs fed the CEL and KF diets. Pigs fed the CEL diet had 4-fold higher (P ≤ 0.05) hindgut valeric acid production than pigs fed the other diets. CONCLUSIONS Ileal fermentation is quantitatively significant. Partial substitution of CEL with more fermentable fibers influences both ileal and hindgut microbial communities and the fermentation in growing pigs.
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Affiliation(s)
- Anna M E Hoogeveen
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand.,Riddet Institute, Te Ohu Rangahau Kai, Massey University, Palmerston North, New Zealand
| | - Paul J Moughan
- Riddet Institute, Te Ohu Rangahau Kai, Massey University, Palmerston North, New Zealand
| | - Sharon J Henare
- Riddet Institute, Te Ohu Rangahau Kai, Massey University, Palmerston North, New Zealand.,School of Health Sciences, Massey University, Palmerston North, New Zealand
| | - Philipp Schulze
- Riddet Institute, Te Ohu Rangahau Kai, Massey University, Palmerston North, New Zealand
| | - Warren C McNabb
- Riddet Institute, Te Ohu Rangahau Kai, Massey University, Palmerston North, New Zealand
| | - Carlos A Montoya
- Riddet Institute, Te Ohu Rangahau Kai, Massey University, Palmerston North, New Zealand.,Smart Foods, AgResearch Limited, Te Ohu Rangahau Kai, Massey University, Palmerston North, New Zealand
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8
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Sierocinski P, Soria Pascual J, Padfield D, Salter M, Buckling A. The impact of propagule pressure on whole community invasions in biomethane-producing communities. iScience 2021; 24:102659. [PMID: 34151242 PMCID: PMC8192723 DOI: 10.1016/j.isci.2021.102659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/29/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
Microbes can invade as whole communities, but the ecology of whole community invasions is poorly understood. Here, we investigate how invader propagule pressure (the number of invading organisms) affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of propagule pressure, which varied between 0.01 and 10% of the size resident community. Invasion resulted in enhanced biogas production (to the level of the pure invading community) but only when propagule pressure was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower richness of invading taxa at lower propagule pressures, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings. Complex communities can successfully invade other communities Invasions change the community composition independently of propagule pressure Number of taxa invading increases with increased propagule pressure Larger propagule pressure impacts both the community structure and function
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Affiliation(s)
- Pawel Sierocinski
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Jesica Soria Pascual
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Daniel Padfield
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | | | - Angus Buckling
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
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9
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Jones ML, Rivett DW, Pascual-García A, Bell T. Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. eLife 2021; 10:71811. [PMID: 34662276 PMCID: PMC8523168 DOI: 10.7554/elife.71811] [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: 06/30/2021] [Accepted: 09/19/2021] [Indexed: 01/03/2023] Open
Abstract
Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.
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Affiliation(s)
- Matt Lloyd Jones
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Damian William Rivett
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Alberto Pascual-García
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
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10
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O'Connor LMJ, Fugère V, Gonzalez A. Evolutionary Rescue Is Mediated by the History of Selection and Dispersal in Diversifying Metacommunities. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.517434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rapid evolution can sometimes prevent population extirpation in stressful environments, but the conditions leading to “evolutionary rescue” in metacommunities are unclear. Here we studied the eco-evolutionary response of microbial metacommunities adapting to selection by the antibiotic streptomycin. Our experiment tested how the history of antibiotic selection and contrasting modes of dispersal influenced diversification and subsequent evolutionary rescue in microbial metacommunities undergoing adaptive radiation. We first tracked the change in diversity and density of Pseudomonas fluorescens morphotypes selected on a gradient of antibiotic stress. We then examined the recovery of these metacommunities following abrupt application of a high concentration of streptomycin lethal to the ancestral organisms. We show that dispersal increases diversity within the stressed metacommunities, that exposure to stress alters diversification dynamics, and that community composition, dispersal, and past exposure to stress mediate the speed at which evolutionary rescue occurs, but not the final outcome of recovery in abundance and diversity. These findings extend recent experiments on evolutionary rescue to the case of metacommunities undergoing adaptive diversification, and should motivate new theory on this question. Our findings are also relevant to evolutionary conservation biology and research on antimicrobial resistance.
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11
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Abstract
Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens. Interactions between plant pathogens and root-associated microbes play an important role in determining disease outcomes. While several studies have suggested that steering these interactions may improve plant health, such approaches have remained challenging in practice. Because of low iron availability in most soils, competition for iron via secreted siderophore molecules might influence microbial interaction outcomes. Here, we tested if bacterial interactions mediated by iron-scavenging siderophores can be used to predict the disease suppressiveness of microbial consortia against soilborne Ralstonia solanacearum, a bacterial pathogen in the tomato rhizosphere. Iron availability significantly affected the interactions within inoculated consortia and between the consortia and the pathogen. We observed contrasting effects of siderophores and other nonsiderophore metabolites on the pathogen growth, while the siderophore effects were relatively much stronger. Specifically, disease incidence was reduced in vivo when the inoculated consortia produced siderophores that the pathogen could not use for its own growth. Employing siderophore-mediated interactions to engineer functionally robust microbial inoculants shows promise in protecting plants from soilborne pathogens. IMPORTANCE Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens.
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12
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Richness, phylogenetic diversity, and abundance all have positive effects on invader performance in an arid ecosystem. Ecosphere 2020. [DOI: 10.1002/ecs2.3045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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13
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Lear L, Hesse E, Shea K, Buckling A. Disentangling the mechanisms underpinning disturbance-mediated invasion. Proc Biol Sci 2020; 287:20192415. [PMID: 31992171 PMCID: PMC7015320 DOI: 10.1098/rspb.2019.2415] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Disturbances can play a major role in biological invasions: by destroying biomass, they alter habitat and resource abundances. Previous field studies suggest that disturbance-mediated invader success is a consequence of resource influxes, but the importance of other potential covarying causes, notably the opening up of habitats, have yet to be directly tested. Using experimental populations of the bacterium Pseudomonas fluorescens, we determined the relative importance of disturbance-mediated habitat opening and resource influxes, plus any interaction between them, for invader success of two ecologically distinct morphotypes. Resource addition increased invasibility, while habitat opening had little impact and did not interact with resource addition. Both invaders behaved similarly, despite occupying different ecological niches in the microcosms. Treatment also affected the composition of the resident population, which further affected invader success. Our results provide experimental support for the observation that resource input is a key mechanism through which disturbance increases invasibility.
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Affiliation(s)
- Luke Lear
- Department of Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Elze Hesse
- Department of Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Katriona Shea
- Department of Biology and Center for Infectious Disease Dynamics, 208 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Angus Buckling
- Department of Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
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14
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Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community. Cell Syst 2019; 9:521-533.e10. [PMID: 31838145 DOI: 10.1016/j.cels.2019.11.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/26/2019] [Accepted: 11/07/2019] [Indexed: 12/15/2022]
Abstract
The composition of an ecosystem is thought to be important for determining its resistance to invasion. Studies of natural ecosystems, from plant to microbial communities, have found that more diverse communities are more resistant to invasion. In some cases, more diverse communities resist invasion by more completely consuming the resources necessary for the invader. We show that Escherichia coli can successfully invade cultures of the alga Chlamydomonas reinhardtii (phototroph) or the ciliate Tetrahymena thermophila (predator) but cannot invade a community where both are present. The invasion resistance of the algae-ciliate community arises from a higher-order interaction between species (interaction modification) that is unrelated to resource consumption. We show that the mode of this interaction is the algal inhibition of bacterial aggregation, which leaves bacteria vulnerable to predation. This mode requires both the algae and the ciliate to be present and provides an example of invasion resistance through an interaction modification.
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15
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Xie JJ, Liu QQ, Liao S, Fang HH, Yin P, Xie SW, Tian LX, Liu YJ, Niu J. Effects of dietary mixed probiotics on growth, non-specific immunity, intestinal morphology and microbiota of juvenile pacific white shrimp, Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2019; 90:456-465. [PMID: 31075403 DOI: 10.1016/j.fsi.2019.04.301] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 04/25/2019] [Accepted: 04/28/2019] [Indexed: 06/09/2023]
Abstract
This study was conducted to elucidate the effects of dietary mixed probiotics on growth, non-specific immunity, intestinal morphology and microbiota of juvenile pacific white shrimp, Litopenaeus vannamei. Juvenile shrimp (initial body weight 1.21 ± 0.01 g) were fed diets containing graded probiotics (F1: 0 mg/kg probiotics; F2: 1000 mg/kg probiotics; F3: 2000 mg/kg probiotics; F4: 4000 mg/kg compound probiotics; F5: 6000 mg/kg probiotics; F6: 8000 mg/kg probiotics) for 8 weeks. The result of this trial showed that the growth performance (SGR, WG, FBW) of shrimp fed diets containing probiotics (F2∼F6) were significantly higher than that of shrimp fed diet without supplemental probiotics (F1) (P < 0.05), and the highest values of the growth performance (SGR, WG, FBW) and lowest FCR were found in shrimp fed the diet containing 2000 mg/kg probiotics. Total antioxidant capacity of shrimp fed diet F2 and F3 were significantly higher than that of shrimp fed the basal diets (P < 0.05). Superoxide dismutase in F4 treatment was significantly higher than that of basal treatment (P < 0.05). Catalase of shrimp in all probiotics supplemented (F2∼F6) treatments were significantly higher than that of the control one (F1) (P < 0.05). Malondialdehyde in F5 groups was significantly lower than that of F1 groups (P < 0.05). Alkline phosphatase and acid phosphatase in F3 treatments were significantly higher than those of the basal one (P < 0.05). Lysozyme of shrimp fed F2∼F6 were significantly higher than that of shrimp fed F1 diet (P < 0.05). The lipase and amylase activities in 2000 mg/kg probiotics groups showed the highest activities and were significantly higher than that of control one (P < 0.05). Intestinal villi height in F3∼F6 treatments were significantly higher than that of control one (P < 0.05). Alpha diversity indices including observed species, chao1, ACE and shannon indices showed that F2 and F3 groups had higher microbial diversity in their intestines, both richness and evenness. PCA plot showed that there was a clear shift of F2 and F3 groups from the control groups in microbial community structure. The dominant phyla in pacific white shrimp are proteobacteria, bacteroidetes and actinobacteria, the dominant genus were algoriphagus and vibrio. As the probiotics increased, the gemmatimonadetes, acidobacteria, deltaproteobacteria and xanthomonadales firstly increased and then decreased, with the highest content in F2 group, which was no significant difference to F3 group (P > 0.05) while significantly higher than other groups (P < 0.05). In conclusion, the supplement of mixed species probiotics can promote growth performance, enhance the non-specific immunity, influence the microbiota of the pacific white shrimps and the recommended optimum dosage in diet of Litopenaeus vannamei was 2000 mg/kg.
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Affiliation(s)
- Jia-Jun Xie
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Qiang-Qiang Liu
- Tianjin Agricultural University, Tianjin, 300384, China; Guangdong Yuehai Feed Group, Zhanjiang, 524017, China
| | - Shiyu Liao
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Hao-Hang Fang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Peng Yin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shi-Wei Xie
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Xia Tian
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Yong-Jian Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jin Niu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China.
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16
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Munzi S, Cruz C, Corrêa A. When the exception becomes the rule: An integrative approach to symbiosis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:855-861. [PMID: 30978547 DOI: 10.1016/j.scitotenv.2019.04.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Symbiosis, mainly due to the advances in -omics technology and to the microbiome revolution, is being increasingly acknowledged as fundamental to explain any aspect of life existence. Previously considered an exception, a peculiar characteristic of few systems like lichens, corals and mycorrhizas, symbiosis is nowadays recognized as the rule, with the microbiome being part of all living entities and systems. However, our knowledge of the ecological meaning and functioning of many symbiotic systems is still limited. Here, we discuss a new, integrative approach based on current findings that looks at commonalities among symbiotic systems to produce theoretical models and conceptual knowledge that would allow a more efficient exploitation of symbiosis-based biotechnologies. The microbiome recruitment and assemblage processes are indicated as one of the potential targets where a holistic approach could bring advantages. Finally, we reflect on the potential socio-economic and environmental consequences of a symbiotic view of the world, where co-dependence is the matrix of life.
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Affiliation(s)
- Silvana Munzi
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Cristina Cruz
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Ana Corrêa
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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17
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Tomasetto F, Duncan RP, Hulme PE. Resolving the invasion paradox: pervasive scale and study dependence in the native‐alien species richness relationship. Ecol Lett 2019; 22:1038-1046. [DOI: 10.1111/ele.13261] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/02/2019] [Accepted: 02/21/2019] [Indexed: 02/04/2023]
Affiliation(s)
| | - Richard P. Duncan
- Bio‐Protection Research Centre Lincoln University PO Box 84 Lincoln7647 New Zealand
- Institute for Applied Ecology University of Canberra Canberra ACT2601 Australia
| | - Philip E. Hulme
- Bio‐Protection Research Centre Lincoln University PO Box 84 Lincoln7647 New Zealand
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18
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Castledine M, Buckling A, Padfield D. A shared coevolutionary history does not alter the outcome of coalescence in experimental populations of Pseudomonas fluorescens. J Evol Biol 2019; 32:58-65. [PMID: 30346633 PMCID: PMC7379710 DOI: 10.1111/jeb.13394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/13/2018] [Accepted: 10/08/2018] [Indexed: 11/30/2022]
Abstract
Community coalescence, the mixing of multiple communities, is ubiquitous in natural microbial communities. During coalescence, theory suggests the success of a population will be enhanced by the presence of species it has coevolved with (relative to foreign species), because coevolution will result in greater resource specialization to minimize competition. Thus, more coevolved communities should dominate over less coevolved communities during coalescence events. We test these hypotheses using the bacterium Pseudomonas fluorescens which diversifies into coexisting niche-specialist morphotypes. We first evolved replicate populations for ~40 generations and then isolated evolved genotypes. In a series of competition trials, we determined if using coevolved versus random genotypes affected the relative performance of "communities" of single and multiple genotypes. We found no effect of coevolutionary history on either genotype fitness or community performance, which suggests parallel (co)evolution between communities. However, fitness was enhanced by the presence of other genotypes of the same strain type (wild-type or an isogenic strain with a LacZ marker; the inclusion of the latter necessary to distinguish genotypes during competition), indicative of local adaptation with respect to genetic background. Our results are the first to investigate the effect of (co)evolution on the outcome of coalescence and suggest that when input populations are functionally similar and added at equal mixing ratios, the outcome community may not be asymmetrically dominated by either input population.
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Affiliation(s)
- Meaghan Castledine
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynCornwallUK
| | - Angus Buckling
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynCornwallUK
| | - Daniel Padfield
- Environment and Sustainability InstituteUniversity of ExeterPenrynCornwallUK
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19
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Haruta S, Yamamoto K. Model Microbial Consortia as Tools for Understanding Complex Microbial Communities. Curr Genomics 2018; 19:723-733. [PMID: 30532651 PMCID: PMC6225455 DOI: 10.2174/1389202919666180911131206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023] Open
Abstract
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.
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Affiliation(s)
- Shin Haruta
- Address correspondence to this author at the Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; Tel: +81-42-677-2580; Fax: +81-42-677-2559; E-mail:
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20
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Reese AT, Dunn RR. Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance. mBio 2018; 9:e01294-18. [PMID: 30065092 PMCID: PMC6069118 DOI: 10.1128/mbio.01294-18] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 06/29/2018] [Indexed: 01/16/2023] Open
Abstract
The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers and, in turn, affects ecosystem functioning. Yet, patterns of alpha diversity in host-associated microbial communities (microbiomes) are poorly studied and the appropriateness of general theory is untested. Expanding diversity theory to include microbiomes is essential as diversity is a frequently cited metric of their status. Here, we review and newly analyze reports of alpha diversity for animal gut microbiomes. We demonstrate that both diet and body size affect diversity in the gut but that gut physiology (fermenter versus simple) is the most important driver. We also assess the advantages of various diversity metrics. The importance of diversity in microbiomes is often assumed but has not been tested outright. Therefore, we close by discussing how to integrate microbiomes into the field of biodiversity-ecosystem functioning to more clearly understand when and why a host supports diverse microbial communities.
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Affiliation(s)
- Aspen T Reese
- Society of Fellows, Harvard University, Cambridge, Massachusetts
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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21
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Sierocinski P, Milferstedt K, Bayer F, Großkopf T, Alston M, Bastkowski S, Swarbreck D, Hobbs PJ, Soyer OS, Hamelin J, Buckling A. A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities. Curr Biol 2017; 27:3390-3395.e4. [PMID: 29107553 DOI: 10.1016/j.cub.2017.09.056] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/06/2017] [Accepted: 09/26/2017] [Indexed: 11/30/2022]
Abstract
The ecology of microbes frequently involves the mixing of entire communities (community coalescence), for example, flooding events, host excretion, and soil tillage [1, 2], yet the consequences of this process for community structure and function are poorly understood [3-7]. Recent theory suggests that a community, due to coevolution between constituent species, may act as a partially cohesive unit [8-11], resulting in one community dominating after community coalescence. This dominant community is predicted to be the one that uses resources most efficiently when grown in isolation [11]. We experimentally tested these predictions using methanogenic communities, for which efficient resource use, quantified by methane production, requires coevolved cross-feeding interactions between species [12]. After propagation in laboratory-scale anaerobic digesters, community composition (determined from 16S rRNA sequencing) and methane production of mixtures of communities closely resembled that of the single most productive community grown in isolation. Analysis of each community's contribution toward the final mixture suggests that certain combinations of taxa within a community might be co-selected as a result of coevolved interactions. As a corollary of these findings, we also show that methane production increased with the number of inoculated communities. These findings are relevant to the understanding of the ecological dynamics of natural microbial communities, as well as demonstrating a simple method of predictably enhancing microbial community function in biotechnology, health, and agriculture [13].
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Affiliation(s)
| | - Kim Milferstedt
- Laboratoire de Biotechnologie de l'Environnement (LBE), Institut National de la Recherche Agronomique (IRNA), 11100 Narbonne, France
| | - Florian Bayer
- Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Tobias Großkopf
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Mark Alston
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Jérôme Hamelin
- Laboratoire de Biotechnologie de l'Environnement (LBE), Institut National de la Recherche Agronomique (IRNA), 11100 Narbonne, France
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
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22
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Jones ML, Ramoneda J, Rivett DW, Bell T. Biotic resistance shapes the influence of propagule pressure on invasion success in bacterial communities. Ecology 2017; 98:1743-1749. [DOI: 10.1002/ecy.1852] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/24/2017] [Accepted: 03/31/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Matt L. Jones
- Department of Life Sciences; Imperial College London, Silwood Park Campus; Ascot United Kingdom
| | - Josep Ramoneda
- Department of Life Sciences; Imperial College London, Silwood Park Campus; Ascot United Kingdom
| | - Damian W. Rivett
- Department of Life Sciences; Imperial College London, Silwood Park Campus; Ascot United Kingdom
| | - Thomas Bell
- Department of Life Sciences; Imperial College London, Silwood Park Campus; Ascot United Kingdom
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23
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Yang T, Wei Z, Friman V, Xu Y, Shen Q, Kowalchuk GA, Jousset A. Resource availability modulates biodiversity‐invasion relationships by altering competitive interactions. Environ Microbiol 2017; 19:2984-2991. [DOI: 10.1111/1462-2920.13708] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Tianjie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University210095Nanjing People's Republic of China
- Institute for Environmental Biology, Ecology & BiodiversityUtrecht UniversityPadualaan 8, 3584 CH Utrecht The Netherlands
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University210095Nanjing People's Republic of China
| | | | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University210095Nanjing People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University210095Nanjing People's Republic of China
| | - George A. Kowalchuk
- Institute for Environmental Biology, Ecology & BiodiversityUtrecht UniversityPadualaan 8, 3584 CH Utrecht The Netherlands
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University210095Nanjing People's Republic of China
- Institute for Environmental Biology, Ecology & BiodiversityUtrecht UniversityPadualaan 8, 3584 CH Utrecht The Netherlands
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24
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Bongrand C, Koch EJ, Moriano-Gutierrez S, Cordero OX, McFall-Ngai M, Polz MF, Ruby EG. A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior. THE ISME JOURNAL 2016; 10:2907-2917. [PMID: 27128997 PMCID: PMC5148191 DOI: 10.1038/ismej.2016.69] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 11/09/2022]
Abstract
Newly hatched Euprymna scolopes squid obtain their specific light-organ symbionts from an array of Vibrio (Allivibrio) fischeri strains present in their environment. Two genetically distinct populations of this squid species have been identified, one in Kaneohe Bay (KB), and another in Maunaloa Bay (MB), Oahu. We asked whether symbionts isolated from squid in each of these populations outcompete isolates from the other population in mixed-infection experiments. No relationship was found between a strain's host source (KB or MB) and its ability to competitively colonize KB or MB juveniles in a mixed inoculum. Instead, two colonization behaviors were identified among the 11 KB and MB strains tested: a 'dominant' outcome, in which one strain outcompetes the other for colonization, and a 'sharing' outcome, in which two strains co-colonize the squid. A genome-level comparison of these and other V. fischeri strains suggested that the core genomic structure of this species is both syntenous and highly conserved over time and geographical distance. We also identified ~250 Kb of sequence, encoding 194 dispersed orfs, that was specific to those strains that expressed the dominant colonization behavior. Taken together, the results indicate a link between the genome content of V. fischeri strains and their colonization behavior when initiating a light-organ symbiosis.
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Affiliation(s)
- Clotilde Bongrand
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Eric J Koch
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Silvia Moriano-Gutierrez
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret McFall-Ngai
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Edward G Ruby
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
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25
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Kadowaki K, Barbera CG, Godsoe W, Delsuc F, Mouquet N. Predicting biotic interactions and their variability in a changing environment. Biol Lett 2016; 12:rsbl.2015.1073. [PMID: 27220858 DOI: 10.1098/rsbl.2015.1073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/27/2016] [Indexed: 11/12/2022] Open
Abstract
Global environmental change is altering the patterns of biodiversity worldwide. Observation and theory suggest that species' distributions and abundances depend on a suite of processes, notably abiotic filtering and biotic interactions, both of which are constrained by species' phylogenetic history. Models predicting species distribution have historically mostly considered abiotic filtering and are only starting to integrate biotic interaction. However, using information on present interactions to forecast the future of biodiversity supposes that biotic interactions will not change when species are confronted with new environments. Using bacterial microcosms, we illustrate how biotic interactions can vary along an environmental gradient and how this variability can depend on the phylogenetic distance between interacting species.
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Affiliation(s)
- Kohmei Kadowaki
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan Institut des Sciences de l'Evolution, UMR 5554, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Claire G Barbera
- Institut des Sciences de l'Evolution, UMR 5554, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - William Godsoe
- BioProtection Research Centre, Lincoln University, Lincoln, Canterbury, New Zealand
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Nicolas Mouquet
- Institut des Sciences de l'Evolution, UMR 5554, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France MARBEC (MARine Biodiversity Exploitation and Conservation), UMR IRD-CNRS-UM-IFREMER 9190, Université Montpellier, CC 093, 34095 Montpellier Cedex 5, France
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26
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Zha Y, Berga M, Comte J, Langenheder S. Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities. PLoS One 2016; 11:e0155239. [PMID: 27182596 PMCID: PMC4868275 DOI: 10.1371/journal.pone.0155239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/26/2016] [Indexed: 12/04/2022] Open
Abstract
Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted.
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Affiliation(s)
- Yinghua Zha
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Mercè Berga
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Jérôme Comte
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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27
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A conceptual framework for invasion in microbial communities. ISME JOURNAL 2016; 10:2773-2775. [PMID: 27137125 DOI: 10.1038/ismej.2016.75] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/06/2016] [Accepted: 03/23/2016] [Indexed: 12/24/2022]
Abstract
There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process.
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28
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Keiser CN, Shearer TA, DeMarco AE, Brittingham HA, Knutson KA, Kuo C, Zhao K, Pruitt JN. Cuticular bacteria appear detrimental to social spiders in mixed but not monoculture exposure. Curr Zool 2016; 62:377-384. [PMID: 29491926 PMCID: PMC5829440 DOI: 10.1093/cz/zow015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/22/2015] [Indexed: 12/15/2022] Open
Abstract
Much of an animal’s health status, life history, and behavior are dictated by
interactions with its endogenous and exogenous bacterial communities. Unfortunately,
interactions between hosts and members of their resident bacterial community are often
ignored in animal behavior and behavioral ecology. Here, we aim to identify the nature of
host–microbe interactions in a nonmodel organism, the African social spider
Stegodyphus dumicola. We collected and identified bacteria from the
cuticles of spiders in situ and then exposed spiders to bacterial
monocultures cultures via topical application or injection. We also topically inoculated
spiders with a concomitant “cocktail” of bacteria and measured the behavior of spiders
daily for 24 days after inoculation. Lastly, we collected and identified bacteria from the
cuticles of prey items in the capture webs of spiders, and then fed spiders domestic
crickets which had been injected with these bacteria. We also injected 1 species of
prey-borne bacteria into the hemolymph of spiders. Only Bacillus
thuringiensis caused increased mortality when injected into the hemolymph of
spiders, whereas no bacterial monocultures caused increased mortality when applied
topically, relative to control solutions. However, a bacterial cocktail of cuticular
bacteria caused weight loss and mortality when applied topically, yet did not detectibly
alter spider behavior. Consuming prey injected with prey-borne bacteria was associated
with an elongated lifespan in spiders. Thus, indirect evidence from multiple experiments
suggests that the effects of these bacteria on spider survivorship appear contingent on
their mode of colonization and whether they are applied in monoculture or within a mixed
cocktail. We urge that follow-up studies should test these host–microbe interactions
across different social contexts to determine the role that microbes play in colony
performance.
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Affiliation(s)
- Carl N Keiser
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Taylor A Shearer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Alexander E DeMarco
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Hayley A Brittingham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Karen A Knutson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Candice Kuo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Katherine Zhao
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Jonathan N Pruitt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
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Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms. Sci Rep 2016; 6:23012. [PMID: 26972977 PMCID: PMC4789748 DOI: 10.1038/srep23012] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/26/2016] [Indexed: 11/08/2022] Open
Abstract
The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.
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Rungrassamee W, Klanchui A, Maibunkaew S, Karoonuthaisiri N. Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure. J Invertebr Pathol 2015; 133:12-9. [PMID: 26585302 DOI: 10.1016/j.jip.2015.11.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 11/04/2015] [Accepted: 11/12/2015] [Indexed: 01/02/2023]
Abstract
The intestinal microbiota play important roles in health of their host, contributing to maintaining the balance and resilience against pathogen. To investigate effects of pathogen to intestinal microbiota, the bacterial dynamics upon a shrimp pathogen, Vibrio harveyi, exposures were determined in two economically important shrimp species; the black tiger shrimp (BT) and the Pacific white shrimp (PW). Both shrimp species were reared under the same diet and environmental conditions. Shrimp survival rates after the V. harveyi exposure revealed that the PW shrimp had a higher resistance to the pathogen than the BT shrimp. The intestinal bacterial profiles were determined by denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing of the 16S rRNA sequences under no pathogen challenge control and under pathogenic V. harveyi challenge. The DGGE profiles showed that the presence of V. harveyi altered the intestinal bacterial patterns in comparison to the control in BT and PW intestines. This implies that bacterial balance in shrimp intestines was disrupted in the presence of V. harveyi. The barcoded pyrosequencing analysis showed the similar bacterial community structures in intestines of BT and PW shrimp under a normal condition. However, during the time course exposure to V. harveyi, the relative abundance of bacteria belong to Vibrio genus was higher in the BT intestines at 12h after the exposure, whereas relative abundance of vibrios was more stable in PW intestines. The principle coordinates analysis based on weighted-UniFrac analysis showed that intestinal bacterial population in the BT shrimp lost their ability to restore their bacterial balance during the 72-h period of exposure to the pathogen, while the PW shrimp were able to reestablish their bacterial population to resemble those seen in the unexposed control group. This observation of bacterial disruption might correlate to different mortality rates observed between the two shrimp species. Our findings provide evidence of intestinal bacterial population altered by a presence of the pathogen in shrimp intestines and intestinal bacterial stability might provide colonization resistance against the invading pathogen in the host shrimp. Hence, intestinal microbial ecology management may potentially contribute to disease prevention in aquaculture.
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Affiliation(s)
- Wanilada Rungrassamee
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand.
| | - Amornpan Klanchui
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Sawarot Maibunkaew
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
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Galand PE, Salter I, Kalenitchenko D. Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters. Mol Ecol 2015; 24:5785-95. [PMID: 26289961 DOI: 10.1111/mec.13347] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/31/2015] [Accepted: 08/16/2015] [Indexed: 01/02/2023]
Abstract
Understanding the link between community diversity and ecosystem function is a fundamental aspect of ecology. Systematic losses in biodiversity are widely acknowledged but the impact this may exert on ecosystem functioning remains ambiguous. There is growing evidence of a positive relationship between species richness and ecosystem productivity for terrestrial macro-organisms, but similar links for marine micro-organisms, which help drive global climate, are unclear. Community manipulation experiments show both positive and negative relationships for microbes. These previous studies rely, however, on artificial communities and any links between the full diversity of active bacterial communities in the environment, their phylogenetic relatedness and ecosystem function remain hitherto unexplored. Here, we test the hypothesis that productivity is associated with diversity in the metabolically active fraction of microbial communities. We show in natural assemblages of active bacteria that communities containing more distantly related members were associated with higher bacterial production. The positive phylogenetic diversity-productivity relationship was independent of community diversity calculated as the Shannon index. From our long-term (7-year) survey of surface marine bacterial communities, we also found that similarly, productive communities had greater phylogenetic similarity to each other, further suggesting that the traits of active bacteria are an important predictor of ecosystem productivity. Our findings demonstrate that the evolutionary history of the active fraction of a microbial community is critical for understanding their role in ecosystem functioning.
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Affiliation(s)
- Pierre E Galand
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Sorbonne Universités, UPMC Univ Paris 06, Banyuls sur Mer, F-66650, France
| | - Ian Salter
- CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Sorbonne Universités, UPMC Univ Paris 06, Banyuls sur Mer, F-66650, France.,Alfred-Wegener-Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Dimitri Kalenitchenko
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Sorbonne Universités, UPMC Univ Paris 06, Banyuls sur Mer, F-66650, France
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Cooper VS, Staples RK, Traverse CC, Ellis CN. Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms. Genomics 2014; 104:447-52. [PMID: 25263109 DOI: 10.1016/j.ygeno.2014.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 12/31/2022]
Abstract
A common phenotype within bacterial biofilms is the small, "wrinkly" colony, which may associate with worse prognoses from biofilm-associated infections. The mechanisms that produce these variants in Burkholderia are undefined. Here we report the mutational and ecological causes of wrinkly (W) colonies that evolved during experimental biofilm evolution of Burkholderia cenocepacia. Mutations clustered in a homologous pathway to the Pseudomonas wsp operon but with a distinct terminal signaling mechanism, and their parallel evolution suggested that they inhabited an equivalent biofilm niche. We tested this hypothesis of niche complementarity by measuring effects of substituting different W variants in the same evolved biofilm community. Despite phenotypic differences among W mutants growing alone, fitness of reconstituted mixed biofilms did not differ significantly. In conclusion, the evolution of small-colony variants in Burkholderia biofilms appears to be driven by an ecological opportunity that generates strong selection for constitutive wsp mutants to inhabit a common niche.
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Affiliation(s)
- Vaughn S Cooper
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03820, USA.
| | - Rachel K Staples
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Charles C Traverse
- Department of Microbiology, University of Texas at Austin, Austin, TX, USA
| | - Crystal N Ellis
- Massachusetts General Hospital, Department of Medicine, Division of Infectious Diseases, 55 Fruit Street, Boston, MA 02114, USA
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Awasthi A, Singh M, Soni SK, Singh R, Kalra A. Biodiversity acts as insurance of productivity of bacterial communities under abiotic perturbations. ISME JOURNAL 2014; 8:2445-52. [PMID: 24926862 DOI: 10.1038/ismej.2014.91] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 12/17/2022]
Abstract
Anthropogenic disturbances are detrimental to the functioning and stability of natural ecosystems. Critical ecosystem processes driven by microbial communities are subjected to these disturbances. Here, we examine the stabilizing role of bacterial diversity on community biomass in the presence of abiotic perturbations such as addition of heavy metals, NaCl and warming. Bacterial communities with a diversity gradient of 1-12 species were subjected to the different treatments, and community biomass (OD600) was measured after 24 h. We found that initial species richness and phylogenetic structure impact the biomass of communities. Under abiotic perturbations, the presence of tolerant species in community largely contributed in community biomass production. Bacterial diversity stabilized the biomass across the treatments, and differential response of bacterial species to different perturbations was the key reason behind these effects. The results suggest that biodiversity is crucial for maintaining the stability of ecosystem functioning and acts as ecological insurance under abiotic perturbations. Biodiversity in natural ecosystems may also uphold the ecosystem functioning under anthropogenic disturbance.
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Affiliation(s)
- Ashutosh Awasthi
- Department of Microbial Technology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Mangal Singh
- Department of Microbial Technology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Sumit K Soni
- Department of Microbial Technology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Rakshapal Singh
- Department of Microbial Technology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Alok Kalra
- Department of Microbial Technology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
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He X, McLean JS, Guo L, Lux R, Shi W. The social structure of microbial community involved in colonization resistance. ISME JOURNAL 2013; 8:564-574. [PMID: 24088624 DOI: 10.1038/ismej.2013.172] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 07/15/2013] [Accepted: 08/30/2013] [Indexed: 12/20/2022]
Abstract
It is well established that host-associated microbial communities can interfere with the colonization and establishment of microbes of foreign origins, a phenomenon often referred to as bacterial interference or colonization resistance. However, due to the complexity of the indigenous microbiota, it has been extremely difficult to elucidate the community colonization resistance mechanisms and identify the bacterial species involved. In a recent study, we have established an in vitro mice oral microbial community (O-mix) and demonstrated its colonization resistance against an Escherichia coli strain of mice gut origin. In this study, we further analyzed the community structure of the O-mix by using a dilution/regrowth approach and identified the bacterial species involved in colonization resistance against E. coli. Our results revealed that, within the O-mix there were three different types of bacterial species forming unique social structure. They act as 'Sensor', 'Mediator' and 'Killer', respectively, and have coordinated roles in initiating the antagonistic action and preventing the integration of E. coli. The functional role of each identified bacterial species was further confirmed by E. coli-specific responsiveness of the synthetic communities composed of different combination of the identified players. The study reveals for the first time the sophisticated structural and functional organization of a colonization resistance pathway within a microbial community. Furthermore, our results emphasize the importance of 'Facilitation' or positive interactions in the development of community-level functions, such as colonization resistance.
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Affiliation(s)
- Xuesong He
- UCLA School of Dentistry, Los Angeles, CA, USA
| | | | - Lihong Guo
- UCLA School of Dentistry, Los Angeles, CA, USA
| | - Renate Lux
- UCLA School of Dentistry, Los Angeles, CA, USA
| | - Wenyuan Shi
- UCLA School of Dentistry, Los Angeles, CA, USA.
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Horňák K, Corno G. Every coin has a back side: invasion by Limnohabitans planktonicus promotes the maintenance of species diversity in bacterial communities. PLoS One 2012; 7:e51576. [PMID: 23251582 PMCID: PMC3520937 DOI: 10.1371/journal.pone.0051576] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/01/2012] [Indexed: 11/18/2022] Open
Abstract
One of the earliest challenges for ecologists has been to study the impact of invasive species on microbial communities. Although bacteria are fundamental in biological processes, current knowledge on invasion effects by aquatic non-pathogenic bacteria is still limited. Using pure cultures of diverse planktonic bacteria as model organisms at two different carbon concentration levels, we tested the response of an assembled community to the invasion by Limnohabitans planktonicus, an opportunistic bacterium, successful in freshwaters. The invader, introduced at the early stationary growth phase of the resident community, caused a strong decrement of the abundance of the dominant species. This was due to competition for nutrients and a potential allelopathic interaction. Simultaneously, resident species formerly unable to successfully compete within the community, thus potentially exposed to competitive exclusion, increased their abundances. The overall result of the invasion was preservation of species diversity, the higher the lower was the substrate content available. Our study provides new insights into bacterial invasions, offering an alternative interpretation of invasions for community ecology.
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Affiliation(s)
- Karel Horňák
- Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic.
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Eisenhauer N, Schulz W, Scheu S, Jousset A. Niche dimensionality links biodiversity and invasibility of microbial communities. Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.02060.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wiebke Schulz
- J.F. Blumenbach Institute of Zoology and Anthropology; Georg August University Göttingen; Berliner Str. 28; 37073; Göttingen; Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology; Georg August University Göttingen; Berliner Str. 28; 37073; Göttingen; Germany
| | - Alexandre Jousset
- J.F. Blumenbach Institute of Zoology and Anthropology; Georg August University Göttingen; Berliner Str. 28; 37073; Göttingen; Germany
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Eisenhauer N, Scheu S, Jousset A. Bacterial diversity stabilizes community productivity. PLoS One 2012; 7:e34517. [PMID: 22470577 PMCID: PMC3314632 DOI: 10.1371/journal.pone.0034517] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/02/2012] [Indexed: 11/19/2022] Open
Abstract
Background Stability is a crucial ecosystem feature gaining particular importance in face of increasing anthropogenic stressors. Biodiversity is considered to be a driving biotic force maintaining stability, and in this study we investigate how different indices of biodiversity affect the stability of communities in varied abiotic (composition of available resources) and biotic (invasion) contexts. Methodology/Principal Findings We set up microbial microcosms to study the effects of genotypic diversity on the reliability of community productivity, defined as the inverse of the coefficient of variation of across-treatment productivity, in different environmental contexts. We established a bacterial diversity gradient ranging from 1 to 8 Pseudomonas fluorescens genotypes and grew the communities in different resource environments or in the presence of model invasive species. Biodiversity significantly stabilized community productivity across treatments in both experiments. Path analyses revealed that different aspects of diversity determined stability: genotypic richness stabilized community productivity across resource environments, whereas functional diversity determined stability when subjected to invasion. Conclusions/Significance Biodiversity increases the stability of microbial communities against both biotic and abiotic environmental perturbations. Depending on stressor type, varying aspects of biodiversity contribute to the stability of ecosystem functions. The results suggest that both genetic and functional diversity need to be preserved to ensure buffering of communities against abiotic and biotic stresses.
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Affiliation(s)
- Nico Eisenhauer
- Georg August University Göttingen, J. F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany.
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Becker J, Eisenhauer N, Scheu S, Jousset A. Increasing antagonistic interactions cause bacterial communities to collapse at high diversity. Ecol Lett 2012; 15:468-74. [PMID: 22394557 DOI: 10.1111/j.1461-0248.2012.01759.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biodiversity is a major determinant of ecosystem functioning. Species-rich communities often use resources more efficiently thereby improving community performance. However, high competition within diverse communities may also reduce community functioning. We manipulated the genotypic diversity of Pseudomonas fluorescens communities, a plant mutualistic species inhibiting pathogens. We measured antagonistic interactions in vitro, and related these interactions to bacterial community productivity (root colonisation) and ecosystem service (host plant protection). Antagonistic interactions increased disproportionally with species richness. Mutual poisoning between competitors lead to a 'negative complementarity effect', causing a decrease in bacterial density by up to 98% in diverse communities and a complete loss of plant protection. The results emphasize that antagonistic interactions may determine community functioning and cause negative biodiversity-ecosystem functioning relationships. Interference competition may thus be an additional key for predicting the dynamics and performance of natural assemblages and needs to be implemented in future biodiversity models.
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Affiliation(s)
- Joachim Becker
- J.F. Blumenbach Institute for Zoology and Anthropology, Georg August University Göttingen, Berliner Str. 28, 37073 Göttingen, Germany
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The importance of dispersal for bacterial community composition and functioning. PLoS One 2011; 6:e25883. [PMID: 21998714 PMCID: PMC3188564 DOI: 10.1371/journal.pone.0025883] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 09/13/2011] [Indexed: 01/31/2023] Open
Abstract
We conducted a metacommunity experiment to investigate the role of dispersal for bacterial community composition (BCC) and function of freshwater bacteria. Bacteria were dispersed from a common source pool into three different lake communities in their natural lake water. The experiment was conducted in dialysis bags to enable a decoupling between a change in the local environment and dispersal. BCC was determined by terminal restriction fragment length polymorphism (tRFLP) of the 16S rRNA gene. We show that the greatest changes in BCC occurred between 10% and 43% of dispersal of standing stock per day. Functioning, measured as growth rate, was also affected by dispersal in all three communities but the qualitative pattern differed between communities, sometimes showing a hump-shaped relationship to dispersal and sometimes decreasing with increasing dispersal. In all waters, functioning was related to BCC. Our results show that dispersal does affect BCC and functioning but that high dispersal rates are needed. Further, the effect of dispersal on BCC and function seem to depend on the quality of the habitat to which bacteria disperse into.
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Jousset A, Schmid B, Scheu S, Eisenhauer N. Genotypic richness and dissimilarity opposingly affect ecosystem functioning. Ecol Lett 2011; 14:537-45. [PMID: 21435139 DOI: 10.1111/j.1461-0248.2011.01613.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biodiversity is an essential determinant of ecosystem functioning. Numerous studies described positive effects of diversity on the functioning of communities arising from complementary resource use and facilitation. However, high biodiversity may also increase competitive interactions, fostering antagonism and negatively affecting community performance. Using experimental bacterial communities we differentiated diversity effects based on genotypic richness and dissimilarity. We show that these diversity characteristics have opposite effects on ecosystem functioning. Genotypic dissimilarity governed complementary resource use, improving ecosystem functioning in complex resource environments. Contrastingly, genotypic richness drove allelopathic interactions, mostly reducing ecosystem functioning. The net biodiversity effect on community performance resulted from the interplay between the genetic structure of the community and resource complexity. These results demonstrate that increasing richness, without concomitantly increasing dissimilarity, can decrease ecosystem functioning in simple environments due to antagonistic interactions, an effect insufficiently considered so far in mechanistic models of the biodiversity-ecosystem functioning relationship.
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Affiliation(s)
- A Jousset
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August- University Göttingen, Berliner Straße 28, 37073 Göttingen, Germany.
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Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. ISME JOURNAL 2011; 5:1108-14. [PMID: 21346790 DOI: 10.1038/ismej.2011.9] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biological invasions can lead to extinction events in resident communities and compromise ecosystem functioning. We tested the effect of two widespread biodiversity measurements, genotypic richness and genotypic dissimilarity on community invasibility. We manipulated the genetic structure of bacterial communities (Pseudomonas fluorescens) and submitted them to invasion by Serratia liquefaciens. We show that the two diversity measures impact on invasibility via distinct and additive mechanisms. Genotypic dissimilarity of the resident communities linearly increased productivity and in parallel decreased invasion success, indicating that high dissimilarity prevents invasion through niche pre-emption. By contrast, genotypic richness exerted a hump-shaped effect on invasion and was linked to the production of toxins antagonistic to the invader. This effect peaked at intermediate richness, suggesting that high richness levels may increase invasibility. Invasibility could be well predicted by the combination of these two mechanisms, documenting that both genotypic richness and dissimilarity need to be considered, if we are to understand the biotic properties determining the susceptibility of ecosystems to biological invasions.
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Abstract
One of the oldest ideas in invasion biology, known as Darwin's naturalization hypothesis, suggests that introduced species are more successful in communities in which their close relatives are absent. We conducted the first experimental test of this hypothesis in laboratory bacterial communities varying in phylogenetic relatedness between resident and invading species with and without a protist bacterivore. As predicted, invasion success increased with phylogenetic distance between the invading and the resident bacterial species in both the presence and the absence of protistan bacterivory. The frequency of successful invader establishment was best explained by average phylogenetic distance between the invader and all resident species, possibly indicating limitation by the availability of the unexploited niche (i.e., organic substances in the medium capable of supporting the invader growth); invader abundance was best explained by phylogenetic distance between the invader and its nearest resident relative, possibly indicating limitation by the availability of the unexploited optimal niche (i.e., the subset of organic substances supporting the best invader growth). These results were largely driven by one resident bacterium (a subspecies of Serratia marcescens) posting the strongest resistance to the alien bacterium (another subspecies of S. marcescens). Overall, our findings support phylogenetic relatedness as a useful predictor of species invasion success.
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Affiliation(s)
- Lin Jiang
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Bell T, Lilley AK, Hector A, Schmid B, King L, Newman JA. A linear model method for biodiversity-ecosystem functioning experiments. Am Nat 2010; 174:836-49. [PMID: 19842969 DOI: 10.1086/647931] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Experiments that manipulate species richness and measure ecosystem functioning attempt to separate the effects of species richness (the number of species) from those of species identity. We introduce an experimental design that ensures that each species is selected the same number of times at each level of species richness. In combination with a linear model analysis, this approach is able to unambiguously partition the variance due to different species identities and the variance due to nonlinear species richness, a proxy measure for interactions among species. Our design and analysis provide several advantages over methods that are currently used. First, the linear model method has the potential to directly estimate the role of various ecological mechanisms (e.g., competition, facilitation) rather than the consequences of those mechanisms (e.g., the "complementarity effect"). Second, unlike other methods that are currently used, this one is able to estimate the impact of diversity when the contribution of individual species in a mixture is unknown.
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Affiliation(s)
- Thomas Bell
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX13PS, United Kingdom.
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Zhang QG, Buckling A, Ellis RJ, Godfray HCJ. COEVOLUTION BETWEEN COOPERATORS AND CHEATS IN A MICROBIAL SYSTEM. Evolution 2009; 63:2248-56. [DOI: 10.1111/j.1558-5646.2009.00708.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Zhang QG, Buckling A, Godfray HCJ. Quantifying the relative importance of niches and neutrality for coexistence in a model microbial system. Funct Ecol 2009. [DOI: 10.1111/j.1365-2435.2009.01579.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Conrad R, Klose M, Noll M. Functional and structural response of the methanogenic microbial community in rice field soil to temperature change. Environ Microbiol 2009; 11:1844-53. [PMID: 19508556 DOI: 10.1111/j.1462-2920.2009.01909.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microbial community in anoxic rice field soil produces CH(4) over a wide temperature range up to 55°C. However, at temperatures higher than about 40°C, the methanogenic path changes from CH(4) production by hydrogenotrophic plus acetoclastic methanogenesis to exclusively hydrogenotrophic methanogenesis and simultaneously, the methanogenic community consisting of Methanosarcinaceae, Methanoseataceae, Methanomicrobiales, Methanobacteriales and Rice Cluster I (RC-1) changes to almost complete dominance of RC-1. We studied changes in structure and function of the methanogenic community with temperature to see whether microbial members of the community were lost or their function impaired by exposure to high temperature. We characterized the function of the community by the path of CH(4) production measuring δ(13)C in CH(4) and CO(2) and calculating the apparent fractionation factor (α(app)) and the structure of the community by analysis of the terminal restriction fragment length polymorphism (T-RFLP) of the microbial 16S rRNA genes. Shift of the temperature from 45°C to 35°C resulted in a corresponding shift of function and structure, especially when some 35°C soil was added to the 45°C soil. The bacterial community (T-RFLP patterns), which was much more diverse than the archaeal community, changed in a similar manner upon temperature shift. Incubation of a mixture of 35°C and 50°C pre-incubated methanogenic rice field soil at different temperatures resulted in functionally and structurally well-defined communities. Although function changed from a mixture of acetoclastic and hydrogenotrophic methanogenesis to exclusively hydrogenotrophic methanogenesis over a rather narrow temperature range of 42-46°C, each of these temperatures also resulted in only one characteristic function and structure. Our study showed that temperature conditions defined structure and function of the methanogenic microbial community.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany.
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Replansky T, Bell G. The relationship between environmental complexity, species diversity and productivity in a natural reconstructed yeast community. OIKOS 2009. [DOI: 10.1111/j.1600-0706.2008.16948.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Brockhurst MA, Buckling A, Racey D, Gardner A. Resource supply and the evolution of public-goods cooperation in bacteria. BMC Biol 2008; 6:20. [PMID: 18479522 PMCID: PMC2409295 DOI: 10.1186/1741-7007-6-20] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 05/14/2008] [Indexed: 11/23/2022] Open
Abstract
Background Explaining public-goods cooperation is a challenge for evolutionary biology. However, cooperation is expected to more readily evolve if it imposes a smaller cost. Such costs of cooperation are expected to decline with increasing resource supply, an ecological parameter that varies widely in nature. We experimentally tested the effect of resource supply on the evolution of cooperation using two well-studied bacterial public-good traits: biofilm formation by Pseudomonas fluorescens and siderophore production by Pseudomonas aeruginosa. Results The frequency of cooperative bacteria increased with resource supply in the context of both bacterial public-good traits. In both cases this was due to decreasing costs of investment into public-goods cooperation with increasing resource supply. Conclusion Our empirical tests with bacteria suggest that public-goods cooperation is likely to increase with increasing resource supply due to reduced costs of cooperation, confirming that resource supply is an important factor in the evolution of cooperation.
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Affiliation(s)
- Michael A Brockhurst
- School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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Benmayor R, Buckling A, Bonsall MB, Brockhurst MA, Hodgson DJ. The interactive effects of parasites, disturbance, and productivity on experimental adaptive radiations. Evolution 2007; 62:467-77. [PMID: 18039322 DOI: 10.1111/j.1558-5646.2007.00268.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Disturbance, productivity, and natural enemies are significant determinants of the evolution of diversity, but their interactive effect remains unresolved. We develop a simple, qualitative model assuming trade-offs between growth rate, competitive ability and parasite resistance, to address the interactive effects of these variables on the evolution of host diversity. Consistent with previous studies our model predicts maximum diversity at intermediate levels of disturbance and productivity in the absence of parasitism. However, parasites break down these unimodal diversity relationships with productivity and disturbance, as selection for parasite resistance reduces the importance of growth rate-competitive ability trade-offs. We tested these predictions using the bacterium Pseudomonas fluorescens, which undergoes an adaptive radiation into spatial niche specialists under laboratory conditions. This is the first study of adaptive radiation in response to experimental manipulation of the three-way interaction between productivity, disturbance, and natural enemies. As hypothesized, unimodal diversity relationships with disturbance and productivity were weakened or disappeared in the presence of parasitic phages. This was the result of phages increasing diversity at environmental extremes, by imposing selection for phage-resistant variants, but decreasing diversity in less stressful environments, probably through reductions in resource competition. Phages had a net effect of increasing host diversity. Parasites and other natural enemies are therefore likely to have a large effect in mitigating the influence of other environmental variables on the evolution and maintenance of diversity.
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Affiliation(s)
- Rebecca Benmayor
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.
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