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Barbosa M, Fernandes GW, Morris RJ. Experimental evidence for a hidden network of higher-order interactions in a diverse arthropod community. Curr Biol 2023; 33:381-388.e4. [PMID: 36563693 DOI: 10.1016/j.cub.2022.11.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/25/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
Transcending pairwise interactions in ecological networks remains a challenge.1,2,3,4,5 Higher-order interactions (HOIs), the modulation of a pairwise interaction by a third species,6 are thought to play a particularly important role in stabilizing coexistence and maintaining species diversity.7,8,9,10,11,12 However, HOIs have so far only been demonstrated in models9,10,11,12,13,14 or isolated experimental systems including only a few interacting species.7,8,15 Their ubiquity and importance at a community level in the real world remain unknown. We hypothesized that a complex network of HOIs could be constantly modifying pairwise interactions and shaping ecological communities and that consequently the outcome of pairwise interactions would be a product of many influences from distinct sources. Using field experiments, we tested how multiple interactions within a diverse arthropod community associated with the tropical shrub Baccharis dracunculifolia D.C. (Asteraceae) were modified by the removal of ant species or live or hatched insect galls (a non-trophic engineering effect) of the dominant galler species. We revealed an extensive hidden network of HOIs modifying each other and the "visible" pairwise interactions. Most pairwise interactions were affected indirectly by the manipulation of non-interacting taxonomic groups. The pervasiveness of these interaction modifications challenges pairwise approaches to understanding interaction outcomes and could shift our thinking about the structure and persistence of ecological communities. Investigating coexistence mechanisms involving interaction modulation by HOIs may be key to elucidating the underlying causes of the stability and persistence of ecological communities.
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Affiliation(s)
- Milton Barbosa
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK; Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, CP 486, 30161-970 Belo Horizonte, Brazil.
| | - Geraldo Wilson Fernandes
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, CP 486, 30161-970 Belo Horizonte, Brazil
| | - Rebecca Jane Morris
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK; School of Biological Sciences, University of Southampton, Highfield Campus, Life Sciences Building 85, Southampton SO17 1BJ, UK
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2
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Baker HK, Li SS, Samu SC, Jones NT, Symons CC, Shurin JB. Prey naiveté alters the balance of consumptive and non‐consumptive predator effects and shapes trophic cascades in freshwater plankton. OIKOS 2022. [DOI: 10.1111/oik.09173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henry K. Baker
- Section of Ecology, Behavior and Evolution, Univ. of California San Diego CA USA
| | - Stephanie S. Li
- Section of Ecology, Behavior and Evolution, Univ. of California San Diego CA USA
- School of Environment and Natural Resources, The Ohio State Univ. Columbus OH USA
| | - Stefan C. Samu
- Section of Ecology, Behavior and Evolution, Univ. of California San Diego CA USA
| | - Natalie T. Jones
- Section of Ecology, Behavior and Evolution, Univ. of California San Diego CA USA
- School of Biological Sciences, Univ. of Queensland St. Lucia QLD Australia
| | - Celia C. Symons
- Dept of Ecology and Evolutionary Biology, Univ. of California Irvine CA USA
| | - Jonathan B. Shurin
- Section of Ecology, Behavior and Evolution, Univ. of California San Diego CA USA
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3
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Koskella B, Hernandez CA, Wheatley RM. Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems. Annu Rev Virol 2022; 9:57-78. [PMID: 35584889 DOI: 10.1146/annurev-virology-091919-075914] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, USA;
| | - Catherine A Hernandez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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4
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Behavioral Interactions between Bacterivorous Nematodes and Predatory Bacteria in a Synthetic Community. Microorganisms 2021; 9:microorganisms9071362. [PMID: 34201688 PMCID: PMC8307948 DOI: 10.3390/microorganisms9071362] [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: 03/12/2021] [Revised: 06/07/2021] [Accepted: 06/12/2021] [Indexed: 11/17/2022] Open
Abstract
Theory and empirical studies in metazoans predict that apex predators should shape the behavior and ecology of mesopredators and prey at lower trophic levels. Despite the ecological importance of microbial communities, few studies of predatory microbes examine such behavioral res-ponses and the multiplicity of trophic interactions. Here, we sought to assemble a three-level microbial food chain and to test for behavioral interactions between the predatory nematode Caenorhabditis elegans and the predatory social bacterium Myxococcus xanthus when cultured together with two basal prey bacteria that both predators can eat—Escherichia coli and Flavobacterium johnsoniae. We found that >90% of C. elegans worms failed to interact with M. xanthus even when it was the only potential prey species available, whereas most worms were attracted to pure patches of E. coli and F. johnsoniae. In addition, M. xanthus altered nematode predatory behavior on basal prey, repelling C. elegans from two-species patches that would be attractive without M. xanthus, an effect similar to that of C. elegans pathogens. The nematode also influenced the behavior of the bacterial predator: M. xanthus increased its predatory swarming rate in response to C. elegans in a manner dependent both on basal-prey identity and on worm density. Our results suggest that M. xanthus is an unattractive prey for some soil nematodes and is actively avoided when other prey are available. Most broadly, we found that nematode and bacterial predators mutually influence one another’s predatory behavior, with likely consequences for coevolution within complex microbial food webs.
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Meroz N, Tovi N, Sorokin Y, Friedman J. Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales. Nat Commun 2021; 12:2891. [PMID: 33976223 PMCID: PMC8113234 DOI: 10.1038/s41467-021-23247-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Managing and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium, and how repeatable and predictable are changes when they occur. Here, we address this knowledge gap by tracking the composition of 87 two- and three-species bacterial communities, with 3-18 replicates each, for ~400 generations. We find that community composition typically changed during evolution, but that the composition of replicate communities remained similar. Furthermore, these changes were predictable in a bottom-up approach-changes in the composition of trios were consistent with those that occurred in pairs during coevolution. Our results demonstrate that simple assembly rules can hold even on evolutionary timescales, suggesting it may be possible to forecast the evolution of microbial communities.
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Affiliation(s)
- Nittay Meroz
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Nesli Tovi
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yael Sorokin
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
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6
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Aghaee BL, Khan Mirzaei M, Alikhani MY, Mojtahedi A, Maurice CF. Improving the Inhibitory Effect of Phages against Pseudomonas aeruginosa Isolated from a Burn Patient Using a Combination of Phages and Antibiotics. Viruses 2021; 13:334. [PMID: 33670028 PMCID: PMC7926668 DOI: 10.3390/v13020334] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance causes around 700,000 deaths a year worldwide. Without immediate action, we are fast approaching a post-antibiotic era in which common infections can result in death. Pseudomonas aeruginosa is the leading cause of nosocomial infection and is also one of the three bacterial pathogens in the WHO list of priority bacteria for developing new antibiotics against. A viable alternative to antibiotics is to use phages, which are bacterial viruses. Yet, the isolation of phages that efficiently kill their target bacteria has proven difficult. Using a combination of phages and antibiotics might increase treatment efficacy and prevent the development of resistance against phages and/or antibiotics, as evidenced by previous studies. Here, in vitro populations of a Pseudomonas aeruginosa strain isolated from a burn patient were treated with a single phage, a mixture of two phages (used simultaneously and sequentially), and the combination of phages and antibiotics (at sub-minimum inhibitory concentration (MIC) and MIC levels). In addition, we tested the stability of these phages at different temperatures, pH values, and in two burn ointments. Our results show that the two-phages-one-antibiotic combination had the highest killing efficiency against the P. aeruginosa strain. The phages tested showed low stability at high temperatures, acidic pH values, and in the two ointments. This work provides additional support for the potential of using combinations of phage-antibiotic cocktails at sub-MIC levels for the treatment of multidrug-resistant P. aeruginosa infections.
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Affiliation(s)
- Bahareh Lashtoo Aghaee
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 65178-38678, Iran;
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764 Neuherberg, Germany;
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 0B1, Canada
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 65178-38678, Iran;
| | - Ali Mojtahedi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht 41938-33697, Iran
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 0B1, Canada
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7
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Williams MA, Holland CV, Donohue I. Warming can alter host behavior in a similar manner to infection with behavior-manipulating parasites. Oecologia 2020; 194:65-74. [PMID: 32876762 DOI: 10.1007/s00442-020-04745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022]
Abstract
Parasites are ecologically ubiquitous and, by modifying the physiology and behavior of their host organisms, act as key regulators of the dynamics and stability of ecosystems. It is, however, as yet unclear how parasitic relationships will act to moderate or accelerate the ecological impacts of global climate change. Here, we explore experimentally how the effects of parasites on both the physiology and behavior of their hosts can be moderated by warming, utilising a well-established aquatic host-parasite model system-the ecologically important amphipod Gammarus duebeni and its acanthocephalan parasite Polymorphus minutus. We show that, while only warming affected measured components of host physiology, parasite infection and warming both supressed predator-avoidance behavior of the host independently, yet in a similar manner. Six degrees of warming altered geotactic behaviors to the same extent as infection with behavior-manipulating parasites. These results indicate a novel mechanism by which parasites impact their ecosystems that could be critical to predicting the ecological impacts of warming. Our findings highlight the need for holistic knowledge of interaction networks, incorporating multiple interaction types and behaviors, to predict the effects of both warming and parasitism on the dynamics and stability of ecosystems.
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Affiliation(s)
- Maureen A Williams
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Dublin 2, Ireland. .,School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA.
| | - Celia V Holland
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Dublin 2, Ireland
| | - Ian Donohue
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Dublin 2, Ireland
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8
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Gorter FA, Manhart M, Ackermann M. Understanding the evolution of interspecies interactions in microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190256. [PMID: 32200743 DOI: 10.1098/rstb.2019.0256] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microbial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of interspecies interactions in communities. Specifically, we propose that to understand the evolution of interspecies interactions, it is important to distinguish between direct and indirect fitness effects of a mutation. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Florien A Gorter
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Michael Manhart
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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9
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Kurm V, van der Putten WH, Weidner S, Geisen S, Snoek BL, Bakx T, Hol WHG. Competition and predation as possible causes of bacterial rarity. Environ Microbiol 2019; 21:1356-1368. [PMID: 30803145 PMCID: PMC6850713 DOI: 10.1111/1462-2920.14569] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/21/2019] [Indexed: 12/05/2022]
Abstract
We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.
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Affiliation(s)
- Viola Kurm
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Wim H. van der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityP.O. Box 8123, 6700 ES, WageningenThe Netherlands
| | - Simone Weidner
- Institute of Environmental Biology, Ecology and BiodiversityUtrecht UniversityPadualaan 8, 3584 CH, UtrechtThe Netherlands
| | - Stefan Geisen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Basten L. Snoek
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityP.O. Box 8123, 6700 ES, WageningenThe Netherlands
- Theoretical Biology and BioinformaticsUtrecht UniversityPadualaan 8, 3584 CH, UtrechtThe Netherlands
| | - Tanja Bakx
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Wilhelmina H. Gera Hol
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
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