1
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Lear L, Inamine H, Shea K, Buckling A. Diversity loss from multiple interacting disturbances is regime-dependent. Ecol Lett 2023; 26:2056-2065. [PMID: 37847646 DOI: 10.1111/ele.14325] [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: 09/26/2022] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
Abstract
Anthropogenic activities expose many ecosystems to multiple novel disturbances simultaneously. Despite this, how biodiversity responds to simultaneous disturbances remains unclear, with conflicting empirical results on their interactive effects. Here, we experimentally test how one disturbance (an invasive species) affects the diversity of a community over multiple levels of another disturbance regime (pulse mortality). Specifically, we invade stably coexisting bacterial communities under four different pulse frequencies, and compare their final resident diversity to uninvaded communities under the same pulse mortality regimes. Our experiment shows that the disturbances synergistically interact, such that the invader significantly reduces resident diversity at high pulse frequency, but not at low. This work therefore highlights the need to study simultaneous disturbance effects over multiple disturbance regimes as well as to carefully document unmanipulated disturbances, and may help explain the conflicting results seen in previous multiple-disturbance work.
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Affiliation(s)
- Luke Lear
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
| | - Hidetoshi Inamine
- Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Katriona Shea
- Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Angus Buckling
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
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2
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Venkataram S, Kryazhimskiy S. Evolutionary repeatability of emergent properties of ecological communities. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220047. [PMID: 37004728 PMCID: PMC10067272 DOI: 10.1098/rstb.2022.0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 04/04/2023] Open
Abstract
Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
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3
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Eckert EM, Galafassi S, Bastidas Navarro M, Di Cesare A, Corno G. Increased similarity of aquatic bacterial communities of different origin after antibiotic disturbance. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120568. [PMID: 36351482 DOI: 10.1016/j.envpol.2022.120568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/28/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Stochastic or deterministic processes control the bacterial community assembly in waters and their understanding is a fundamental question to correctly manage aquatic environments exposed to the release of antibiotics from anthropogenic sources. It has been suggested that microdiversity (i.e. the rare biosphere) convers freshwater communities with stability, meaning that previously rare taxa bloom when the community is disturbed. Since there might be a seed bank of similar, but not abundant, bacterial taxa in different waters, we tested whether a disturbance by an antibiotic cocktail would increase similarity in bacterial communities from different freshwater systems (a wastewater effluent and two lakes). In a continuous culture set-up in chemostats, we show that disturbance with antibiotics causes communities from different environments to become more similar. Once the antibiotic pressure is released the communities tend to become more dissimilar again. This shows that there is a similar shift in community composition even in waters from very different origins when they are disturbed by antibiotics, even at low concentrations. Antibiotics impact the bacterial communities at the cell and the community level, independently by the original degree of anthropogenic stress they are adapted to, altering the original phenotypes, genotypes, and the relations between bacteria.
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Affiliation(s)
- Ester M Eckert
- National Research Council of Italy, Water Research Institute, (CNR-IRSA), L.go Tonolli 50, 28922, Verbania, Italy
| | - Silvia Galafassi
- National Research Council of Italy, Water Research Institute, (CNR-IRSA), L.go Tonolli 50, 28922, Verbania, Italy
| | - Marcela Bastidas Navarro
- Laboratorio de Limnología, INIBIOMA, CONICET-Universidad Nacional Del Comahue, Quintral 1250, 8400, Bariloche, Argentina
| | - Andrea Di Cesare
- National Research Council of Italy, Water Research Institute, (CNR-IRSA), L.go Tonolli 50, 28922, Verbania, Italy
| | - Gianluca Corno
- National Research Council of Italy, Water Research Institute, (CNR-IRSA), L.go Tonolli 50, 28922, Verbania, Italy.
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4
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Bonforti A, Solé R. Unicellular-multicellular evolutionary branching driven by resource limitations. J R Soc Interface 2022; 19:20220018. [PMID: 35642429 DOI: 10.1098/rsif.2022.0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Multicellular life forms have evolved many times on our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for the emergence of multicellularity (MC). In this paper, we address the problem of how the first precondition for MC, namely 'stay together', might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell-cell adhesion among growing and dividing cells that exploit a localized resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localized portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients.
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Affiliation(s)
- Adriano Bonforti
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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5
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Inamine H, Miller A, Roxburgh S, Buckling A, Shea K. Pulse and press disturbances have different effects on transient community dynamics. Am Nat 2022; 200:571-583. [DOI: 10.1086/720618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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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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7
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Liao J, Barabás G, Bearup D. Competition-colonization dynamics and multimodality in diversity-disturbance relationships. Ecology 2022; 103:e3672. [PMID: 35233766 DOI: 10.1002/ecy.3672] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/08/2021] [Accepted: 12/01/2021] [Indexed: 11/11/2022]
Abstract
Disturbance has long been recognized as a critical driver of species diversity in community ecology. Recently, it has been found that the well-known intermediate disturbance hypothesis, which predicts a unimodal diversity-disturbance relationship (DDR), fails to describe numerous experimental observations, as empirical DDRs are diverse. Consequently, the precise form of the DDR remains a topic of debate. Here we develop a simple yet comprehensive metacommunity framework that can account for complex competition patterns. Using both numerical simulations and analytical arguments, we show that strongly multimodal DDRs arise naturally, and this multimodality is quite robust to changing parameters or relaxing the assumption of a strict competitive hierarchy. Having multimodality as a robust property of DDRs in competition models suggests that much of the noise observed in empirical DDRs could be a critical signature of the underlying competitive dynamics.
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Affiliation(s)
- Jinbao Liao
- Research Center for Theoretical Ecology, Jiangxi Normal University, Ziyang Road 99, Nanchang, China
| | - György Barabás
- Division of Theoretical Biology, Department IFM, Linköping University, Linköping, Sweden.,MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1A, Budapest, Hungary
| | - Daniel Bearup
- University of Kent, School of Mathematics, Statistics and Actuarial Sciences, Parkwood Road, Canterbury, UK
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8
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Freedy AM, Liau BB. Discovering new biology with drug-resistance alleles. Nat Chem Biol 2021; 17:1219-1229. [PMID: 34799733 PMCID: PMC9530778 DOI: 10.1038/s41589-021-00865-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/21/2021] [Indexed: 02/08/2023]
Abstract
Small molecule drugs form the backbone of modern medicine's therapeutic arsenal. Often less appreciated is the role that small molecules have had in advancing basic biology. In this Review, we highlight how resistance mutations have unlocked the potential of small molecule chemical probes to discover new biology. We describe key instances in which resistance mutations and related genetic variants yielded foundational biological insight and categorize these examples on the basis of their role in the discovery of novel molecular mechanisms, protein allostery, physiology and cell signaling. Next, we suggest ways in which emerging technologies can be leveraged to systematically introduce and characterize resistance mutations to catalyze basic biology research and drug discovery. By recognizing how resistance mutations have propelled biological discovery, we can better harness new technologies and maximize the potential of small molecules to advance our understanding of biology and improve human health.
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Affiliation(s)
- Allyson M. Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Brian B. Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Correspondence should be addressed to Brian B. Liau,
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9
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Dubé CE, Ziegler M, Mercière A, Boissin E, Planes S, Bourmaud CAF, Voolstra CR. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun 2021; 12:6402. [PMID: 34737272 PMCID: PMC8568919 DOI: 10.1038/s41467-021-26543-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.
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Affiliation(s)
- C. E. Dubé
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia ,grid.23856.3a0000 0004 1936 8390Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, G1V 0A6 Canada
| | - M. Ziegler
- grid.8664.c0000 0001 2165 8627Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, 35392 Giessen, Germany ,grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia
| | - A. Mercière
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - E. Boissin
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - S. Planes
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. A. -F. Bourmaud
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. R. Voolstra
- grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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10
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Roman J. The benefits of disturbance. Science 2021; 374:256-257. [PMID: 34648323 DOI: 10.1126/science.abm2257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Joe Roman
- Gund Institute for Environment, University of Vermont, Burlington, VT 05477, USA
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11
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Blumenfeld AJ, Eyer PA, Helms AM, Buczkowski G, Vargo EL. Consistent signatures of urban adaptation in a native, urban invader ant Tapinoma sessile. Mol Ecol 2021; 31:4832-4850. [PMID: 34551170 DOI: 10.1111/mec.16188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022]
Abstract
Biological invasions are becoming more prevalent due to the rise of global trade and expansion of urban areas. Ants are among the most prolific invaders with many exhibiting a multiqueen colony structure, dependent colony foundation and reduced internest aggression. Although these characteristics are generally associated with the invasions of exotic ants, they may also facilitate the spread of native ants into novel habitats. Native to diverse habitats across North America, the odorous house ant Tapinoma sessile has become abundant in urban environments throughout the United States. Natural colonies typically have a small workforce, inhabit a single nest, and are headed by a single queen, whereas urban colonies tend to be several orders of magnitude larger, inhabit multiple nests (i.e., polydomy) and are headed by multiple queens (i.e., polygyny). Here, we explore and compare the population genetic and breeding structure of T. sessile within and between urban and natural environments in several localities across its distribution range. We found the social structure of a colony to be a plastic trait in both habitats, although extreme polygyny was confined to urban habitats. Additionally, polydomous colonies were only present in urban habitats, suggesting T. sessile can only achieve supercoloniality within urbanized areas. Finally, we identified strong differentiation between urban and natural populations in each locality and continent-wide, indicating cities may restrict gene flow and exert intense selection pressure. Overall, our study highlights urbanization's influence in charting the evolutionary course for species.
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Affiliation(s)
| | - Pierre-André Eyer
- Department of Entomology, TAMU, Texas A&M University, College Station, Texas, USA
| | - Anjel M Helms
- Department of Entomology, TAMU, Texas A&M University, College Station, Texas, USA
| | | | - Edward L Vargo
- Department of Entomology, TAMU, Texas A&M University, College Station, Texas, USA
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12
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Phillips KN, Cooper TF. The cost of evolved constitutive lac gene expression is usually, but not always, maintained during evolution of generalist populations. Ecol Evol 2021; 11:12497-12507. [PMID: 34594515 PMCID: PMC8462147 DOI: 10.1002/ece3.7994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/13/2023] Open
Abstract
Beneficial mutations can become costly following an environmental change. Compensatory mutations can relieve these costs, while not affecting the selected function, so that the benefits are retained if the environment shifts back to be similar to the one in which the beneficial mutation was originally selected. Compensatory mutations have been extensively studied in the context of antibiotic resistance, responses to specific genetic perturbations, and in the determination of interacting gene network components. Few studies have focused on the role of compensatory mutations during more general adaptation, especially as the result of selection in fluctuating environments where adaptations to different environment components may often involve trade-offs. We examine whether costs of a mutation in lacI, which deregulated the expression of the lac operon in evolving populations of Escherichia coli bacteria, were compensated. This mutation occurred in multiple replicate populations selected in environments that fluctuated between growth on lactose, where the mutation was beneficial, and on glucose, where it was deleterious. We found that compensation for the cost of the lacI mutation was rare, but, when it did occur, it did not negatively affect the selected benefit. Compensation was not more likely to occur in a particular evolution environment. Compensation has the potential to remove pleiotropic costs of adaptation, but its rarity indicates that the circumstances to bring about the phenomenon may be peculiar to each individual or impeded by other selected mutations.
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Affiliation(s)
- Kelly N. Phillips
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
| | - Tim F. Cooper
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
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13
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Chu XL, Zhang QG, Buckling A, Castledine M. Interspecific Niche Competition Increases Morphological Diversity in Multi-Species Microbial Communities. Front Microbiol 2021; 12:699190. [PMID: 34394041 PMCID: PMC8362326 DOI: 10.3389/fmicb.2021.699190] [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: 04/23/2021] [Accepted: 07/02/2021] [Indexed: 12/03/2022] Open
Abstract
Intraspecific competition for limited niches has been recognized as a driving force for adaptive radiation, but results for the role of interspecific competition have been mixed. Here, we report the adaptive diversification of the model bacteria Pseudomonas fluorescens in the presence of different numbers and combinations of four competing bacterial species. Increasing the diversity of competitive community increased the morphological diversity of focal species, which is caused by impeding the domination of a single morphotype. Specifically, this pattern was driven by more diverse communities being more likely to contain key species that occupy the same niche as otherwise competitively superior morphotype, and thus preventing competitive exclusion within the focal species. Our results suggest that sympatric adaptive radiation is driven by the presence or absence of niche-specific competitors.
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Affiliation(s)
- Xiao-Lin Chu
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, United Kingdom.,State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China
| | - Angus Buckling
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Meaghan Castledine
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, United Kingdom
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14
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Zhou D, Zhang Q. Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation. Ecol Evol 2021; 11:9689-9696. [PMID: 34306654 PMCID: PMC8293784 DOI: 10.1002/ece3.7792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbor very low genetic diversity compared with their parental populations. The present study addresses how population size and within-population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment and then imposed a one-individual-size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity-diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a "holey" fitness landscape under the antibiotic stress.
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Affiliation(s)
- Dong‐Hao Zhou
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life SciencesBeijing Normal UniversityBeijingChina
| | - Quan‐Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life SciencesBeijing Normal UniversityBeijingChina
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15
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Chavhan Y, Malusare S, Dey S. Interplay of population size and environmental fluctuations: A new explanation for fitness cost rarity in asexuals. Ecol Lett 2021; 24:1943-1954. [PMID: 34145720 DOI: 10.1111/ele.13831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/19/2021] [Accepted: 05/22/2021] [Indexed: 11/29/2022]
Abstract
Theoretical models of ecological specialisation commonly assume that adaptation to one environment leads to fitness reductions (costs) in others. However, experiments often fail to detect such costs. We addressed this conundrum using experimental evolution with Escherichia coli in several constant and fluctuating environments at multiple population sizes. We found that in fluctuating environments, smaller populations paid significant costs, but larger ones avoided them altogether. Contrastingly, in constant environments, larger populations paid more costs than the smaller ones. Overall, large population sizes and fluctuating environments led to cost avoidance only when present together. Mutational frequency distributions obtained from whole-genome whole-population sequencing revealed that the primary mechanism of cost avoidance was the enrichment of multiple beneficial mutations within the same lineage. Since the conditions revealed by our study for avoiding costs are widespread, it provides a novel explanation of the conundrum of why the costs expected in theory are rarely detected in experiments.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sarthak Malusare
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
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16
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Weisse T, Lukić D, Lu X. Container volume may affect growth rates of ciliates and clearance rates of their microcrustacean predators in microcosm experiments. JOURNAL OF PLANKTON RESEARCH 2021; 43:288-299. [PMID: 33814976 PMCID: PMC8009685 DOI: 10.1093/plankt/fbab017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 12/22/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
We studied the effect of volume in small containers (microcosms) on five common planktonic freshwater ciliates and three zooplankton species, namely Daphnia sp., the calanoid copepod Eudiaptomus sp., and the cyclopoid copepod Cyclops sp. We measured ciliate specific growth rates and their loss rates due to microcrustacean predation in short-term experiments. We hypothesized that container volume ranging from 10 to 200 mL would not affect the activity of our prey and predator species. We found that the response to volume was species-specific; growth rates of three ciliate species were sensitive to volume. However, the volume effect was not unequivocal because different timing of the microcosm experiments (block effects) may have caused random bias due to varying morphological and/or physiological conditions of the ciliates and their predators. For predator clearance rate, the volume effect was insignificant in the filter-feeding Daphnia and Eudiaptomus but was significant for the predatory copepod Cyclops, which was hampered in the smallest experimental containers. Total crustacean clearance rates averaged over all treatments appeared unaffected by predator species, while ciliate species significantly affected the results. Our growth and clearance rates are close to previous findings with the same or similar planktonic prey and predator species.
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Affiliation(s)
| | - Dunja Lukić
- University of Innsbruck, Research Department for Limnology, Mondseestr. 9, A-5310 Mondsee, Austria
| | - Xiaoteng Lu
- University of Innsbruck, Research Department for Limnology, Mondseestr. 9, A-5310 Mondsee, Austria
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17
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van Houte S, Padfield D, Gómez P, Luján AM, Brockhurst MA, Paterson S, Buckling A. Compost spatial heterogeneity promotes evolutionary diversification of a bacterium. J Evol Biol 2020; 34:246-255. [PMID: 33111439 PMCID: PMC7984246 DOI: 10.1111/jeb.13722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/20/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
Spatial resource heterogeneity is expected to be a key driver for the evolution of diversity. However, direct empirical support for this prediction is limited to studies carried out in simplified laboratory environments. Here, we investigate how altering spatial heterogeneity of potting compost-by the addition of water and mixing-affects the evolutionary diversification of a bacterial species, Pseudomonas fluorescens, that is naturally found in the environment. There was a greater propensity of resource specialists to evolve in the unmanipulated compost, while more generalist phenotypes dominated the compost-water mix. Genomic data were consistent with these phenotypic findings. Competition experiments strongly suggest these results are due to diversifying selection as a result of resource heterogeneity, as opposed to other covariables. Overall, our findings corroborate theoretical and in vitro findings, but in semi-natural, more realistic conditions.
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Affiliation(s)
| | | | - Pedro Gómez
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
| | - Adela M Luján
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
| | | | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Angus Buckling
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
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18
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Wang C, Wang S, Jiao X, Yang B, Liang S, Luo Z, Mao L. Periodic density as an endpoint of customized plankton community responses to petroleum hydrocarbons: A level of toxic effect should be matched with a suitable time scale. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110723. [PMID: 32485490 DOI: 10.1016/j.ecoenv.2020.110723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/28/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
As an endpoint of community response to contaminants, average periodic density of populations (APDP) has been introduced to model species interactions in a community with 4 planktonic species. An ecological model for the community was developed by means of interspecific relationship including competition and predation to calculate the APDP. As a case study, we reported here the ecotoxicological effects of petroleum hydrocarbons (PHC) collected from Bohai oil field on densities of two algae, Platymonas subcordiformis and Isochrysis galbana, a rotifer, Brachionus plicatilis, and of a cladocera, Penilia avirostris, in single species and a microcosm experiment. Time scales expressing toxic effect increased with increasing levels of toxic effect from molecule to community. Remarkable periodic changes in densities were found during the tests in microcosm experiment, revealing a strong species reaction. The minimum time scale characterizing toxic effect at a community level should be the common cycle of population densities of the microcosm. In addition, the cycles of plankton densities shortened in general with increasing PHC, showing an evident toxic effect on the microcosm. Using APDP as the endpoint, a threshold concentration for the modeled microcosm was calculated to be 0.404 mg-PHC L-1. The APDP was found to be more sensitive and reliable than the standing crops of populations as the endpoint. This indicated that the APDP, an endpoint at the community level, could be quantitatively related to the endpoints at the population level, and led to the quantitative concentration-toxic effect relationship at the community level.
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Affiliation(s)
- Changyou Wang
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Siwen Wang
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xinming Jiao
- Jiangsu Environmental Monitoring Center, Nanjing, 210036, China
| | - Bin Yang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535011, China
| | - Shengkang Liang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Zhuhua Luo
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Longjiang Mao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
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19
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Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community. ISME JOURNAL 2020; 14:2877-2889. [PMID: 32884114 DOI: 10.1038/s41396-020-00755-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 08/05/2020] [Accepted: 08/21/2020] [Indexed: 11/09/2022]
Abstract
Rapid within-species evolution can alter community structure, yet the mechanisms underpinning this effect remain unknown. Populations that rapidly evolve large amounts of phenotypic diversity are likely to interact with more species and have the largest impact on community structure. However, the evolution of phenotypic diversity is, in turn, influenced by the presence of other species. Here, we investigate how microbial community structure changes as a consequence of rapidly evolved within-species diversity using Pseudomonas fluorescens as a focal species. Evolved P. fluorescens populations showed substantial phenotypic diversification in resource-use (and correlated genomic change) irrespective of whether they were pre-adapted in isolation or in a community context. Manipulating diversity revealed that more diverse P. fluorescens populations had the greatest impact on community structure, by suppressing some bacterial taxa, but facilitating others. These findings suggest that conditions that promote the evolution of high within-population diversity should result in a larger impact on community structure.
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20
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Jacquet C, Altermatt F. The ghost of disturbance past: long-term effects of pulse disturbances on community biomass and composition. Proc Biol Sci 2020; 287:20200678. [PMID: 32635861 DOI: 10.1098/rspb.2020.0678] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Current global change is associated with an increase in disturbance frequency and intensity, with the potential to trigger population collapses and to cause permanent transitions to new ecosystem states. However, our understanding of ecosystem responses to disturbances is still incomplete. Specifically, there is a mismatch between the diversity of disturbance regimes experienced by ecosystems and the one-dimensional description of disturbances used in most studies on ecological stability. To fill this gap, we conducted a full factorial experiment on microbial communities, where we varied the frequency and intensity of disturbances affecting species mortality, resulting in 20 different disturbance regimes. We explored the direct and long-term effects of these disturbance regimes on community biomass. While most communities were able to recover biomass and composition states similar to undisturbed controls after a halt of the disturbances, we identified some disturbance thresholds that had long-lasting legacies on communities. Using a model based on logistic growth, we identified qualitatively the sets of disturbance frequency and intensity that had equivalent long-term negative impacts on experimental communities. Our results show that an increase in disturbance intensity is a bigger threat for biodiversity and biomass recovery than the occurrence of more frequent but less intense disturbances.
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Affiliation(s)
- Claire Jacquet
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Florian Altermatt
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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21
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Gloria‐Soria A, Mendiola SY, Morley VJ, Alto BW, Turner PE. Prior evolution in stochastic versus constant temperatures affects RNA virus evolvability at a thermal extreme. Ecol Evol 2020; 10:5440-5450. [PMID: 32607165 PMCID: PMC7319105 DOI: 10.1002/ece3.6287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
It is unclear how historical adaptation versus maladaptation in a prior environment affects population evolvability in a novel habitat. Prior work showed that vesicular stomatitis virus (VSV) populations evolved at constant 37°C improved in cellular infection at both 29°C and 37°C; in contrast, those evolved under random changing temperatures between 29°C and 37°C failed to improve. Here, we tested whether prior evolution affected the rate of adaptation at the thermal-niche edge: 40°C. After 40 virus generations in the new environment, we observed that populations historically evolved at random temperatures showed greater adaptability. Deep sequencing revealed that most of the newly evolved mutations were de novo. Also, two novel evolved mutations in the VSV glycoprotein and replicase genes tended to co-occur in the populations previously evolved at constant 37°C, whereas this parallelism was not seen in populations with prior random temperature evolution. These results suggest that prior adaptation under constant versus random temperatures constrained the mutation landscape that could improve fitness in the novel 40°C environment, perhaps owing to differing epistatic effects of new mutations entering genetic architectures that earlier diverged. We concluded that RNA viruses maladapted to their previous environment could "leapfrog" over counterparts of higher fitness, to achieve faster adaptability in a novel environment.
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Affiliation(s)
- Andrea Gloria‐Soria
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Present address:
Department of Environmental Sciences, Center for Vector Biology and Zoonotic DiseasesThe Connecticut Agricultural Experiment StationNew HavenCTUSA
| | - Sandra Y. Mendiola
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Present address:
Department of BiologyEmory UniversityAtlantaGA30322USA
| | - Valerie J. Morley
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Present address:
Department of BiologyPennsylvania State UniversityUniversity ParkPA16802USA
| | - Barry W. Alto
- Florida Medical Entomology LaboratoryUniversity of FloridaVero BeachFLUSA
| | - Paul E. Turner
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Program in MicrobiologyYale School of MedicineNew HavenCTUSA
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22
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Haber LT, Fahey RT, Wales SB, Correa Pascuas N, Currie WS, Hardiman BS, Gough CM. Forest structure, diversity, and primary production in relation to disturbance severity. Ecol Evol 2020; 10:4419-4430. [PMID: 32489607 PMCID: PMC7246213 DOI: 10.1002/ece3.6209] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 11/12/2022] Open
Abstract
Differential disturbance severity effects on forest vegetation structure, species diversity, and net primary production (NPP) have been long theorized and observed. Here, we examined these factors concurrently to explore the potential for a mechanistic pathway linking disturbance severity, changes in light environment, leaf functional response, and wood NPP in a temperate hardwood forest.Using a suite of measurements spanning an experimental gradient of tree mortality, we evaluated the direction and magnitude of change in vegetation structural and diversity indexes in relation to wood NPP. Informed by prior observations, we hypothesized that forest structural and species diversity changes and wood NPP would exhibit either a linear, unimodal, or threshold response in relation to disturbance severity. We expected increasing disturbance severity would progressively shift subcanopy light availability and leaf traits, thereby coupling structural and species diversity changes with primary production.Linear or unimodal changes in three of four vegetation structural indexes were observed across the gradient in disturbance severity. However, disturbance-related changes in vegetation structure were not consistently correlated with shifts in light environment, leaf traits, and wood NPP. Species diversity indexes did not change in response to rising disturbance severity.We conclude that, in our study system, the sensitivity of wood NPP to rising disturbance severity is generally tied to changing vegetation structure but not species diversity. Changes in vegetation structure are inconsistently coupled with light environment and leaf traits, resulting in mixed support for our hypothesized cascade linking disturbance severity to wood NPP.
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Affiliation(s)
- Lisa T. Haber
- Department of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Robert T. Fahey
- Department of Natural Resources and the Environment & Center for Environmental Sciences and EngineeringUniversity of ConnecticutStorrsCTUSA
| | - Shea B. Wales
- Department of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | | | - William S. Currie
- School for Environment and SustainabilityUniversity of MichiganAnn ArborMIUSA
| | - Brady S. Hardiman
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
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23
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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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24
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Eckert EM, Quero GM, Di Cesare A, Manfredini G, Mapelli F, Borin S, Fontaneto D, Luna GM, Corno G. Antibiotic disturbance affects aquatic microbial community composition and food web interactions but not community resilience. Mol Ecol 2019; 28:1170-1182. [PMID: 30697889 DOI: 10.1111/mec.15033] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/13/2018] [Accepted: 01/14/2019] [Indexed: 01/17/2023]
Abstract
Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with potential risks to human health. We therefore tested resilience of microbial communities challenged by the presence of an antibiotic. In a continuous culture experiment, we compared the abundance, composition and diversity of microbial communities undisturbed or disturbed by the constant addiction of tetracycline in low (10 µg/L) or intermediate (100 µg/L) concentration (press disturbance). Further, the bacterial communities in the three treatments had to face the sudden pulse disturbance of adding an allochthonous bacterium (Escherichia coli). Tetracycline, even at low concentrations, affected microbial communities by changing their phylogenetic composition and causing cell aggregation. This, however, did not coincide with a reduced microbial diversity, but was mainly caused by a shift in dominance of specific bacterial families. Moreover, the less disturbed community (10 µg/L tetracycline) was sometimes more similar to the control and sometimes more similar to heavily disturbed community (100 µg/L tetracycline). All in all, we could not see a pattern where the communities disturbed with antibiotics were less resilient to a second disturbance introducing E. coli, but they seemed to be able to buffer the input of the allochthonous strain in a similar manner as the control.
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Affiliation(s)
- Ester M Eckert
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Grazia M Quero
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn (SZN), Napoli, Italy
| | - Andrea Di Cesare
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy.,Department of Environmental and Life Sciences (DISTAV), University of Genoa, Genova, Italy
| | - Giuliana Manfredini
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano, Italy
| | - Diego Fontaneto
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Gian Marco Luna
- National Research Council, Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Ancona, Italy
| | - Gianluca Corno
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
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25
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Hester ER, Jetten MSM, Welte CU, Lücker S. Metabolic Overlap in Environmentally Diverse Microbial Communities. Front Genet 2019; 10:989. [PMID: 31681424 PMCID: PMC6811665 DOI: 10.3389/fgene.2019.00989] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022] Open
Abstract
The majority of microbial communities consist of hundreds to thousands of species, creating a massive network of organisms competing for available resources within an ecosystem. In natural microbial communities, it appears that many microbial species have highly redundant metabolisms and seemingly are capable of utilizing the same substrates. This is paradoxical, as theory indicates that species requiring a common resource should outcompete one another. To better understand why microbial species can coexist, we developed metabolic overlap (MO) as a new metric to survey the functional redundancy of microbial communities at the genome scale across a wide variety of ecosystems. Using metagenome-assembled genomes, we surveyed nearly 1,000 studies across nine ecosystem types. We found the highest MO in extreme (i.e., low pH/high temperature) and aquatic environments, while the lowest MO was observed in communities associated with animal hosts, the built/engineered environment, and soil. In addition, different metabolism subcategories were explored for their degree of MO. For instance, overlap in nitrogen metabolism was among the lowest in animal and engineered ecosystems, while species from the built environment had the highest overlap. Together, we present a metric that utilizes whole genome information to explore overlapping niches of microbes. This provides a detailed picture of potential metabolic competition and cooperation between species present in an ecosystem, indicates the main substrate types sustaining the community, and serves as a valuable tool to generate hypotheses for future research.
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Affiliation(s)
- Eric R Hester
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
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26
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Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site. Sci Rep 2019; 9:14138. [PMID: 31578444 PMCID: PMC6775442 DOI: 10.1038/s41598-019-50740-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022] Open
Abstract
The microbial colonization of plastic wastes has been extensively studied in marine environments, while studies on aged terrestrial wastes are scarce, and mostly limited to the isolation of plastic-degrading microorganisms. Here we have applied a multidisciplinary approach involving culturomics, next-generation sequencing analyses and fine-scale physico-chemical measurements to characterize plastic wastes retrieved in landfill abandoned for more than 35 years, and to assess the composition of bacterial communities thriving as biofilms on the films’ surfaces. All samples were characterized by different colors but were all of polyethylene; IR and DSC analyses identified different level of degradation, while FT-Raman spectroscopy and X-ray fluorescence further assessed the degradation level and the presence of pigments. Each plastic type harbored distinct bacterial communities from the others, in agreement with the differences highlighted by the physico-chemical analyses. Furthermore, the most degraded polyethylene films were found to host a bacterial community more similar to the surrounding soil as revealed by both α- and β-diversity NGS analyses. This work confirms the novel hypothesis that different polyethylene terrestrial waste samples select for different bacterial communities, and that structure of these communities can be correlated with physico-chemical properties of the plastics, including the degradation degree.
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27
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Rillig MC, de Souza Machado AA, Lehmann A, Klümper U. Evolutionary implications of microplastics for soil biota. ENVIRONMENTAL CHEMISTRY (COLLINGWOOD, VIC.) 2019; 16:3-7. [PMID: 31231167 PMCID: PMC6588528 DOI: 10.1071/en18118] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Microplastic pollution is increasingly considered to be a factor of global change: in addition to aquatic ecosystems, this persistent contaminant is also found in terrestrial systems and soils. Microplastics have been chiefly examined in soils in terms of the presence and potential effects on soil biota. Given the persistence and widespread distribution of microplastics, it is also important to consider potential evolutionary implications of the presence of microplastics in soil; we offer such a perspective for soil microbiota. We discuss the range of selection pressures likely to act upon soil microbes, highlight approaches for the study of evolutionary responses to microplastics, and present the obstacles to be overcome. Pondering the evolutionary consequences of microplastics in soils can yield new insights into the effects of this group of pollutants, including establishing 'true' baselines in soil ecology, and understanding future responses of soil microbial populations and communities.
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Affiliation(s)
- Matthias C. Rillig
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
- Corresponding author.
| | - Anderson Abel de Souza Machado
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Anika Lehmann
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Uli Klümper
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, United Kingdom
- European Centre for Environment and Human Health, University of Exeter, Truro, TR1 3HD, United Kingdom
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28
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Pisa H, Hermisson J, Polechová J. The influence of fluctuating population densities on evolutionary dynamics. Evolution 2019; 73:1341-1355. [PMID: 31148149 PMCID: PMC6771508 DOI: 10.1111/evo.13756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/20/2019] [Indexed: 11/26/2022]
Abstract
The causes and consequences of fluctuating population densities are an important topic in ecological literature. Yet, the effects of such fluctuations on maintenance of variation in spatially structured populations have received little analytic treatment. We analyze what happens when two habitats coupled by migration not only differ in their trade‐offs in selection but also in their demographic stability—and show that equilibrium allele frequencies can change significantly due to ecological feedback arising from locally fluctuating population sizes. When an ecological niche exhibits such fluctuations, these drive an asymmetry in the relative impact of gene flow, and therefore, the equilibrium frequency of the locally adapted type decreases. Our results extend the classic conditions on maintenance of diversity under selection and migration by including the effect of fluctuating population densities. We find simple analytic conditions in terms of the strength of selection, immigration, and the extent of fluctuations between generations in a continent‐island model. Although weak fluctuations hardly affect coexistence, strong recurrent fluctuations lead to extinction of the type better adapted to the fluctuating niche—even if the invader is locally maladapted. There is a disadvantage to specialization to an unstable habitat, as it makes the population vulnerable to swamping from more stable habitats.
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Affiliation(s)
- Hanja Pisa
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria
| | - Joachim Hermisson
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria
| | - Jitka Polechová
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria
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29
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Mortality causes universal changes in microbial community composition. Nat Commun 2019; 10:2120. [PMID: 31073166 PMCID: PMC6509412 DOI: 10.1038/s41467-019-09925-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/20/2019] [Indexed: 12/20/2022] Open
Abstract
All organisms are sensitive to the abiotic environment, and a deteriorating environment can cause extinction. However, survival in a multispecies community depends upon interactions, and some species may even be favored by a harsh environment that impairs others, leading to potentially surprising community transitions as environments deteriorate. Here we combine theory and laboratory microcosms to predict how simple microbial communities will change under added mortality, controlled by varying dilution. We find that in a two-species coculture, increasing mortality favors the faster grower, confirming a theoretical prediction. Furthermore, if the slower grower dominates under low mortality, the outcome can reverse as mortality increases. We find that this tradeoff between growth and competitive ability is prevalent at low dilution, causing outcomes to shift dramatically as dilution increases, and that these two-species shifts propagate to simple multispecies communities. Our results argue that a bottom-up approach can provide insight into how communities change under stress. Environmental stress can affect the outcome of ecological competition. Here, the authors use theory and experiments with a synthetic microbial community to show that a tradeoff between growth rate and competitive ability determines which species prevails when the population faces variable mortality rates.
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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: 15] [Impact Index Per Article: 3.0] [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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Palasio RGS, Xavier IG, Chiaravalotti-Neto F, Tuan R. Diversity of Biomphalaria spp. freshwater snails and associated mollusks in areas with schistosomiasis risk, using molecular and spatial analysis tools. BIOTA NEOTROPICA 2019. [DOI: 10.1590/1676-0611-bn-2019-0746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Abstract: The Middle Paranapanema River region of São Paulo, Brazil is home to significant diversity of Biomphalaria species and is very vulnerable to health and environmental impacts such as schistosomiasis. This study updates freshwater malacological surveys for ecosystems in one portion of the Middle Paranapanema River Basin, with emphasis on the genus Biomphalaria. Snails were collected from 114 distinct bodies of water between 2015 and 2018. Biomphalaria specimens were identified according to morphological and molecular characteristics, while animals in other genera (Drepanotrema, Lymnaea, Melanoides, Physa and Pomacea) were identified solely according to shell characteristics. A geographic information system was used to update intermediate host colonization sites and consequently assist in identifying probable hotspots for intermediate hosts of schistosomiasis. The sequences of the COI gene relating to the DNA barcode stretch were tested for similarity against sequences found in GenBank, for monophyly through Maximum Likelihood phylogenetic inference, and analyzed in ABDG, bPTP and GMYC for the delimitation of putative species. Of the 10,722 snails collected, 86.7% were in the Planorbidae family (75.5% Biomphalaria and 11.2% Drepanotrema) and 13.3% were other non-Planorbidae species (Lymnaea, Melanoides, Physa and Pomacea). The taxonomic COI reference sequences in the NCBI nucleotide database used for DNA sequence comparison, and phylogenetic analysis used to test the monophyly of the groups, resulted in more reliable taxonomic units than delimitation of the COI sequences in MOTUs using statistical taxonomic models. Analysis of the species distribution shows that B. glabrata and B. tenagophila are heterogeneously distributed in the study area. B. glabrata colonizes only five water bodies, in the study area, most of them in Ourinhos, while B. tenagophila predominates in water bodies in Ipaussu. Contrasting with this, B. straminea, B. occidentalis and B. peregrina are evenly distributed throughout the study area.
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Affiliation(s)
| | | | | | - Roseli Tuan
- Superintendência de Controle de Endemias, Brasil
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Liu Z, Cichocki N, Hübschmann T, Süring C, Ofiţeru ID, Sloan WT, Grimm V, Müller S. Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis. Environ Microbiol 2018; 21:164-181. [PMID: 30289191 PMCID: PMC7379589 DOI: 10.1111/1462-2920.14437] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/03/2018] [Accepted: 09/30/2018] [Indexed: 12/22/2022]
Abstract
In completely insular microbial communities, evolution of community structure cannot be shaped by the immigration of new members. In addition, when those communities are run in steady state, the influence of environmental factors on their assembly is reduced. Therefore, one would expect similar community structures under steady‐state conditions. Yet, in parallel setups, variability does occur. To reveal ecological mechanisms behind this phenomenon, five parallel reactors were studied at the single‐cell level for about 100 generations and community structure variations were quantified by ecological measures. Whether community variability can be controlled was tested by implementing soft temperature stressors as potential synchronizers. The low slope of the lognormal rank‐order abundance curves indicated a predominance of neutral mechanisms, i.e., where species identity plays no role. Variations in abundance ranks of subcommunities and increase in inter‐community pairwise β‐diversity over time support this. Niche differentiation was also observed, as indicated by steeper geometric‐like rank‐order abundance curves and increased numbers of correlations between abiotic and biotic parameters during initial adaptation and after disturbances. Still, neutral forces dominated community assembly. Our findings suggest that complex microbial communities in insular steady‐state environments can be difficult to synchronize and maintained in their original or desired structure, as they are non‐equilibrium systems.
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Affiliation(s)
- Zishu Liu
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Nicolas Cichocki
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Christine Süring
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Irina Dana Ofiţeru
- School of Engineering, Environmental Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - William T Sloan
- Department of Civil Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Volker Grimm
- Helmholtz Centre for Environmental Research-UFZ, Department of Ecological Modeling, Permoserstraße 15, 04318, Leipzig, Germany
| | - Susann Müller
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
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Zhang QG, Lu HS, Buckling A. Temperature drives diversification in a model adaptive radiation. Proc Biol Sci 2018; 285:rspb.2018.1515. [PMID: 30185639 DOI: 10.1098/rspb.2018.1515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/15/2018] [Indexed: 01/10/2023] Open
Abstract
The warmer regions harbour more species, attributable to accelerated speciation and increased ecological opportunities for coexistence. While correlations between temperature and energy availability and habitat area have been suggested as major drivers of these biodiversity patterns, temperature can theoretically also have direct effects on the evolution of diversity. Here, we experimentally studied the evolution of diversity in a model adaptive radiation of the bacterium Pseudomonas fluorescens across a temperature gradient. Diversification increased at higher temperatures, driven by both faster generation of genetic variation and stronger diversifying selection. Specifically, low temperatures could limit the generation of diversity, suggested by the observation that supply of genetic variation through immigration increased diversity at low, but not high temperatures. The two major determinants of mutation supply, population size and mutation rate, both showed a positive temperature dependence. Stronger diversifying selection in warmer environments was suggested by promoted coexistence, and further explicitly inferred by the ability of evolved phenotypes to invade the ancestral type from rare. We discuss possible physiological and environmental mechanisms underlying the findings, most of which are likely to be general.
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Affiliation(s)
- Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Han-Shu Lu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Angus Buckling
- ESI and CEC, Biosciences, University of Exeter, Penryn, Cornwall TR10 9EZ, UK
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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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Koza A, Kusmierska A, McLaughlin K, Moshynets O, Spiers AJ. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation. FEMS Microbiol Lett 2018; 364:3850210. [PMID: 28535292 DOI: 10.1093/femsle/fnx109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function.
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Affiliation(s)
- Anna Koza
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kusmierska
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Kimberley McLaughlin
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kiev 03143, Ukraine
| | - Andrew J Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
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36
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Edrada-Ebel R, Ævarsson A, Polymenakou P, Hentschel U, Carettoni D, Day J, Green D, Hreggviðsson GÓ, Harvey L, McNeil B. SeaBioTech: From Seabed to Test-Bed: Harvesting the Potential of Marine Biodiversity for Industrial Biotechnology. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites. mSystems 2017; 2:mSystems00129-17. [PMID: 29152587 PMCID: PMC5686522 DOI: 10.1128/msystems.00129-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/24/2017] [Indexed: 11/25/2022] Open
Abstract
Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion a range of research to investigate how the diversity of a microbiome and interactions among its members impact its function, where function can be measured as exometabolites. The system allows for community exometabolite profiling to be coupled with genome mining, transcript analysis, and measurements of member productivity and population size. It can also facilitate discovery of natural products that are only produced within microbial consortia. Thus, this synthetic community system has utility to address fundamental questions about a diversity of possible microbial interactions that occur in both natural and engineered ecosystems. Though most microorganisms live within a community, we have modest knowledge about microbial interactions and their implications for community properties and ecosystem functions. To advance understanding of microbial interactions, we describe a straightforward synthetic community system that can be used to interrogate exometabolite interactions among microorganisms. The filter plate system (also known as the Transwell system) physically separates microbial populations, but allows for chemical interactions via a shared medium reservoir. Exometabolites, including small molecules, extracellular enzymes, and antibiotics, are assayed from the reservoir using sensitive mass spectrometry. Community member outcomes, such as growth, productivity, and gene regulation, can be determined using flow cytometry, biomass measurements, and transcript analyses, respectively. The synthetic community design allows for determination of the consequences of microbiome diversity for emergent community properties and for functional changes over time or after perturbation. Because it is versatile, scalable, and accessible, this synthetic community system has the potential to practically advance knowledge of microbial interactions that occur within both natural and artificial communities. IMPORTANCE Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion a range of research to investigate how the diversity of a microbiome and interactions among its members impact its function, where function can be measured as exometabolites. The system allows for community exometabolite profiling to be coupled with genome mining, transcript analysis, and measurements of member productivity and population size. It can also facilitate discovery of natural products that are only produced within microbial consortia. Thus, this synthetic community system has utility to address fundamental questions about a diversity of possible microbial interactions that occur in both natural and engineered ecosystems. Author Video: An author video summary of this article is available.
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Dutilleul M, Réale D, Goussen B, Lecomte C, Galas S, Bonzom J. Adaptation costs to constant and alternating polluted environments. Evol Appl 2017; 10:839-851. [PMID: 29151875 PMCID: PMC5680423 DOI: 10.1111/eva.12510] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 06/19/2017] [Indexed: 11/28/2022] Open
Abstract
Some populations quickly adapt to strong and novel selection pressures caused by anthropogenic stressors. However, this short-term evolutionary response to novel and harsh environmental conditions may lead to adaptation costs, and evaluating these costs is important if we want to understand the evolution of resistance to anthropogenic stressors. In this experimental evolution study, we exposed Caenorhabditis elegans populations to uranium (U populations), salt (NaCl populations) and alternating uranium/salt treatments (U/NaCl populations) and to a control environment (C populations), over 22 generations. In parallel, we ran common-garden and reciprocal-transplant experiments to assess the adaptive costs for populations that have evolved in the different environmental conditions. Our results showed rapid evolutionary changes in life history characteristics of populations exposed to the different pollution regimes. Furthermore, adaptive costs depended on the type of pollutant: pollution-adapted populations had lower fitness than C populations, when the populations were returned to their original environment. Fitness in uranium environments was lower for NaCl populations than for U populations. In contrast, fitness in salt environments was similar between U and NaCl populations. Moreover, fitness of U/NaCl populations showed similar or higher fitness in both the uranium and the salt environments compared to populations adapted to constant uranium or salt environments. Our results show that adaptive evolution to a particular stressor can lead to either adaptive costs or benefits once in contact with another stressor. Furthermore, we did not find any evidence that adaptation to alternating stressors was associated with additional adaption costs. This study highlights the need to incorporate adaptive cost assessments when undertaking ecological risk assessments of pollutants.
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Affiliation(s)
- Morgan Dutilleul
- Laboratoire d’écotoxicologie des radionucléidesInstitut de Radioprotection et de Sûreté Nucléaire, CadaracheSaint‐Paul‐lez‐Durance CedexFrance
- Département des Sciences BiologiquesUniversité du Québec À MontréalMontréalQCCanada
- Faculté de pharmacieLaboratoire de ToxicologieUniversité de Montpellier 1Montpellier Cedex 5France
- Present address:
Environment DepartmentUniversity of YorkHeslingtonYorkUK
| | - Denis Réale
- Département des Sciences BiologiquesUniversité du Québec À MontréalMontréalQCCanada
| | - Benoit Goussen
- Laboratoire d’écotoxicologie des radionucléidesInstitut de Radioprotection et de Sûreté Nucléaire, CadaracheSaint‐Paul‐lez‐Durance CedexFrance
- Unit “Models for ecotoxicology and toxicology” (METO) INERIS Parc ALATAVerneuil‐en‐HalatteFrance
- Present address:
Environment DepartmentUniversity of YorkHeslingtonYorkUK
- Present address:
Safety and Environmental Assurance CentreUnileverSharnbrookBedfordshireUK
| | - Catherine Lecomte
- Laboratoire d’écotoxicologie des radionucléidesInstitut de Radioprotection et de Sûreté Nucléaire, CadaracheSaint‐Paul‐lez‐Durance CedexFrance
| | - Simon Galas
- Faculté de pharmacieLaboratoire de ToxicologieUniversité de Montpellier 1Montpellier Cedex 5France
| | - Jean‐Marc Bonzom
- Laboratoire d’écotoxicologie des radionucléidesInstitut de Radioprotection et de Sûreté Nucléaire, CadaracheSaint‐Paul‐lez‐Durance CedexFrance
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Abstract
Uropathogenic Escherichia coli (UPEC) are opportunistic human pathogens that primarily circulate as part of commensal intestinal microbiota. Though they have the ability to survive and proliferate in various urinary tract compartments, the urinary tract is a transient, occasional habitat for UPEC. Because of this, most of the UPEC traits have originally evolved to serve in intestinal colonization and transmission. Some of these bacterial traits serve as virulence factors - they are critical to or assist in survival of UPEC as pathogens, and the structure and/or function may be specialized for the infection. Other traits could serve as anti-virulence factors - they represent liability in the urinary tract and are under selection to be lost or inactivated during the infection. Inactivation, variation, or other changes of the bacterial genes that increase the pathogen's fitness during the infection are called pathoadaptive mutations. This chapter describes examples of pathoadaptive mutations in UPEC and provides rationale for their further in-depth study.
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Cho H, Kim M, Tripathi B, Adams J. Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency. MICROBIAL ECOLOGY 2017; 74:62-77. [PMID: 28062901 DOI: 10.1007/s00248-016-0919-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/12/2016] [Indexed: 06/06/2023]
Abstract
Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been little studied experimentally. We subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. We analyzed the fungal community structure using Illumina HiSeq sequencing of the ITS1 region. Fungal diversity was found to decline with the increasing disturbance frequencies, with no sign of the "humpback" pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance-which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.
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Affiliation(s)
- Hyunjun Cho
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 151-742, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute (KOPRI), Incheon, 460-840, Republic of Korea
| | - Binu Tripathi
- Korea Polar Research Institute (KOPRI), Incheon, 460-840, Republic of Korea
| | - Jonathan Adams
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 151-742, South Korea.
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Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach. Sci Rep 2017; 7:2260. [PMID: 28536449 PMCID: PMC5442152 DOI: 10.1038/s41598-017-02262-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/10/2017] [Indexed: 12/19/2022] Open
Abstract
There has been little study of effects of disturbance on soil biota combining closely controlled experimental conditions and DNA-based methods. We sampled pots of soil at varying times following an initial simulated mass mortality event. Soil DNA was extracted at intervals up to 24 weeks after the event, and shotgun metagenomes sequenced using NextSeq. Compared to initial conditions, we found: consistent, sequential changes in functional metagenome and community structure over time, indicating successional niche differentiation amongst soil biota. As predicted, early successional systems had greater abundance of genes associated with motility, but fewer genes relating to DNA/RNA/protein metabolism, cell division and cell cycle. Contrary to predictions, there were no significant differences in cell signaling, virulence and defense-related genes. Also, stress related genes were less abundant in later succession. The early successional system had lower taxonomic diversity but higher functional gene diversity. Over time, community characteristics changed progressively, but by the end of the experiment had not returned to the ‘original’ state of the system before disturbance. Results indicated a predictable sequence of gene functions and taxa following disturbance, analogous to ecosystem succession for large organisms. It is unclear if and when the system would return to its pre-disturbance state.
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Martínez-García R, Tarnita CE. Seasonality can induce coexistence of multiple bet-hedging strategies in Dictyostelium discoideum via storage effect. J Theor Biol 2017; 426:104-116. [PMID: 28536035 DOI: 10.1016/j.jtbi.2017.05.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 02/06/2023]
Abstract
The social amoeba Dictyostelium discoideum has been recently suggested as an example of bet-hedging in microbes. In the presence of resources, amoebae reproduce as unicellular organisms. Resource depletion, however, leads to a starvation phase in which the population splits between aggregators, which form a fruiting body made of a stalk and resistant spores, and non-aggregators, which remain as vegetative cells. Spores are favored when starvation periods are long, but vegetative cells can exploit resources in environments where food replenishes quickly. The investment in aggregators versus non-aggregators can therefore be understood as a bet-hedging strategy that evolves in response to stochastic starvation times. A genotype (or strategy) is defined by the balance between each type of cells. In this framework, if the ecological conditions on a patch are defined in terms of the mean starvation time (i.e. time between the onset of starvation and the arrival of a new food pulse), a single genotype dominates each environment, which is inconsistent with the huge genetic diversity observed in nature. Here we investigate whether seasonality, represented by a periodic, wet-dry alternation in the mean starvation times, allows the coexistence of several strategies in a single patch. We study this question in a non-spatial (well-mixed) setting in which different strains compete for a common pool of resources over a sequence of growth-starvation cycles. We find that seasonality induces a temporal storage effect that can promote the stable coexistence of multiple genotypes. Two conditions need to be met in our model. First, there has to be a temporal niche partitioning (two well-differentiated habitats within the year), which requires not only different mean starvation times between seasons but also low variance within each season. Second, each season's well-adapted strain has to grow and create a large enough population that permits its survival during the subsequent unfavorable season, which requires the number of growth-starvation cycles within each season to be sufficiently large. These conditions allow the coexistence of two bet-hedging strategies. Additional tradeoffs among life-history traits can expand the range of coexistence and increase the number of coexisting strategies, contributing toward explaining the genetic diversity observed in D. discoideum. Although focused on this cellular slime mold, our results are general and may be easily extended to other microbes.
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Affiliation(s)
- Ricardo Martínez-García
- Department of Ecology and Evolutionary Biology, Princeton University. Princeton NJ 08544, USA
| | - Corina E Tarnita
- Department of Ecology and Evolutionary Biology, Princeton University. Princeton NJ 08544, USA.
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Zhao D, Xu H, Zeng J, Cao X, Huang R, Shen F, Yu Z. Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake. FEMS Microbiol Ecol 2017; 93:3814240. [DOI: 10.1093/femsec/fix062] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/09/2017] [Indexed: 11/12/2022] Open
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Catania V, Sarà G, Settanni L, Quatrini P. Bacterial communities in sediment of a Mediterranean marine protected area. Can J Microbiol 2017; 63:303-311. [DOI: 10.1139/cjm-2016-0406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) “Capo Gallo–Isola delle Femmine” was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.
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Affiliation(s)
- Valentina Catania
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
| | - Gianluca Sarà
- Dipartimento di Scienze della Terra e del Mare (DISTEM), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
| | - Luca Settanni
- Dipartimento di Scienze Agrarie e Forestali (SAF), Università degli Studi di Palermo, Viale delle Scienze Ed.4 - 90128 Palermo, Italia
| | - Paola Quatrini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
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Bono LM, Smith LB, Pfennig DW, Burch CL. The emergence of performance trade‐offs during local adaptation: insights from experimental evolution. Mol Ecol 2017; 26:1720-1733. [DOI: 10.1111/mec.13979] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Lisa M. Bono
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Leno B. Smith
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - David W. Pfennig
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Christina L. Burch
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
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Ling H, Zhang P, Guo B, Xu H, Ye M, Deng X. Negative feedback adjustment challenges reconstruction study from tree rings: A study case of response of Populus euphratica to river discontinuous flow and ecological water conveyance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 574:109-119. [PMID: 27639018 DOI: 10.1016/j.scitotenv.2016.09.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
Drought stress changes the relationship between the growth of tree rings and variations in ambient temperature. However, it is not clear how the growth of trees changes in response to drought of varying intensities, especially in arid areas. Therefore, Tree rings were studied for 6years in Populus euphratica to assess the impacts of abrupt changes in environment on tree rings using the theories and methods in dendrohydrology, ecology and phytophysiology. The width of tree rings increased by 8.7% after ecological water conveyance downstream of Tarim River compared to that when the river water had been cut off. However, during intermediate drought, as the depth of the groundwater increases, the downward trend in the tree rings was reversed because of changes in the physiology of the tree. Therefore, the growth of tree rings shows a negative feedback to intermediate drought stress, an observation that challenges the homogenization theory of tree ring reconstruction based on the traditional methods. Owing to the time lag, the cumulative effect and the negative feedback between the growth of tree rings and drought stress, the reconstruction of past environment by studying the patterns of tree rings is often inaccurate. Our research sets out to verify the hypothesis that intermediate drought stress results in a negative feedback adjustment and thus to answers two scientific questions: (1) How does the negative feedback adjustment promote the growth of tree rings as a result of intermediate drought stress? (2) How does the negative feedback adjustment lower the accuracy with which the past is reconstructed based on tree rings? This research not only enriches the connotations of intermediate disturbance hypothesis and reconstruction theory of tree rings, but also provides a scientific basis for the conservation of desert riparian forests worldwide.
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Affiliation(s)
- Hongbo Ling
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi 830011, China
| | - Pei Zhang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Department of Water Resources, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Bin Guo
- College of Geomatics, Shandong University of Science and Technology, Qingdao 266590, China
| | - Hailiang Xu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi 830011, China.
| | - Mao Ye
- School of Geography Science and Tourism, Xinjiang Normal University, Urumqi 830054, China
| | - Xiaoya Deng
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Department of Water Resources, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
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Abstract
Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems. The diversity of microbial communities is linked to the functioning and stability of ecosystems. As humanity continues to impact ecosystems worldwide, and as diet and disease perturb our own commensal microbial communities, the ability to predict how microbial diversity will respond to disturbance is of critical importance. Using microbial microcosm experiments, we find that community diversity responds to different disturbance regimes in a reproducible and predictable way. Maximum diversity occurs when two communities, each suited to different environmental conditions, are mixed due to disturbance. This maximum diversity is transient except under specific regimes. Using a simple mathematical model, we show that transient unimodality is likely a common feature of microbial diversity-disturbance relationships in fluctuating environments.
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Bell T, Tylianakis JM. Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems. Proc Biol Sci 2016; 283:20160896. [PMID: 27928044 PMCID: PMC5204138 DOI: 10.1098/rspb.2016.0896] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022] Open
Abstract
Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. We review what is known about spatial flows of microbes and their response to land-use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesize that intensified agriculture selects for certain taxa and genes, which then 'spill over' into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields. Consequently, the spatial configuration and management intensity of different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which can impact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer. Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impacting the consistent provisioning of ecosystem services. While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes should be taken into consideration to ensure that ecosystem functioning and services are maintained in agri-ecosystem mosaics.
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Affiliation(s)
- Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Jason M Tylianakis
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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50
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Smith CR, Blair PL, Boyd C, Cody B, Hazel A, Hedrick A, Kathuria H, Khurana P, Kramer B, Muterspaw K, Peck C, Sells E, Skinner J, Tegeler C, Wolfe Z. Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem. Ecol Evol 2016; 6:8075-8084. [PMID: 27878079 PMCID: PMC5108259 DOI: 10.1002/ece3.2553] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022] Open
Abstract
The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms.
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Affiliation(s)
- Chris R Smith
- Department of Biology Earlham College Richmond IN USA
| | - Peter L Blair
- Department of Biology Earlham College Richmond IN USA
| | - Charlie Boyd
- Department of Biology Earlham College Richmond IN USA
| | - Brianne Cody
- Department of Biology Earlham College Richmond IN USA
| | - Alexander Hazel
- Department of Biology Earlham College Richmond IN USA; Present address: Department of Entomology University of Illinois Urbana Champaign IL USA
| | | | - Hitesh Kathuria
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Parul Khurana
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Brent Kramer
- Department of Biology Earlham College Richmond IN USA
| | | | - Charles Peck
- Department of Computer Science Earlham College Richmond IN USA
| | - Emily Sells
- Department of Biology Earlham College Richmond IN USA
| | - Jessica Skinner
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Cara Tegeler
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Zoe Wolfe
- Department of Biology Earlham College Richmond IN USA
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