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Porter SS, Dupin SE, Denison RF, Kiers ET, Sachs JL. Host-imposed control mechanisms in legume-rhizobia symbiosis. Nat Microbiol 2024:10.1038/s41564-024-01762-2. [PMID: 39095495 DOI: 10.1038/s41564-024-01762-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/17/2024] [Indexed: 08/04/2024]
Abstract
Legumes are ecologically and economically important plants that contribute to nutrient cycling and agricultural sustainability, features tied to their intimate symbiosis with nitrogen-fixing rhizobia. Rhizobia vary dramatically in quality, ranging from highly growth-promoting to non-beneficial; therefore, legumes must optimize their symbiosis with rhizobia through host mechanisms that select for beneficial rhizobia and limit losses to non-beneficial strains. In this Perspective, we examine the considerable scientific progress made in decoding host control over rhizobia, empirically examining both molecular and cellular mechanisms and their effects on rhizobia symbiosis and its benefits. We consider pre-infection controls, which require the production and detection of precise molecular signals by the legume to attract and select for compatible rhizobia strains. We also discuss post-infection mechanisms that leverage the nodule-level and cell-level compartmentalization of symbionts to enable host control over rhizobia development and proliferation in planta. These layers of host control each contribute to legume fitness by directing host resources towards a narrowing subset of more-beneficial rhizobia.
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Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Simon E Dupin
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - R Ford Denison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Joel L Sachs
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, USA.
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2
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Holden EM, Salimbayeva K, Brown C, Stotz GC, Cahill JF. Vegetative growth drives the negative effects of an invasive species on resident community diversity and is not limited by plant-soil feedbacks: A temporal assessment. Ecol Evol 2024; 14:e70070. [PMID: 39041020 PMCID: PMC11262830 DOI: 10.1002/ece3.70070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/28/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
Many pathways of invasion have been posited, but ecologists lack an experimental framework to identify which mechanisms are dominant in a given invasion scenario. Plant-soil feedbacks (PSFs) are one such mechanism that tend to initially facilitate, but over time attenuate, invasive species' impacts on plant diversity and ecosystem function. PSFs are typically measured under greenhouse conditions and are often assumed to have significant effects under field conditions that change over time. However, direct tests of PSFs effects in natural settings and their change over time are rare. Here we compare the role of PSFs with the effects of biomass in limiting the dominance of an invasive species and impacts on resident species diversity. We characterized the effects of the invader Bromus inermis (Leyss.) on native plant communities over time and measured changes in its conspecific PSFs and vegetative growth to understand their integrated effects on community diversity. To do so, we combined data from a 6-year field study documenting the rate and impacts of invasion with a short-term greenhouse experiment quantifying PSF as a function of time since invasion in the field. We found that the nature and strength of B. inermis PSFs did not change over time and were not mediated by soil microbial communities. Though PSFs impacted B. inermis reproduction, they did not sufficiently limit vegetative growth to diminish the negative impacts of B. inermis biomass on native species. B. inermis experienced the full strength of its negative PSFs immediately upon invasion, but they were ineffective at reducing B. inermis vigor to facilitate the recovery of the native plant community. We recommend that conservation efforts focus on limiting B. inermis vegetative growth to facilitate community recovery.
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Affiliation(s)
- Emily M. Holden
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Karina Salimbayeva
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Charlotte Brown
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Départment de BiologieUniversité de SherbrookeSherbrookeQuebecCanada
| | - Gisela C. Stotz
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Centro de Investigación Para la Sustentabilidad, Facultad de Ciencias de la VidaUniversidad Andrés BelloSantiagoChile
| | - James F. Cahill
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
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Rúa MA, Hoeksema JD. Interspecific selection in a diverse mycorrhizal symbiosis. Sci Rep 2024; 14:12151. [PMID: 38802437 PMCID: PMC11130337 DOI: 10.1038/s41598-024-62815-4] [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: 07/31/2023] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
Coevolution describes evolutionary change in which two or more interacting species reciprocally drive each other's evolution, potentially resulting in trait diversification and ecological speciation. Much progress has been made in analysis of its dynamics and consequences, but relatively little is understood about how coevolution works in multispecies interactions, i.e., those with diverse suites of species on one or both sides of an interaction. Interactions among plant hosts and their mutualistic ectomycorrhizal fungi (ECM) may provide an ecologically unique arena to examine the nature of selection in multispecies interactions. Using native genotypes of Monterey pine (Pinus radiata), we performed a common garden experiment at a field site that contains native stands to investigate selection from ECM fungi on pine traits. We planted seedlings from all five native populations, as well as inter-population crosses to represent intermediate phenotypes/genotypes, and measured seedling traits and ECM fungal traits to evaluate the potential for evolution in the symbiosis. We then combined field estimates of selection gradients with estimates of heritability and genetic variance-covariance matrices for multiple traits of the mutualism to determine which fungal traits drive plant fitness variation. We found evidence that certain fungal operational taxonomic units, families and species-level morphological traits by which ECM fungi acquire and transport nutrients exert selection on plant traits related to growth and allocation patterns. This work represents the first field-based, community-level study measuring multispecific coevolutionary selection in nutritional symbioses.
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Affiliation(s)
- Megan A Rúa
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
| | - Jason D Hoeksema
- Department of Biology, University of Mississippi, P.O. Box 1848, University, MS, 38677, USA
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Zobel M, Koorem K, Moora M, Semchenko M, Davison J. Symbiont plasticity as a driver of plant success. THE NEW PHYTOLOGIST 2024; 241:2340-2352. [PMID: 38308116 DOI: 10.1111/nph.19566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024]
Abstract
We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant-associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.
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Affiliation(s)
- Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
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Caudill V, Ralph PL. Genetic architecture, spatial heterogeneity, and the coevolutionary arms race between newts and snakes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.07.570693. [PMID: 38106105 PMCID: PMC10723474 DOI: 10.1101/2023.12.07.570693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Coevolution between two species can lead to exaggerated phenotypes that vary in a correlated manner across space. However, the conditions under which we expect such spatially varying coevolutionary patterns in polygenic traits are not well-understood. We investigate the coevolutionary dynamics between two species undergoing reciprocal adaptation across space and time, using simulations inspired by the Taricha newt - Thamnophis garter snake system. One striking observation from this system is that newts in some areas carry much more tetrodotoxin than in other areas, and garter snakes that live near more toxic newts tend to be more resistant to this toxin, a correlation seen across several broad geographic areas. Furthermore, snakes seem to be "winning" the coevolutionary arms race, i.e., having a high level of resistance compared to local newt toxicity, despite substantial variation in both toxicity and resistance across the range. We explore how possible genetic architectures of the toxin and resistance traits would affect the coevolutionary dynamics by manipulating both mutation rate and effect size of mutations across many simulations. We find that coevolutionary dynamics alone were not sufficient in our simulations to produce the striking mosaic of levels of toxicity and resistance observed in nature, but simulations with ecological heterogeneity (in trait costliness or interaction rate) did produce such patterns. We also find that in simulations, newts tend to "win" across most combinations of genetic architectures, although the species with higher mutational genetic variance tends to have an advantage.
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Shi Y, Ma L, Zhou M, He Z, Zhao Y, Hong J, Zou X, Zhang L, Shu L. Copper stress shapes the dynamic behavior of amoebae and their associated bacteria. THE ISME JOURNAL 2024; 18:wrae100. [PMID: 38848278 PMCID: PMC11197307 DOI: 10.1093/ismejo/wrae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/15/2024] [Accepted: 06/06/2024] [Indexed: 06/09/2024]
Abstract
Amoeba-bacteria interactions are prevalent in both natural ecosystems and engineered environments. Amoebae, as essential consumers, hold significant ecological importance within ecosystems. Besides, they can establish stable symbiotic associations with bacteria. Copper plays a critical role in amoeba predation by either killing or restricting the growth of ingested bacteria in phagosomes. However, certain symbiotic bacteria have evolved mechanisms to persist within the phagosomal vacuole, evading antimicrobial defenses. Despite these insights, the impact of copper on the symbiotic relationships between amoebae and bacteria remains poorly understood. In this study, we investigated the effects of copper stress on amoebae and their symbiotic relationships with bacteria. Our findings revealed that elevated copper concentration adversely affected amoeba growth and altered cellular fate. Symbiont type significantly influenced the responses of the symbiotic relationships to copper stress. Beneficial symbionts maintained stability under copper stress, but parasitic symbionts exhibited enhanced colonization of amoebae. Furthermore, copper stress favored the transition of symbiotic relationships between amoebae and beneficial symbionts toward the host's benefit. Conversely, the pathogenic effects of parasitic symbionts on hosts were exacerbated under copper stress. This study sheds light on the intricate response mechanisms of soil amoebae and amoeba-bacteria symbiotic systems to copper stress, providing new insights into symbiotic dynamics under abiotic factors. Additionally, the results underscore the potential risks of copper accumulation in the environment for pathogen transmission and biosafety.
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Affiliation(s)
- Yijing Shi
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Lu Ma
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Min Zhou
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanchen Zhao
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Junyue Hong
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xinyue Zou
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
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8
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Song Q, Zhao F, Hou L, Miao M. Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates. THE ISME JOURNAL 2024; 18:wrae117. [PMID: 38916437 PMCID: PMC11253213 DOI: 10.1093/ismejo/wrae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental conditions. The integration of acquired phototrophy with intrinsic phagotrophy results in a trophic mode known as mixotrophy. Additionally, ciliates can harbor thousands of bacteria in various intracellular regions, including the cytoplasm and nucleus, exhibiting species specificity. Under prolonged and specific selective pressure within hosts, bacterial endosymbionts evolve unique lifestyles and undergo particular reductions in metabolic activities. Investigating the research advancements in various endosymbiotic cases within ciliates will contribute to elucidate patterns in cellular interaction and unravel the evolutionary origins of complex traits.
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Affiliation(s)
- Qi Song
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
| | - Fangqing Zhao
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
- Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, No. 1 Xiangshan Road, Hangzhou 310024, China
| | - Lina Hou
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
| | - Miao Miao
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
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Forero-Muñoz NR, Muylaert RL, Seifert SN, Albery GF, Becker DJ, Carlson CJ, Poisot T. The coevolutionary mosaic of bat betacoronavirus emergence risk. Virus Evol 2023; 10:vead079. [PMID: 38361817 PMCID: PMC10868545 DOI: 10.1093/ve/vead079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 09/01/2023] [Accepted: 12/18/2023] [Indexed: 02/17/2024] Open
Abstract
Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Coronavirus disease 2019 (COVID-19), we examine the global biogeography of bat-origin betacoronaviruses, and find that coevolutionary principles suggest geographies of risk that are distinct from the hotspots and coldspots of host richness. Further, our framework helps explain patterns like a unique pool of merbecoviruses in the Neotropics, a recently discovered lineage of divergent nobecoviruses in Madagascar, and-most importantly-hotspots of diversification in southeast Asia, sub-Saharan Africa, and the Middle East that correspond to the site of previous zoonotic emergence events. Our framework may help identify hotspots of future risk that have also been previously overlooked, like West Africa and the Indian subcontinent, and may more broadly help researchers understand how host ecology shapes the evolution and diversity of pandemic threats.
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Affiliation(s)
- Norma R Forero-Muñoz
- Département de Sciences Biologiques, Université de Montréal, 1375 Avenue Thérèse-Lavoie-Roux, Montréal (Québec) H2V 0B3, Canada
- Québec Centre for Biodiversity Sciences
| | - Renata L Muylaert
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand
| | - Stephanie N Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, United States
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Colin J Carlson
- Department of Biology, Georgetown University, Washington, DC, USA
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| | - Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, 1375 Avenue Thérèse-Lavoie-Roux, Montréal (Québec) H2V 0B3, Canada
- Québec Centre for Biodiversity Sciences
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Zhao Y, Ji X, Liu X, Qin L, Tan D, Wu D, Bai C, Yang J, Xie J, He Y. Age-dependent dendrobine biosynthesis in Dendrobium nobile: insights into endophytic fungal interactions. Front Microbiol 2023; 14:1294402. [PMID: 38149273 PMCID: PMC10749937 DOI: 10.3389/fmicb.2023.1294402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction Dendrobium nobile (D. nobile), a valued Chinese herb known for its diverse pharmacological effects, owes much of its potency to the bioactive compound dendrobine. However, dendrobine content varies significantly with plant age, and the mechanisms governing this variation remain unclear. This study delves into the potential role of endophytic fungi in shaping host-microbe interactions and influencing plant metabolism. Methods Using RNA-seq, we examined the transcriptomes of 1-year-old, 2-year-old, and 3-year-old D. nobile samples and through a comprehensive analysis of endophytic fungal communities and host gene expression in D. nobile stems of varying ages, we aim to identify associations between specific fungal taxa and host genes. Results The results revealing 192 differentially expressed host genes. These genes exhibited a gradual decrease in expression levels as the plants aged, mirroring dendrobine content changes. They were enriched in 32 biological pathways, including phagosome, fatty acid degradation, alpha-linolenic acid metabolism, and plant hormone signal transduction. Furthermore, a significant shift in the composition of the fungal community within D. nobile stems was observed along the age gradient. Olipidium, Hannaella, and Plectospherella dominated in 1-year-old plants, while Strelitziana and Trichomerium prevailed in 2-year-old plants. Conversely, 3-year-old plants exhibited additional enrichment of endophytic fungi, including the genus Rhizopus. Two gene expression modules (mediumpurple3 and darkorange) correlated significantly with dominant endophytic fungi abundance and dendrobine accumulation. Key genes involved in dendrobine synthesis were found associated with plant hormone synthesis. Discussion This study suggests that the interplay between different endophytic fungi and the hormone signaling system in D. nobile likely regulates dendrobine biosynthesis, with specific endophytes potentially triggering hormone signaling cascades that ultimately influence dendrobine synthesis.
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Affiliation(s)
- Yongxia Zhao
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaolong Ji
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaoqi Liu
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Lin Qin
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Daopeng Tan
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Di Wu
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Chaojun Bai
- Guangxi Shenli Pharmaceutical Co., Ltd., Yulin, China
| | - Jiyong Yang
- Chishui Xintian Chinese Medicine Industry Development Co., Ltd., Zunyi, China
| | - Jian Xie
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
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11
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Hanusch M, He X, Janssen S, Selke J, Trutschnig W, Junker RR. Exploring the Frequency and Distribution of Ecological Non-monotonicity in Associations among Ecosystem Constituents. Ecosystems 2023; 26:1819-1840. [PMID: 38106357 PMCID: PMC10721710 DOI: 10.1007/s10021-023-00867-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/06/2023] [Indexed: 12/19/2023]
Abstract
Complex links between biotic and abiotic constituents are fundamental for the functioning of ecosystems. Although non-monotonic interactions and associations are known to increase the stability, diversity, and productivity of ecosystems, they are frequently ignored by community-level standard statistical approaches. Using the copula-based dependence measure qad, capable of quantifying the directed and asymmetric dependence between variables for all forms of (functional) relationships, we determined the proportion of non-monotonic associations between different constituents of an ecosystem (plants, bacteria, fungi, and environmental parameters). Here, we show that up to 59% of all statistically significant associations are non-monotonic. Further, we show that pairwise associations between plants, bacteria, fungi, and environmental parameters are specifically characterized by their strength and degree of monotonicity, for example, microbe-microbe associations are on average stronger than and differ in degree of non-monotonicity from plant-microbe associations. Considering directed and non-monotonic associations, we extended the concept of ecosystem coupling providing more complete insights into the internal order of ecosystems. Our results emphasize the importance of ecological non-monotonicity in characterizing and understanding ecosystem patterns and processes. Supplementary Information The online version contains supplementary material available at 10.1007/s10021-023-00867-9.
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Affiliation(s)
- Maximilian Hanusch
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Xie He
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Stefan Janssen
- Algorithmic Bioinformatics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Julian Selke
- Algorithmic Bioinformatics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Wolfgang Trutschnig
- Department for Artificial Intelligence & Human Interfaces, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Robert R. Junker
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043 Marburg, Germany
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12
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Six DL, Biedermann PHW. Fidelity or love the one you're with? Biotic complexity and tradeoffs can drive strategy and specificity in beetle-fungus by-product mutualisms. Ecol Evol 2023; 13:e10345. [PMID: 37492462 PMCID: PMC10363798 DOI: 10.1002/ece3.10345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023] Open
Abstract
By-product mutualisms are ubiquitous yet seldom considered in models of mutualism. Most models represent conditional mutualisms that shift between mutualism and antagonism in response to shifts in costs and benefits resulting from changes in environmental quality. However, in by-product mutualisms, benefits arise as a part of normal life processes that may be costly to produce but incur little-to-no additional costs in response to the interaction. Without costs associated with the interaction, they do not have antagonistic alternate states. Here, we present a conceptual model that differs from traditional conditional models in three ways: (1) partners exchange by-product benefits, (2) interactions do not have alternate antagonistic states, and (3) tradeoffs are allowed among factors that influence environmental quality (rather than all factors that contribute to environmental quality being combined into a single gradient ranging from high to low). We applied this model to bark and ambrosia beetles (Curculionidae: Scolytinae), a diverse group that associates with fungi and that has repeatedly developed two distinct pathways to by-product mutualism. We used independent axes for each major factor influencing environmental quality in these systems, including those that exhibit tradeoffs (tree defense and nutritional quality). For these symbioses, tradeoffs in these two factors are key to which mutualism pathway is taken.
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Affiliation(s)
- Diana L. Six
- Department of Ecosystem and Conservation ScienceUniversity of MontanaMissoulaMontanaUSA
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13
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Rogério F, Van Oosterhout C, Ciampi-Guillardi M, Correr FH, Hosaka GK, Cros-Arteil S, Rodrigues Alves Margarido G, Massola Júnior NS, Gladieux P. Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen. Mol Ecol 2023; 32:2428-2442. [PMID: 35076152 DOI: 10.1111/mec.16366] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
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Affiliation(s)
- Flávia Rogério
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
- Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | | | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Nelson S Massola Júnior
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | - Pierre Gladieux
- UMR PHIM, University of Montpellier, INRAE, CIRAD, Montpellier, France
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14
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Riley AB, Grillo MA, Epstein B, Tiffin P, Heath KD. Discordant population structure among rhizobium divided genomes and their legume hosts. Mol Ecol 2023; 32:2646-2659. [PMID: 36161739 DOI: 10.1111/mec.16704] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.
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Affiliation(s)
- Alex B Riley
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
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15
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Burrill HM, Wang G, Bever JD. Rapid differentiation of soil and root microbiomes in response to plant composition and biodiversity in the field. ISME COMMUNICATIONS 2023; 3:31. [PMID: 37076650 PMCID: PMC10115818 DOI: 10.1038/s43705-023-00237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/15/2023] [Accepted: 03/29/2023] [Indexed: 04/21/2023]
Abstract
Research suggests that microbiomes play a major role in structuring plant communities and influencing ecosystem processes, however, the relative roles and strength of change of microbial components have not been identified. We measured the response of fungal, arbuscular mycorrhizal fungal (AMF), bacteria, and oomycete composition 4 months after planting of field plots that varied in plant composition and diversity. Plots were planted using 18 prairie plant species from three plant families (Poaceae, Fabaceae, and Asteraceae) in monoculture, 2, 3, or 6 species richness mixtures and either species within multiple families or one family. Soil cores were collected and homogenized per plot and DNA were extracted from soil and roots of each plot. We found that all microbial groups responded to the planting design, indicating rapid microbiome response to plant composition. Fungal pathogen communities were strongly affected by plant diversity. We identified OTUs from genera of putatively pathogenic fungi that increased with plant family, indicating likely pathogen specificity. Bacteria were strongly differentiated by plant family in roots but not soil. Fungal pathogen diversity increased with planted species richness, while oomycete diversity, as well as bacterial diversity in roots, decreased. AMF differentiation in roots was detected with individual plant species, but not plant family or richness. Fungal saprotroph composition differentiated between plant family composition in plots, providing evidence for decomposer home-field advantage. The observed patterns are consistent with rapid microbiome differentiation with plant composition, which could generate rapid feedbacks on plant growth in the field, thereby potentially influencing plant community structure, and influence ecosystem processes. These findings highlight the importance of native microbial inoculation in restoration.
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16
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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17
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Cross Cultivation on Homologous/Heterologous Plant-Based Culture Media Empowers Host-Specific and Real Time In Vitro Signature of Plant Microbiota. DIVERSITY 2022. [DOI: 10.3390/d15010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alliances of microbiota with plants are masked by the inability of in vitro cultivation of their bulk. Pure cultures piled in international centers originated from dissimilar environments/hosts. Reporting that plant root/leaf-based culture media support the organ-specific growth of microbiota, it was of interest to further investigate if a plant-based medium prepared from homologous (maize) supports specific/adapted microbiota compared to another prepared from heterologous plants (sunflower). The culture-independent community of maize phyllosphere was compared to communities cross-cultivated on plant broth-based media: CFU counts and taxa prevalence (PCR-DGGE; Illumina MiSeq amplicon sequencing). Similar to total maize phyllospheric microbiota, culture-dependent communities were overwhelmed by Proteobacteria (>94.3–98.3%); followed by Firmicutes (>1.3–3.7%), Bacteroidetes (>0.01–1.58%) and Actinobacteria (>0.06–0.34%). Differential in vitro growth on homologous versus heterologous plant-media enriched/restricted various taxa. In contrast, homologous cultivation over represented members of Proteobacteria (ca. > 98.0%), mainly Pseudomonadaceae and Moraxellaceae; heterologous cultivation and R2A enriched Firmicutes (ca. > 3.0%). The present strategy simulates/fingerprints the chemical composition of host plants to expand the culturomics of plant microbiota, advance real-time in vitro cultivation and lab-keeping of compatible plant microbiota, and identify preferential pairing of plant-microbe partners toward future synthetic community (SynComs) research and use in agriculture.
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18
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Different faces, same attitudes: behavioral mimicry and description of a new termitophilous species of the remarkable rove beetle genus Thyreoxenus (Staphylinidae, Aleocharinae, Corotocini) from Brazil with notes on post-imaginal growth. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2022; 109:53. [DOI: 10.1007/s00114-022-01820-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/17/2022] [Accepted: 09/09/2022] [Indexed: 11/06/2022]
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19
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Pruvost O, Ibrahim YE, Sharafaddin AH, Boyer K, Widyawan A, Al‐Saleh MA. Molecular epidemiology of the citrus bacterial pathogen Xanthomonas citri pv. citri from the Arabian Peninsula reveals a complex structure of specialist and generalist strains. Evol Appl 2022; 15:1423-1435. [PMID: 36187189 PMCID: PMC9488683 DOI: 10.1111/eva.13451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 06/16/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022] Open
Abstract
Molecular epidemiology studies are essential to refine our understanding of migrations of phytopathogenic bacteria, the major determining factor in their emergence, and to understand the factors that shape their population structure. Microsatellite and minisatellite typing are useful techniques for deciphering the population structure of Xanthomonas citri pv. citri, the causal agent of Asiatic citrus canker. This paper presents a molecular epidemiology study, which has improved our understanding of the history of the pathogen's introductions into the Arabian Peninsula, since it was first reported in the 1980s. An unexpectedly high genetic diversity of the pathogen was revealed. The four distinct genetic lineages within X. citri pv. citri, which have been reported throughout the world, were identified in the Arabian Peninsula, most likely as the result of multiple introductions. No copper-resistant X. citri pv. citri strains were identified. The pathogen's population structure on Mexican lime (their shared host species) was closely examined in two countries, Saudi Arabia and Yemen. We highlighted the marked prevalence of specialist pathotype A* strains in both countries, which suggests that specialist strains of X. citri pv. citri may perform better than generalist strains when they occur concomitantly in this environment. Subclade 4.2 was the prevailing lineage identified. Several analyses (genetic structure deciphered by discriminant analysis of principal components, RST-based genetic differentiation, geographic structure) congruently suggested the role of human activities in the pathogen's spread. We discuss the implications of these results on the management of Asiatic citrus canker in the region.
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Affiliation(s)
| | - Yasser Eid Ibrahim
- Department of Plant Protection, College of Food and Agriculture SciencesKing Saud UniversityRiyadhSaudi Arabia
| | - Anwar Hamoud Sharafaddin
- Department of Plant Protection, College of Food and Agriculture SciencesKing Saud UniversityRiyadhSaudi Arabia
| | | | - Arya Widyawan
- Department of Plant Protection, College of Food and Agriculture SciencesKing Saud UniversityRiyadhSaudi Arabia
| | - Mohammed Ali Al‐Saleh
- Department of Plant Protection, College of Food and Agriculture SciencesKing Saud UniversityRiyadhSaudi Arabia
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20
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Epstein B, Burghardt LT, Heath KD, Grillo MA, Kostanecki A, Hämälä T, Young ND, Tiffin P. Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis. Mol Ecol 2022. [PMID: 35793264 DOI: 10.1111/mec.16602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.
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Affiliation(s)
- Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Liana T Burghardt
- Department of Plant Sciences, The University of Pennsylvania, University Park, Pennsylvania, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Adam Kostanecki
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Nevin D Young
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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21
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Semchenko M, Barry KE, de Vries FT, Mommer L, Moora M, Maciá-Vicente JG. Deciphering the role of specialist and generalist plant-microbial interactions as drivers of plant-soil feedback. THE NEW PHYTOLOGIST 2022; 234:1929-1944. [PMID: 35338649 DOI: 10.1111/nph.18118] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density-dependence and species co-existence. Such effects are often attributed to the accumulation of host-specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host-specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host-specificity in plant-associated microbes and propose that specific plant-soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant-soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant-microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant-soil feedback and the ways it contributes to plant co-existence.
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Affiliation(s)
- Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Kathryn E Barry
- Ecology and Biodiversity, Department of Biology, Institute of Science, Utrecht University, Padualaan 8, Utrecht, the Netherlands
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Liesje Mommer
- Plant Ecology and Nature Conservation, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
| | - Jose G Maciá-Vicente
- Plant Ecology and Nature Conservation, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
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22
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Nakayama R, Nakano T, Asakura A. Substrate variety and host preference of the epizoic limpet Lottia tenuisculpta (Patellogastropoda: Lottiidae). MOLLUSCAN RESEARCH 2022. [DOI: 10.1080/13235818.2022.2036308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ryo Nakayama
- Department of Zoology, Division of Biological Science, Graduate School of Science, Kyoto University, Kitashirakawa, Japan
- Seto Marine Biological Laboratory, Field Science Education & Research Centre, Kyoto University, Wakayama, Japan
- Agriculture and Fisheries, Research Institute of Environment, Osaka, Japan
| | - Tomoyuki Nakano
- Seto Marine Biological Laboratory, Field Science Education & Research Centre, Kyoto University, Wakayama, Japan
| | - Akira Asakura
- Seto Marine Biological Laboratory, Field Science Education & Research Centre, Kyoto University, Wakayama, Japan
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23
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Liu Y, Ma B, Chen W, Schlaeppi K, Erb M, Stirling E, Hu L, Wang E, Zhang Y, Zhao K, Lu Z, Ye S, Xu J. Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean. Front Microbiol 2021; 12:709012. [PMID: 34925249 PMCID: PMC8678110 DOI: 10.3389/fmicb.2021.709012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.
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Affiliation(s)
- Yuanhui Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.,China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Ministry of Agriculture Key Laboratory of Soil Microbiology, Beijing, China
| | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.,Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, México
| | - Yunzeng Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Zhijiang Lu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Shudi Ye
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
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24
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Tarkka MT, Bonkowski M, Ge T, Knief C, Razavi BS, Vetterlein D. Editorial: Rhizosphere Spatiotemporal Organisation. FRONTIERS IN PLANT SCIENCE 2021; 12:795136. [PMID: 34868189 PMCID: PMC8639225 DOI: 10.3389/fpls.2021.795136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Mika T. Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Tida Ge
- Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Bahar S. Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian- Albrechts-University of Kiel, Kiel, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
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25
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Trevenen EJ, Veneklaas EJ, Teste FP, Dobrowolski M, Mucina L, Renton M. Positive heterospecific interactions can increase long‐term diversity of plant communities more than negative conspecific interactions alone. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Elizabeth J. Trevenen
- School of Biological Sciences The University of Western Australia Perth WA Australia
| | - Erik J. Veneklaas
- School of Biological Sciences The University of Western Australia Perth WA Australia
- School of Agriculture and Environment The University of Western Australia Perth WA Australia
| | - François P. Teste
- School of Biological Sciences The University of Western Australia Perth WA Australia
- Grupo de Estudios Ambientales IMASL‐CONICET & Universidad Nacional de San Luis San Luis Argentina
- Swift Current Research and Development Centre Agriculture and Agri‐Food Canada Swift Current SK Canada
| | - Mark P. Dobrowolski
- School of Biological Sciences The University of Western Australia Perth WA Australia
- Iluka Resources Limited Perth WA Australia
- Harry Butler Institute Murdoch University Perth WA Australia
| | - Ladislav Mucina
- School of Biological Sciences The University of Western Australia Perth WA Australia
- Harry Butler Institute Murdoch University Perth WA Australia
- Department of Geography & Environmental Studies Stellenbosch University Stellenbosch South Africa
| | - Michael Renton
- School of Biological Sciences The University of Western Australia Perth WA Australia
- School of Agriculture and Environment The University of Western Australia Perth WA Australia
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26
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Huang S, Farrell M, Stephens PR. Infectious disease macroecology: parasite diversity and dynamics across the globe. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200350. [PMID: 34538145 PMCID: PMC8450632 DOI: 10.1098/rstb.2020.0350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shan Huang
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Maxwell Farrell
- Ecology and Evolutionary Biology, University Toronto, Toronto, Ontario, Canada
| | - Patrick R. Stephens
- Odum School of Ecology and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
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27
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Boco SR, Pitt KA, Melvin SD. Ocean acidification impairs the physiology of symbiotic phyllosoma larvae of the lobster Thenus australiensis and their ability to detect cues from jellyfish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148679. [PMID: 34328968 DOI: 10.1016/j.scitotenv.2021.148679] [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: 10/22/2020] [Revised: 06/01/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Ocean acidification (OA) can alter the behaviour and physiology of marine fauna and impair their ability to interact with other species, including those in symbiotic and predatory relationships. Phyllosoma larvae of lobsters are symbionts to many invertebrates and often ride and feed on jellyfish, however OA may threaten interactions between phyllosomas and jellyfish. Here, we tested whether OA predicted for surface mid-shelf waters of Great Barrier Reef, Australia, under ∆ pH = -0.1 (pH ~7.9) and ∆pH = -0.3 (pH ~7.7) relative to the present pH (~8.0) (P) impaired the survival, moulting, respiration, and metabolite profiles of phyllosoma larvae of the slipper lobster Thenus australiensis, and the ability of phyllosomas to detect chemical cues of fresh jellyfish tissue. We discovered that OA was detrimental to survival of phyllosomas with only 20% survival under ∆pH = -0.3 compared to 49.2% and 45.3% in the P and ∆pH = -0.1 treatments, respectively. The numbers of phyllosomas that moulted in the P and ∆pH = -0.1 treatments were 40% and 34% higher, respectively, than those in the ∆pH = -0.3 treatment. Respiration rates varied between pH treatments, but were not consistent through time. Respiration rates in the ∆pH = -0.3 and ∆pH = -0.1 treatments were initially 40% and 22% higher, respectively, than in the P treatment on Day 2 and then rates varied to become 26% lower (∆pH = -0.3) and 17% (∆pH = -0.1) higher towards the end of the experiment. Larvae were attracted to jellyfish tissue in treatments P and ∆pH = -0.1 but avoided jellyfish at ∆pH = -0.3. Moreover, OA conditions under ∆pH = -0.1 and ∆pH = -0.3 levels reduced the relative abundances of 22 of the 34 metabolites detected in phyllosomas via Nuclear Magnetic Resonance (NMR) spectroscopy. Our study demonstrates that the physiology and ability to detect jellyfish tissue by phyllosomas of the lobster T. australiensis may be impaired under ∆pH = -0.3 relative to the present conditions, with potential negative consequences for adult populations of this commercially important species.
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Affiliation(s)
- Sheldon Rey Boco
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland 4215, Australia.
| | - Kylie A Pitt
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland 4215, Australia
| | - Steven D Melvin
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland 4215, Australia
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Drew GC, Stevens EJ, King KC. Microbial evolution and transitions along the parasite-mutualist continuum. Nat Rev Microbiol 2021; 19:623-638. [PMID: 33875863 PMCID: PMC8054256 DOI: 10.1038/s41579-021-00550-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Virtually all plants and animals, including humans, are home to symbiotic microorganisms. Symbiotic interactions can be neutral, harmful or have beneficial effects on the host organism. However, growing evidence suggests that microbial symbionts can evolve rapidly, resulting in drastic transitions along the parasite-mutualist continuum. In this Review, we integrate theoretical and empirical findings to discuss the mechanisms underpinning these evolutionary shifts, as well as the ecological drivers and why some host-microorganism interactions may be stuck at the end of the continuum. In addition to having biomedical consequences, understanding the dynamic life of microorganisms reveals how symbioses can shape an organism's biology and the entire community, particularly in a changing world.
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Affiliation(s)
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, UK.
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29
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Raduła M, Świerszcz S, Nobis M, Nowak S, Nobis A, Nowak A. Palaeoclimate has a major effect on the diversity of endemic species in the hotspot of mountain biodiversity in Tajikistan. Sci Rep 2021; 11:18684. [PMID: 34548515 PMCID: PMC8455614 DOI: 10.1038/s41598-021-98027-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
In a period of ongoing climate changes, identifying drivers of overall and endemic species diversity is a key element in constructing new ecological patterns and determining the main goals of conservation. Such studies are especially crucial if they concern biodiversity hotspot areas. In this study, we explore patterns and drivers of plant endemism (the proportion of endemic plant species to overall plant species richness; PE) in Tajikistan. We used three groups of climatic measures featuring the contemporary and glacial climates as well as climatic changes since the Last Glacial Maximum in the Pleistocene (LGM). To explore relationships between PE and climatic groups, and the most important climatic variables, we applied the Generalised Additive Model and regression trees method respectively. Glacial climate predicted PE variation the most (74.3%), followed by climate stability (55.4%) and current climate (62.4%). The most important variables represented change in precipitation of driest quarter, glacial mean annual temperature and current annual precipitation. LGM climate and its change to date have the greatest influence on contemporary PE patterns in Tajikistan, revealing the evolutionary dependencies between limited-range plants and past climate. Accordingly, annual temperature and precipitation regimes have been the most crucial drivers of PE since the LGM until today. The study revealed the dependence of the PE on a stabilized water-energy supply. The changing temperature and precipitations regimes during the ongoing climate warming may, therefore, increases the threat to geographically isolated cryophilous plants of Tajikistan, while their escape potential to suitable cold habitats is highly topographically limited.
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Affiliation(s)
- Małgorzata Raduła
- grid.413454.30000 0001 1958 0162Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-976 Warszawa, Poland ,grid.8505.80000 0001 1010 5103Department of Ecology, Biogeochemistry and Environmental Protection, University of Wrocław, Kanonia 6/8, 50-328 Wrocław, Poland
| | - Sebastian Świerszcz
- grid.413454.30000 0001 1958 0162Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-976 Warszawa, Poland ,grid.107891.60000 0001 1010 7301Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland
| | - Marcin Nobis
- grid.5522.00000 0001 2162 9631Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland ,grid.77602.340000 0001 1088 3909Research Laboratory ‘Herbarium’, National Research Tomsk State University, Tomsk, 634050 Russia
| | - Sylwia Nowak
- grid.107891.60000 0001 1010 7301Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland
| | - Agnieszka Nobis
- grid.5522.00000 0001 2162 9631Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Arkadiusz Nowak
- grid.413454.30000 0001 1958 0162Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-976 Warszawa, Poland ,grid.107891.60000 0001 1010 7301Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland
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30
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Dang BT, Truong OT, Tran SQ, Glenner H. Comparative population genetics of swimming crab host ( Portunus pelagicus) and common symbiotic barnacle ( Octolasmis angulata) in Vietnam. PeerJ 2021; 9:e11671. [PMID: 34277149 PMCID: PMC8272463 DOI: 10.7717/peerj.11671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background By comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms. Methods Here, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages. Results Based on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R2 = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively).
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Affiliation(s)
- Binh Thuy Dang
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Oanh Thi Truong
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Sang Quang Tran
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Henrik Glenner
- Department of Biological Science, University of Bergen, Bergen, Norway
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31
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Six DL, Klepzig KD. Context Dependency in Bark Beetle-Fungus Mutualisms Revisited: Assessing Potential Shifts in Interaction Outcomes Against Varied Genetic, Ecological, and Evolutionary Backgrounds. Front Microbiol 2021; 12:682187. [PMID: 34054789 PMCID: PMC8149605 DOI: 10.3389/fmicb.2021.682187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Context dependency occurs when biological interactions shift in sign or magnitude depending upon genetic, abiotic, and biotic context. Most models of mutualism address systems where interaction outcomes slide along a mutualism-antagonism continuum as environmental conditions vary altering cost-benefit relationships. However, these models do not apply to the many mutualisms that involve by-product benefits and others that do not have antagonistic alternate states. The ubiquity of such mutualisms indicates a need for different approaches and models to understand how environmental variability influences their strength, stability, and ecological roles. In this paper, we apply the concept of context dependency to mutualisms among bark beetles and fungi that span a variety of life strategies and exposures to environmental variability. Bark beetles and their mutualist fungi co-construct a niche based on by-product benefits that allows them to exist in a resource that is otherwise intractable or inaccessible. For the closest of these partnerships, this has resulted in some of the most influential agents of forest mortality in conifer forests worldwide. Understanding these symbioses is key to understanding their influence on forest structure and dynamics and responses to change. We found no evidence that bark beetle mutualisms change in sign as conditions vary, only in magnitude, and that the "closest" (and most environmentally influential) of these partnerships have evolved behaviors and mechanisms to reduce context-dependency and stabilize benefit delivery. The bark beetle-fungus symbioses most likely to slide along a mutualism-antagonism continuum are those involving loosely associated facultative symbionts that may provide benefits under some circumstances and that are horizontally transmitted by the beetle host. Additionally, some symbiotic fungi are never mutualists - these "third party" fungi are exploiters and may shift from commensalism to antagonism depending on environmental context. Our assessment indicates that a careful differentiation between bark beetle-fungus partnerships is crucial to understanding how they influence forests and respond to environmental variability.
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Affiliation(s)
- Diana L Six
- Department of Ecosystem and Conservation Science, The University of Montana, Missoula, MT, United States
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32
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Hayward A, Poulin R, Nakagawa S. A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence. Ecol Lett 2021; 24:1681-1696. [PMID: 33987932 DOI: 10.1111/ele.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/21/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023]
Abstract
Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.
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Affiliation(s)
- Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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Oita S, Ibáñez A, Lutzoni F, Miadlikowska J, Geml J, Lewis LA, Hom EFY, Carbone I, U'Ren JM, Arnold AE. Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale. Commun Biol 2021; 4:313. [PMID: 33750915 PMCID: PMC7943826 DOI: 10.1038/s42003-021-01826-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves-fungal endophytes-that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and taxonomic composition reflect both temperature seasonality and climate (mean annual temperature and precipitation). Overall our findings highlight the vital role of climate-related factors in shaping the hyperdiversity of these important and little-known symbionts of the trees that, in turn, form the foundations of tropical forest biodiversity.
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Affiliation(s)
- Shuzo Oita
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | | | - József Geml
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, Eger, Hungary
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Erik F Y Hom
- Department of Biology, Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Jana M U'Ren
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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Benning JW, Moeller DA. Microbes, mutualism, and range margins: testing the fitness consequences of soil microbial communities across and beyond a native plant's range. THE NEW PHYTOLOGIST 2021; 229:2886-2900. [PMID: 33225448 DOI: 10.1111/nph.17102] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/04/2020] [Indexed: 05/28/2023]
Abstract
Interactions between plants and soil fungi and bacteria are ubiquitous and have large effects on individual plant fitness. However, the degree to which spatial variation in soil microbial communities modulates plant species' distributions remains largely untested. Using the California native plant Clarkia xantiana ssp. xantiana we paired glasshouse and field reciprocal transplants of plant populations and soils to test whether plant-microbe interactions affect the plant's geographic range limit and whether there is local adaptation between plants and soil microbe communities. In the field and glasshouse, one of the two range interior inocula had a positive effect on plant fitness. In the field, this benefit was especially pronounced at the range edge and beyond, suggesting possible mutualist limitation. In the glasshouse, soil inocula from beyond-range tended to increase plant growth, suggesting microbial enemy release beyond the range margin. Amplicon sequencing revealed stark variation in microbial communities across the range boundary. Plants dispersing beyond their range limit are likely to encounter novel microbial communities. In C. x. xantiana, our results suggest that range expansion may be facilitated by fewer pathogens, but could also be hindered by a lack of mutualists. Both negative and positive plant-microbe interactions will likely affect contemporary range shifts.
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Affiliation(s)
- John W Benning
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Labs, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Labs, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
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35
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Lajoie G, Kembel SW. Host neighborhood shapes bacterial community assembly and specialization on tree species across a latitudinal gradient. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1443] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Geneviève Lajoie
- Département des sciences biologiques Université du Québec à Montréal 141, Avenue du Président‐Kennedy Montréal QuébecH2X 1Y4Canada
| | - Steven W. Kembel
- Département des sciences biologiques Université du Québec à Montréal 141, Avenue du Président‐Kennedy Montréal QuébecH2X 1Y4Canada
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36
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García-Parisi PA, Gavilán SA, Casas C, Gundel PE, Omacini M. A fungal endophyte of an annual weed reduces host competitive ability and confers associational protection to wheat. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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37
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Vaidya P, Stinchcombe JR. The Potential for Genotype-by-Environment Interactions to Maintain Genetic Variation in a Model Legume-Rhizobia Mutualism. PLANT COMMUNICATIONS 2020; 1:100114. [PMID: 33367267 PMCID: PMC7747969 DOI: 10.1016/j.xplc.2020.100114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/10/2020] [Accepted: 10/08/2020] [Indexed: 05/10/2023]
Abstract
The maintenance of genetic variation in mutualism-related traits is key for understanding mutualism evolution, yet the mechanisms maintaining variation remain unclear. We asked whether genotype-by-environment (G×E) interaction is a potential mechanism maintaining variation in the model legume-rhizobia system, Medicago truncatula-Ensifer meliloti. We planted 50 legume genotypes in a greenhouse under ambient light and shade to reflect reduced carbon availability for plants. We found an expected reduction under shaded conditions for plant performance traits, such as leaf number, aboveground and belowground biomass, and a mutualism-related trait, nodule number. We also found G×E for nodule number, with ∼83% of this interaction due to shifts in genotype fitness rank order across light environments, coupled with strong positive directional selection on nodule number regardless of light environment. Our results suggest that G×E can maintain genetic variation in a mutualism-related trait that is under consistent positive directional selection across light environments.
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Affiliation(s)
- Priya Vaidya
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S3B2, Canada
- Corresponding author
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S3B2, Canada
- Koffler Scientific Reserve at Joker's Hill, University of Toronto, Toronto, ON M5S3B2, Canada
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38
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Sanaei E, Charlat S, Engelstädter J. Wolbachia
host shifts: routes, mechanisms, constraints and evolutionary consequences. Biol Rev Camb Philos Soc 2020; 96:433-453. [DOI: 10.1111/brv.12663] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Ehsan Sanaei
- School of Biological Sciences The University of Queensland Saint Lucia Brisbane QLD 4067 Australia
| | - Sylvain Charlat
- Laboratoire de Biométrie et Biologie Evolutive Université de Lyon, Université Lyon 1, CNRS, UMR 5558 43 boulevard du 11 novembre 1918 Villeurbanne F‐69622 France
| | - Jan Engelstädter
- School of Biological Sciences The University of Queensland Saint Lucia Brisbane QLD 4067 Australia
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Koskella B, Bergelson J. The study of host-microbiome (co)evolution across levels of selection. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190604. [PMID: 32772660 PMCID: PMC7435161 DOI: 10.1098/rstb.2019.0604] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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Pérez LI, Gundel PE, Zabalgogeazcoa I, Omacini M. An ecological framework for understanding the roles of Epichloë endophytes on plant defenses against fungal diseases. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Abrego N, Huotari T, Tack AJM, Lindahl BD, Tikhonov G, Somervuo P, Martin Schmidt N, Ovaskainen O, Roslin T. Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient. Ecol Evol 2020; 10:8989-9002. [PMID: 32884673 PMCID: PMC7452766 DOI: 10.1002/ece3.6604] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 06/02/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022] Open
Abstract
How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.
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Affiliation(s)
- Nerea Abrego
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
- Centre for Biodiversity DynamicsDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Tea Huotari
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Ayco J. M. Tack
- Department of EcologyEnvironment and Plant SciencesStockholm UniversityStockholmSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Gleb Tikhonov
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Computational Systems Biology groupDepartment of Computer ScienceAalto UniversityEspooFinland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | | | - Otso Ovaskainen
- Centre for Biodiversity DynamicsDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | - Tomas Roslin
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
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Parmentier T, De Laender F, Bonte D. The topology and drivers of ant-symbiont networks across Europe. Biol Rev Camb Philos Soc 2020; 95:1664-1688. [PMID: 32691527 DOI: 10.1111/brv.12634] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/21/2022]
Abstract
Intimate associations between different species drive community composition across ecosystems. Understanding the ecological and evolutionary drivers of these symbiotic associations is challenging because their structure eventually determines stability and resilience of the entire species network. Here, we compiled a detailed database on naturally occurring ant-symbiont networks in Europe to identify factors that affect symbiont network topology. These networks host an unrivalled diversity of macrosymbiotic associations, spanning the entire mutualism-antagonism continuum, including: (i) myrmecophiles - commensalistic and parasitic arthropods; (ii) trophobionts - mutualistic aphids, scale insects, planthoppers and caterpillars; (iii) social parasites - parasitic ant species; (iv) parasitic helminths; and (v) parasitic fungi. We dissected network topology to investigate what determines host specificity, symbiont species richness, and the capacity of different symbiont types to switch hosts. We found 722 macrosymbionts (multicellular symbionts) associated with European ants. Symbiont type explained host specificity and the average relatedness of the host species. Social parasites were associated with few hosts that were phylogenetically highly related, whereas the other symbiont types interacted with a larger number of hosts across a wider taxonomic distribution. The hosts of trophobionts were the least phylogenetically related across all symbiont types. Colony size, host range and habitat type predicted total symbiont richness: ant hosts with larger colony size, a larger distribution range or with a wider habitat range contained more symbiont species. However, we found that different sets of host factors affected diversity in the different types of symbionts. Ecological factors, such as colony size, host range and niche width predominantly determined myrmecophile species richness, whereas host phylogeny was the most important predictor of mutualistic trophobiont, social parasite and parasitic helminth species richness. Lastly, we found that hosts with a common biogeographic history support a more similar community of symbionts. Phylogenetically related hosts also shared more trophobionts, social parasites and helminths, but not myrmecophiles. Taken together, these results suggest that ecological and evolutionary processes structure host specificity and symbiont richness in large-scale ant-symbiont networks, but these drivers may shift in importance depending on the type of symbiosis. Our findings highlight the potential of well-characterized bipartite networks composed of different types of symbioses to identify candidate processes driving community composition.
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Affiliation(s)
- Thomas Parmentier
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, Ghent, B-9000, Belgium.,Research Unit of Environmental and Evolutionary Biology, Namur Institute of Complex Systems, and Institute of Life, Earth, and the Environment, University of Namur, Namur, 5000, Belgium
| | - Frederik De Laender
- Research Unit of Environmental and Evolutionary Biology, Namur Institute of Complex Systems, and Institute of Life, Earth, and the Environment, University of Namur, Namur, 5000, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, Ghent, B-9000, Belgium
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43
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Nishad R, Ahmed T, Rahman VJ, Kareem A. Modulation of Plant Defense System in Response to Microbial Interactions. Front Microbiol 2020; 11:1298. [PMID: 32719660 PMCID: PMC7350780 DOI: 10.3389/fmicb.2020.01298] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/20/2020] [Indexed: 01/09/2023] Open
Abstract
At different stages throughout their life cycle, plants often encounter several pathogenic microbes that challenge plant growth and development. The sophisticated innate plant immune system prevents the growth of harmful microbes via two interconnected defense strategies based on pathogen perception. These strategies involve microbe-associated molecular pattern-triggered immunity and microbial effector-triggered immunity. Both these immune responses induce several defense mechanisms for restricting pathogen attack to protect against pathogens and terminate their growth. Plants often develop immune memory after an exposure to pathogens, leading to systemic acquired resistance. Unlike that with harmful microbes, plants make friendly interactions with beneficial microbes for boosting their plant immune system. A spike in recent publications has further improved our understanding of the immune responses in plants as triggered by interactions with microbes. The present study reviews our current understanding of how plant–microbe interactions can activate the sophisticated plant immune system at the molecular level. We further discuss how plant-microbe interaction boost the immune system of plants by demonstrating the examples of Mycorrhizal and Rhizobial association and how these plant-microbe interactions can be exploited to engineer disease resistance and crop improvement.
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Affiliation(s)
- Resna Nishad
- Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha, Qatar
| | - Talaat Ahmed
- Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha, Qatar.,Environmental Science Centre, Qatar University, Doha, Qatar
| | | | - Abdul Kareem
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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44
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Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
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Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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45
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Bodawatta KH, Synek P, Bos N, Garcia-Del-Rey E, Koane B, Marki PZ, Albrecht T, Lifjeld J, Poulsen M, Munclinger P, Sam K, Jønsson KA. Spatiotemporal patterns of avian host-parasite interactions in the face of biogeographical range expansions. Mol Ecol 2020; 29:2431-2448. [PMID: 32470165 DOI: 10.1111/mec.15486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 11/27/2022]
Abstract
Exploration of interactions between hosts and parasitic symbionts is important for our understanding of the temporal and spatial distribution of organisms. For example, host colonization of new geographical regions may alter levels of infections and parasite specificity, and even allow hosts to escape from co-evolved parasites, consequently shaping spatial distributions and community structure of both host and parasite. Here we investigate the effect of host colonization of new regions and the elevational distribution of host-parasite associations between birds and their vector-transmitted haemosporidian blood parasites in two geological and geographical settings: mountains of New Guinea and the Canary Islands. Our results demonstrate that bird communities in younger regions have significantly lower levels of parasitism compared to those of older regions. Furthermore, host-parasite network analyses demonstrate that blood parasites may respond differently after arriving to a new region, through adaptations that allow for either expanding (Canary Islands) or retaining (New Guinea) their host niches. The spatial prevalence patterns along elevational gradients differed in the two regions, suggesting that region-specific biotic (e.g., host community) and abiotic factors (e.g., temperature) govern prevalence patterns. Our findings suggest that the spatiotemporal range dynamics in host-parasite systems are driven by multiple factors, but that host and parasite community compositions and colonization histories are of particular importance.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Petr Synek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nick Bos
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eduardo Garcia-Del-Rey
- Macaronesian Institute of Field Ornithology, Santa Cruz de Tenerife, Canary Islands, Spain
| | - Bonny Koane
- The New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Petter Z Marki
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Lifjeld
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Pavel Munclinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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46
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Cappelli SL, Pichon NA, Kempel A, Allan E. Sick plants in grassland communities: a growth-defense trade-off is the main driver of fungal pathogen abundance. Ecol Lett 2020; 23:1349-1359. [PMID: 32455502 DOI: 10.1111/ele.13537] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/29/2020] [Accepted: 04/30/2020] [Indexed: 01/21/2023]
Abstract
Aboveground fungal pathogens can substantially reduce biomass production in grasslands. However, we lack a mechanistic understanding of the drivers of fungal pathogen infection and impact. Using a grassland global change and biodiversity experiment we show that the trade-off between plant growth and defense is the main determinant of infection incidence. In contrast, nitrogen addition only indirectly increased incidence via shifting plant communities towards faster growing species. Plant diversity did not decrease incidence, likely because spillover of generalist pathogens or dominance of susceptible plants counteracted negative diversity effects. A fungicide treatment increased plant biomass production and high levels of infection incidence were associated with reduced biomass. However, pathogen impact was context dependent and infection incidence reduced biomass more strongly in diverse communities. Our results show that a growth-defense trade-off is the key driver of pathogen incidence, but pathogen impact is determined by several mechanisms and may depend on pathogen community composition.
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Affiliation(s)
- Seraina L Cappelli
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Noémie A Pichon
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Anne Kempel
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Eric Allan
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
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47
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Schroeder JW, Dobson A, Mangan SA, Petticord DF, Herre EA. Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model. Nat Commun 2020; 11:2204. [PMID: 32371877 PMCID: PMC7200732 DOI: 10.1038/s41467-020-16047-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023] Open
Abstract
Empirical studies show that plant-soil feedbacks (PSF) can generate negative density dependent (NDD) recruitment capable of maintaining plant community diversity at landscape scales. However, the observation that common plants often exhibit relatively weaker NDD than rare plants at local scales is difficult to reconcile with the maintenance of overall plant diversity. We develop a spatially explicit simulation model that tracks the community dynamics of microbial mutualists, pathogens, and their plant hosts. We find that net PSF effects vary as a function of both host abundance and key microbial traits (e.g., host affinity) in ways that are compatible with both common plants exhibiting relatively weaker local NDD, while promoting overall species diversity. The model generates a series of testable predictions linking key microbial traits and the relative abundance of host species, to the strength and scale of PSF and overall plant community diversity.
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Affiliation(s)
- John W Schroeder
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama.
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Andrew Dobson
- Princeton University, Princeton, NJ, USA
- Santa Fe Institute, Hyde Park Road, Santa Fe, NM, USA
| | - Scott A Mangan
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
- Washington University, St. Louis, MO, USA
| | - Daniel F Petticord
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
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48
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Muggia L, Nelsen MP, Kirika PM, Barreno E, Beck A, Lindgren H, Lumbsch HT, Leavitt SD. Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): An impetus for developing an integrated taxonomy. Mol Phylogenet Evol 2020; 149:106821. [PMID: 32294545 DOI: 10.1016/j.ympev.2020.106821] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022]
Abstract
Lichens provide valuable systems for studying symbiotic interactions. In lichens, these interactions are frequently described in terms of availability, selectivity and specificity of the mycobionts and photobionts towards one another. The lichen-forming, green algal genus Trebouxia Puymaly is among the most widespread photobiont, associating with a broad range of lichen-forming fungi. To date, 29 species have been described, but studies consistently indicate that the vast majority of species-level lineages still lack formal description, and new, previously unrecognized lineages are frequently reported. To reappraise the diversity and the evolutionary relationships of species-level lineages in Trebouxia, we assembled DNA sequence data from over 1600 specimens, compiled from a range of sequences from previously published studies, axenic algal cultures, and lichens collected from poorly sampled regions. From these samples, we selected representatives of the currently known genetic diversity in the lichenized Trebouxia and inferred a phylogeny from multi-locus sequence data (ITS, rbcL, cox2). We demonstrate that the current formally described species woefully underrepresent overall species-level diversity in this important lichen-forming algal genus. We anticipate that an integrative taxonomic approach, incorporating morphological and physiological data from axenic cultures with genetic data, will be required to establish a robust, comprehensive taxonomy for Trebouxia. The data presented here provide an important impetus and reference dataset for more reliably characterizing diversity in lichenized algae and in using lichens to investigate the evolution of symbioses and holobionts.
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Affiliation(s)
- Lucia Muggia
- University of Trieste, Department of Life Sciences, via Giorgieri 10, 34127 Trieste, Italy
| | | | - Paul M Kirika
- Botany Department, EA Herbarium, National Museums of Kenya, P.O. Box 40658-00100, Nairobi, Kenya
| | - Eva Barreno
- Botánica, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Fac. CC. Biológicas, Universitat de València, C/ Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Andreas Beck
- Botanische Staatssammlung München, SNSB-BSM, Menzinger Str. 67, D-80638 Munich, Germany
| | | | | | - Steven D Leavitt
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA.
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49
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Affiliation(s)
- Takefumi Nakazawa
- Dept of Life Sciences, National Cheng Kung Univ. No.1, University Road Tainan City 701 Taiwan
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50
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Heath KD, Podowski JC, Heniff S, Klinger CR, Burke PV, Weese DJ, Yang WH, Lau JA. Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis. AMERICAN JOURNAL OF BOTANY 2020; 107:229-238. [PMID: 32072629 DOI: 10.1002/ajb2.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/08/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen. Because partner quality in mutualisms is genotype-dependent, within-species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here we ask whether partner quality variation in rhizobia mediates the response of host plants to changing light availability, and conversely, whether light alters the expression of partner quality variation. METHODS We inoculated clover hosts with 11 strains of Rhizobium leguminosarum that differed in partner quality, grew plants under either ambient or low light conditions in the greenhouse, and measured plant growth, nodule traits, and foliar nutrient composition. RESULTS Light availability and rhizobium inoculum interactively determined plant growth, and variation in rhizobium partner quality was more apparent in ambient light. CONCLUSIONS Our results suggest that variation in the costs and benefits of rhizobium symbionts mediate host responses to light availability and that rhizobium strain variation might more important in higher-light environments. Our work adds to a growing appreciation for the role of microbial intraspecific and interspecific diversity in mediating extended phenotypes in their hosts and suggests an important role for light availability in the ecology and evolution of legume-rhizobium symbiosis.
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Affiliation(s)
- Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Justin C Podowski
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Stephanie Heniff
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Christie R Klinger
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Patricia V Burke
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Dylan J Weese
- Department of Biology, St. Ambrose University, Davenport, IA, 52803, USA
| | - Wendy H Yang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Jennifer A Lau
- W. K. Kellogg Biological Station and Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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