1
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Chen M, Yang J, Xue C, Tu T, Su Z, Feng H, Shi M, Zeng G, Zhang D, Qian X. Community composition of phytopathogenic fungi significantly influences ectomycorrhizal fungal communities during subtropical forest succession. Appl Microbiol Biotechnol 2024; 108:99. [PMID: 38204135 PMCID: PMC10781812 DOI: 10.1007/s00253-023-12992-5] [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: 01/27/2023] [Revised: 11/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Ectomycorrhizal fungi (EMF) can form symbiotic relationships with plants, aiding in plant growth by providing access to nutrients and defense against phytopathogenic fungi. In this context, factors such as plant assemblages and soil properties can impact the interaction between EMF and phytopathogenic fungi in forest soil. However, there is little understanding of how these fungal interactions evolve as forests move through succession stages. In this study, we used high-throughput sequencing to investigate fungal communities in young, intermediate, and old subtropical forests. At the genus level, EMF communities were dominated by Sebacina, Russula, and Lactarius, while Mycena was the most abundant genus in pathogenic fungal communities. The relative abundances of EMF and phytopathogenic fungi in different stages showed no significant difference with the regulation of different factors. We discovered that interactions between phytopathogenic fungi and EMF maintained a dynamic balance under the influence of the differences in soil quality attributed to each forest successional stage. The community composition of phytopathogenic fungi is one of the strong drivers in shaping EMF communities over successions. In addition, the EMF diversity was significantly related to plant diversity, and these relationships varied among successional stages. Despite the regulation of various factors, the positive relationship between the diversity of phytopathogenic fungi and EMF remained unchanged. However, there is no significant difference in the ratio of the abundance of EMF and phytopathogenic fungi over the course of successions. These results will advance our understanding of the biodiversity-ecosystem functioning during forest succession. KEY POINTS: •Community composition of both EMF and phytopathogenic fungi changed significantly over forest succession. •Phytopathogenic fungi is a key driver in shaping EMF community. •The effect of plant Shannon's diversity on EMF communities changed during the forest aging process.
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Affiliation(s)
- Meirong Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiazhi Yang
- Guangdong Forestry Survey and Planning Institute, Guangzhou, China
| | - Chunquan Xue
- Guangdong Forestry Survey and Planning Institute, Guangzhou, China.
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiyao Su
- South China Agriculture University, Guangzhou, China
| | - Hanhua Feng
- Guangdong Forestry Survey and Planning Institute, Guangzhou, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gui Zeng
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xin Qian
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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2
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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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3
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Cui G, Mi J, Moret A, Menzies J, Zhong H, Li A, Hung SH, Al-Babili S, Aranda M. A carbon-nitrogen negative feedback loop underlies the repeated evolution of cnidarian-Symbiodiniaceae symbioses. Nat Commun 2023; 14:6949. [PMID: 37914686 PMCID: PMC10620218 DOI: 10.1038/s41467-023-42582-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Symbiotic associations with Symbiodiniaceae have evolved independently across a diverse range of cnidarian taxa including reef-building corals, sea anemones, and jellyfish, yet the molecular mechanisms underlying their regulation and repeated evolution are still elusive. Here, we show that despite their independent evolution, cnidarian hosts use the same carbon-nitrogen negative feedback loop to control symbiont proliferation. Symbiont-derived photosynthates are used to assimilate nitrogenous waste via glutamine synthetase-glutamate synthase-mediated amino acid biosynthesis in a carbon-dependent manner, which regulates the availability of nitrogen to the symbionts. Using nutrient supplementation experiments, we show that the provision of additional carbohydrates significantly reduces symbiont density while ammonium promotes symbiont proliferation. High-resolution metabolic analysis confirmed that all hosts co-incorporated glucose-derived 13C and ammonium-derived 15N via glutamine synthetase-glutamate synthase-mediated amino acid biosynthesis. Our results reveal a general carbon-nitrogen negative feedback loop underlying these symbioses and provide a parsimonious explanation for their repeated evolution.
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Affiliation(s)
- Guoxin Cui
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia.
| | - Jianing Mi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, the BioActives Lab, Center for Desert Agriculture, Thuwal, 23955- 6900, Saudi Arabia
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Alessandro Moret
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Jessica Menzies
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Huawen Zhong
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Angus Li
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Shiou-Han Hung
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, the BioActives Lab, Center for Desert Agriculture, Thuwal, 23955- 6900, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, the Plant Science Program, Thuwal, 23955- 6900, Saudi Arabia
| | - Manuel Aranda
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia.
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4
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Van Cauwenberghe J, Simms EL. How might bacteriophages shape biological invasions? mBio 2023; 14:e0188623. [PMID: 37812005 PMCID: PMC10653932 DOI: 10.1128/mbio.01886-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Ellen L. Simms
- Department of Integrative Biology, University of California, Berkeley, California, USA
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5
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Rahman A, Manci M, Nadon C, Perez IA, Farsamin WF, Lampe MT, Le TH, Torres Martínez L, Weisberg AJ, Chang JH, Sachs JL. Competitive interference among rhizobia reduces benefits to hosts. Curr Biol 2023; 33:2988-3001.e4. [PMID: 37490853 DOI: 10.1016/j.cub.2023.06.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
The capacity of beneficial microbes to compete for host infection-and the ability of hosts to discriminate among them-introduces evolutionary conflict that is predicted to destabilize mutualism. We investigated fitness outcomes in associations between legumes and their symbiotic rhizobia to characterize fitness impacts of microbial competition. Diverse Bradyrhizobium strains varying in their capacity to fix nitrogen symbiotically with a common host plant, Acmispon strigosus, were tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations. We analyzed the effects of interstrain competition and host discrimination on symbiotic-interaction outcomes by relativizing fitness proxies to clonally infected and uninfected controls. More than one thousand root nodules of coinoculated plants were genotyped to quantify strain occupancy, and the Bradyrhizobium strain genome sequences were analyzed to uncover the genetic bases of interstrain competition outcomes. Strikingly, interstrain competition favored a fast-growing, minimally beneficial rhizobia strain. Host benefits were significantly diminished in coinoculation treatments relative to expectations from clonally inoculated controls, consistent with competitive interference among rhizobia that reduced both nodulation and plant growth. Competition traits appear polygenic, linked with inter-strain allelopathic interactions in the rhizosphere. This study confirms that competition among strains can destabilize mutualism by favoring microbes that are superior in colonizing host tissues but provide minimal benefits to host plants. Moreover, our findings help resolve the paradox that despite efficient host control post infection, legumes nonetheless encounter rhizobia that vary in their nitrogen fixation.
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Affiliation(s)
- Arafat Rahman
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Max Manci
- Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Cassandra Nadon
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Ivan A Perez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Warisha F Farsamin
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew T Lampe
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Tram H Le
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Lorena Torres Martínez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, St. Mary's College of Maryland, St. Mary's City, MD 20686, USA
| | - Alexandra J Weisberg
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joel L Sachs
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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6
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Montoya AP, Wendlandt CE, Benedict AB, Roberts M, Piovia-Scott J, Griffitts JS, Porter SS. Hosts winnow symbionts with multiple layers of absolute and conditional discrimination mechanisms. Proc Biol Sci 2023; 290:20222153. [PMID: 36598018 PMCID: PMC9811631 DOI: 10.1098/rspb.2022.2153] [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] [Indexed: 01/05/2023] Open
Abstract
In mutualism, hosts select symbionts via partner choice and preferentially direct more resources to symbionts that provide greater benefits via sanctions. At the initiation of symbiosis, prior to resource exchange, it is not known how the presence of multiple symbiont options (i.e. the symbiont social environment) impacts partner choice outcomes. Furthermore, little research addresses whether hosts primarily discriminate among symbionts via sanctions, partner choice or a combination. We inoculated the legume, Acmispon wrangelianus, with 28 pairs of fluorescently labelled Mesorhizobium strains that vary continuously in quality as nitrogen-fixing symbionts. We find that hosts exert robust partner choice, which enhances their fitness. This partner choice is conditional such that a strain's success in initiating nodules is impacted by other strains in the social environment. This social genetic effect is as important as a strain's own genotype in determining nodulation and has both transitive (consistent) and intransitive (idiosyncratic) effects on the probability that a symbiont will form a nodule. Furthermore, both absolute and conditional partner choice act in concert with sanctions, among and within nodules. Thus, multiple forms of host discrimination act as a series of sieves that optimize host benefits and select for costly symbiont cooperation in mixed symbiont populations.
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Affiliation(s)
- Angeliqua P. Montoya
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Camille E. Wendlandt
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Alex B. Benedict
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Miles Roberts
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Jonah Piovia-Scott
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Stephanie S. Porter
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
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7
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Warrington S, Ellis AG, Keet JH, Le Roux JJ. How does familiarity in rhizobial interactions impact the performance of invasive and native legumes? NEOBIOTA 2022. [DOI: 10.3897/neobiota.72.79620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mutualisms can be disrupted when non-native plants are introduced into novel environments, potentially impacting their establishment success. Introduced species can reassemble mutualisms by forming novel associations with resident biota or by maintaining familiar associations when they are co-introduced with their mutualists. Invasive Australian Acacia species in South Africa have formed nitrogen-fixing rhizobium mutualisms using both pathways.
Here we examined the contributions of novel vs familiar rhizobial associations to the performance of Acacia saligna across different soils within South Africa’s Core Cape Subregion (CCR), and the concomitant impacts of exotic rhizobia on the endemic legume, Psoralea pinnata. We grew each legume with and without Australian Bradyrhizobium strains across various CCR soil types in a glasshouse. We identified root nodule rhizobium communities associating with seedlings grown in each treatment combination using next-generation sequencing (NGS) techniques.
Our results show that different CCR soils affected growth performances of seedlings for both species while the addition of Australian bradyrhizobia affected growth performances of A. saligna, but not P. pinnata. NGS data revealed that each legume associated mostly with their familiar rhizobial partners, regardless of soil conditions or inoculum treatment. Acacia saligna predominantly associated with Australian bradyrhizobia, even when grown in soils without inoculum, while P. pinnata largely associated with native South African Mesorhizobium strains.
Our study suggests that exotic Australian bradyrhizobia are already present and widespread in pristine CCR soils, and that mutualist limitation is not an impediment to further acacia invasion in the region. The ability of P. pinnata to sanction Australian Bradyrhizobium strains suggests that this species may be a good candidate for restoration efforts following the removal of acacias in CCR habitats.
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8
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Wendlandt CE, Gano-Cohen KA, Stokes PJN, Jonnala BNR, Zomorrodian AJ, Al-Moussawi K, Sachs JL. Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition. Oecologia 2022; 198:419-430. [PMID: 35067801 DOI: 10.1007/s00442-022-05116-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
Natural landscapes are increasingly impacted by nitrogen enrichment from aquatic and airborne pollution sources. Nitrogen enrichment in the environment can eliminate the net benefits that plants gain from nitrogen-fixing microbes such as rhizobia, potentially altering host-mediated selection on nitrogen fixation. However, we know little about the long-term effects of nitrogen enrichment on this critical microbial service. Here, we sampled populations of the legume Acmispon strigosus and its associated soil microbial communities from sites spanning an anthropogenic nitrogen deposition gradient. We measured the net growth benefits plants obtained from their local soil microbial communities and quantified plant investment into nodules that house nitrogen-fixing rhizobia. We found that plant growth benefits from sympatric soil microbes did not vary in response to local soil nitrogen levels, and instead varied mainly among plant lines. Soil nitrogen levels positively predicted the number of nodules formed on sympatric plant hosts, although this was likely due to plant genotypic variation in nodule formation, rather than variation among soil microbial communities. The capacity of all the tested soil microbial communities to improve plant growth is consistent with plant populations imposing strong selection on rhizobial nitrogen fixation despite elevated soil nitrogen levels, suggesting that host control traits in A. strigosus are stable under long-term nutrient enrichment.
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Affiliation(s)
- Camille E Wendlandt
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Kelsey A Gano-Cohen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Peter J N Stokes
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Basava N R Jonnala
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Avissa J Zomorrodian
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Khadija Al-Moussawi
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Joel L Sachs
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA. .,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA. .,Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA.
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9
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Basile LA, Lepek VC. Legume-rhizobium dance: an agricultural tool that could be improved? Microb Biotechnol 2021; 14:1897-1917. [PMID: 34318611 PMCID: PMC8449669 DOI: 10.1111/1751-7915.13906] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The specific interaction between rhizobia and legume roots leads to the development of a highly regulated process called nodulation, by which the atmospheric nitrogen is converted into an assimilable plant nutrient. This capacity is the basis for the use of bacterial inoculants for field crop cultivation. Legume plants have acquired tools that allow the entry of compatible bacteria. Likewise, plants can impose sanctions against the maintenance of nodules occupied by rhizobia with low nitrogen-fixing capacity. At the same time, bacteria must overcome different obstacles posed first by the environment and then by the legume. The present review describes the mechanisms involved in the regulation of the entire legume-rhizobium symbiotic process and the strategies and tools of bacteria for reaching the nitrogen-fixing state inside the nodule. Also, we revised different approaches to improve the nodulation process for a better crop yield.
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Affiliation(s)
- Laura A. Basile
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
| | - Viviana C. Lepek
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
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10
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The evolution of parasitism from mutualism in wasps pollinating the fig, Ficus microcarpa, in Yunnan Province, China. Proc Natl Acad Sci U S A 2021; 118:2021148118. [PMID: 34341115 DOI: 10.1073/pnas.2021148118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Theory identifies factors that can undermine the evolutionary stability of mutualisms. However, theory's relevance to mutualism stability in nature is controversial. Detailed comparative studies of parasitic species that are embedded within otherwise mutualistic taxa (e.g., fig pollinator wasps) can identify factors that potentially promote or undermine mutualism stability. We describe results from behavioral, morphological, phylogenetic, and experimental studies of two functionally distinct, but closely related, Eupristina wasp species associated with the monoecious host fig, Ficus microcarpa, in Yunnan Province, China. One (Eupristina verticillata) is a competent pollinator exhibiting morphologies and behaviors consistent with observed seed production. The other (Eupristina sp.) lacks these traits, and dramatically reduces both female and male reproductive success of its host. Furthermore, observations and experiments indicate that individuals of this parasitic species exhibit greater relative fitness than the pollinators, in both indirect competition (individual wasps in separate fig inflorescences) and direct competition (wasps of both species within the same fig). Moreover, phylogenetic analyses suggest that these two Eupristina species are sister taxa. By the strictest definition, the nonpollinating species represents a "cheater" that has descended from a beneficial pollinating mutualist. In sharp contrast to all 15 existing studies of actively pollinated figs and their wasps, the local F. microcarpa exhibit no evidence for host sanctions that effectively reduce the relative fitness of wasps that do not pollinate. We suggest that the lack of sanctions in the local hosts promotes the loss of specialized morphologies and behaviors crucial for pollination and, thereby, the evolution of cheating.
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11
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Quides KW, Weisberg AJ, Trinh J, Salaheldine F, Cardenas P, Lee HH, Jariwala R, Chang JH, Sachs JL. Experimental evolution can enhance benefits of rhizobia to novel legume hosts. Proc Biol Sci 2021; 288:20210812. [PMID: 34034525 PMCID: PMC8150021 DOI: 10.1098/rspb.2021.0812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a full-factorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes that vary in regulation of nodule formation. We evaluated phenotypic evolution of rhizobia by quantifying fitness, growth effects and histological features on hosts, and molecular evolution via genome resequencing. Rhizobia evolved enhanced host benefits and caused changes in nodule development in one of the four host–symbiont combinations, that appeared to be driven by reduced costs during symbiosis, rather than increased nitrogen fixation. Descendant populations included genetic changes that could alter rhizobial infection or proliferation in host tissues, but lack of evidence for fixation of these mutations weakens the results. Evolution of enhanced rhizobial benefits occurred only in a subset of experiments, suggesting a role for host–symbiont genotype interactions in mediating the evolution of enhanced benefits from symbionts.
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Affiliation(s)
- Kenjiro W Quides
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jerry Trinh
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Fathi Salaheldine
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Paola Cardenas
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Hsu-Han Lee
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Ruchi Jariwala
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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12
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Tsiknia M, Tsikou D, Papadopoulou KK, Ehaliotis C. Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant - microbiome - soil continuum. FEMS Microbiol Ecol 2021; 97:5957530. [PMID: 33155054 DOI: 10.1093/femsec/fiaa222] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/03/2020] [Indexed: 01/02/2023] Open
Abstract
Mutualistic relationships of legume plants with, either bacteria (like rhizobia) or fungi (like arbuscular mycorrhizal fungi), have been investigated intensively, usually as bi-partite interactions. However, diverse symbiotic interactions take place simultaneously or sequentially under field conditions. Their collective, but not additive, contribution to plant growth and performance remains hard to predict, and appears to be furthermore affected by crop species and genotype, non-symbiotic microbial interactions and environmental variables. The challenge is: (i) to unravel the complex overlapping mechanisms that operate between the microbial symbionts as well as between them, their hosts and the rhizosphere (ii) to understand the dynamics of the respective mechanisms in evolutionary and ecological terms. The target for agriculture, food security and the environment, is to use this insight as a solid basis for developing new integrated technologies, practices and strategies for the efficient use of beneficial microbes in legumes and other plants. We review recent advances in our understanding of the symbiotic interactions in legumes roots brought about with the aid of molecular and bioinformatics tools. We go through single symbiont-host interactions, proceed to tripartite symbiont-host interactions, appraise interactions of symbiotic and associative microbiomes with plants in the root-rhizoplane-soil continuum of habitats and end up by examining attempts to validate community ecology principles in the legume-microbe-soil biosystem.
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Affiliation(s)
- Myrto Tsiknia
- Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75 st., Athens 11855, Greece
| | - Daniela Tsikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Kalliope K Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Constantinos Ehaliotis
- Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75 st., Athens 11855, Greece
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13
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Quides KW, Salaheldine F, Jariwala R, Sachs JL. Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs. Evolution 2021; 75:1189-1200. [PMID: 33521949 DOI: 10.1111/evo.14173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 10/31/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Microbial mutualists provide substantial benefits to hosts that feed back to enhance the fitness of the associated microbes. In many systems, beneficial microbes colonize symbiotic organs, specialized host structures that house symbionts and mediate resources exchanged between parties. Mutualisms are characterized by net benefits exchanged among members of different species, however, inequalities in the magnitude of these exchanges could result in evolutionary conflict, destabilizing the mutualism. We investigated joint fitness effects of root nodule formation, the symbiotic organ of legumes that house nitrogen-fixing rhizobia in planta. We quantified host and symbiont fitness parameters dependent on the number of nodules formed using near-isogenic Lotus japonicus and Mesorhizobium loti mutants, respectively. Empirically estimated fitness functions suggest that legume and rhizobia fitness is aligned as the number of nodules formed increases from zero until the host optimum is reached, a point where aligned fitness interests shift to diverging fitness interests between host and symbiont. However, fitness conflict was only inferred when analyzing wild-type hosts along with their mutants dysregulated for control over nodule formation. These data demonstrate that to avoid conflict, hosts must tightly regulate investment into symbiotic organs maximizing their benefit to cost ratio of associating with microbes.
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Affiliation(s)
- Kenjiro W Quides
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA.,Current Institution: Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Fathi Salaheldine
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA
| | - Ruchi Jariwala
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA
| | - Joel L Sachs
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, California, 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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14
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Burghardt LT. Evolving together, evolving apart: measuring the fitness of rhizobial bacteria in and out of symbiosis with leguminous plants. THE NEW PHYTOLOGIST 2020; 228:28-34. [PMID: 31276218 DOI: 10.1111/nph.16045] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/20/2019] [Indexed: 05/11/2023]
Abstract
Most plant-microbe interactions are facultative, with microbes experiencing temporally and spatially variable selection. How this variation affects microbial evolution is poorly understood. Given its tractability and ecological and agricultural importance, the legume-rhizobia nitrogen-fixing symbiosis is a powerful model for identifying traits and genes underlying bacterial fitness. New technologies allow high-throughput measurement of the relative fitness of bacterial mutants, strains and species in mixed inocula in the host, rhizosphere and soil environments. I consider how host genetic variation (G × G), other environmental factors (G × E), and host life-cycle variation may contribute to the maintenance of genetic variation and adaptive trajectories of rhizobia - and, potentially, other facultative symbionts. Lastly, I place these findings in the context of developing beneficial inoculants in a changing climate.
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Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN, 55108, USA
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15
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Brown SP, Grillo MA, Podowski JC, Heath KD. Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula. MICROBIOME 2020; 8:139. [PMID: 32988416 PMCID: PMC7523075 DOI: 10.1186/s40168-020-00915-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/01/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. RESULTS Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. CONCLUSIONS Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes. Video Abstract.
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Affiliation(s)
- Shawn P. Brown
- Department of Plant Biology, University of Illinois, 505 S. Goodwin Ave, Urbana, IL 61801 USA
- Department of Biological Sciences, The University of Memphis, 3774 Walker Ave, Memphis, TN 38152 USA
- Center for Biodiversity Research, The University of Memphis, 3774 Walker Ave, Memphis, TN 38152 USA
| | - Michael A. Grillo
- Department of Plant Biology, University of Illinois, 505 S. Goodwin Ave, Urbana, IL 61801 USA
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60618 USA
| | - Justin C. Podowski
- Department of Plant Biology, University of Illinois, 505 S. Goodwin Ave, Urbana, IL 61801 USA
- Department of Geophysical Sciences, University of Chicago, 5734 S Ellis Ave, Chicago, IL 60637 USA
| | - Katy D. Heath
- Department of Plant Biology, University of Illinois, 505 S. Goodwin Ave, Urbana, IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Dr, Urbana, IL 61801 USA
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16
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Chomicki G, Werner GDA, West SA, Kiers ET. Compartmentalization drives the evolution of symbiotic cooperation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190602. [PMID: 32772665 DOI: 10.1098/rstb.2019.0602] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Across the tree of life, hosts have evolved mechanisms to control and mediate interactions with symbiotic partners. We suggest that the evolution of physical structures that allow hosts to spatially separate symbionts, termed compartmentalization, is a common mechanism used by hosts. Such compartmentalization allows hosts to: (i) isolate symbionts and control their reproduction; (ii) reward cooperative symbionts and punish or stop interactions with non-cooperative symbionts; and (iii) reduce direct conflict among different symbionts strains in a single host. Compartmentalization has allowed hosts to increase the benefits that they obtain from symbiotic partners across a diversity of interactions, including legumes and rhizobia, plants and fungi, squid and Vibrio, insects and nutrient provisioning bacteria, plants and insects, and the human microbiome. In cases where compartmentalization has not evolved, we ask why not. We argue that when partners interact in a competitive hierarchy, or when hosts engage in partnerships which are less costly, compartmentalization is less likely to evolve. We conclude that compartmentalization is key to understanding the evolution of symbiotic cooperation. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Guillaume Chomicki
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Gijsbert D A Werner
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK.,Netherlands Scientific Council for Government Policy, Buitenhof 34, 2513 AH Den Haag, The Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - E Toby Kiers
- Department of Ecological Science, VU University, Amsterdam, The Netherlands
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17
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Agtuca BJ, Stopka SA, Evans S, Samarah L, Liu Y, Xu D, Stacey MG, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. Metabolomic profiling of wild-type and mutant soybean root nodules using laser-ablation electrospray ionization mass spectrometry reveals altered metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1937-1958. [PMID: 32410239 DOI: 10.1111/tpj.14815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 05/18/2023]
Abstract
The establishment of the nitrogen-fixing symbiosis between soybean and Bradyrhizobium japonicum is a complex process. To document the changes in plant metabolism as a result of symbiosis, we utilized laser ablation electrospray ionization-mass spectrometry (LAESI-MS) for in situ metabolic profiling of wild-type nodules, nodules infected with a B. japonicum nifH mutant unable to fix nitrogen, nodules doubly infected by both strains, and nodules formed on plants mutated in the stearoyl-acyl carrier protein desaturase (sacpd-c) gene, which were previously shown to have an altered nodule ultrastructure. The results showed that the relative abundance of fatty acids, purines, and lipids was significantly changed in response to the symbiosis. The nifH mutant nodules had elevated levels of jasmonic acid, correlating with signs of nitrogen deprivation. Nodules resulting from the mixed inoculant displayed similar, overlapping metabolic distributions within the sectors of effective (fix+ ) and ineffective (nifH mutant, fix- ) endosymbionts. These data are inconsistent with the notion that plant sanctioning is cell autonomous. Nodules lacking sacpd-c displayed an elevation of soyasaponins and organic acids in the central necrotic regions. The present study demonstrates the utility of LAESI-MS for high-throughput screening of plant phenotypes. Overall, nodules disrupted in the symbiosis were elevated in metabolites related to plant defense.
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Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Laith Samarah
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Minviluz G Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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18
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Younginger BS, Friesen ML. Connecting signals and benefits through partner choice in plant-microbe interactions. FEMS Microbiol Lett 2020; 366:5626345. [PMID: 31730203 DOI: 10.1093/femsle/fnz217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
Abstract
Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.
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Affiliation(s)
- Brett S Younginger
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, PO Box 646420, 115 Johnson Hall, Pullman, WA 99164, USA
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19
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Perez-Lamarque B, Selosse MA, Öpik M, Morlon H, Martos F. Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy. THE NEW PHYTOLOGIST 2020; 226:1822-1835. [PMID: 32022272 DOI: 10.1111/nph.16474] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/20/2020] [Indexed: 05/27/2023]
Abstract
Although mutualistic interactions are widespread and essential in ecosystem functioning, the emergence of uncooperative cheaters threatens their stability, unless there are some physiological or ecological mechanisms limiting interactions with cheaters. In this framework, we investigated the patterns of specialization and phylogenetic distribution of mycoheterotrophic cheaters vs noncheating autotrophic plants and their respective fungi, in a global arbuscular mycorrhizal network with> 25 000 interactions. We show that mycoheterotrophy evolved repeatedly among vascular plants, suggesting low phylogenetic constraints for plants. However, mycoheterotrophic plants are significantly more specialized than autotrophic plants, and they tend to be associated with specialized and closely related fungi. These results raise new hypotheses about the mechanisms (e.g. sanctions, or habitat filtering) that actually limit the interaction of mycoheterotrophic plants and their associated fungi with the rest of the autotrophic plants. Beyond mycorrhizal symbiosis, this unprecedented comparison of mycoheterotrophic vs autotrophic plants provides a network and phylogenetic framework to assess the presence of constraints upon cheating emergences in mutualisms.
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Affiliation(s)
- Benoît Perez-Lamarque
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP39, 57 rue Cuvier, 75 005, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75 005, Paris, France
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP39, 57 rue Cuvier, 75 005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Maarja Öpik
- University of Tartu, 40 Lai Street, 51 005, Tartu, Estonia
| | - Hélène Morlon
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75 005, Paris, France
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP39, 57 rue Cuvier, 75 005, Paris, France
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20
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Gano-Cohen KA, Wendlandt CE, Al Moussawi K, Stokes PJ, Quides KW, Weisberg AJ, Chang JH, Sachs JL. Recurrent mutualism breakdown events in a legume rhizobia metapopulation. Proc Biol Sci 2020; 287:20192549. [PMID: 31992172 DOI: 10.1098/rspb.2019.2549] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet, microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium isolates gathered from a 700 km transect in California spanning 10 sampled A. strigosus populations. We clonally inoculated each Bradyrhizobium isolate onto A. strigosus hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six Bradyrhizobium isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on A. strigosus. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood.
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Affiliation(s)
- Kelsey A Gano-Cohen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Camille E Wendlandt
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Khadija Al Moussawi
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
| | - Peter J Stokes
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Kenjiro W Quides
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joel L Sachs
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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21
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Rebolleda-Gómez M, Forrester NJ, Russell AL, Wei N, Fetters AM, Stephens JD, Ashman TL. Gazing into the anthosphere: considering how microbes influence floral evolution. THE NEW PHYTOLOGIST 2019; 224:1012-1020. [PMID: 31442301 DOI: 10.1111/nph.16137] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
The flower is the hallmark of angiosperms and its evolution is key to their diversification. As knowledge of ecological interactions between flowers and their microbial communities (the anthosphere) expands, it becomes increasingly important to consider the evolutionary impacts of these associations and their potential eco-evolutionary dynamics. In this Viewpoint we synthesize current knowledge of the anthosphere within a multilevel selection framework and illustrate the potential for the extended floral phenotype (the phenotype expressed from the genes of the plant and its associated flower microbes) to evolve. We argue that flower microbes are an important, but understudied, axis of variation that shape floral trait evolution and angiosperm reproductive ecology. We highlight knowledge gaps and discuss approaches that are critical for gaining a deeper understanding of the role microbes play in mediating plant reproduction, ecology, and evolution.
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Affiliation(s)
- María Rebolleda-Gómez
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Avery L Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Andrea M Fetters
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jessica D Stephens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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22
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Ansorge R, Romano S, Sayavedra L, Porras MÁG, Kupczok A, Tegetmeyer HE, Dubilier N, Petersen J. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Nat Microbiol 2019; 4:2487-2497. [DOI: 10.1038/s41564-019-0572-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/28/2019] [Indexed: 12/13/2022]
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23
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Garcia JR, Larsen TJ, Queller DC, Strassmann JE. Fitness costs and benefits vary for two facultative Burkholderia symbionts of the social amoeba, Dictyostelium discoideum. Ecol Evol 2019; 9:9878-9890. [PMID: 31534701 PMCID: PMC6745654 DOI: 10.1002/ece3.5529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Hosts and their associated microbes can enter into different relationships, which can range from mutualism, where both partners benefit, to exploitation, where one partner benefits at the expense of the other. Many host-microbe relationships have been presumed to be mutualistic, but frequently only benefits to the host, and not the microbial symbiont, have been considered. Here, we address this issue by looking at the effect of host association on the fitness of two facultative members of the Dictyostelium discoideum microbiome (Burkholderia agricolaris and Burkholderia hayleyella). Using two indicators of bacterial fitness, growth rate and abundance, we determined the effect of D. discoideum on Burkholderia fitness. In liquid culture, we found that D. discoideum amoebas lowered the growth rate of both Burkholderia species. In soil microcosms, we tracked the abundance of Burkholderia grown with and without D. discoideum over a month and found that B. hayleyella had larger populations when associating with D. discoideum while B. agricolaris was not significantly affected. Overall, we find that both B. agricolaris and B. hayleyella pay a cost to associate with D. discoideum, but B. hayleyella can also benefit under some conditions. Understanding how fitness varies in facultative symbionts will help us understand the persistence of host-symbiont relationships. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://openscholarship.wustl.edu/data/15/.
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Affiliation(s)
- Justine R. Garcia
- Department of BiologyWashington University in St. LouisSt. LouisMOUSA
- Present address:
Department of BiologyNew Mexico Highlands UniversityLas VegasNMUSA
| | - Tyler J. Larsen
- Department of BiologyWashington University in St. LouisSt. LouisMOUSA
| | - David C. Queller
- Department of BiologyWashington University in St. LouisSt. LouisMOUSA
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24
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Ye S, Badhiwala KN, Robinson JT, Cho WH, Siemann E. Thermal plasticity of a freshwater cnidarian holobiont: detection of trans-generational effects in asexually reproducing hosts and symbionts. THE ISME JOURNAL 2019; 13:2058-2067. [PMID: 31015561 PMCID: PMC6775974 DOI: 10.1038/s41396-019-0413-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/16/2019] [Accepted: 03/15/2019] [Indexed: 11/08/2022]
Abstract
Understanding factors affecting the susceptibility of organisms to thermal stress is of enormous interest in light of our rapidly changing climate. When adaptation is limited, thermal acclimation and deacclimation abilities of organisms are critical for population persistence through a period of thermal stress. Holobionts (hosts plus associated symbionts) are key components of various ecosystems, such as coral reefs, yet the contributions of their two partners to holobiont thermal plasticity are poorly understood. Here, we tested thermal plasticity of the freshwater cnidarian Hydra viridissima (green hydra) using individual behavior and population responses. We found that algal presence initially reduced hydra thermal tolerance. Hydra with algae (symbiotic hydra) had comparable acclimation rates, deacclimation rates, and thermal tolerance after acclimation to those without algae (aposymbiotic hydra) but they had higher acclimation capacity. Acclimation of the host (hydra) and/or symbiont (algae) to elevated temperatures increased holobiont thermal tolerance and these effects persisted for multiple asexual generations. In addition, acclimated algae presence enhanced hydra fitness under prolonged sublethal thermal stress, especially when food was limited. Our study indicates while less intense but sublethal stress may favor symbiotic organisms by allowing them to acclimate, sudden large, potentially lethal fluctuations in climate stress likely favor aposymbiotic organisms. It also suggests that thermally stressed colonies of holobionts could disperse acclimated hosts and/or symbionts to other colonies, thereby reducing their vulnerability to climate change.
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Affiliation(s)
- Siao Ye
- Department of Biosciences, Rice University, Houston, TX, 77005, USA.
| | | | - Jacob T Robinson
- Bioengineering Department, Rice University, Houston, TX, 77005, USA
- Electrical and Computer Engineering Department, Rice University, Houston, TX, 77005, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Won Hee Cho
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
| | - Evan Siemann
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
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Gano‐Cohen KA, Wendlandt CE, Stokes PJ, Blanton MA, Quides KW, Zomorrodian A, Adinata ES, Sachs JL. Interspecific conflict and the evolution of ineffective rhizobia. Ecol Lett 2019; 22:914-924. [DOI: 10.1111/ele.13247] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/07/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Kelsey A. Gano‐Cohen
- Department of Microbiology and Plant Pathology University of California Riverside CA USA
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Camille E. Wendlandt
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside CA USA
| | - Peter J. Stokes
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Mia A. Blanton
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Kenjiro W. Quides
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Avissa Zomorrodian
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Eunice S. Adinata
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
| | - Joel L. Sachs
- Department of Microbiology and Plant Pathology University of California Riverside CA USA
- Department of Evolution Ecology & Organismal Biology University of California Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside CA USA
- Institute for Integrative Genome Biology University of California Riverside CA USA
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME JOURNAL 2019; 13:1831-1844. [PMID: 30877285 DOI: 10.1038/s41396-019-0398-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.
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Wendlandt CE, Regus JU, Gano-Cohen KA, Hollowell AC, Quides KW, Lyu JY, Adinata ES, Sachs JL. Host investment into symbiosis varies among genotypes of the legume Acmispon strigosus, but host sanctions are uniform. THE NEW PHYTOLOGIST 2019; 221:446-458. [PMID: 30084172 DOI: 10.1111/nph.15378] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/05/2018] [Indexed: 05/26/2023]
Abstract
Efficient host control predicts the extirpation of ineffective symbionts, but they are nonetheless widespread in nature. We tested three hypotheses for the maintenance of symbiotic variation in rhizobia that associate with a native legume: partner mismatch between host and symbiont, such that symbiont effectiveness varies with host genotype; resource satiation, whereby extrinsic sources of nutrients relax host control; and variation in host control among host genotypes. We inoculated Acmispon strigosus from six populations with three Bradyrhizobium strains that vary in symbiotic effectiveness on sympatric hosts. We measured proxies of host and symbiont fitness in single- and co-inoculations under fertilization treatments of zero added nitrogen (N) and near-growth-saturating N. We examined two components of host control: 'host investment' into nodule size during single- and co-inoculations, and 'host sanctions' against less effective strains during co-inoculations. The Bradyrhizobium strains displayed conserved growth effects on hosts, and host control did not decline under experimental fertilization. Host sanctions were robust in all hosts, but host lines from different populations varied significantly in measures of host investment in both single- and co-inoculation experiments. Variation in host investment could promote variation in symbiotic effectiveness and prevent the extinction of ineffective Bradyrhizobium from natural populations.
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Affiliation(s)
- Camille E Wendlandt
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - John U Regus
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Kelsey A Gano-Cohen
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Amanda C Hollowell
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Kenjiro W Quides
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Jonathan Y Lyu
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Eunice S Adinata
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Joel L Sachs
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
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Sachs JL, Quides KW, Wendlandt CE. Legumes versus rhizobia: a model for ongoing conflict in symbiosis. THE NEW PHYTOLOGIST 2018; 219:1199-1206. [PMID: 29845625 DOI: 10.1111/nph.15222] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/04/2018] [Indexed: 05/21/2023]
Abstract
Contents Summary 1199 I. Introduction 1199 II. Selecting beneficial symbionts: one problem, many solutions 1200 III. Control and conflict over legume nodulation 1201 IV. Control and conflict over nodule growth and senescence 1204 V. Conclusion 1204 Acknowledgements 1205 References 1205 SUMMARY: The legume-rhizobia association is a powerful model of the limits of host control over microbes. Legumes regulate the formation of root nodules that house nitrogen-fixing rhizobia and adjust investment into nodule development and growth. However, the range of fitness outcomes in these traits reveals intense conflicts of interest between the partners. New work that we review and synthesize here shows that legumes have evolved varied mechanisms of control over symbionts, but that host control is often subverted by rhizobia. An outcome of this conflict is that both legumes and rhizobia have evolved numerous traits that can improve their own short-term fitness in this interaction, but little evidence exists for any net improvement in the joint trait of nitrogen fixation.
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Affiliation(s)
- Joel L Sachs
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Kenjiro W Quides
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Camille E Wendlandt
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
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Masson-Boivin C, Sachs JL. Symbiotic nitrogen fixation by rhizobia-the roots of a success story. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:7-15. [PMID: 29289792 DOI: 10.1016/j.pbi.2017.12.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 05/12/2023]
Abstract
By evolving the dual capacity of intracellular survival and symbiotic nitrogen fixation in legumes, rhizobia have achieved an ecological and evolutionary success that has reshaped our biosphere. Despite complex challenges, including a dual lifestyle of intracellular infection separated by a free-living phase in soil, rhizobial symbiosis has spread horizontally to hundreds of bacterial species and geographically throughout the globe. This symbiosis has also persisted and been reshaped through millions of years of history. Here, we summarize recent advances in our understanding of the molecular mechanisms, ecological settings, and evolutionary pathways that are collectively responsible for this symbiotic success story. We offer predictions of how this symbiosis can evolve under new influences and for the benefit of a burgeoning human population.
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Affiliation(s)
| | - Joel L Sachs
- Department of Evolution Ecology and Organismal Biology, University of California, Riverside, CA, USA
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30
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Pahua VJ, Stokes PJN, Hollowell AC, Regus JU, Gano‐Cohen KA, Wendlandt CE, Quides KW, Lyu JY, Sachs JL. Fitness variation among host species and the paradox of ineffective rhizobia. J Evol Biol 2018; 31:599-610. [DOI: 10.1111/jeb.13249] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 01/12/2018] [Accepted: 01/29/2018] [Indexed: 01/31/2023]
Affiliation(s)
- V. J. Pahua
- Department of Evolution Ecology and Organismal Biology University of California Riverside CA USA
| | - P. J. N. Stokes
- Department of Botany and Plant Sciences University of California Riverside CA USA
| | - A. C. Hollowell
- Department of Evolution Ecology and Organismal Biology University of California Riverside CA USA
| | - J. U. Regus
- Department of Evolution Ecology and Organismal Biology University of California Riverside CA USA
| | - K. A. Gano‐Cohen
- Department of Evolution Ecology and Organismal Biology University of California Riverside CA USA
| | - C. E. Wendlandt
- Department of Botany and Plant Sciences University of California Riverside CA USA
| | - K. W. Quides
- Department of Evolution Ecology and Organismal Biology University of California Riverside CA USA
| | - J. Y. Lyu
- Department of Evolution Ecology and Organismal Biology University of California Riverside CA USA
| | - J. L. Sachs
- Department of Evolution Ecology and Organismal Biology University of California Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside CA USA
- Institute for Integrative Genome Biology University of California Riverside CA USA
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31
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Forrester NJ, Ashman TL. The direct effects of plant polyploidy on the legume-rhizobia mutualism. ANNALS OF BOTANY 2018; 121:209-220. [PMID: 29182713 PMCID: PMC5808787 DOI: 10.1093/aob/mcx121] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/08/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Polyploidy is known to significantly alter plant genomes, phenotypes and interactions with the abiotic environment, yet the impacts of polyploidy on plant-biotic interactions are less well known. A particularly important plant-biotic interaction is the legume-rhizobia mutualism, in which rhizobia fix atmospheric nitrogen in exchange for carbon provided by legume hosts. This mutualism regulates nutrient cycles in natural ecosystems and provides nitrogen to agricultural environments. Despite the ecological, evolutionary and agricultural importance of plant polyploidy and the legume-rhizobia mutualism, it is not yet fully understood whether plant polyploidy directly alters mutualism traits or the consequences on plant growth. SCOPE The aim was to propose a conceptual framework to understand how polyploidy might directly enhance the quantity and quality of rhizobial symbionts hosted by legume plants, resulting in increased host access to fixed nitrogen (N). Mechanistic hypotheses have been devised to examine how polyploidy can directly alter traits that impact the quantity (e.g. nodule number, nodule size, terminal bacteroid differentiation) and quality of symbionts (e.g. nodule environment, partner choice, host sanctions). To evaluate these hypotheses, an exhaustive review of studies testing the effects of plant polyploidy on the mutualism was conducted. In doing so, overall trends were synthesized, highlighting the limited understanding of the mechanisms that underlie variation in results achieved thus far, revealing striking gaps in knowledge and uncovering areas ripe for future research. CONCLUSIONS Plant polyploidy can immediately alter nodule size, N fixation rate and the identity of rhizobial symbionts hosted by polyploid legumes, but many of the mechanistic hypotheses proposed here, such as bacteroid number and enhancements of the nodule environment, remain unexplored. Although current evidence supports a role of plant polyploidy in enhancing key aspects of the legume-rhizobia mutualism, the underlying mechanisms and effects on host benefit from the mutualism remain unresolved.
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Affiliation(s)
- Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- For correspondence. E-mail
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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Stefan A, Van Cauwenberghe J, Rosu CM, Stedel C, Labrou NE, Flemetakis E, Efrose RC. Genetic diversity and structure of Rhizobium leguminosarum populations associated with clover plants are influenced by local environmental variables. Syst Appl Microbiol 2018; 41:251-259. [PMID: 29452714 DOI: 10.1016/j.syapm.2018.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 11/15/2022]
Abstract
The identification and conservation of indigenous rhizobia associated with legume plants and their application as biofertilizers is becoming an agricultural worldwide priority. However, little is known about the genetic diversity and phylogeny of rhizobia in Romania. In the present study, the genetic diversity and population composition of Rhizobium leguminosarum symbiovar trifolii isolates from 12 clover plants populations located across two regions in Romania were analyzed. Red clover isolates were phenotypically evaluated and genotyped by sequencing 16S rRNA gene, 16S-23S intergenic spacer, three chromosomal genes (atpD, glnII and recA) and two plasmid genes (nifH and nodA). Multilocus sequence typing (MLST) analysis revealed that red clover plants are nodulated by a wide genetic diversity of R. leguminosarum symbiovar trifolii sequence types (STs), highly similar to the ones previously found in white clover. Rhizobial genetic variation was found mainly within the two clover populations for both chromosomal and plasmid types. Many STs appear to be unique for this region and the genetic composition of rhizobia differs significantly among the clover populations. Furthermore, our results showed that both soil pH and altitude contributed to plasmid sequence type composition while differences in chromosomal composition were affected by the altitude and were strongly correlated with distance.
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Affiliation(s)
- Andrei Stefan
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n Col. Chamilpa, Cuernavaca, Morelos CP 62210, Mexico; Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Craita M Rosu
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Catalina Stedel
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Rodica C Efrose
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania.
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Werner GDA, Zhou Y, Pieterse CMJ, Kiers ET. Tracking plant preference for higher-quality mycorrhizal symbionts under varying CO 2 conditions over multiple generations. Ecol Evol 2018; 8:78-87. [PMID: 29321853 PMCID: PMC5756855 DOI: 10.1002/ece3.3635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 01/14/2023] Open
Abstract
The symbiosis between plants and root-colonizing arbuscular mycorrhizal (AM) fungi is one of the most ecologically important examples of interspecific cooperation in the world. AM fungi provide benefits to plants; in return plants allocate carbon resources to fungi, preferentially allocating more resources to higher-quality fungi. However, preferential allocations from plants to symbionts may vary with environmental context, particularly when resource availability affects the relative value of symbiotic services. We ask how differences in atmospheric CO 2-levels influence root colonization dynamics between AMF species that differ in their quality as symbiotic partners. We find that with increasing CO 2-conditions and over multiple plant generations, the more beneficial fungal species is able to achieve a relatively higher abundance. This suggests that increasing atmospheric carbon supply enables plants to more effectively allocate carbon to higher-quality mutualists, and over time helps reduce lower-quality AM abundance. Our results illustrate how environmental context may affect the extent to which organisms structure interactions with their mutualistic partners and have potential implications for mutualism stability and persistence under global change.
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Affiliation(s)
- Gijsbert D. A. Werner
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
- Department of ZoologyUniversity of OxfordOxfordUK
| | - Yeling Zhou
- Plant‐Microbe InteractionsDepartment of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Corné M. J. Pieterse
- Plant‐Microbe InteractionsDepartment of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - E. Toby Kiers
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
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Quides KW, Stomackin GM, Lee HH, Chang JH, Sachs JL. Lotus japonicus alters in planta fitness of Mesorhizobium loti dependent on symbiotic nitrogen fixation. PLoS One 2017; 12:e0185568. [PMID: 28957401 PMCID: PMC5619806 DOI: 10.1371/journal.pone.0185568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/14/2017] [Indexed: 12/19/2022] Open
Abstract
Rhizobial bacteria are known for their capacity to fix nitrogen for legume hosts. However ineffective rhizobial genotypes exist and can trigger the formation of nodules but fix little if any nitrogen for hosts. Legumes must employ mechanisms to minimize exploitation by the ineffective rhizobial genotypes to limit fitness costs and stabilize the symbiosis. Here we address two key questions about these host mechanisms. What stages of the interaction are controlled by the host, and can hosts detect subtle differences in nitrogen fixation? We provide the first explicit evidence for adaptive host control in the interaction between Lotus japonicus and Mesorhizobium loti. In both single inoculation and co-inoculation experiments, less effective rhizobial strains exhibited reduced in planta fitness relative to the wildtype M. loti. We uncovered evidence of host control during nodule formation and during post-infection proliferation of symbionts within nodules. We found a linear relationship between rhizobial fitness and symbiotic effectiveness. Our results suggest that L. japonicus can adaptively modulate the fitness of symbionts as a continuous response to symbiotic nitrogen fixation.
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Affiliation(s)
- Kenjiro W. Quides
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
| | - Glenna M. Stomackin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
| | - Hsu-Han Lee
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Joel L. Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, CA, United States of America
- * E-mail:
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35
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Regus JU, Quides KW, O'Neill MR, Suzuki R, Savory EA, Chang JH, Sachs JL. Cell autonomous sanctions in legumes target ineffective rhizobia in nodules with mixed infections. AMERICAN JOURNAL OF BOTANY 2017; 104:1299-1312. [PMID: 29885243 DOI: 10.3732/ajb.1700165] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/11/2017] [Indexed: 05/22/2023]
Affiliation(s)
- John U. Regus
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Kenjiro W. Quides
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Matthew R. O'Neill
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Rina Suzuki
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Elizabeth A. Savory
- Department of Botany and Plant Pathology, Cordley Hall, 2701 SW Campus Way, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Cordley Hall, 2701 SW Campus Way, Oregon State University, Corvallis, Oregon 97331 USA
| | - Joel L. Sachs
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
- Department of Botany and Plant Sciences, 2142 Batchelor Hall, University of California, Riverside, California 92521 USA
- Institute for Integrative Genome Biology, 5406 Boyce Hall, University of California, Riverside, California 92521 USA
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Role of plant-fungal nutrient trading and host control in determining the competitive success of ectomycorrhizal fungi. ISME JOURNAL 2017; 11:2666-2676. [PMID: 28731478 DOI: 10.1038/ismej.2017.116] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/04/2017] [Accepted: 06/04/2017] [Indexed: 11/08/2022]
Abstract
Multiple ectomycorrhizal fungi (EMF) compete to colonise the roots of a host plant, but it is not known whether their success is under plant or fungal control, or a combination of both. We assessed whether plants control EMF colonisation by preferentially allocating more carbon to more beneficial partners in terms of nitrogen supply or if other factors drive competitive success. We combined stable isotope labelling and RNA-sequencing approaches to characterise nutrient exchange between the plant host Eucalyptus grandis and three Pisolithus isolates when growing alone and when competing either indirectly (with a physical barrier) or directly. Overall, we found that nitrogen provision to the plant does not explain the amount of carbon that an isolate receives nor the number of roots that it colonises. Differences in nutrient exchange among isolates were related to differences in expression of key fungal and plant nitrogen and carbon transporter genes. When given a choice of partners, the plant was able to limit colonisation by the least cooperative isolate. This was not explained by a reduction in allocated carbon. Instead, our results suggest that partner choice in EMF could operate through the upregulation of defence-related genes against those fungi providing fewer nutrients.
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Batstone RT, Dutton EM, Wang D, Yang M, Frederickson ME. The evolution of symbiont preference traits in the model legume Medicago truncatula. THE NEW PHYTOLOGIST 2017; 213:1850-1861. [PMID: 27864973 DOI: 10.1111/nph.14308] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/23/2016] [Indexed: 05/25/2023]
Abstract
Many hosts preferentially associate with or reward better symbionts, but how these symbiont preference traits evolve is an open question. Legumes often form more nodules with or provide more resources to rhizobia that fix more nitrogen (N), but they also acquire N from soil via root foraging. It is unclear whether root responses to abiotically and symbiotically derived N evolve independently. Here, we measured root foraging and both preferential allocation of root resources to and preferential association with an effective vs an ineffective N-fixing Ensifer meliloti strain in 35 inbred lines of the model legume Medicago truncatula. We found that M. truncatula is an efficient root forager and forms more nodules with the effective rhizobium; root biomass increases with the number of effective, but not ineffective, nodules, indicating preferential allocation to roots harbouring effective rhizobia; root foraging is not genetically correlated with either preferential allocation or association; and selection favours plant genotypes that form more effective nodules. Root foraging and symbiont preference traits appear to be genetically uncoupled in M. truncatula. Rather than evolving to exclude ineffective partners, our results suggest that preference traits probably evolve to take better advantage of effective symbionts.
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Affiliation(s)
- Rebecca T Batstone
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Emily M Dutton
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Donglin Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Molly Yang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Jandér KC, Herre EA. Host sanctions in Panamanian Ficus are likely based on selective resource allocation. AMERICAN JOURNAL OF BOTANY 2016; 103:1753-1762. [PMID: 27562207 DOI: 10.3732/ajb.1600082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Fig trees and their pollinators, fig wasps, present a powerful model system for studying mutualism stability: both partners depend on each other for reproduction, cooperation levels can be manipulated, and the resulting field-based fitness quantified. Previous work has shown that fig trees can severely reduce the fitness of wasps that do not pollinate by aborting unpollinated figs or reducing the number and size of wasp offspring. Here we evaluated four hypotheses regarding the mechanism of sanctions in four Panamanian fig species. METHODS We examined wasp and fig samples from field experiments with manipulated levels of pollination. KEY RESULTS In unpollinated figs, the fig wall and the wasp offspring had a lower dry mass. Unpollinated figs had as many initiated wasp galls as pollinated figs but fewer galls that successfully produced live wasp offspring. Across three experimentally increasing levels of pollination, we found nonlinear increases in fig wall mass, the proportion of wasp galls that develop, and wasp mass. CONCLUSIONS Our data did not support the hypotheses that lack of pollination prevents gall formation or that fertilized endosperm is required for wasp development. While our data are potentially consistent with the hypothesis that trees produce a wasp-specific toxin in response to lack of pollination, we found the hypothesis that sanctions are a consequence of trees allocating more resources to better-pollinated figs more parsimonious with the aggregate data. Our findings are completely analogous to the selective resource allocation to more beneficial tissues documented in other mutualistic systems.
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Affiliation(s)
- K Charlotte Jandér
- Department of Organismic and Evolutionary Biology, Level 4 MCZ Labs, 26 Oxford Street, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut USA
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, DPO, AA 34002-9998 USA
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, DPO, AA 34002-9998 USA
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Grillo MA, Stinchcombe JR, Heath KD. Nitrogen addition does not influence pre-infection partner choice in the legume-rhizobium symbiosis. AMERICAN JOURNAL OF BOTANY 2016; 103:1763-1770. [PMID: 27671532 DOI: 10.3732/ajb.1600090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/09/2016] [Indexed: 05/26/2023]
Abstract
PREMISE OF THE STUDY Resource mutualisms such as the symbiosis between legumes and nitrogen-fixing rhizobia are context dependent and are sensitive to various aspects of the environment, including nitrogen (N) addition. Mutualist hosts such as legumes are also thought to use mechanisms such as partner choice to discriminate among potential symbionts that vary in partner quality (fitness benefits conferred to hosts) and thus impose selection on rhizobium populations. Together, context dependency and partner choice might help explain why the legume-rhizobium mutualism responds evolutionarily to N addition, since plant-mediated selection that shifts in response to N might be expected to favor different rhizobium strains in different N environments. METHODS We test for the influence of context dependency on partner choice in the model legume, Medicago truncatula, using a factorial experiments with three plant families across three N levels with a mixed inoculation of three rhizobia strains. KEY RESULTS Neither the relative frequencies of rhizobium strains occupying host nodules, nor the size of those nodules, differed in response to N level. CONCLUSIONS Despite the lack of context dependence, plant genotypes respond very differently to mixed populations of rhizobia, suggesting that these traits are genetically variable and thus could evolve in response to longer-term increases in N.
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Affiliation(s)
- Michael A Grillo
- University of Illinois, Department of Plant Biology, Urbana, Illinois 61801, USA
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Katy D Heath
- University of Illinois, Department of Plant Biology, Urbana, Illinois 61801, USA
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40
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Nonnodulating Bradyrhizobium spp. Modulate the Benefits of Legume-Rhizobium Mutualism. Appl Environ Microbiol 2016; 82:5259-68. [PMID: 27316960 DOI: 10.1128/aem.01116-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Rhizobia are best known for nodulating legume roots and fixing atmospheric nitrogen for the host in exchange for photosynthates. However, the majority of the diverse strains of rhizobia do not form nodules on legumes, often because they lack key loci that are needed to induce nodulation. Nonnodulating rhizobia are robust heterotrophs that can persist in bulk soil, thrive in the rhizosphere, or colonize roots as endophytes, but their role in the legume-rhizobium mutualism remains unclear. Here, we investigated the effects of nonnodulating strains on the native Acmispon-Bradyrhizobium mutualism. To examine the effects on both host performance and symbiont fitness, we performed clonal inoculations of diverse nonnodulating Bradyrhizobium strains on Acmispon strigosus hosts and also coinoculated hosts with mixtures of sympatric nodulating and nonnodulating strains. In isolation, nonnodulating Bradyrhizobium strains did not affect plant performance. In most cases, coinoculation of nodulating and nonnodulating strains reduced host performance compared to that of hosts inoculated with only a symbiotic strain. However, coinoculation increased host performance only under one extreme experimental treatment. Nearly all estimates of nodulating strain fitness were reduced in the presence of nonnodulating strains. We discovered that nonnodulating strains were consistently capable of coinfecting legume nodules in the presence of nodulating strains but that the fitness effects of coinfection for hosts and symbionts were negligible. Our data suggest that nonnodulating strains most often attenuate the Acmispon-Bradyrhizobium mutualism and that this occurs via competitive interactions at the root-soil interface as opposed to in planta IMPORTANCE Rhizobia are soil bacteria best known for their capacity to form root nodules on legume plants and enhance plant growth through nitrogen fixation. Yet, most rhizobia in soil do not have this capacity, and their effects on this symbiosis are poorly understood. We investigated the effects of diverse nonnodulating rhizobia on a native legume-rhizobium symbiosis. Nonnodulating strains did not affect plant growth in isolation. However, compared to inoculations with symbiotic rhizobia, coinoculations of symbiotic and nonnodulating strains often reduced plant and symbiont fitness. Coinoculation increased host performance only under one extreme treatment. Nonnodulating strains also invaded nodule interiors in the presence of nodulating strains, but this did not affect the fitness of either partner. Our data suggest that nonnodulating strains may be important competitors at the root-soil interface and that their capacity to attenuate this symbiosis should be considered in efforts to use rhizobia as biofertilizers.
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Estrela S, Kerr B, Morris JJ. Transitions in individuality through symbiosis. Curr Opin Microbiol 2016; 31:191-198. [DOI: 10.1016/j.mib.2016.04.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 11/29/2022]
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42
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Van Cauwenberghe J, Lemaire B, Stefan A, Efrose R, Michiels J, Honnay O. Symbiont abundance is more important than pre-infection partner choice in a Rhizobium - legume mutualism. Syst Appl Microbiol 2016; 39:345-9. [PMID: 27269381 DOI: 10.1016/j.syapm.2016.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 11/30/2022]
Abstract
It is known that the genetic diversity of conspecific rhizobia present in root nodules differs greatly among populations of a legume species, which has led to the suggestion that both dispersal limitation and the local environment affect rhizobial genotypic composition. However, it remains unclear whether rhizobial genotypes residing in root nodules are representative of the entire population of compatible symbiotic rhizobia. Since symbiotic preferences differ among legume populations, the genetic composition of rhizobia found within nodules may reflect the preferences of the local hosts, rather than the full diversity of potential nodulating rhizobia present in the soil. Here, we assessed whether Vicia cracca legume hosts of different provenances select different Rhizobium leguminosarum genotypes than sympatric V. cracca hosts, when presented a natural soil rhizobial population. Through combining V. cracca plants and rhizobia from adjacent and more distant populations, we found that V. cracca hosts are relatively randomly associated with rhizobial genotypes. This indicates that pre-infection partner choice is relatively weak in certain legume hosts when faced with a natural population of rhizobia.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium.
| | - Benny Lemaire
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Andrei Stefan
- Faculty of Biology, Alexandru Ioan Cuza University of Iasi, Bd. Carol I 20A, 700505 Iasi, Romania
| | - Rodica Efrose
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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Hollowell AC, Regus JU, Turissini D, Gano-Cohen KA, Bantay R, Bernardo A, Moore D, Pham J, Sachs JL. Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities. Proc Biol Sci 2016; 283:20160496. [PMID: 27122562 PMCID: PMC4855393 DOI: 10.1098/rspb.2016.0496] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/04/2016] [Indexed: 01/05/2023] Open
Abstract
Root nodule-forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across more than 800 km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis loci expressed in planta and encoded on an integrated 'symbiosis island' (SI). We uncovered a massive clonal expansion restricted to the Bradyrhizobium chromosome, with a single chromosomal haplotype dominating populations, ranging more than 700 km, and acquiring 42 divergent SI haplotypes, none of which were spatially widespread. For focal genotypes, we quantified utilization of 190 sole-carbon sources relevant to soil fitness. Chromosomal haplotypes that were both widespread and dominant exhibited superior growth on diverse carbon sources, whereas these patterns were not mirrored among SI haplotypes. Abundance, spatial range and catabolic superiority of chromosomal, but not symbiosis genotypes suggests that fitness in the soil environment, rather than symbiosis with hosts, might be the key driver of Bradyrhizobium dominance.
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Affiliation(s)
- Amanda C Hollowell
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - John U Regus
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - David Turissini
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Roxanne Bantay
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Andrew Bernardo
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Devora Moore
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Jonathan Pham
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Joel L Sachs
- Department of Biology, University of California, Riverside, CA 92521, USA Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Miranda-Sánchez F, Rivera J, Vinuesa P. Diversity patterns ofRhizobiaceaecommunities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes. Environ Microbiol 2015; 18:2375-91. [DOI: 10.1111/1462-2920.13061] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/17/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Fabiola Miranda-Sánchez
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Javier Rivera
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Pablo Vinuesa
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
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45
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Mueller U, Sachs J. Engineering Microbiomes to Improve Plant and Animal Health. Trends Microbiol 2015; 23:606-617. [DOI: 10.1016/j.tim.2015.07.009] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/08/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
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46
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Jones EI, Afkhami ME, Akçay E, Bronstein JL, Bshary R, Frederickson ME, Heath KD, Hoeksema JD, Ness JH, Pankey MS, Porter SS, Sachs JL, Scharnagl K, Friesen ML. Cheaters must prosper: reconciling theoretical and empirical perspectives on cheating in mutualism. Ecol Lett 2015; 18:1270-1284. [PMID: 26388306 DOI: 10.1111/ele.12507] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/13/2015] [Accepted: 08/13/2015] [Indexed: 01/21/2023]
Abstract
Cheating is a focal concept in the study of mutualism, with the majority of researchers considering cheating to be both prevalent and highly damaging. However, current definitions of cheating do not reliably capture the evolutionary threat that has been a central motivation for the study of cheating. We describe the development of the cheating concept and distill a relative-fitness-based definition of cheating that encapsulates the evolutionary threat posed by cheating, i.e. that cheaters will spread and erode the benefits of mutualism. We then describe experiments required to conclude that cheating is occurring and to quantify fitness conflict more generally. Next, we discuss how our definition and methods can generate comparability and integration of theory and experiments, which are currently divided by their respective prioritisations of fitness consequences and traits. To evaluate the current empirical evidence for cheating, we review the literature on several of the best-studied mutualisms. We find that although there are numerous observations of low-quality partners, there is currently very little support from fitness data that any of these meet our criteria to be considered cheaters. Finally, we highlight future directions for research on conflict in mutualisms, including novel research avenues opened by a relative-fitness-based definition of cheating.
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Affiliation(s)
- Emily I Jones
- Department of BioSciences, Rice University, Houston, TX, 77005, USA.,Wissenschaftskolleg zu Berlin, Institute for Advanced Study, 14193, Berlin, Germany.,Department of Entomology, Washington State University, Pullman, WA, 99164, USA
| | - Michelle E Afkhami
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Judith L Bronstein
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Redouan Bshary
- Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Megan E Frederickson
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | - Katy D Heath
- Department of Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Jason D Hoeksema
- Department of Biology, University of Mississippi, University, MS, 38677, USA
| | - Joshua H Ness
- Department of Biology, Skidmore College, Saratoga Springs, NY, 12866, USA
| | - M Sabrina Pankey
- Department of Molecular, Cell and Biomedical Sciences, University of New Hampshire, Durham, NH, 08624, USA
| | - Stephanie S Porter
- Department of Biology, University of California, Riverside, CA, 92521, USA
| | - Joel L Sachs
- Department of Biology, University of California, Riverside, CA, 92521, USA
| | - Klara Scharnagl
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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Simonsen AK, Stinchcombe JR. Standing genetic variation in host preference for mutualist microbial symbionts. Proc Biol Sci 2015; 281:rspb.2014.2036. [PMID: 25355477 DOI: 10.1098/rspb.2014.2036] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many models of mutualisms show that mutualisms are unstable if hosts lack mechanisms enabling preferential associations with mutualistic symbiotic partners over exploitative partners. Despite the theoretical importance of mutualism-stabilizing mechanisms, we have little empirical evidence to infer their evolutionary dynamics in response to exploitation by non-beneficial partners. Using a model mutualism-the interaction between legumes and nitrogen-fixing soil symbionts-we tested for quantitative genetic variation in plant responses to mutualistic and exploitative symbiotic rhizobia in controlled greenhouse conditions. We found significant broad-sense heritability in a legume host's preferential association with mutualistic over exploitative symbionts and selection to reduce frequency of associations with exploitative partners. We failed to detect evidence that selection will favour the loss of mutualism-stabilizing mechanisms in the absence of exploitation, as we found no evidence for a fitness cost to the host trait or indirect selection on genetically correlated traits. Our results show that genetic variation in the ability to preferentially reduce associations with an exploitative partner exists within mutualisms and is under selection, indicating that micro-evolutionary responses in mutualism-stabilizing traits in the face of rapidly evolving mutualistic and exploitative symbiotic bacteria can occur in natural host populations.
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Affiliation(s)
- Anna K Simonsen
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Canada M5S 3B2
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology & Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, Canada M5S 3B2
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48
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Wernegreen JJ. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann N Y Acad Sci 2015; 1360:16-35. [PMID: 25866055 DOI: 10.1111/nyas.12740] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes--mutation, selection, genetic drift, and recombination--and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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49
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Bever JD. Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts. THE NEW PHYTOLOGIST 2015; 205:1503-1514. [PMID: 25561086 DOI: 10.1111/nph.13239] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/15/2014] [Indexed: 05/09/2023]
Abstract
The common occurrence of mutualistic interactions between plants and root symbionts is problematic. As the delivery of benefit to hosts involves costs to symbionts, symbionts that provide reduced benefit to their host are expected to increase in frequency. Plants have been shown to allocate preferentially to the most efficient symbiont and this preferential allocation may stabilize the mutualism. I construct a general model of the interactive feedbacks of host preferential allocation and the dynamics of root symbiont populations to evaluate the stability of nutritional mutualisms. Preferential allocation can promote the evolution of mutualism even when the cost to the symbiont is very large. Moreover, the physiological plasticity of preferential allocation likely leads to coexistence of beneficial and nonbeneficial symbionts. For arbuscular mycorrhizal fungi, which facilitate plant uptake of phosphorus (P), the model predicts greater P transfer from these fungi per unit carbon invested with decreasing concentrations of soil P and with increasing concentrations of atmospheric CO2 , patterns that have been observed in laboratory and field studies. This framework connects physiological plasticity in plant allocation to population processes that determine mutualism stability and, as such, represents a significant step in understanding the stability and environmental patterns in mutualism.
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Affiliation(s)
- James D Bever
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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50
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Regus JU, Gano KA, Hollowell AC, Sofish V, Sachs JL. Lotus
hosts delimit the mutualism-parasitism continuum of Bradyrhizobium. J Evol Biol 2015; 28:447-56. [DOI: 10.1111/jeb.12579] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 10/15/2014] [Accepted: 12/22/2014] [Indexed: 01/24/2023]
Affiliation(s)
- J. U. Regus
- Department of Biology; University of California; Riverside CA USA
| | - K. A. Gano
- Department of Biology; University of California; Riverside CA USA
| | - A. C. Hollowell
- Department of Biology; University of California; Riverside CA USA
| | - V. Sofish
- Department of Biology; University of California; Riverside CA USA
| | - J. L. Sachs
- Department of Biology; University of California; Riverside CA USA
- Institute for Integrative Genome Biology; University of California; Riverside CA USA
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