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Stindt KR, McClean MN. Tuning interdomain conjugation to enable in situ population modification in yeasts. mSystems 2024; 9:e0005024. [PMID: 38747597 PMCID: PMC11326116 DOI: 10.1128/msystems.00050-24] [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: 01/09/2024] [Accepted: 04/15/2024] [Indexed: 05/28/2024] Open
Abstract
The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to the widespread use of IDC is its limited efficiency. In this work, we manipulated metabolic and physical interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture and model how these tunable controls can predictably yield a range of IDC outcomes. Furthermore, we demonstrate that these controls can be utilized to irreversibly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.IMPORTANCEFungi are important but often unaddressed members of most natural and synthetic microbial communities. This work highlights opportunities for modifying yeast microbiome populations through bacterial conjugation. While conjugation has been recognized for its capacity to deliver engineerable DNA to a range of cells, its dependence on cell contact has limited its efficiency. Here, we find "knobs" to control DNA transfer, by engineering the metabolic dependence between bacterial donors and yeast recipients and by changing their ability to physically adhere to each other. Importantly, we functionally validate these "knobs" by irreversibly altering yeast populations. We use these controls to "rescue" a failing yeast population, demonstrate the capacity of conjugated CRISPR/Cas9 to depress or collapse populations, and show that conjugation can be easily interrupted by disrupting cell-to-cell binding. These results offer building blocks toward in situ mycobiome editing, with significant implications for clinical treatments of fungal pathogens and other fungal system engineering.
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Affiliation(s)
- Kevin R Stindt
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Doctoral Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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Stindt KR, McClean MN. Tuning Interdomain Conjugation Toward in situ Population Modification in Yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557379. [PMID: 37745509 PMCID: PMC10515866 DOI: 10.1101/2023.09.12.557379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes, and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to widespread use of IDC is its limited efficiency. In this work, we utilize interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture, and model how these tunable controls can predictably yield a range of IDC outcomes. Further, we demonstrate that these lessons can be utilized to lastingly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.
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Hulting KA, Mason SD, Story CM, Keller GS. Wetland cohesion is associated with increased probability of infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis. DISEASES OF AQUATIC ORGANISMS 2022; 151:97-109. [PMID: 36226838 DOI: 10.3354/dao03692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) poses a substantial threat to amphibian populations. Understanding the landscape conditions that facilitate Bd transmission and persistence is crucial for predicting Bd trends in amphibian populations. Here, we investigated the interactions between land use, wetland connectivity, and Bd occurrence and infection intensity. In northeastern Massachusetts, we sampled Pseudacris crucifer, Lithobates sylvaticus, L. clamitans, and L. pipiens from 24 sites. We found an overall 30.6% Bd prevalence at our sites, with prevalence differing among species. Bd occurrence increased with wetland-patch cohesion, potentially due to microclimate shifts from decreased forest or changes in host movement. Bd infection intensity was not mediated by landscape context. Overall, our results highlight the importance of landscape structure for Bd dynamics, suggesting that certain landscapes may facilitate transmission and harbor Bd more than others. To mitigate the impacts of Bd on amphibian populations, conservation efforts should account for interactions between Bd and landscape variables.
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Affiliation(s)
- Katherine A Hulting
- Landscape Ecology Lab, Department of Life, Health, and Physical Sciences, Gordon College, Wenham, MA 01984, USA
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Garnham JI, Bower DS, Stockwell MP, Pickett EJ, Pollard CJ, Clulow J, Mahony MJ. Seasonal variation in the prevalence of a fungal pathogen and unexpected clearance from infection in a susceptible frog species. DISEASES OF AQUATIC ORGANISMS 2022; 148:1-11. [PMID: 35142293 DOI: 10.3354/dao03628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) causes the disease chytridiomycosis, which is a primary driver for amphibian population declines and extinctions worldwide. For highly susceptible species, such as the green and golden bell frog Litoria aurea, large numbers of Bd-related mortalities are thought to occur during the colder season (winter), when low temperatures favour the growth of the pathogen. However, extant L. aurea populations are persisting with Bd. We measured Bd prevalence and infection levels of wild L. aurea using capture-mark-recapture and radio-tracking methods. Using this information, we sought to determine host and environmental correlates of Bd prevalence and infection load. Mean ± SE infection load was higher in frogs sampled in autumn (431.5 ± 310.4 genomic equivalents; GE) and winter (1147.5 ± 735.8 GE), compared to spring (21.8 ± 19.3 GE) and summer (0.9 ± 0.8 GE). Furthermore, prevalence of Bd infection in L. aurea was highest in winter (43.6%; 95% CI 33.1-54.7%) and lowest in summer (11.2%; 95% CI 6.8-17.9%). Both prevalence and infection load decreased with increasing temperature. Seven frogs cleared their fungal infection during the coolest months when Bd prevalence was highest; however, these clearances were not permanent, as 5 frogs became infected again. Understanding the factors that allow amphibians to clear their Bd infections when temperatures are optimal for Bd growth presents the potential for manipulating such factors and provides an important step in future research.
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Affiliation(s)
- James I Garnham
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
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Rodriguez KM, Voyles J. The amphibian complement system and chytridiomycosis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 333:706-719. [PMID: 33052039 PMCID: PMC7821119 DOI: 10.1002/jez.2419] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/26/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]
Abstract
Understanding host immune function and ecoimmunology is increasingly important at a time when emerging infectious diseases (EIDs) threaten wildlife. One EID that has emerged and spread widely in recent years is chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), which is implicated unprecedented amphibian declines around the world. The impacts of Bd have been severe for many amphibian species, but some populations have exhibited signs of persistence, and even recovery, in some regions. Many mechanisms may underpin this pattern and amphibian immune responses are likely one key component. Although we have made great strides in understanding amphibian immunity, the complement system remains poorly understood. The complement system is a nonspecific, innate immune defense that is known to enhance other immune responses. Complement activation can occur by three different biochemical pathways and result in protective mechanisms, such as inflammation, opsonization, and pathogen lysis, thereby providing protection to the host. We currently lack an understanding of complement pathway activation for chytridiomycosis, but several studies have suggested that it may be a key part of an early and robust immune response that confers host resistance. Here, we review the available research on the complement system in general as well as amphibian complement responses to Bd infection. Additionally, we propose future research directions that will increase our understanding of the amphibian complement system and other immune responses to Bd. Finally, we suggest how a deeper understanding of amphibian immunity could enhance the conservation and management of amphibian species that are threatened by chytridiomycosis.
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Affiliation(s)
| | - Jamie Voyles
- Department of Biology, University of Nevada-Reno, Reno, Nevada, USA
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Verbrugghe E, Van Rooij P, Favoreel H, Martel A, Pasmans F. In vitro modeling of Batrachochytrium dendrobatidis infection of the amphibian skin. PLoS One 2019; 14:e0225224. [PMID: 31725762 PMCID: PMC6855447 DOI: 10.1371/journal.pone.0225224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/30/2019] [Indexed: 11/19/2022] Open
Abstract
The largest current disease-induced loss of vertebrate biodiversity is due to chytridiomycosis and despite the increasing understanding of the pathogenesis, knowledge unravelling the early host-pathogen interactions remains limited. Batrachochytrium dendrobatidis (Bd) zoospores attach to and invade the amphibian epidermis, with subsequent invasive growth in the host skin. Availability of an in vitro assay would facilitate in depth study of this interaction while reducing the number of experimental animals needed. We describe a fluorescent cell-based in vitro infection model that reproduces host-Bd interactions. Using primary keratinocytes from Litoria caerulea and the epithelial cell line A6 from Xenopus laevis, we reproduced different stages of host cell infection and intracellular growth of Bd, resulting in host cell death, a key event in chytridiomycosis. The presented in vitro models may facilitate future mechanistic studies of host susceptibility and pathogen virulence.
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Affiliation(s)
- Elin Verbrugghe
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- * E-mail:
| | - Pascale Van Rooij
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Herman Favoreel
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Wu NC, McKercher C, Cramp RL, Franklin CE. Mechanistic basis for loss of water balance in green tree frogs infected with a fungal pathogen. Am J Physiol Regul Integr Comp Physiol 2019; 317:R301-R311. [PMID: 31141416 DOI: 10.1152/ajpregu.00355.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chytridiomycosis, a lethal skin disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), disrupts skin function of amphibians, interfering with ionic and osmotic regulation. To regulate fungal loads, amphibians increase their rate of skin sloughing. However, sloughing also causes a temporary loss of ionic and osmotic homeostasis due to disruption of the skin, a key osmoregulatory organ. The combined effects of increased sloughing frequency and chytridiomycosis contribute to the high rates of mortality from Bd infections. However, the mechanisms responsible for the loss of cutaneous osmotic regulation remain unknown. We measured the changes in whole animal water uptake rates, in vitro transcutaneous water fluxes across the ventral skin, and the mRNA expression of epithelial water transport proteins (aquaporins, AQPs) and junctional proteins in Bd-infected and uninfected Litoria caerulea skin. We hypothesize that infected frogs would show reduction/inhibition in cutaneous water transporters responsible for regulating water balance, and sloughing would exacerbate cutaneous water fluxes. We found that infected, nonsloughing frogs had an impaired rate of water uptake and showed increased rates of in vitro water efflux across the ventral skin. In uninfected frogs, the expression of AQPs and junction genes increased significantly with sloughing, which may assist in regulating cutaneous water movements and barrier function in the newly exposed skin. In contrast, infected frogs did not show this postsloughing increase in AQP gene expression. The combination of increased sloughing frequency, impaired water uptake rates, and increased rates of water loss likely contributes to the loss of osmotic homeostasis in frogs infected with Bd.
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Affiliation(s)
- Nicholas C Wu
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Callum McKercher
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Rebecca L Cramp
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Craig E Franklin
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
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