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Eleftherakos K, Polymeni RM, Mikropoulou EV, Vougogiannopoulou K, Georgiadis C, Petrakis EA, Skaltsounis LA, Halabalaki M. A skin secretion metabolome analysis of the Greek Dodecanese Lycian salamanders: Preliminary evidence of dietary alkaloid sequestration in urodeles. PLoS One 2024; 19:e0300278. [PMID: 39208286 PMCID: PMC11361651 DOI: 10.1371/journal.pone.0300278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/25/2024] [Indexed: 09/04/2024] Open
Abstract
Lyciasalamandra species, like most amphibians, secrete a wide array of compounds from their granular and mucous skin glands, including the internally synthesized samandarine alkaloids, making their skin a complex organ performing a variety of functions. Lyciasalamandra helverseni and L. luschani basoglui are insular endemics of the Dodecanese islands of SE Greece, bearing distinct isolated populations, with well-documented phylogenetic profiles. Here, we employ a metabolomics approach, utilizing UPLC-ESI-HRMS/MS data of the skin secretions sampled from a number of specimens found in the islands of Karpathos, Kasos and Kastellorizo, in an effort to reveal aspects of their chemistry and diversity across populations. The results indicated statistically significant variation between all taxa examined, based on various secreted compounds. The underlying factors of variation highlighted by the multivariate analysis were differences in samandarine and other alkaloid content as well as in animal size. Metabolite annotation, based on dereplication tools and most importantly HRMS and HRMS/MS spectra, yielded a number of known samandarine alkaloids, reported for the first time in the currently studied Lyciasalamandra species. We also present documentation for novel members of the samandarine alkaloid family, as well as preliminary evidence for a possible dietary alkaloid sequestration. This work can set the basis for further research of this often-neglected endemic species of the Salamandridae, as well as the structural investigation of the samandarine alkaloid group.
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Affiliation(s)
- Karolos Eleftherakos
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Roza Maria Polymeni
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni V. Mikropoulou
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Vougogiannopoulou
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Georgiadis
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleftherios A. Petrakis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Leandros A. Skaltsounis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Halabalaki
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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Jones KR, Belden LK, Hughey MC. Priority effects alter microbiome composition and increase abundance of probiotic taxa in treefrog tadpoles. Appl Environ Microbiol 2024; 90:e0061924. [PMID: 38757977 PMCID: PMC11218634 DOI: 10.1128/aem.00619-24] [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: 03/29/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024] Open
Abstract
Host-associated microbial communities, like other ecological communities, may be impacted by the colonization order of taxa through priority effects. Developing embryos and their associated microbiomes are subject to stochasticity during colonization by bacteria. For amphibian embryos, often developing externally in bacteria-rich environments, this stochasticity may be particularly impactful. For example, the amphibian microbiome can mitigate lethal outcomes from disease for their hosts; however, this may depend on microbiome composition. Here, we examined the assembly of the bacterial community in spring peeper (Pseudacris crucifer) embryos and tadpoles. First, we reared embryos from identified mating pairs in either lab or field environments to examine the relative impact of environment and parentage on embryo and tadpole bacterial communities. Second, we experimentally inoculated embryos to determine if priority effects (i) could be used to increase the relative abundance of Janthinobacterium lividum, an amphibian-associated bacteria capable of preventing fungal infection, and (ii) would lead to observed differences in the relative abundances of two closely related bacteria from the genus Pseudomonas. Using 16S rRNA gene amplicon sequencing, we observed differences in community composition based on rearing location and parentage in embryos and tadpoles. In the inoculation experiment, we found that priority inoculation could increase the relative abundance of J. lividum, but did not find that either Pseudomonas isolate was able to prevent colonization by the other when given priority. These results highlight the importance of environmental source pools and parentage in determining microbiome composition, while also providing novel methods for the administration of a known amphibian probiotic. IMPORTANCE Harnessing the functions of host-associated bacteria is a promising mechanism for managing disease outcomes across different host species. In the case of amphibians, certain frog-associated bacteria can mitigate lethal outcomes of infection by the fungal pathogen Batrachochytrium dendrobatidis. Successful probiotic applications require knowledge of community assembly and an understanding of the ecological mechanisms that structure these symbiotic bacterial communities. In our study, we show the importance of environment and parentage in determining bacterial community composition and that community composition can be influenced by priority effects. Further, we provide support for the use of bacterial priority effects as a mechanism to increase the relative abundance of target probiotic taxa in a developing host. While our results show that priority effects are not universally effective across all host-associated bacteria, our ability to increase the relative abundance of specific probiotic taxa may enhance conservation strategies that rely on captive rearing of endangered vertebrates.
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Affiliation(s)
- Korin Rex Jones
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Myra C. Hughey
- Department of Biology, Vassar College, Poughkeepsie, New York, USA
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Wan B, Chen G, Poon ESK, Fung HS, Lau A, Sin SYW. Environmental factors and host sex influence the skin microbiota structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia. Integr Zool 2024. [PMID: 38872359 DOI: 10.1111/1749-4877.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, poses a significant threat to amphibian biodiversity worldwide. Antifungal bacteria found on the skin of chytrid-resistant amphibians could potentially provide defense against chytridiomycosis and lower mortality rates among resistant individuals. The Hong Kong newt (Paramesotriton hongkongensis) is native to East Asia, a region suspected to be the origin of chytrids, and has exhibited asymptomatic infection, suggesting a long-term coexistence with the chytrids. Therefore, the skin microbiota of this resistant species warrant investigation, along with other factors that can affect the microbiota. Among the 149 newts sampled in their natural habitats in Hong Kong, China, putative antifungal bacteria were found in all individuals. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria; abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiota compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites that could be vital to P. hongkongensis. The dominant cores included the family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiota compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as developing probiotic treatments for susceptible species.
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Affiliation(s)
- Bowen Wan
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Guoling Chen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Emily Shui Kei Poon
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Hon Shing Fung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Anthony Lau
- Science Unit, Lingnan University, Hong Kong, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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4
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Hotopp AM, Olsen BJ, Ishaq SL, Frey SD, Kovach AI, Kinnison MT, Gigliotti FN, Roeder MR, Cammen KM. Plumage microorganism communities of tidal marsh sparrows. iScience 2024; 27:108668. [PMID: 38230264 PMCID: PMC10790016 DOI: 10.1016/j.isci.2023.108668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/02/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024] Open
Abstract
Microorganism communities can shape host phenotype evolution but are often comprised of thousands of taxa with varied impact on hosts. Identification of taxa influencing host evolution relies on first describing microorganism communities and acquisition routes. Keratinolytic (keratin-degrading) microorganisms are hypothesized to be abundant in saltmarsh sediments and to contribute to plumage evolution in saltmarsh-adapted sparrows. Metabarcoding was used to describe plumage bacterial (16S rRNA) and fungal (ITS) communities in three sparrow species endemic to North America's Atlantic coast saltmarshes. Results describe limited within-species variability and moderate host species-level patterns in microorganism diversity and community composition. A small percentage of overall microorganism diversity was comprised of potentially keratinolytic microorganisms, warranting further functional studies. Distinctions between plumage and saltmarsh sediment bacteria, but not fungal, communities were detected, suggesting multiple bacterial acquisition routes and/or vertebrate host specialization. This research lays groundwork for future testing of causal links between microorganisms and avian host evolution.
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Affiliation(s)
- Alice M. Hotopp
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Brian J. Olsen
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Suzanne L. Ishaq
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Serita D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael T. Kinnison
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Franco N. Gigliotti
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Kristina M. Cammen
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
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5
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Troitsky TS, Laine VN, Lilley TM. When the host's away, the pathogen will play: the protective role of the skin microbiome during hibernation. Anim Microbiome 2023; 5:66. [PMID: 38129884 PMCID: PMC10740296 DOI: 10.1186/s42523-023-00285-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
The skin of animals is enveloped by a symbiotic microscopic ecosystem known as the microbiome. The host and microbiome exhibit a mutualistic relationship, collectively forming a single evolutionary unit sometimes referred to as a holobiont. Although the holobiome theory highlights the importance of the microbiome, little is known about how the skin microbiome contributes to protecting the host. Existing studies focus on humans or captive animals, but research in wild animals is in its infancy. Specifically, the protective role of the skin microbiome in hibernating animals remains almost entirely overlooked. This is surprising, considering the massive population declines in hibernating North American bats caused by the fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome. Hibernation offers a unique setting in which to study the function of the microbiome because, during torpor, the host's immune system becomes suppressed, making it susceptible to infection. We conducted a systematic review of peer-reviewed literature on the protective role of the skin microbiome in non-human animals. We selected 230 publications that mentioned pathogen inhibition by microbes residing on the skin of the host animal. We found that the majority of studies were conducted in North America and focused on the bacterial microbiome of amphibians infected by the chytrid fungus. Despite mentioning pathogen inhibition by the skin microbiome, only 30.4% of studies experimentally tested the actual antimicrobial activity of symbionts. Additionally, only 7.8% of all publications studied defensive cutaneous symbionts during hibernation. With this review, we want to highlight the knowledge gap surrounding skin microbiome research in hibernating animals. For instance, research looking to mitigate the effects of white-nose syndrome in bats should focus on the antifungal microbiome of Palearctic bats, as they survive exposure to the Pseudogymnoascus destructans -pathogen during hibernation. We also recommend future studies prioritize lesser-known microbial symbionts, such as fungi, and investigate the effects of a combination of anti-pathogen microbes, as both areas of research show promise as probiotic treatments. By incorporating the protective skin microbiome into disease mitigation strategies, conservation efforts can be made more effective.
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Affiliation(s)
- T S Troitsky
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - V N Laine
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - T M Lilley
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
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Campos PM, Lucid MK, Ehlers S, Walke JB. Low-level pathogen infection and geographic location correlate with the skin microbiomes of Columbia spotted frogs ( Rana luteiventris) in a montane landscape. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100213. [PMID: 38187998 PMCID: PMC10770434 DOI: 10.1016/j.crmicr.2023.100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
The skin microbiome of amphibians can influence host susceptibility towards the fungal pathogen Batrachochytrium dendrobatidis (Bd), while simultaneously having the potential to be altered by Bd. Severe Bd infections are known to alter the amphibian skin microbiome; however, little is known about microbiome interactions in amphibians with low infection intensity. In addition to disease dynamics, environmental factors may influence the microbiome. To test for patterns in bacterial diversity based on pathogen infection and environmental factors, 399 Columbia spotted frogs (Rana luteiventris) were sampled throughout northern Idaho and northeastern Washington across two years. Bd prevalence and intensity were measured in 376 frogs, revealing a prevalence of 69%, but generally low infection intensity (Mean = 127 Bd zoospore equivalents among infected frogs). Skin bacterial communities were characterized in 92 frogs using 16S rRNA gene amplicon sequencing. Our results indicated correlations of decreasing Shannon diversity and evenness as infection intensity increased. Latitude was correlated with bacterial richness and Faith's Phylogenetic Diversity measures, indicating increased diversity in northern locations. Beta diversity (UniFrac) analyses revealed that skin microbiomes were distinct between infected and uninfected frogs, and infection intensity had a significant effect on microbiome composition. Site explained the majority of microbiome variation (weighted UniFrac: 57.5%), suggesting a combination of local habitat conditions explain variation, as only small proportions of variation could be explained by year, month, temperature, elevation, and latitude individually. Bacterial genera with potential for Bd-inhibitory properties were found with differential relative abundance in infected and uninfected frogs, with higher Stenotrophomonas and lower Pseudomonas relative abundance observed in infected frogs. Further study may indicate if Bd inhibition by members of the skin microbiome is an influence behind the low infection intensities observed and whether low Bd infection intensities are capable of altering skin microbiome composition.
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Affiliation(s)
- Philip M. Campos
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
| | - Michael K. Lucid
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- Selkirk Wildlife Science, LLC, PO Box 733, Sandpoint, ID 83864, USA
| | - Shannon Ehlers
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- U.S. Fish and Wildlife Service, 287 Westside Rd., Bonners Ferry, ID 83805, USA
| | - Jenifer B. Walke
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
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Lin Z, He M, Zhong C, Li Y, Tang S, Kang X, Wu Z. Responses of gut microbiota in crocodile lizards ( Shinisaurus crocodilurus) to changes in temperature. Front Microbiol 2023; 14:1263917. [PMID: 38033565 PMCID: PMC10684959 DOI: 10.3389/fmicb.2023.1263917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
The gut microbiota plays an essential role in maintaining the health and fitness of the host organism. As a critical environmental variable, temperature exerts significant effects on animal survival and reproduction. Elevated temperatures can influence the composition and function of the animal gut microbiota, which may have potentially detrimental effects on the host. The crocodile lizard (Shinisaurus crocodilurus) is an ancient and currently endangered reptile species due to human hunting and habitat destruction. Given the predicted shifts in global temperatures in the next century, it is important to understand how warming affects the gut microbiota of these vulnerable lizards, which remains unclear. To determine how the microbial communities change in crocodile lizards in response to warming, we analyzed the gut microbiota under five temperature conditions (22°C, 24°C, 26°C, 28°C, and 30°C) using 16S rRNA high-throughput sequencing. Results showed that the dominant phyla, Proteobacteria and Bacteroidetes, in gut microbiota were not significantly affected by temperature variations, but increasing temperature altered the structure and increased the community richness of the gut microbiota. In addition, warming changed the abundance of Pseudomonas aeruginosa and Actinobacteria, which may have negative effects on the physiological health of the crocodile lizards. Functional prediction analysis demonstrated that the functional pathways enriched in crocodile lizards were mainly related to metabolism, with no significant differences observed in these pathways at KEGG pathway level 1 after warming. These results provide valuable insights into the ecological adaptations and regulatory mechanisms employed by crocodile lizards in response to warming, which may be of benefit for their conservation.
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Affiliation(s)
- Zhengzhong Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Mingxian He
- College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi, China
| | - Chunying Zhong
- College of Vocational and Technical Education, Guangxi Science and Technology Normal University, Guangxi, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Sanqi Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Xindan Kang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
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Robak MJ, Saenz V, de Cortie E, Richards-Zawacki CL. Effects of temperature on the interaction between amphibian skin bacteria and Batrachochytrium dendrobatidis. Front Microbiol 2023; 14:1253482. [PMID: 37942072 PMCID: PMC10628663 DOI: 10.3389/fmicb.2023.1253482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
Symbiotic relationships between animals and microbes are important for a range of functions, from digestion to protection from pathogens. However, the impact of temperature variation on these animal-microbe interactions remains poorly understood. Amphibians have experienced population declines and even extinctions on a global scale due to chytridiomycosis, a disease caused by chytrid fungi in the genus Batrachochytrium. Variation in susceptibility to this disease exists within and among host species. While the mechanisms generating differences in host susceptibility remain elusive, differences in immune system components, as well as variation in host and environmental temperatures, have been associated with this variation. The symbiotic cutaneous bacteria of amphibians are another potential cause for variation in susceptibility to chytridiomycosis, with some bacterial species producing antifungal metabolites that prevent the growth of Bd. The growth of both Bd and bacteria are affected by temperature, and thus we hypothesized that amphibian skin bacteria may be more effective at preventing Bd growth at certain temperatures. To test this, we collected bacteria from the skins of frogs, harvested the metabolites they produced when grown at three different temperatures, and then grew Bd in the presence of those metabolites under those same three temperatures in a three-by-three fully crossed design. We found that both the temperature at which cutaneous bacteria were grown (and metabolites produced) as well as the temperature at which Bd is grown can impact the ability of cutaneous bacteria to inhibit the growth of Bd. While some bacterial isolates showed the ability to inhibit Bd growth across multiple temperature treatments, no isolate was found to be inhibitive across all combinations of bacterial incubation or Bd challenge temperatures, suggesting that temperature affects both the metabolites produced and the effectiveness of those metabolites against the Bd pathogen. These findings move us closer to a mechanistic understanding of why chytridiomycosis outbreaks and related amphibian declines are often limited to certain climates and seasons.
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Affiliation(s)
- Matthew J. Robak
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
| | - Veronica Saenz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biology, The Pennsylvania State University, State College, PA, United States
| | - Esmee de Cortie
- Falk School of Sustainability and Environment, Chatham University, Pittsburgh, PA, United States
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McMahon TA, Nordheim CL, Detmering SE, Johnson PTJ, Rohr JR, Civitello DJ. Pseudacris regilla metamorphs acquire resistance to Batrachochytrium dendrobatidis after exposure to the killed fungus. DISEASES OF AQUATIC ORGANISMS 2023; 155:193-198. [PMID: 37767886 DOI: 10.3354/dao03753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
The pathogenic fungus Batrachochytrium dendrobatidis (Bd) is associated with drastic global amphibian declines. Prophylactic exposure to killed zoospores and the soluble chemicals they produce (Bd metabolites) can induce acquired resistance to Bd in adult Cuban treefrogs Osteopilus septentrionalis. Here, we exposed metamorphic frogs of a second species, the Pacific chorus frog Pseudacris regilla, to one of 2 prophylactic treatments prior to live Bd exposures: killed Bd zoospores with metabolites, killed zoospores alone, or a water control. Prior exposure to killed Bd zoospores with metabolites reduced Bd infection intensity in metamorphic Pacific chorus frogs by 60.4% compared to control frogs. Interestingly, Bd intensity in metamorphs previously exposed to killed zoospores alone did not differ in magnitude relative to the control metamorphs, nor to those treated with killed zoospores plus metabolites. Previous work indicated that Bd metabolites alone can induce acquired resistance in tadpoles, and so these findings together indicate that it is possible that the soluble Bd metabolites may contain immunomodulatory components that drive this resistance phenotype. Our results expand the generality of this prophylaxis work by identifying a second amphibian species (Pacific chorus frog) and an additional amphibian life stage (metamorphic frog) that can acquire resistance to Bd after metabolite exposure. This work increases hopes that a Bd-metabolite prophylaxis might be widely effective across amphibian species and life stages.
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Affiliation(s)
- Taegan A McMahon
- Connecticut College, Department of Biology, New London, Connecticut 06320, USA
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Ujszegi J, Boros Z, Fodor A, Vajna B, Hettyey A. Metabolites of Xenorhabdus bacteria are potent candidates for mitigating amphibian chytridiomycosis. AMB Express 2023; 13:88. [PMID: 37615904 PMCID: PMC10449739 DOI: 10.1186/s13568-023-01585-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
Chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has caused extreme losses in amphibian biodiversity. Finding bacteria that produce metabolites with antifungal properties may turn out to be invaluable in the fight against this devastating disease. The entomopathogenic bacteria, Xenorhabdus szentirmaii and X. budapestensis produce secondary metabolites that are effective against a wide range of fungal plant pathogens. To assess whether they may also be effective against Bd, we extracted cell-free culture media (CFCM) from liquid cultures of X. szentirmaii and X. budapestensis and tested their ability to inhibit Bd growth in vitro. As a second step, using juvenile common toads (Bufo bufo) experimentally infected with Bd we also tested the in vivo antifungal efficacy of X. szentirmaii CFCM diluted to 2 and 10% (v/v), while also assessing possible malign side effects on amphibians. Results of the in vitro experiment documented highly effective growth inhibition by CFCMs of both Xenorhabdus species. The in vivo experiment showed that treatment with CFCM of X. szentirmaii applied at a dilution of 10% resulted in infection intensities reduced by ca. 73% compared to controls and to juvenile toads treated with CFCM applied at a dilution of 2%. At the same time, we detected no negative side effects of treatment with CFCM on toad survival and development. Our results clearly support the idea that metabolites of X. szentirmaii, and perhaps of several other Xenorhabdus species as well, may prove highly useful for the treatment of Bd infected amphibians.
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Affiliation(s)
- János Ujszegi
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary.
| | - Zsófia Boros
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - András Fodor
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Attila Hettyey
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary
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11
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Gajewski Z, Johnson LR, Medina D, Crainer WW, Nagy CM, Belden LK. Skin bacterial community differences among three species of co-occurring Ranid frogs. PeerJ 2023; 11:e15556. [PMID: 37465150 PMCID: PMC10351513 DOI: 10.7717/peerj.15556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 07/20/2023] Open
Abstract
Skin microbial communities are an essential part of host health and can play a role in mitigating disease. Host and environmental factors can shape and alter these microbial communities and, therefore, we need to understand to what extent these factors influence microbial communities and how this can impact disease dynamics. Microbial communities have been studied in amphibian systems due to skin microbial communities providing some resistance to the amphibian chytrid fungus, Batrachochytrium dendrobatidis. However, we are only starting to understand how host and environmental factors shape these communities for amphibians. In this study, we examined whether amphibian skin bacterial communities differ among host species, host infection status, host developmental stage, and host habitat. We collected skin swabs from tadpoles and adults of three Ranid frog species (Lithobates spp.) at the Mianus River Gorge Preserve in Bedford, New York, USA, and used 16S rRNA gene amplicon sequencing to determine bacterial community composition. Our analysis suggests amphibian skin bacterial communities change across host developmental stages, as has been documented previously. Additionally, we found that skin bacterial communities differed among Ranid species, with skin communities on the host species captured in streams or bogs differing from the communities of the species captured on land. Thus, habitat use of different species may drive differences in host-associated microbial communities for closely-related host species.
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Affiliation(s)
- Zachary Gajewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - Leah R. Johnson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
- Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - Daniel Medina
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - William W. Crainer
- Department of Animal Sciences, Cornell University, Ithaca, New York, United States
| | | | - Lisa K. Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
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12
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Fiedler AW, Drågen MKR, Lorentsen ED, Vadstein O, Bakke I. The stability and composition of the gut and skin microbiota of Atlantic salmon throughout the yolk sac stage. Front Microbiol 2023; 14:1177972. [PMID: 37485532 PMCID: PMC10358989 DOI: 10.3389/fmicb.2023.1177972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
The bacterial colonization of newly hatched fish is important for the larval development and health. Still, little is known about the ontogeny of the early microbiota of fish. Here, we conducted two independent experiments with yolk sac fry of Atlantic salmon that were (1) either reared conventionally, with the eggs as the only source for bacteria (egg-derived microbiota; EDM) or (2) hatched germ-free and re-colonized using lake water (lake-derived microbiota; LDM). First, we characterized the gut and skin microbiota at 6, 9, and 13 weeks post hatching based on extracted RNA. In the second experiment, we exposed fry to high doses of either a fish pathogen or a commensal bacterial isolate and sampled the microbiota based on extracted DNA. The fish microbiota differed strongly between EDM and LDM treatments. The phyla Proteobacteria, Bacteroidetes, and Actinobacteria dominated the fry microbiota, which was found temporarily dynamic. Interestingly, the microbiota of EDM fry was more stable, both between replicate rearing flasks, and over time. Although similar, the skin and gut microbiota started to differentiate during the yolk sac stage, several weeks before the yolk was consumed. Addition of high doses of bacterial isolates to fish flasks had only minor effects on the microbiota.
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13
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Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. MICROBIAL ECOLOGY 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
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Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
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14
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Hardman RH, Reinert LK, Irwin KJ, Oziminski K, Rollins-Smith L, Miller DL. Disease state associated with chronic toe lesions in hellbenders may alter anti-chytrid skin defenses. Sci Rep 2023; 13:1982. [PMID: 36737574 PMCID: PMC9898527 DOI: 10.1038/s41598-023-28334-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
Hellbenders (Cryptobranchus alleganiensis) are large, aquatic salamanders from the eastern United States. Both subspecies, eastern and Ozark hellbenders, have experienced declines resulting in federal listing of Ozark hellbenders. The globally distributed chytrid fungus, Batrachochytrium dendrobatidis (Bd) has been detected in both subspecies, and Batrachochytrium salamandrivorans (Bsal) poses a new threat if introduced into North America. Ozark hellbenders also suffer a high prevalence of toe lesions of unknown etiology, with changes in host immunocompetence hypothesized to contribute. Antimicrobial peptides (AMPs) secreted from dermal granular glands may play a role in hellbender health. We collected skin secretions from free-ranging hellbenders and enriched them for small cationic peptides used for growth inhibition assays against Bd and Bsal. Generalized linear mixed models revealed the presence of active toe lesions as the strongest and only significant predictor of decreased Bd inhibition by skin peptides. We also found skin secretions were more inhibitory of Bsal than Bd. MALDI-TOF mass spectrometry revealed candidate peptides responsible for anti-chytrid activity. Results support the hypothesis that hellbender skin secretions are important for innate immunity against chytrid pathogens, and decreased production or release of skin peptides may be linked to other sub-lethal effects of disease associated with toe lesions.
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Affiliation(s)
- Rebecca H Hardman
- Department of Biomedical and Diagnostic Sciences, University of Tennessee College of Veterinary Medicine, Knoxville, TN, 37996, USA. .,Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL, 33701, USA.
| | - Laura K Reinert
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Kelly J Irwin
- Arkansas Game and Fish Commission, Benton, AR, 72015, USA
| | - Kendall Oziminski
- Department of Biomedical and Diagnostic Sciences, University of Tennessee College of Veterinary Medicine, Knoxville, TN, 37996, USA
| | - Louise Rollins-Smith
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Debra L Miller
- Department of Biomedical and Diagnostic Sciences, University of Tennessee College of Veterinary Medicine, Knoxville, TN, 37996, USA.,School of Natural of Resources, University of Tennessee, Knoxville, Tennessee, 37996, USA
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15
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Loudon AH, Terrell KA, Davis RW, Umile TP, Lipps GJ, Greathouse J, Chapman E, Roblee K, Kleopfer JD, Bales EK, Hyman OJ, Harris RN, Minbiole KPC. Metabolite compositions on skins of eastern hellbenders Cryptobranchus alleganiensis alleganiensis differ with location and captivity. DISEASES OF AQUATIC ORGANISMS 2023; 153:9-16. [PMID: 36727687 DOI: 10.3354/dao03715] [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: 06/18/2023]
Abstract
Eastern hellbenders Cryptobranchus alleganiensis alleganiensis, large aquatic salamanders, are declining over most of their range. The amphibian-killing fungus Batrachochytrium dendrobatidis (Bd) has contributed to global amphibian declines and has been detected on eastern hellbenders, but infection intensities were lower than those of species that are more susceptible to Bd. The factors limiting Bd on hellbenders may include antifungal metabolites produced by their skin microbiota. We used a metabolite fingerprinting technique to noninvasively identify the presence, but not identity, of metabolites associated with eastern hellbenders. We surveyed the skin of wild eastern hellbenders to test whether the composition and richness (i.e. number of metabolites) of their metabolites are explained by Bd status or location. Furthermore, we surveyed for metabolites on captive eastern hellbenders to test whether metabolite compositions were different between captive and wild eastern hellbenders. Bd detection was not associated with either metabolite richness or composition. Both metabolite composition and richness differed significantly on hellbenders from different locations (i.e. states). For metabolite composition, there was a statistical interaction between location and Bd status. Metabolite richness was greater on captive eastern hellbenders compared to wild hellbenders, and metabolite compositions differed between wild and captive eastern hellbenders. The methods we employed to detect metabolite profiles effectively grouped individuals by location even though metabolite composition and richness have high levels of intraspecific variation. Understanding the drivers and functional consequences of assemblages of skin metabolites on amphibian health will be an important step toward understanding the mechanisms that result in disease vulnerability.
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Affiliation(s)
- Andrew H Loudon
- Biology Department, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
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16
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Alexiev A, Chen MY, Korpita T, Weier AM, McKenzie VJ. Together or Alone: Evaluating the Pathogen Inhibition Potential of Bacterial Cocktails against an Amphibian Pathogen. Microbiol Spectr 2023; 11:e0151822. [PMID: 36719234 PMCID: PMC10100949 DOI: 10.1128/spectrum.01518-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 12/11/2022] [Indexed: 02/01/2023] Open
Abstract
The amphibian fungal skin disease Batrachochytrium dendrobatidis (Bd) has caused major biodiversity losses globally. Several experimental trials have tested the use of Janthinobacterium lividum to reduce mortality due to Bd infections, usually in single-strain amendments. It is well-characterized in terms of its anti-Bd activity mechanisms. However, there are many other microbes that inhibit Bd in vitro, and not all experiments have demonstrated consistent results with J. lividum. We used a series of in vitro assays involving bacterial coculture with Bd lawns, bacterial growth tests in liquid broth, and Bd grown in bacterial cell-free supernatant (CFS) to determine: (i) which skin bacteria isolated from a locally endangered amphibian, namely, the Colorado boreal toad (Anaxyrus boreas boreas), are able to inhibit Bd growth; (ii) whether multistrain combinations are more effective than single-strains; and (iii) the mechanism behind microbe-microbe interactions. Our results indicate that there are some single strain and multistrain probiotics (especially including strains from Pseudomonas, Chryseobacterium, and Microbacterium) that are potentially more Bd-inhibitive than is J. lividum alone and that some combinations may lead to a loss of inhibition, potentially through antagonistic metabolite effects. Additionally, if J. lividum continues being developed as a wild boreal toad probiotic, we should investigate it in combination with Curvibacter CW54D, as they inhibited Bd additively and grew at a higher rate when combined than did either alone. This highlights the fact that combinations of probiotics function in variable and unpredictable ways as well as the importance of considering the potential for interactions among naturally resident host microbiota and probiotic additions. IMPORTANCE Batrachochytrium dendrobatidis (Bd) is a pathogen that infects amphibians globally and is causing a biodiversity crisis. Our research group studies one of the species affected by Bd, namely, the Colorado boreal toad (Anaxyrus boreas boreas). Many researchers focus their studies on one probiotic bacterial isolate called Janthinobacterium lividum, which slows Bd growth in lab cultures and is currently being field tested in Colorado boreal toads. Although promising, J. lividum is not consistently effective across all amphibian individuals or species. For Colorado boreal toads, we addressed whether there are other bacterial strains that also inhibit Bd (potentially better than does J. lividum) and whether we can create two-strain probiotics that function better than do single-strain probiotics. In addition, we evaluate which types of interactions occur between two-strain combinations and what these results mean in the context of adding a probiotic to an existing amphibian skin microbiome.
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Affiliation(s)
- Alexandra Alexiev
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Melissa Y. Chen
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Timothy Korpita
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Andrew M. Weier
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Valerie J. McKenzie
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
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17
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Crim MJ, Hart ML. Health Monitoring for Laboratory Salamanders. Methods Mol Biol 2023; 2562:41-74. [PMID: 36272067 DOI: 10.1007/978-1-0716-2659-7_3] [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] [Indexed: 06/16/2023]
Abstract
Laboratory animal health monitoring programs are necessary to protect animal health and welfare, the validity of experimental data, and human health against zoonotic infections. Health monitoring programs should be designed based on a risk assessment and knowledge about the biology and transmission of salamander pathogens. Both traditional and molecular diagnostic platforms are available for salamanders, and they provide complementary information. A comprehensive approach to health monitoring leverages the advantages of multiple platforms to provide a more complete picture of colony health and pathogen status. This chapter presents key considerations in the design and implementation of a colony health monitoring program for laboratory salamanders, including protocols for necropsy and sample collection.
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18
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Evidente A. Microbial and Plant Derived Low Risk Pesticides Having Nematocidal Activity. Toxins (Basel) 2022; 14:toxins14120849. [PMID: 36548747 PMCID: PMC9787815 DOI: 10.3390/toxins14120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Microorganisms, virus, weeds, parasitic plants, insects, and nematodes are among the enemies that induce severe economic losses to agrarian production. Farmers have been forced to combat these enemies using different methods, including mechanical and agronomic strategies, since the beginning of agriculture. The development of agriculture, due to an increased request for food production, which is a consequence to the rapid and noteworthy growth of the world's population, requires the use of more efficient methods to strongly elevate the yield production. Thus, in the last five-to-six decades, a massive and extensive use of chemicals has occurred in agriculture, resulting in heavy negative consequences, such as the increase in environmental pollution and risks for human and animal health. These problems increased with the repetition of treatments, which is due to resistance that natural enemies developed against this massive use of pesticides. There are new control strategies under investigation to develop products, namely biopesticides, with high efficacy and selectivity but based on natural products which are not toxic, and which are biodegradable in a short time. This review is focused on the microbial and plant metabolites with nematocidal activity with potential applications in suitable formulations in greenhouses and fields.
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Affiliation(s)
- Antonio Evidente
- Department of Chemical Science, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy;
- Institute of Sciences of Food Production, National Research Council, Via Amendola 122/O, 70125 Bari, Italy
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19
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Cevallos MA, Basanta MD, Bello-López E, Escobedo-Muñoz AS, González-Serrano FM, Nemec A, Romero-Contreras YJ, Serrano M, Rebollar EA. Genomic characterization of antifungal Acinetobacter bacteria isolated from the skin of the frogs Agalychnis callidryas and Craugastor fitzingeri. FEMS Microbiol Ecol 2022; 98:6775075. [PMID: 36288213 DOI: 10.1093/femsec/fiac126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/09/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023] Open
Abstract
Chytridiomycosis, a lethal fungal disease caused by Batrachochytrium dendrobatidis (Bd), is responsible for population declines and extinctions of amphibians worldwide. However, not all amphibian species are equally susceptible to the disease; some species persist in Bd enzootic regions with no population reductions. Recently, it has been shown that the amphibian skin microbiome plays a crucial role in the defense against Bd. Numerous bacterial isolates with the capacity to inhibit the growth of Batrachochytrium fungi have been isolated from the skin of amphibians. Here, we characterized eight Acinetobacter bacteria isolated from the frogs Agalychnis callidryas and Craugastor fitzingeri at the genomic level. A total of five isolates belonged to Acinetobacter pittii,Acinetobacter radioresistens, or Acinetobactermodestus, and three were not identified as any of the known species, suggesting they are members of new species. We showed that seven isolates inhibited the growth of Bd and that all eight isolates inhibited the growth of the phytopathogen fungus Botrytis cinerea. Finally, we identified the biosynthetic gene clusters that could be involved in the antifungal activity of these isolates. Our results suggest that the frog skin microbiome includes Acinetobacter isolates that are new to science and have broad antifungal functions, perhaps driven by distinct genetic mechanisms.
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Affiliation(s)
- M A Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M D Basanta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México.,Department of Biology, University of Nevada Reno, 1664 N Virgina St, Reno, NV 89557, United States
| | - E Bello-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A S Escobedo-Muñoz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - F M González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 00 Prague 10, Czechia.,Department of Medical Microbiology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Úvalu 84, 150 06 Prague 5, Czechia
| | - Y J Romero-Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - E A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
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20
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Wu-Chuang A, Bates KA, Obregon D, Estrada-Peña A, King KC, Cabezas-Cruz A. Rapid evolution of a novel protective symbiont into keystone taxon in Caenorhabditis elegans microbiota. Sci Rep 2022; 12:14045. [PMID: 35982076 PMCID: PMC9388637 DOI: 10.1038/s41598-022-18269-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
Protective microbes have a major role in shaping host-pathogen interactions, but their relative importance in the structure of the host microbiota remains unclear. Here, we used a network approach to characterize the impact of a novel, experimentally evolved 'protective microbial symbiont' (Enterococcus faecalis) on the structure and predicted function of the natural microbiota of the model organism Caenorhabditis elegans. We used microbial network analysis to identify keystone taxa and describe the hierarchical placement of protective and non-protective symbionts in the microbiota. We found that early colonization with symbionts produce statistically significant changes in the structure of the community. Notably, only the protective E. faecalis became a keystone taxon in the nematode microbiota. Non-protective lineages of the same bacterial species remained comparatively unimportant to the community. Prediction of functional profiles in bacterial communities using PICRUSt2 showed that the presence of highly protective E. faecalis decreased the abundance of ergothioneine (EGT) biosynthesis pathway involved in the synthesis of the antioxidant molecule EGT, a potential public good. These data show that in addition to direct antagonism with virulent pathogens, keystone protective symbionts are linked to modified bacterial community structure and possible reductions in public goods, potentially driving decreased antioxidant defense. We suggest that this response could suppress infection via wholesale microbial community changes to further benefit the host. These findings extend the concept of protective symbionts beyond bodyguards to ecosystem engineers.
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Affiliation(s)
- Alejandra Wu-Chuang
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Kieran A Bates
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Dasiel Obregon
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France.
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21
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LaForgia ML, Kang H, Ettinger CL. Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome. MICROBIAL ECOLOGY 2022; 84:496-508. [PMID: 34505915 PMCID: PMC9436828 DOI: 10.1007/s00248-021-01853-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses grown in a shade-house both individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition. We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Furthermore, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.
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Affiliation(s)
- Marina L LaForgia
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
- Department of Plant Sciences, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Hannah Kang
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Cassandra L Ettinger
- Genome Center, University of California, Davis, CA, USA.
- Department of Evolution and Ecology, University of California, Davis, CA, USA.
- Microbiology & Plant Pathology, University of California, Riverside, CA, USA.
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22
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McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak. Ecosphere 2022. [DOI: 10.1002/ecs2.4037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Donald T. McKnight
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Roger Huerlimann
- College of Science and Engineering James Cook University Townsville Queensland Australia
- Marine Climate Change Unit Okinawa Institute of Science and Technology Onnason Okinawa Japan
| | - Deborah S. Bower
- College of Science and Engineering James Cook University Townsville Queensland Australia
- School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Lin Schwarzkopf
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Ross A. Alford
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Kyall R. Zenger
- College of Science and Engineering James Cook University Townsville Queensland Australia
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23
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Martins RA, Greenspan SE, Medina D, Buttimer S, Marshall VM, Neely WJ, Siomko S, Lyra ML, Haddad CFB, São-Pedro V, Becker CG. Signatures of functional bacteriome structure in a tropical direct-developing amphibian species. Anim Microbiome 2022; 4:40. [PMID: 35672870 PMCID: PMC9172097 DOI: 10.1186/s42523-022-00188-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species.
Results
Intensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization.
Conclusions
Our findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.
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Orlandi VT, Martegani E, Giaroni C, Baj A, Bolognese F. Bacterial pigments: A colorful palette reservoir for biotechnological applications. Biotechnol Appl Biochem 2022; 69:981-1001. [PMID: 33870552 PMCID: PMC9544673 DOI: 10.1002/bab.2170] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 04/09/2021] [Indexed: 12/12/2022]
Abstract
Synthetic derivatives are currently used instead of pigments in many applicative fields, from food to feed, from pharmaceutical to diagnostic, from agronomy to industry. Progress in organic chemistry allowed to obtain rather cheap compounds covering the whole color spectrum. However, several concerns arise from this chemical approach, as it is mainly based on nonrenewable resources such as fossil oil, and the toxicity or carcinogenic properties of products and/or precursors may be harmful for personnel involved in the productive processes. In this scenario, microorganisms and their pigments represent a colorful world to discover and reconsider. Each living bacterial strain may be a source of secondary metabolites with peculiar functions. The aim of this review is to link the physiological role of bacterial pigments with their potential use in different biotechnological fields. This enormous potential supports the big challenge for the development of strategies useful to identify, produce, and purify the right pigment for the desired application. At the end of this ideal journey through the world of bacterial pigments, the attention will be focused on melanin compounds, whose production relies upon different techniques ranging from natural producers, heterologous hosts, or isolated enzymes. In a green workflow, the microorganisms represent the starting and final point of pigment production.
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Affiliation(s)
| | - Eleonora Martegani
- Department of Biotechnologies and Life SciencesUniversity of InsubriaVareseItaly
| | - Cristina Giaroni
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
| | - Andreina Baj
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
| | - Fabrizio Bolognese
- Department of Biotechnologies and Life SciencesUniversity of InsubriaVareseItaly
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25
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Chen MY, Kueneman JG, González A, Humphrey G, Knight R, McKenzie VJ. Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians. Mol Ecol 2022; 31:2140-2156. [PMID: 35076975 DOI: 10.1111/mec.16372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/16/2021] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
Pathogen success (risk and severity) is influenced by host-associated microbiota, but the degree to which variation in microbial community traits predict future infection presence/absence (risk) and load (severity) for the host is unknown. We conducted a time-series experiment by sampling the skin-associated bacterial communities of five amphibian species before and after exposure to the fungal pathogen, Batrachochytrium dendrobaditis (Bd). We ask whether microbial community traits are predictors of, or are affected by, Bd infection risk and intensity. Our results show that richness of putative Bd-inhibitory bacteria strongly predicts infection risk, while the proportion of putative Bd-inhibitory bacteria predicts future infection intensity. Variation in microbial community composition is high across time and individual, and bacterial prevalence is low. Our findings demonstrate how ecological community traits of host-associated microbiota may be used to predict infection risk by pathogenic microbes.
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Affiliation(s)
- Melissa Y Chen
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA
| | - Jordan G Kueneman
- Smithsonian Tropical Research Institute, Luis Clement Avenue, Bldg. 401 Tupper, Balboa Ancon, Panama, Republic of Panama
| | - Antonio González
- Department of Pediatrics, Bioengineering and Computer Science and Engineering, and Center for Microbiome Innovation, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093, USA
| | - Greg Humphrey
- Department of Pediatrics, Bioengineering and Computer Science and Engineering, and Center for Microbiome Innovation, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, Bioengineering and Computer Science and Engineering, and Center for Microbiome Innovation, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093, USA
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA
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26
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Buttimer S, Hernández-Gómez O, Rosenblum EB. Skin bacterial metacommunities of San Francisco Bay Area salamanders are structured by host genus and habitat quality. FEMS Microbiol Ecol 2021; 97:6464136. [PMID: 34918086 DOI: 10.1093/femsec/fiab162] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Host-associated microbial communities can influence physiological processes of macroorganisms, including contributing to infectious disease resistance. For instance, some bacteria that live on amphibian skin produce antifungal compounds that inhibit two lethal fungal pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). Therefore, differences in microbiome composition among host species or populations within a species can contribute to variation in susceptibility to Bd/Bsal. This study applies 16S rRNA sequencing to characterize the skin bacterial microbiomes of three widespread terrestrial salamander genera native to the western United States. Using a metacommunity structure analysis, we identified dispersal barriers for these influential bacteria between salamander families and localities. We also analyzed the effects of habitat characteristics such as percent natural cover and temperature seasonality on the microbiome. We found that certain environmental variables may influence the skin microbial communities of some salamander genera more strongly than others. Each salamander family had a somewhat distinct community of putative anti-Bd skin bacteria, suggesting that salamanders may select for a functional assembly of cutaneous symbionts that could differ in its ability to protect these amphibians from disease. Our observations raise the need to consider host identity and environmental heterogeneity during the selection of probiotics to treat wildlife diseases.
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Affiliation(s)
- Shannon Buttimer
- Department of Environmental Science, Policy, and Management - The University of California, Berkeley, Berkeley, CA, U.S.A.,Department of Biological Sciences - The University of Alabama, Tuscaloosa, AL, U.S.A
| | - Obed Hernández-Gómez
- Department of Environmental Science, Policy, and Management - The University of California, Berkeley, Berkeley, CA, U.S.A.,School of Health and Natural Sciences - Dominican University of California, San Rafael, CA, U.S.A
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management - The University of California, Berkeley, Berkeley, CA, U.S.A
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27
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Weitzman CL, Rostama B, Thomason CA, May M, Belden LK, Hawley DM. Experimental test of microbiome protection across pathogen doses reveals importance of resident microbiome composition. FEMS Microbiol Ecol 2021; 97:6385755. [PMID: 34626186 DOI: 10.1093/femsec/fiab141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/07/2021] [Indexed: 01/04/2023] Open
Abstract
The commensal microbes inhabiting a host tissue can interact with invading pathogens and host physiology in ways that alter pathogen growth and disease manifestation. Prior work in house finches (Haemorhous mexicanus) found that resident ocular microbiomes were protective against conjunctival infection and disease caused by a relatively high dose of Mycoplasma gallisepticum. Here, we used wild-caught house finches to experimentally examine whether protective effects of the resident ocular microbiome vary with the dose of invading pathogen. We hypothesized that commensal protection would be strongest at low M. gallisepticum inoculation doses because the resident microbiome would be less disrupted by invading pathogen. Our five M. gallisepticum dose treatments were fully factorial with an antibiotic treatment to perturb resident microbes just prior to M. gallisepticum inoculation. Unexpectedly, we found no indication of protective effects of the resident microbiome at any pathogen inoculation dose, which was inconsistent with the prior work. The ocular bacterial communities at the beginning of our experiment differed significantly from those previously reported in local wild-caught house finches, likely causing this discrepancy. These variable results underscore that microbiome-based protection in natural systems can be context dependent, and natural variation in community composition may alter the function of resident microbiomes in free-living animals.
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Affiliation(s)
- Chava L Weitzman
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Bahman Rostama
- Department of Biomedical Sciences, University of New England, Biddeford - 04005, ME, USA
| | - Courtney A Thomason
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA.,Division of Remediation, Tennessee Department of Environment and Conservation, Oak Ridge - 37830, TN, USA
| | - Meghan May
- Department of Biomedical Sciences, University of New England, Biddeford - 04005, ME, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Dana M Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
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28
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Becker MH, Brophy JAN, Barrett K, Bronikowski E, Evans M, Glassey E, Kaganer AW, Klocke B, Lassiter E, Meyer AJ, Muletz-Wolz CR, Fleischer RC, Voigt CA, Gratwicke B. Genetically modifying skin microbe to produce violacein and augmenting microbiome did not defend Panamanian golden frogs from disease. ISME COMMUNICATIONS 2021; 1:57. [PMID: 37938636 PMCID: PMC9723765 DOI: 10.1038/s43705-021-00044-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 04/21/2023]
Abstract
We designed two probiotic treatments to control chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) on infected Panamanian golden frogs (Atelopus zeteki), a species that is thought to be extinct in the wild due to Bd. The first approach disrupted the existing skin microbe community with antibiotics then exposed the frogs to a core golden frog skin microbe (Diaphorobacter sp.) that we genetically modified to produce high titers of violacein, a known antifungal compound. One day following probiotic treatment, the engineered Diaphorobacter and the violacein-producing pathway could be detected on the frogs but the treatment failed to improve frog survival when exposed to Bd. The second approach exposed frogs to the genetically modified bacterium mixed into a consortium with six other known anti-Bd bacteria isolated from captive A. zeteki, with no preliminary antibiotic treatment. The consortium treatment increased the frequency and abundance of three probiotic isolates (Janthinobacterium, Chryseobacterium, and Stenotrophomonas) and these persisted on the skin 4 weeks after probiotic treatment. There was a temporary increase in the frequency and abundance of three other probiotics isolates (Masillia, Serratia, and Pseudomonas) and the engineered Diaphorobacter isolate, but they subsequently disappeared from the skin. This treatment also failed to reduce frog mortality upon exposure.
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Affiliation(s)
- Matthew H Becker
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
- Liberty University Department of Biology and Chemistry, Lynchburg, VA, USA
| | - Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ed Bronikowski
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Matthew Evans
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alyssa W Kaganer
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
| | - Blake Klocke
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Elliot Lassiter
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Adam J Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carly R Muletz-Wolz
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Conservation Genetics, Washington, DC, 20001, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Conservation Genetics, Washington, DC, 20001, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA.
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29
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Chimetto Tonon LA, Rua C, Crnkovic CM, Bernardi DI, Pires Junior OR, Haddad CFB, Pedrosa CSG, Souza LRQ, Rehen SK, de Azevedo GPR, Thompson CC, Thompson FL, Berlinck RGS. Microbiome associated with the tetrodotoxin-bearing anuran Brachycephalus pitanga. Toxicon 2021; 203:139-146. [PMID: 34653444 DOI: 10.1016/j.toxicon.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/15/2022]
Abstract
The genus Brachycephalus includes small species of aposematic anurans known as microendemic, occurring in the mountains of the Atlantic Forest. Brachycephalus ephippium, B. nodoterga and B. pernix have been reported to contain the neurotoxin tetrodotoxin in skin and viscera. The biological conservation of several Brachycephalus species is currently threatened by climate change, deforestation, and the pandemic caused by the fungus Batrachochytrium dendrobatidis (Bd). Despite the well-known importance of amphibians' associated bacteria in the defensive role against pathogens, there is still a poor understanding of amphibian microbiome composition. The present study investigated the composition of B. pitanga microbial community and the presence of TTX in the host and in cultures of bacterial isolates, using a combination of metagenomics, bacterial culture isolation, mass spectrometry and metabolomic analyses. Results of culture-dependent and -independent analyses characterized the microbial communities associated with the skin and viscera of B. pitanga. Mass spectrometry analysis indicated the presence of TTX in host tissues, while bacterial production of TTX was not observed under the experimental conditions used in this investigation. This is the first report confirming the occurrence of TTX in B. pitanga.
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Affiliation(s)
- Luciane A Chimetto Tonon
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
| | - Cintia Rua
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Camila M Crnkovic
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Departamento de Tecnologia Bioquímico-Farmacêutica (FBT), Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Osmindo R Pires Junior
- Laboratório de Toxinologia, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | | | | | - Stevens K Rehen
- Instituto D'Or de Pesquisa e Ensino (IDOR), RJ, Brazil; Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Gustavo P R de Azevedo
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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30
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Ward CS, Rolison K, Li M, Rozen S, Fisher CL, Lane TW, Thelen MP, Stuart RK. Janthinobacter additions reduce rotifer grazing of microalga Microchloropsis salina in biotically complex communities. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Gabriel A, Costa S, Henriques I, Lopes I. Effects of Long-Term Exposure to Increased Salinity on the Amphibian Skin Bacterium Erwinia toletana. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 80:779-788. [PMID: 33877369 DOI: 10.1007/s00244-021-00845-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Amphibian's skin bacterial community may help them to cope with several types of environmental perturbations, including osmotic stress caused by increased salinity. This work assessed whether an amphibian skin bacterium could increase its tolerance to NaCl after a long-term exposure to this salt. A strain of Erwinia toletana, isolated from the skin of Pelophylax perezi, was exposed to two salinity scenarios (with 18 g/L of NaCl): (1) long-term exposure (for 46 days; Et-NaCl), and (2) long-term exposure followed by a recovery period (exposure for 30 days to NaCl and then to LB medium for 16 days; Et-R). After exposure, the sensitivity of E. toletana clonal populations to NaCl was assessed by exposing them to 6 NaCl concentrations (LB medium spiked with NaCl) plus a control (LB medium). Genotypic alterations were assessed by PCR-based molecular typing method (BOX-PCR). The results showed that tolerance of E. toletana to NaCl slightly increased after the long-term exposure, EC50 for growth were: 22.5 g/L (8.64-36.4) for Et-LB; 30.3 g/L (23.2-37.4) for Et-NaCl; and 26.1 g/L (19.332.9) for Et-R. Differences in metabolic activity were observed between Et-LB and Et-R and between Et-NaCl and Et-R, suggesting the use of different substrates by this bacterium when exposed to salinized environments. NaCl-induced genotypic alterations were not detected. This work suggests that E. toletana exposed to low levels of salinity, activate different metabolic pathways to cope with osmotic stress. These findings may be further explored to be used in bioaugmentation procedures through the supplementation with this bacterium of the skin microbiome of natural populations of amphibians exposed to salinization.
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Affiliation(s)
- Antonieta Gabriel
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal.
| | - Sara Costa
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| | - Isabel Henriques
- Department of Life Sciences, CESAM, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Isabel Lopes
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
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32
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Medina D, Greenspan SE, Carvalho T, Becker CG, Toledo LF. Co-infecting pathogen lineages have additive effects on host bacterial communities. FEMS Microbiol Ecol 2021; 97:6134751. [PMID: 33580951 DOI: 10.1093/femsec/fiab030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/11/2021] [Indexed: 01/08/2023] Open
Abstract
Amphibian skin bacteria may confer protection against the fungus Batrachochytrium dendrobatidis (Bd), but responses of skin bacteria to different Bd lineages are poorly understood. The global panzootic lineage (Bd-GPL) has caused amphibian declines and extinctions globally. However, other lineages are enzootic (Bd-Asia-2/Brazil). Increased contact rates between Bd-GPL and enzootic lineages via globalization pose unknown consequences for host-microbiome-pathogen dynamics. We conducted a laboratory experiment and used 16S rRNA amplicon-sequencing to assess: (i) whether two lineages (Bd-Asia-2/Brazil and Bd-GPL) and their recombinant, in single and mixed infections, differentially affect amphibian skin bacteria; (ii) and the changes associated with the transition to laboratory conditions. We determined no clear differences in bacterial diversity among Bd treatments, despite differences in infection intensity. However, we observed an additive effect of mixed infections on bacterial alpha diversity and a potentially antagonistic interaction between Bd genotypes. Additionally, observed changes in community composition suggest a higher ability of Bd-GPL to alter skin bacteria. Lastly, we observed a drastic reduction in bacterial diversity and a change in community structure in laboratory conditions. We provide evidence for complex interactions between Bd genotypes and amphibian skin bacteria during coinfections, and expand on the implications of experimental conditions in ecological studies.
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Affiliation(s)
- Daniel Medina
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil.,Sistema Nacional de Investigación, SENACYT, Building 205, City of Knowledge, Clayton, Panama, Republic of Panama
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, 1339 Science and Engineering Complex, Tuscaloosa 35487, Alabama, USA
| | - Tamilie Carvalho
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil
| | - C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, 1339 Science and Engineering Complex, Tuscaloosa 35487, Alabama, USA
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil
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33
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The Fungicide Chlorothalonil Changes the Amphibian Skin Microbiome: A Potential Factor Disrupting a Host Disease-Protective Trait. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The skin microbiome is an important part of amphibian immune defenses and protects against pathogens such as the chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the skin disease chytridiomycosis. Alteration of the microbiome by anthropogenic factors, like pesticides, can impact this protective trait, disrupting its functionality. Chlorothalonil is a widely used fungicide that has been recognized as having an impact on amphibians, but so far, no studies have investigated its effects on amphibian microbial communities. In the present study, we used the amphibian Lithobates vibicarius from the montane forest of Costa Rica, which now appears to persist despite ongoing Bd-exposure, as an experimental model organism. We used 16S rRNA amplicon sequencing to investigate the effect of chlorothalonil on tadpoles’ skin microbiome. We found that exposure to chlorothalonil changes bacterial community composition, with more significant changes at a higher concentration. We also found that a larger number of bacteria were reduced on tadpoles’ skin when exposed to the higher concentration of chlorothalonil. We detected four presumed Bd-inhibitory bacteria being suppressed on tadpoles exposed to the fungicide. Our results suggest that exposure to a widely used fungicide could be impacting host-associated bacterial communities, potentially disrupting an amphibian protective trait against pathogens.
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34
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Chatragadda R, Dufossé L. Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments. Microorganisms 2021; 9:637. [PMID: 33803896 PMCID: PMC8003166 DOI: 10.3390/microorganisms9030637] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), Council of Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d’Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France
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35
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Park H, Park S, Yang YH, Choi KY. Microbial synthesis of violacein pigment and its potential applications. Crit Rev Biotechnol 2021; 41:879-901. [PMID: 33730942 DOI: 10.1080/07388551.2021.1892579] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Violacein is a pigment synthesized by Gram-negative bacteria such as Chromobacterium violaceum. It has garnered significant interest owing to its unique physiological and biological activities along with its synergistic effects with various antibiotics. In addition to C. violaceum, several microorganisms, including: Duganella sp., Pseudoalteromonas sp., Iodobacter sp., and Massilia sp., are known to produce violacein. Along with the identification of violacein-producing strains, the genetic regulation, quorum sensing mechanism, and sequence of the vio-operon involved in the biosynthesis of violacein have been elucidated. From an engineering perspective, the heterologous production of violacein using the genetically engineered Escherichia coli or Citrobacter freundii host has also been attempted. Genetic engineering of host cells involves the heterologous expression of genes involved in the vio operon and the optimization of metabolic pathways and gene regulation. Further, the crystallography of VioD and VioE was revealed, and mass production by enzyme engineering has been accelerated. In this review, we highlight the biologically assisted end-use applications of violacein (such as functional fabric development, nanoparticles, functional polymer composites, and sunscreen ingredients) and violacein activation mechanisms, production strains, and the results of mass production with engineered methods. The prospects for violacein research and engineering applications have also been discussed.
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Affiliation(s)
- HyunA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - SeoA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea.,Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Suwon, South Korea
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36
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Choi SY, Lim S, Yoon KH, Lee JI, Mitchell RJ. Biotechnological Activities and Applications of Bacterial Pigments Violacein and Prodigiosin. J Biol Eng 2021; 15:10. [PMID: 33706806 PMCID: PMC7948353 DOI: 10.1186/s13036-021-00262-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
In this review, we discuss violacein and prodigiosin, two chromogenic bacterial secondary metabolites that have diverse biological activities. Although both compounds were "discovered" more than seven decades ago, interest into their biological applications has grown in the last two decades, particularly driven by their antimicrobial and anticancer properties. These topics will be discussed in the first half of this review. The latter half delves into the current efforts of groups to produce these two compounds. This includes in both their native bacterial hosts and heterogeneously in other bacterial hosts, including discussing some of the caveats related to the yields reported in the literature, and some of the synthetic biology techniques employed in this pursuit.
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Affiliation(s)
- Seong Yeol Choi
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Sungbin Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Kyoung-Hye Yoon
- Department of Physiology, Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Gangwon-do, South Korea.
| | - Jin I Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus, Wonju, Gangwon-do, South Korea.
| | - Robert J Mitchell
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
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37
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Proença DN, Fasola E, Lopes I, Morais PV. Characterization of the Skin Cultivable Microbiota Composition of the Frog Pelophylax perezi Inhabiting Different Environments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18052585. [PMID: 33807539 PMCID: PMC7967507 DOI: 10.3390/ijerph18052585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 12/20/2022]
Abstract
Microorganisms that live in association with amphibian skin can play important roles in protecting their host. Within the scenarios of global change, it is important to understand how environmental disturbances, namely, metal pollution, can affect this microbiota. The aim of this study is to recognize core bacteria in the skin cultivable microbiota of the Perez frog (Pelophylax perezi) that are preserved regardless of the environmental conditions in which the frogs live. The characterization of these isolates revealed characteristics that can support their contributions to the ability of frogs to use metal impacted environments. Frog’s skin swabs were collected from P. perezi populations that inhabit a metal-polluted site and three reference (non-metal polluted) sites. Bacterial strains were isolated, identified, and subjected to an acid mine drainage tolerance (AMD) test, collected upstream from a site heavily contaminated with metals, and tested to produce extracellular polymeric substances (exopolysaccharide, EPS). All frog populations had Acinetobacter in their cutaneous cultivable microbiota. Significant growth inhibition was observed in all bacterial isolates exposed to 75% of AMD. EPS production was considered a characteristic of several isolates. The data obtained is a preliminary step but crucial to sustain that the cultivable microbiota is a mechanism for protecting frogs against environmental contamination.
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Affiliation(s)
- Diogo Neves Proença
- Department of Life Sciences and Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal;
| | - Emanuele Fasola
- CESAM and Department of Biology, University of Aveiro, 3810-005 Aveiro, Portugal; (E.F.); (I.L.)
| | - Isabel Lopes
- CESAM and Department of Biology, University of Aveiro, 3810-005 Aveiro, Portugal; (E.F.); (I.L.)
| | - Paula V. Morais
- Department of Life Sciences and Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal;
- Correspondence: ; Tel.: +35-1239240700
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38
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Abarca JG, Whitfield SM, Zuniga-Chaves I, Alvarado G, Kerby J, Murillo-Cruz C, Pinto-Tomás AA. Genotyping and differential bacterial inhibition of Batrachochytrium dendrobatidis in threatened amphibians in Costa Rica. MICROBIOLOGY-SGM 2021; 167. [PMID: 33529150 DOI: 10.1099/mic.0.001017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Amphibians have declined around the world in recent years, in parallel with the emergence of an epidermal disease called chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). This disease has been associated with mass mortality in amphibians worldwide, including in Costa Rica, and Bd is considered an important contributor to the disappearance of this group of vertebrates. While many species are susceptible to the disease, others show tolerance and manage to survive infection with the pathogen. We evaluated the pathogen Bd circulating in Costa Rica and the capacity of amphibian skin bacteria to inhibit the growth of the pathogen in vitro. We isolated and characterized - genetically and morphologically - several Bd isolates from areas with declining populations of amphibians. We determined that the circulating chytrid fungus in Costa Rica belongs to the virulent strain Bd-GPL-2, which has been related to massive amphibian deaths worldwide; however, the isolates obtained showed genetic and morphological variation. Furthermore, we isolated epidermal bacteria from 12 amphibian species of surviving populations, some in danger of extinction, and evaluated their inhibitory activity against the collection of chytrid isolates. Through bioassays we confirmed the presence of chytrid-inhibitory bacterial genera in Costa Rican amphibians. However, we observed that the inhibition varied between different isolates of the same bacterial genus, and each bacterial isolation inhibited fungal isolation differently. In total, 14 bacterial isolates belonging to the genera Stenotrophomonas, Streptomyces, Enterobacter, Pseudomonas and Klebsiella showed inhibitory activity against all Bd isolates. Given the observed variation both in the pathogen and in the bacterial inhibition capacity, it is highly relevant to include local isolates and to consider the origin of the microorganisms when performing in vivo infection tests aimed at developing and implementing mitigation strategies for chytridiomycosis.
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Affiliation(s)
- Juan G Abarca
- Laboratorio de Recursos Naturales y Vida Silvestre (LARNAVISI), Escuela de Ciencias Biológicas, Universidad Nacional, Heredia, Costa Rica
| | - Steven M Whitfield
- Conservation and Research Department, Zoo Miami, St, Miami, FL 33177, USA
| | - Ibrahim Zuniga-Chaves
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Gilbert Alvarado
- Laboratorio de Patología Experimental y Comparada (LAPECOM), Escuela de Biología, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Jacob Kerby
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, San Pedro, Costa Rica.,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, San Pedro, Costa Rica.,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
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39
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Female Salamanders Experience Higher Parasitism Compared to Males: A Cost of Female Reproduction? J HERPETOL 2020. [DOI: 10.1670/19-072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Preuss JF, Greenspan SE, Rossi EM, Lucas Gonsales EM, Neely WJ, Valiati VH, Woodhams DC, Becker CG, Tozetti AM. Widespread Pig Farming Practice Linked to Shifts in Skin Microbiomes and Disease in Pond-Breeding Amphibians. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11301-11312. [PMID: 32845628 DOI: 10.1021/acs.est.0c03219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Farming practices may reshape the structure of watersheds, water quality, and the health of aquatic organisms. Nutrient enrichment from agricultural pollution increases disease pressure in many host-pathogen systems, but the mechanisms underlying this pattern are not always resolved. For example, nutrient enrichment should strongly influence pools of aquatic environmental bacteria, which has the potential to alter microbiome composition of aquatic animals and their vulnerability to disease. However, shifts in the host microbiome have received little attention as a link between nutrient enrichment and diseases of aquatic organisms. We examined nutrient enrichment through the widespread practice of integrated pig-fish farming and its effects on microbiome composition of Brazilian amphibians and prevalence of the globally distributed amphibian skin pathogen Batrachochytrium dendrobatidis (Bd). This farming system drove surges in fecal coliform bacteria, disturbing amphibian skin bacterial communities such that hosts recruited higher proportions of Bd-facilitative bacteria and carried higher Bd prevalence. Our results highlight previously overlooked connections between global trends in land use change, microbiome dysbiosis, and wildlife disease. These interactions may be particularly important for disease management in the tropics, a region with both high biodiversity and continually intensifying anthropogenic pressures on aquatic wildlife habitats.
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Affiliation(s)
- Jackson F Preuss
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS 93022-750, Brazil
- Departamento de Ciências da Vida, Universidade do Oeste de Santa Catarina, São Miguel do Oeste, SC 89900-000, Brazil
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Eliandra M Rossi
- Departamento de Ciências da Vida, Universidade do Oeste de Santa Catarina, São Miguel do Oeste, SC 89900-000, Brazil
| | - Elaine M Lucas Gonsales
- Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, RS 98300-000, Brazil
| | - Wesley J Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Victor Hugo Valiati
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS 93022-750, Brazil
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, United States
| | - C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Alexandro M Tozetti
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS 93022-750, Brazil
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41
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Loudon AH, Kurtz A, Esposito E, Umile TP, Minbiole KPC, Parfrey LW, Sheafor BA. Columbia spotted frogs (Rana luteiventris) have characteristic skin microbiota that may be shaped by cutaneous skin peptides and the environment. FEMS Microbiol Ecol 2020; 96:5894915. [DOI: 10.1093/femsec/fiaa168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/13/2020] [Indexed: 01/20/2023] Open
Abstract
ABSTRACT
Global amphibian declines due to the fungal pathogen Batrachochytrium dendrobatidis (Bd) have led to questions about how amphibians defend themselves against skin diseases. A total of two amphibian defense mechanisms are antimicrobial peptides (AMPs), a component of amphibian innate immune defense and symbiotic skin bacteria, which can act in synergy. We characterized components of these factors in four populations of Columbia spotted frogs (Rana luteiventris) to investigate their role in disease defense. We surveyed the ability of their AMPs to inhibit Bd, skin bacterial community composition, skin metabolite profiles and presence and intensity of Bd infection. We found that AMPs from R. luteiventris inhibited Bd in bioassays, but inhibition did not correlate with Bd intensity on frogs. R. luteiventris had two prevalent and abundant core bacteria: Rhizobacter and Chryseobacterium. Rhizobacter relative abundance was negatively correlated with AMP's ability to inhibit Bd, but was not associated with Bd status itself. There was no relationship between metabolites and Bd. Bacterial communities and Bd differ by location, which suggests a strong environmental influence. R. luteiventris are dominated by consistent core bacteria, but also house transient bacteria that are site specific. Our emergent hypothesis is that host control and environmental factors shape the microbiota on R. luteiventris.
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Affiliation(s)
- A H Loudon
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - A Kurtz
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - E Esposito
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - T P Umile
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - K P C Minbiole
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - L W Parfrey
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - B A Sheafor
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
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42
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de Souza Valente C, Rodiles A, Freire Marques MR, Merrifield DL. White spot syndrome virus (WSSV) disturbs the intestinal microbiota of shrimp (Penaeus vannamei) reared in biofloc and clear seawater. Appl Microbiol Biotechnol 2020; 104:8007-8023. [PMID: 32789745 DOI: 10.1007/s00253-020-10816-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 01/18/2023]
Abstract
White spot syndrome virus (WSSV) is one of the most virulent pathogens afflicting shrimp farming. Understanding its influence on shrimp intestinal microbiota is paramount for the advancement of aquaculture, since gut dysbiosis can negatively impact shrimp development, physiology, and immunological response. Thereupon, the data presented herein assesses the influence of WSSV infection and different rearing systems on the intestinal microbiota of Penaeus vannamei. Our study aimed to describe and correlate the composition of shrimp (Penaeus vannamei) gut microbiota, when reared in biofloc and clear seawater, before and (48 h) after WSSV experimental infection. Shrimp were kept in two different systems (biofloc and clear seawater) and experimentally infected with WSSV. Intestine and water samples were characterized by 16S rRNA gene sequencing, before and after viral infection. We observed (i) WSSV induced higher mortality among shrimp reared in biofloc; (ii) WSSV led to a loss of intestinal microbiota heterogeneity, at the genus level, in shrimp kept in clear seawater; (iii) there was a prevalence of Cetobacterium and Bacillus in the intestine of shrimp from both systems; (iv) WSSV did not cause significant changes in intestinal microbiota diversity or richness; (v) regardless of the type of system and time of infection, intestinal microbiota was dissimilar to that of the surrounding water, despite being influenced by the type of system. Therefore, WSSV infection leads to punctual dysbiotic changes in shrimp microbiota, although the virus is sufficiently virulent to cause high mortalities even in well-managed systems, such as a balanced experimental biofloc system. KEY POINTS: • WSSV infection leads to a perturbed gut microbiota in shrimp. • WSSV infection greater impacts microbiota of shrimp reared in CSW than those in BFT. • WSSV infection caused higher mortality levels in shrimp reared in BFT than in CSW. • Rearing system influences shrimp gut microbiota composition. Graphical abstract.
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Affiliation(s)
- Cecília de Souza Valente
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry, Department of Biochemistry, Federal University of Santa Catarina, Florianopolis, SC, Brazil.
| | - Ana Rodiles
- School of Biological & Marine Sciences, Faculty of Science & Engineering, University of Plymouth, Plymouth, UK.,Lallemand Animal Nutrition, Lallemand SAS, 31702, Blagnac, France
| | - Maria Risoleta Freire Marques
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry, Department of Biochemistry, Federal University of Santa Catarina, Florianopolis, SC, Brazil
| | - Daniel Lee Merrifield
- School of Biological & Marine Sciences, Faculty of Science & Engineering, University of Plymouth, Plymouth, UK
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43
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Li Z, Wang H, Ding D, Liu Y, Fang H, Chang Z, Chen T, Zhang D. Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway. ACTA ACUST UNITED AC 2020; 47:525-535. [DOI: 10.1007/s10295-020-02288-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022]
Abstract
Abstract
The shikimate pathway is indispensable for the biosynthesis of natural products with aromatic moieties. These products have wide current and potential applications in food, cosmetics and medicine, and consequently have great commercial value. However, compounds extracted from various plants or synthesized from petrochemicals no longer satisfy the requirements of contemporary industries. As a result, an increasing number of studies has focused on this pathway to enable the biotechnological manufacture of natural products, especially in E. coli. Furthermore, the development of synthetic biology, systems metabolic engineering and high flux screening techniques has also contributed to improving the biosynthesis of high-value compounds based on the shikimate pathway. Here, we review approaches based on a combination of traditional and new metabolic engineering strategies to increase the metabolic flux of the shikimate pathway. In addition, applications of this optimized pathway to produce aromatic amino acids and a range of natural products is also elaborated. Finally, this review sums up the opportunities and challenges facing this field.
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Affiliation(s)
- Zhu Li
- grid.33763.32 0000 0004 1761 2484 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education); SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin China
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Huiying Wang
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Dongqin Ding
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.410726.6 0000 0004 1797 8419 University of Chinese Academy of Sciences 100049 Beijing China
| | - Yongfei Liu
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Huan Fang
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Zhishuai Chang
- grid.33763.32 0000 0004 1761 2484 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education); SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin China
| | - Tao Chen
- grid.33763.32 0000 0004 1761 2484 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education); SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin China
| | - Dawei Zhang
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.410726.6 0000 0004 1797 8419 University of Chinese Academy of Sciences 100049 Beijing China
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44
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Rebollar EA, Martínez-Ugalde E, Orta AH. The Amphibian Skin Microbiome and Its Protective Role Against Chytridiomycosis. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.167] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Emanuel Martínez-Ugalde
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Alberto H. Orta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
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45
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Dahan D, Preston GM, Sealey J, King KC. Impacts of a novel defensive symbiosis on the nematode host microbiome. BMC Microbiol 2020; 20:159. [PMID: 32539750 PMCID: PMC7296725 DOI: 10.1186/s12866-020-01845-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Bacteria adapted to live within animals can protect their hosts against harmful infections. Beyond antagonism with pathogens, a 'defensive' bacterial symbiont could engage in additional interactions with other colonizing micro-organisms. A single bacterium might thus have cascading ecological impacts on the whole microbiome that are rarely investigated. Here, we assess the role of a defensive symbiont as a driver of host-associated microbiota composition by using a bacterial species (Enterococcus faecalis) that was previously experimentally adapted to a nematode host model (Caenorhabditis elegans). RESULTS An analysis of 16S rRNA data from C. elegans exposed to E. faecalis and subsequently reared in soil, reveal that symbiont adaptation to host environment or its protective potential had minimal impact on microbiota diversity. Whilst the abundance of Pseudomonas was higher in the microbiota of hosts with protective E.faecalis (and another protective species tested), a few other genera - including Serratia and Salinispora - were less abundant in hosts colonized by all E. faecalis strains. In addition, the protective effect of E. faecalis against virulent Staphylococcus aureus pathogens was maintained despite multi-species interactions within the microbiota. CONCLUSIONS Our results reveal the degree to which a new, evolving symbiont can colonise and maintain pathogen-resistance with minimal disruption to host microbiota diversity.
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Affiliation(s)
- Dylan Dahan
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305-5124, USA
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Jordan Sealey
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.
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46
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Lankau EW, Xue D, Christensen R, Gevens AJ, Lankau RA. Management and Soil Conditions Influence Common Scab Severity on Potato Tubers Via Indirect Effects on Soil Microbial Communities. PHYTOPATHOLOGY 2020; 110:1049-1055. [PMID: 31939718 DOI: 10.1094/phyto-06-19-0223-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Common scab, caused by Streptomyces scabies and related species, is a potato tuber blemish disease that causes reductions in marketable yield worldwide. Evidence of suppression of common scab by indigenous soil microbial populations has been found in several studies. However, we lack a comprehensive understanding of how common scab severity relates functionally to potato varieties, farming systems, soil physical and chemical properties, and soil microbial communities. These factors may affect disease directly or indirectly by affecting one of the other variables. We performed a survey of 30 sampling locations across 12 fields in Wisconsin and used structural equation modeling to disentangle the direct effects of potato market classes, farm management (conventional versus organic), and soil physiochemical properties on common scab severity from their indirect effects mediated through soil bacterial and fungal communities. We found that, although potato market classes affected disease severity directly, the effects of farm management and soil physiochemistry were best explained as indirect, mediated by their impacts on soil bacterial communities. This suggests that evaluating the consequences of specific management practices for soil microbial communities may be useful for understanding disease pressure across fields.
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Affiliation(s)
- Emily W Lankau
- Department of Animal Sciences, University of Wisconsin, Madison, WI
- Department of Plant Pathology, University of Wisconsin, Madison, WI
| | - Dianne Xue
- Department of Plant Pathology, University of Wisconsin, Madison, WI
| | | | - Amanda J Gevens
- Department of Plant Pathology, University of Wisconsin, Madison, WI
| | - Richard A Lankau
- Department of Plant Pathology, University of Wisconsin, Madison, WI
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47
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Mueller EA, Wisnoski NI, Peralta AL, Lennon JT. Microbial rescue effects: How microbiomes can save hosts from extinction. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13493] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Jay T. Lennon
- Department of Biology Indiana University Bloomington IN USA
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48
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Choi SY, Lim S, Cho G, Kwon J, Mun W, Im H, Mitchell RJ. Chromobacterium violaceum delivers violacein, a hydrophobic antibiotic, to other microbes in membrane vesicles. Environ Microbiol 2020; 22:705-713. [PMID: 31814287 DOI: 10.1111/1462-2920.14888] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 12/01/2022]
Abstract
This study describes Chromobacterium violaceum's use of extracellular membrane vesicles (MVs) to both solubilize and transport violacein to other microorganisms. Violacein is a hydrophobic bisindole with known antibiotic activities against other microorganisms. Characterization of the MVs found they carried more violacein than protein (1.37 ± 0.19-fold), suggesting they may act as a reservoir for this compound. However, MVs are not produced in response to violacein - a ΔvioA isogenic mutant, which is incapable of making violacein, actually produced significantly more MVs (3.2-fold) than the wild-type strain. Although violacein is insoluble in water (Log Poctanol:water = 3.34), 79.5% remained in the aqueous phase when it was present within the C. violaceum MVs, an increase in solubility of 1740-fold. Moreover, tests with a strain of Staphylococcus aureus showed MV-associated violacein is bactericidal, with 3.1 mg/l killing 90% of S. aureus in 6 h. Tests with the ΔvioA MVs found no loss in the S. aureus viability, even when its MVs were added at much higher concentrations, demonstrating violacein is the active component within the wild-type MVs. In conclusion, our study clearly demonstrates C. violaceum produces MVs and uses them as vehicles to solubilize violacein and transport this hydrophobic antibiotic to other microbes.
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Affiliation(s)
- Seong Yeol Choi
- Applied and Environmental Microbiology Lab, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Sungbin Lim
- Applied and Environmental Microbiology Lab, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Gayoung Cho
- Applied and Environmental Microbiology Lab, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Jisoo Kwon
- Applied and Environmental Microbiology Lab, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Wonsik Mun
- Applied and Environmental Microbiology Lab, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Hansol Im
- Applied and Environmental Microbiology Lab, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Robert J Mitchell
- Applied and Environmental Microbiology Lab, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
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49
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Kruger A. Functional Redundancy of Batrachochytrium dendrobatidis Inhibition in Bacterial Communities Isolated from Lithobates clamitans Skin. MICROBIAL ECOLOGY 2020; 79:231-240. [PMID: 31165187 DOI: 10.1007/s00248-019-01387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
The cutaneous microbial community can influence the health of amphibians exposed to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that has contributed to recent amphibian declines. Resistance to Bd in amphibian populations is correlated with the presence of anti-Bd cutaneous microbes, which confer disease resistance by inhibiting Bd growth. I aimed to determine if green frogs (Lithobates clamitans), an abundant and widely distributed species in New Jersey, harbored bacteria that inhibit Bd and whether the presence and identity of these microbes varied among sites. I used in vitro challenge assays to determine if bacteria isolated from green frog skin could inhibit or enhance the growth of Bd. I found that green frogs at all sites harbored anti-Bd bacteria. However, there were differences in Bd inhibition capabilities among bacterial isolates identified as the same operational taxonomic unit (OTU), lending support to the idea that phylogenetic relatedness does not always predict Bd inhibition status. Additionally, anti-Bd bacterial richness did not vary by site, but the composition of anti-Bd bacterial taxa was distinct at each site. This suggests that there is functional redundancy of Bd inhibition across unique communities of anti-Bd symbionts found on frogs at different sites. These findings highlight the need to better elucidate the structure-function relationship of microbiomes and their role in disease resistance.
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Affiliation(s)
- Ariel Kruger
- Graduate Program in Ecology and Evolution, Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901, USA.
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50
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Harrison XA, Price SJ, Hopkins K, Leung WTM, Sergeant C, Garner TWJ. Diversity-Stability Dynamics of the Amphibian Skin Microbiome and Susceptibility to a Lethal Viral Pathogen. Front Microbiol 2019; 10:2883. [PMID: 31956320 PMCID: PMC6951417 DOI: 10.3389/fmicb.2019.02883] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022] Open
Abstract
Variation among animals in their host-associated microbial communities is increasingly recognized as a key determinant of important life history traits including growth, metabolism, and resistance to disease. Quantitative estimates of the factors shaping the stability of host microbiomes over time at the individual level in non-model organisms are scarce. Addressing this gap in our knowledge is important, as variation among individuals in microbiome stability may represent temporal gain or loss of key microbial species and functions linked to host health and/or fitness. Here we use controlled experiments to investigate how both heterogeneity in microbial species richness of the environment and exposure to the emerging pathogen Ranavirus influence the structure and temporal dynamics of the skin microbiome in a vertebrate host, the European common frog (Rana temporaria). Our evidence suggests that altering the bacterial species richness of the environment drives divergent temporal microbiome dynamics of the amphibian skin. Exposure to ranavirus effects changes in skin microbiome structure irrespective of total microbial diversity, but individuals with higher pre-exposure skin microbiome diversity appeared to exhibit higher survival. Higher diversity skin microbiomes also appear less stable over time compared to lower diversity microbiomes, but stability of the 100 most abundant ("core") community members was similar irrespective of microbiome richness. Our study highlights the importance of extrinsic factors in determining the stability of host microbiomes over time, which may in turn have important consequences for the stability of host-microbe interactions and microbiome-fitness correlations.
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Affiliation(s)
- Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, United Kingdom.,Centre for Ecology and Conservation, University of Exeter, Exeter, United Kingdom
| | - Stephen J Price
- Institute of Zoology, Zoological Society of London, London, United Kingdom.,UCL Genetics Institute, University College London, London, United Kingdom
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - William T M Leung
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Chris Sergeant
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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