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Yu M, Li W, He X, He G, Yao Y, Wang Y, Shao M, Xiong T, Xu H, Zhao J. Metabarcoding of protozoa and helminth in black-necked cranes: a high prevalence of parasites and free-living amoebae. Parasite 2024; 31:28. [PMID: 38819296 PMCID: PMC11141520 DOI: 10.1051/parasite/2024028] [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: 11/27/2023] [Accepted: 05/04/2024] [Indexed: 06/01/2024] Open
Abstract
Parasites and free-living amoebae (FLA) are common pathogens that pose threats to wildlife and humans. The black-necked crane (Grus nigricollis) is a near-threatened species and there is a shortage of research on its parasite diversity. Our study aimed to use noninvasive methods to detect intestinal parasites and pathogenic FLA in G. nigricollis using high-throughput sequencing (HTS) based on the 18S rDNA V9 region. A total of 38 fresh fecal samples were collected in Dashanbao, China, during the overwintering period (early-, middle I-, middle II-, and late-winter). Based on the 18S data, eight genera of parasites were identified, including three protozoan parasites: Eimeria sp. (92.1%) was the dominant parasite, followed by Tetratrichomonas sp. (36.8%) and Theileria sp. (2.6%). Five genera of helminths were found: Echinostoma sp. (100%), Posthodiplostomum sp. (50.0%), Euryhelmis sp. (26.3%), Eucoleus sp. (50.0%), and Halomonhystera sp. (2.6%). Additionally, eight genera of FLA were detected, including the known pathogens Acanthamoeba spp. (n = 13) and Allovahlkampfia spp. (n = 3). Specific PCRs were used to further identify the species of some parasites and FLA. Furthermore, the 18S data indicated significant changes in the relative abundance and genus diversity of the protozoan parasites and FLA among the four periods. These results underscore the importance of long-term monitoring of pathogens in black-necked cranes to protect this near-endangered species.
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Affiliation(s)
- Mengshi Yu
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Wenhao Li
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Xin He
- Sichuan Academy of Grassland Sciences Chengdu 610000 PR China
| | - Guiwen He
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University Zhaotong 657000 PR China
| | - Yonfang Yao
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Junsong Zhao
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University Zhaotong 657000 PR China
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Bass D, Christison KW, Stentiford GD, Cook LSJ, Hartikainen H. Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology. Trends Parasitol 2023; 39:285-304. [PMID: 36759269 DOI: 10.1016/j.pt.2022.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 02/11/2023]
Abstract
Detection of pathogens, parasites, and other symbionts in environmental samples via eDNA/eRNA (collectively eNA) is an increasingly important source of information about their occurrence and activity. There is great potential for using such detections as a proxy for infection of host organisms in connected habitats, for pathogen monitoring and surveillance, and for early warning systems for disease. However, many factors require consideration, and appropriate methods developed and verified, in order that eNA detections can be reliably interpreted and adopted for surveillance and assessment of disease risk, and potentially inclusion in international standards, such as the World Organisation for Animal Health guidelines. Disease manifestation results from host-symbiont-environment interactions between hosts, demanding a multifactorial approach to interpretation of eNA signals.
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Affiliation(s)
- David Bass
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
| | - Kevin W Christison
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa; Department of Forestry, Fisheries and the Environment, Private Bag X2, Vlaeberg, 8012, South Africa
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
| | - Lauren S J Cook
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, UK
| | - Hanna Hartikainen
- University of Nottingham, School of Life Sciences, University Park, NG7 2RD, Nottingham, UK
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Holt CC, Boscaro V, Van Steenkiste NWL, Herranz M, Mathur V, Irwin NAT, Buckholtz G, Leander BS, Keeling PJ. Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi. MICROBIOME 2022; 10:161. [PMID: 36180959 PMCID: PMC9523941 DOI: 10.1186/s40168-022-01363-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. RESULTS Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. CONCLUSIONS Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
| | - Niels W L Van Steenkiste
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Maria Herranz
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Gracy Buckholtz
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
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Protists in the Insect Rearing Industry: Benign Passengers or Potential Risk? INSECTS 2022; 13:insects13050482. [PMID: 35621816 PMCID: PMC9144225 DOI: 10.3390/insects13050482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023]
Abstract
Simple Summary As human populations grow and the climate crisis deepens, humans will need to look to alternative sustainable sources of protein. The insect rearing industry is now rapidly growing to generate more sustainable sources of food and feed, and, as it does so, there will be an urgent need to better understand the role that microorganisms play in both maintaining insect health and generating disease. Protists are microbes that are neither viral, bacterial nor fungal and, therefore, are sometimes overlooked when considering microbial fauna. In this paper, we review the literature on protists that have been uncovered within insects that are being considered for rearing as food and feed. We discuss what is known about how they interact with hosts, how they may affect industrially reared insects in the future and which tools now need to be developed to better study them. Abstract As the insects for food and feed industry grows, a new understanding of the industrially reared insect microbiome is needed to better comprehend the role that it plays in both maintaining insect health and generating disease. While many microbiome projects focus on bacteria, fungi or viruses, protists (including microsporidia) can also make up an important part of these assemblages. Past experiences with intensive invertebrate rearing indicate that these parasites, whilst often benign, can rapidly sweep through populations, causing extensive damage. Here, we review the diversity of microsporidia and protist species that are found in reared insect hosts and describe the current understanding of their host spectra, life cycles and the nature of their interactions with hosts. Major entomopathogenic parasite groups with the potential to infect insects currently being reared for food and feed include the Amoebozoa, Apicomplexa, Ciliates, Chlorophyta, Euglenozoa, Ichtyosporea and Microsporidia. However, key gaps exist in the understanding of how many of these entomopathogens affect host biology. In addition, for many of them, there are very limited or even no molecular data, preventing the implementation of molecular detection methods. There is now a pressing need to develop and use novel molecular tools, coupled with standard molecular diagnostic methods, to help unlock their biology and predict the effects of these poorly studied protist parasites in intensive insect rearing systems.
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Briscoe AG, Nichols S, Hartikainen H, Knipe H, Foster R, Green AJ, Okamura B, Bass D. High-Throughput Sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds. Mol Ecol Resour 2021; 22:1303-1318. [PMID: 34758191 DOI: 10.1111/1755-0998.13548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.
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Affiliation(s)
- Andrew G Briscoe
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Core Research Laboratories, Natural History Museum, London, United Kingdom
| | - Sarah Nichols
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Hanna Hartikainen
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Eawag and Institute for Integrative Biology, Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Hazel Knipe
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Rachel Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, 41092, Sevilla, Spain
| | - Beth Okamura
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Centre for Environment, Aquaculture and Fisheries Science (Cefas), Weymouth, UK
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