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Engstrom CB, Raymond BB, Albeitshawish J, Bogdanovic A, Quarmby LM. Rosetta gen. nov. (Chlorophyta): Resolving the identity of red snow algal rosettes. JOURNAL OF PHYCOLOGY 2024; 60:275-298. [PMID: 38439561 DOI: 10.1111/jpy.13438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
Thick-walled rosette-like snow algae were long thought to be a life stage of various other species of snow algae. Rosette-like cells have not been cultured, but by manually isolating cells from 38 field samples in southern British Columbia, we assigned a variety of rosette morphologies to DNA sequence. Phylogenetic analysis of Rubisco large-subunit (rbcL) gene, ribosomal internal transcribed spacer 2 (ITS2) rRNA region, and 18S rRNA gene revealed that the rosette-like cells form a new clade within the phylogroup Chloromonadinia. Based on these data, we designate a new genus, Rosetta, which comprises five novel species: R. castellata, R. floranivea, R. stellaria, R. rubriterra, and R. papavera. In a survey of 762 snow samples from British Columbia, we observed R. floranivea exclusively on snow overlying high-elevation glaciers, whereas R. castellata was observed at lower elevations, near the tree line. The other three species were rarely observed. Spherical red cells enveloped in a thin translucent sac were conspecific with Rosetta, possibly a developmental stage. These results highlight the unexplored diversity among snow algae and emphasize the utility of single-cell isolation to advance the centuries-old problem of disentangling life stages and cryptic species.
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Affiliation(s)
- Casey B Engstrom
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Breanna B Raymond
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Joud Albeitshawish
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anastasia Bogdanovic
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Lynne M Quarmby
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Quaresma A, Ankenbrand MJ, Garcia CAY, Rufino J, Honrado M, Amaral J, Brodschneider R, Brusbardis V, Gratzer K, Hatjina F, Kilpinen O, Pietropaoli M, Roessink I, van der Steen J, Vejsnæs F, Pinto MA, Keller A. Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. Sci Data 2024; 11:129. [PMID: 38272945 PMCID: PMC10810873 DOI: 10.1038/s41597-024-02962-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.
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Affiliation(s)
- Andreia Quaresma
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, S/N, Edifício FC4, 4169-007, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Vila do Conde, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Vila do Conde, Portugal
| | - Markus J Ankenbrand
- Center for Computational and Theoretical Biology, Faculty of Biology, Julius-Maximilians-Universität Würzburg, Klara-Oppenheimer-Weg 32, 97074, Würzburg, Germany
| | - Carlos Ariel Yadró Garcia
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - José Rufino
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Research Centre in Digitalization and Intelligent Robotics (CeDRI), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Mónica Honrado
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Joana Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Robert Brodschneider
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Valters Brusbardis
- Latvian Beekeepers' Association (LBA), Rigas iela 22, LV-3004, Jelgava, Latvia
| | - Kristina Gratzer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Fani Hatjina
- Ellinikos Georgikos Organismos DIMITRA (ELGO- DIMITRA), Kourtidou 56-58, GR-11145, Athina, Greece
| | - Ole Kilpinen
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - Marco Pietropaoli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri" (IZSLT), Via Appia Nuova 1411, IT-00178, Roma, Italy
| | - Ivo Roessink
- Wageningen Environmental Research, WageningenUniversity&Research, Droevendaalsesteeg 3, 6700 AA, Wageningen, Netherlands
| | | | - Flemming Vejsnæs
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Alexander Keller
- Cellular and Organismic Interactions, Biocenter, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany.
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Zograf JK, Semenchenko AA, Mordukhovich VV. New deep-sea species of Aborjinia (Nematoda, Leptosomatidae) from the North-Western Pacific: an integrative taxonomy and phylogeny. Zookeys 2024; 1189:231-256. [PMID: 38282715 PMCID: PMC10809327 DOI: 10.3897/zookeys.1189.111825] [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: 08/29/2023] [Accepted: 11/15/2023] [Indexed: 01/30/2024] Open
Abstract
Marimermithid nematodes parasitising invertebrates are mainly found in the deep-sea environments. Several adult and juvenile specimens marimermithids of the genus Aborjinia have been found in bottom sediments and inside Polychaeta during recent cruises to the Kuril-Kamchatka trench and the Kuril Basin (the Sea of Okhotsk). New species are described based on integrative study. Aborjiniaprofundasp. nov. differs from A.eulagiscae by the location of the ventral gland cell bodies (posterior to the nerve ring vs posterior to the cardia), by the smaller body size (23-28 mm vs 103-132 mm) and shorter tail (193-263 µm vs 500-850 µm). BI and ML phylogenetic analyses based on 18S and 28S rDNA suggest that genus Aborjinia belongs to the family Leptosomatidae. Based on molecular and morphological characters the new genus Paraborjiniagen. nov. is proposed for A.corallicola. Within the family Leptosomatidae the new genus differs from all genera except Aborjinia by its endoparasitic lifestyle and hologonic ovaries. Paraborjiniagen. nov. differs from Aborjinia by the position of cephalic sensitive organs (outer labial and cephalic papillae in two separate circles vs outer labial and cephalic papillae in one circle) and by the parasitic adult (vs free-living in Aborjinia).
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Affiliation(s)
- Julia K. Zograf
- A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, 690041, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine BiologyVladivostokRussia
| | - Alexander A. Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022, Vladivostok, RussiaFederal Scientific Center of the East Asia Terrestrial BiodiversityVladivostokRussia
| | - Vladimir V. Mordukhovich
- A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, 690041, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine BiologyVladivostokRussia
- Far Eastern Federal University, 690922, Vladivostok, RussiaFar Eastern Federal UniversityVladivostokRussia
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Brusati A, Agostinetto G, Bruno A, Casiraghi M, Pescini D, Sandionigi A, Balech B. Exploration and Retrieval of Virus-Related Molecular Data Using ExTaxsI: The Monkeypox Use Case. Methods Mol Biol 2024; 2732:145-154. [PMID: 38060123 DOI: 10.1007/978-1-0716-3515-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Retrieval and visualization of biological data are essential for understanding complex systems. With the increasing volume of data generated from high-throughput sequencing technologies, effective and optimized data visualization tools have become indispensable. This is particularly relevant in the COVID-19 postpandemic period, where understanding the diversity and interactions of microbial communities (i.e., viral and bacterial) constitutes an important asset to develop and plan suitable interventions.In this chapter, we show the usage and the potentials of ExTaxsI (Exploring Taxonomy Information) tool to retrieve viral biodiversity data stored in National Center for Biotechnology Information (NCBI) databases and create the related visualization. In addition, by integrating different functions and modules, the tool generates relevant types of visualization plots to facilitate the exploration of microbial biodiversity communities useful to deep dive into ecological and taxonomic relationships among different species and identify potential significant targets.Using the Monkeypox virus as a case study, this work points out significant perspectives on biological data visualization, which can be used to gain insights into the ecology, evolution, and pathogenesis of viruses. Accordingly, we show the potentiality of ExTaxsI to organize and describe the available/downloaded data in an easy, simple, and interpretable way allowing the user to interact dynamically with the visualization plots through specific filters, zoom, and explore functions.
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Affiliation(s)
- Alberto Brusati
- University of Pavia, Department of Brain and Behavioral Sciences, Pavia, Italy
| | - Giulia Agostinetto
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy.
| | - Antonia Bruno
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
| | - Maurizio Casiraghi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
| | - Dario Pescini
- University of Milano-Bicocca, Department of Statistics and Quantitative Methods, Milan, Italy
| | - Anna Sandionigi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
- Quantia Consulting srl, Department of Data Science and Education, Remote Company, Milan, Italy
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (CNR), Bari, Italy
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5
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Wasti QZ, Sabar MF, Farooq A, Khan MU. Stepping towards pollen DNA metabarcoding: A breakthrough in forensic sciences. Forensic Sci Med Pathol 2023:10.1007/s12024-023-00770-8. [PMID: 38147285 DOI: 10.1007/s12024-023-00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
This review is engaged in determining the capability of plant pollen as a significant source of evidence for the linkage between suspects and crime location in forensic sciences. Research and review articles were collected from Google Scholar, the Web of Science, and PubMed. Articles were searched using specific keywords such as "Forensic Palynology," "Pollen metabarcoding," "Plant forensics," and "Pollen" AND "criminal investigation." Boolean logic was also utilized to narrow the articles to be included in this review article. Through the literature and exploratory research, it has been observed in the current study that with advancements in technology, forensic palynology has found its application in creating an association between the crime scene and suspected individuals to have a link to it, as pollen DNA is a long-lasting investigative tool that can effectively help forensic investigations. Moreover, the literature shows that the DNA of pollen and spores has helped forensic scientists link suspects to crime scenes, and the introduction of pollen DNA metabarcoding tools has eased the efforts of palynologists to analyze pollen DNA. The introduction of DNA metabarcoding techniques to analyze pollen from plants has helped identify the geological locations of the plants and ultimately identify the culprit.
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Affiliation(s)
- Qandeel Zaineb Wasti
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Abeera Farooq
- Punjab University College of Pharmacy, University of the Punjab, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
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6
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Xiao Y, Sun L, Xin X, Xu L, Du S. Physicochemical characteristics and microbial community succession during oat silage prepared without or with Lactiplantibacillus plantarum or Lentilactobacillus buchneri. Microbiol Spectr 2023; 11:e0222823. [PMID: 37947518 PMCID: PMC10714795 DOI: 10.1128/spectrum.02228-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/07/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Ensiled whole-plant oats are an important feedstuff for ruminants in large parts of the world. Oat silage is rich in dietary fibers, minerals, vitamins, and phytochemicals beneficial to animal health. The fermentation of oat silage is a complex biochemical process that includes interactions between various microorganisms. The activity of many microbes in silage may cause an extensive breakdown of nutrition and lead to undesirable fermentation. Moreover, it is difficult to make high-quality oat silage because the number of epiphytic lactic acid bacterium microflora was lower than the requirement. Understanding the complex microbial community during the fermentation process and its relationship with community functions is therefore important in the context of developing improved fermentation biotechnology systems. These results suggested that the addition of Lactobacillus plantarum or Lactobacillus buchneri regulated the ensiling performance and microbial community in oat silage by shaping the metabolic pathways.
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Affiliation(s)
- Yanzi Xiao
- College of Agriculture and Forestry, Hulunbuir University, Hulunber, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Science, Hulunber Grassland Ecosystem Observation and Research Station, Beijing, China
| | - Lin Sun
- Inner Mongolia Academy of Agricultural Science & Animal Husbandry, Hohhot, China
| | - Xiaoping Xin
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Science, Hulunber Grassland Ecosystem Observation and Research Station, Beijing, China
| | - Lijun Xu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Science, Hulunber Grassland Ecosystem Observation and Research Station, Beijing, China
| | - Shuai Du
- />Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Yong RQY, Martin SB, Smit NJ. A new species of Siphoderina Manter, 1934 (Digenea: Cryptogonimidae) infecting the Dory Snapper Lutjanus fulviflamma (Teleostei: Lutjanidae) from the east coast of South Africa. Syst Parasitol 2023; 100:673-686. [PMID: 37845589 PMCID: PMC10613151 DOI: 10.1007/s11230-023-10116-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023]
Abstract
Parasitological assessment of marine fishes at Sodwana Bay in the iSimangaliso Marine Protected Area on the east coast of South Africa revealed a new species of cryptogonimid trematode infecting the pyloric caeca of the Dory Snapper, Lutjanus fulviflamma (Forsskål) (Lutjanidae). The new species is morphologically consistent with the concept of the large genus Siphoderina Manter, 1934; its phylogenetic position within this genus was validated through molecular sequencing of the ITS2 and partial 28S ribosomal DNA sub-regions. We name this species Siphoderina nana n. sp. and comment on the current state of understanding for this genus of cryptogonimids.
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Affiliation(s)
- Russell Q-Y Yong
- Water Research Group, Unit for Environmental Sciences & Management, North-West University, Potchefstroom, 2520, South Africa.
| | - Storm B Martin
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Nico J Smit
- Water Research Group, Unit for Environmental Sciences & Management, North-West University, Potchefstroom, 2520, South Africa
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Liu Y, Liang N, Xian Q, Zhang W. GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2. BMC PLANT BIOLOGY 2023; 23:608. [PMID: 38036992 PMCID: PMC10691020 DOI: 10.1186/s12870-023-04634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/26/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Despite GC variation constitutes a fundamental element of genome and species diversity, the precise mechanisms driving it remain unclear. The abundant sequence data available for the ITS2, a commonly employed phylogenetic marker in plants, offers an exceptional resource for exploring the GC variation across angiosperms. RESULTS A comprehensive selection of 8666 species, comprising 165 genera, 63 families, and 30 orders were used for the analyses. The alignment of ITS2 sequence-structures and partitioning of secondary structures into paired and unpaired regions were performed using 4SALE. Substitution rates and frequencies among GC base-pairs in the paired regions of ITS2 were calculated using RNA-specific models in the PHASE package. The results showed that the distribution of ITS2 GC contents on the angiosperm phylogeny was heterogeneous, but their increase was generally associated with ITS2 sequence homogenization, thereby supporting the occurrence of GC-biased gene conversion (gBGC) during the concerted evolution of ITS2. Additionally, the GC content in the paired regions of the ITS2 secondary structure was significantly higher than that of the unpaired regions, indicating the selection of GC for thermodynamic stability. Furthermore, the RNA substitution models demonstrated that base-pair transformations favored both the elevation and fixation of GC in the paired regions, providing further support for gBGC. CONCLUSIONS Our findings highlight the significance of secondary structure in GC investigation, which demonstrate that both gBGC and structure-based selection are influential factors driving angiosperm ITS2 GC content.
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Affiliation(s)
- Yubo Liu
- Marine College, Shandong University, Weihai, 264209, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Nan Liang
- Marine College, Shandong University, Weihai, 264209, China
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qing Xian
- Marine College, Shandong University, Weihai, 264209, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, 264209, China.
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Liu X, Yang M, Liu R, Zhou F, Zhu H, Wang X. The impact of Parkinson's disease-associated gut microbiota on the transcriptome in Drosophila. Microbiol Spectr 2023; 11:e0017623. [PMID: 37754772 PMCID: PMC10581176 DOI: 10.1128/spectrum.00176-23] [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: 01/13/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease in middle-aged and elderly people, and many studies have confirmed that the disorder of gut microbiota is involved in the pathophysiological process of PD. However, the molecular mechanism of gut microbiota in regulating the pathogenesis of PD is still lacking. In this study, to investigate the impact of PD-associated gut microbiota on host transcriptome, we established various PD models with fecal microbiota transplantation (FMT) in the model organism Drosophila followed by integrative data analysis of microbiome and transcriptome. We first constructed rotenone-induced PD models in Drosophila followed by FMT in different groups. Microbial analysis by 16S rDNA sequencing showed that gut microbiota from PD Drosophila could affect bacterial structure of normal Drosophila, and gut microbiota from normal Drosophila could affect bacterial structure of PD Drosophila. Transcriptome analysis revealed that PD-associated gut microbiota influenced expression patterns of genes enriched in neuroactive ligand-receptor interaction, lysosome, and diverse metabolic pathways. Importantly, to verify our findings, we transplanted Drosophila with fecal samples from clinical PD patients. Compared to the control, Drosophila transplanted with fecal samples from PD patients had reduced microbiota Acetobacter and Lactobacillus, and differentially expressed genes enriched in diverse metabolic pathways. In summary, our results reveal the influence of PD-associated gut microbiota on host gene expression, and this study can help better understand the link between gut microbiota and PD pathogenesis through gut-brain axis. IMPORTANCE Gut microbiota plays important roles in regulating host gene expression and physiology through complex mechanisms. Recently, it has been suggested that disorder of gut microbiota is involved in the pathophysiological process of Parkinson's disease (PD). However, the molecular mechanism of gut microbiota in regulating the pathogenesis of PD is still lacking. In this study, to investigate the impact of PD-associated gut microbiota on host transcriptome, we established various PD models with fecal microbiota transplantation in the model organism Drosophila followed by integrative data analysis of microbiome and transcriptome. We also verified our findings by transplanting Drosophila with fecal samples from clinical PD patients. Our results demonstrated that PD-associated gut microbiota can induce differentially expressed genes enriched in diverse metabolic pathways. This study can help better understand the link between gut microbiota and PD pathogenesis through gut-brain axis.
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Affiliation(s)
- Xin Liu
- South China Normal University-Panyu Central Hospital Joint Laboratory of Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Meng Yang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Runzhou Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Fan Zhou
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haibing Zhu
- South China Normal University-Panyu Central Hospital Joint Laboratory of Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China
- Department of Psychiatry, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Xiaoyun Wang
- South China Normal University-Panyu Central Hospital Joint Laboratory of Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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Guo L, Tóth T, Yang F, Wang Z. Effects of different types of vegetation cover on soil microorganisms and humus characteristics of soda-saline land in the Songnen Plain. Front Microbiol 2023; 14:1163444. [PMID: 37808294 PMCID: PMC10551454 DOI: 10.3389/fmicb.2023.1163444] [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: 02/10/2023] [Accepted: 08/15/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction In the soda-saline grasslands of the Songnen Plain, Jilin Province, China, the prohibition of grazing has led to significant changes in plant communities and soil properties. However, the intricate interplay between soil physical and chemical attributes, the soil microbial community, and their combined influence on soil humus composition remains poorly understood. Methods Our study aimed to evaluate the impact of natural vegetation restoration on soil properties, microbial community diversity, and composition in the soda-saline soil region of the Songnen Plain. We conducted assessments of soil physical and chemical properties, analyzed community diversity, and composition at a soil depth range of 0-20 cm. The study covered soils with dominant soda-saline vegetation species, including Suaeda glauca Bunge, Puccinellia chinampoensis Ohwi, Chloris virgata Swarta, Phragmites australis (Clay.), Leymus chinensis (Trin.), and Tzvelev. We compared these vegetated soils to bare land devoid of any plants. Results We found that soil organic content (SOC) in vegetation restoration areas was higher than in bare land, with SOC content varying between 3.64 and 11.15 g/kg in different vegetated areas. Notably, soil pH emerged as a pivotal factor, explaining 11.4% and 12.2% of the variance in soil bacteria and fungi, respectively. There were correlations between SOC content and the relative abundance of specific microbial groups, with Acidobacteria and Mortierella showing a positive correlation, while Actinobacteria, Gemmatimonadetes, and Ascomycota exhibited significant negative correlations with SOC. Discussion The disparities in SOC composition and content among the soda-saline vegetation types were primarily attributed to variations in pH. Consequently, reducing soil pH is identified as a critical step in the process of vegetation restoration in soda-saline land. Prohibiting grazing has the potential to increase soda-saline SOC content and enhance microbial diversity, with Leymus chinensis and Phragmites australis showing particularly promising results in terms of higher SOC carbon content and microbial diversity.
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Affiliation(s)
- Liangliang Guo
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tibor Tóth
- Centre for Agricultural Research, Institute for Soil Sciences, Budapest, Hungary
| | - Fan Yang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Zhichun Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Jiménez-Gaona Y, Vivanco-Galván O, Cruz D, Armijos-Carrión A, Suárez JP. Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota). J Fungi (Basel) 2023; 9:894. [PMID: 37755002 PMCID: PMC10532482 DOI: 10.3390/jof9090894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella. OBJECTIVES The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella. METHODOLOGY Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale. RESULTS AND CONCLUSIONS The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.
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Affiliation(s)
- Yuliana Jiménez-Gaona
- Departamento de Química, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Oscar Vivanco-Galván
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Darío Cruz
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Angelo Armijos-Carrión
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada;
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
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Abdullah N, Teng ST, Hanifah AH, Law IK, Tan TH, Krock B, Harris TM, Nagai S, Lim PT, Tillmann U, Leaw CP. Thecal plate morphology, molecular phylogeny, and toxin analyses reveal two novel species of Alexandrium (Dinophyceae) and their potential for toxin production. HARMFUL ALGAE 2023; 127:102475. [PMID: 37544675 DOI: 10.1016/j.hal.2023.102475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
This study describes two novel species of marine dinophytes in the genus Alexandrium. Morphological characteristics and phylogenetic analyses support the placement of the new taxa, herein designated as Alexandrium limii sp. nov. and A. ogatae sp. nov. Alexandrium limii, a species closely related to A. taylorii, is distinguished by having a shorter 2'/4' suture length, narrower plates 1' and 6'', with larger length: width ratios, and by the position of the ventral pore (Vp). Alexandrium ogatae is distinguishable with its metasert plate 1' having almost parallel lateral margins, and by lacking a Vp. Production of paralytic shellfish toxins (PSTs), cycloimines, and goniodomins (GDs) in clonal cultures of A. ogatae, A. limii, and A. taylorii were examined analytically and the results showed that all strains contained GDs, with GDA as major variants (6-14 pg cell-1) for all strains except the Japanese strain of A. limii, which exclusively had a desmethyl variant of GDA (1.4-7.3 pg cell-1). None of the strains contained detectable levels of PSTs and cycloimines.
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Affiliation(s)
- Nursyahida Abdullah
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Afiqah Hamilton Hanifah
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Ing Kuo Law
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Toh Hii Tan
- Department of Animal Science and Fishery, Faculty of Agricultural Science and Forestry, Universiti Putra Malaysia, 97008, Bintulu, Sarawak, Malaysia
| | - Bernd Krock
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
| | - Thomas M Harris
- Department of Chemistry, Vanderbilt, University, Nashville, Tennessee, 37235, United States; Virginia Institute of Marine Science (VIMS), Gloucester Point, Virginia, 23062, United States
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Urban Tillmann
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia.
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Mai XC, Shen CR, Liu CL, Trinh DM, Nguyen ML. "DNA signaturing" database construction for Tetradesmus species identification and phylogenetic relationships of Scenedesmus-like green microalgae (Scenedesmaceae, Chlorophyta). JOURNAL OF PHYCOLOGY 2023; 59:775-784. [PMID: 37261838 DOI: 10.1111/jpy.13354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Species identification of Scenedesmus-like microalgae, comprising Desmodesmus, Tetradesmus, and Scenedesmus, has been challenging due to their high morphological and genetic similarity. After developing a DNA signaturing tool for Desmodesmus identification, we built a DNA signaturing database for Tetradesmus. The DNA signaturing tool contained species-specific nucleotide sequences of Tetradesmus species or strain groups with high similarity in ITS2 sequences. To construct DNA signaturing, we collected data on ITS2 sequences, aligned the sequences, organized the data by ITS2 sequence homology, and determined signature sequences according to hemi-compensatory base changes (hCBC)/CBC data from previous studies. Four Tetradesmus species and 11 strain groups had DNA signatures. The signature sequence of the genus Tetradesmus, TTA GAG GCT TAA GCA AGG ACCC, recognized 86% (157/183) of the collected Tetradesmus strains. Phylogenetic analysis of Scenedesmus-like species revealed that the Tetradesmus species were monophyletic and closely related to each other based on branch lengths. Desmodesmus was suggested to split into two subgenera due to their genetic and morphological distinction. Scenedesmus must be analyzed along with other genera of the Scenedesmaceae family to determine their genetic relationships. Importantly, DNA signaturing was integrated into a database for identifying Scenedesmus-like species through BLAST.
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Affiliation(s)
- Xuan Cuong Mai
- Department and Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Rui Shen
- Department and Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chao-Lin Liu
- Department of Chemical Engineering and Biochemical Technology R&D Center, Ming Chi University of Technology, New Taipei City, Taiwan
| | - Dang Mau Trinh
- Department of Biotechnology, Faculty of Biology and Environmental Science, The University of Danang - University of Science and Education, Danang, Vietnam
| | - Minh Ly Nguyen
- Department of Biotechnology, Faculty of Biology and Environmental Science, The University of Danang - University of Science and Education, Danang, Vietnam
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Zhu B, Chen Y, Zhou C, Li H, Ali S, Wu J. Gut Bacterial Diversity of Insecticide-Susceptible and Insecticide-Resistant Megalurothrips usitatus (Thysanoptera: Thripidae) and Elucidation of Their Putative Functional Roles. INSECTS 2023; 14:669. [PMID: 37623379 PMCID: PMC10455865 DOI: 10.3390/insects14080669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023]
Abstract
The gut bacterial microbiota of insects plays a crucial role in physiological, metabolic, and innate immune processes. In the current study, the gut bacterial communities of an insecticide-susceptible (IS), and a resistant (IR) population of a major legume pest, Megalurothrips usitatus (Bagnall), were evaluated. The 16S rDNA V3 + V4 regions of M. usitatus infected with Beauveria brongniartii along with the intestinal flora of both populations were sequenced based on a High-throughput sequencing platform. Toxicological bioassays revealed that the IR population exhibited resistance to acetamiprid and B. brongniartii isolate SB010 at levels of 138.0-fold and 55.6-fold higher, respectively, compared to the IS population. Through 16S High-throughput sequencing, the results indicate that both resistant populations, as well as B. brongniartii infestation, reduce the number of species of M. usitatus gut microbes. Using KEGG function prediction, it was found that most intestinal bacteria were involved in various metabolic activities, and the abundance of resistant populations was higher than that of sensitive populations. The bacteria in the gut of M. usitatus are mainly involved in various metabolic activities to achieve the degradation of B. brongniartii. This study provides valuable insights into the interaction between gut bacteria, insecticide resistance, and Beauveria. brongniartii infection in Megalurothrips usitatus, which can help inform future pest control strategies.
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Affiliation(s)
- Bifeng Zhu
- Engineering Research Center of Biological Control, Ministry of Education and Guangdong Province, South China Agricultural University, Guangzhou 510642, China; (B.Z.); (C.Z.); (H.L.)
| | - Yueyin Chen
- Meizhou Depot of Guangdong Grain Reserve Management Group Co., Ltd., Meizhou 514071, China;
| | - Chenyan Zhou
- Engineering Research Center of Biological Control, Ministry of Education and Guangdong Province, South China Agricultural University, Guangzhou 510642, China; (B.Z.); (C.Z.); (H.L.)
| | - Haolong Li
- Engineering Research Center of Biological Control, Ministry of Education and Guangdong Province, South China Agricultural University, Guangzhou 510642, China; (B.Z.); (C.Z.); (H.L.)
| | - Shaukat Ali
- Engineering Research Center of Biological Control, Ministry of Education and Guangdong Province, South China Agricultural University, Guangzhou 510642, China; (B.Z.); (C.Z.); (H.L.)
| | - Jianhui Wu
- Engineering Research Center of Biological Control, Ministry of Education and Guangdong Province, South China Agricultural University, Guangzhou 510642, China; (B.Z.); (C.Z.); (H.L.)
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15
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Magro L, Cutmore SC, Carrasson M, Cribb TH. Integrated characterisation of nine species of the Schistorchiinae (Trematoda: Apocreadiidae) from Indo-Pacific fishes: two new species, a new genus, and a resurrected but 'cryptic' genus. Syst Parasitol 2023:10.1007/s11230-023-10093-5. [PMID: 37160818 DOI: 10.1007/s11230-023-10093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
We report nine species of the Schistorchiinae Yamaguti, 1942 (Apocreadiidae Skrjabin, 1942) from Indo-Pacific marine fishes. Molecular data (ITS2 and 28S rDNA and cox1 mtDNA) are provided for all species and the genus-level classification of the subfamily is revised. For Schistorchis Lühe, 1906, we report the type-species Sch. carneus Lühe, 1906 and Sch. skrjabini Parukhin, 1963. For Sphinteristomum Oshmarin, Mamaev & Parukhin, 1961 we report the type-species, Sph. acollum Oshmarin, Mamaev & Parukhin, 1961. We report and re-recognise Lobatotrema Manter, 1963, for the type and only species, L. aniferum Manter, 1963, previously a synonym of Sph. acollum. Lobatotrema aniferum is phylogenetically distant from, but morphologically similar to, Sph. acollum and Lobatotrema is recognised as a 'cryptic genus'. We propose Blendiella n. gen. for B. trigintatestis n. sp. and B. tridecimtestis n. sp. These species are broadly consistent with the present morphological concept of Schistorchis but are phylogenetically distant from the type-species; a larger number of testes and some other subtle morphological characters in species of Blendiella serve to distinguish the two genera. We report three species of Paraschistorchis Blend, Karar & Dronen, 2017: P. stenosoma (Hanson, 1953) Blend, Karar & Dronen, 2017 (type-species), P. seychellesiensis (Toman, 1989) Blend, Karar & Dronen, 2017, and P. zancli (Hanson, 1953) Blend, Karar & Dronen, 2017. Lobatotrema aniferum, P. stenosoma, and Sch. carneus each have two distinct cox1 populations either over geographical range or in sympatry. Available evidence suggests that most of these species, but not all, are widespread in the tropical Indo-Pacific.
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Affiliation(s)
- Lori Magro
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Scott C Cutmore
- Queensland Museum, Biodiversity and Geosciences Program, South Brisbane, QLD, 4101, Australia
| | - Maite Carrasson
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Thomas H Cribb
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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16
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Stenhouse EH, Bellamy P, Kirby W, Vaughan IP, Symondson WOC, Orozco-terWengel P. Herbivorous dietary selection shown by hawfinch ( Coccothraustes coccothraustes) within mixed woodland habitats. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230156. [PMID: 37181798 PMCID: PMC10170347 DOI: 10.1098/rsos.230156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Abstract
Knowledge of diet and dietary selectivity is vital, especially for the conservation of declining species. Accurately obtaining this information, however, is difficult, especially if the study species feeds on a wide range of food items within heterogeneous and inaccessible environments, such as the tree canopy. Hawfinches (Coccothraustes coccothraustes), like many woodland birds, are declining for reasons that are unclear. We investigated the possible role that dietary selection may have in these declines in the UK. Here, we used a combination of high-throughput sequencing of 261 hawfinch faecal samples assessed against tree occurrence data from quadrats sampled in three hawfinch population strongholds in the UK to test for evidence of selective foraging. This revealed that hawfinches show selective feeding and consume certain tree genera disproportionally to availability. Positive selection was shown for beech (Fagus), cherry (Prunus), hornbeam (Carpinus), maples (Acer) and oak (Quercus), while Hawfinch avoided ash (Fraxinus), birch (Betula), chestnut (Castanea), fir (Abies), hazel (Corylus), rowan (Sorbus) and lime (Tilia). This approach provided detailed information on hawfinch dietary choice and may be used to predict the effects of changing food resources on other declining passerines populations in the future.
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Affiliation(s)
- Ewan H. Stenhouse
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Paul Bellamy
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Will Kirby
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Ian P. Vaughan
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
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Tie J, Qiao Y, Jin N, Gao X, Liu Y, Lyu J, Zhang G, Hu L, Yu J. Yield and Rhizosphere Soil Environment of Greenhouse Zucchini in Response to Different Planting and Breeding Waste Composts. Microorganisms 2023; 11:microorganisms11041026. [PMID: 37110447 PMCID: PMC10143665 DOI: 10.3390/microorganisms11041026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Composting, planting, and breeding waste for return to the field is the most crucial soil improvement method under the resource utilization of agricultural waste. However, how the vegetable yield and rhizosphere soil environment respond to different composts is still unknown. Therefore, eight formulations were designed for compost fermentation using agricultural waste [sheep manure (SM), tail vegetable (TV), cow manure (CM), mushroom residue (MR), and corn straw (CS)] without fertilizer (CK1) and local commercial organic fertilizer (CK2) as controls to study the yield and rhizosphere soil environment of greenhouse zucchini in response to different planting and breeding waste compost. Applying planting and breeding waste compost significantly increased the soil's organic matter and nutrient content. It inhibited soil acidification, which T4 (SM:TV:CS = 6:3:1) and T7 (SM:TV:MR:CS = 6:2:1:1) treatments affected significantly. Compared to CK2 treatment, T4 and T7 treatments showed a greater increase, with a significant increase of 14.69% and 11.01%, respectively. Therefore, T4, T7, and two control treatments were selected for high-throughput sequencing based on yield performance. Compared with the CK1 treatment, although multiple applications of chemical fertilizers led to a decrease in bacterial and fungal richness, planting and breeding waste compost maintained bacterial diversity and enhanced fungal diversity. Compared to CK2, the relative abundance increased in T7-treated Proteobacteria (Sphingomonas, Pseudomonas, and Lysobacter) and T4-treated Bacteroidetes (Flavobacterium) among bacteria. An increase in T4-treated Ascomycota (Zopfiella and Fusarium) and Basidiomycota among fungi and a decrease in T7-treated Mortierellomycota have been observed. Functional predictions of the bacterial Tax4Fun and fungal FUNGuild revealed that applying planting and breeding waste compost from the T4 treatment significantly increased the abundance of soil bacterial Metabolism of Cities, Genetic Information Processing, and Cellular Processes decreased the abundance of Pathotroph and Saprotroph-Symbiotroph fungi and increased the abundance of Saprotroph fungi. Overall, planting and breeding waste compost increased zucchini yield by improving soil fertility and microbial community structure. Among them, T4 treatment has the most significant effect, so T4 treatment can be selected as the optimized formulation of local commercial organic fertilizer. These findings have valuable implications for sustainable agricultural development.
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Affiliation(s)
- Jianzhong Tie
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yali Qiao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Xueqin Gao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yayu Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Guobin Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Linli Hu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
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Percy DM, Cronk QCB. Report of two distinct ribotypes in ITS sequences of Phalarisarundinacea (Poaceae) in western Canada and Alaska. Biodivers Data J 2023; 11:e101257. [PMID: 38327306 PMCID: PMC10848705 DOI: 10.3897/bdj.11.e101257] [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: 01/31/2023] [Accepted: 03/28/2023] [Indexed: 02/09/2024] Open
Abstract
Background Phalarisarundinacea L. (reed canary grass) is a widely occurring grass throughout the Northern Hemisphere. In North America, it is thought to consist of introduced agricultural forms from Europe as well as native populations. New information During a survey of Phalarisarundinacea in western Canada, we discovered two distinct ribotypes in the sequences of the internal transcribed spacer (ITS) of the nuclear ribosomal DNA: one full length (ITS-long) and one with a seven base pair deletion (ITS-short). In addition, ITS-long plants have fixed heterozygosity indicating possible polyploidy. Phylogenetic analysis reveals that ITS-short is a unique ribotype that characterises an intraspecific clade. We designed an efficient PCR-based assay that allows sizing of a 238/245 base pair fragment in a capillary sequencer. This approach provides a novel marker that could be useful in future surveys of Phalarisarundinacea.
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Affiliation(s)
- Diana M. Percy
- Department of Botany, University of British Columbia, Vancouver, CanadaDepartment of Botany, University of British ColumbiaVancouverCanada
| | - Quentin C. B. Cronk
- Department of Botany, University of British Columbia, Vancouver, CanadaDepartment of Botany, University of British ColumbiaVancouverCanada
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, CanadaBeaty Biodiversity Museum, University of British ColumbiaVancouverCanada
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Prudnikow L, Pannicke B, Wünschiers R. A primer on pollen assignment by nanopore-based DNA sequencing. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1112929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
The possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by chemical treatment methods. This procedure for identification of pollen grains is both time-consuming and requires expert knowledge of morphological features. Additionally, these microscopically recognizable features usually have a low resolution at species-level. Since a few decades, DNA has been used for the identification of pollen taxa, as sequencing technologies evolved both in their handling and affordability. We discuss advantages and challenges of pollen DNA analyses compared to traditional methods. With readers with little experience in this field in mind, we present a hands-on primer for genetic pollen analysis by nanopore sequencing. As our lab mainly works with pollen collected within agroecological research projects, we focus on pollen collected by pollinating insects. We briefly consider sample collection, storage and processing in the laboratory as well as bioinformatic aspects. Currently, pollen metabarcoding is mostly conducted with next-generation sequencing methods that generate short sequence reads (<1 kb). Increasingly, however, pollen DNA analysis is carried out using the long-read generating (several kb), low-budget and mobile MinION nanopore sequencing platform by Oxford Nanopore Technologies. Therefore, we are focusing on aspects for palynology with the MinION DNA sequencing device.
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Rackevei AS, Karnkowska A, Wolf M. 18S rDNA sequence-structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida). J Eukaryot Microbiol 2023; 70:e12959. [PMID: 36478494 DOI: 10.1111/jeu.12959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence-structure data are encoded and automatically aligned. Here, we present a sequence-structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence-structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.
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Affiliation(s)
- Antonia S Rackevei
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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21
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Successful identification of the species of the semipetrified amber medicinal resin benzoin using molecular diagnostic technology. Sci Rep 2023; 13:2943. [PMID: 36808137 PMCID: PMC9941088 DOI: 10.1038/s41598-023-30034-y] [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: 08/13/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Benzoin is an incomplete lithified resin secreted from the trunk of the Styrax Linn. that is known as "semipetrified amber" and has been widely used in medicine due to its blood circulation-promoting and pain-relieving properties. However, the lack of an effective species identification method due to the numerous sources of benzoin resin and the difficulty of DNA extraction has led to the uncertainty of species of benzoin in the trade process. Here, we report the successful extraction of DNA from benzoin resin containing bark-like residues and the evaluation of commercially available benzoin species using molecular diagnostic techniques. By performing a BLAST alignment of ITS2 primary sequences and homology prediction analysis of ITS2 secondary structures, we found that commercially available benzoin species were derived from Styrax tonkinensis (Pierre) Craib ex Hart. and Styrax japonicus Sieb. et Zucc. of the genus Styrax Linn. In addition, some of the benzoin samples were mixed with plant tissues from other genera, accounting for 29.6%. Therefore, this study provides a new method to solve the problem of species identification of semipetrified amber benzoin using information from bark residues.
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Triapitsyn SV, Rugman-Jones PF, Kusuhara H, Nakano R, Janšta P, Arikawa S, Adachi-Hagimori T. Genetic analysis reveals conspecificity of two nominal species of Anaphes fairyflies (Hymenoptera: Mymaridae), egg parasitoids of Oulema leaf beetle (Coleoptera: Chrysomelidae) pests of cereal crops in Europe and of rice in East Asia. PLoS One 2023; 18:e0273823. [PMID: 36706103 PMCID: PMC9882753 DOI: 10.1371/journal.pone.0273823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/16/2022] [Indexed: 01/28/2023] Open
Abstract
Anaphes (Anaphes) flavipes (Foerster), a fairyfly (Hymenoptera: Mymaridae) native of Europe, is an economically important egg parasitoid for the natural control of Oulema spp. leaf beetle (Coleoptera: Chrysomelidae) pests of cereal crops such as barley, oats, rye, and wheat in Europe, and for the classical biological control of the invasive Oulema melanopus (L.) in North America. A morphologically very similar Anaphes (Anaphes) nipponicus Kuwayama, known from mainland China, Japan, Republic of Korea, Far East of Russia and Taiwan, is an egg parasitoid of Oulema oryzae (Kuwayama), a pest of rice mainly in temperate parts of East Asia. The nuclear 28S-D2 and ITS2 and the mitochondrial COI genes were used as markers to compare specimens of A. (Anaphes) flavipes reared from eggs of an Oulema sp. on barley in Germany with those of A. (Anaphes) nipponicus reared from eggs of O. oryzae on rice in Honshu Island, Japan. Because the resulting sequences are practically identical, within an expected intraspecific genetic variability, conspecificity of these two nominal species has been confirmed, and consequently A. (Anaphes) nipponicus Kuwayama, 1932, syn. n. is synonymized with A. (Anaphes) flavipes (Foerster, 1841). Taxonomic notes and illustrations are provided for the specimens of both sexes of A. (Anaphes) flavipes from Japan to facilitate their recognition.
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Affiliation(s)
- S. V. Triapitsyn
- Department of Entomology, University of California, Riverside, California, United States of America
- * E-mail:
| | - P. F. Rugman-Jones
- Department of Entomology, University of California, Riverside, California, United States of America
| | - H. Kusuhara
- Laboratory of Insect Natural Enemies, Institute of Biological Control, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - R. Nakano
- Laboratory of Applied Entomology, University of Miyazaki, Miyazaki, Japan
- Shida-Haibara Agriculture and Forestry Office, Shizuoka, Japan
| | - P. Janšta
- Department of Entomology, State Museum of Natural History Stuttgart, Stuttgart, Germany
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - S. Arikawa
- Laboratory of Insect Natural Enemies, Institute of Biological Control, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - T. Adachi-Hagimori
- Laboratory of Applied Entomology, University of Miyazaki, Miyazaki, Japan
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Lee SK, Woo C, Lee EJ, Yamamoto N. Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison. Sci Rep 2022; 12:22271. [PMID: 36564425 PMCID: PMC9789119 DOI: 10.1038/s41598-022-26862-z] [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: 03/28/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The Korean water deer (Hydropotes inermis argyropus) is considered a vermin in Korea because it damages crops, but also listed as a vulnerable species on the IUCN's red list. Therefore, it is indispensable to manage them appropriately by understanding the ecology such as food habits. Here, we aimed to apply high-throughput sequencing (HTS), a sensitive and objective method, to investigate the dietary composition of the Korean water deer inhabiting the lowland and forest areas in summer and winter. We targeted the internal transcribed spacer 2 (ITS2) region for plant identification. From a total of 40 fecal samples analyzed, 63 plant genera were identified, with Morus being the most abundant, and some of the plant taxa identified by HTS were detected for the first time as the diets of Korean water deer. By type, woody plants (68.6%) were the most predominant, followed by forbs (7.0%) and graminoids (0.7%). We found that the deer in the forest area ate more woody plants (84.6%) than those in the lowland area (52.7%). It was also found that the type of woody plants that the deer ate changed by season. Overall, our results indicate that the Korean water deer is a browser that is seasonally adaptable and feeds on a wide variety of woody plants. We expect that the results and genetics methods reported here, by parallelly investigating their habitat range and reproductive behavior in the future, will help the management and conservation of the Korean water deer, which is in contradictory situations.
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Affiliation(s)
- Seung-Kyung Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Cheolwoon Woo
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea
| | - Eun Ju Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Naomichi Yamamoto
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Institute of Health and Environment, Seoul National University, Seoul, South Korea
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Devi MP, Dasgupta M, Mohanty S, Sharma SK, Hegde V, Roy SS, Renadevan R, Kumar KB, Patel HK, Sahoo MR. DNA Barcoding and ITS2 Secondary Structure Predictions in Taro ( Colocasia esculenta L. Schott) from the North Eastern Hill Region of India. Genes (Basel) 2022; 13:genes13122294. [PMID: 36553561 PMCID: PMC9778394 DOI: 10.3390/genes13122294] [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: 10/15/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022] Open
Abstract
Taro (Colocasia esculenta L. Schott, Araceae), an ancient root and tuber crop, is highly polygenic, polyphyletic, and polygeographic in nature, which leads to its rapid genetic erosion. To prevent the perceived loss of taro diversity, species discrimination and genetic conservation of promising taro genotypes need special attention. Reports on genetic discrimination of taro at its center of origin are still untapped. We performed DNA barcoding of twenty promising genotypes of taro indigenous to the northeastern hill region of India, deploying two chloroplast-plastid genes, matK and rbcL, and the ribosomal nuclear gene ITS2. The secondary structure of ITS2 was determined and molecular phylogeny was performed to assess genetic discrimination among the taro genotypes. The matK and rbcL genes were highly efficient (>90%) in amplification and sequencing. However, the ITS2 barcode region achieved significant discrimination among the tested taro genotypes. All the taro genotypes displayed most similar sequences at the conserved matK and rbcL loci. However, distinct sequence lengths were observed in the ITS2 barcode region, revealing accurate discriminations among the genotypes. Multiple barcode markers are unrelated to one another and change independently, providing different estimations of heritable traits and genetic lineages; thus, they are advantageous over a single locus in genetic discrimination studies. A dynamic programming algorithm that used base-pairing interactions within a single nucleic acid polymer or between two polymers transformed the secondary structures into the symbol code data to predict seven different minimum free energy secondary structures. Our analysis strengthens the potential of the ITS2 gene as a potent DNA barcode candidate in the prediction of a valuable secondary structure that would help in genetic discrimination between the genotypes while augmenting future breeding strategies in taro.
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Affiliation(s)
- Mayengbam Premi Devi
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- College of Agriculture, Central Agricultural University (CAU-Imphal), Kyrdemkulai 793105, India
| | - Madhumita Dasgupta
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
| | - Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, India
| | - Susheel Kumar Sharma
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- ICAR—Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Vivek Hegde
- ICAR—Central Tuber Crops Research Institute, Thiruvananthapuram 695017, India
- ICAR—Indian Institute of Horticultural Research, Bengaluru 560089, India
| | - Subhra Saikat Roy
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
| | - Rennya Renadevan
- Centre for Cellular and Molecular Biology, Hyderabad 570007, India
| | | | - Hitendra Kumar Patel
- Centre for Cellular and Molecular Biology, Hyderabad 570007, India
- Correspondence: (H.K.P.); (M.R.S.); Tel.: +91-674-247-1867 (M.R.S.); Fax: +91-674-247-1712 (M.R.S.)
| | - Manas Ranjan Sahoo
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, India
- Correspondence: (H.K.P.); (M.R.S.); Tel.: +91-674-247-1867 (M.R.S.); Fax: +91-674-247-1712 (M.R.S.)
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Fermentation Characteristics, Microbial Compositions, and Predicted Functional Profiles of Forage Oat Ensiled with Lactiplantibacillus plantarum or Lentilactobacillus buchneri. FERMENTATION 2022. [DOI: 10.3390/fermentation8120707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
This study aimed to investigate the effects of lactic acid bacteria (LAB) inoculants on the fermentation quality, microbial compositions, and predicted functional profiles of forage oat. The forage oat was inoculated with distilled water, Lentilactobacillus buchneri (LB), and Lactiplantibacillus plantarum (LP) as the control (CON), LB and LP treatments, respectively, and the addition of Lentilactobacillus buchneri (LB) or Lactiplantibacillus plantarum (LP) resulted in 1 × 106 colony-forming units/g of fresh weight. After 30 days of fermentation, the lowest pH (4.23) and the lowest content of ammoniacal nitrogen (NH3-N) in dry matter (DM, 4.39%) were observed in the LP treatment. Interestingly, there was a significant (p < 0.05) difference in lactic acid (LA) concentration among the three treatments. The LP treatment had the highest lactate concentration (7.49% DM). At the same time, a markedly (p < 0.05) elevated acetic acid (AA) concentration (2.48% DM) was detected in the LB treatment. The Shannon and Chao1 indexes of bacterial and fungal communities in all the silage samples decreased compared to those in the fresh materials (FM). Proteobacteria was the dominant phylum in the FM group and shifted from Proteobacteria to Firmicutes after ensiling. Lactobacillus (64.87%) and Weissella (18.93%) were the predominant genera in the CON, whereas Lactobacillus dominated the fermentation process in the LB (94.65%) and LP (99.60%) treatments. For the fungal community structure, the major genus was Apiotrichum (21.65% and 60.66%) in the FM and CON groups after 30 days of fermentation. Apiotrichum was the most predominant in the LB and LP treatments, accounting for 52.54% and 34.47%, respectively. The genera Lactococcus, Pediococcus, and Weissella were negatively associated with the LA content. The genus Ustilago and Bulleromyces were positively associated with the LA content. These results suggest that the addition of LAB regulated the microbial community in oat silage, which influenced the ensiling products, and LP was more beneficial for decreasing the pH and NH3-N and increasing the LA concentration than LB in forage oat silage.
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Martynenko N, Gusev E, Kapustin D, Kulikovskiy M. A New Cryptic Species of the Genus Mychonastes (Chlorophyceae, Sphaeropleales). PLANTS (BASEL, SWITZERLAND) 2022; 11:3363. [PMID: 36501404 PMCID: PMC9741059 DOI: 10.3390/plants11233363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
A new species of green coccoid algae, Mychonastes hindakii sp. nov., was isolated from the River Moscow (Russia, Moscow). The taxon is described using morphological and molecular methods. Mychonastes hindakii sp. nov. belongs to the group of species of the genus Mychonastes with spherical single cells joined with mucilaginous, irregularly shaped stalks. A comparison of ITS2 rDNA sequences and its secondary structures combined with the compensatory base changes approach confirms the separation between Mychonastes hindakii and other species of the genus. Mychonastes hindakii sp. nov. represents a cryptic species that can only be reliably identified using molecular data.
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Affiliation(s)
- Nikita Martynenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Evgeniy Gusev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Dmitry Kapustin
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanical Street 35, 127276 Moscow, Russia
| | - Maxim Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanical Street 35, 127276 Moscow, Russia
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Dubois B, Debode F, Hautier L, Hulin J, Martin GS, Delvaux A, Janssen E, Mingeot D. A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data. BMC Genom Data 2022; 23:53. [PMID: 35804326 PMCID: PMC9264521 DOI: 10.1186/s12863-022-01067-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence. Results We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids ‘black box’ systems that are sometimes encountered. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets. Conclusion This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01067-5.
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Zeng L, Feng Z, Zhuo M, Wen Z, Zhu C, Tang C, Liu L, Wang Y. Fecal fungal microbiota alterations associated with clinical phenotypes in Crohn's disease in southwest China. PeerJ 2022; 10:e14260. [PMID: 36275466 PMCID: PMC9586077 DOI: 10.7717/peerj.14260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/27/2022] [Indexed: 01/24/2023] Open
Abstract
Although previous studies reported that gut fungal microbiota was associated with Crohn's disease (CD), only a few studies have focused on the correlation between gut fungi and clinical phenotypes of CD. Here, we aimed to analyze the association between intestinal fungi and the occurrence of CD, disease activity, biological behaviors, and perianal lesions. Stool samples from subjects meeting the inclusion and exclusion criteria were collected for running internal transcribed spacer 2 (ITS2) high-throughput sequencing. Then, correlation analysis was conducted between intestinal fungi and different clinical groups. There were 45 patients with CD and 17 healthy controls (HCs) enrolled. Results showed that two phyla, Rozellomycota and Mortierellomycota, were not present in patients with CD compared to HCs. At the same time, there was a higher abundance of fungal genera and species belonging to the phylum Ascomycota in patients with CD. SparCC network analysis showed fewer interactions among the fungal communities in patients with CD compared to HCs. Exophiala dermatitidis was positively associated with the clinical active stage and platelet count. The genus Candida was with significantly higher abundance in the non-B1 CD group based on the Montreal classification. Clonostachys, Humicola, and Lophiostoma were significantly enriched in patients with CD with perianal lesions. Our results demonstrated that the composition of the intestinal fungal microbiota in patients with CD and HCs was markedly different, some of which might play a pathogenic role in the occurrence of CD and perianal lesions. Exophiala dermatitidis and genus Candida might be associated with active disease stage and type non-B1 CD (CD with intestinal stenosis or penetrating lesions, or both), respectively.
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Affiliation(s)
- Li Zeng
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China
| | - Zhe Feng
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China
| | - Ma Zhuo
- Department of Gastroenterology, Lhasa People’s Hospital, Lhasa, Tibet Autonomous Region, China.
| | - Zhonghui Wen
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China
| | - Cairong Zhu
- School of Public Health and Community Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Chengwei Tang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China
| | - Ling Liu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China
| | - Yufang Wang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China
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Cheng H, Dai Y, Ruan X, Duan X, Zhang C, Li L, Huang F, Shan J, Liang K, Jia X, Wang Q, Zhao H. Effects of nanoplastic exposure on the immunity and metabolism of red crayfish (Cherax quadricarinatus) based on high-throughput sequencing. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 245:114114. [PMID: 36179446 DOI: 10.1016/j.ecoenv.2022.114114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Previous studies have shown that nanoplastics (NPs) are harmful pollutants that threaten aquatic organisms and ecosystems, however, less research has been conducted on the hazards of NPs for aquaculture animals. In this study, Cherax quadricarinatus was used as an experimental model to evaluate the possible effects of three concentrations (25, 250 and 2500 μg/L) of NPs on red crayfish. The toxicological effects of NPs on this species were investigated based on transcriptomics and microbiome. A total of 67,668 genes were obtained from the transcriptome. The annotation rate of the four major libraries (Nr, KEGG, KOG, Swissprot) was 40.17 %, and the functions of differential genes were mainly related to antioxidant activity, metabolism and immune processes. During the experiment, the activities of superoxide dismutase (SOD) and catalase (CAT) in the high concentration group were significantly decreased, while the concentration of malondialdehyde (MDA) increased after nanoplastics (NPs) exposure, and SOD1, Jafrac1 were significantly reduced at high concentrations. expression is inhibited. The immune genes LYZ and PPO2 were highly expressed at low concentrations and suppressed at high concentrations. After 14 days of exposure to NPs, significant changes in gut microbiota were observed, such as decreased abundances of Actinobacteria, Bacteroidetes, and Firmicutes. NPs compromise host health by inducing changes in microbial communities and the production of beneficial bacterial metabolites. Overall, these results suggest that NPs affect immune-related gene expression and antioxidant enzyme activity in red crayfish and cause redox imbalance in the body, altering the composition and diversity of the gut microbiota.
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Affiliation(s)
- Huitao Cheng
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Yuantang Dai
- Modern Agriculture Comprehensive Service Center of Dongyuan County, Heyuan 517500, China.
| | - Xinhe Ruan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xuzhuo Duan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chunli Zhang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Lihua Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Fengqi Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jinhong Shan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Kaishan Liang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xianze Jia
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qing Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou 510642, China.
| | - Huihong Zhao
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
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Boff S, Keller A, Raizer J, Lupi D. Decreased efficiency of pollen collection due to Sulfoxaflor exposure leads to a reduction in the size of bumble bee workers in late European summer. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.842563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bumble bees (Bombus terrestris) are important pollinators of wild and crop plants. Despite their importance in the process of fruit and seed production on crop sites, their activity may be impaired due to exposure to pesticides. This species has a yearly life cycle and colony success may rely on effective foraging of workers on ruderal plants late in summer when most crops are no longer flowering. In the current study, we investigated the effect of chronic exposure to Sulfoxaflor on aspects of the foraging behavior of bumble bees and whether Sulfoxaflor influences the body size of workers of B. terrestris in a crop landscape. We found that 2 weeks of continuous exposure to Sulfoxaflor influenced workers’ foraging dynamics and collection of resources. However, there was no evidence that the 5 ppb dose of the pesticide impacted the ability of bees to handle flowers with different traits. Workers from colonies exposed to Sulfoxaflor were smaller. The effect on worker size may be explained as a consequence of the reduced pollen income per unit of worker foraging. Thus, if the effects of Sulfoxaflor applied directly to crops had the same effect as that observed on commercial bumble bees after our chronic exposure, it might negatively impact colony success due to the impact on pollen collection and the reduction in the size of workers.
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König S, Krauss J, Keller A, Bofinger L, Steffan-Dewenter I. Phylogenetic relatedness of food plants reveals highest insect herbivore specialization at intermediate temperatures along a broad climatic gradient. GLOBAL CHANGE BIOLOGY 2022; 28:4027-4040. [PMID: 35429201 DOI: 10.1111/gcb.16199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
The composition and richness of herbivore and plant assemblages change along climatic gradients, but knowledge about associated shifts in specialization is scarce and lacks controlling for the abundance and phylogeny of interaction partners. Thus, we aimed to test whether the specialization of phytophagous insects in insect-plant interaction networks decreases toward cold habitats as predicted by the 'altitude niche-breadth hypothesis' to forecast possible consequences of interaction rewiring under climate change. We used a non-invasive, standardized metabarcoding approach to reconstruct dietary relationships of Orthoptera species as a major insect herbivore taxon along a broad temperature gradient (~12°C) in Southern Germany. Based on Orthoptera surveys, feeding observations, collection of fecal pellets from >3,000 individuals of 54 species, and parallel vegetation surveys on 41 grassland sites, we quantified plant resource availability and its use by herbivores. Herbivore assemblages were richer in species and individuals at sites with high summer temperatures, while plant richness peaked at intermediate temperatures. Corresponding interaction networks were most specialized in warm habitats. Considering phylogenetic relationships of plant resources, however, the specialization pattern was not linear but peaked at intermediate temperatures, mediated by herbivores feeding on a narrow range of phylogenetically related resources. Our study provides empirical evidence of resource specialization of insect herbivores along a climatic gradient, demonstrating that resource phylogeny, availability, and temperature interactively shape the specialization of herbivore assemblages. Instead of low specialization levels only in cold, harsh habitats, our results suggest increased generalist feeding due to intraspecific changes and compositional differences at both ends of the microclimatic gradient. We conclude that this nonlinear change of phylogeny-based resource specialization questions predictions derived from the 'altitude-niche breadth hypothesis' and highlights the currently limited understanding of how plant-herbivore interactions will change under future climatic conditions.
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Affiliation(s)
- Sebastian König
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alexander Keller
- Organismic and Cellular Interactions, Biocenter, Ludwig-Maximilians-Universität München, Planegg, Germany
| | | | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
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Cao R, Tong S, Luan T, Zheng H, Zhang W. Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070929. [PMID: 35406909 PMCID: PMC9003356 DOI: 10.3390/plants11070929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 05/27/2023]
Abstract
A compensatory base change (CBC) that coevolves in the secondary structure of ribosomal internal transcribed spacer 2 (ITS2) influences the estimation of genetic distance and thus challenges the phylogenetic use of this most popular genetic marker. To date, however, the CBC effect on ITS2 genetic distance is still unclear. Here, ITS2 sequences of 46 more recent angiosperm lineages were screened from 5677 genera and phylogenetically analyzed in sequence-structure format, including secondary structure prediction, structure-based alignment and sequence partition of paired and unpaired regions. ITS2 genetic distances were estimated comparatively by using both conventional DNA substitution models and RNA-specific models, which were performed in the PHASE package. Our results showed that the existence of the CBC substitution inflated the ITS2 genetic distances to different extents, and the deviation could be 180% higher if the relative ratio of substitution rate in ITS2 secondary structure stems was threefold higher than that in the loops. However, the CBC effect was minor if that ratio was below two, indicating that the DNA model is still applicable in recent lineages in which few CBCs occur. We thus provide a general empirical threshold to take account of CBC before ITS2 phylogenetic analyses.
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Xie T, Shen S, Hao Y, Li W, Wang J. Comparative Analysis of Microbial Community Diversity and Dynamics on Diseased Tubers During Potato Storage in Different Regions of Qinghai China. Front Genet 2022; 13:818940. [PMID: 35273638 PMCID: PMC8902257 DOI: 10.3389/fgene.2022.818940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Effective storage of potatoes is very important for the food industry. Given the problems involving rotten potatoes and low quality during storage, harvested potatoes from the main potato-producing areas in the Qinghai Plateau were treated by selection and air drying (Group "A") and the others were stored directly as controls (Group "C"). Then, the microbial community structure and diversity of diseased potato tubers from four main production areas were analyzed by high-throughput sequencing technology in different storage stages. The results showed that the community composition and diversity of microbes in different regions and storage periods were different, and the dominant fungi in diseased potato tubers were Boeremia in Huangyuan (HY), Maying (MY) and Zhongling (ZL) and Apiotrichum in Huangzhong (HZ) at the genus level. The dominant bacterial genus was Pseudomonas, but its abundance varied in samples from different regions and storage periods. In the analysis of indicator species, there were some common species and endemic species in each region and period, and the period with the largest number of different species was the third period. Among the four storage periods, the region with the largest number of different species was HZ. Some fungi, especially Fusarium and other potato pathogens, were more abundant in control Group "C" than in treatment Group "A." In the diversity analysis, the α diversity of fungi in Group "C" was higher than that in Group "A," but the α diversity of bacteria in Group "A" was higher than that in Group "C," and there was no obvious regularity with storage time. The β diversity varied significantly among different regions. In addition, through functional prediction analysis, it was found that a plant pathogen was one of the main nutritional types of fungi, which indicated that treatment by selection and drying could significantly reduce phytopathogenic microbe and other microorganisms and could be used as an effective measure for potato storage compared with the prevention and control by drugs that can cause environmental pollution. Further analysis of co-occurrence network showed that pathogenic fungi Fusarium was negatively correlated with pathogenic bacteria Erwinia, and there is also a negative correlation between pathogens and antagonistic microorganisms indicated that there were various symbiotic relationships among microorganisms in diseased potatoes. This study may provide a theoretical basis for biological control of potato cellar diseases and the maintenance of potato quality during long-term storage.
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Affiliation(s)
- Tianyan Xie
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,Key Laboratory of Potato Breeding of Qinghai Province, Xining, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, China.,Northwest Potato Engineering Research Center, Ministry of Education, Xining, China
| | - Shuo Shen
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,Key Laboratory of Potato Breeding of Qinghai Province, Xining, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, China.,Northwest Potato Engineering Research Center, Ministry of Education, Xining, China
| | - Yufan Hao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,Key Laboratory of Potato Breeding of Qinghai Province, Xining, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, China.,Northwest Potato Engineering Research Center, Ministry of Education, Xining, China
| | - Wei Li
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,Key Laboratory of Potato Breeding of Qinghai Province, Xining, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, China.,Northwest Potato Engineering Research Center, Ministry of Education, Xining, China
| | - Jian Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,Key Laboratory of Potato Breeding of Qinghai Province, Xining, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, China.,Northwest Potato Engineering Research Center, Ministry of Education, Xining, China
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Detection and Molecular Phylogenetic-Morphometric Characterization of Rhizoctonia tuliparum, Causal Agent of Gray Bulb Rot of Tulips and Bulbous Iris. J Fungi (Basel) 2022; 8:jof8020163. [PMID: 35205917 PMCID: PMC8880388 DOI: 10.3390/jof8020163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
Gray bulb rot of tulips and bulbous iris is caused by the soil-borne fungal pathogen, Rhizoctonia tuliparum (Rtul). Sclerotia present in infected bulbs, as well as overwintering sclerotia in soil and field debris, are the primary sources of infection. A method for accurate and sensitive detection of Rtul from soil and infected bulbs, and estimation of inoculum threshold levels, is needed for the management of disease caused by this pathogen. We designed a unique set of primers targeting the ITS2 region of the Rtul genome and developed a highly sensitive quantitative PCR (qPCR)-based method for Rtul identification using these primers, where the threshold of detection was approximately 1 fg Rtul DNA. The assay was more sensitive with sclerotia collected from the field (natural) than with those grown in the lab, and more sensitive with natural-light than natural-dark sclerotia. Also, the detection method was more sensitive when sclerotia were extracted from soil than from bulb tissue. The qPCR method was highly specific, as no PCR amplification was detected when genomic DNA from 62 non-Rtul Rhizoctonia isolates from a wide range of anastomosis groups were tested. To understand the evolutionary relationships and genomic diversity of Rtul, we performed phylogenetics of the ITS1-5.8S-ITS2 region and ITS2-molecular morphometric characterization (MMC) of Rtul isolates. The three Rtul isolates whose ITS sequences were available in GenBank formed a distinct phylogenetic clade with Ceratobasidium anceps as the nearest relative. Furthermore, MMC analysis revealed genetic divergence among these three Rtul isolates.
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Singh V, Lakshman DK, Roberts DP, Ismaiel A, Hooda KS, Gogoi R. Morphopathological and Molecular Morphometric Characterization of Waitea circinata var. prodigus Causing a Novel Sheath Spot Disease of Maize in India. PLANT DISEASE 2022; 106:526-534. [PMID: 34261356 DOI: 10.1094/pdis-05-21-0951-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Maize brown sheath spot (MBSS), a new disease of maize, was discovered while surveying for maize leaf and sheath blight diseases in the Indian states of Assam, Jharkhand, Meghalaya, Manipur, and Odisha. Maize is the third most important cereal after rice and wheat in India. Unlike banded leaf and sheath blight disease caused by Rhizoctonia solani, MBSS symptoms on maize were discrete and limited to sheaths only. Symptoms of MBSS in the field were initially water-soaked necrotic lesions of 1 to 2 cm in diameter on the lowermost leaf sheaths, which then progressed to the upper sheaths. Lesions coalesced and covered approximately 2 to 5% of the sheath area. Infected dried lower leaves were shed, whereas infected upper leaves remained on the stem. The pathogen was isolated, characterized morphologically, pathologically, and molecularly, and identified as Waitea circinata var. prodigus, a basidiomycete known to cause basal leaf blight of seashore paspalum. The internal transcribed spacer (ITS) sequence 2 (ITS2) of rDNA from MBSS isolates formed a well supported clade with known W. circinata var. prodigus isolates. Molecular morphometric analysis of the ITS2 regions of the five known varieties of W. circinata detected distinguishing variations in GC content, compensatory base changes (CBCs), hemi- CBCs, indels, and altered base-pairing of helices. Variation in these characteristics may indicate that varieties are distinct biological species within W. circinata sensu lato. The geographical distribution and potential impacts of MBSS on the maize crop in India necessitate further investigations of pathogen identification and disease management.
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Affiliation(s)
- Vimla Singh
- Department of Botany and Plant Physiology, Chaudhary Charan Singh Haryana Agricultural University, Regional Research Station, Karnal 132001, India
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Adnan Ismaiel
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - K S Hooda
- Germplasm Evaluation Division, Indian Council of Agricultural Research, National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Robin Gogoi
- Division of Plant Pathology, Indian Council of Agricultural Research, Indian Agricultural Research Institute, New Delhi 110012, India
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Huang Y, Dong Y, Ren Y, Wang S, Li Y, Du K, Lin X, Yang M. Niches and Seasonal Changes, Rather Than Transgenic Events, Affect the Microbial Community of Populus × euramericana ‘Neva’. Front Microbiol 2022; 12:805261. [PMID: 35154035 PMCID: PMC8831546 DOI: 10.3389/fmicb.2021.805261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/27/2021] [Indexed: 01/05/2023] Open
Abstract
Exploring the complex spatiotemporal changes and colonization mechanism of microbial communities will enable microbial communities to be better used to serve agricultural and ecological operations. In addition, evaluating the impact of transgenic plants on endogenous microbial communities is necessary for their commercial application. In this study, microbial communities of Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-BADH genes (ECAA1 line), Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-NTHK1 genes (ECAB1 line), and non-transgenic Populus × euramericana ‘Neva’ from rhizosphere soil, roots, and phloem collected in different seasons were compared and analyzed. Our analyses indicate that the richness and diversity of bacterial communities were higher in the three Populus × euramericana ‘Neva’ habitats than in those of fungi. Bacterial and fungal genetic-distance-clustering results were similar; rhizosphere soil clustered in one category, with roots and phloem in another. The diversity and evenness values of the microbial community were: rhizosphere soil > phloem > root system. The bacterial communities in the three habitats were dominated by the Proteobacteria, and fungal communities were dominated by the Ascomycota. The community composition and abundance of each part were quite different; those of Populus × euramericana ‘Neva’ were similar among seasons, but community abundance fluctuated. Seasonal fluctuation in the bacterial community was greatest in rhizosphere soil, while that of the fungal community was greatest in phloem. The transgenic lines ECAA1 and ECAB1 had a bacterial and fungal community composition similar to that of the control samples, with no significant differences in community structure or diversity among the lines. The abundances of operational taxonomic units (OTUs) were low, and differed significantly among the lines. These differences did not affect the functioning of the whole specific community. Sampling time and location were the main driving factors of changes in the Populus × euramericana ‘Neva’ microbial community. Transgenic events did not affect the Populus × euramericana ‘Neva’ rhizosphere or endophytic microbial communities. This study provides a reference for the safety evaluation of transgenic plants and the internal colonization mechanism of microorganisms in plants.
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Affiliation(s)
- Yali Huang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yan Dong
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yachao Ren
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Shijie Wang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yongtan Li
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Kejiu Du
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Xin Lin
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Agricultural Office of Kenfeng Subdistrict Office, Tangshan, China
| | - Minsheng Yang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
- *Correspondence: Minsheng Yang,
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37
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Agostinetto G, Brusati A, Sandionigi A, Chahed A, Parladori E, Balech B, Bruno A, Pescini D, Casiraghi M. ExTaxsI: an exploration tool of biodiversity molecular data. Gigascience 2022; 11:giab092. [PMID: 35077538 PMCID: PMC8848311 DOI: 10.1093/gigascience/giab092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/16/2021] [Accepted: 11/30/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The increasing availability of multi-omics data is leading to regularly revised estimates of existing biodiversity data. In particular, the molecular data enable novel species to be characterized and the information linked to those already observed to be increased with new genomics data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy-to-use IT tools have become a key point to design future research. The more users are able to access biodiversity-related information, the greater the ability of the scientific community to expand its knowledge in this area. RESULTS In this article we focus on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool that can retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. We use 3 case studies to show how an efficient organization of the available data can lead to obtaining new information that is fundamental as a starting point for new research. Using this approach highlights the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad-spectrum studies such as metagenomics. CONCLUSIONS ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim of helping researchers to improve experimental designs and highlight the main gaps in the coverage of available data.
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Affiliation(s)
- Giulia Agostinetto
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Alberto Brusati
- Istituto Auxologico Italiano - IRCCS, Via Giuseppe Zucchi 18, 20095 Cusano Milanino, Italy
- Università degli Studi di Pavia, Dipartimento di Scienze del Sistema Nervoso e del Comportamento, Via Agostino Bassi 21, 27100 Pavia, Italy
| | - Anna Sandionigi
- Quantia Consulting srl, Via F. Petrarca 20, 22066 Mariano Comense, Italy
| | - Adam Chahed
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Elena Parladori
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Antonia Bruno
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Dario Pescini
- University of Milano-Bicocca, Department of Statistics and Quantitative Methods, Piazza dell'Ateneo Nuovo 1, 20126 Milan, Italy
| | - Maurizio Casiraghi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
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Savchenko A, Zamora J, Shirouzu T, Spirin V, Malysheva V, Kõljalg U, Miettinen O. Revision of Cerinomyces ( Dacrymycetes, Basidiomycota) with notes on morphologically and historically related taxa. Stud Mycol 2021; 99:100117. [PMID: 34934464 PMCID: PMC8645972 DOI: 10.1016/j.simyco.2021.100117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cerinomyces (Dacrymycetes, Basidiomycota) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family Cerinomycetaceae is paraphyletic. Aiming for a more concise delimitation, we revise Cerinomyces s.l. with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α). We establish that monophyletic Cerinomyces s.s. is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments. In our updated definition, Cerinomyces s.s. encompasses five well-supported phylogenetic clades divided into two morphological groups: (i-iii) taxa with arid corticioid basidiocarps, including the generic type C. pallidus; and (iv-v) newly introduced members with gelatinous basidiocarps, like Dacrymyces enatus and D. tortus. The remaining corticioid species of Cerinomyces s.l. are morphologically distinct and belong to the Dacrymycetaceae: our analysis places the carotenoid-rich Cerinomyces canadensis close to Femsjonia, and we transfer the clamps-lacking C. grandinioides group to Dacrymyces. In addition, we address genera related to Cerinomyces s.l. historically and morphologically, such as Ceracea, Dacryonaema and Unilacryma. Overall, we describe twenty-four new species and propose nine new combinations in both Cerinomycetaceae and Dacrymycetaceae.
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Affiliation(s)
- A. Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Natural History Museum, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
- Correspondence: A. Savchenko
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-75236, Uppsala, Sweden
| | - T. Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan
| | - V. Spirin
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
| | - V. Malysheva
- Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova str. 2, RU-197376, St. Petersburg, Russia
| | - U. Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Natural History Museum, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - O. Miettinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
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Plieger T, Wolf M. 18S and ITS2 rDNA sequence-structure phylogeny of Prototheca (Chlorophyta, Trebouxiophyceae). Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00971-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractProtothecosis is an infectious disease caused by organisms currently classified within the green algal genus Prototheca. The disease can manifest as cutaneous lesions, olecranon bursitis or disseminated or systemic infections in both immunocompetent and immunosuppressed patients. Concerning diagnostics, taxonomic validity is important. Prototheca, closely related to the Chlorella species complex, is known to be polyphyletic, branching with Auxenochlorella and Helicosporidium. The phylogeny of Prototheca was discussed and revisited several times in the last decade; new species have been described. Phylogenetic analyses were performed using ribosomal DNA (rDNA) and partial mitochondrial cytochrome b (cytb) sequence data. In this work we use Internal Transcribed Spacer 2 (ITS2) as well as 18S rDNA data. However, for the first time, we reconstruct phylogenetic relationships of Prototheca using primary sequence and RNA secondary structure information simultaneously, a concept shown to increase robustness and accuracy of phylogenetic tree estimation. Using encoded sequence-structure data, Neighbor-Joining, Maximum-Parsimony and Maximum-Likelihood methods yielded well-supported trees in agreement with other trees calculated on rDNA; but differ in several aspects from trees using cytb as a phylogenetic marker. ITS2 secondary structures of Prototheca sequences are in agreement with the well-known common core structure of eukaryotes but show unusual differences in their helix lengths. An elongation of the fourth helix of some species seems to have occurred independently in the course of evolution.
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Gong L, Zhang D, Ding X, Huang J, Guan W, Qiu X, Huang Z. DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province. PeerJ 2021; 9:e12325. [PMID: 34721994 PMCID: PMC8541303 DOI: 10.7717/peerj.12325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
Background Amomum villosum Lour. is the plant that produces the famous traditional Chinese medicine Amomi Fructus. Frequent habitat destruction seriously threatens A. villosum germplasm resources. Genetic diversity is very important to the optimization of germplasm resources and population protection, but the range of inherited traits within A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library as a resource for conservation efforts. Methods DNA barcoding and Inter-Simple Sequence Repeat (ISSR) markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and used in the construction of a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity index (H), and Shannon’s polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by measuring Nei’s gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs), and gene flow (Nm). Analysis of molecular variance (AMOVA), Mantel tests, unweighted pair-group method with arithmetic mean (UPGMA) dendrogram, and principal co-ordinates (PCoA) analysis were used to elucidate the genetic differentiation and relationship among populations. Results A total of 531 sequences were obtained from the five DNA barcodes with no variable sites from any of the barcode sequences. A total of 66 ISSR bands were generated from A. villosum populations using the selected six ISSR primers; 56 bands, 84.85% for all the seven A. villosum populations were polymorphic. The A. villosum populations showed high genetic diversity (H = 0.3281, I = 0.4895), whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated that there is obvious genetic differentiation amongA. villosum populations and more genetic variations existed within each population. The genetic relationship of each population was relatively close as the genetic distances were between 0.0844 and 0.3347.
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Affiliation(s)
- Lu Gong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China.,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medicial Products Administration, Guangzhou, China.,Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, China
| | - Danchun Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China.,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medicial Products Administration, Guangzhou, China
| | - Xiaoxia Ding
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juan Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China.,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medicial Products Administration, Guangzhou, China.,Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, China
| | - Wan Guan
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohui Qiu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China.,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medicial Products Administration, Guangzhou, China.,Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, China
| | - Zhihai Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China.,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medicial Products Administration, Guangzhou, China.,Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, China
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Tian L, Ou J, Sun X, Miao Y, Pei J, Zhao L, Huang L. The discovery of pivotal fungus and major determinant factor shaping soil microbial community composition associated with rot root of American ginseng. PLANT SIGNALING & BEHAVIOR 2021; 16:1952372. [PMID: 34304705 PMCID: PMC8525955 DOI: 10.1080/15592324.2021.1952372] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
American ginseng, a valuable medicinal and food plant, is threatened by rot root, which affects its yield and quality. However, limited studies have investigated the changes in soil microbial community and physiochemical properties between healthy and rot root American ginseng. Here, high-throughput sequencing and soil physiochemical properties were used to characterize these changes. The soil physiochemical properties showed significance differences between the soil of healthy and rot root, in which the pH, available potassium, available phosphorus, soil organic carbon and soil organic matter were significantly higher in healthy root soil. Besides, fungal α-diversity was also higher in healthy root soil than that in rot root. Importantly, the dominant fungal genera differed between soils of healthy and rot root of American ginseng, and LEfSe further indicated that six fungal genera (Devriesia, Chrysosporium, Dichotomopilus, Pseudeurotium, Acaulium and Scedosporium) were significantly enriched in the soil of healthy plants, whereas six fungal genera (Gibellulopsis, Fusarium, Plectosphaerella, Tetracladium, Gibberella and Ilyonectri) were significantly enriched in the soil of rot root, suggesting that an increase in the relative abundance of these pathogenic fungi (Fusarium, Plectosphaerella, and Ilyonectri) may be associated with ginseng rot root. Notably, this study is the first to report that an increase in the relative abundances of Gibellulopsis and Gibberella in the rot root soil of American ginseng may be associated with the onset of rot root symptoms in this plant. The functional profile prediction showed that the there was a significantly Pathotrophs increase in the rot root soil compared with healthy root soil and Saprotrophs were more abundant in the healthy root soil. Finally, correlation analyses revealed that soil cation exchange capacity was an important factors affecting the composition of rot root of American ginseng soil microbial communities. This study not only used a new approach to explore the new fungal associated with rot root in American ginseng but also excavated the major soil physiochemical properties affecting the microbiome diversity, providing foundation for developing biocontrol strategies against rot root.
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Affiliation(s)
- Lixia Tian
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiarong Ou
- Tongren Municipal People’s Hospital, Tongren, China
| | - Xiao Sun
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yujing Miao
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jin Pei
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lei Zhao
- Central Medical District of Chinese PLA General Hospital, Beijing, China
| | - Linfang Huang
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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42
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Shirazi S, Meyer RS, Shapiro B. Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding. Ecol Evol 2021; 11:15766-15779. [PMID: 34824788 PMCID: PMC8601883 DOI: 10.1002/ece3.8239] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is an increasingly popular tool for measuring and cataloguing biodiversity. Because the environments and substrates in which DNA is preserved differ considerably, eDNA research often requires bespoke approaches to generating eDNA data. Here, we explore how two experimental choices in eDNA study design-the number of PCR replicates and the depth of sequencing of PCR replicates-influence the composition and consistency of taxa recovered from eDNA extracts. We perform 24 PCR replicates from each of six soil samples using two of the most common metabarcodes for Fungi and Viridiplantae (ITS1 and ITS2), and sequence each replicate to an average depth of ~84,000 reads. We find that PCR replicates are broadly consistent in composition and relative abundance of dominant taxa, but that low abundance taxa are often unique to one or a few PCR replicates. Taxa observed in one out of 24 PCR replicates make up 21-29% of the total taxa detected. We also observe that sequencing depth or rarefaction influences alpha diversity and beta diversity estimates. Read sampling depth influences local contribution to beta diversity, placement in ordinations, and beta dispersion in ordinations. Our results suggest that, because common taxa drive some alpha diversity estimates, few PCR replicates and low read sampling depths may be sufficient for many biological applications of eDNA metabarcoding. However, because rare taxa are recovered stochastically, eDNA metabarcoding may never fully recover the true amplifiable alpha diversity in an eDNA extract. Rare taxa drive PCR replicate outliers of alpha and beta diversity and lead to dispersion differences at different read sampling depths. We conclude that researchers should consider the complexity and unevenness of a community when choosing analytical approaches, read sampling depths, and filtering thresholds to arrive at stable estimates.
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Affiliation(s)
- Sabrina Shirazi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of California Santa CruzSanta CruzCaliforniaUSA
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Casanelles‐Abella J, Müller S, Keller A, Aleixo C, Alós Orti M, Chiron F, Deguines N, Hallikma T, Laanisto L, Pinho P, Samson R, Tryjanowski P, Van Mensel A, Pellissier L, Moretti M. How wild bees find a way in European cities: Pollen metabarcoding unravels multiple feeding strategies and their effects on distribution patterns in four wild bee species. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joan Casanelles‐Abella
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Institute of Terrestrial Ecosystems ETH Zurich Zurich Switzerland
| | - Stefanie Müller
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Alexander Keller
- Organismic and Cellular Interactions Biocenter Faculty of Biology Ludwig‐Maximilians‐Universität München Martinsried Germany
| | - Cristiana Aleixo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Marta Alós Orti
- Institute of Agricultural and Environmental Sciences Estonian University of Life Sciences Tartu Estonia
| | - François Chiron
- Université Paris‐SaclayCNRSAgroParisTechEcologie Systématique Evolution Orsay France
| | - Nicolas Deguines
- Université Paris‐SaclayCNRSAgroParisTechEcologie Systématique Evolution Orsay France
- Laboratoire Ecologie et Biologie des Interactions Equipe Ecologie Evolution Symbiose Université de PoitiersUMR CNRS Nouvelle‐Aquitaine France
| | - Tiit Hallikma
- Institute of Agricultural and Environmental Sciences Estonian University of Life Sciences Tartu Estonia
| | - Lauri Laanisto
- Institute of Agricultural and Environmental Sciences Estonian University of Life Sciences Tartu Estonia
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Roeland Samson
- Laboratory of Environmental and Urban Ecology Department of Bioscience Engineering University of Antwerp Antwerp Belgium
| | - Piotr Tryjanowski
- Department of Zoology Poznan University of Life Sciences Poznań Poland
| | - Anskje Van Mensel
- Laboratory of Environmental and Urban Ecology Department of Bioscience Engineering University of Antwerp Antwerp Belgium
| | - Loïc Pellissier
- Institute of Terrestrial Ecosystems ETH Zurich Zurich Switzerland
- Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
| | - Marco Moretti
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
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Bray RA, Cutmore SC, Cribb TH. A paradigm for the recognition of cryptic trematode species in tropical Indo-west Pacific fishes: the problematic genus Preptetos (Trematoda: Lepocreadiidae). Int J Parasitol 2021; 52:169-203. [PMID: 34656610 DOI: 10.1016/j.ijpara.2021.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 11/30/2022]
Abstract
Molecular data have transformed approaches to trematode taxonomy by providing objective evidence for the delineation of species. However, although the data are objective, the interpretation of these data regarding species boundaries is subjective, especially when different markers conflict. Conserved markers can lead to an underestimation of richness and those used for finer species delineation have the capacity to inflate species recognition, perhaps unrealistically. Here we examine molecular and morphological evidence for species recognition in an especially confusing system, the lepocreadiid genus Preptetos Pritchard, 1960 in acanthuriform fishes of the tropical Indo-west Pacific. We consider species boundaries within this genus based on combined data (ITS2 and 28S rDNA; cox1 mtDNA and morphometrics) for substantial new collections. Delineation of species using only morphological data suggest fewer species than analysis of the sequence data; the latter suggests the presence of potential cryptic species and analysis of different markers suggests the presence of differing numbers of species. We conclude that an integrative interpretation creates the most satisfying taxonomic hypothesis. In the light of the new data, we have chosen and propose a model of trematode species recognition that demands reciprocal monophyly in the most discriminating available molecular marker plus distinction in morphology or host distribution. By invoking these criteria, we distinguish eight species in our new tropical Indo-west Pacific collections. Six of these are new (Preptetos allocaballeroi n. sp., Preptetos paracaballeroi n. sp., Preptetos pearsoni n. sp., Preptetos prudhoei n. sp., Preptetos quandamooka n. sp. and Preptetos zebravaranus n. sp.) and we continue to recognise Preptetos cannoni Barker, Bray & Cribb, 1993 and Preptetos laguncula Bray and Cribb, 1996. Notably; two of the new species, P. allocaballeroi n. sp. and P. paracaballeroi n. sp., are morphologically cryptic relative to each other. Our criteria lead us to recognise, as species, populations with unvarying morphology and similar host relationships but which may have a complex population structure over their range. In our view, this paradigm has the capacity to render tractable the interpretation of the species status of the huge trematode fauna of the tropical Indo-west Pacific.
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Affiliation(s)
- Rodney A Bray
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Scott C Cutmore
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
| | - Thomas H Cribb
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
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45
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Blanke M, Morgenstern B. App-SpaM: phylogenetic placement of short reads without sequence alignment. BIOINFORMATICS ADVANCES 2021; 1:vbab027. [PMID: 36700102 PMCID: PMC9710606 DOI: 10.1093/bioadv/vbab027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 01/28/2023]
Abstract
Motivation Phylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. A major field of application of such methods is, for example, the taxonomic identification of reads in metabarcoding or metagenomic studies. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them requires a multiple sequence alignment of the references as input. However, calculating multiple alignments is not only time-consuming but also limits the applicability of these approaches. Results Herein, we propose Alignment-free phylogenetic placement algorithm based on Spaced-word Matches (App-SpaM), an efficient algorithm for the phylogenetic placement of short sequencing reads on a tree of a set of reference sequences. App-SpaM produces results of high quality that are on a par with the best available approaches to phylogenetic placement, while our software is two orders of magnitude faster than these existing methods. Our approach neither requires a multiple alignment of the reference sequences nor alignments of the queries to the references. This enables App-SpaM to perform phylogenetic placement on a broad variety of datasets. Availability and implementation The source code of App-SpaM is freely available on Github at https://github.com/matthiasblanke/App-SpaM together with detailed instructions for installation and settings. App-SpaM is furthermore available as a Conda-package on the Bioconda channel. Contact matthias.blanke@biologie.uni-goettingen.de. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Matthias Blanke
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen 37077, Germany,International Max Planck Research School for Genome Science, Göttingen 37077, Germany,To whom correspondence should be addressed.
| | - Burkhard Morgenstern
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen 37077, Germany,Campus-Institute Data Science (CIDAS), Göttingen 37077, Germany
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Magalhães K, Santos AL, Vaulot D, Oliveira MC. Hemiselmis aquamarina sp. nov. (Cryptomonadales, Cryptophyceae), A Cryptophyte with A Novel Phycobiliprotein Type (Cr-PC 564). Protist 2021; 172:125832. [PMID: 34597847 DOI: 10.1016/j.protis.2021.125832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/07/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
Cryptophytes are a small group of photosynthetic biflagellate organisms distributed worldwide in fresh, brackish and marine waters. Although members of this class are easily distinguished from other groups, species identification is difficult and studies concerning their diversity are scarce. Two strains of an undescribed Hemiselmis species were isolated from the marine waters off Brazil and Japan. Analyses of morphology, phycobiliprotein spectral characterization, molecular phylogeny and ITS2 secondary structure comparisons were performed to assist the identification. The morphological features of Hemiselmis aquamarina sp. nov. matches that of other species from the same genus, but it has a new type of phycocyanin. Molecular phylogeny and ITS2 secondary structure support H. aquamarina as a distinct species. Furthermore, phylogenetic inferences indicate H. aquamarina as closely related to H. tepida, H. andersenii and H. rufescens. Currently, all Hemiselmis species have been described from the Northern Hemisphere and most from the subtropical region. H. aquamarina is the first species of this genus described from the South Atlantic.
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Affiliation(s)
- Karoline Magalhães
- Laboratório de Algas Marinhas Edison José de Paula, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, Butantã, São Paulo, SP, Brazil.
| | - Adriana Lopes Santos
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR 7144, ECOMAP Team Station Biologique de Roscoff, Roscoff, France; Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Mariana Cabral Oliveira
- Laboratório de Algas Marinhas Edison José de Paula, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, Butantã, São Paulo, SP, Brazil
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Yakimovich KM, Gauthier NPG, Engstrom CB, Leya T, Quarmby LM. A Molecular Analysis of Microalgae from Around the Globe to Revise Raphidonema (Trebouxiophyceae, Chlorophyta). JOURNAL OF PHYCOLOGY 2021; 57:1419-1432. [PMID: 33988850 DOI: 10.1111/jpy.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
We isolated five microalgal strains from alpine snow near Vancouver, Canada, which display morphological features suggestive of the genera Koliella and Raphidonema. Due to variations in cell size and shape, we could not make a clear delimitation based on morphology. We proceeded to a molecular analysis and included 22 strains from the CCCryo culture collection, previously identified as members of four closely related genera: Raphidonema, Koliella, Stichococcus, and Pseudochlorella. For greater taxonomic context in our phylogenetic analysis, we also obtained authentic strains for the type species of Koliella and Pseudochlorella, but were unable to find one for Raphidonema. To examine generic boundaries, we did a phylogenetic analysis on the rbcL gene for all strains, establishing distinct lineages. Our novel isolates fell within Raphidonema, and so we analyzed the ITS2 gene of all Raphidonema strains to delimit species. To support species delimitations, we did a Compensatory Base Change analysis using the secondary structure of the ITS2 gene to assist in aligning the sequence. We also computed a maximum likelihood phylogenetic tree to examine species clades of Raphidonema. We assigned epitypes for two Raphidonema species based on the best morphological match to strains in the ITS2 clades. We then amended their diagnoses so they can be more reliably identified using DNA sequence data. We also propose two new species, R. catena and R. monicae, that formed their own species clades according to our ITS2 analysis.
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Affiliation(s)
- Kurt M Yakimovich
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Sciences Building room 8166, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Nick P G Gauthier
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Sciences Building room 8166, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Casey B Engstrom
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Sciences Building room 8166, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Thomas Leya
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Extremophile Research & Biobank CCCryo, Am Muehlenberg 13, Potsdam-Golm, 14476, Germany
| | - Lynne M Quarmby
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Sciences Building room 8166, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
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Sahin E. Putative Group I Introns in the Nuclear Internal Transcribed Spacer of the Basidiomycete Fungus Gautieria Vittad. CYTOL GENET+ 2021. [DOI: 10.3103/s009545272105011x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Kolter A, Gemeinholzer B. Internal transcribed spacer primer evaluation for vascular plant metabarcoding. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.68155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.
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Q-Y Yong R, Cribb TH, Cutmore SC. Molecular phylogenetic analysis of the problematic genus Cardicola (Digenea: Aporocotylidae) indicates massive polyphyly, dramatic morphological radiation and host-switching. Mol Phylogenet Evol 2021; 164:107290. [PMID: 34371186 DOI: 10.1016/j.ympev.2021.107290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/07/2021] [Accepted: 08/04/2021] [Indexed: 11/26/2022]
Abstract
Novel multi-locus sequence data were used to assess the molecular phylogenetic relationships of fish blood flukes showing similarity to the genus Cardicola Short, 1953 (Trematoda: Aporocotylidae). Analyses of three ribosomal (ITS2, 28S & 18S) subregions and one mitochondrial (cox1) DNA subregion shows that the hitherto-monophyletic clade formed by species of Cardicola Short, 1953 also includes species of three other genera - Braya Nolan & Cribb, 2006, Elaphrobates Bullard & Overstreet, 2003 and Rhaphidotrema Yong & Cribb, 2011 - as well as a new, morphologically distinct species discovered from the heart of the yellowfin tripodfish, Tripodichthys angustifrons (Tetraodontiformes: Triacanthidae). In the context of conflicting morphological, molecular and ecological data, we argue that the recognition of seven genera produces a more satisfactory taxonomy for these parasites than considering them all as species of Cardicola. We thus recognise Cardicola (as an explicitly polyphyletic taxon) together with Braya, Elaphrobates, Rhaphidotrema and three new genera. We propose Allocardicola n. gen. for A. johnpagei n. sp. from T. angustifrons, Chanicola n. gen. for three species of Cardicola that infect the chanid Chanos chanos, and Spirocaecum n. gen. for six species of Cardicola that infect siganid fishes. We interpret the pattern of diversification seen in the clade of these seven genera as one of multiple host-switching events followed by diversification among closely-related hosts and differing levels of morphological divergence.
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Affiliation(s)
- Russell Q-Y Yong
- The University of Queensland, School of Biological Sciences, Brisbane, Queensland 4072, Australia.
| | - Thomas H Cribb
- The University of Queensland, School of Biological Sciences, Brisbane, Queensland 4072, Australia
| | - Scott C Cutmore
- The University of Queensland, School of Biological Sciences, Brisbane, Queensland 4072, Australia
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