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Gross M, Dunthorn M, Mauvisseau Q, Stoeck T. Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers. Environ Microbiol 2024; 26:e16619. [PMID: 38649189 DOI: 10.1111/1462-2920.16619] [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: 11/27/2023] [Accepted: 03/16/2024] [Indexed: 04/25/2024]
Abstract
Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour-intensive, time-consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per-cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per-cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.
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Affiliation(s)
- Megan Gross
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
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2
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Collier JL, Rest JS, Gallot-Lavallée L, Lavington E, Kuo A, Jenkins J, Plott C, Pangilinan J, Daum C, Grigoriev IV, Filloramo GV, Novák Vanclová AMG, Archibald JM. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Curr Biol 2023; 33:5199-5207.e4. [PMID: 37913769 DOI: 10.1016/j.cub.2023.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.1 50 years ago, "herpes-type" viral particles2 were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes,3,4 but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ∼300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.
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Affiliation(s)
- Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA.
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA.
| | - Lucie Gallot-Lavallée
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
| | - Erik Lavington
- Department of Ecology and Evolution, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; HudsonAlpha Institute for Biotechnology, Genome Way Northwest, Huntsville, AL 35806, USA
| | - Chris Plott
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; HudsonAlpha Institute for Biotechnology, Genome Way Northwest, Huntsville, AL 35806, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, University Avenue, Berkeley, CA 94720, USA
| | - Gina V Filloramo
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
| | | | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
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3
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Yang DL, Huang K, Deng D, Zeng Y, Wang Z, Zhang Y. DNA-dependent RNA polymerases in plants. THE PLANT CELL 2023; 35:3641-3661. [PMID: 37453082 PMCID: PMC10533338 DOI: 10.1093/plcell/koad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/09/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023]
Abstract
DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.
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Affiliation(s)
- Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenxing Wang
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Das B, Kumar N, Solanki JB, Jadav MM, Kalyani IH. Morphological and molecular characterization of Haemonchus contortus isolated from the small ruminants of south Gujarat, India. Helminthologia 2023; 60:175-188. [PMID: 37745222 PMCID: PMC10516478 DOI: 10.2478/helm-2023-0020] [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: 11/29/2022] [Accepted: 05/30/2023] [Indexed: 09/26/2023] Open
Abstract
The successful design of strategic control measures against the blood-sucking gastrointestinal nematode, Haemonchus contortus in small ruminants can be facilitated by revealing its general features from morphology to the molecular level. In the south Gujarat region of India, a total of 2408 H. contortus were collected from 84 slaughtered sheep's abomasum, consisting of 347 males and 2061 females (1:6 ratio) (p<0.05). Furthermore, 726 H. contortus were collected from 61 goats, comprising 145 males and 581 females (1:4 ratio) (p<0.05). The male worms were approximately 12±0.06 mm long, while female worms were about 20±0.09 mm long. The vulvar morphotypes of the female worms were found to be 17.7% linguiform, 76.6 % knobbed/button (p<0.05), and 5.7 % smooth type, demonstrating common features of H. contortus. The nucleotide sequences of the Internal Transcribed Spacer 1 (ITS-1) of 165 bp or ITS-2 plus of 256 bp were aligned, and it was found that the genotypes of male and female specimens of either sheep or goat origin were identical, with a 100 % match. The present isolates shared >95 % and >94 % homology with published sequences of ITS-1 and ITS-2 plus of H. contortus, respectively, with more nucleotide transitions than transversions in the aligned sequences. The reconstructed phylogram of either ITS-1 or ITS-2 plus revealed two major clades, one for H. contortus and another for other nematodes, with Haemonchus placei showing its proximity with the clade of H. contortus. The study established the role of morphological and molecular features in identifying and differentiating H. contortus parasite at the local level.
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Affiliation(s)
- B. Das
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Navsari-396 450, Gujarat, India
| | - N. Kumar
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Navsari-396 450, Gujarat, India
| | - J. B. Solanki
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Navsari-396 450, Gujarat, India
| | - M. M. Jadav
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Navsari-396 450, Gujarat, India
| | - I. H. Kalyani
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Navsari-396 450, Gujarat, India
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Maurer M, Klassert TE, Löffler B, Slevogt H, Tuchscherr L. Extraction of High-Quality RNA from S. aureus Internalized by Endothelial Cells. Microorganisms 2023; 11:microorganisms11041020. [PMID: 37110443 PMCID: PMC10143013 DOI: 10.3390/microorganisms11041020] [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: 03/12/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Staphylococcus aureus evades antibiotic therapy and antimicrobial defenses by entering human host cells. Bacterial transcriptomic analysis represents an invaluable tool to unravel the complex interplay between host and pathogen. Therefore, the extraction of high-quality RNA from intracellular S. aureus lays the foundation to acquire meaningful gene expression data. In this study, we present a novel and straightforward strategy to isolate RNA from internalized S. aureus after 90 min, 24 h, and 48 h postinfection. Real-time PCR data were obtained for the target genes agrA and fnba, which play major roles during infection. The commonly used reference genes gyrB, aroE, tmRNA, gmk, and hu were analyzed under different conditions: bacteria from culture (condition I), intracellular bacteria (condition II), and across both conditions I and II. The most stable reference genes were used for the normalization of agrA and fnbA. Delta Cq (quantification cycle) values had a relatively low variability and thus demonstrated the high quality of the extracted RNA from intracellular S. aureus during the early phase of infection. The established protocol allows the extraction and purification of intracellular staphylococcal RNA while minimizing the amount of host RNA in the sample. This approach can leverage reproducible gene expression data to study host-pathogen interactions.
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Affiliation(s)
- Michelle Maurer
- Institute for Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Tilman E Klassert
- Department of Respiratory Medicine, Medizinische Hochschule Hannover, 30625 Hannover, Germany
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Bettina Löffler
- Institute for Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Hortense Slevogt
- Department of Respiratory Medicine, Medizinische Hochschule Hannover, 30625 Hannover, Germany
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Lorena Tuchscherr
- Institute for Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
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6
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McGee JP, Armache JP, Lindner SE. Ribosome heterogeneity and specialization of Plasmodium parasites. PLoS Pathog 2023; 19:e1011267. [PMID: 37053161 PMCID: PMC10101515 DOI: 10.1371/journal.ppat.1011267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Affiliation(s)
- James P McGee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
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7
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Bi YH, Li Z, Zhou ZG. Karyotype analysis of the brown seaweed Saccharina (or Laminaria) japonica. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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8
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Guerra-Slompo E, Cesaro G, Guimarães B, Zanchin N. Dissecting Trypanosoma brucei RRP44 function in the maturation of segmented ribosomal RNA using a regulated genetic complementation system. Nucleic Acids Res 2023; 51:396-419. [PMID: 36610751 PMCID: PMC9841430 DOI: 10.1093/nar/gkac1217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Trypanosoma brucei belongs to a group of protozoans presenting fragmented large subunit rRNA. Its LSU rRNA equivalent to the 25S/28S rRNA of other eukaryotes is split into six fragments, requiring additional processing for removal of the extra spacer sequences. We have used a genetic complementation strategy to further investigate the T. brucei RRP44 nuclease in pre-rRNA maturation. TbRRP44 contains both a PIN and a RNB domain whose homologues are found in association with the exosome complex. We found that the exonucleolytic activity of the RNB domain as well as the physical presence of the PIN domain are essential for TbRRP44 function, while a catalytic site mutation in the PIN domain has no detectable effect on cell growth. A new endonucleolytic cleavage site in ITS1 was identified. In addition to the 5.8S rRNA 3'-end maturation, TbRRP44 is required for degradation of the excised 5'-ETS and for removal of part of ITS1 during maturation of the 18S rRNA 3'-end. TbRRP44 deficiency leads to accumulation of many LSU intermediate precursors, most of them not detected in control cells. TbRRP44 is also required for U3 snoRNA and spliced leader processing, indicating that TbRRP44 may have a wide role in RNA processing in T. brucei.
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Affiliation(s)
- Eloise Pavão Guerra-Slompo
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil
| | - Giovanna Cesaro
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil,Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba-PR, Brazil
| | - Beatriz Gomes Guimarães
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil,Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba-PR, Brazil
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9
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Exploring LSU and ITS rDNA Sequences for Acanthamoeba Identification and Phylogeny. Microorganisms 2022; 10:microorganisms10091776. [PMID: 36144378 PMCID: PMC9502406 DOI: 10.3390/microorganisms10091776] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/22/2022] Open
Abstract
The identification and classification of strains of Acanthamoeba, a potentially pathogenic ubiquitous free-living amoeba, are largely based on the analysis of 18S rDNA sequences, currently delineating 23 genotypes, T1 to T23. In this study, the sequences of the ITS region, i.e., the 5.8S rDNA and the two internal transcribed spacers (ITS-1 and ITS-2), and those of the large subunit (LSU) rDNA of Acanthamoeba were recovered from amoeba genomes; the sequences are available in GenBank. The complete ITS–LSU sequences could be obtained for 15 strains belonging to 7 distinct lineages (T4A, T4D, T4F, T4G, T2, T5, and T18), and the site of the hidden break producing the 26Sα and 26Sβ was identified. For the other lines, either the LSU is partial (T2/T6, T7) or the ITS is fragmentary (T7, T10, T22). It is noteworthy that a number of sequences assigned to fungi turned out to actually be Acanthamoeba, only some of which could be affiliated with known genotypes. Analysis of the obtained sequences indicates that both ITS and LSU are promising for diagnostic and phylogenetic purposes.
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10
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Lagunas-Rangel FA. Ribosomal RNA Transcription Machineries in Intestinal Protozoan Parasites: A Bioinformatic Analysis. Acta Parasitol 2022; 67:1788-1799. [PMID: 36028726 DOI: 10.1007/s11686-022-00612-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Ribosome biogenesis is a key process in all living organisms, energetically expensive and tightly regulated. Currently, little is known about the components of the ribosomal RNA (rRNA) transcription machinery that are present in intestinal parasites, such as Giardia duodenalis, Cryptosporidium parvum, and Entamoeba histolytica. Thus, in the present work, an analysis was carried out looking for the components of the rRNA transcription machinery that are conserved in intestinal parasites and if these could be used to design new treatment strategies. METHODS The different components of the rRNA transcription machinery were searched in the studied parasites with the NCBI BLAST tool in the EuPathDB Bioinformatics Resource Center database. The sequences of the RRN3 and POLR1F orthologs were aligned and important regions identified. Subsequently, three-dimensional models were built with different bioinformatic tools and a structural analysis was performed. RESULTS Among the protozoa examined, C. parvum is the parasite with the fewest identifiable components of the rRNA transcription machinery. TBP, RRN3, POLR1A, POLR1B, POLR1C, POLR1D, POLR1F, POLR1H, POLR2E, POLR2F and POLR2H subunits were identified in all species studied. Furthermore, the interaction regions between RRN3 and POLR1F were found to be conserved and could be used to design drugs that inhibit rRNA transcription in the parasites studied. CONCLUSION The inhibition of the rRNA transcription machinery in parasites might be a new therapeutic strategy against these microorganisms.
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11
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Sharma D, Denmat SHL, Matzke NJ, Hannan K, Hannan RD, O'Sullivan JM, Ganley ARD. A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations. Genomics 2022; 114:110430. [PMID: 35830947 DOI: 10.1016/j.ygeno.2022.110430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/23/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations.
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Affiliation(s)
- Diksha Sharma
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sylvie Hermann-Le Denmat
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross D Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168, Australia
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand; Maurice Wilkins Center, University of Auckland, New Zealand; MRC Lifecourse Unit, University of Southampton, United Kingdom; Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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12
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Hałakuc P, Karnkowska A, Milanowski R. Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans. BMC Ecol Evol 2022; 22:59. [PMID: 35534840 PMCID: PMC9082867 DOI: 10.1186/s12862-022-02014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
Background Members of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of the large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal transcribed spacers (ITSs) in the rDNA. Diplonemea is the third of the main groups of Euglenozoa and its members are known to be among the most abundant and diverse protists in the oceans. Despite that, the rRNA of only one diplonemid species, Diplonema papillatum, has been examined so far and found to exhibit continuous 28S rRNA. Currently, the rDNA organization has not been researched for any diplonemid. Herein we investigate the structure of rRNA genes in classical (Diplonemidae) and deep-sea diplonemids (Eupelagonemidae), representing the majority of known diplonemid diversity. The results fill the gap in knowledge about diplonemid rDNA and allow better understanding of the evolution of the fragmented structure of the rDNA in Euglenozoa. Results We used available genomic (culture and single-cell) sequencing data to assemble complete or almost complete rRNA operons for three classical and six deep-sea diplonemids. The rDNA sequences acquired for several euglenids and kinetoplastids were used to provide the background for the analysis. In all nine diplonemids, 28S rRNA seems to be contiguous, with no additional ITSs detected. Similarly, no additional ITSs were detected in basal prokinetoplastids. However, we identified five additional ITSs in the 28S rRNA of all analysed metakinetoplastids, and up to twelve in euglenids. Only three of these share positions, and they cannot be traced back to their common ancestor. Conclusions Presented results indicate that independent origin of additional ITSs in euglenids and kinetoplastids seems to be the most likely. The reason for such unmatched fragmentation remains unknown, but for some reason euglenozoan ribosomes appear to be prone to 28S rRNA fragmentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02014-9.
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Jüttner M, Ferreira-Cerca S. Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis. Mol Biol Evol 2022; 39:6547259. [PMID: 35275997 PMCID: PMC8997704 DOI: 10.1093/molbev/msac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.
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Affiliation(s)
- Michael Jüttner
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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14
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Kasselimi E, Pefani DE, Taraviras S, Lygerou Z. Ribosomal DNA and the nucleolus at the heart of aging. Trends Biochem Sci 2022; 47:328-341. [DOI: 10.1016/j.tibs.2021.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022]
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15
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Feist SM, Lance RF. Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum. HARMFUL ALGAE 2021; 110:102124. [PMID: 34887004 DOI: 10.1016/j.hal.2021.102124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Recurrence and severity of harmful algal blooms (HABs) are increasing due to a number of factors, including human practices and climate change. Sensitive and robust methods that allow for early and expedited HAB detection across large landscape scales are needed. Among the suite of HAB detection tools available, a powerful option exists in genetics-based approaches utilizing environmental sampling, also termed environmental DNA (eDNA). Here we provide a detailed methodological review of three HAB eDNA approaches (quantitative PCR, high throughput sequencing, and isothermal amplification). We then summarize and synthesize recently published eDNA applications covering a variety of HAB surveillance and research objectives, all with a specific emphasis in the detection of two widely problematic freshwater species, Microcystis aeruginosa and Prymnesium parvum. In our summary and conclusion we build on this literature by discussing ways in which eDNA methods could be advanced to improve HAB detection. We also discuss ways in which eDNA data could be used to potentially provide novel insight into the ecology, mitigation, and prediction of HABs.
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Affiliation(s)
- Sheena M Feist
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States.
| | - Richard F Lance
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States
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16
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Briscoe AG, Nichols S, Hartikainen H, Knipe H, Foster R, Green AJ, Okamura B, Bass D. High-Throughput Sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds. Mol Ecol Resour 2021; 22:1303-1318. [PMID: 34758191 DOI: 10.1111/1755-0998.13548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.
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Affiliation(s)
- Andrew G Briscoe
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Core Research Laboratories, Natural History Museum, London, United Kingdom
| | - Sarah Nichols
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Hanna Hartikainen
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Eawag and Institute for Integrative Biology, Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Hazel Knipe
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Rachel Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, 41092, Sevilla, Spain
| | - Beth Okamura
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Centre for Environment, Aquaculture and Fisheries Science (Cefas), Weymouth, UK
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17
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Luttermann T, Rückert C, Wibberg D, Busche T, Schwarzhans JP, Friehs K, Kalinowski J. Establishment of a near-contiguous genome sequence of the citric acid producing yeast Yarrowia lipolytica DSM 3286 with resolution of rDNA clusters and telomeres. NAR Genom Bioinform 2021; 3:lqab085. [PMID: 34661101 PMCID: PMC8515841 DOI: 10.1093/nargab/lqab085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 09/01/2021] [Accepted: 10/13/2021] [Indexed: 11/29/2022] Open
Abstract
Yarrowia lipolytica is an oleaginous yeast that is particularly suitable for the sustainable production of secondary metabolites. The genome of this yeast is characterized by its relatively large size and its high number of different rDNA clusters located in its telomeric regions. However, due to the presence of long repetitive elements in the sub-telomeric regions, rDNA clusters and telomeres are missing in current genome assemblies of Y. lipolytica. Here, we present the near-contiguous genome sequence of the biotechnologically relevant strain DSM 3286. We employed a hybrid assembly strategy combining Illumina and nanopore sequencing reads to integrate all six rDNA clusters as well as telomeric repeats into the genome sequence. By fine-tuning of DNA isolation and library preparation protocols, we were able to create ultra-long reads that not only contained multiples of mitochondrial genomes but also shed light on the inter- and intra-chromosomal diversity of rDNA cluster types. We show that there are ten different rDNA units present in this strain that additionally appear in a predefined order in a cluster. Based on single reads, we also demonstrate that the number of rDNA repeats in a specific cluster varies from cell to cell within a population.
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Affiliation(s)
- Tobias Luttermann
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
| | | | - Karl Friehs
- Fermentation Engineering, Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
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18
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Martin K, Schmidt K, Toseland A, Boulton CA, Barry K, Beszteri B, Brussaard CPD, Clum A, Daum CG, Eloe-Fadrosh E, Fong A, Foster B, Foster B, Ginzburg M, Huntemann M, Ivanova NN, Kyrpides NC, Lindquist E, Mukherjee S, Palaniappan K, Reddy TBK, Rizkallah MR, Roux S, Timmermans K, Tringe SG, van de Poll WH, Varghese N, Valentin KU, Lenton TM, Grigoriev IV, Leggett RM, Moulton V, Mock T. The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. Nat Commun 2021; 12:5483. [PMID: 34531387 PMCID: PMC8446083 DOI: 10.1038/s41467-021-25646-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.
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Affiliation(s)
- Kara Martin
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bánk Beszteri
- Department of Biology, University of Duisburg-Essen, Essen, Essen, Germany
| | | | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris G Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley Eloe-Fadrosh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Fong
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Brian Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bryce Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael Ginzburg
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia N Ivanova
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Supratim Mukherjee
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishnaveni Palaniappan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mariam R Rizkallah
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaas Timmermans
- Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Willem H van de Poll
- Centre for Isotope Research - Oceans, Energy and Sustainability Research Institute Groningen, Faculty of Science and Engineering, University of Groningen, AG Groningen, The Netherlands
| | - Neha Varghese
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaus U Valentin
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | | | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Biology Department, University of California, Berkeley, CA, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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19
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Vaulot D, Geisen S, Mahé F, Bass D. pr2-primers: An 18S rRNA primer database for protists. Mol Ecol Resour 2021; 22:168-179. [PMID: 34251760 DOI: 10.1111/1755-0998.13465] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023]
Abstract
Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R-based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set (https://app.pr2-primers.org). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations.
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Affiliation(s)
- Daniel Vaulot
- UMR 7144, ECOMAP, Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France.,Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.,Nanjing Agricultural University, Nanjing, China
| | - Frédéric Mahé
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK.,Department of Life Sciences, The Natural History Museum, London, UK
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20
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Mthethwa NP, Amoah ID, Reddy P, Bux F, Kumari S. A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives. J Microbiol Methods 2021; 187:106269. [PMID: 34129906 DOI: 10.1016/j.mimet.2021.106269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/23/2023]
Abstract
The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and large eukaryotic genome, the prevalence of small parasite populations in environmental samples compared to bacteria, difficulties in extracting DNA from (oo)cysts, and limited reference databases for parasites. This calls for further research to develop optimized methods specifically looking at protozoan parasites in the environment. This study reviews the current workflow, methods and provide recommendations for the standardization of techniques. The article identifies and summarizes the key methods, advantages, and limitations associated with metagenomic analysis, like sample pre-processing, DNA extraction, sequencing approaches, and analysis methods. The study enhances the understanding and application of standardized protocols for profiling of protozoan parasite community from highly complexe samples and further creates a resourceful comparison among datasets without any biases.
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Affiliation(s)
- N P Mthethwa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa; Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - I D Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - P Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - F Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - S Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
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21
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Abstract
Tritrichomonas foetus is a venereal trichomonad parasite which causes reproductive issues in cattle. No other trichomonads are known to be urogenital pathogens in cattle, but there are several reports of Tetratrichomonas and Pentatrichomonas isolates of unclear origin from the cattle urogenital tract (UGT) in the Americas. This study reports the first case of a non-T. foetus cattle urogenital trichomonad isolate in Europe. Molecular analysis of the internal transcribed spacer (ITS) 1-5.8S ribosomal RNA-ITS 2 and 18S ribosomal RNA loci suggest that the isolate is a Tetratrichomonas species from a lineage containing other previously described bull preputial isolates. We identified close sequence similarity between published urogenital and gastrointestinal Tetratrichomonas spp., and this is reviewed alongside further evidence regarding the gastrointestinal origin of non-T. foetus isolates. Routine screening for T. foetus is based on culture and identification by microscopy, and so considering other trichomonad parasites of the bovine UGT is important to avoid misdiagnosis.
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22
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The extrachromosomal elements of the Naegleria genus: How little we know. Plasmid 2021; 115:102567. [PMID: 33617907 DOI: 10.1016/j.plasmid.2021.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/20/2022]
Abstract
There are currently 47 characterized species in the Naegleria genus of free-living amoebae. Each amoeba has thousands of extrachromosomal elements that are closed circular structures comprised of a single ribosomal DNA (rDNA) copy and a large non-rDNA sequence. Despite the presence of putative open reading frames and introns, ribosomal RNA is the only established transcript. A single origin of DNA replication (ori) has been mapped within the non-rDNA sequence for one species (N. gruberi), a finding that strongly indicates that these episomes replicate independently of the cell's chromosomal DNA component. This article reviews that which has been published about these interesting DNA elements and by analyzing available sequence data, discusses the possibility that different phylogenetically related clusters of Naegleria species individually conserve ori structures and suggests where the rRNA promoter and termination sites may be located.
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23
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Colabella C, Casagrande Pierantoni D, Corte L, Roscini L, Conti A, Bassetti M, Tascini C, Robert V, Cardinali G. Single Strain High-Depth NGS Reveals High rDNA (ITS-LSU) Variability in the Four Prevalent Pathogenic Species of the Genus Candida. Microorganisms 2021; 9:microorganisms9020302. [PMID: 33540602 PMCID: PMC7912828 DOI: 10.3390/microorganisms9020302] [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: 12/31/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 01/08/2023] Open
Abstract
Ribosomal RNA in fungi is encoded by a series of genes and spacers included in a large operon present in 100 tandem repeats, normally in a single locus. The multigene nature of this locus was somehow masked by Sanger sequencing, which produces a single sequence reporting the prevalent nucleotide of each site. The introduction of next generation sequencing led to deeper knowledge of the individual sequences (reads) and therefore of the variants between the same DNA sequences located in different tandem repeats. In this framework, NGS sequencing of the rDNA region was used to elucidate the extent of intra- and inter-genomic variation at both the strain and species level. Specifically, the use of an innovative NGS technique allowed the high-throughput high-depth sequencing of the ITS1-LSU D1/D2 amplicons of 252 strains belonging to four opportunistic yeast species of the genus Candida. Results showed the presence of a large extent of variability among strains and species. These variants were differently distributed throughout the analyzed regions with a higher concentration within the Internally Transcribed Spacer (ITS) region, suggesting that concerted evolution was not able to totally homogenize these sequences. Both the internal variability and the SNPs between strain can be used for a deep typing of the strains and to study their ecology.
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Affiliation(s)
- Claudia Colabella
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
| | - Debora Casagrande Pierantoni
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Luca Roscini
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Matteo Bassetti
- Department Science and Health, University of Genoa and Genoa Hospital, 16100 Genova, Italy;
| | - Carlo Tascini
- Department of Medical Art, University of Udine and Udine Hospital, 33100 Udine, Italy;
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
- CEMIN Excellence Research Centre, University of Perugia, 06123 Perugia, Italy
- Correspondence: ; Tel.: +39-075-585-6484
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24
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de Bustos A, Figueroa RI, Sixto M, Bravo I, Cuadrado Á. The 5S rRNA genes in Alexandrium: their use as a FISH chromosomal marker in studies of the diversity, cell cycle and sexuality of dinoflagellates. HARMFUL ALGAE 2020; 98:101903. [PMID: 33129460 DOI: 10.1016/j.hal.2020.101903] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/25/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Chromosomal markers of the diversity and evolution of dinoflagellates are scarce because the genomes of these organisms are unique among eukaryotes in terms of their base composition and chromosomal structure. Similarly, a lack of appropriate tools has hindered studies of the chromosomal localization of 5S ribosomal DNA (rDNA) in the nucleosome-less chromosomes of dinoflagellates. In this study, we isolated and cloned 5S rDNA sequences from various toxin-producing species of the genus Alexandrium and developed a fluorescence in situ hybridization (FISH) probe that allows their chromosomal localization. Our results can be summarized as follows: 1) The 5S rDNA unit is composed of a highly conserved 122-bp coding region and an intergenic spacer (IGS), the length and sequence of which are variable even within strains. 2) Three different IGS types, one containing the U6 small nuclear RNA (snRNA) gene, were found among four of the studied species (A. minutum, A. tamarense, A. catenella and A. pacificum). 3) In all strains investigated by FISH (A. minutum, A. tamarense, A. pacificum, A. catenella, A. andersonii and A. ostenfeldii), 5S rDNA gene arrays were separate from the nucleolar organizer region, which contains the genes for the large 45S pre-ribosomal RNA. 4) One to three 5S rDNA sites per haploid genome were detected, depending on the strains/species. Intraspecific variability in the number of 5S rDNA sites was determined among strains of A. minutum and A. pacificum. 5) 5S rDNA is a useful chromosomal marker of mitosis progression and can be employed to differentiate vegetative (haploid) vs. planozygotes (diploid) cells. Thus, the FISH probe (oligo-Dino5Smix5) developed in this study facilitates analyses of the diversity, cell cycle and life stages of the genus Alexandrium.
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Affiliation(s)
- Alfredo de Bustos
- Universidad de Alcalá (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain.
| | - Rosa I Figueroa
- Instituto Español de Oceanografía (IEO), Subida a Radio Faro 50, 36390 Vigo, Spain.
| | - Marta Sixto
- Instituto Español de Oceanografía (IEO), Subida a Radio Faro 50, 36390 Vigo, Spain; Campus do Mar, Facultad de Ciencias del Mar, Universidad de Vigo, 36311 Vigo, Spain.
| | - Isabel Bravo
- Instituto Español de Oceanografía (IEO), Subida a Radio Faro 50, 36390 Vigo, Spain.
| | - Ángeles Cuadrado
- Universidad de Alcalá (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain.
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25
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Sipiczki M. Metschnikowia pulcherrima and Related Pulcherrimin-Producing Yeasts: Fuzzy Species Boundaries and Complex Antimicrobial Antagonism. Microorganisms 2020; 8:E1029. [PMID: 32664630 PMCID: PMC7409158 DOI: 10.3390/microorganisms8071029] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/30/2022] Open
Abstract
Yeasts affiliated with the Metschnikowia pulcherrima clade (subclade) of the large ascomycetous genus Metschnikowia frequently turn out to produce the characteristic maroon-red pulcherrimin when tested for pigment production and prove to exert antagonistic effects on many types of microorganisms. The determination of the exact taxonomic position of the strains is hampered by the shortage of distinctive morphological and physiological properties of the species of the clade and the lack of rDNA barcode gaps. The rDNA repeats of the type strains of the species are not homogenized and are assumed to evolve by a birth-and-death mechanism combined with reticulation. The taxonomic division is further hampered by the incomplete biological (reproductive) isolation of the species: certain type strains can be hybridized and genome sequencing revealed chimeric genome structures in certain strains that might have evolved from interspecies hybrids (alloploid genome duplication). Various mechanisms have been proposed for the antimicrobial antagonism. One is related to pulcherrimin production. The diffusible precursor of pulcherrimin, the pulcherriminic acid is secreted by the cells into the environment where it forms the insoluble pulcherrimin with the ferric ions. The lack of free iron caused by the immobilization of ferric ions inhibits the growth of many microorganisms. Recent results of research into the complexity of the taxonomic division of the pulcherrimin-producing Metschnikowia yeasts and the mechanism(s) underlying their antimicrobial antagonism are discussed in this review.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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Evidence of Intra-individual SSU Polymorphisms in Dark-spored Myxomycetes (Amoebozoa). Protist 2019; 170:125681. [PMID: 31586669 DOI: 10.1016/j.protis.2019.125681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 11/24/2022]
Abstract
The nuclear small subunit rRNA gene (SSU or 18S) is a marker frequently used in phylogenetic and barcoding studies in Amoebozoa, including Myxomycetes. Despite its common usage and the confirmed existence of divergent copies of ribosomal genes in other protists, the potential presence of intra-individual SSU variability in Myxomycetes has never been studied before. Here we investigated the pattern of nucleotide polymorphism in the 5' end fragment of SSU by cloning and sequencing a total of 238 variants from eight specimens, each representing a species of the dark-spored orders Stemonitidales and Physarales. After excluding singletons, a relatively low SSU intra-individual variability was found but our data indicate that this might be a widely distributed phenomenon in Myxomycetes as all samples analyzed possessed various ribotypes. To determine if the occurrence of multiple SSU variants within a single specimen has a negative effect on the circumscription of species boundaries, we conducted phylogenetic analyses that revealed that clone variation may be detrimental for inferring phylogenetic relationships among some of the specimens analyzed. Despite that intra-individual variability should be assessed in additional taxa, our results indicate that special care should be taken for species identification when working with closely related species.
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Corsaro D, Venditti D. Putative group I introns in the eukaryote nuclear internal transcribed spacers. Curr Genet 2019; 66:373-384. [PMID: 31463775 DOI: 10.1007/s00294-019-01027-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/05/2019] [Accepted: 08/17/2019] [Indexed: 11/28/2022]
Abstract
Group I introns are mobile genetic elements that interrupt genes encoding proteins and RNAs. In the rRNA operon, introns can insert in the small subunit (SSU) and large subunit (LSU) of a wide variety of protists and various prokaryotes, but they were never found in the ITS region. In this study, unusually long ITS regions of fungi and closely related unicellular organisms (Polychytrium aggregatum, Mitosporidium daphniae, Amoeboaphelidium occidentale and Nuclearia simplex) were analysed. While the insertion of repeats is responsible for long ITS in other eukaryotes, the increased size of the sequences analysed herein seems rather due to the presence of introns in ITS-1 or ITS-2. The identified insertions can be folded in secondary structures according to group I intron models, and they cluster within introns in conserved core-based phylogeny. In addition, for Mitosporidium, Amoeboaphelidium and Nuclearia, more conventional ITS-2 structures can be deduced once spacer introns are removed. Sequences of five shark species were also analysed for their structure and included in phylogeny because of unpublished work reporting introns in their ITS, obtaining congruent results. Overall, the data presented herein indicate that spacer regions may contain introns.
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Affiliation(s)
- Daniele Corsaro
- CHLAREAS, 12 rue du Maconnais, Vandoeuvre-lès-Nancy, 54500, France.
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Martínez-Calvillo S, Florencio-Martínez LE, Nepomuceno-Mejía T. Nucleolar Structure and Function in Trypanosomatid Protozoa. Cells 2019; 8:cells8050421. [PMID: 31071985 PMCID: PMC6562600 DOI: 10.3390/cells8050421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleolus is the conspicuous nuclear body where ribosomal RNA genes are transcribed by RNA polymerase I, pre-ribosomal RNA is processed, and ribosomal subunits are assembled. Other important functions have been attributed to the nucleolus over the years. Here we review the current knowledge about the structure and function of the nucleolus in the trypanosomatid parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania ssp., which represent one of the earliest branching lineages among the eukaryotes. These protozoan parasites present a single nucleolus that is preserved throughout the closed nuclear division, and that seems to lack fibrillar centers. Trypanosomatids possess a relatively low number of rRNA genes, which encode rRNA molecules that contain large expansion segments, including several that are trypanosomatid-specific. Notably, the large subunit rRNA (28S-type) is fragmented into two large and four small rRNA species. Hence, compared to other organisms, the rRNA primary transcript requires additional processing steps in trypanosomatids. Accordingly, this group of parasites contains the highest number ever reported of snoRNAs that participate in rRNA processing. The number of modified rRNA nucleotides in trypanosomatids is also higher than in other organisms. Regarding the structure and biogenesis of the ribosomes, recent cryo-electron microscopy analyses have revealed several trypanosomatid-specific features that are discussed here. Additional functions of the nucleolus in trypanosomatids are also reviewed.
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Affiliation(s)
- Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Luis E Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Tomás Nepomuceno-Mejía
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
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Symonová R. Integrative rDNAomics-Importance of the Oldest Repetitive Fraction of the Eukaryote Genome. Genes (Basel) 2019; 10:genes10050345. [PMID: 31067804 PMCID: PMC6562748 DOI: 10.3390/genes10050345] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
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Mullican JC, Chapman NM, Tracy S. Mapping the Single Origin of Replication in the Naegleria gruberi Extrachromosomal DNA Element. Protist 2019; 170:141-152. [DOI: 10.1016/j.protis.2019.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/28/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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Comparison of Loop-Mediated Isothermal Amplification and Real-Time PCR Assays for Detection of Strongyloides Larvae in Different Specimen Matrices. J Clin Microbiol 2019; 57:JCM.01173-18. [PMID: 30728195 DOI: 10.1128/jcm.01173-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/29/2019] [Indexed: 12/27/2022] Open
Abstract
Strongyloides stercoralis can cause disease that ranges from asymptomatic chronic infection to fatal hyperinfection. Diagnosis from stool can be challenging because the most sensitive conventional tests require live larvae to be effective and there can be low larval output in chronic infection. Nucleic acid amplification tests (NAAT) have been developed to complement existing diagnostic methods. We compared a recently developed loop-mediated isothermal amplification (LAMP) assay with a real-time PCR that has previously been validated with larval microscopy. The limits of detection-quantified using serial dilutions of DNA extracts from single Strongyloides ratti third-stage (L3) larvae spiked into approximately 250 µl of 5 different S. stercoralis-negative stool specimens-were 10-3 (1/5 replicates) and 10-2 (1/5 replicates) dilutions for PCR and LAMP, respectively. PCR was positive for 4/5 replicates at 10-2 LAMP was compared to PCR using extracts from 396 stool specimens collected in Bangladesh and Australia, of which 53 were positive and 343 were negative by PCR. The positive percentage agreement of LAMP was 77.3% (95% score confidence interval [CI], 64.5 to 86.6). The negative percentage agreement was 100% (95% CI, 98.9 to 100). In a preliminary investigation, PCR and LAMP assays were positive using DNA extracted from serum (PCR, 3/16 extracts; LAMP, 2/16 extracts) and bronchoalveolar lavage fluid (PCR and LAMP, 2/2 extracts), demonstrating proof of concept. Compared to PCR, the lower number of positive results using the LAMP assay may have been due to reaction inhibitors and DNA degradation, and strategies to improve the LAMP assay are discussed.
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Amato P, Besaury L, Joly M, Penaud B, Deguillaume L, Delort AM. Metatranscriptomic exploration of microbial functioning in clouds. Sci Rep 2019; 9:4383. [PMID: 30867542 PMCID: PMC6416334 DOI: 10.1038/s41598-019-41032-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/27/2019] [Indexed: 01/19/2023] Open
Abstract
Clouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.
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Affiliation(s)
- Pierre Amato
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France.
| | - Ludovic Besaury
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | - Muriel Joly
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | - Benjamin Penaud
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | | | - Anne-Marie Delort
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
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Wang Y, Wang C, Jiang Y, Katz LA, Gao F, Yan Y. Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. SCIENCE CHINA-LIFE SCIENCES 2019; 62:203-214. [PMID: 30671886 DOI: 10.1007/s11427-018-9422-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/06/2018] [Indexed: 11/26/2022]
Abstract
Sequence-based approaches, such as analyses of ribosome DNA (rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities. However, recent studies demonstrate both rDNA copy number variation and intra-individual (intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA (SSU rDNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that: (i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa; (ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template; (iii) compared with the most common version, other variant sequences differ in only 1-3 nucleotides, likely generated during macronuclear (somatic) amplification; (iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses; (v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall, these analyses indicate the need for careful consideration of SSU rDNA variation in analyses of the role of ciliates in ecosystems.
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Affiliation(s)
- Yurui Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Chundi Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA.
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Wutkowska M, Vader A, Mundra S, Cooper EJ, Eidesen PB. Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil. Front Microbiol 2019; 9:3243. [PMID: 30671045 PMCID: PMC6333106 DOI: 10.3389/fmicb.2018.03243] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/13/2018] [Indexed: 11/15/2022] Open
Abstract
Describing dynamics of belowground organisms, such as fungi, can be challenging. Results of studies based on environmental DNA (eDNA) may be biased as the template does not discriminate between metabolically active cells and dead biomass. We analyzed ribosomal DNA (rDNA) and ribosomal RNA (rRNA) coextracted from 48 soil samples collected from a manipulated snow depth experiment in two distinct vegetation types in Svalbard, in the High Arctic. Our main goal was to compare if the rDNA and rRNA metabarcoding templates produced congruent results that would lead to consistent ecological interpretation. Data derived from both rDNA and rRNA clustered according to vegetation types. Different sets of environmental variables explained the community composition based on the metabarcoding template. rDNA and rRNA-derived community composition of symbiotrophs and saprotrophs, unlike pathotrophs, clustered together in a similar way as when the community composition was analyzed using all OTUs in the study. Mean OTU richness was higher for rRNA, especially in symbiotrophs. The metabarcoding template was more important than vegetation type in explaining differences in richness. The proportion of symbiotrophic, saprotrophic and functionally unassigned reads differed between rDNA and rRNA, but showed similar trends. There was no evidence for increased snow depth influence on fungal community composition or richness. Our findings suggest that template choice may be especially important for estimating biodiversity, such as richness and relative abundances, especially in Helotiales and Agaricales, but not for inferring community composition. Differences in study results originating from rDNA or rRNA may directly impact the ecological conclusions of one’s study, which could potentially lead to false conclusions on the dynamics of microbial communities in a rapidly changing Arctic.
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Affiliation(s)
- Magdalena Wutkowska
- Department of Arctic Biology, The University Centre in Svalbard (UNIS), Longyearbyen, Norway.,Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard (UNIS), Longyearbyen, Norway
| | - Sunil Mundra
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Elisabeth J Cooper
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Pernille B Eidesen
- Department of Arctic Biology, The University Centre in Svalbard (UNIS), Longyearbyen, Norway
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Antonia AL, Wang L, Ko DC. A real-time PCR assay for quantification of parasite burden in murine models of leishmaniasis. PeerJ 2018; 6:e5905. [PMID: 30430041 PMCID: PMC6231426 DOI: 10.7717/peerj.5905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic parasites in the genus Leishmania place approximately 350 million people per year at risk of disease. In addition to their global health significance, Leishmania spp. have served as an important model for delineating basic concepts in immunology such as T-helper cell polarization. There have been many qPCR-based assays reported for measuring parasite burden in humans and animals. However, these are largely optimized for use in clinical diagnosis and not specifically for animal models. This has led several of these assays to have suboptimal characteristics for use in animal models. For example, multi-copy number genes have been frequently used to increase sensitivity but are subject to greater plasticity within the genome and thus may confound effects of experimental manipulations in animal models. In this study, we developed a sybr-green based quantitative touchdown PCR assay for a highly conserved and single-copy putative RNA-binding protein, DRBD3. With primers that share greater than 90% sequence identity across all sequenced Leishmania spp., we demonstrate that this assay has a lower limit of detection of 100 fg of parasite DNA for Leishmania major, L. donovani, L. venezuelensis, and L. panamensis. Using C57BL6/J mice, we used this assay to monitor parasite burden over 1 month of infection with two strains of L. major (Seidman and Friedlin), and L. venezeuelensis. These characteristics rival the sensitivity of previously reported qPCR based methods of parasite quantitation while amplifying a stable, single copy gene. Use of this protocol in the future will lead to improved accuracy in animal based models and help to tease apart differences in biology of host-parasite interactions.
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Affiliation(s)
- Alejandro L. Antonia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, NC, USA
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Skibiel AL, Peñagaricano F, Amorín R, Ahmed BM, Dahl GE, Laporta J. In Utero Heat Stress Alters the Offspring Epigenome. Sci Rep 2018; 8:14609. [PMID: 30279561 PMCID: PMC6168509 DOI: 10.1038/s41598-018-32975-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022] Open
Abstract
Exposure to intrauterine heat stress during late gestation affects offspring performance into adulthood. However, underlying mechanistic links between thermal insult in fetal life and postnatal outcomes are not completely understood. We examined morphology, DNA methylation, and gene expression of liver and mammary gland for bull calves and heifers that were gestated under maternal conditions of heat stress or cooling (i.e. in utero heat stressed vs. in utero cooled calves). Mammary tissue was harvested from dairy heifers during their first lactation and liver from bull calves at birth. The liver of in utero heat stressed bull calves contained more cells and the mammary glands of in utero heat stressed heifers were comprised of smaller alveoli. We identified more than 1,500 CpG sites differently methylated between maternal treatment groups. These CpGs were associated with approximately 400 genes, which play a role in processes, such as development, innate immune defense, cell signaling, and transcription and translation. We also identified over 100 differentially expressed genes in the mammary gland with similar functions. Interestingly, fifty differentially methylated genes were shared by both bull calf liver and heifer mammary gland. Intrauterine heat stress alters the methylation profile of liver and mammary DNA and programs their morphology in postnatal life, which may contribute to the poorer performance of in utero heat stressed calves.
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Affiliation(s)
- A L Skibiel
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - F Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - R Amorín
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - B M Ahmed
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - G E Dahl
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.
| | - J Laporta
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.
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Shin JH, Lee SE, Kim TS, Ma DW, Cho SH, Chai JY, Shin EH. Development of Molecular Diagnosis Using Multiplex Real-Time PCR and T4 Phage Internal Control to Simultaneously Detect Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis from Human Stool Samples. THE KOREAN JOURNAL OF PARASITOLOGY 2018; 56:419-427. [PMID: 30419727 PMCID: PMC6243187 DOI: 10.3347/kjp.2018.56.5.419] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 11/25/2022]
Abstract
This study aimed to develop a new multiplex real-time PCR detection method for 3 species of waterborne protozoan parasites (Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis) identified as major causes of traveler's diarrhea. Three target genes were specifically and simultaneously detected by the TaqMan probe method for multiple parasitic infection cases, including Cryptosporidium oocyst wall protein for C. parvum, glutamate dehydrogenase for G. lamblia, and internal transcribed spacer 1 for C. cayetanensis. Gene product 21 for bacteriophage T4 was used as an internal control DNA target for monitoring human stool DNA amplification. TaqMan probes were prepared using 4 fluorescent dyes, FAMTM, HEXTM, Cy5TM, and CAL Fluor Red® 610 on C. parvum, G. lamblia, C. cayetanensis, and bacteriophage T4, respectively. We developed a novel primer-probe set for each parasite, a primer-probe cocktail (a mixture of primers and probes for the parasites and the internal control) for multiplex real-time PCR analysis, and a protocol for this detection method. Multiplex real-time PCR with the primer-probe cocktail successfully and specifically detected the target genes of C. parvum, G. lamblia, and C. cayetanensis in the mixed spiked human stool sample. The limit of detection for our assay was 2×10 copies for C. parvum and for C. cayetanensis, while it was 2×103 copies for G. lamblia. We propose that the multiplex real-time PCR detection method developed here is a useful method for simultaneously diagnosing the most common causative protozoa in traveler's diarrhea.
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Affiliation(s)
- Ji-Hun Shin
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul 03080, Korea
| | - Sang-Eun Lee
- Division of Vectors and Parasitic Diseases, Korea Centers for Disease Control and Prevention, Cheongju 28159, Korea
| | - Tong Soo Kim
- Department of Tropical Medicine and Inha Research Institute for Medical Sciences, Inha University School of Medicine, Incheon 22212, Korea
| | - Da-Won Ma
- Division of Vectors and Parasitic Diseases, Korea Centers for Disease Control and Prevention, Cheongju 28159, Korea
| | - Shin-Hyeong Cho
- Division of Vectors and Parasitic Diseases, Korea Centers for Disease Control and Prevention, Cheongju 28159, Korea
| | - Jong-Yil Chai
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul 03080, Korea
| | - Eun-Hee Shin
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul 03080, Korea
- Seoul National University Bundang Hospital, Seongnam 13620, Korea
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Flaherty BR, Talundzic E, Barratt J, Kines KJ, Olsen C, Lane M, Sheth M, Bradbury RS. Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. MICROBIOME 2018; 6:164. [PMID: 30223888 PMCID: PMC6142370 DOI: 10.1186/s40168-018-0540-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/29/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Targeted amplicon deep sequencing (TADS) of the 16S rRNA gene is commonly used to explore and characterize bacterial microbiomes. Meanwhile, attempts to apply TADS to the detection and characterization of entire parasitic communities have been hampered since conserved regions of many conserved parasite genes, such as the 18S rRNA gene, are also conserved in their eukaryotic hosts. As a result, targeted amplification of 18S rRNA from clinical samples using universal primers frequently results in competitive priming and preferential amplification of host DNA. Here, we describe a novel method that employs a single pair of universal primers to capture all blood-borne parasites while reducing host 18S rRNA template and enhancing the amplification of parasite 18S rRNA for TADS. This was achieved using restriction enzymes to digest the 18S rRNA gene at cut sites present only in the host sequence prior to PCR amplification. RESULTS This method was validated against 16 species of blood-borne helminths and protozoa. Enzyme digestion prior to PCR enrichment and Illumina amplicon deep sequencing led to a substantial reduction in human reads and a corresponding 5- to 10-fold increase in parasite reads relative to undigested samples. This method allowed for discrimination of all common parasitic agents found in human blood, even in cases of multi-parasite infection, and markedly reduced the limit of detection in digested versus undigested samples. CONCLUSIONS The results herein provide a novel methodology for the reduction of host DNA prior to TADS and establish the validity of a next-generation sequencing-based platform for universal parasite detection.
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Affiliation(s)
- Briana R Flaherty
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
- Oak Ridge Institute for Science and Education, 100 ORAU Way, Oak Ridge, TN, 37830, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
- Oak Ridge Institute for Science and Education, 100 ORAU Way, Oak Ridge, TN, 37830, USA
| | - Kristine J Kines
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Christian Olsen
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA
| | - Meredith Lane
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
- IHRC, Inc., 2 Ravinia Drive, Atlanta, GA, 30346, USA
| | - Mili Sheth
- Biotechnology Core Facility, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Richard S Bradbury
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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Arroyo AS, López-Escardó D, Kim E, Ruiz-Trillo I, Najle SR. Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Sipiczki M, Horvath E, Pfliegler WP. Birth-and-Death Evolution and Reticulation of ITS Segments of Metschnikowia andauensis and Metschnikowia fructicola rDNA Repeats. Front Microbiol 2018; 9:1193. [PMID: 29946303 PMCID: PMC6005844 DOI: 10.3389/fmicb.2018.01193] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high degree of sequence diversity in the D1/D2 domains of two pulcherrimin-producing Metschnikowia (Saccharomycotina) species which appeared to evolve by reticulation. The major goals of this study were the examination of the diversity of the ITS segments and their evolution. We show that the ITS sequences of these species are not homogenized either, differ from each other by up to 38 substitutions and indels which have dramatic effects on the predicted secondary structures of the transcripts. The high intragenomic diversity makes the D1/D2 domains and the ITS spacers unsuitable for barcoding of these species and therefore the taxonomic position of strains previously assigned to them needs revision. By analyzing the genome sequence of the M. fructicola type strain, we also show that the rDNA of this species is fragmented, contains pseudogenes and thus evolves by the birth-and-death mechanism rather than by homogenisation, which is unusual in yeasts. The results of the network analysis of the sequences further indicate that the ITS regions are also involved in reticulation. M. andauensis and M. fructicola can form interspecies hybrids and their hybrids segregate, providing thus possibilities for reticulation of the rDNA repeats.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Eniko Horvath
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Walter P Pfliegler
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
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Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. mSphere 2018; 3:mSphere00092-18. [PMID: 29600282 PMCID: PMC5874442 DOI: 10.1128/msphere.00092-18] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/05/2018] [Indexed: 02/07/2023] Open
Abstract
A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon's second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults. IMPORTANCE We sought to identify the fungi that colonize healthy GI tracts and that have a sustained influence on the diverse functions of the gut microbiome. Instead, we found that all fungi in the stool of healthy volunteers could be explained by their presence in oral and dietary sources and that our results, together with those from other analyses, support the model that there is little or no gastrointestinal colonization by fungi. This may be due to Westernization, primate evolution, fungal ecology, and/or the strong defenses of a healthy immune system. Importantly, fungal colonization of the GI tract may often be indicative of disease. As fungi can cause serious infections in immunocompromised individuals and are found at increased abundance in multiple disorders of the GI tract, understanding normal fungal colonization is essential for proper treatment and prevention of fungal pathogenesis.
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Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev 2018; 42:293-323. [DOI: 10.1093/femsre/fuy006] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel 2000, Switzerland
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, Canada
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Straße, 67663 Kaiserslautern, Germany
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Avenida Viel 1497, Santiago, Chile
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, 37073 Göttingen, Germany
| | - David Singer
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, United States of America
| | - Julia Walochnik
- Molecular Parasitology, Institute of Tropical Medicine, Medical University, 1090 Vienna, Austria
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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43
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Seah BKB, Schwaha T, Volland JM, Huettel B, Dubilier N, Gruber-Vodicka HR. Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis. Proc Biol Sci 2018; 284:rspb.2017.0764. [PMID: 28701560 PMCID: PMC5524500 DOI: 10.1098/rspb.2017.0764] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/06/2017] [Indexed: 12/03/2022] Open
Abstract
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected in the Mediterranean and Caribbean, and symbiont sequences from 13 of these morphospecies. We discovered a new Kentrophoros morphotype where the symbiont-bearing surface is folded into pouch-like compartments, illustrating the variability of the basic body plan. Phylogenetic analyses revealed that all investigated Kentrophoros belonged to a single clade, despite the remarkable morphological diversity of these hosts. The symbionts were also monophyletic and belonged to a new clade within the Gammaproteobacteria, with no known cultured representatives. Each host morphospecies had a distinct symbiont phylotype, and statistical analyses revealed significant support for host–symbiont codiversification. Given that these symbioses were collected from two widely separated oceans, our results indicate that symbiotic associations in unicellular hosts can be highly specific and stable over long periods of evolutionary time.
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Affiliation(s)
- Brandon K B Seah
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Thomas Schwaha
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jean-Marie Volland
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
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Identification of bat trypanosomes from Minas Gerais state, Brazil, based on 18S rDNA and Cathepsin-L-like targets. Parasitol Res 2018; 117:737-746. [PMID: 29340783 DOI: 10.1007/s00436-017-5744-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/29/2017] [Indexed: 10/18/2022]
Abstract
Several bat species can be infected by trypanosomes, but there is not much information about which of these parasites infect bats from Triângulo Mineiro and Alto Paranaíba, Minas Gerais state, Brazil, a formerly endemic region for Trypanosoma cruzi, the causative agent of Chagas disease. The aim of this study was to describe, characterize, and identify the presence of trypanosomes in bats. The captured bats (448) belong to four families and to 19 different species. Of those, 37 bats were found to be positive for trypanosomes by microhematocrit, (infection rate 8.3%) and 27 were positive after hemoculture analysis. Initially, the isolates were identified by PCR (18S rDNA, 24Sα rDNA, spliced leader, COII RFLP-PCR) using primers originally designed for T. cruzi. PCRs (18S rDNA, 24Sα rDNA) showed compatible bands for TcI, whereas COII RFLP-PCR showed a similar pattern associated to TcII. However, there was no DNA amplification using spliced leader as a target, revealing a discrepancy between the results. Phylogenetic analysis of Cathepsin L-like and 18S rDNA sequences proved that 15 of the isolates corresponded to Trypanosoma cruzi marinkellei and one to Trypanosoma dionisii. These results revealed that the diversity of trypanosome species in a region considered endemic for Chagas disease is greater than previous descriptions. All this can confirm the necessity of using DNA sequencing approaches in order to determinate trypanosomes species isolated from bats.
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45
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Tucker SJ, McManus GB, Katz LA, Grattepanche JD. Distribution of Abundant and Active Planktonic Ciliates in Coastal and Slope Waters Off New England. Front Microbiol 2017; 8:2178. [PMID: 29250036 PMCID: PMC5715329 DOI: 10.3389/fmicb.2017.02178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 10/23/2017] [Indexed: 11/18/2022] Open
Abstract
Despite their important role of linking microbial and classic marine food webs, data on biogeographical patterns of microbial eukaryotic grazers are limited, and even fewer studies have used molecular tools to assess active (i.e., those expressing genes) community members. Marine ciliate diversity is believed to be greatest at the chlorophyll maximum, where there is an abundance of autotrophic prey, and is often assumed to decline with depth. Here, we assess the abundant (DNA) and active (RNA) marine ciliate communities throughout the water column at two stations off the New England coast (Northwest Atlantic)—a coastal station 43 km from shore (40 m depth) and a slope station 135 km off shore (1,000 m). We analyze ciliate communities using a DNA fingerprinting technique, Denaturing Gradient Gel Electrophoresis (DGGE), which captures patterns of abundant community members. We compare estimates of ciliate communities from SSU-rDNA (abundant) and SSU-rRNA (active) and find complex patterns throughout the water column, including many active lineages below the photic zone. Our analyses reveal (1) a number of widely-distributed taxa that are both abundant and active; (2) considerable heterogeneity in patterns of presence/absence of taxa in offshore samples taken 50 m apart throughout the water column; and (3) three distinct ciliate assemblages based on position from shore and depth. Analysis of active (RNA) taxa uncovers biodiversity hidden to traditional DNA-based approaches (e.g., clone library, rDNA amplicon studies).
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Affiliation(s)
- Sarah J Tucker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, United States
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46
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Borg Dahl M, Brejnrod AD, Unterseher M, Hoppe T, Feng Y, Novozhilov Y, Sørensen SJ, Schnittler M. Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies. Mol Ecol Resour 2017; 18:306-318. [PMID: 29024429 DOI: 10.1111/1755-0998.12725] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 09/26/2017] [Accepted: 10/01/2017] [Indexed: 12/18/2022]
Abstract
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Asker D Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Thomas Hoppe
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yun Feng
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
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47
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Moreno Y, Moreno-Mesonero L, Amorós I, Pérez R, Morillo JA, Alonso JL. Multiple identification of most important waterborne protozoa in surface water used for irrigation purposes by 18S rRNA amplicon-based metagenomics. Int J Hyg Environ Health 2017; 221:102-111. [PMID: 29066287 DOI: 10.1016/j.ijheh.2017.10.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/04/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
Understanding waterborne protozoan parasites (WPPs) diversity has important implications in public health. In this study, we evaluated a NGS-based method as a detection approach to identify simultaneously most important WPPs using 18S rRNA high-throughput sequencing. A set of primers to target the V4 18S rRNA region of WPPs such as Cryptosporidium spp., Giardia sp., Blastocystis sp., Entamoeba spp, Toxoplasma sp. and free-living amoebae (FLA) was designed. In order to optimize PCR conditions before sequencing, both a mock community with a defined composition of representative WPPs and a real water sample inoculated with specific WPPs DNA were prepared. Using the method proposed in this study, we have detected the presence of Giardia intestinalis, Acanthamoeba castellanii, Toxoplasma gondii, Entamoeba histolytica and Blastocystis sp. at species level in real irrigation water samples. Our results showed that untreated surface irrigation water in open fields can provide an important source of WPPs. Therefore, the methodology proposed in this study can establish a basis for an accurate and effective diagnostic of WPPs to provide a better understanding of the risk associated to irrigation water.
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Affiliation(s)
- Y Moreno
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - L Moreno-Mesonero
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - I Amorós
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - R Pérez
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - J A Morillo
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (EEZA-CSIC), Carretera de Sacramento s/n, La Cañada, Almería, Spain
| | - J L Alonso
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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Polinski MP, Meyer GR, Lowe GJ, Abbott CL. Seawater detection and biological assessments regarding transmission of the oyster parasite Mikrocytos mackini using qPCR. DISEASES OF AQUATIC ORGANISMS 2017; 126:143-153. [PMID: 29044044 DOI: 10.3354/dao03167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mikrocytos mackini is an intracellular parasite of oysters and causative agent of Denman Island disease in Pacific oysters Crassostrea gigas. Although M. mackini has been investigated for decades, its natural mode of transmission, mechanism for host entry, and environmental stability are largely unknown. We explored these biological characteristics of M. mackini using a recently described quantitative PCR (qPCR) assay. We detected M. mackini in the flow-through tank water of experimentally infected oysters and during disease remission in host tissues following 6 wk of elevated water temperature. Waterborne exposure of oysters to M. mackini further confirmed the potential for extracellular seawater transmission of this parasite and also identified host gill to have the highest early and continued prevalence for M. mackini DNA compared to stomach, mantle, labial palps, or adductor muscle samples. However, infections following waterborne challenge were slow to develop despite a substantial exposure (>106 M. mackini l-1 for 24 h), and further investigation demonstrated that M. mackini occurrence and infectivity severely declined following extracellular seawater incubation of more than 24 h. This study demonstrates a potential for using qPCR to monitor M. mackini in wild or farmed oyster populations during periods of disease remission or from environmental seawater samples. This work also suggests that gill tissues may provide a primary site for waterborne entry and possibly shedding of M. mackini in oysters. Further, although extracellular seawater transmission of M. mackini was possible, poor environmental stability and infection efficiency likely restricts the geographic transmission of M. mackini between oysters in natural environs and may help to explain localized areas of infection.
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Affiliation(s)
- Mark P Polinski
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
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Eyvazi S, Kazemi B, Bandehpour M, Dastmalchi S. Identification of a novel single chain fragment variable antibody targeting CD24-expressing cancer cells. Immunol Lett 2017; 190:240-246. [DOI: 10.1016/j.imlet.2017.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 05/29/2017] [Accepted: 08/28/2017] [Indexed: 02/06/2023]
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50
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Feng X, Norose K, Li K, Hikosaka K. Utility of the cytochrome c oxidase subunit I gene for the diagnosis of toxoplasmosis using PCR. J Microbiol Methods 2017; 141:82-86. [PMID: 28803790 DOI: 10.1016/j.mimet.2017.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/23/2017] [Accepted: 08/06/2017] [Indexed: 11/26/2022]
Abstract
Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii, which belongs to the phylum Apicomplexa. Since this parasite causes severe clinical symptoms in immunocompromised patients, early diagnosis of toxoplasmosis is essential. PCR is currently used for early diagnosis, but there is no consensus regarding the most effective method for amplifying Toxoplasma DNA. In this study, we considered the utility of the cytochrome c subunit I (cox1) gene, which is encoded in the mitochondrial DNA of this parasite, as a novel target of PCR for the diagnosis of toxoplasmosis. To do this, we compared its copy number per haploid nuclear genome and the detection sensitivity of cox1-PCR with the previously reported target genes B1 and 18S rRNA and the AF146527 repeat element. We found that the copy number of cox1 was high and that the PCR using cox1 primers was more efficient at amplifying Toxoplasma DNA than the other PCR targets examined. In addition, PCR using clinical samples indicated that the cox1 gene would be useful for the diagnosis of toxoplasmosis. These findings suggest that use of cox1-PCR would facilitate the diagnosis of toxoplasmosis in clinical laboratories.
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Affiliation(s)
- Xue Feng
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Kazumi Norose
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Kexin Li
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Kenji Hikosaka
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan.
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