scholarly journals Molecular Identification and Hidden Diversity of Novel Daphnia Parasites from European Lakes

2009 ◽  
Vol 75 (22) ◽  
pp. 7051-7059 ◽  
Author(s):  
Justyna Wolinska ◽  
Sabine Giessler ◽  
Henrike Koerner
Keyword(s):  
Sequence Variation ◽  
Local Population ◽  
Its Region ◽  
Small Subunit ◽  
Diagnostic Tools ◽  
Rrna Gene ◽  
Natural Systems ◽  
Parasite Communities ◽  
Host Parasite ◽  
Sequence Similarities

ABSTRACT Parasites play important roles in local population dynamics and genetic structure. However, due to insufficient diagnostic tools, detailed host-parasite interactions may remain concealed by hidden parasite diversity in natural systems. Microscopic examination of 19 European lake Daphnia populations revealed the presence of three groups of parasites: fungi, microsporidia, and oomycetes. For most of these parasites no genetic markers have been described so far. Based on sequence similarities of the nuclear small-subunit and internal transcribed spacer (ITS) rRNA gene regions, one fungus, four microsporidian, and nine oomycete taxa were discovered in 147 infected Daphnia (and/or three other zooplankton crustaceans). Additionally, cloning of rRNA gene regions revealed parasite sequence variation within host individuals. This was most pronounced in the ITS region of one microsporidian taxon, where the within-host sequence variation ranged from 1.7% to 5.3% polymorphic sites for parasite isolates from 14 different geographical locations. Interestingly, the parasite isolates from close locations grouped together based on sequence similarities, suggesting that there was parasite dispersal. Taken together, the data obtained in this study revealed hidden diversity of parasite communities in Daphnia lake populations. Moreover, a higher level of resolution for identifying parasite strains makes it possible to test new hypotheses with respect to parasite dispersal, transmission routes, and coinfection.

Community-Level Interactions and Disease Dynamics

2021 ◽  
pp. 145-170
Author(s):  
Karen D. McCoy
Keyword(s):  
Local Area ◽  
Community Level ◽  
Disease Dynamics ◽  
Biological Communities ◽  
Natural Systems ◽  
Parasite Communities ◽  
Almost All ◽  
Host Parasite ◽  
Natural Communities ◽  
Over Time

An ecological community includes all individuals of all species that interact within a single patch or local area of habitat. Understanding the outcome of host–parasite interactions and predicting disease dynamics is particularly challenging at this biological scale because the different component species interact both directly and indirectly in complex ways. Current shifts in biodiversity due to global change, and its associated modifications to biological communities, will alter these interactions, including the probability of disease emergence, its dynamics over time, and its community-level consequences. Birds are integral component species of almost all natural communities. Due to their ubiquity and specific life history traits, they are defining actors in the ecology, evolution, and epidemiology of parasitic species. To better understand this role, this chapter examines the relative importance of birds and parasites in natural communities, revisiting basic notions in community ecology. The impact of changes in diversity for disease dynamics, including the debate surrounding dilution and amplification effects are specifically addressed. By considering the intrinsic complexities of natural communities, the importance of combining data from host and parasite communities to better understand how natural systems function over time and space is highlighted. The different elements in each section of the chapter are illustrated with brief, concrete examples from avian species, with a detailed example from marine bird communities in which Lyme disease bacteria circulate.

scholarly journals Small Subunit Ribosomal DNA Sequence ShowsParacoccidioides brasiliensis Closely Related toBlastomyces dermatitidis

2000 ◽  
Vol 38 (9) ◽  
pp. 3190-3193 ◽  
Author(s):  
Ralf Bialek ◽  
Aida Ibricevic ◽  
Annette Fothergill ◽  
Dominik Begerow
Keyword(s):  
Histoplasma Capsulatum ◽  
Paracoccidioides Brasiliensis ◽  
Large Subunit ◽  
Close Relation ◽  
Small Subunit ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Rrna Gene ◽  
Dimorphic Fungus ◽  
The Family

The similarities of paracoccidioidomycosis and blastomycosis are highly suggestive of a close relation of the two etiological agents. Whereas the agent of the first disease is exclusively endemic in Latin America, the agent of the latter one is endemic in North America and Africa. In symptomatic travelers visiting both areas of endemicity, differentiation of the diseases might be impossible, even though therapy and prognosis for these two diseases differ significantly. In order to identify differences in the 18S rRNA gene (rDNA) for use as molecular diagnostic tools, we sequenced this gene from five isolates of Paracoccidioides brasiliensis and compared them to known sequences of other fungi. Neighbor-joining, maximum parsimony, and maximum likelihood analyses and, finally, the Kishino-Hasegawa test revealed that P. brasiliensis, Blastomyces dermatitidis, and Emmonsia parva are more closely related than Histoplasma capsulatum and B. dermatitidis, whose teleomorphic forms belong to one genus,Ajellomyces. In accordance with the work of other investigators who have used internal transcribed spacer and large subunit rDNA sequences, our small subunit rDNA data show that the dimorphic fungus P. brasiliensis must be grouped within the order Onygenales and is closely related to members of the family Onygenaceae. There are hints in the molecular phylogenetic analysis that the family Onygenaceae might be further divided into two families. The subgroup that includes P. brasiliensis comprises all zoopathogenic species. The differences in the 18S rDNAs appear to be too small to allow species identification of the members of the family Onygenaceae pathogenic for humans by use of target sequences within this gene.

Genetic differentiation within the Paralia longispina (Bacillariophyta) species complex

Botany ◽  
2012 ◽  
Vol 90 (3) ◽  
pp. 205-222 ◽  
Author(s):  
Michael L. MacGillivary ◽  
Irena Kaczmarska
Keyword(s):  
Large Subunit ◽  
Morphological Diversity ◽  
Its Region ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Tropical Species ◽  
Rrna Gene ◽  
Rbcl Gene ◽  
Extant Species ◽  
Practical Implications

We report on undiscovered genetic and morphological diversity within a diatom taxon known as Paralia longispina and propose three new, extant species of Paralia — Paralia allisonii sp. nov., Paralia crawfordii sp. nov., and Paralia ehrmanii sp. nov. — obtained from subtropical and tropical coasts of the Atlantic and Pacific oceans. Comprehensive examination and hierarchical clustering of frustule characters separated these three species from each other and from P. longispina. Each species possessed one or two unique morphological diagnostic characters. The internal transcribed spacer (ITS) region and a fragment of the small subunit (18S rRNA gene) of nuclear encoded rRNA and a portion of the 5′ end of the large subunit of the ribulose bisophosphate carboxylase (rbcL) gene of the chloroplast genome were related to the morphological groupings of monoclonal isolates of P. allisonii and P. crawfordii. The ITS2 secondary structure of the cultured clones of these two species had four helices. They differed by five hemicompensatory base changes (HCBCs) and substantial changes to the distal end of helix I, the region between helix II and helix III, and nearly all of helix IV. Our results better our understanding of the distribution of subtropical and tropical species of Paralia and have practical implications for the conservation of native microbial florae and for the possibility of ship ballast in human-mediated dispersal of these diatoms.

Genetic variation in relation to substratum preferences of Hypogymnia physodes

2009 ◽  
Vol 41 (5) ◽  
pp. 547-555 ◽  
Author(s):  
Jan-Eric MATTSSON ◽  
Anne-Charlotte HANSSON ◽  
Louise LINDBLOM
Keyword(s):  
Dna Sequences ◽  
Sequence Variation ◽  
Its Region ◽  
Small Subunit ◽  
Hypogymnia Physodes ◽  
Gene Fragment ◽  
Statistical Parsimony ◽  
Total Dna ◽  
Study Sites ◽  
Group 1

AbstractGenetic variability and its relationship to substratum preferences within and among populations of the sorediate foliose lichen Hypogymnia physodes was investigated using sequence variation in the complete nrDNA internal transcribed spacer (ITS) region. A few samples of the putatively closely related, sorediate, H. tubulosa were also included. Samples were collected from each tree species in study sites in Estonia, Finland, and Sweden. In total, DNA sequences from 104 individuals of H. physodes and 16 of H. tubulosa were obtained. A group 1 intron situated at the end of the small subunit (SSU) of the nrDNA was detected in both species. Within-species variability was observed in both species: fifteen haplotypes were found for H. physodes and seven for H. tubulosa for the combined alignment of the intron and the ITS. Possible recombination within the total gene fragment was detected and hence the different regions (intron, ITS1, 5.8S, ITS2) were analysed separately. They show a different degree of variability both between each other and between the species. The number of haplotypes of H. physodes in the four regions are 5, 5, 1, and 5 and for H. tubulosa 5, 2, 1 and 2, respectively. A statistical parsimony estimation resulted in two unconnected networks; one containing all the samples of H. physodes and one containing all H. tubulosa samples. It was not possible to show different potentials of the different haplotypes for establishment on different substrata as the network of H. physodes indicates recombination within the ITS region which may be frequent enough to make this primarily clonally reproducing species to behave like a sexual species.

scholarly journals Nakazawaea Odontotermitis f.a., sp. nov., a Novel Yeast Isolated from the Gut of Odontotermes Horni in India.

2021 ◽  
Author(s):  
Snigdha Tiwari ◽  
Bhaskar C. Behera ◽  
Abhishek Baghela
Keyword(s):  
New Species ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Its Region ◽  
Small Subunit ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
Ascomycetous Yeast ◽  
Lsu Rrna Gene

Abstract Three strains SMT1.3, SMT1.10, and SMT2.2, representing a novel asexual ascomycetous yeast species, were isolated from the gut of a termite Odontotermes horni in Maharashtra, India. Phylogenetic analyses of the LSU, ITS and SSU sequences revealed that they belonged to the genus Nakazawaea, with N. siamensis as the closest relative. The new species differed from the type strain of N. siamensis (DMKU-RK467T) by 1.93% nucleotide substitutions in the D1/D2 region of the large subunit (LSU) rRNA gene, 0.53% nucleotide substitutions in the small subunit (SSU) rRNA gene and 12.6% nucleotide substitutions in the internal transcribed spacer (ITS) region. Notable physiological differences were also observed between N. siamensis and the new species. Hence, the species Nakazawaea odontotermitis f.a., sp. nov. is proposed. The type strain is SMT1.3T (MTCC 13105 = NFCCI 5011). The GenBank accession numbers of the LSU and ITS and SSU sequences of Nakazawaea odontotermitis f.a., sp. nov. are MZ234240, MZ234239 and OK384663. The MycoBank number is MB 841926.

scholarly journals “Enterocytozoon bieneusi and Cryptosporidium: a cross-sectional study conducted throughout Thailand”

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Rapeepun Prasertbun ◽  
Hirotake Mori ◽  
Yaowalark Sukthana ◽  
Supaluk Popruk ◽  
Teera Kusolsuk ◽  
...  
Keyword(s):  
Rural Areas ◽  
Its Region ◽  
Epidemiological Data ◽  
Cross Sectional Study ◽  
Small Subunit ◽  
Enterocytozoon Bieneusi ◽  
Rrna Gene ◽  
Intestinal Protozoa ◽  
Cross Sectional ◽  
Epidemiological Characteristics

Abstract Background Enterocytozoon bieneusi and Cryptosporidium spp. are prevalent zoonotic parasites associated with a high burden among children. To date only limited molecular epidemiological data on E. bieneusi and Cryptosporidium spp. in humans living in Thailand has been published. Methods PCR-based tools were used to detect and characterize E. bieneusi and Cryptosporidium spp. The internal transcribed spacer (ITS) region of the rRNA gene was used to investigate E. bieneusi, and the small subunit (SSU) rRNA gene was used to investigate Cryptosporidium spp., and 697 fecal samples from villagers and school children in rural areas in Thailand were analyzed. Results The infection rates were 2.15% (15/697) for E. bieneusi and 0.14% (1/697) for Cryptosporidium spp. The prevalence of E. bieneusi was significantly high in Loei province. Sequence analysis indicated that the Cryptosporidium isolate was C. parvum. Nine E. bieneusi genotypes were identified, EbpC, Peru12, TMH6, TMH3, TMH7, H, D, and two novel genotypes TMLH1 and TMLH2. E. bieneusi prevalence was significantly higher in male participants than in female participants, and in children aged 3–15 years than in participants aged > 15 years. Conclusions The prevalence, genotypes, and zoonotic potential of E. bieneusi were found to vary significantly high even in one country. Transmission routes and key animal carriers of E. bieneusi may be associated with differences in hygiene, sanitation, and cultural behaviors. Further molecular studies including longitudinal studies will be required to unveil epidemiological characteristics of these opportunistic intestinal protozoa in all over the countries.

scholarly journals Suhomyces drosophilae sp. nov., isolated from Drosophila flies feeding on a stinkhorn mushroom

2020 ◽  
Vol 70 (9) ◽  
pp. 4908-4913
Author(s):  
Reshma Jadhav ◽  
Snigdha Tiwari ◽  
Rameshwar Avchar ◽  
Marizeth Groenewald ◽  
Abhishek Baghela
Keyword(s):  
Sequence Variation ◽  
Biochemical Characterization ◽  
Novel Species ◽  
Large Subunit ◽  
Its Region ◽  
Rrna Gene ◽  
The Novel ◽  
Nucleotide Substitutions ◽  
Yeast Strains ◽  
Large Subunit Rrna

The majority of Suhomyces species have been isolated from fungus-feeding insects and particularly from the gut of beetles. In the present study, seven yeast strains were isolated from the gut of Drosophila species feeding on gleba, the spore-bearing inner mass, of a stinkhorn mushroom belonging to the family Phallaceae. Based on phenotypic, biochemical characterization and sequence analysis of the D1/D2 region of the large subunit rRNA gene and the internal transcribed spacer (ITS) region, two of these yeast strains, DGY3 and DGY4, represented a novel species of the genus Suhomyces. The novel species is closely related to an undescribed species of Candida ST-370 (DQ404513) and with Suhomyces canberraensis, wherein, the novel species differs from S. canberraensis by 40 nucleotide substitutions and three gaps (7.7 % sequence variation) in the D1/D2 region and 50 nucleotide substitutions and seven gaps (13.7 % sequence variation) in the ITS region. Several morphological and physiological differences were also observed between S. canberraensis and the strains obtained during this study. These data support the proposal of Suhomyces drosophilae as a novel species, with DGY3T as the holotype and CBS 16329T and MCC 1871T as ex-type strains.

Molecular detection of Murshidia linstowi in a free-ranging dead elephant calf

2020 ◽  
Vol 12 (3) ◽  
pp. 15359-15363
Author(s):  
Sourabh Ranjan Hota ◽  
Sonali Sahoo ◽  
Manojita Dash ◽  
Avishek Pahari ◽  
Bijayendranath Mohanty ◽  
...  
Keyword(s):  
Average Length ◽  
Its Region ◽  
Buccal Capsule ◽  
Nematode Species ◽  
Phylogenetic Study ◽  
Gastrointestinal Helminths ◽  
Pcr Product ◽  
Maximum Similarity ◽  
Host Parasite ◽  
Free Ranging

Gastrointestinal helminths are ubiquitous in both domestic and wild animals. Infections are often sub-clinical except in circumstances of destabilization of host-parasite equilibrium by innate or environmental factors. The present case deals with microscopic and molecular diagnosis of Murshidia linstowi recovered from an elephant. A post-mortem examination of a free-ranging juvenile male elephant calf that had died of electrocution in Athagarh Wildlife Division revealed the presence of slender, whitish nematodes in the stomach. No gross lesions were noticed either in the site of predilection or any other internal organs. The average length of the parasites was 3.8cm.  These parasites were collected for further gross as well as microscopic examination following routine parasitological techniques. Temporary mounts prepared after cleaning the nematodes in lactophenol were observed under a microscope. Morphological features such as a well-developed mouth collar, large and globular buccal capsule with fine tubercles, cone shaped oesophageal funnel, short bursa having indistinctly divided lobes and closely apposed ventral rays and stout spicules with club shaped tips bent dorsally corroborated with that of M.linstowi (male). Amplification of the rDNA from the internal transcribed spacer (ITS) region using universal nematode primers NC2 and NC5 revealed a product size of 870bp. The PCR product was subjected to sequencing followed by NCBI-BLAST which revealed 98% homology with M. linstowi. A phylogenetic study showed a maximum similarity with M.linstowi recovered from elephants in Kenya. This particular nematode species belonging to the family Strongylidae and sub-family Cyathostominae appears to be the first documented report in India.

scholarly journals New Chitosan-Degrading Strains That Produce Chitosanases Similar to ChoA of Mitsuaria chitosanitabida

2005 ◽  
Vol 71 (9) ◽  
pp. 5138-5144 ◽  
Author(s):  
ChoongSoo Yun ◽  
Daiki Amakata ◽  
Yasuhiro Matsuo ◽  
Hideyuki Matsuda ◽  
Makoto Kawamukai
Keyword(s):  
Southern Hybridization ◽  
Glycosyl Hydrolase ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Glycosyl Hydrolase Family ◽  
Broad Variety ◽  
Hydrolase Family ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

ABSTRACT The betaproteobacterium Mitsuaria chitosanitabida (formerly Matsuebacter chitosanotabidus) 3001 produces a chitosanase (ChoA) that is classified in glycosyl hydrolase family 80. While many chitosanase genes have been isolated from various bacteria to date, they show limited homology to the M. chitosanitabida 3001 chitosanase gene (choA). To investigate the phylogenetic distribution of chitosanases analogous to ChoA in nature, we identified 67 chitosan-degrading strains by screening and investigated their physiological and biological characteristics. We then searched for similarities to ChoA by Western blotting and Southern hybridization and selected 11 strains whose chitosanases showed the most similarity to ChoA. PCR amplification and sequencing of the chitosanase genes from these strains revealed high deduced amino acid sequence similarities to ChoA ranging from 77% to 99%. Analysis of the 16S rRNA gene sequences of the 11 selected strains indicated that they are widely distributed in the β and γ subclasses of Proteobacteria and the Flavobacterium group. These observations suggest that the ChoA-like chitosanases that belong to family 80 occur widely in a broad variety of bacteria.

scholarly journals Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions

2020 ◽  
Vol 9 (1) ◽  
pp. 21
Author(s):  
Abdul Ghafar ◽  
Anson V. Koehler ◽  
Ross S. Hall ◽  
Charles G. Gauci ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Water Buffalo ◽  
Hypervariable Region ◽  
Small Subunit ◽  
Rrna Gene ◽  
Next Generation ◽  
Small Subunit Rrna ◽  
Tropical Theileriosis ◽  
Ecological Zones ◽  
Generation Sequencing

Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.

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