Pseudomonas mandelii SW-3, isolated from the Napahai plateau wetland, can survive in cold environments. The mechanisms underlying the survival of bacteria in low temperatures and high altitudes are not yet fully understood. In this study, the whole genome of SW-3 was sequenced to identify the genomic features that may contribute to survival in cold environments. The results showed that the genome size of strain SW-3 was 6,538,059 bp with a GC content of 59%. A total of 67 tRNAs, a 34,110 bp prophage sequence, and a large number of metabolic genes were found. Based on 16S rRNA gene phylogeny and average nucleotide identity analysis among P. mandelii, SW-3 was identified as a strain belonging to P. mandelii. In addition, we clarified the mechanisms by which SW-3 survived in a cold environment, providing a basis for further investigation of host-phage interaction. P. mandelii SW-3 showed stress resistance mechanisms, including glycogen and trehalose metabolic pathways, and antisense transcriptional silencing. Furthermore, cold shock proteins and glucose 6-phosphate dehydrogenase may play pivotal roles in facilitating adaptation to cold environmental conditions. The genome-wide analysis provided us with a deeper understanding of the cold-adapted bacterium.
- MeSH
- DNA, Bacterial genetics MeSH
- Phylogeny * MeSH
- Adaptation, Physiological * genetics MeSH
- Genome, Bacterial * MeSH
- Cold Temperature * MeSH
- Prophages genetics MeSH
- Pseudomonas * genetics classification MeSH
- RNA, Ribosomal, 16S * genetics MeSH
- Whole Genome Sequencing MeSH
- Base Composition MeSH
- Publication type
- Journal Article MeSH
The two stork species that nest in Central Europe, Ciconia ciconia and Ciconia nigra, have been repeatedly shown to host the digenetic trematode Cathaemasia hians (Rudolphi, 1809) in their esophagus and muscular stomach. These host species differ in their habitat and food preferences, and the morphologic characters of C. hians isolates ex Ci. nigra and Ci. ciconia are not identical. These differences led to a previous proposal of two subspecies, Cathaemasia hians longivitellata Macko, 1960, and Cathaemasia hians hians Macko, 1960. We hypothesize that the Cathaemasia hians isolates ex Ci. nigra and Ci. ciconia represent two independent species. Therefore, in the present study, we performed the first molecular analyses of C. hians individuals that were consistent with the diagnosis of C. hians hians (ex Ci. nigra) and C. hians longivitellata (ex Ci. ciconia). The combined molecular and comparative morphological analyses of the central European Cathaemasia individuals ex Ci. nigra and Ci. ciconia led to the proposal of a split of C. hians into C. hians sensu stricto (formerly C. hians hians) and C. longivitellata sp. n. (formerly C. hians longivitellata). Morphological analyses confirmed that the length of the vitellaria is the key identification feature of the two previously mentioned species. Both Cathaemasia spp. substantially differ at the molecular level and have strict host specificity, which might be related to differences in the habitat and food preferences of the two stork species.
- MeSH
- DNA, Helminth genetics MeSH
- Species Specificity MeSH
- Phylogeny * MeSH
- Host Specificity * MeSH
- Birds parasitology MeSH
- Trematoda * anatomy & histology classification genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
In this study, we use an integrative taxonomic approach to redescribe Schyzocotyle nayarensis (Malhotra, 1983) (Cestoda: Bothriocephalidae), based on newly collected specimens from the type-host Raiamas bola (Hamilton, 1822) (Cypriniformes: Danionidae) in Fulbari, Siliguri, West Bengal, India. The detailed morphological assessment, from whole mounts, histology and scanning electron microscopy, offers additional insights into the scolex structure, vitelline follicles, and egg morphology. Molecular data from this and previous studies corroborate the identity and systematics of S. nayarensis as a bothriocephalid closely related to the Asian Fish Tapeworm, Schyzocotyle acheilognathi (Yamaguti, 1934). This study elucidates the historical context and taxonomic ambiguities surrounding S. nayarensis, emphasizing the key role of the scolex in both generic and species identification. Amendments to the diagnosis of Schyzocotyle Akhmerov, 1960 are proposed. A differential diagnosis of the two valid species within the genus, namely S. acheilognathi and S. nayarensis, is also provided. An evaluation of the taxonomic status of Bothriocephalus teleostei Malhotra, 1984, and Capooria barilii Malhotra, 1985 suggests that they may be S. nayarensis. Finally, we posit that none of the ten species of Ptychobothrium Lönnberg, 1889 described from Indian freshwater teleosts belong to this genus but instead appear to be a mix of species belonging to Schyzocotyle, Senga Dollfus, 1934, and possibly even Proteocephalidae La Rue, 1911; all require further study based on newly collected, properly fixed specimens and an integrated taxonomic approach. Finally, future survey studies may reveal hidden diversity of Schyzocotyle species in Indian cyprinoids.
- MeSH
- Cestoda * classification anatomy & histology ultrastructure isolation & purification genetics MeSH
- Cestode Infections * veterinary parasitology MeSH
- Phylogeny * MeSH
- Cypriniformes parasitology MeSH
- Microscopy, Electron, Scanning * veterinary MeSH
- Fish Diseases * parasitology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- India MeSH
Species of the genus Morishitium Witenberg, 1928 are parasites of the body cavity, air sacs, and lungs of birds. At least 14 species are considered valid, but molecular confirmation of their status is lacking. Here, we provide the first molecular data on Morishitium dollfusi isolated from their type host Pica pica, compared them with previously reported molecular data from Morishitium polonicum isolated from their type and paratype hosts, Turdus merula and Turdus philomelos, and performed extensive measurements of 511 individuals of Morishitium spp. across a broad host spectrum, at multiple infection intensities, and year-round. We analyzed the molecular phylogenetics of Morishitium spp. adults isolated from bird hosts of Czech origin and provide comparative measurements of the analyzed specimens. Based on the molecular examination of morphologically identified specimens of M. dollfusi and M. polonicum (CO1, ND1, and ITS2 markers), we propose synonymization of Morishitium dollfusi (Timon-David, 1950) with Morishitium polonicum (Machalska, 1980) (isolates of European origin). The three markers were either identical (CO1, ITS2) or formed haplotypes shared by the two species (ND1). Morphological analyses revealed a continuum of key identification features for the two above-named species, although we used specimens matching the original descriptions and isolated them from the type hosts. Therefore, Morishitium polonicum is a junior synonym of Morishitium dollfusi. Attention is needed regarding the status of East Asian isolates identified previously as M. polonicum (or M. polonicum malayense). The molecular analysis revealed that these isolates form a distinct clade, and further research is needed to produce data allowing the likely separation of the malayense clade as a separate species.
This paper represents the results of screening a diversity of fungal endophytes associated with Vitis vinifera leaves and canes in the Czech Republic. The characterization of strains is based on morphological and phylogenetic analyses of ITS, EF1α and TUB2 sequence data. Our strain selection covers 16 species and seven orders belonging to Ascomycota and Basidiomycota. Together with ubiquitous fungi, we report on several poorly known plant-associated fungi, Angustimassarina quercicola (= A. coryli, a synonym proposed in this study) and Pleurophoma pleurospora. Other species, such as Didymella negriana, D. variabilis, Neosetophoma sp. (species identical or sister to N. rosae), Phragmocamarosporium qujingensis and Sporocadus rosigena, have so far been little known and rarely found, but are frequent on V. vinifera in different parts of the world and obviously belong to a microbiota with a strong preference for this plant. Detailed taxonomical identification allowed us to identify species with apparent stable associations with V. vinifera, for which further interactions with V. vinifera can be expected. Our study is the first to focus on V. vinifera endophytes in Central Europe and expands the knowledge about their taxonomy, ecology and geography.
- MeSH
- Basidiomycota * MeSH
- Endophytes genetics MeSH
- Phylogeny MeSH
- Fungi MeSH
- Vitis * microbiology MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined and verified using high-throughput sequencing. The genomic organization of BCRV2 was characteristic of cytorhabdoviruses (family Rhabdoviridae) and included seven genes: 3 ́- N-P ́-P-P3-M-G-L -5 ́. BLASTP analysis revealed that the putative L protein had the highest amino acid sequence identity (75 %) with strawberry virus 2. BCRV2 was detected in Cryptomyzusgaleopsidis, but efficient transmission by this aphid was not confirmed. Of note, we observed coinfection of the KB1 line with blackcurrant-associated rhabdovirus (BCaRV) by RT-PCR. This is likely the first evidence of the presence of a cyto- and a nucleorhabdovirus in a single host.
The genus Cytorhabdovirus includes plant viruses with an unsegmented, single-stranded, negative-sense RNA genome that infect various plant hosts. In this work, we report the detection of a new cytorhabdovirus infecting elderberry (Sambucus nigra L.). Total RNA was purified from infected leaves and, after ribodepletion, sequenced using an Illumina system. The RNA genome of viral isolate B15 is 12,622 nucleotides (nt) long, and that of isolate B42 is 12,621 nt long. A nearly complete sequence (12,592 nt) was also obtained for a third isolate (B160). The RNA genomes of all three isolates showed an organisation typical of cytorhabdoviruses, harbouring all six of the expected genes (3 ́ N-P-P3-M-G-L 5 ́), separated by intergenic regions. These isolates were closely related to each other (99.5-99.6% nt sequence identity) and showed the highest overall similarity to trichosanthes associated rhabdovirus 1 (63.5% identity) and Wuhan insect virus 5 (58% identity), and similar results were obtained when comparing individual coding sequences or proteins. Phylogenetic analysis confirmed that this elderberry virus, for which we propose the name "sambucus virus 1" belongs to the genus Cytorhabdovirus and fulfils the criteria to represent a novel species.
- MeSH
- Sambucus nigra * MeSH
- Sambucus * genetics MeSH
- Phylogeny MeSH
- Genome, Viral MeSH
- Plant Diseases MeSH
- Open Reading Frames MeSH
- Rhabdoviridae * MeSH
- RNA MeSH
- Viral Proteins genetics MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794T, Streptomyces laculatispora NRRL B-24909T, and Streptomyces brevispora NRRL B-24910T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04T (=DSM 111306T = CCM 9048T) as the type strain.
- MeSH
- Antibiosis * MeSH
- DNA, Bacterial genetics MeSH
- Phylogeny MeSH
- Nucleic Acid Hybridization MeSH
- Methicillin-Resistant Staphylococcus aureus MeSH
- Multigene Family MeSH
- Porifera * microbiology MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Sequence Analysis, DNA MeSH
- Streptomyces * classification isolation & purification MeSH
- Bacterial Typing Techniques MeSH
- Base Composition MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
Bats host many viruses pathogenic to humans, and increasing evidence suggests that rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America, and Africa were PCR-positive for RVA, and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, which included evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite various levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.IMPORTANCE The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens. The current effort to characterize bat rotavirus strains from 3 continents sheds light on the vast genetic diversity of rotaviruses and also hints at a bat origin for several atypical rotaviruses in humans and animals, implying that zoonoses of bat rotaviruses might occur more frequently than currently realized.
- MeSH
- Chiroptera virology MeSH
- COVID-19 transmission virology MeSH
- Phylogeny MeSH
- Genetic Variation MeSH
- Genome, Viral MeSH
- Genotype MeSH
- Horses MeSH
- Middle East Respiratory Syndrome Coronavirus isolation & purification MeSH
- Humans MeSH
- Metagenomics MeSH
- Diarrhea virology MeSH
- Rotavirus Infections transmission virology MeSH
- Rotavirus genetics MeSH
- SARS-CoV-2 isolation & purification MeSH
- Zoonoses transmission virology MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Silver gulls carry phylogenetically diverse Escherichia coli, including globally dominant extraintestinal pathogenic E. coli (ExPEC) sequence types and pandemic ExPEC-ST131 clades; however, our large-scale study (504 samples) on silver gulls nesting off the coast of New South Wales identified E. coli ST457 as the most prevalent. A phylogenetic analysis of whole-genome sequences (WGS) of 138 ST457 samples comprising 42 from gulls, 2 from humans (Australia), and 14 from poultry farmed in Paraguay were compared with 80 WGS deposited in public databases from diverse sources and countries. E. coli ST457 strains are phylogenetic group F, carry fimH145, and partition into five main clades in accordance to predominant flagella H-antigen carriage. Although we identified considerable phylogenetic diversity among the 138 ST457 strains, closely related subclades (<100 SNPs) suggested zoonotic or zooanthroponosis transmission between humans, wild birds, and food-producing animals. Australian human clinical and gull strains in two of the clades were closely related (≤80 SNPs). Regarding plasmid content, country, or country/source, specific connections were observed, including I1/ST23, I1/ST314, and I1/ST315 disseminating blaCMY-2 in Australia, I1/ST113 carrying blaCTX-M-8 and mcr-5 in Paraguayan poultry, and F2:A-:B1 plasmids of Dutch origin being detected across multiple ST457 clades. We identified a high prevalence of nearly identical I1/ST23 plasmids carrying blaCMY-2 among Australian gull and clinical human strains. In summary, ST457 is a broad host range, geographically diverse E. coli lineage that can cause human extraintestinal disease, including urinary tract infection, and displays a remarkable ability to capture mobile elements that carry and transmit genes encoding resistance to critically important antibiotics.
- MeSH
- Anti-Bacterial Agents pharmacology MeSH
- beta-Lactamases genetics MeSH
- beta-Lactams MeSH
- Animals, Wild MeSH
- Escherichia coli * genetics MeSH
- Phylogeny MeSH
- Escherichia coli Infections * veterinary MeSH
- Humans MeSH
- Plasmids genetics MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Australia MeSH
