New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida)

Biofilm-Inhibitory Activity of Wild Mushroom Extracts against Pathogenic Bacteria

Objective

This study aims to investigate the bacterial biofilm-inhibitory effect of mushroom extracts.

Methods

Mushrooms were collected from Arabuko-Sokoke and Kakamega forests and identified using morphological and molecular approaches. Auricularia auricula-judae, Microporus xanthopus, Termitomyces umkowaani, Trametes elegans, and Trametes versicolor were extracted by chloroform, 70% ethanol, and hot water. Extracts were tested against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus (ATCC25923). Data were analyzed using SPSS ver. 20.0.

Results

Chloroform, 70% ethanol, and hot water extracts of A. auricula-judae (50 μg/mL) showed statistically significant antibiofilm activities against P. aeruginosa, E. coli, and S. aureus (p ≤ 0.05). M. xanthopus extracts (250 μg/mL) revealed significantly significant antibiofilm activities against each test bacterium (p ≤ 0.05). All extracts of T. umkowaani (250 μg/mL) exhibited statistically significant antibiofilm activities against S. aureus only (p ≤ 0.05). Chloroform extract of T. elegans (250 μg/mL) showed the best antibiofilm activity (69.75 ± 0.01%) against S. aureus. All T. versicolor extracts (250 μg/mL) indicated the best antibiofilm activities against S. aureus.

Conclusions

Being the first study of its kind to be conducted in Kenya, it added a novel concept to the body of knowledge already known about medical biotechnology research. It offers a fresh understanding of the various varieties of mushrooms found in Kenya, their potential biological function in the production of drugs, particularly those that combat drug resistance, and perhaps even a peek at their bioactive elements. Wild mushrooms, a hidden gem, might help to reopen the pipeline of new antibiotics that have been on the decline. However, further research is required to determine the potential mechanism(s) of action of the extracts that are in charge of the apparent antibiofilm activity.

Global species delimitation of the cosmopolitan marine littoral earthworm Pontodrilus litoralis (Grube, 1855)

The marine littoral earthworm Pontodrilus litoralis (Grube, 1855) is widely distributed and is reported as a single species. This study utilized an integrative taxonomic approach based upon morphological examination, phylogenetic reconstruction, and molecular species delimitation, to test whether the taxon is a single species or a species complex. For this, a total of 114 P. litoralis specimens collected from North America, Africa, Australia and Oceania, Europe and Asia were used. The phylogenetic analyses revealed deeply divergent mitochondrial lineages and a high level of genetic diversity among P. litoralis populations. Both single and multi-locus species delimitation analyses yielded several molecular operational taxonomic units. Therefore, due to the homogeneity of morphological characteristics, it is likely that the morphospecies P. litoralis is a complex of four or more cryptic species, suggesting that more sampling is required and that the population structure genetic data and gene flow need to be investigated.

Cryptic carnivores: Intercontinental sampling reveals extensive novel diversity in a genus of freshwater annelids

Freshwater annelids are globally widespread in aquatic ecosystems, but their diversity is severely underestimated. Obvious morphological features to define taxa are sparse, and molecular phylogenetic analyses regularly discover cryptic diversity within taxa. Despite considerable phylogenetic work on certain clades, many groups of freshwater annelids remain poorly understood. Included among these are water nymph worms of the genus Chaetogaster (Clitellata: Tubificida: Naididae: Naidinae). These worms have diverged from the detritivorous diet of most oligochaetes to become more predatory and exist as omnivores, generalist predators, parasites, or symbionts on other invertebrates. Despite their unusual trophic ecology, the true diversity of Chaetogaster and the phylogenetic relationships within the genus are uncertain. Only three species are commonly referenced in the literature (Chaetogaster diaphanus, Chaetogaster limnaei, and Chaetogaster diastrophus), but additional species have been described and prior molecular data suggests that there is cryptic diversity within named species. To clarify the phylogenetic diversity of Chaetogaster, we generated the first molecular phylogeny of the genus using mitochondrial and nuclear sequence data from 128 worms collected primarily across North America and Europe. Our phylogenetic analyses suggest that the three commonly referenced species are a complex of 24 mostly cryptic species. In our dataset, Chaetogaster "diaphanus" is represented by two species, C. "limnaei" is represented by three species, and C. "diastrophus" is represented by 19 species. North American and European sequences are largely interspersed across the phylogeny, with four pairs of clades involving distinct North American and European sister groupings. Overall, our study demonstrates that the species diversity of Chaetogaster has been underestimated and that carnivory has evolved at least twice in the genus. Chaetogaster is being used as a model for symbiotic evolution and the loss of regenerative ability, and our study indicates that researchers must be careful to identify which species of Chaetogaster they are working with in future studies.

Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland

The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophoracarrionii and Lichenotheliaconvexa. New mycobiont-specific primers (mt-SSU-581-5' and mt-SSU-1345-3') were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics.

The pharmacophylogenetic relationships of two edible medicinal plants in the genus Artemisia

Artemisia argyi and Artemisia indica are edible medicinal plants belonging to the genus Artemisia in the Asteraceae. There are many similarities in their morphology, traditional curative effect, and modern pharmacological treatment. In this study, we built distribution maps of A. argyi and A. indica in China and a phylogenetic tree of common medicinal plants in Asteraceae. Then, we verified the chemical composition changes of A. argyi and A. indica via their metabolome. Traditional efficacy and modern pharmacological action were verified by network pharmacology and in vitro using RAW264.7 cells. The results showed that A. argyi and A. indica are widely distributed in China, and they shared pharmaphylogeny, which provides theoretical support for the mixed use of A. argyi and A. indica in most regions of China. Furthermore, there were both similarities and differences in volatile oil and flavonoid composition between A. argyi and A. indica. The network pharmacology results showed that A. argyi and A. indica had 23 common active compounds and that both had pharmacological effects on chronic gastritis (CG). Molecular docking analyses showed that quercetin, luteolin, and kaempferol have strong binding affinities with the target proteins JUN, TP53, AKT1, MAPK3, TNF, MAPK, and IL6. The cell experiment results further demonstrated that A. argyi and A. indica treat CG via the NOD-like receptor pathway. Based on the theory of pharmaphylogeny, this study explored the pharmaphylogeny between A. argyi and A. indica from various perspectives to provide a basis for the substitution of A. argyi and A. indica.

DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifextubifex and Lumbriculusvariegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

New insights into the systematics of Lumbricillus and Marionina (Clitellata: Enchytraeidae) inferred from Southern Hemisphere samples, including three new species

Enchytraeid worms collected in South Africa and on the Marion, South Orkney, South Georgia and South Shetland Islands during 2008–2015 were studied using morphology and seven genetic markers. Nine species were recognized: one terrestrial (Christensenidrilus blocki) and all the others marine littoral (five Lumbricillus and three Marionina s.s.). An estimated phylogeny including other enchytraeids from the Northern Hemisphere, many of which are members of Lumbricillus and some representing Marionina s.l., confirmed a non-monophyletic Lumbricillus, with some of its current species closely related to Grania or Marionina s.s. The phylogeny also corroborated a non-monophyletic Marionina s.l., with Marionina s.s. closely related to Grania and Lumbricillus s.l., but not to the remaining sequenced ‘Marionina’ or to Ch. blocki. These results provide a long-needed starting point for a revision of both Marionina and Lumbricillus. We provide morphological descriptions of all nine species, three of which are new to science: Lumbricillus finisafricae sp. nov., Lumbricillus nivalis sp. nov., and Marionina fusca sp. nov. Comments on three related species of Marionina s.s. based on re-examined type material are also provided.

New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida)

Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.