Floristic Composition, Diversity and Plant Community Along Elevational Gradients in the Afro-alpine Vegetation of Abohoy Gara Mountain, northern Ethiopia

This research was conducted in Afro-alpine vegetation of Abohoy Gara Mountain in northern Ethiopia with the aim of analyzing floristic composition along elevational gradients, threats and conservation methods. Data were collected from 53 quadrats (15 m x 15 m) laid at 100 m interval along parallel vertical transects spaced at 500m to each other to record shrubs and trees, whereas 1 m x 1 m plots were used to record herbs. Cover abundance data were used to do community analysis using R version 3.1.2 software. Analysis of variance (ANOVA) was employed to determine significant level of species richness; abundance and Shannon diversity index along elevational gradient, whereas pearson’s correlation test was applied to check the relationship between environmental variables with species richness, species abundance and Shannon diversity index (H’) using SPSS v20. Ninety-seven plant species composed of 82 genera under 40 families were recorded. The mean number of plant species showed significant difference along elevational gradient (P < 0.05). Besides, significant (P < 0.05) negative correlation of elevation with the plant richness, abundance as well as Shannon diversity index had been observed. Based on dominant species, a total of five plant communities were identified. The maximum plant diversity occurred in community type III (3.79), whereas the least plant diversity occurred in community type IV and community type V. Vegetation cover and species composition of Abohoy Gara Mountain is being endangered by agricultural expansion, over grazing and logging of wood for construction material. Hence, it needs application of complementary on-site and offsite conservation approaches. This calls for further joint management of the Abohoy Gara Mountain by the local people and administrative bodies in the overall conservation actions that can save and rehabilitate the plant resources and their habitats.

Assessment of Open Grown Trees Composition and Diversity in Selected Research Institutes in Peri-Urban Ibadan, Oyo state, Nigeria

Urban green spaces are rapidly deteriorating in most parts of Nigeria. The study assessed open grown trees composition and diversity in selected Research Institutes within Ibadan Region with the aim of comparing the ecological diversity in the study locations. This was achieved through species identification and mensuration of all open grown trees species that were accessible in the study areas. Open grown trees with Diameter at breast height ≥ 10cm were assessed for growth characteristics of total height and diameter at breast height. Basal area and volume were estimated from measured growth characteristics. Tree species were identified by a taxonomist at Federal Herbarium in Ibadan. Biodiversity indices of Shannon diversity index, species evenness and species dominance were computed to see variation in tree community of the areas. The Shannon diversity index calculated was higher in IITA with a value of 3.04 compared to that of CRIN with a value of 2.36. A dominance value of 0.15 and 0.05 was obtained for CRIN and IITA respectively. The study concludes that both institutes are repository of large diversity of tree species thereby, helping in the conservation of biodiversity while ameliorating weather. It is recommended that educational institutions from all levels located within the region as well as private organizations and individuals should plant trees within their domains in order to create conducive green environments that would promote sustainable environment in the region. This is possible when government provide adequate incentive and annual rewards for establishments with the best green environments.

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya

Background There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans. Methods Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3–V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database. Results cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys. Conclusion This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.

Ethnobotanical Study and Plant Diversity in the Forest of Kedarnath Valley, Garhwal Himalaya, India

The present study was carried out in the forest of Kedarnath valley in Garhwal Himalaya. The aim of the study was to access the diversity status and ecological status. The study was conducted following the stratified sampling techniques by placing quadrates (1m×1m) for herbs, (5m×5m) for shrubs, and (10m×10m) size for trees in the forest area. A total number of 221 plant species were recorded during the floristic survey in the project area. Plant diversity of the project area encompasses 49 species of trees, 28 species of shrubs, and 144 species of herbs. Important value index, the Shannon diversity index, and total basal area species were recorded. The tree density in the present study was highest in the Kedarnath valley which ranged from 0.3 to 8.5 no./ha. Shrub density in the present study varied from 0.4 to 13.5 no./ha, whereas herb density ranged between 0.2 to 22.4 no.ha-1. Total basal cover (TBC) for trees showed a range of 9.542 to 0.075 m2.ha-1, and the Shannon diversity index (H) for tree species was recorded from a minimum of 0.976 to a maximum of 3.048. The horrific disaster in the Kedarnath valley in 2013 caused a lot of damage to the bugyals (High altitude grass) and forests of the valley. About 500 species of vesicular medicinal plants, fodder plants, and other important plant species were washed away (Botanical Survey of India 2015). The current study is a pioneer in the aspect and can be helpful in making district forest plans, protocols, and implementation of forest policy to protect the forest by local people.

Prevalence of Diarrhoeagenic Escherichia Coli and Associated Risk Factors in Dug Wells in Ile-Ife, Southwestern Nigeria

BackgroundDiarrhoeagenic Escherichia coli (DEC) strains are common bacterial causes of morbidity and mortality in young children. Waterborne DEC could pose a potential health risk to humans through domestic use of contaminated water. However, epidemiological studies on DEC strains in drinking water are scarce in Nigeria. This study determined the prevalence, diversity and factors associated with the presence of DEC in dug wells in Ile-Ife, southwestern Nigeria.MethodsWe assessed 143 wells for safety by coliform count using the multiple tube technique. A standardized questionnaire was used to obtain relevant information about the wells and their owners. Contaminating isolates were identified as E. coli by amplifying their 16S rRNA gene. Five DEC pathotypes comprising enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC) enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC) and Shiga-toxin producing E. coli (STEC) were detected using two sets of multiplex PCR assays. Isolates diversity was determined by (GTG)5 Repetitive element palindromic PCR and Shannon diversity index. Multivariate logistic regression analysis was used to identify associated risk factors. Results Fifty-eight (40.6%) wells were contaminated by diarrhoeagenic E. coli. Wells with dirty platforms, damaged by erosion and sited near septic tanks significantly harboured DEC (p<0.05). There was a preponderance of STEC among the isolates with nine isolates carrying multiple diarrhoeagenic genes and 10 (17.2%) wells contaminated by multiple DEC strains. The (GTG)5-PCR fingerprinting assigned all DEC strains into six clades, with an overall Shannon diversity index of 18.87. A diverse profile was obtained among and between the isolates recovered from different sources.ConclusionsThe presence of DEC strains in drinking water highlights the risk to human health associated with the use of untreated water. There was a high degree of genetic diversity among the isolates implying multiple sources of contamination. There is a need for periodic sanitation and inspection of wells for cracks to prevent seepages and possible outbreaks of waterborne diseases.

Water Beetles: Species Diversity and Response to Physico-Chemical Parameters in Different Freshwater Habitats in Samtse, Bhutan

Bhutan is located between the two zoogeographic regions which are assumed to be rich in diversity of water beetles. The study aimed to determine the diversity and distribution pattern of water beetles in different freshwater habitats in Namgaychholing under Samtse district, Bhutan. The study also analysed the association of water beetles with the physico-chemical parameters. The data were collected from four different habitats with sample plot of 3 m × 1 m for a standard time of 1 hour in every plot. A total of 30 species belonging to 7 families were recorded of which Dytiscidae (n=626, RA=51) was the most abundant family and Lacconectus basalis (n=416, RA=34.13) was the most abundant species. The overall Shannon diversity index of the study area was H ′=2.48. Amongst the different habitats, marshy area had the highest Shannon diversity index (H ′=2.45) and stream had the lowest (H ′=1.82). A Kruskal Wallis test on diversity among different habitats showed no significant difference (p<.05). Through a cluster analysis, the species composition between the river and waterlogged showed 100% similarity index. Canonical correspondence analysis showed temperature as a main determining factor affecting the distribution of water beetles. With broad families encompassing the water beetles, similar study on water beetles in different regions of the country is recommended with particular emphasis on different families. Moreover, Bhutan falls in junction of Palearctic and Oriental Zoogeographic regions, which are known to be rich in diversity of water beetles. Hence, study in high-altitude lakes, which are assumed to be rich in diversity of water beetles are recommended despite social beliefs to keep lakes isolated and undisturbed.

Metagenomic Shotgun Sequencing Analysis of Canalicular Concretions in Lacrimal Canaliculitis Cases

Lacrimal canaliculitis is a rare infection of the lacrimal canaliculi with canalicular concretions formed by aggregation of organisms. Metagenomic shotgun sequencing analysis using next-generation sequencing has been used to detect pathogens directly from clinical samples. Using this technology, we report cases of successful pathogen detection of canalicular concretions in lacrimal canaliculitis cases. We investigated patients with primary lacrimal canaliculitis examined in the eye clinics of four hospitals from February 2015 to July 2017. Eighteen canalicular concretion specimens collected from 18 eyes of 17 patients were analyzed by shotgun metagenomics sequencing using the MiSeq platform (Illumina). Taxonomic classification was performed using the GenBank NT database. The canalicular concretion diversity was characterized using the Shannon diversity index. This study included 18 eyes (17 patients, 77.1 ± 6.1 years): 82.4% were women with lacrimal canaliculitis; canalicular concretions were obtained from 12 eyes using lacrimal endoscopy and six eyes using canaliculotomy with curettage. Sequencing analysis detected bacteria in all samples (Shannon diversity index, 0.05–1.47). The following genera of anaerobic bacteria (>1% abundance) were identified: Actinomyces spp. in 15 eyes, Propionibacterium spp., Parvimonas spp. in 11 eyes, Prevotella spp. in 9 eyes, Fusobacterium spp. in 6 eyes, Selenomonas spp. in 5 eyes, Aggregatibacter spp. in 3 eyes, facultative and aerobic bacteria such as Streptococcus spp. in 13 eyes, Campylobacter spp. in 6 eyes, and Haemophilus spp. in 3 eyes. The most common combinations were Actinomyces spp. and Streptococcus spp. and Parvinomonas spp. and Streptococcus spp., found in 10 cases. Pathogens were identified successfully using metagenomic shotgun sequencing analysis in patients with canalicular concretions. Canalicular concretions are polymicrobial with anaerobic and facultative, aerobic bacteria.

On a Variational Definition for the Jensen-Shannon Symmetrization of Distances Based on the Information Radius

We generalize the Jensen-Shannon divergence and the Jensen-Shannon diversity index by considering a variational definition with respect to a generic mean, thereby extending the notion of Sibson’s information radius. The variational definition applies to any arbitrary distance and yields a new way to define a Jensen-Shannon symmetrization of distances. When the variational optimization is further constrained to belong to prescribed families of probability measures, we get relative Jensen-Shannon divergences and their equivalent Jensen-Shannon symmetrizations of distances that generalize the concept of information projections. Finally, we touch upon applications of these variational Jensen-Shannon divergences and diversity indices to clustering and quantization tasks of probability measures, including statistical mixtures.

Diversity and Abundance of Insects at the Campus of Higher Polytechnic Institute of Manica, Mozambique

The aim of this study was to assess insect diversity and abundance at the Campus of Higher Polytechnic Institute of Manica, Mozambique. Collection of insects was carried out by pitfall traps a long linear transects and sweep nets during 21 days of October 2019. Data were analyzed using descriptive statistical and Shannon diversity index. A total of 1780 individuals of insects belonging to 8 orders, 15 families and 27 species were collected. Highest relative abundance was observed in Hymenoptera order (92.64%), and the least were Blattodea (2.70%), Diptera (2.13%), Coleoptera (0.82%), Orthoptera (1.52%), Phasmatodea (0.06%), Mantodea (0.28%) and Hemiptera (0.11%). The abundant specie was Crematogaster peringueyi (Hymenoptera) with 89.83% follwed by Macrotermes natalensis (Blattodea) and Chrysonmya chloropyga (Diptera) with 2.47% and 1.63% respectively. Higher insect diversity was observed in Orthoptera order (Shannon, H'=1.76), while the orders Coleoptera, Diptera, Hymenoptera, Blattodea, Phasmatodea, Hemiptera, had the lowest diversity (Shannon, H'<1). Further work need to be done in the study area, expanding the duration of the study and applying diversity sampling techniques.

Effects of invasion level of Prosopis juliflora on native species diversity and regeneration in Afar region, Northeast Ethiopia

The study aimed to assess (i) the effects of Prosopis juliflora invasion on the diversity of plant species, and floristic composition at Awash Fentale and the Amibara districts of the Afar region and (ii) the effects of P. juliflora invasion on the regeneration potential of native woody species. Sample collection was performed in habitats of P. juliflora thicket, P. juliflora mixed with native species stands, non-invaded woodlands, and open grazing lands. A stratified random sampling technique was used for data collection. Among species of plants, the highest proportion of species, 87 (27.4%), was recorded under non-invaded woodlands, but the lowest proportion of species, 70 (22%), was recorded under open grazing lands. The invasion level of P. juliflora caused significantly reduced Shannon diversity index. The mean values of Shannon diversity index and species richness under P. juliflora mixed with native species (H’=2.22, R=14) and non-invaded woodlands (H’=2.23, R=13) were significantly higher than P. juliflora thicket (H’=1.96, R=12) and open grazing lands (H’=1.84, R=10). In this study, 102 trees ha-1native woody species were recorded under P. juliflora thicket, but 1252 trees ha-1native species were recorded under non-invaded woodlands. If the present effects of the invasion of P. juliflora on native species diversity were to continue coupled with a drier climate, plant diversity of the Afar flora region will be highly affected. As a result the ecosystem services will be under threat. Thus, the participation of all stakeholders and multidisciplinary research approaches should be designed for the management of invaded rangelands to reverse the situation.