Browsing by Author "Kipnyargis, Alex C."

Now showing 1 - 5 of 5
  • No Thumbnail Available
    Item
    Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya
    (Heliyon, 2022-11) Kenya, Eucharia U.; Kinyanjui, Grace; Kipnyargis, Alex C.; Kinyua, Franklin; Mwangi, Mary; Khamis, Fathiya; Mwirichia, Romano K.
    Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R ¼ 0.559, p ¼ 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.
  • Thumbnail Image
    Item
    Diversity of esterase and lipase producing haloalkaliphilic bacteria from Lake Magadi in Kenya
    (2019-09) Kiplimo, Denis; Mugweru, Julius; Kituyi, Sarah; Kipnyargis, Alex C.; Mwirichia, Romano K.
    Lipids are hydrocarbons comprised of long‐chain fatty acids and are found in all living things. In the environment, microorganisms degrade them to obtain energy using esterases and lipases. These enzymes are nowadays used in different industrial applications. We report isolation of 24 bacteria with esteresic and lipolytic activity from Lake Magadi, Kenya. The isolates were characterised using morphological, biochemical, and molecular methods. Isolates grew at an optimum salt concentration of 5–8% (w/v), pH range of 8.0–9.0, and temperature range of 35–40°C. The isolates were positive for esterase and lipase assay as well as other extracellular enzymes. Phylogenetic analysis of the 16S ribosomal RNA gene showed that the isolates were affiliated to the genus Bacillus, Alkalibacterium, Staphylococcus, Micrococcus, Halomonas, and Alkalilimnicola. None of the bacterial isolates produced antimicrobial agents, and all of them were resistant to trimethoprim and nalidixic acid but susceptible to streptomycin, amoxillin, chloramphenicol, and cefotaxime. Growth at elevated pH, salt, and temperature is an indicator that the enzymes from these organisms could function well under haloalkaline conditions. Therefore, Lake Magadi could be a good source of isolates with the potential to produce unique biocatalysts for the biotechnology industry.
  • Thumbnail Image
    Item
    Genetic diversity of aphid (Hemiptera: Aphididae) species attacking amaranth and nightshades in different agro-ecological zones of Kenya and Tanzania
    (Entomological Society of Southern Africa, 2018-12) Kipnyargis, Alex C.; Kenya, Eucharia U.; Khamis, F. M.; Ekesi, S.; Fiaboe, K.K.M.
    Aphids are major pests of African indigenous vegetables. Information on the genetic diversity and the role of host crop and environmental differentiation in their diversity in East Africa is scanty. The knowledge on genetic diversity is a critical component in the development of sound and sustainable integrated pest management strategy, from detection to control. A portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene was used to characterise the species of aphids on amaranth and nightshades at different agro-ecological zones of Kenya and Tanzania. Aphid samples were collected in localities growing the vegetables in low, mid and high altitude agro-ecological zones. Total DNA was isolated and amplified using universal barcoding primers targeting the 5’ end of the COI barcode region. Nucleotide sequences of the COI barcode, using the Basic Local Alignment Search Tool model, found high homology to four species of aphids: Myzus persicae, Aphis fabae, Aphis craccivora and Macrosiphum euphorbiae. Three subspecies of the A. fabae were also detected. Intraspecific diversity depicted M. euphorbiae having the lowest value, while A. fabae showed the highest diversity. Interspecific diversity between A. fabae and A. craccivora was the lowest while between A. craccivora and M. persicae it was the highest. The phylogenetic tree showed each species clustering together irrespective of the host crop or site where collected. Principal component analysis and haplotype network analyses confirmed these results. Low genetic diversity revealed by COI suggests that the environment or host crop contribute less to the genetic diversity of aphids in both countries
  • Thumbnail Image
    Item
    Genetic Diversity of Aphid Species Attacking Amaranth and Nightshades in Different Agro-Ecological Zones of Kenya and Tanzania
    (University of Embu, 2016-09) Kipnyargis, Alex C.
    Aphids are the major pests of vegetables leading to a significant yield loss in African indigenous vegetables including amaranth and nightshades. Information on the types of aphids that infest these vegetables and their genetic diversity in Kenya and Tanzania is scanty. This is an important diagnostic component in developing management strategies such as integrated pest management and early detection and control of invasive species. This study used a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene region called the barcode region to characterize the species of aphids that attack amaranth and nightshades in different agro-ecological regions of Kenya and Tanzania. Individual aphid samples were collected in 22 localities of amaranth and nightshade growing zones of the two countries, representing low, mid and high altitude agro-ecological zones. Total DNA was isolated and amplified using universal barcoding primers targeting the 5’ end of the COI barcode region. There was a strong homology (≥ 98% identity) in nucleotide sequences of the barcode region using the Basic Local Alignment Search tool for nucleotides (BLASTn) in the GenBank to four main species of aphids namely: Myzus persicae, Aphis fabae, Aphis craccivora and Macrosiphum euphorbiae. Further, three subspecies of the black bean aphid were identified as A. fabae fabae, A. fabae ciirciacanthoidis and A. fabae solanella. Intra-specific nucleotide diversity indicated that M. euphorbiae had no genetic diversity (0.0%); while A. fabae had the highest diversity (0.8%). The lowest inter-specific diversity was observed between A. fabae and A. craccivora (6.3%) while the highest was observed between A. craccivora and M. persicase (10.6%). The phylogenetic tree constructed using the maximum likelihood model showed each individual species clustering in robust clades irrespective of the host crop or the locality from which it was collected. This confirmed the BLASTn results. The principal coordinate analysis (PCoA) and the haplotype network analyses further confirmed these results by showing species clustering together in their space and haplotypes, respectively. Overall, COI successfully identified the species of aphid infesting amaranth and nightshades. This forms an important diagnostic tool for management strategies, early detection of newly evolving biotypes, deployment of resistant crop cultivars and containment of invasive species.
  • Thumbnail Image
    Item
    Genetic Diversity of Aphid Species Attacking Amaranth and Nightshades in Different Agro-Ecological Zones of Kenya and Tanzania
    (University of Embu, 2016-09) Kipnyargis, Alex C.
    Aphids are the major pests of vegetables leading to a significant yield loss in African indigenous vegetables including amaranth and nightshades. Information on the types of aphids that infest these vegetables and their genetic diversity in Kenya and Tanzania is scanty. This is an important diagnostic component in developing management strategies such as integrated pest management and early detection and control of invasive species. This study used a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene region called the barcode region to characterize the species of aphids that attack amaranth and nightshades in different agro-ecological regions of Kenya and Tanzania. Individual aphid samples were collected in 22 localities of amaranth and nightshade growing zones of the two countries, representing low, mid and high altitude agro-ecological zones. Total DNA was isolated and amplified using universal barcoding primers targeting the 5’ end of the COI barcode region. There was a strong homology (≥ 98% identity) in nucleotide sequences of the barcode region using the Basic Local Alignment Search tool for nucleotides (BLASTn) in the GenBank to four main species of aphids namely: Myzus persicae, Aphis fabae, Aphis craccivora and Macrosiphum euphorbiae. Further, three subspecies of the black bean aphid were identified as A. fabae fabae, A. fabae ciirciacanthoidis and A. fabae solanella. Intra-specific nucleotide diversity indicated that M. euphorbiae had no genetic diversity (0.0%); while A. fabae had the highest diversity (0.8%). The lowest inter-specific diversity was observed between A. fabae and A. craccivora (6.3%) while the highest was observed between A. craccivora and M. persicase (10.6%). The phylogenetic tree constructed using the maximum likelihood model showed each individual species clustering in robust clades irrespective of the host crop or the locality from which it was collected. This confirmed the BLASTn results. The principal coordinate analysis (PCoA) and the haplotype network analyses further confirmed these results by showing species clustering together in their space and haplotypes, respectively. Overall, COI successfully identified the species of aphid infesting amaranth and nightshades. This forms an important diagnostic tool for management strategies, early detection of newly evolving biotypes, deployment of resistant crop cultivars and containment of invasive species.