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  1. Home
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Browsing by Author "Mwirichia, Romano K."

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    16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species)
    (Springer Netherlands, 2013-08-14) Makonde, Huxley M.; Boga, Hamadi I.; Mwirichia, Romano K.; Mackenzie, Lucy; Göker, Markus; Klenk, Hans-Peter
    The interaction between termites and their gut symbionts has continued to attract the curiosity of researchers over time. The aim of this study was to characterize and compare the bacterial diversity and community structure in the guts of three termites (Odontotermes somaliensis, Odontotermes sp. and Microtermes sp.) using 16S rRNA gene sequencing of clone libraries. Clone libraries were screened by restriction fragment length polymorphism and representative clones from O. somaliensis (100 out of 330 clones), Odontotermes sp. (100 out of 359 clones) and Microtermes sp. (96 out 336 clones) were sequenced. Phylogenetic analysis indicated seven bacterial phyla were represented: Bacteroidetes, Spirochaetes, Firmicutes, Proteobacteria, Synergistetes, Planctomycetes and Actinobacteria. Sequences representing the phylum Bacteroidetes (>60 %) were the most abundant group in Odontotermes while those of Spirochaetes (29 %) and Firmicutes (23 %) were the abundant groups in Microtermes. The gut bacterial community structure within the two Odontotermes species investigated here was almost identical at the phylum level, but the Microtermes sp. had a unique bacterial community structure. Bacterial diversity was higher in Odontotermes than in Microtermes. The affiliation and clustering of the sequences, often with those from other termites’ guts, indicate a majority of the gut bacteria are autochthonous having mutualistic relationships with their hosts. The findings underscore the presence of termite-specific bacterial lineages, the majority of which are still uncultured.
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    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.
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    Archaeal Diversity in the Haloalkaline Lake Elmenteita in Kenya
    (Springer-Verlag, 2009-10-06) Mwirichia, Romano K.; Cousin, Sylvie; Muigai, Ann W.; Boga, Hamadi I.; Stackebrandt, Erko
    A non-culture approach was used to study the archaeal diversity in Lake Elmenteita, Kenya. Five different sampling points were selected randomly within the lake. Wet sediments and water samples were collected from each sampling point. In addition, dry mud cake was collected from three points where the lake had dried. DNA was extracted from these samples and the 16S rRNA genes were amplified using primers described to be Domain-specific for Archaea. Eleven clone libraries were constructed using PCR-amplified 16S rRNA genes. A total of 1,399 clones were picked and analysed via ARDRA. 170 ARDRA patterns were unique and the respective clones were selected for sequencing. 149 clones gave analysable sequences. BLAST analysis showed that 49 belong to the Domain Archaea while the others were either chimera or affiliated to eukaryotic taxa. Comparative sequence analysis of archaeal clones affiliated them to a wide range of genera. The order Halobacteriales was represented by members of the genera Natronococcus, Halovivax, Halobiforma, Halorubrum, and Halalkalicoccus. The highest percentage (46%) of the clones, however, belonged to uncultured members of the Domain Archaea in the order Halobacteriales. The results show that the archaeal diversity in the lake could be higher than previously reported.
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    Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
    (BioMed Central, 2016-06) Mwirichia, Romano K.; Kasili, Remmy W.; Karanja, Edward N.; Makonde, Huxley M.; Boga, Hamadi I.; Kambura, Anne K.
    Background: Lake Magadi and little Magadi are hypersaline, alkaline lakes situated in the southern part of Kenyan Rift Valley. Solutes are supplied mainly by a series of alkaline hot springs with temperatures as high as 86 °C. Previous culture-dependent and culture-independent studies have revealed diverse groups of microorganisms thriving under these conditions. Previous culture independent studies were based on the analysis of 16S rDNA but were done on less saline lakes. For the first time, this study combined illumina sequencing and analysis of amplicons of both total community rDNA and 16S rRNA cDNA to determine the diversity and community structure of bacteria and archaea within 3 hot springs of L. Magadi and little Magadi. Methods: Water, wet sediments and microbial mats were collected from springs in the main lake at a temperature of 45.1 °C and from Little Magadi “Nasikie eng’ida” (temperature of 81 °C and 83.6 °C). Total community DNA and RNA were extracted from samples using phenol-chloroform and Trizol RNA extraction protocols respectively. The 16S rRNA gene variable region (V4 – V7) of the extracted DNA and RNA were amplified and library construction performed following Illumina sequencing protocol. Sequences were analyzed done using QIIME while calculation of Bray-Curtis dissimilarities between datasets, hierarchical clustering, Non Metric Dimensional Scaling (NMDS) redundancy analysis (RDA) and diversity indices were carried out using the R programming language and the Vegan package. Results: Three thousand four hundred twenty-six and one thousand nine hundred thirteen OTUs were recovered from 16S rDNA and 16S rRNA cDNA respectively. Uncultured diversity accounted for 89.35 % 16S rDNA and 87.61 % 16S rRNA cDNA reads. The most abundant phyla in both the 16S rDNA and 16S rRNA cDNA datasets included: Proteobacteria (8.33–50 %), Firmicutes 3.52–28.92 %, Bacteroidetes (3.45–26.44 %), Actinobacteria (0.98–28.57 %) and Euryarchaeota (3.55–34.48 %) in all samples. NMDS analyses of taxonomic composition clustered the taxa into three groups according to sample types (i.e. wet sediments, mats and water samples) with evident overlap of clusters between wet sediments and microbial mats from the three sample types in both DNA and cDNA datasets. The hot spring (45.1 °C) contained less diverse populations compared to those in Little Magadi (81–83 °C). Conclusion: There were significant differences in microbial community structure at 95 % level of confidence for both total diversity (P value, 0.009) based on 16S rDNA analysis and active microbial diversity (P value, 0.01) based on 16S rRNA cDNA analysis, within the three hot springs. Differences in microbial composition and structure were observed as a function of sample type and temperature, with wet sediments harboring the highest diversity.
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    Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
    (2016-07) Mwirichia, Romano K.; Kambura, Anne Kelly; Kasili, Remmy Wekesa; Karanja, Edward Nderitu; Makonde, Huxley Mae; Boga, Hamadi Iddi
    Background: Lake Magadi and little Magadi are hypersaline, alkaline lakes situated in the southern part of Kenyan Rift Valley. Solutes are supplied mainly by a series of alkaline hot springs with temperatures as high as 86 °C. Previous culture-dependent and culture-independent studies have revealed diverse groups of microorganisms thriving under these conditions. Previous culture independent studies were based on the analysis of 16S rDNA but were done on less saline lakes. For the first time, this study combined illumina sequencing and analysis of amplicons of both total community rDNA and 16S rRNA cDNA to determine the diversity and community structure of bacteria and archaea within 3 hot springs of L. Magadi and little Magadi. Methods: Water, wet sediments and microbial mats were collected from springs in the main lake at a temperature of 45.1 °C and from Little Magadi “Nasikie eng’ida” (temperature of 81 °C and 83.6 °C). Total community DNA and RNA were extracted from samples using phenol-chloroform and Trizol RNA extraction protocols respectively. The 16S rRNA gene variable region (V4 – V7) of the extracted DNA and RNA were amplified and library construction performed following Illumina sequencing protocol. Sequences were analyzed done using QIIME while calculation of Bray-Curtis dissimilarities between datasets, hierarchical clustering, Non Metric Dimensional Scaling (NMDS) redundancy analysis (RDA) and diversity indices were carried out using the R programming language and the Vegan package. Results: Three thousand four hundred twenty-six and one thousand nine hundred thirteen OTUs were recovered from 16S rDNA and 16S rRNA cDNA respectively. Uncultured diversity accounted for 89.35 % 16S rDNA and 87.61 % 16S rRNA cDNA reads. The most abundant phyla in both the 16S rDNA and 16S rRNA cDNA datasets included: Proteobacteria (8.33–50 %), Firmicutes 3.52–28.92 %, Bacteroidetes (3.45–26.44 %), Actinobacteria (0.98–28.57 %) and Euryarchaeota (3.55–34.48 %) in all samples. NMDS analyses of taxonomic composition clustered the taxa into three groups according to sample types (i.e. wet sediments, mats and water samples) with evident overlap of clusters between wet sediments and microbial mats from the three sample types in both DNA and cDNA datasets. The hot spring (45.1 °C) contained less diverse populations compared to those in Little Magadi (81–83 °C). Conclusion: There were significant differences in microbial community structure at 95 % level of confidence for both total diversity (P value, 0.009) based on 16S rDNA analysis and active microbial diversity (P value, 0.01) based on 16S rRNA cDNA analysis, within the three hot springs. Differences in microbial composition and structure were observed as a function of sample type and temperature, with wet sediments harboring the highest diversity.
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    Bacterial Diversity in the Haloalkaline Lake Elmenteita
    (Springer-Verlag, 2010-06) Mwirichia, Romano K.; Cousin, S.; Muigai, A.W.; Boga, Hamadi I.; Stackebrandt, Erko
    Lake Elmenteita is one of the alkaline saline lakes within the Kenyan Rift valley. The lake is situated on the floor of the Kenyan Rift Valley at 1,776 m above sea level and has no direct outlet. The microbial diversity of the lake was investigated using a culture-independent approach. Five different sampling points were selected randomly within the lake. Wet sediments and water samples were collected from each sampling point. In addition, dry mud cake was collected from three points where the lake had dried. DNA was extracted from the samples and the 16S rRNA genes amplified using universal primers for Bacteria. Thirteen clone libraries were constructed using the PCR amplified 16S rRNA genes. A total of 1,663 clones were picked. Representative clones were selected using ARDRA technique for sequencing. 655 partial and non-chimeric clone sequences indicated the presence of 37 orders in the Domain Bacteria. Cyanobacteria were the most abundant clones in terms of numbers whereas members of the phylum Firmicutes group were the second in terms of numbers but the most diverse in terms of genera represented. All clones affiliated to the class Betaproteobacteria originated from DNA obtained from the water samples. Analysis using BLAST showed that 93.1% of the sequenced clones had similarity values below 98% to both cultured and as yet uncultured bacteria, resulting in 596 phylotypes. Therefore, it can be concluded that Lake Elmenteita harbours phylogenetically diverse groups of bacteria involved in complex metabolic interactions within the Lake’s ecosystem.
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    Biocementation Influence on Flexural Strength and Chloride Ingress by Lysinibacillus sphaericus and Bacillus megaterium in Mortar Structures
    (Hindawi, 2020-05) Mutitu, Daniel Karanja; Wachira, Jackson M.; Mwirichia, Romano K.; Thiong’o, Joseph Karanja; Munyao, Onesmus Mulwa; Genson, Muriithi
    The concrete/mortar durability performance depends mainly on the environmental conditions, the microstructures, and its chemistry. Cement structures are subject to deterioration by the ingress of aggressive media. This study focused on the effects of Bacillus megaterium and Lysinibacillus sphaericus on flexural strength and chloride ingress in mortar prisms. Microbial solutions with a concentration of 1.0 × 107 cells/ml were mixed with ordinary Portland cement (OPC 42.5 N) to make mortar prisms at a water/cement ratio of 0.5. Four mortar categories were obtained from each bacterium based on mix and curing solution. Mortar prisms of 160 mm × 40 mm × 40 mm were used in this study. Flexural strength across all mortar categories was determined at the 14th, 28th, and 56th day of curing. Mortars prepared and cured using bacterial solution across all curing ages exhibited the highest flexural strength as well as the highest percent flexural strength gain. Lysinibacillus sphaericus mortars across all mortar categories showed higher flexural strength and percent flexural strength gain than Bacillus megaterium mortars. The highest percent flexural strength gain of 33.3% and 37.0% was exhibited by the 28th and 56th day of curing, respectively. The mortars were subjected to laboratory prepared 3.5% by mass of sodium chloride solution under the accelerated ion migration test method for thirty-six hours using a 12 V Direct Current power source after their 28th day of curing. After subjecting the mortar cubes to Cl media, their core powder was analyzed for Cl content. From these results, the apparent diffusion coefficient, Dapp, was approximated from solutions to Fick’s 2nd Law using the error function. Bacillus megaterium mortars across all mortar categories showed lower apparent diffusion coefficient values with the lowest being 2.6456 × 10–10 while the highest value for Lysinibacillus sphaericus mortars was 2.8005 × 10–10. Both of the test bacteria lowered the ordinary Portland cement Cl-ingress but Bacillus megaterium was significantly more effective than Lysinibacillus sphaericus in inhibition.
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    Characterization of various Bacillus thuringiensis strains having larvicidal activity on Chilo partellus first-instar larvae, after culture on cost-effective medium, in Kenya
    (2011) Anyika, D.; Boga, Hamadi I.; Mwirichia, Romano K.
    Bacillus thuringiensis strains are widely used in many larvicidal pest control programs. However, the large-scale production of these biolarvicides is very expensive due to the high cost of the production synthetic medium. In this study, we developed cost-effective media, based on locally available raw materials namely legumes, potato, and whey. The optical density, protein concentration yield, sporulation and Chilo partellus larvicidal action were studied by growing bacterial strains in these waste product and in comparison with the conventional medium (NYSM). Protein concentration yield of 27.60 μg/ ml, spore count of 5.60 × 108 and Chilo partellus larvicidal activity (LC50) of 78 μg/ l against first-instar larvae were obtained with a 72 h culture of this bacterium. Production of Bt Insecticidal Crystal Proteins in NYSM was comparable to the test media and mean values were not significantly different for spore counts: F (media) = 25.19 P>0.01. One-way ANOVA (repeated measures) difference in percentage larval mortalities of Bacillus thuringiensis subspecies kurstaki (F = 26.88, P>0.05) and Bt isolates was not statistically significant. The SDS-PAGE profiles indicated that spore-crystal product from each treatment consisted of proteins with molecular weights of approximately 110-120 kDa and 60-70 kDa. Therefore the investigation suggests that legume, potato and whey-based culture media are more economical for the industrial production of Bt Insecticidal Crystal Proteins.
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    Characterization, Enzymatic Activity, and Secondary Metabolites of Fungal Isolates from Lake Sonachi in Kenya
    (2015-03) Ndwigah, Ireri F.; Bogai, Hamadi I.; Wanyoike, Wanjiru; Mwirichia, Romano K.
    The soda lakes of Kenya provide an extreme environment where diverse groups of microorganisms thrive. They are characterized by great variation in temperature, halophillic and alkaliphilic- extreme conditions. Lake Sonachi has been the study site for this research. The study sort to isolate, characterize and identify fungi, screen for potential exo-enzymes and secondary metabolites production that may be of industrial application. Malt extract agar was used in the isolation of fungi and six (6) isolates were recovered. Inhibition zones were used to measure the enzymatic and antimicrobial activity of the isolates. GC-MC analysis was done on the filtrates extracted from the fungi to identify secondary metabolites. Molecular characterization of the 18s rDNA was done using fungal primers and sequencing PCR products.s .Phylogenetic tree was inferred using neighbor- joining method. The fungal isolates were alighned to diferrent genera, Acrimonies sp., Scopulariopsissp, Verticilium sp. Fusariumsp and Paecilomyces sp. The fungal isolates produce different types of enzymes (cellulases, proteases, pectinases and lipases) and metabolites (acids, ketones, quinones, alcohols, esters etc) .Antimicrobial assay showed that most of the fungal isolates produced inhibition zones ranging from 0.1 to 4mm, an indication of presence of compounds with antimicrobial activity against most of the test organisms, E.coli, B. subtilis, S.aureasetc, used in this study. Results indicate that Lake Sonachi, a soda lake has fungal species that are capable of producing enzymes and metabolites with antimicrobial activity.
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    Complete genome sequence of Oceanithermus profundus type strain (506T)
    (2011) Pati, A.; Zhang, X.; Lapidus, A.; Nolan, M.; Lucas, S.; Del Rio, T.G.; Tice, H.; Cheng, J.F.; Tapia, R.; Han, C.; Goodwin, L.; Pitluck, S.; Liolios, K.; Pagani, I.; Kyrpides, N.C.; Klenk, H.P.; Land, M.; Mwirichia, Romano K.
    Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Ocea-nithermus, which belongs to the family Thermaceae. The genus currently comprises two spe-cies whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbo-hydrates, some proteinaceous substrates, organic acids and alcohols. This is the first com-pleted genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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    Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae
    (2014) Scheuner, C.; Tindall, B.J.; Lu, Megan; Nolan, M.; Lapidus, A.; Mwirichia, Romano K.; et al.
    Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
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    Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)
    (2011) Han, C.; Mwirichia, Romano K.; Chertkov, O.; Lapidus, A.; Nolan, M.; Brambilla, Evelyne-Marie; et al.
    Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of tree of life. When grown in pure culture with glyoxylate as carbon source the organism utilizes glyoxylate through fermentative oxidation, whereas, when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria, it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic or inorganic carbon source is utilized by S. glycolicus. The subdivision of the family Peptococcaceae into genera does not reflect the natural relationships, particularly re-garding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in signifi-cant conflict with the 16S rRNA data. S. glycolicus is already the ninth member of the family Peptococcaceae with a completely sequenced and publicly available genome. The 3,406,739 bp long genome with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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    Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)
    (2011) Woyke, T.; Chertkov, Olga; Lapidus, A.; Nolan, Matt; Lucas, S.; Mwirichia, Romano K.; et al.
    Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic lo-cation in the genome-sequenced fraction of the tree of life. Strain RW262T forms a monophy-letic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na+ ions. All other genera in the fami-ly Cryomorphaceae are from marine habitats and have an absolute requirement for Na+ ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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    Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent
    (2011) Göker, M.; Daligault, H.; Mwirichia, Romano K.; Lapidus, A.; Lucas, S.; Deshpande, S.; et al.
    Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the ge-nus Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of interest because it represents the first thermophilic bacterium that can act as a primary pro-ducer in the temperature range of 45-75 °C (optimum 70°C) and is incapable of growing un-der microaerophilic conditions. Strain BSAT preferentially synthesizes high-melting-point fatty acids (C18 and C20) which is hypothesized to be a strategy to ensure the functionality of the membrane at high growth temperatures. This is the second completed genome sequence of a member of the family Desulfurobacteriaceae and the first sequence from the genus Desulfu-robacterium. The 1,541,968 bp long genome harbors 1,543 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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    Development of cost-effective media for the culture of Chilo partellus larvicide in Kenya
    (Academic Journals, 2013-03) Anyika, D.; Boga, Hamadi I.; Mwirichia, Romano K.
    Stem borers (Chilo partellus) are important field insect pests of maize (Zea mays L.) and sorghum (Sorghum bicolor L.) in Africa. They account for more than 30% yield losses depending on the composition of the pest community. C. partellus larvicide like Bacillus thuringiensis have been widely and effectively used in C. partellus control programs, but the industrial production of theses bacilli is expensive. Here we have attempted to develop three cost-effective media, based on legumes, potato, and whey. Growth and production of the insecticidal proteins from these bacteria were satisfactory; protein concentration yields of 27.60 mg/ml, spore counts of 5.60 × 108 CFU/ ml and first-instar Chilo partellus larvicidal activity (LC50) of 78 μg/l were obtained with a 72 h culture of this bacterium. Therefore, this investigation suggests that legume, potato and whey-based culture media are more economical and effective for the industrial production of B. thuringiensis insecticidal crystal proteins.
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    Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya
    (PLOS, 2020-08) Karanja, Edward N.; Fliessbach, Andreas; Adamtey, Noah; Kambura, Anne Kelly; Musyoka, Martha; Fiaboe, Komi; Mwirichia, Romano K.
    Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs application are known to influence diversity and function of soil microbial populations. In this study, we investigated the effect of conventional versus organic farming systems at low and high input levels on structure and diversity of prokaryotic microbial communities. Soil samples were collected from the ongoing long-term farming system comparison trials established in 2007 at Chuka and Thika in Kenya. Physicochemical parameters for each sample were analyzed. Total DNA and RNA amplicons of variable region (V4—V7) of the 16S rRNA gene were generated on an Illumina platform using the manufacturer’s instructions. Diversity indices and statistical analysis were done using QIIME2 and R packages, respectively. A total of 29,778,886 high quality reads were obtained and assigned to 16,176 OTUs at 97% genetic distance across both 16S rDNA and 16S rRNA cDNA datasets. The results pointed out a histrionic difference in OTUs based on 16S rDNA and 16S rRNA cDNA. Precisely, while 16S rDNA clustered by site, 16S rRNA cDNA clustered by farming systems. In both sites and systems, dominant phylotypes were affiliated to phylum Actinobacteria, Proteobacteria and Acidobacteria. Conventional farming systems showed a higher species richness and diversity compared to organic farming systems, whilst 16S rRNA cDNA datasets were similar. Physiochemical factors were associated differently depending on rRNA and rDNA. Soil pH, electrical conductivity, organic carbon, nitrogen, potassium, aluminium, zinc, iron, boron and micro-aggregates showed a significant influence on the observed microbial diversity. The observed higher species diversity in the conventional farming systems can be attributed to the integration of synthetic and organic agricultural inputs. These results show that the type of inputs used in a farming system not only affect the soil chemistry but also the microbial population dynamics and eventually the functional roles of these microbes.
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    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.
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    Diversity of fungi in sediments and water sampled from the hot springs of Lake Magadi and Little Magadi in Kenya
    (2016-02) Mwirichia, Romano K.; Kambura, Ann K.; Kasili, Remmy W.; Boga, Hamadi Iddi; Karanja, Edward N.; Makonde, Huxley M.
    Lake Magadi and Little Magadi are saline, alkaline lakes lying in the southern part of Kenyan Rift Valley. Their solutes are supplied by a series of alkaline hot springs with temperatures as high as 86°C. Previous culture-dependent and independent studies have revealed diverse prokaryotic groups adapted to these conditions. However, very few studies have examined the diversity of fungi in these soda lakes. In this study, amplicons of Internal Transcribed Spacer (ITS) region on Total Community DNA using Illumina sequencing were used to explore the fungal community composition within the hot springs. Operational taxonomic units (OTUs) were analyzed using QIIME 1.8.0, taxonomy assigned via BLASTn against SILVA 119 Database and hierarchical clustering was done using R programming software. A total of 334, 394 sequence reads were obtained from which, 151 OTUs were realized at 3% genetic distance. Taxonomic analysis revealed that 80.33% of the OTUs belonged to the Phylum Ascomycota, 11.48% Basidiomycota while the remaining consisted of Chytridiomycota, Glomeromycota and early diverging fungal lineages. The most abundant Ascomycota groups consisted of Aspergillus (18.75%), Stagonospora and Ramularia (6.25% each) in wet sediment at 83.6°C, while Penicillium and Trichocomaceae (14.29% each) were dominant in wet sediment at 45.1°C. The results revealed representatives of thermophilic and alkaliphilic fungi within the hot springs of Lake Magadi and Little Magadi. This suggests their ability to adapt to high alkalinity, temperature and salinity.
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    Diversity of Termitomyces Associated with Fungus- Farming Termites Assessed by Cultural and Culture- Independent Methods
    (2013) Makonde, H.M.; Boga, Hamadi I.; Osiemo, Z.; Mwirichia, Romano K.; Stielow, J.B.; Go¨ ker, Markus; et al.
    Background: Fungus-cultivating termites make use of an obligate mutualism with fungi from the genus Termitomyces, which are acquired through either vertical transmission via reproductive alates or horizontally transmitted during the formation of new mounds. Termitomyces taxonomy, and thus estimating diversity and host specificity of these fungi, is challenging because fruiting bodies are rarely found. Molecular techniques can be applied but need not necessarily yield the same outcome than morphological identification. Methodology: Culture-dependent and culture-independent methods were used to comprehensively assess host specificity and gut fungal diversity. Termites were identified using mitochondrial cytochrome oxidase II (COII) genes. Twenty-three Termitomyces cultures were isolated from fungal combs. Internal transcribed spacer (ITS) clone libraries were constructed from termite guts. Presence of Termitomyces was confirmed using specific and universal primers. Termitomyces species boundaries were estimated by cross-comparison of macromorphological and sequence features, and ITS clustering parameters accordingly optimized. The overall trends in coverage of Termitomyces diversity and host associations were estimated using Genbank data. Results and Conclusion: Results indicate a monoculture of Termitomyces in the guts as well as the isolation sources (fungal combs). However, cases of more than one Termitomyces strains per mound were observed since mounds can contain different termite colonies. The newly found cultures, as well as the clustering analysis of GenBank data indicate that there are on average between one and two host genera per Termitomyces species. Saturation does not appear to have been reached, neither for the total number of known Termitomyces species nor for the number of Termitomyces species per host taxon, nor for the number of known hosts per Termitomyces species. Considering the rarity of Termitomyces fruiting bodies, it is suggested to base the future taxonomy of the group mainly on well-characterized and publicly accessible cultures.
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    Effects of biocementation on some properties of cement-based materials incorporating Bacillus Species bacteria – a review
    (Taylor and Francis, 2019-11) Mutitu, Karanja D.; Munyao, Mulwa O.; Wachira, Jackson M.; Mwirichia, Romano K.; Thiong'o, Karanja J.
    There is a growing need in the construction industry to improve transfer and durability aspects of Portland pozzolana cement. Ureolytic bacteria have recently emerged as potential micro-organisms well known for precipitation of calcium carbonate through microbiologically induced calcite precipitation (MICP) process. MICP process has emerged as a viable mechanism for improvement of the PPC performance. This paper presents an in-depth discussion on the effects of Bacillus pseudofirmus, Bacillus sphaericus, Sporosarcina pasteurii, Bacillus cereus, Bacillus megaterium and Bacillus subtilis on some selected physico-mechanical properties of cement-based materials. These properties include standard consistency, setting time, compressive strength, water absorptivity, porosity and chloride ingress. The influence of pH, temperature and various bacteria nutrient requirements on optimum MICP process is also presented. In conclusion, benefits and drawbacks on the use of MICP has been discussed. MICP as a potential technique for improvement of physico-mechanical properties as well as repair of cracked cement-based structures has been discussed.
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