Rhodococcus opacus strain RW, a resorcinol-degrading bacterium from the gut of Macrotermes michaelseni

The population of resorcinol degrading bacteria in the intestinal tract of fungi-cultivating termite, Macrotermes michaelseni, was estimated to be 6.8 × 102 cells/ml. A gram-positive bacterium designated RW, capable of degrading resorcinol, was isolated from the highest positive dilution. Isolate RW could also degrade phenol and benzoic acid aerobically, and anaerobically using nitrate as an electron acceptor. The isolate is a rod-shaped bacterium that exhibited evolutionary relatedness with the genus Rhodococcus, as determined by phenotypic traits and physiological tests, and a 16S rRNA gene sequence similarity value of 99.6% to the closest Rhodococcus opacus strain. On the basis of these results isolate RW is proposed as a new strain in the species R. opacus. The ability of the isolate to degrade resorcinol, phenol and benzoic acid makes it a potential candidate for use in bioremediation of environments contaminated by such or related compounds.African Journal of Biotechnology Vol. 4 (7), pp. 639-645, 200

Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

Active diversity relative abundance of microbial taxa at family level in various samples collected from the three hot springs (83.6, 81 and 45.1 °C) of L. Magadi and Little Magadi. ‘No blast hit/Others’ represent unclassified sequences in both data sets. (XLSX 32 kb

Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation

Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented.This workwas funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health

Nocardiopsis mwathae sp. nov., isolated from the haloalkaline Lake Elmenteita in the African Rift Valley.

During a screening for novel and biotechnologically useful bacteria in haloalkaline lakes, strain No.156(T) was isolated from a sediment sample from lake Elmenteita in the African Rift Valley and studied by a polyphasic taxonomic approach. The strain was observed to form yellow aerial and substrate mycelia; optimal growth was found to be at 30-35 °C in salt concentrations of 6-9 % (w/v) and at pH 7-9. The DNA G+C content of the novel strain was 71 mol%. Analysis of 16S rRNA sequences indicated that the isolate belongs to the genus Nocardiopsis with sequence similarities below 98 % to the type strains of all other representatives of the genus. Mycolic acids were not detected in whole cell methanolysates. The peptidoglycan was found to contain meso-diaminopimelic acid as the diamino acid with no diagnostic sugars. The main polar lipids were identified as phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol but no diphosphatidylglycerol. The predominant menaquinones were MK-11(H8), MK-11(H6), MK-10(H8) and MK-10(H6). Cellular fatty acids were found to consist of saturated and monounsaturated iso- and anteiso-branched acids with 16-18 C-length, tuberculostearic acid (Me18:0), and straight-chain saturated (16:0, 18:0) acids. These characteristics match those of the genus Nocardiopsis. Based on 16S rRNA gene sequence analysis and phenotypic characteristics, a novel species with the name Nocardiopsis mwathae is proposed. The type strain is No.156(T) (=DSM 46659(T) = CECT 8552(T)). The INSDC accession number for the 16S rRNA gene sequence of strain No.156(T) is KF976731

Belliella kenyensis sp. nov., isolated from an alkaline lake.

A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164(T), was isolated from sediment sample from the alkaline Lake Elmenteita located in the Kenyan Rift Valley. Results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Belliella, with the highest sequence similarity (97 %) to Belliella pelovolcani DSM 46698(T). Optimal growth temperature was 30-35 °C, at pH 7.0-12.0 in the presence of 0-4 % (w/v) NaCl. Flexirubins were absent. The respiratory menaquinone (MK-7), predominant cellular fatty acids (iso-C15 : 0, anteiso-C15 : 0 and a mixture of C16 : 1ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38.1 mol%) of strain No.164(T) were consistent with those of other members of the genus Belliella. The polar lipids consisted of phosphatidylethanolamine, eight unspecified lipids and one unspecified phospholipid. Several phenotypic characteristics can be used to differentiate this isolate from those of other species of the genus Belliella. The results of polyphasic analyses presented in this study indicated that this isolate should be classified as representing a novel species of the genus Belliella. The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164(T) ( = DSM 46651(T) = CECT 8551(T))

African Journal of Microbiology Research Diversity of fungi in sediments and water sampled from the hot springs of Lake Magadi and Little Magadi in Kenya

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

Isolation, characterization and analysis of bacteriophages from the haloalkaline lake Elmenteita, Kenya.

As a step towards better understanding of diversity and biology of phages and their hosts in haloalkaline Lake Elmenteita, phages were isolated from sediment samples and overlying water using indigenous bacteria as hosts. 17 seemingly different phages of diverse morphotypes with different dimensions and partly exhibiting remarkably unusual ultrastructures were revealed by transmission electron microscopy. 12 clonal phage isolates were further characterized. Infection capability of the phages was optimum at 30–35°C and in alkali condition with optimum at pH 10–12. Structural protein profiles and restriction fragment length polymorphism analyses patterns were distinct for each of the phage type. Complete nucleotide sequences of phages vB-VmeM-32, vB_EauS-123 and vB_BhaS-171 genomes varied in size from 30,926–199,912 bp and G + C content of between 36.25–47.73%. A range of 56–260 potential open reading frames were identified and annotated. The results showed that the 12 phages were distinct from each other and confirmed the presence and diversity of phages in extreme environment of haloalkaline Lake Elmenteita. The phages were deposited at the German Collection of Microorganisms and Cell Cultures and three of their genomes uploaded to NCBI GenBank.As a step towards better understanding of diversity and biology of phages and their hosts in haloalkaline Lake Elmenteita, phages were isolated from sediment samples and overlying water using indigenous bacteria as hosts. 17 seemingly different phages of diverse morphotypes with different dimensions and partly exhibiting remarkably unusual ultrastructures were revealed by transmission electron microscopy. 12 clonal phage isolates were further characterized. Infection capability of the phages was optimum at 30-35°C and in alkali condition with optimum at pH 10-12. Structural protein profiles and restriction fragment length polymorphism analyses patterns were distinct for each of the phage type. Complete nucleotide sequences of phages vB-VmeM-32, vB_EauS-123 and vB_BhaS-171 genomes varied in size from 30,926-199,912 bp and G + C content of between 36.25-47.73%. A range of 56-260 potential open reading frames were identified and annotated. The results showed that the 12 phages were distinct from each other and confirmed the presence and diversity of phages in extreme environment of haloalkaline Lake Elmenteita. The phages were deposited at the German Collection of Microorganisms and Cell Cultures and three of their genomes uploaded to NCBI GenBank

Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya.

We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other. Comparison to other nucleotide sequences in GenBank database showed no significant similarities hence novel. At the amino acid level, phages of our study revealed mosaicism to genes with conserved domains to already described phages. Phylogenetic analyses of large terminase gene responsible for DNA packaging and DNA polymerase gene for replication further showed diversity among the bacteriophages. Our results give insight into diversity of bacteriophages in Lake Elmenteita and provide information on their evolution. By providing primary sequence information, this study not only provides novel sequences for biotechnological exploitation, but also sets stage for future studies aimed at better understanding of virus diversity and genomes from haloalkaline lakes in the Rift Valley

Potential human pathogenic bacteria in five hot springs in Eritrea revealed by next generation sequencing

<div><p>Human pathogens can survive and grow in hot springs. For water quality assessment, <i>Escherichia coli</i> or <i>Enterococci</i> are the main thermotolerant enteric bacteria commonly used to estimate the load of pathogenic bacteria in water. However, most of the environmental bacteria are unculturable thus culture methods may cause bias in detection of most pathogens. Illumina sequencing can provide a more comprehensive and accurate insight into environmental bacterial pathogens, which can be used to develop better risk assessment methods and promote public health awareness. In this study, high-throughput Illumina sequencing was used to identify bacterial pathogens from five hot springs; Maiwooi, Akwar, Garbanabra, Elegedi and Gelti, in Eritrea. Water samples were collected from the five hot springs. Total community DNA was extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4—V7) of the extracted DNA was amplified and library construction done according to Illumina sequencing protocol. The sequence reads (length >200 bp) from Illumina sequencing libraries ranged from 22,091 sequences in the wet sediment sample from Garbanabra to 155,789 sequences in the mat sample from Elegedi. Taxonomy was assigned to each OTU using BLASTn against a curated database derived from GreenGenes, RDPII, SILVA SSU Reference 119 and NCBI. The proportion of potential pathogens from the water samples was highest in Maiwooi (17.8%), followed by Gelti (16.7%), Akwar (13.6%) and Garbanabra (10.9%). Although the numbers of DNA sequence reads from Illumina sequencing were very high for the Elegedi (104,328), corresponding proportion of potential pathogens very low (3.6%). Most of the potential pathogenic bacterial sequences identified were from <i>Proteobacteria</i> and <i>Firmicutes</i>. <i>Legionella</i> and <i>Clostridium</i> were the most common detected genera with different species. Most of the potential pathogens were detected from the water samples. However, sequences belonging to <i>Clostridium</i> were observed more abundantly from the mat samples. This study employed high-throughput sequencing technologies to determine the presence of pathogenic bacteria in the five hot springs in Eritrea.</p></div