Control of Alternaria Leaf Spot of the Common Bean (Phaseolus vulgaris L.) Using Soil-Derived Biological Agents.

Phaseolus vulgaris L. is considered one of the most essential legume crops in Kenya. Alternaria alternata is an economically significant plant pathogen that causes Alternaria leaf spot which accounts for over 70% yield losses of beans in Kenya. Chemical fungicides based on copper and sulfur are used to control Alternaria leaf spot in bean plants, but their prolonged use has adversely affected the environment and the health of workers. Herein, we tested the biocontrol potential of bacterial agents from soil planted with Rosecoco bean plants infected with A. alternata. Using bacterial suspensions at different time intervals, we evaluated the putative bacterial biocontrol activity against A. alternata under greenhouse conditions. B. subtilis and B. velezensis bacterial biocontrol agents significantly suppressed disease severity by 20% and 21.2% on the 45th day, respectively. Our study demonstrates that B. subtilis and B. velezensis are promising biocontrol agents that could be integrated in the management of Alternaria leaf spot.

Management of bacterial wilt caused by Curtobacterium flaccumfacienspv.flaccumfaciens in common bean (Phaseolus vulgaris) using rhizobacterial biocontrol agents.

The bacterial wilt of common bean, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens(Cff) is one of the most severe diseases affecting Phaseolus vulgaris production worldwide. This study aimed at evaluating the biocontrol potential of strains of rhizobacteria against bacterial wilt of common bean. Sequence analysis of the 16S rRNA gene was used to identify Cff isolates and also the bacterial antagonists. A soft agar overlay assay was used to select three biocontrol isolates based on their antagonistic activity against Cff. Our findings demonstrate that seed treatment using rhizobacterial P. fluorescens, Bacillus cereus, and Paenibacillus polymyxa species coupled with foliar application significantly reduced Cff disease incidence and disease severity. Therefore, biocontrol methods are potentially a safe, effective, and sustainable alternative to chemicals for controlling bacterial wilt of beans.

Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya.

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 = 0.559, p = 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.

Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya.

An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.

Complete Genome Sequence of Alkalihalobacillus sp. Strain LMS39, a Haloalkaliphilic Bacterium Isolated from a Hypersaline Lake.

Here, we report the complete genome sequence of a haloalkaliphilic bacterium (Alkalihalobacillus sp. strain LMS39) isolated from Lake Magadi, a hypersaline lake in Kenya. The genome comprised 4,850,562 bp with a GC content of 37%.

Amplicon-Based Analysis of the Fungal Diversity across Four Kenyan Soda Lakes.

Microorganisms have been able to colonize and thrive in extreme environments characterized by low/high pH, temperature, salt, or pressure. Examples of extreme environments are soda lakes and soda deserts. The objective of this study was to explore the fungal diversity across soda lakes Magadi, Elmenteita, Sonachi, and Bogoria in Kenya. A new set of PCR primers was designed to amplify a fragment long enough for the 454-pyrosequencing technology. Analysis of the amplicons generated showed that the new primers amplified for diverse fungal groups. A total of 153,634 quality-filtered, nonchimeric sequences derived from the 18S region of the rRNA region were used for community diversity analysis. The sequence reads were clustered into 502 OTUs at 97% similarity cut-off using BLASTn analysis of which 432 were affiliated to known fungal phylotypes and the rest to other eukaryotes. Fungal OTUs were distributed across 107 genera affiliated to the phyla Ascomycota, Basidiomycota, Glomeromycota, and and other unclassified groups refred to as Incertae sedis. The phylum Ascomycota was the most abundant in terms of OTUs. Overall, fifteen genera (Chaetomium, Monodictys, Arthrinium, Cladosporium, Fusarium, Myrothecium, Phyllosticta, Coniochaeta, Diatrype, Sarocladium, Sclerotinia, Aspergillus, Preussia, and Eutypa) accounted for 65.3% of all the reads. The genus Cladosporium was detected across all the samples at varying percentages with the highest being water from Lake Bogoria (51.4%). Good's coverage estimator values ranged between 97 and 100%, an indication that the dominant phylotypes were represented in the data. These results provide useful insights that can guide cultivation-dependent studies to understand the physiology and biochemistry of the as-yet uncultured taxa.

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya.

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.

Study on the effect of Thiobacillus intermedius bacteria on the physico-mechanical properties of mortars of ordinary portland cement.

Most of concrete structural failures are attributed to poor workmanship and poor engineering designs. Some microorganisms present in sewer systems can degrade the concrete and/or mortar. Concrete failures due to microbial attack has not attracted much attention especially in developing countries such as Kenya. This study investigated the effect of Thiobacillus intermedius bacteria on the performance of Ordinary Portland Cement (OPC). Preparation of test mortar prisms was done using the bacterial solution as either mix water, curing water or both. The control mortar prisms were prepared and cured in distilled water. Compressive strength test was done after 7th, 28th, 56th and 90th days of curing respectively. Results showed significant drop in compressive strength for the mortar prisms prepared and cured in bacterial solution as compared to the control mortar samples. Soundness and normal consistency increased significantly for the bacterial treated cement paste as compared to the control sample. Scanning Electron Microscopy (SEM) analysis showed severe damage on the bacterial treated cement mortar. This was characterized by formation of deleterious expansive products like ettringite and gypsum. Control mortar sample exhibited even formation of hydration products within the pore system.

Isolation of haloalkaliphilic fungi from Lake Magadi in Kenya.

In this study we explored the cultivable fungal diversity in Lake Magadi and their secondary metabolite production. Isolation was done on alkaline media (Potato dextrose agar, Malt extract agar, Oatmeal agar and Sabouraud dextrose agar). A total of 52 unique isolates were recovered from the lake and were characterized using different techniques. Growth was observed at pH, temperature and salinity ranges of between 6 - 10, 25 °C - 40 °C and 0%-20% respectively. Phylogenetically, the isolates were affiliated to 18 different genera with Aspergillus, Penicillium, Cladosporium, Phoma and Acremonium being dominant. A screen for the ability to produce extracellular enzymes showed that different isolates could produce proteases, chitinases, cellulases, amylases, pectinases and lipases. Production of antimicrobial metabolites was noted for isolate 11M affiliated to Penicillium chrysogenum (99%). Cell free extracts and crude extracts from this isolate had inhibitory effects on Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp., Shigella spp., Candida albicans and fungal plant pathogens Schizophyllum commune, Epicoccum sorghinum strain JME-11, Aspergillus fumigatus strain EG11-4, Cladosporium halotolerans CBS 119416, Phoma destructive and Didymella glomerata). In this study we showed that different cultivation strategies can lead to recovery of more phylotypes from the extreme environments. Growth under different physiological characteristics typical of the soda lake environment (elevated temperature, pH and salts) confirmed the haloalkaliphilic nature of the fungal isolates. The use of suitable antimicrobial production media can also lead to discovery of more phylotypes producing diverse biocatalysts and bioactive metabolites.

Influence of Lysinibacillus sphaericus on compressive strength and water sorptivity in microbial cement mortar.

Cement structures are subject to degradation either by aggressive media or development of micro/macro cracks which create external substance ingress pathways. Microbiocementation can be employed as a self-intelligent solution to this deterioration process. This paper presents study results on the effects of Lysinibacillus sphaericus microbiocementation on Ordinary Portland cement (OPC), normal consistency, setting time, soundness, compressive strength and water sorptivity. Microbial solutions with a concentration of 1.0 × 107 cells/ml were mixed with OPC to make prisms at a water/cement ratio of 0.5. Mortar prisms of 160 mm × 40 mm x 40mm were used in this study. A maximum compressive strength gain of 17% and 19.8% was observed on the microbial prism at the 28th and 56th day of curing respectively. A minimum of 0.0190 and a maximum of 0.0355 water sorptivity coefficient was observed on the OPC microbial prism and OPC control prism, after 28th day of curing respectively. Scanning electron microscope images taken after the 28th day of curing showed formation of vast calcium silicate hydrates and more calcite deposits on microbial mortars. Statistical findings of this study indicate that Lysinibacillus sphaericus significantly retarded both the setting time and normal consistency, but has no influence on the mortar soundness.

Diversity of esterase and lipase producing haloalkaliphilic bacteria from Lake Magadi in Kenya.

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.

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

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.

Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea.

The candidate Division MSBL1 (Mediterranean Sea Brine Lakes 1) comprises a monophyletic group of uncultured archaea found in different hypersaline environments. Previous studies propose methanogenesis as the main metabolism. Here, we describe a metabolic reconstruction of MSBL1 based on 32 single-cell amplified genomes from Brine Pools of the Red Sea (Atlantis II, Discovery, Nereus, Erba and Kebrit). Phylogeny based on rRNA genes as well as conserved single copy genes delineates the group as a putative novel lineage of archaea. Our analysis shows that MSBL1 may ferment glucose via the Embden-Meyerhof-Parnas pathway. However, in the absence of organic carbon, carbon dioxide may be fixed via the ribulose bisphosphate carboxylase, Wood-Ljungdahl pathway or reductive TCA cycle. Therefore, based on the occurrence of genes for glycolysis, absence of the core genes found in genomes of all sequenced methanogens and the phylogenetic position, we hypothesize that the MSBL1 are not methanogens, but probably sugar-fermenting organisms capable of autotrophic growth. Such a mixotrophic lifestyle would confer survival advantage (or possibly provide a unique narrow niche) when glucose and other fermentable sugars are not available.

454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils.

Termites constitute part of diverse and economically important termite fauna in Africa, but information on gut microbiota and their associated soil microbiome is still inadequate. In this study, we assessed and compared the bacterial diversity and community structure between termites' gut, their mounds and surrounding soil using the 454 pyrosequencing-based analysis of 16S rRNA gene sequences. A wood-feeder termite (Microcerotermes sp.), three fungus-cultivating termites (Macrotermes michaelseni, Odontotermes sp. and Microtermes sp.), their associated mounds and corresponding savannah soil samples were analyzed. The pH of the gut homogenates and soil physico-chemical properties were determined. The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples. Soil samples (Chao1 index ranged from 1359 to 2619) had higher species richness than gut samples (Chao1 index ranged from 461 to 1527). The bacterial composition and community structure in the gut of Macrotermes michaelseni and Odontotermes sp. were almost identical but different from that of Microtermes and Microcerotermes species, which had unique community structures. The most predominant bacterial phyla in the gut were Bacteroidetes (40-58 %), Spirochaetes (10-70 %), Firmicutes (17-27 %) and Fibrobacteres (13 %) while in the soil samples were Acidobacteria (28-45 %), Actinobacteria (20-40 %) and Proteobacteria (18-24 %). Some termite gut-specific bacterial lineages belonging to the genera Dysgonomonas, Parabacteroides, Paludibacter, Tannerella, Alistipes, BCf9-17 termite group and Termite Treponema cluster were observed. The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated. Therefore, combined efforts using both culture and culture-independent methods are suggested to comprehensively characterize the bacterial species and their specific roles in these environments.

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), 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.

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 1448(T), 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 G enomic E ncyclopedia 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.

16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species).

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.

Diversity of Termitomyces associated with fungus-farming termites assessed by cultural and culture-independent methods.

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.

Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).

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 location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic 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 family 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.

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).

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 regarding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in significant 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.

Complete genome sequence of Oceanithermus profundus type strain (506).

Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species 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 carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed 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.