A thermophilic,motile strain ofMicrobacterium

Summary A thermophilic, motile organism producing catalase is described. It belongs certainly to the genusMicrobacterium by reason of its catalase production, although in its morphology, in some secondary characters and in its fermentative properties it more nearly resembles members of the genusLactobacillus. The nameMicrobacterium mobile is proposed for this organism.     

The use of Beneckea natriegens for practical exercises in microbiology and biochemistry

Beneckea natriegens is a rapidly growing, nonpathogenic marine bacterium which can be used with advantage to replace Escherichia coli in many of the microbiology experiments which are performed in undergraduate courses. Some recommendations for the handling and growth of this organism together with some examples of experiments are described. The potential value of this organism as a subject for student research projects is also discussed.     

Physiological properties,conjugation and taxonomy ofCephaloascus fragrans Hanawa 1920 (syn:Ascocybe grovesii Wells 1954)

Summary It has been established that the type cultures ofCephaloascus fragrans Hanawa 1920,Ascocybe grovesii Wells 1954 and a culture isolated from oakwood from Japan are identical. Conjugation in this organism has been observed. The taxonomic position of this organism in theAscomycetes was discussed. If this organism is incorporated in the classification ofLodder andKreger-van Rij, it seems justified by taxonomical reasons to create a new subfamily: theCephaloascoideae.     

The cell cycle of Entamoeba histolytica

Entamoeba histolytica, is a microaerophilic protist, which causes amoebic dysentery in humans. This unicellular organism proliferates in the human intestine as the motile trophozoite and survives the hostile environment outside the human host as the dormant quadri-nucleate cyst. Lack of organelles – such as mitochondria and Golgi bodies – and an unequal mode of cell division, led to the popular belief, that this organism preceded other eukaryotes during evolution. However, data from several laboratories have shown that, contrary to this belief, E. histolytica is remarkable in its divergence from other eukaryotes. This uniqueness is witnessed in many aspects of its biochemical pathways, cellular biology and genetic diversity. In this context, I have analysed the cell division cycle of this organism and compared it to that of other eukaryotes. Studies on E. histolytica, suggest that in its proliferative phase, this organism may accumulate polyploid cells. Thus 'checkpoints' regulating alternation of genome duplication and cell division appear to be absent in this unicellular protist. Sequence homologs of several cell cycle regulating proteins have been identified in amoeba, but their structural divergence suggests that they may not have equivalent function in this organism. The regulation of cell proliferation in E. histolytica, may be ideally suited to survival of a parasite in a complex host. Analysis of these molecular details may offer solutions for eradicating the pathogen by hitherto unknown methods.     

Morphological,Molecular and Pathological Characterization of Phytophthora amaranthi sp. nov. from Amaranth in Taiwan

In the spring of 2007, a serious disease on amaranth was noticed in several farms in the major amaranth production area in central Taiwan. Abundant oospores were found in the disease tissues. A species of Phytophthora was consistently isolated from disease tissues. The organism formed abundant oospores with smooth walls and with amphigynous antheridia in single culture. Sporangia were partially deciduous with short‐ to medium‐length pedicels. Morphological characteristics of this organism did not match any reported Phytophthora species, and the organism was named Phytophthora amaranthi. Pathogenicity tests and molecular characterization confirmed the identity of the organism as a new pathogen of amaranth and a new species of Phytophthora.     

Interaction of <Emphasis Type="Italic">Klebsiella oxytoca</Emphasis> and <Emphasis Type="Italic">Burkholderia cepacia</Emphasis> in Dual-Species Batch Cultures and Biofilms as a Function of Growth Rate and Substrate Concentration

Dual-species microbial interactions have been extensively reported for batch and continuous culture environments. However, little research has been performed on dual-species interaction in a biofilm. This research examined the effects of growth rate and substrate concentration on dual-species population densities in batch and biofilm reactors. In addition, the feasibility of using batch reactor kinetics to describe dual-species biofilm interactions was explored. The scope of the research was directed toward creating a dual-species biofilm for the biodegradation of trichloroethylene, but the findings are a significant contribution to the study of dual-species interactions in general. The two bacterial species used were Burkholderia cepacia PR1-pTOM_31c, an aerobic organism capable of constitutively mineralizing trichloroethylene (TCE), and Klebsiella oxytoca, a highly mucoid, facultative anaerobic organism. The substrate concentrations used were different dilutions of a nutrient-rich medium resulting in dissolved organic carbon (DOC) concentrations on the order of 30, 70, and 700 mg/L. Presented herein are single- and dual-species population densities and growth rates for these two organisms grown in batch and continuous-flow biofilm reactors. In batch reactors, planktonic growth rates predicted dual-species planktonic species dominance, with the faster-growing organism (K. oxytoca) outcompeting the slower-growing organism (B. cepacia). In a dual-species biofilm, however, dual-species planktonic growth rates did not predict which organism would have the higher dual-species biofilm population density. The relative fraction of each organism in a dual-species biofilm did correlate with substrate concentration, with B. cepacia having a greater proportional density in the dual-species culture with K. oxytoca at low (30 and 70 mg/L DOC) substrate concentrations and K. oxytoca having a greater dual-species population density at a high (700 mg/L DOC) substrate concentration. Results from this research demonstrate the effectiveness of using substrate concentration to control population density in this dual-species biofilm.     

Characterization ofClostridium bifermentans and its biotransformation of 2,4,6-trinitrotoluene (TNT) and 1,3,5-triaza-1,3,5-trinitrocyclohexane (RDX)

Summary We have determined that an organism able to degrade both RDX and TNT in a pure culture is a strain ofClostridium bifermentans. The consortium from which this organism is derived also degrades these compounds, and we suspect thatC. bifermentans is also the responsible organism within that consortium. The bioconversion of RDX and TNT occurs under anaerobic conditions both in the consortium and in pure culture without the need of an added reductant. The presence of co-metabolites speeded these biotransformations.     

A metabolic study to decipher amino acid catabolism-directed biofuel synthesis in Acetoanaerobium sticklandii DSM 519

Acetoanaerobium sticklandii DSM 519 is a hyper-ammonia-producing anaerobe. It has the ability to produce organic solvents and acids from protein catabolism through Stickland reactions and specialized pathways. Nevertheless, its protein catabolism-directed biofuel production has not yet been understood. The present study aimed to decipher such growth-associated metabolic potential of this organism at different growth phases using metabolic profiling. A seed culture of this organism was grown separately in metabolic assay media supplemented with gelatin and or a mixture of amino acids. The extracellular metabolites produced by this organism were qualitatively analyzed by gas chromatography–mass spectrometry platform. The residual amino acids after protein degradation and amino acids assimilation were identified and quantitatively measured by high-performance liquid chromatography (HPLC). Organic solvents and acids produced by this organism were detected and the quantity of them determined with HPLC. Metabolic profiling data confirmed the presence of amino acid catabolic products including tyramine, cadaverine, methylamine, and putrescine in fermented broth. It also found products including short-chain fatty acids and organic solvents of the Stickland reactions. It reported that amino acids were more appropriate for its growth yield compared to gelatin. Results of quantitative analysis of amino acids indicated that many amino acids either from gelatin or amino acid mixture were catabolised at a log-growth phase. Glycine and proline were poorly consumed in all growth phases. This study revealed that apart from Stickland reactions, a specialized system was established in A. sticklandii for protein catabolism-directed biofuel production. Acetone–butanol–ethanol (ABE), acetic acid, and butyric acid were the most important biofuel components produced by this organism. The production of these components was achieved much more on gelatin than amino acids. Thus, A. sticklandii is suggested herein as a potential organism to produce butyric acid along with ABE from protein-based wastes (gelatin) in bio-energy sectors.

     

Sequence of the gene encoding the 16S rRNA of the beer spoilage organismMegasphaera cerevisiae

The 16S ribosomal RNA gene from the beer-spoilage organism,Megasphaera cerevisiae was polymerase chain reaction (PCR)-amplified and sequenced. Analysis confirmed the phylogenetic position ofM. cerevisiae as a sister taxon ofMegasphaera elsdenii, within the obligately anaerobic, Gram-negative cocci. The sequence obtained should facilitate the development of DNA probes for early detection of this spoilage organism.     

Vibrio natriegens: an ultrafast-growing marine bacterium as emerging synthetic biology chassis

The marine bacterium Vibrio natriegens is the fastest-growing non-pathogenic bacterium known to date and is gaining more and more attention as an alternative chassis organism to Escherichia coli. A recent wave of synthetic biology efforts has focused on the establishment of molecular biology tools in this fascinating organism, now enabling exciting applications – from speeding up our everyday laboratory routines to increasing the pace of biotechnological production cycles. In this review, we seek to give a broad overview on the literature on V. natriegens, spanning all the way from its initial isolation to its latest applications. We discuss its natural ecological niche and interactions with other organisms, unveil some of its extraordinary traits, review its genomic organization and give insight into its diverse metabolism – key physiological insights required to further develop this organism into a synthetic biology chassis. By providing a comprehensive overview on the established genetic tools, methods and applications we highlight the current possibilities of this organism, but also identify some of the gaps that could drive future lines of research, hopefully stimulating the growth of the V. natriegens research community.     

Gephyrocapsa huxleyi (Emiliania huxleyi) as a model system for coccolithophore biology

Coccolithophores are the most abundant calcifying organisms in modern oceans and are important primary producers in many marine ecosystems. Their ability to generate a cellular covering of calcium carbonate plates (coccoliths) plays a major role in marine biogeochemistry and the global carbon cycle. Coccolithophores also play an important role in sulfur cycling through the production of the climate-active gas dimethyl sulfide. The primary model organism for coccolithophore research is Emiliania huxleyi, now named Gephyrocapsa huxleyi. G. huxleyi has a cosmopolitan distribution, occupying coastal and oceanic environments across the globe, and is the most abundant coccolithophore in modern oceans. Research in G. huxleyi has identified many aspects of coccolithophore biology, from cell biology to ecological interactions. In this perspective, we summarize the key advances made using G. huxleyi and examine the emerging tools for research in this model organism. We discuss the key steps that need to be taken by the research community to advance G. huxleyi as a model organism and the suitability of other species as models for specific aspects of coccolithophore biology.     

Yeast Systems Biology: Model Organism and Cell Factory

For thousands of years, the yeast Saccharomyces cerevisiae (S. cerevisiae) has served as a cell factory for the production of bread, beer, and wine. In more recent years, this yeast has also served as a cell factory for producing many different fuels, chemicals, food ingredients, and pharmaceuticals. S. cerevisiae, however, has also served as a very important model organism for studying eukaryal biology, and even today many new discoveries, important for the treatment of human diseases, are made using this yeast as a model organism. Here a brief review of the use of S. cerevisiae as a model organism for studying eukaryal biology, its use as a cell factory, and how advances in systems biology underpin developments in both these areas, is provided.     

Regulation of synthesis of endo-xylanase and β-xylosidase in <Emphasis Type="Italic">Cellulomonas flavigena</Emphasis>: a kinetic study

Regulation of xylanase, and β-xylosidase synthesis in Cellulomonas flavigenawas studied by culturing non-induced cells on mono-, oligo-, and poly-saccharides. The concomitant formation of these enzymes occurred on polysaccharides having structural resemblances with lignocellulosics, namely, cellulose, cellodextrin and xylan. Among disaccharides, cellobiose was the best inducer for their synthesis. Increased levels of enzymes were synthesized by the organism even under repressed conditions. Cell-free supernatants of the organism exhibited greater endo-xylanase than cell-associated β-xylosidase activity. Among inexpensive materials produced on saline lands, the salt tolerant grass Leptochloa fusca supported maximum xylanolytic activities followed by Sesbania aculeate (dhancha). The former could be effectively used for bulk production of xylanolytic enzymes by this organism.     

Pneumocystis carinii: Genetic Diversity and Cell Biology

As an important opportunistic pulmonary pathogen, Pneumocystis carinii has been the focus of extensive research over the decades. The use of laboratory animal models has permitted a detailed understanding of the host–parasite interaction but an understanding of the basic biology of P. carinii has lagged due in large part to the inability of the organism to grow well in culture and to the lack of a tractable genetic system. Molecular techniques have demonstrated extensive heterogeneity among P. carinii organisms isolated from different host species. Characterization of the genes and genomes of the Pneumocystis family has supported the notion that the family comprises different species rather than strains within the genus Pneumocystis and contributed to the understanding of the pathophysiology of infection. Many of the technical obstacles in the study of the organisms have been overcome in the past decade and the pace of research into the basic biology of the organism has accelerated. Biochemical pathways have been inferred from the presence of key enzyme activities or gene sequences, and attempts to dissect cellular pathways have been initiated. The Pneumocystis genome project promises to be a rich source of information with regard to the functional activity of the organism and the presence of specific biochemical pathways. These advances in our understanding of the biology of this organism should provide for future studies leading to the control of this opportunistic pathogen.     

A simple medium for isolation and identification of Candida albicans directly from clinical specimens

A simple and specific medium consisting of chitosan, trypticase, Tween-80 and agar is devised to isolate the organisms directly from the clinical specimens and to produce germ tubes and chlamydospores for rapid differentiation and identification of Candida albicans from other closely related Candida species. By manipulating the incubating conditions, the specific phase of the organism can be produced in liquid or on solid medium at different time intervals to study the physiology of the organism.Many methods and media have been proposed in the past for identification of Candida albicans and to differentiate this from the closely related species of Candida (5–8, 15). Taschdjian, Burchall&Kozinn (15) showed that C. albicans produces germ tube within an hour or two when it is grown in human or animal serum or serum substitutes. The specificity of this germ tube test was later confirmed by various workers by using different media (3–5). The distinctive feature that differentiates C. albicans from other species is the production of chlamydospores (14). However, in all these studies three types of media were required to isolate the organisms from clinical specimens and to produce germ tubes and chlamydospores for identification. Recently studies have shown that a single medium can be employed to produce both structural components of the organism from the primary isolation medium but the preparation of the medium is more exhaustive (1) and time consuming (13) than the medium to be described here. The present investigation was therefore undertaken to develop a simple and specific medium to isolate the organism directly from the clinical specimens and to produce various morphological phases of Candida albicans to differentiate from other closely related Candida species for clinical diagnosis and to provide a medium to study the physiology and metabolism of the organism under in vitro conditions.Supported in part by Grant CA 20917, National Cancer Institute, National Institutes of Health and ALSAC.     

Characterization ofPseudomonas geomorphus: A novel groundwater bacterium

Strain ABS10, a Gram-negative, pleomorphic bacterium isolated from a pristine aquifer in Ada, Oklahoma, was studied as a candidate for the introduction and expression of plasmid DNA in a native ground water isolate. This organism was originally typed as anArthrobacter sp. due to its morphological phase change and Gram-variable reaction upon Gram staining. The fatty acid methyl ester profile of ABS10 revealed a high similarity withPseudomonas putida. DNA-DNA hybridization showed 81% homology between ABS10 andP. putida. 16S rRNA sequence analysis showed ABS 10 to be a member of the Gamma division of the purple photosynthetic bacteria. The organism has been designatedPseudomonas geomorphus due to its isolation from a subterranean sample and the morphological phase change from rods in young cultures to cocci in older cultures. The broad host range plasmid RP4 was introduced into ABS10 and stably maintained, indicating that RP4 may serve as a vehicle for the introduction of catabolic genes into this organism.     

Progress inDrosophila genome manipulation

The introduction of cloned and manipulated genetic material into the germline of an experimental organism is one of the most powerful tools of modern biology. In the case of the fruit fly,Drosophila melanogaster, there is also an unparalleled range of sophisticated genetic tools to facilitate subsequent analysis. In consequence,Drosophila remains a most favourable model organism for the dissection of gene structure and functionin vivo. In this review we look at some of the achievements to date inDrosophila genome manipulation, and at what may be possible in the near future.     

Contamination of a hospital environment byClostridium difficile

Clostridium difficile was recovered from a variety of environmental sites in three hospital rooms occupied by a patient who had colitis due to this organism.C. difficile was detected for 40 days after the patient was moved from one of these rooms. These findings suggest that the contaminated hospital environment may be a clinically significant reservoir forC. difficile and that this organism may be a nosocomial pathogen. Isolation of patients and adequate decontamination of rooms may be needed to minimize risk to other patients.     

Biochemical studies on the effect of various carbon sources on growth,nitrogen fixtion,and main cellular constituents of azotobacter vinelandii,strain IV grown under various cultivation conditions

The accessibility of different carbon compounds to Azotobacter vinelandii and the productivity of nitrogen fixation were studied under static and shaking culture conditions. The nature of the carbon source applied was found to affect the yield of bacterial mass and nitrogen metabolism of the tested organism. On the basis of the efficiency of dinitrogen fixation and the yield efficiency ratio it was obvious that (sucrose + mannitol) as a source of carbon is optimum for both growth and dinitrogen fixation by A. vinelandii grown under static and shaking culture conditions. Furthermore, it was found that the highest crude protein efficiency ratio (14.6) and total carbohydrates efficiency ratio (4.3) were obtained with (sucrose + mannitol) as energy source for this organism under shaking culture condition. The experimental organism is able to convert the soluble nitrogenus substances present in molasses into more complex protein as well as to utilize the molasses as a source of energy for the fixtion of atmospheric nitrogen. The tested organism was unable to utilize sodium salicylate as the sole source of carbon.     

Functional expression of heterologous UDP-galactose-4-epimerase in Agrobacterium sp. via a broad host-range expression vector

We report here the first functional expression of a heterologous protein in an Agrobacterium sp. strain (LTU261). A 1014 bp gene coding for the dimeric 79 kDa UDP-galactose-4-epimerase from E. coli was successfully cloned into a 11 kb broad host-range expression vector. Both expression level and activity level in Agrobacterium sp. LTU 261 were about one-tenth of the level obtained in E. coli from the same plasmid. The success of the heterologous expression in Agrobacterium sp. opens up possibilities for introducing new products into this organism and offers opportunities for improvement in production and modification of the existing bioproducts from this organism.