Peptidoglycan types and cytochrome patterns of strains of Oerskovia turbata and O. xanthineolytica

Determination of the primary structure of the peptidoglycan of 15 strains of Oerskovia showed that three different peptidoglycan types occur. Oerskovia xanthineolytica strains contain the l-Lys-d-Ser--d-Asp type, whereas Oerskovia turbata strains show the new peptidoglycan types l-Lys-l-Thr--d-Asp or l-Lys-l-Thr--d-Glu, respectively. Research on the cytochromes of Oerskovia revealed the presence of a, b and c types. O. turbata can be clearly distinguished from O. xanthineolytica by the occurrence of cytochrome a ₁ in cells, isolated from the stationary phase. The following conclusions were made: O. turbata and O. xanthineolytica can be clearly separated on the basis of different peptidoglycan types and cytochrome patterns. This distinction is in perfect correlation with the classical separation method of O. turbata and O. xanthineolytica on the basis of xanthine degradation. l-Lys-d-Ser--d-Asp peptidoglycan type does not only occur in O. xanthineolytica but also in some coryneform bacteria such as Corynebacterium manihot (Fiedler et al. 1970), Cellulomonas cartae (Stackebrandt et al. 1978; Stackebrandt and Kandler 1980), Brevibacterium fermentans and Nocardia cellulans.This paper is respectively dedicated to Professor Dr. O. Kandler, on the occasion of his 60th birthday     

Efficient conversion from polysialogangliosides to monosialotetrahexosylganglioside using Oerskovia xanthineolytica YZ-2

A new sialidase-producing strain isolated from soil was identified as Oerskovia xanthineolytica YZ-2. Sialidase was produced when Oerskovia xanthineolytica YZ-2 was exposed to polysialogangliosides. The sialidase of Oerskovia xanthineolytica YZ-2 hydrolyzed sialic acid linkages in polysialogangliosides, and released monosialotetrahexosylganglioside (GM1). The sialidase had the capability of product specificity because it did not attack the sialic acid linkage in GM1. Therefore, Oerskovia xanthineolytica YZ-2 was used for GM1 production from polysialogangliosides. In flasks cultivation phase, it was proved that Oerskovia xanthineolytica YZ-2 could convert polysialogangliosides to GM1 efficiently. Scaling-up the bioprocess with 8% crude ganglioside, polysialogangliosides was converted to GM1 by Oerskovia xanthineolytica YZ-2 in 30 L bioreactor after 18 h. The relative content of GM1 increased from 16.3% in crude ganglioside to 83.7% after Oerskovia xanthineolytica YZ-2 conversion. Therefore, a simple, large-scale conversion process for GM1 production from polysialogangliosides was achieved using Oerskovia xanthineolytica YZ-2 as a biocatalyst.     

Cellular fatty acid composition of Oerskovia species,CDC Coryneform groups A-3, A-4, A-5, Corynebacterium aquaticum,Listeria denitrificans and Brevibacterium acetylicum

Twenty four strains representing eight species of gram positive yellow-pigmented rods (Oerskovia turbata, Oerskovia xanthineolytica, CDC Coryneform groups A-3, A-4, A-5, Listeria denitrificans, Corynebacterium aquaticum and Brevibacterium acetylicum) were divided into two major groups based on the relative amounts of 12 methyltetradecanoate (15:0^a) obtained by capillary gas liquid chromatography. O. turbata, O. xanthineolytica, CDC groups A-3 and A-4, L. denitrificans and C. aquaticum were placed in the first group due to the presence of a higher percentage (29–47%) of 15:0^a, than CDC group A-5 and B. acetylicum. The latter contained 2–6% of this fatty acid, and were placed in the second group.All species in the two groups except C. aquaticum and CDC group A-4, were further separated from each other based on the qualitative and quantitative differences in their fatty acid compositions. In addition, the eight strains of CDC group A-5 revealed four different patterns and were further divided into four subgroups. This study supports the importance of the composition of cellular fatty acids in differentiating some closely related organisms.     

Chitinase Production in Solid-State Fermentation from <Emphasis Type="Italic">Oerskovia xanthineolytica</Emphasis> NCIM 2839 and its Application in Fungal Protoplasts Formation

The present study reports the economic production of thermostable chitinase production from Oerskovia xanthineolytica NCIM 2839 by solid-state fermentation (SSF) technique and its application in fungal protoplasts formation. The Oerskovia xanthineolytica NCIM 2839 was found to produce thermostable chitinase 148 U g⁻¹ of solid substrate in SSF using wheat bran with colloidal chitin as base. Protoplasts of A. niger were formed by using crude chitinase produced in SSF and formed protoplasts were confirmed by using scanning electron microscopy. This is the simple and economical method for protoplast formation which makes it possible applications in strain improvement of various fungi by protoplasts fusion in Biotechnological industries.     

Two extracellular proteases from Oerskovia xanthineolytica LL-G109

Summary Two proteases have been purified to a high specific activity from Oerskovia xanthineolytica LL-G109 culture broth. Both showed banding on SDS PAGE corresponding to molecular weights in the range 11,000–23,000. One (protease IIa or III) had a pI of 6.5 while the other (protease IIb) had two components of pI = 7.1 and 7.8.     

Study of thermostable chitinases from Oerskovia xanthineolytica NCIM 2839

The mesophilic organism, Oerskovia xanthineolytica NCIM 2839, was adapted to grow at moderate thermophilic temperatures. At these elevated temperatures, it was found to produce two thermostable chitinases—C1 and C2. These were purified by ion exchange chromatography using DEAE cellulose. The chitinases C1 and C2 were found to be stable in a pH range from 3.0 to 9.0 with 7.5 and 8.0 being the optimum pH, respectively. The optimum temperatures of the activities of C1 and C2 were 50 and 55°C, respectively. These were activated by Mn⁺⁺ and Cu⁺⁺and inactivated by Hg⁺⁺. This is first report of an extracellular thermostable chitinase being produced by O. xanthineolytica NCIM 2839.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

DNA homologies of 14 strains of Chlorella protothecoides were determined. All strains are related by a high degree of DNA similarity (96–102% D) with the exception of strain 211-11 a which proved to belong to C. kessleri. There is, however, no detectable DNA homology with strains of the genus Prototheca which is supposed to have evolved from C. protothecoides by loss of photosynthetic pigments. Even within Prototheca the low degree of DNA similarity indicates a heterogeneity similar to that observed in the genus Chlorella.     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

DNA-DNA homology studies among strains of Arthrobacter and Brevibacterium

Sixteen named strains of Arthrobacter and two strains of Brevibacterium were investigated by nucleic acid hybridisation. The Arthrobacter strains show homology values ranging between 11 and 55% to the type strain A. globiformis DSM 20124 (ATCC 8010), indicating only a low to moderate relationship. Two strains of A. globiformis, DSM 20124 and DSM 20125, exhibit only poor relationship to one another (30%). Among all the Arthrobacter strains the homology data range between 10 to 70% demonstrating separate status of almost all species. Only A. polychromogenes DSM 20136 was found to be a subspecies of A. oxydans DSM 20119. The type strain of A. citreus, DSM 20133 shows a remarkable lack of homology to four other strains of A. citreus, deposited as ATCC 15170, ATCC 17775, ATCC 21040 and ATCC 21348 (11–13%) which themselves can be separated into two groups according to the homology data (24–31%). Each of the two strains of Brevibacterium share high genetic relatedness with one of these A. citreus groups (71 and 73%, respectively). According to the DNA-DNA homology data, most of the species of Arthrobacter can actually be ranged taxonomically as species.Abbreviation DSM German Collection of Microorganisms, Menzinger Strasse 67, D-8000 Munich 19, FRG - ATCC American Type Culture Collection, Rockville, Maryland, U.S.A. - CCM Czechoslovak Collection of Microorganisms, J. E. Purkyne University, Tr. Obracu miru 10, Brno, CSSR - NCIB National Collection of Industrial Bacteria Aberdeen, Scotland     

Deoxyribonucleic acid reassociation in the classification of coagulase-positive staphylococci

DNA-DNA reassociation studies were performed with coagulase-positive staphylococci belonging to the biotypes A, B, C, D, E and F. These studies present genetic evidence for the existence of at least two distinct species within this group of organisms. The common Staphylococcus aureus strains were represented by organisms from biotypes A to D, and their DNA revealed over 80% nucleotide sequence homology under restrictive conditions. Less than 15% DNA homology was detected between strains from biotypes A to D (S. aureus) and those from biotypes E and F. The DNA of organisms from either the biotypes E or F displayed over 70% homology. Together, both biotypes are considered to represent the species S. intermedius. However, DNA homology values dropped to 50–65% between strains from different biotypes. This may justify the separation of S. intermedius biotypes E and F on a subspecies level.Abbreviations O.D. optical density - SSC standard saline citrate buffer (0.15 M NaCl, 0.015 M sodium citrate, pH 7.0) This work was supported by Deutsche Forschungsgemeinschaft     

DNA-DNA and rRNA-DNA hybridization studies in the genus Ectothiorhodospira and other purple sulfur bacteria

DNA-DNA hybridization reveals low DNA homologies (about 14%) between the species of Ectothiorhodospira genus and indicate clearly that the degree of divergence within this genus exceeds the interspecific level. The degree of genome similarities of E. mobilis and E. vacuolata (more than 80% homology) is high and characteristic for the strains of one and the same species.The results of rRNA-DNA and secondary DNA-DNA hybridization indicate the following: Ectothiorhodospira and Thiocapsa are far less related than the genera of one and the same family; the genus Ectothiorhodospira is equidistant from both families of purple sulfur and nonsulfur bacteria. Thus Ectothiorhodospira is a taxon of a higher rank than a genus; we agree with Imhoff's proposal of a new family Ectothiorhodospiraceae.     

16S rDNA克隆文库方法分析太岁样品中细菌的多样性

通过构建16S rDNA克隆文库的方法,分析太岁样品中细菌的群落结构及多样性。太岁样品中的细菌归属于4个门9个目,优势类群依次是芽胞杆菌目(Bacillales,33.01%)、柄杆菌目(Caulobacterales,32.04%)和伯克霍尔德氏菌目(Burkholderiales,12.62%);优势属为短波单胞菌属(Brevundimonas,30.10%)、葡萄球菌属(Staphylococcus,29.13%)和食酸菌属(Acidovorax,7.77%)。并且其中的5个目中含有未培养的细菌,红杆菌目(Rhodobacterales)、伯克霍尔德氏菌目和红环菌目(Rhodocyclales)的11个克隆子的细菌16S rDNA序列同源性低于97%。研究表明太岁样品中细菌多样性较丰富,且蕴藏着许多未知的微生物资源。     

The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A New Family,Alteromonadaceae fam. nov., Including Marine Proteobacteria of the Genera Alteromonas,Pseudoalteromonas, Idiomarina,and Colwellia

The taxonomic positions of the marine genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia within the gamma subclass of the class Proteobacteria were specified on the basis of their phenotypic, genotypic, and phylogenetic characteristics. Gram-negative aerobic bacteria of the genera Alteromonas, Pseudoalteromonas, and Idiomarina and facultatively anaerobic bacteria of the genus Colwellia were found to form a phylogenetic cluster with a 16S rRNA sequence homology of 90% or higher. The characteristics of these genera presented in this paper allow their reliable taxonomic identification. Based on the analysis of our experimental data and analyses available in the literature, we propose to combine the genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia into a new family, Alteromonadaceae fam. nov., with the type genus Alteromonas.     

Reproductive isolation in the Aegean Ophrys omegaifera complex (Orchidaceae)

The orchid genus Ophrys operates a system of sexual deception by which high specificity of pollination is attained. Reproductive isolation in Ophrys mainly rests upon prezygotic isolation mechanisms. The level of genetic separateness of Ophrys taxa with different pollinators is therefore likely determined by the fidelity of pollinators. The present study employs genetic fingerprinting to investigate this in the east Aegean Ophrys omegaifera s.l. complex, also including O. dryis, a west Mediterranean species of this complex. Ophrys fleischmannii, O. basilissa, and the west Mediterranean O. dyris, are found to be well-separated genetic entities whereas O. omegaifera s.str. and the putative hybrid taxon, O. sitiaca, are found to be genetically inseparable across their entire range of co-occurrence. This suggests that specific pollinators have high enough fidelity to act as effective isolating factors in east Aegean O. omegaifera s.l. as a whole, but that the situation in the species pair of O. sitiaca and O. omegaifera is likely to be more complex.     

Physiological and biochemical contributions to the taxonomy of the genus Prototheca

16 strains of the genus Prototheca do not produce extracellular amylolytic enzymes. The base composition of their DNA shows rather continuous values from 62% to 78% GC (guanine + cytosine). Their assignment to four species and their possible relationship with Chlorella protothecoides are discussed.Abbreviations Used GC guanine + cytosine - SSC saline sodium citrate     

Origin and phylogeny of Oryza species with the CD genome based on multiple-gene sequence data

The CD genome species in the genus Oryza are endemic to Latin America, including O. alta, O. grandiglumis and O. latifolia. Origins and phylogenetic relationship of these species have long been in dispute and are still ambiguous due to their homogeneous genome type, similar morphological characteristics and overlapping distribution. In the present study, we sequenced two chloroplast fragments (matK and trnL-trnF) and portions of three nuclear genes (Adh1, Adh2 and GPA1) from sixteen accessions representing seven species with the C, CD, and E genomes, as well as one G genome species as the outgroup. Phylogenetic analyses using parsimony and distance methods strongly supported that the CD genome originated from a single hybridization event, and that the C genome species (O. officinalis or O. rhizomatis instead of O. eichingeri) served as the maternal parent while the E genome species (O. australiensis) was the paternal donor during the formation of CD genome. In addition, the consistent phylogenetic relationships among the CCDD species indicated that significant divergence existed between O. latifolia and the other two (O. alta and O. grandiglumis), which corroborated the suggestion of treating the latter two as a single species or as taxa within species.We thank Tao Sang of Michigan State University (East Lansing, USA) and Bao-rong Lu of Fudan University (Shanghai, China) for their encouragement and assistance. We are also grateful to the International Rice Research Institute (Manila, Philippines) for providing plant material for this study. This research was supported by the Chinese Academy of Sciences (kscxz-sw-101A), the National Natural Science Foundation of China (30025005) and the Program for Key International S & T Cooperation Project of P. R. China (2001CB711103).     

Purification of the major glucanase of Oerskovia xanthineolytica LL-G109

Summary A major lytic -1,3-glucanase with M_r = 31,000 has been purified to homogeneity from Oerskovia xanthineolytica LL-G109. This enzyme had a specific activity of 11.1 U/mg and a pI of 5.0.     

青藏高原特有属——固沙草属(禾本科)2个类群的修订

固沙草属(Orinus)是禾本科(Poaceae)中一个具有重要经济价值的高山特有属,共记载6个物种,它们均具有较强的抗逆特性,是农业良种繁育、畜牧业牧草改良利用的重要资源,但固沙草属物种形态差异不显著,种间界限较模糊。该研究通过标本研究、野外考察、形态性状分析以及实验的观察研究,对固沙草属2个类群进行了分类修订,将长颖固沙草(O.longiglumis)和西藏固沙草(O.tibeticus)以及高秆固沙草(O.alticulmus)和鸡爪草(O.anomala)分别处理为固沙草(O.thoroldii)和青海固沙草(O.kokonorica)的新异名。     

Rapid procedure for the isolation of high molecular weight RNA and DNA from yeast using lyticase and sodium dodecyl sulfate

Lyticase, an enzyme preparation isolated from the culture supernatant of Oerskovia xanthineolytica, was found to lyse yeast cells in the presence of sodium dodecyl sulfate (SDS). Undegraded nucleic acids could be isolated from the lysate demonstrating the usefulness of the described procedure for the rapid isolation of high molecular weight RNA and DNA from whole cells.