Immunophyletic relationships between actinomycetales and eubacteriales determined by examinations of their cytoplasmic antigens.

Cytoplasms obtained from a total of 205 different strains of Actinomycetales, Eubacteriales, Lower Fungi, and Protozoa were examined against selected anti-cytoplasm antisera using the immunodiffusion and counterimmunoelectrophoresis procedures. Immunological relationships between the different genera have been revealed and, in respect to Eubacteriales, the possible immunophyletic determinants have been discerned. Cytoplasms of Enterobacter, Clostridium, Staphylococcus, and Diplococcus were found to retain the significant linkage determinants between large groups of Eubacteriales and Actinomycetales. Evolutionary implications of the findings are discussed.     

放线菌15个属中线型染色体和线型质粒的检测

在属于放线菌目 (Actinomycetales)链霉菌属 (Streptomyces)下的不同种中发现了约 5 0 0 0种抗生素和生理活性物质 ,其作用包括抗细菌、抗真菌、除草、杀虫、抗肿瘤和免疫抑制剂等[1 ] 。在属于放线菌目的红球菌属 (Rhodococcus)和诺卡氏菌属 (Nocardia)中有许多种可以降解多种工业有毒化合物 ,如苯酚、多卤联苯、脂环烃和硝基芳族等[2 ] 。一般细菌的染色体和质粒DNA为环型结构。近年来 ,人们利用脉冲电泳技术发现在链霉菌等少数细菌中存在线型结构的染色体和质粒[3] ,有的巨大线型质粒上还带有完整的抗生素生物合成基因簇[4 ]或降解多…     

Taxonomic characteristics of soil Mycobacteria and their antibiotic properties]

Morphological, cultural and chemotaxonomic properties of 12 gram-positive soil cultures isolated were studied by using a test system developed for screening the organisms producing broad-spectrum antibiotics among Nocardiaforms (Coryneforms). The cultures were found to belong to Actinomycetales, Nocardioforms, Mycobacteriaceae and Mycobacterium. The saprophytic rapidly growing soil mycobacteria showed antibiotic activity against a large number of gram-positive and gram-negative test microbes including those belonging to Pseudomonas and Proteus resistant to the majority of the antibiotics currently used in medicine.     

海洋放线菌盐孢菌属研究进展

1991年,Jensen等从热带及亚热带海洋样品中分离获得了放线菌目专性海洋放线菌类群MAR1。根据形态学特征、生理生化特征及16S rRNA基因分析,提议该类群为新属——盐孢菌属(Salinospora)。2005年,盐孢菌属被正式报道,并将Salinospora更正为Salinispora。盐孢菌属是放线菌目第一个被报道的专性海洋微生物属,可以产生丰富的活性次级代谢产物,使盐孢菌属成为海洋微生物研究的热点。短短几年内,相继报道了许多研究成果。本文从盐孢菌属的建立过程、属及所含种的分类特征、生理生态学研究、次级代谢产物和分子生物学研究等方面对盐孢菌属的研究进展进行综述。     

Sequence, overproduction and purification of the family 11 endo-beta-1,4-xylanase encoded by the xyl1 gene of Streptomyces sp. S38.

The xyl1 gene encoding the Xyl1 xylanase of Streptomyces sp. strain S38 was cloned by screening an enriched DNA library with a specific DNA probe and sequenced. Three short 5 bp -CGAAA- sequences are located upstream of the Streptomyces sp. S38 xyl1 gene 105, 115 and 250 bp before the start codon. These sequences, named boxes 1, 2 and 3, are conserved upstream of the Actinomycetales xylanase genes and are specifically recognized by a DNA-binding protein (Giannotta et al., 1994. FEMS Microbiol. Lett. 142, 91-97) and could be probably involved in the regulation of xylanase production. The Xyl1 ORF encodes a 228 residue polypeptide and the Xyl1 preprotein contains a 38 residue signal peptide whose cleavage yields a 190 residue mature protein of calculated M(r) = 20,585 and basic pI value of 9.12. The molecular mass of the produced and purified mature protein determined by mass spectrometry (20,586 +/- 1 Da) and its pI (9.8) agree with these calculated values. Its N-terminal amino-acid sequence confirmed the proposed cleavage site between the signal peptide and the mature protein. Comparisons between Xyl1 and the 62 other xylanases belonging to family 11 allowed the construction of a phylogenetic tree and revealed its close relationship with Actinomycetales enzymes. Moreover, nine residues were found to be strictly conserved among the 63 xylanases.     

16S rRNA metagenomic analysis of the symbiotic community structures of bacteria in foregut,midgut, and hindgut of the wood-feeding termite <Emphasis Type="Italic">Bulbitermes</Emphasis> sp.

The termite gut is a highly structured microhabitat with physicochemically distinct regions. It is generally separated into the foregut, midgut and hindgut. The distribution of gut microbiota is greatly influenced by varying physicochemical conditions within the gut. Thus, each gut compartment has a unique microbial population structure. In this study, the bacterial communities of foregut, midgut and hindgut of wood-feeding higher termite, Bulbitermes sp. were analyzed in detail via metagenomic sequencing of the 16S rRNA V3-V4 region. While the microbiomes of the foregut and midgut shared a similar taxonomic pattern, the hindgut possessed more diverse bacterial phylotypes. The communities in the foregut and midgut were dominated by members of the group Bacilli and Clostridia (Firmicutes) as well as taxon Actinomycetales (Actinobacteria). The main bacterial lineage found in hindgut was Spirochaetaceae (Spirochaetes). The significant difference among the three guts was the relative abundance of the potential lignin-degrading bacteria, Actinomycetales, in both the foregut and midgut. This suggests that lignin modification was probably held in the anterior part of termite gut. Predictive functional profiles of the metagenomes using 16S rRNA marker gene showed that cell motility, energy metabolism and metabolism of cofactors and vitamins were found predominantly in hindgut microbiota, whereas xenobiotics degradation and metabolism mostly occurred in the foregut segment. This was compatible with our 16S rRNA metagenomic results showing that the lignocellulose degradation process was initiated by lignin disruption, increasing the accessibility of celluloses and hemicelluloses.     

Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton

The effect of signal compounds and of different incubation conditions on the culturability (i.e., the fraction of all cells capable of growth) of natural bacterioplankton from the eutrophic lake Zwischenahner Meer was investigated over a period of 20 months. Numbers of growing cells were determined by the most-probable-number technique in liquid media containing low concentrations (10 micro M) of the signal compounds N-(oxohexanoyl)-DL-homoserine lactone, N-(butyryl)-DL-homoserine lactone, cyclic AMP (cAMP), or ATP. cAMP was the most effective signal compound, leading to significantly increased cultivation efficiencies of up to 10% of the total bacterial counts. Microautoradiography with [2,8-(3)H]cAMP, combined with fluorescence in situ hybridization, demonstrated that cAMP was taken up by 18% of all cells. The bacterial cAMP uptake systems had a very low K(m) value of 相似文献   

抗生素对于对虾苗池水体细菌区系的影响

以细菌16S rDNA片段作为分子标记,采用PCR结合DGGE（Denaturing gradient gel electrophoresis）的方法构建了细菌区系指纹图谱,研究了对虾苗池使用硫酸链霉素、土霉素和氨苄青霉素3种抗生素后水体细菌区系的变化.结果表明：在120 h试验期内,与对照组相比,苗池水体分别经0.5 mg·L^-1的硫酸链霉素、土霉素和氨苄青霉素处理后,细菌区系均产生了显著变化;对照组水体0～30 h时段的细菌DGGE条带聚为一组,56～120 h取样时的条带聚为一组;而3个处理组水体0～56 h时段的细菌DGGE条带聚为一组,72～120 h聚为一组.对DGGE图谱典型条带进行测序,经BLAST-N比对,表明对虾苗池水体细菌多样性丰富,包括可培养的细菌（主要包括亚硫酸盐杆菌、红假单胞菌、美人鱼发光杆菌、聚球菌、海洋放线菌、黄杆菌、丝状光合细菌、粘细菌、哈氏弧菌）和某些不可培养的其他海洋细菌等.其中,单胞菌、发光杆菌、放线菌、黄杆菌、粘细菌和2种不可培养的其他海洋细菌不受抗生素的影响;而硫细菌、丝状光合细菌和另外8种不可培养的其他海洋细菌则因抗生素种类不同产生了不同的时空变化.     

河西走廊酒泉地区盐碱土未培养放线菌多样性

采用免培养技术对河西走廊酒泉地区的原生盐碱土、次生盐碱土和农田土中的放线菌群落结构及其多样性进行分析.结果表明: 河西走廊酒泉地区原生盐碱土克隆文库分归于19个OTUs,分属于微球菌亚目、丙酸杆菌亚目、棒状杆菌亚目、弗兰克氏菌亚目、假诺卡氏菌亚目和放线菌目未知类群;次生盐碱土克隆文库分归于14个OTUs,分属于微球菌亚目、丙酸杆菌亚目和放线菌目未知类群;农田土克隆文库分归于7个OTUs,分属于微球菌亚目和棒状杆菌亚目;微球菌亚目是3种不同类型土壤中的共有种群,是原生盐碱土和农田土中的优势种群.多样性指数和稀释性曲线分析结果显示,3种不同类型土壤中放线菌种群丰富度为原生盐碱土>次生盐碱土>农田土;原生盐碱土、次生盐碱土的稀释性曲线均未趋于平稳,说明盐碱土中放线菌多样性比实际更加丰富.     

F420H2-dependent degradation of aflatoxin and other furanocoumarins is widespread throughout the actinomycetales

Two classes of F(420)-dependent reductases (FDR-A and FDR-B) that can reduce aflatoxins and thereby degrade them have previously been isolated from Mycobacterium smegmatis. One class, the FDR-A enzymes, has up to 100 times more activity than the other. F(420) is a cofactor with a low reduction potential that is largely confined to the Actinomycetales and some Archaea and Proteobacteria. We have heterologously expressed ten FDR-A enzymes from diverse Actinomycetales, finding that nine can also use F(420)H(2) to reduce aflatoxin. Thus FDR-As may be responsible for the previously observed degradation of aflatoxin in other Actinomycetales. The one FDR-A enzyme that we found not to reduce aflatoxin belonged to a distinct clade (herein denoted FDR-AA), and our subsequent expression and analysis of seven other FDR-AAs from M. smegmatis found that none could reduce aflatoxin. Certain FDR-A and FDR-B enzymes that could reduce aflatoxin also showed activity with coumarin and three furanocoumarins (angelicin, 8-methoxysporalen and imperatorin), but none of the FDR-AAs tested showed any of these activities. The shared feature of the compounds that were substrates was an α,β-unsaturated lactone moiety. This moiety occurs in a wide variety of otherwise recalcitrant xenobiotics and antibiotics, so the FDR-As and FDR-Bs may have evolved to harness the reducing power of F(420) to metabolise such compounds. Mass spectrometry on the products of the FDR-catalyzed reduction of coumarin and the other furanocoumarins shows their spontaneous hydrolysis to multiple products.     

Predominant Catalase-negative Soil Bacteria. III. Agromyces, gen. n., Microorganisms Intermediary to Actinomyces and Nocardia

The occurrence of filamentous, branching, catalase-negative bacteria as a numerically predominant microflora of various soils was demonstrated by using a dilution frequency isolation procedure. The major characteristics of these organisms were those of the order Actinomycetales. However, they could not be placed in any of the present genera of this order and, therefore, a new genus, Agromyces, was proposed for these organisms. This genus includes catalase-negative, nutritionally-fastidious microorganisms whose cells produce a true branching mycelium that fragments into coccoid and diphtheroid forms. Also, they have an oxidative metabolism, are microaerophilic to aerobic, and contain neither diaminopimelic acid nor lysine as major constituents of the cell wall glycopeptide. The type species would be Agromyces ramosus, gen. n., sp. n. The possible importance of these organisms in clarifying certain phylogenetic relationships of the Actinomycetales is discussed.     

Chromosome diversity and similarity within the Actinomycetales

Many chromosomes from Actinomycetales, an order within the Actinobacteria, have been sequenced over the last 10 years and the pace is increasing. This group of Gram-positive and high G+C% bacteria is economically and medically important. However, this group of organisms also is just about the only order in the kingdom Bacteria to have a relatively high proportion of linear chromosomes. Chromosome topology varies within the order according to the genera. Streptomyces, Kitasatospora and Rhodococcus, at least as chromosome sequencing stands at present, have a very high proportion of linear chromosomes, whereas most other genera seem to have circular chromosomes. This review examines chromosome topology across the Actinomycetales and how this affects our concepts of chromosome evolution.     

Inbred strain variation in lung function

The purpose of the present study was to determine the strain-specific phenotype variance of lung function parameters among common inbred laboratory mouse strains. In accordance with the "Mouse Phenome Project" run by The Jackson Laboratory (http://www.jax.org/phenome), lung volumes, lung mechanics, and diffusing capacity of 16 males and 16 females of the strains C3H/HeJ, BALB/cByJ, C57B1/6J, A/J, FVB/J, 129SV/ImJ, and SWR/J were determined in a standardized manner. The defined respiratory maneuvers for lung function testing were performed with a custom-made, computer-controlled servo-ventilator in anesthetized animals. Sex differences within the strains were found in most (83%) of the absolute lung function parameters. Usually, normalization to body or lung size completely compensates for the observed gender differences. There was great diversity between strains for all of the lung function parameters studied; for example, the total lung capacity as well as the pulmonary diffusing capacity for carbon monoxide varied by 50% and the static lung compliance by a factor of almost two among the strains. Little, but statistically significant variability was detectable for the dead space volume and the respiratory system resistance. There was no clear-cut evidence for any strain exhibiting either the smallest or the largest values for all parameters studied, suggesting that there were no simple allometric relationships of lung size between the strains. Well-established genealogical relationships among strains were not constantly reflected in phenotype similarities of pulmonary function. Therefore, these data strongly support heritable genetic traits for pulmonary function. Moreover, it constitutes a basis for further genetic lung function-related studies.     

First report that the wasp Gronotoma guamensis (Hymenoptera: Figitidae: Eucoilinae) parasitizes the orchid‐feeding fly Japanagromyza tokunagai in Japan

Compared with mycorrhizal relationships, the relationships between mycoheterotrophic plants and insects have rarely been studied. Here we report a previously unknown tripartite interaction among an endangered mycoheterotrophic orchid, an orchid‐feeding fly, and a parasitoid wasp. The flowers and stems of Eulophia zollingeri were heavily attacked by Japanagromyza tokunagai (Sasakawa) (Diptera: Agromyzidae), and the parasitoid wasp Gronotoma guamensis (Yoshimoto) (Hymenoptera: Figitidae) was reared from these J. tokunagai individuals. Considering the high infestation rate of J. tokunagai, G. guamensis could be important in suppressing the J. tokunagai population, and positively affect the reproductive success of E. zollingeri.     

PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa

The phylogenetic composition of bacterial communities in the rhizosphere of three potato cultivars grown at two distant field sites was analysed. Ribosomal gene fragments amplified from total community DNA were hybridized to PhyloChips. A total of 2432 operational taxonomic units (OTUs) were detected by the PhyloChips, of which 65% were found in the rhizosphere of all cultivars at both field sites. From all detected OTUs, 9% revealed a cultivar-dependent abundance at the one or the other field site and 4% at both sites. Differential abundance on the three cultivars was mainly observed for OTUs belonging to the Pseudomonadales, Actinomycetales and Enterobacteriales. More than 40% of OTUs belonging to Bradyrhizobiales, Sphingomonadales, Burkholderiales, Rhodocyclales, Xanthomonadales and Actinomycetales differed significantly in their abundance between the sites. A sequence analysis of six 16S rRNA gene clone libraries corresponded well with the taxonomic community structure evidenced by the PhyloChip hybridization. Most ribotypes matched OTUs detected by the PhyloChip. Those OTUs that responded to the potato cultivar at both field sites might be of interest in view of cultivar-specific effects on bacterial biocontrol strains and pathogens.     

Analysis of developmental gene conservation in the Actinomycetales using DNA/DNA microarray comparisons

Based on available genome sequences, Actinomycetales show significant gene synteny across a wide range of species and genera. In addition, many genera show varying degrees of complex morphological development. Using the presence of gene synteny as a basis, it is clear that an analysis of gene conservation across the Streptomyces and various other Actinomycetales will provide information on both the importance of genes and gene clusters and the evolution of morphogenesis in these bacteria. Genome sequencing, although becoming cheaper, is still relatively expensive for comparing large numbers of strains. Thus, a heterologous DNA/DNA microarray hybridization dataset based on a Streptomyces coelicolor microarray allows a cheaper and greater depth of analysis of gene conservation. This study, using both bioinformatical and microarray approaches, was able to classify genes previously identified as involved in morphogenesis in Streptomyces into various subgroups in terms of conservation across species and genera. This will allow the targeting of genes for further study based on their importance at the species level and at higher evolutionary levels.     

Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil

We report the characterisation of Nocardioides sp. SP12, an atrazine-degrading bacteria isolated from atrazine-treated bulk- and maize rhizosphere soil. Based on 16S rDNA alignment, strain SP12 showed close phylogenic relationships with Nocardioides sp. C157 and Nocardioides simplex. Internal transcribed spacer (ITS) sequences of strain SP12 were longer than those of other Nocardioides sp. and present Ala- and Ile-tRNA unlike Actinomycetales. Nocardioides sp. SP12 presents a novel atrazine catabolic pathway combining trzN with atzB and atzC. Atrazine biodegradation ends in a metabolite that co-eluted in HPLC with cyanuric acid. This metabolite shows an absorption spectrum identical to that of cyanuric acid with a maximal absorption at 214.6 nm. The mass of the atrazine metabolite is in concordance with that of cyanuric acid according to mass spectrometry analysis. Quantitative PCR revealed that the ITS sequence of Nocardioides sp. SP12 was at a lower number than the one of trzN in atrazine-treated soil samples. It suggests that trzN could also be present in other atrazine degrading bacteria. The numbers of trzN and ITS sequences of Nocardioides sp. SP12 were higher in the maize rhizosphere than in bulk soil.     

Novel Fusicoccins R and S, and the fusicoccin S aglycon (phomopsiol) from Phomopsis amygdali niigata 2-A, and their seed germination-stimulating activity in the presence of abscisic acid

Our search for new 3-hydroxyfusicoccins structurally related to cotylenin A from a culture of Phomopsis amygdali Niigata 2-A resulted in the isolation of novel 3-hydroxy fusicoccins, called fusicoccins R and S, and the fusicoccin S aglycon, called phomopsiol, together with known 3alpha-hydroxyfusicoccin J. The structure of phomopsiol was identified as that of O-demethyl-3-epicotylenol based on spectroscopic evidence. The structures of fusicoccins R and S were also determined to be those of 3'-deacetyl-3alpha-hydroxyfusicoccin A and 3beta-hydroxy-3-epifusicoccin H. The lettuce seed germination-stimulating activity of fusicoccins R and S, phomopsiol and 3alpha-hydroxyfusicoccin J was examined in the presence of ABA; fusicoccin R and 3alpha-hydroxyfusicoccin J were highly active, while fusicoccin S and phomopsiol were inactive. The possible biosynthetic relationships among these novel fusicoccins having a 3alpha- or 3beta-hydroxy group in their diterpene moiety are briefly discussed.     

Two-component signal transduction systems in <Emphasis Type="Italic">Streptomyces</Emphasis> and related organisms studied using DNA comparative microarray analysis

Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. In this study, we have used DNA/DNA genome microarray analysis to compare 14 Streptomyces species and one closely related genus to Streptomyces coelicolor in order to identify a core group of such systems. This core group is compared to the syntenous and non-syntenous TCSs present in the genome sequences of other Actinomycetales in order to separate the systems into those present in Actinomycetales in general, the Streptomyces specific systems and the species specific systems. Horizontal transfer does not seem to play a very important role in the evolution of the TCS complement analyzed in this study. However, cognate pairs do not necessarily seem to evolve at the same pace, which may indicate the evolutionary responses to environmental variation may be reflected differently in sequence changes within the two components of the TCSs. The overall analysis allowed subclassification of the orphan TCSs and the TCS cognate pairs and identification of possible targets for further study using gene knockouts, gene overexpression, reporter genes and yeast two hybrid analysis. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.