Iron and carbon metabolism by a mineral-oxidizing Alicyclobacillus-like bacterium

A novel iron-oxidizing, moderately thermophilic, acidophilic bacterium (strain “GSM”) was isolated from mineral spoil taken from a gold mine in Montana. Biomolecular analysis showed that it was most closely related to Alicyclobacillus tolerans, although the two bacteria differed in some key respects, including the absence (in strain GSM) of ϖ-alicyclic fatty acids and in their chromosomal base compositions. Isolate GSM was able to grow in oxygen-free media using ferric iron as terminal electron acceptor confirming that it was a facultative anaerobe, a trait not previously described in Alicyclobacillus spp.. The acidophile used both organic and inorganic sources of energy and carbon, although growth and iron oxidation by isolate GSM was uncoupled in media that contained both fructose and ferrous iron. Fructose utilization suppressed iron oxidation, and oxidation of ferrous iron occurred only when fructose was depleted. In contrast, fructose catabolism was suppressed when bacteria were harvested while actively oxidizing iron, suggesting that both ferrous iron- and fructose-oxidation are inducible in this acidophile. Isolate GSM accelerated the oxidative dissolution of pyrite in liquid media either free of, or amended with, organic carbon, although redox potentials were significantly different in these media. The potential of this isolate for commercial mineral processing is discussed.     

Isolation and identification of species of Alicyclobacillus from orchard soil in the Western Cape, South Africa

Alicyclobacilli were isolated from orchard soil collected from an apple and pear farm in Elgin, Western Cape, South Africa. Morphological, biochemical and physiological characteristics of the isolates were used to presumptively classify them as belonging to the genus Alicyclobacillus. Strains were identified to species level by polymerase chain reaction (PCR) with genus-specific primers, and 16S ribosomal RNA (rRNA) gene sequencing. To our knowledge this is the first report on the isolation of Alicyclobacillus acidoterrestris and Alicyclobacillus acidocaldarius from orchard soil. The presence of these organisms in the soil suggests a possible source of contamination for the final fruit juice, concentrate or pulp.     

Fatty acids, unusual glycophospholipids and DNA analyses of thermophilic bacteria isolated from hot springs

The composition of fatty acids in 12 strains of the genera Thermus, Meiothermus, Geobacillus and Alicyclobacillus was analyzed by gas chromatography–mass spectrometry. Major FAs found in the profiles included i-15:0, i-17:0, ai-15:0, i-16:0, 16:0, ai-17:0, together with some minor components. Branched FAs were predominant, forming more than 80% of all FAs measured. Fast atom bombardment-mass spectrometry was used for analysis of unusual glycophospholipids, i.e., acylglycosylcardiolipins from genera Geobacillus and Alicyclobacillus and 1-(hydroxy(2-(O-acylglycosyl-oxy)hexadecyloxy)phosphoryloxy) hexadecan-2-yl esters of C15–C17 acids from genera Thermus and Meiothermus. Cloning and preliminary sequence analysis of 16S rDNA showed that these isolates belong to the genera Thermus, Meiothermus, Geobacillus and Alicyclobacillus.     

Transport and utilization of ferrioxamine-E-bound iron inErwinia herbicola (Pantoea agglomerans)

Summary We have analyzed ferrioxamine-E-mediated iron uptake and metabolization inErwinia herbicola K4 (Pantoea agglomerans) by means of in vivo Mössbauer spectroscopy and radioactive labeling techniques. A comparison of cell spectra with the spectrum of ferrioxamine clearly demonstrates that ferrioxamine E is not accumulated in the cell, indicating a fast metal transfer. Only two major components of iron metabolism can be detected, a ferric and a ferrous species. At 30 min after uptake, 86% of the internalized metal corresponded to a ferrous ion compound and 14% to a ferric iron species. Metal transfer apparently involves a reductive process. With progressing growth, the oxidized species of the two major proteins becomes dominant. The two iron metabolites closely resemble species previously isolated fromEscherichia coli. These components of iron metabolism differ from bacterio-ferritin, cytochromes and most iron-sulfur proteins. All other iron-containing cellular components are at least one order of magnitude lower in concentration. We suggest that the ferrous and ferric iron species correspond to two different oxidation states of a low-molecular mass protein.     

内蒙古岗更诺尔湖泊退化情景下好氧甲烷氧化的微生物过程研究

【目的】内蒙古岗更诺尔湖退化为碱地、草地情景下,研究好氧甲烷氧化过程及其微生物群落的变化规律。【方法】针对湖泊沉积物及其退化后形成的碱地、草地土壤,在不同初始甲烷浓度下培养,研究其甲烷氧化速率,通过实时荧光定量PCR、高通量测序技术分析甲烷氧化菌的群落构成及其变化规律。【结果】湖泊退化过程中,沉积物和碱地的土壤理化性质、甲烷氧化速率变化规律基本一致,但与草地土壤有显著差异。在微生物属水平,甲烷氧化菌Methylococcus的丰度显著增加,在沉积物、碱地和草地中的丰度分别为19.2%、48.8%和78.3%,而Crenothrix的丰度明显降低,依次为54.7%、32.1%、和13.9%。进一步室内模拟不同初始浓度下甲烷氧化过程,发现沉积物中Crenothrix和Methylocaldum的增幅最大;碱地土壤中Methylococcus和Methylomonas的增幅远高于其他甲烷氧化菌;而在草地土壤中,Crenothrix增加高达7.81%,增幅达196倍。这些显著增加的微生物可能在不同浓度甲烷氧化过程中发挥了重要作用。【结论】湖泊退化过程中,甲烷氧化潜力降低。沉积物中的甲烷氧化菌发生了显著分异,Methylococcus逐渐成为碱地和草地的优势微生物,而Crenothrix则逐渐成为弱势类群。然而,草地土壤氧化高浓度甲烷过程中,数量上占弱势的Crenothrix迅速变为优势类群,可能发挥了重要作用。     

Proferrioxamine profiles of Erwinia herbicola and related bacteria

Two strains of Erwinia herbicola effective in the biocontrol of E. amylovora, the etiological agent of fire blight, were screened for proferrioxamine siderophores by on-line liquid chromatography-electrospray mass spectrometry (LC-MS). Type strains of E. herbicola and Pantoea species were included in this study for taxonomic comparisons. Proferrioxamine profiles similar to that previously described for E. amylovora, including tri- and tetrameric hydroxamates and diaminopropane-containing proferrioxamines, were observed for P. agglomerans, but not for other E. herbicola-like species. Biocontrol activity was not correlated with proferrioxamine synthesis. The results of this study are consistent with the notion that some, but not all, biocontrol strains may inhibit E. amylovora via competition for iron. Further studies into the link between biocontrol of fire blight and siderophores are thus warranted. This study also revealed limitations of standard nutrient utilization and fatty acid profile analyses for the differentiation of P. agglomerans, P. dispersa and other E. herbicola-like species from each other. Given these limitations, LC-MS may become a much needed additional diagnostic tool for the identification of E. herbicola-like strains at the species level.     

<Emphasis Type="Italic">FORMOSA</Emphasis> controls cell division and expansion during floral development in <Emphasis Type="Italic">Antirrhinum</Emphasis><Emphasis Type="Italic">majus</Emphasis>

Control of organ size is the product of coordinated cell division and expansion. In plants where one of these pathways is perturbed, organ size is often unaffected as compensation mechanisms are brought into play. The number of founder cells in organ primordia, dividing cells, and the period of cell proliferation determine cell number in lateral organs. We have identified the Antirrhinum FORMOSA (FO) gene as a specific regulator of floral size. Analysis of cell size and number in the fo mutant, which has increased flower size, indicates that FO is an organ-specific inhibitor of cell division and activator of cell expansion. Increased cell number in fo floral organs correlated with upregulation of genes involved in the cell cycle. In Arabidopsis the AINTEGUMENTA (ANT) gene promotes cell division. In the fo mutant increased cell number also correlates with upregulation of an Antirrhinum ANT-like gene (Am-ANT) in inflorescences that is very closely related to ANT and shares a similar expression pattern, suggesting that they may be functional equivalents. Increased cell proliferation is thought to be compensated for by reduced cell expansion to maintain organ size. In Arabidopsis petal cell expansion is inhibited by the BIGPETAL (BPE) gene, and in the fo mutant reduced cell size corresponded to upregulation of an Antirrhinum BPE-like gene (Am-BPE). Our data suggest that FO inhibits cell proliferation by negatively regulating Am-ANT, and acts upstream of Am-BPE to coordinate floral organ size. This demonstrates that organ size is modulated by the organ-specific control of both general and local gene networks. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH

The archaeal community present in a sample of Mixed Thermophilic Culture-B (MTC-B) from a laboratory-scale thermophilic bioleaching reactor was investigated by temperature gradient gel electrophoresis (TGGE) and fluorescence in situ hybridisation (FISH). Both techniques were specifically adapted for use on native state bioleaching samples, with a view to establishing convenient means for monitoring culture composition. Using the TGGE protocol developed, the relative species composition of the thermophilic bioleaching sample was analysed, and included four phylotypes belonging to the Sulfolobales, which were related to Stygiolobus azoricus, Metallosphaera sp. J1, Acidianus infernus and Sulfurisphaera ohwakuensis. However, the St. azoricus-like phylotype was difficult to resolve and some micro-heterogeneity was observed within this phylotype. Specific FISH probes were designed to qualitatively assess the presence of the phylotypes in MTC-B. The sample was dominated by Sf. ohwakuensis-like Archaea. In addition, the St. azoricus-like, Metallosphaera species-like and Acidianus species-like cells appeared in similar low abundance in the community. Most strikingly, FISH identified Sulfolobus shibatae-like cells present in low numbers in the sample even though these were not detected by PCR-dependent TGGE. These results highlight the importance of using more than one molecular technique when investigating the archaeal diversity of complex bioleaching reactor samples.     

基于可培养方法分析云南腾冲小空山火山谷芽胞杆菌分布特征

【目的】为了解云南腾冲小空山火山谷土壤中可培养芽胞杆菌种类分布特征。【方法】采用可培养手段对小空山火山谷阳坡、谷底和阴坡土壤中的芽胞杆菌进行分离培养,根据16S rRNA基因序列同源性对分离菌株进行鉴定,并分析系统发育地位。利用Canoco5软件分析采样点芽胞杆菌种类分布特征与土壤样品理化性质的相关性。【结果】从火山谷土壤样品中共分离获得180株芽胞杆菌,16S rRNA基因测序鉴定结果表明分离菌株隶属于芽胞杆菌纲2个科(芽胞杆菌科和类芽胞杆菌科)、6个属、34个种,其中芽胞杆菌属(Bacillus) 11个种,类芽胞杆菌属(Paenibacillus) 14个种,短芽胞杆菌属(Brevibacillus)3个种,赖氨酸芽胞杆菌属(Lysinibacillus)4个种,嗜冷芽胞杆菌属(Psychrobacillus)1个种和绿芽胞杆菌属(Viridibacillus)2个种,其中7个菌株与其最近模式菌株16SrRNA相似性低于种的界定阈值(98.65%),为芽胞杆菌潜在新物种。优势属为芽胞杆菌属和类芽胞杆菌属,优势种为蕈状芽胞杆菌(Bacillusmycoides),图瓦永芽胞杆菌(Bacillustoyonensis),蜡状芽胞杆菌(Bacilluscereus),解木糖赖氨酸芽胞杆菌(Lysinibacillusxylanilyticus),蜂房类芽胞杆菌(Paenibacillusalvei)和沙地绿芽胞杆菌(Viridibacillus arenosi)。其中16个种分离自阳坡,29个种分离自阴坡,9个种分离自谷底,三者共同种类为6种。阳坡、谷底和阴坡的芽胞杆菌种群分布Bray-Curtis相似性为62.4%,多样性分析结果表明,Shannon指数(H′)大小次序为阴坡阳坡谷底。环境因子分析发现,芽胞杆菌种群分布多样性特征与其土壤的海拔高度、碳氮比和硫含量呈负相关,而和碳源和氮源含量呈正相关。【结论】从以上结果得出,云南腾冲火山谷有着较为丰富的芽胞杆菌资源,且还存在可分离培养的芽胞杆菌的潜在新物种,为利用火山微生物资源提供了保障。     

Taxonomic characterization of Shiraia-like fungi isolated from bamboos in Japan

The molecular phylogeny of nuclear LSU rDNA sequences (D1/D2 domain), ITS regions, and beta-tubulin gene (tub2) showed that the seven strains of Shiraia-like fungi obtained from fresh bamboo tissues as endophytes were closely related to Shiraia bambusicola and had three distinctive lineages (groups A-C). The closest group (group A) to S. bambusicola produced distinctive prawn-shaped conidioma-like structures that differed from conidiomata in the anamorph of S. bambusicola. Currently, none of the morphological structures and molecular database records were compatible with our Shiraia-like fungi. These results reveal that Shiraia-like fungi group A is supposed to be a new species that should be assigned into a novel genus/species related to S. bambusicola.     

Lupinus species differ in their requirements for iron

The effect of iron supply on the growth and nodulation ofLupinus angustifolius L. (Gungurru),Lupinus luteus L. (R-1171) andLupinus pilosus Murr. (P20957) was studied in acid solutions. Plants of the three species were grown together in the same solution and inoculated withBradyrhizobium (Lupinus) WU 425. Plants were then grown with or without applied NH₄NO₃. The lupin species differed greatly in their sensitivity to low iron concentrations in solution withL. pilosus being most tolerant andL. luteus most sensitive.L. pilosus had the highest iron concentration in tissues and had a higher ratio of iron concentration in the youngest fully expanded leaf blades (YEB) to that in roots than the other two species.L. luteus had higher iron concentrations in roots but lower iron concentration in YEB and shoots than didL. angustifolius. The requirements of internal iron for the maximal chlorophyll synthesis in YEB were 65 μg g^-1 forL. angustifolius andL. luteus, and 52 μg g^-1 forL. pilosus. In contrast to effects on growth, the three species had similar external iron requirements for nodule formation in roots and for maximal nitrogen concentrations in shoots. The results indicate that iron tolerant lupin species require lower internal and external iron supply and have a greater ability than sensitive species to translocate iron from roots to shoots.     

Conidiogenesis,nutritional physiology and taxonomy ofAureobasidium andHormonema

Diagnostic criteria for the distinction of the slightly osmophilic species,Aureobasidium pullulans, and the opportunistic pathogen on conifers,Hormonema dematioides, are provided. Reliable identification requires a combination of characters of conidiogenesis, expansion growth and assimilative abilities. Relationships with species ofKabatiella, and with the teleomorph generaPringsheimia, Dothidea andDothiora, all havingHormonema-like cultural states, are discussed. An identification key is provided.     

Hypocrella panamensis sp. nov. (Clavicipitaceae, Hypocreales): a new species infecting scale insects on Piper carrilloanum in Panama

A new species, Hypocrella panamensis, is described from collections and cultures obtained on Barro Colorado Island, Panama. In order to aid in placement of this fungus, phylogenetic analyses were conducted using LSU (rDNA) sequences. Hypocrella panamensis is characterized by possessing pulvinate stromata with a Lecanicillium-like anamorphic state and superficial perithecia. Hypocrella panamensis consistently grouped in a clade containing Hypocrella nectrioides, H. phyllogena, and H. africana (100 % PP). Most species of Hypocrella possess Aschersonia or Hirsutella anamorphs. Hypocrella panamensis is unique in the genus Hypocrella in possession of a Lecanicillium-like anamorphic state. In its biological habit Hypocrella panamensis is similar to other species in Hypocrella in that it infects and degrades the scale insect, then grows superficially on nutrients that emerge to the plant surface through the stylet wound.     

Iron Acquisition and Transport in Staphylococcus aureus

Pathogenic Gram-positive bacteria encounter many obstacles in route to successful invasion and subversion of a mammalian host. As such, bacterial species have evolved clever ways to prevent the host from clearing an infection, including the production of specialized virulence systems aimed at counteracting host defenses or providing protection from host immune mechanisms. Positioned at the interface of bacteria/host interactions is the bacterial cell wall, a dynamic surface organelle that serves a multitude of functions, ranging from physiologic processes such as structural scaffold and barrier to osmotic lysis to pathogenic properties, for example the deposition of surface molecules and the secretion of cytotoxins. In order to succeed in a battle with host defenses, invading bacteria need to acquire the nutrient iron, which is sequestered within host tissues. A cell-wall based iron acquisition and import pathway was uncovered in Staphylococcus aureus. This pathway, termed the isd or iron-responsive surface determinant locus, consists of a membrane transporter, cell wall anchored heme-binding proteins, heme/haptoglobin receptors, two heme oxygenases, and sortase B, a transpeptidase that anchors substrate proteins to the cell wall. Identification of the isd pathway provides an additional function to the already bountiful roles the cell wall plays in bacterial pathogenesis and provides new avenues for therapeutics to combat the rise of antimicrobial resistance in S. aureus. This review focuses on the molecular attributes of this locus, with emphasis placed on the mechanism of iron transport and the role of such a system during infection.     

Kinetics of nitrite oxidation in two Nitrobacter species grown in nitrite-limited chemostats

The influence of growth rate, the presence of acetate and variation in the dissolved oxygen concentration on the kinetics of nitrite oxidation was studied in suspensions of intact cells of Nitrobacter winogradskyi and Nitrobacter hamburgensis. The cells were grown in nitrite-limited chemostats at different dilution rates under chemolithotrophic and mixotrophic conditions. Growth of N. hamburgensis in continuous culture was dependent on the presence of acetate. Acetate hardly affected the maximal nitrite oxidation rate per cell (V _max), but displayed a distinctly negative effect on the saturation constants for nitrite oxidation (K _m ) of both Nitrobacter species. This effect was reversible; when acetate was removed from the suspensions the K _m -values for nitrite oxidation returned to their original values. A reduction of the dissolved oxygen concentration from 100% to 18% air saturation slightly decreased the V _max of chemolithotrophically grown N. winogradskyi cells, whereas a 2.3 fold increase was observed with mixotrophically grown cells of N. hamburgensis. It is suggested that the large variation in K _m encountered in field samples could be due to this observed phenotypic variability. The V _max per cell is not a constant, but apparently is dependent on growth rate and environmental conditions. This implies that potential nitrite oxidation activity and numbers of cells are not necessarily related. Considering their kinetic characteristics, it is unlikely that N. hamburgensis is able to compete succesfully with N. winogradskyi for limiting amounts of nitrite under mixotrophic conditions. However, at reduced partial oxygen tensions, N. hamburgensis may become the better competitor.     

Analysis of the sequence variations in the Mhc DRB1-like gene of the endangered Humboldt penguin (Spheniscus humboldti)

The Major Histocompatibility Complex (Mhc) genomic region of many vertebrates is known to contain at least one highly polymorphic class II gene that is homologous in sequence to one or other of the human Mhc DRB1 class II genes. The diversity of the avian Mhc class II gene sequences have been extensively studied in chickens, quails, and some songbirds, but have been largely ignored in the oceanic birds, including the flightless penguins. We have previously reported that several penguin species have a high degree of polymorphism on exon 2 of the Mhc class II DRB1-like gene. In this study, we present for the first time the complete nucleotide sequences of exon 2, intron 2, and exon 3 of the DRB1-like gene of 20 Humboldt penguins, a species that is presently vulnerable to the dangers of extinction. The Humboldt DRB1-like nucleotide and amino acid sequences reveal at least eight unique alleles. Phylogenetic analysis of all the available avian DRB-like sequences showed that, of five penguin species and nine other bird species, the sequences of the Humboldt penguins grouped most closely to the Little penguin and the mallard, respectively. The present analysis confirms that the sequence variations of the Mhc class II gene, DRB1, are useful for discriminating among individuals within the same penguin population as well those within different penguin population groups and species.The nucleotide sequence and amino acid sequence data reported in this paper have been submitted to the DDBJ database and have been assigned the accession numbers AB088371–AB088374, AB089199, AB154393–AB154399, and AB162144.     

Japanese species of Hypomyces and its anamorph III

Three new species of Hypomyces with KOH-negative subiculi occurring on the Aphyllophorales are described. Hypomyces pseudocorticiicola is characterized by a grayish-yellow to brown subiculum, fusiform ascospores, always with one septum, and its Cladobotryum-anamorph. Hypomyces laeticolor is characterized by a bright-colored subiculum, small apiculi on the ascospores, and well-developed verticillate conidiogenous cells. Hypomyces penicillatus forms a Trichothecium-like anamorph with well-developed verticils of conidiogenous cells.     

<Emphasis Type="Italic">Drosophila</Emphasis> Bys is nuclear and shows dynamic tissue-specific expression during development

Although the bys-like family of genes has been conserved from yeast to humans, it is not apparent to what extent the function of Bys-like proteins has been conserved across phylogenetic groups. Human Bystin is thought to function in a novel cell adhesion complex involved in embryo implantation. The product of the yeast bys-like gene, Enp1, is nuclear and has a role in pre-ribosomal RNA (pre-rRNA) splicing and ribosome biogenesis. To gain insight into the function of the Drosophila melanogaster bys-like family member, termed bys, we examined bys mRNA expression and the localization of Bys protein. In embryos, bys mRNA is expressed in a tissue-specific pattern during gastrulation. In the larval wing imaginal disc, bys mRNA is expressed in the ventral and dorsal regions of the wing pouch, regions that give rise to epithelia that adhere to one another after the wing disc everts. The bys mRNA expression patterns could be interpreted as being consistent with a role for Bys in events requiring cell-cell interactions. However, embryonic bys mRNA expression patterns mirror those of genes that are potential targets of the growth regulator Myc and encode nucleolar proteins implicated in cell growth. Additionally, in Schneider line 2 (S2) cells, an epitope-tagged Bys protein is localized to the nucleus, suggesting that Drosophila Bys function may be conserved with that of yeast Enp1.Edited by D.A. Weisblat