Activity and bacterial diversity of snow around Russian Antarctic stations

The diversity and temporal dynamics of bacterial communities in pristine snow around two Russian Antarctic stations was investigated. Taxonomic analysis of rDNA libraries revealed that snow communities were dominated by bacteria from a small number of operational taxonomic units (OTUs) that underwent dramatic swings in abundance between the 54th (2008–2009) and 55th (2009–2010) Russian Antarctic expeditions. Moreover, analysis of the 55th expedition samples indicated that there was very little, if any, correspondence in abundance of clones belonging to the same OTU present in rDNA and rRNA libraries. The latter result suggests that most rDNA clones originate from bacteria that are not alive and/or active and may have been deposited on the snow surface from the atmosphere. In contrast, clones most abundant in rRNA libraries (mostly belonging to Variovorax, Janthinobacterium, Pseudomonas, and Sphingomonas genera) may be considered as endogenous Antarctic snow inhabitants.     

Microbial diversity of mine water at Zhong Tiaoshan copper mine, China

Microbial diversity of mine water at Zhong Tiaoshan copper mine, Shanxi province, China, was analyzed using a culture-independent 16S rRNA gene (rDNA) based on cloning approach. A total of 59 Operational Taxonomic Units (OTUs) were obtained from 226 clones from all three samples (8 OTUs from sample SX1, 25 from SX2 and 26 from SX3). 46 of them were representative OTUs and were sequenced. 93.5% of the total clones had sequences that were less than 5% difference from those in the nucleic acids database. The percentage of overlapping OTUs among samples was from 12.1% to 35.3%. Phylogenetic analysis indicated that 60.62% of the clones were affiliated with members of the Proteobacteria (alpha -3.10%, beta -24.78%, gamma -31.41%, delta -1.33%), whereas 29.20% of the clones were closely related to the Nitrospira (Leptospirillum ferrooxidans 20.80%, Leptospirillum ferriphilum 0.88% and Leptospirillum group III 7.52%, respectively). The rest clones were affiliated with the Firmicutes (2.65%) and the Bacteroidetes (7.52%). The results of Principal Component Analysis (PCA) based on the percentages of OTUs and biogeochemical data revealed that biogeochemical properties affected the diversity of microbial communities in mine water. Especially, the pH value, temperature and different concentrations of elements such as lead, zinc, sulfur, iron and copper seemed to be key factors affecting the composition and structure of microbial communities in this study.     

Novel prokaryotic diversity in sediments of Tunisian multipond solar saltern

The phylogenetic diversity of a sediment microbial community from two ponds having different salinities, 150–200 g/l (M2) and 250–300 g/l (TS38), of an Sfax (Tunisia) solar saltern, was investigated using 16S rRNA clone libraries. The 16S rRNA genes from 135 bacterial clones and 105 archaeal clones were sequenced and phylogenetically analyzed. 32 operational taxonomic units (OTUs) were generated for Bacteria and 64 for Archaea. The bacterial community in M2 sediment was affiliated only with Bacteroidetes, while that in TS38 sediment was dominated by clones affiliated with Bacteroidetes, (gamma, alpha, delta) Proteobacteria and unclassified bacteria; these represented 56.52, 26.08, 4.34, 4.34 and 8.7% of the OTUs, respectively. In the M2 and TS38 sediments, 44.44 and 43.47% of the bacterial OTUs, respectively, were novel. All archaeal sequences fell into the Euryarchaeota phylum. In both sediments, 38.46 and 72.55% of the OTUs had less than 97% 16S rRNA sequence identity, representing novel OTUs. Two sequences, retrieved from TS38 sediment, were found to be affiliated with the candidate division MSBL-1 defining two OTUs. The sediment phylogenetic study revealed the presence of a highly diverse microbial population in highly salty media.     

High Archaea diversity in Varvara hot spring, Bulgaria

The phylogeny of the latest recognized domain, Archaea, is still complicated and it is largely based on environmental sequences. A culture independent molecular phylogenetic analysis revealed high Archaea diversity in a terrestrial hot spring, village Varvara, Bulgaria. A total of 35 archaeal operational taxonomic units (OTUs) belonging to three of the classified five Archaea phyla were identified. Most of the sequences were affiliated with the phylum Crenarchaeota (23), grouped in four branches. The rest of the sequences showed highest similarity to the unidentified archaeal clones (9), Euryarchaeota (2), and "Korarchaeota " (1). Eight (23%) of the sequenced 16S rDNAs didn't have known close relatives and represented new and diverse OTUs, four of them forming a new archaeal subgroup without close described sequences or culturable relatives. A sequence affiliated with "Korarchaeota " showed low similarity (90%) to the closest neighbor and both sequences formed unique branch in this phylum. Consequently, the constructed archaeal libraries are characterized by (1) high proportion of OTUs representing uncultivated archaeal phylogroups, (2) the abundance of novel phylotype sequences, (3) the presence of high proportions of Crenarchaeota phylotypes unrelated to cultivated organisms and (4) the presence of a sequence only distantly related to "Korarchaeota " phylum.     

慢性HBV感染者肠道真菌菌群生态结构研究

目的 探讨慢性HBV感染者肠道真菌菌群的分子生态结构变化特点.方法 采用真菌18S rDNA通用引物对乙肝肝硬化患者、慢性乙型肝炎患者、HBV携带者和健康志愿者4组研究对象的粪便标本DNA进行PCR扩增,扩增产物进行18S rRNA基因克隆,构建真菌18S rDNA克隆文库,利用限制性片段长度多态性(RFLP)技术筛选阳性克隆子并进行测序,绘制系统发育树,获取各组研究对象肠道真菌菌群结构特征.结果 所有阳性克隆子经过酶切分析和测序,共获得29个操作分类单元(OTUs),归属于3个真菌类群:接合菌纲(3.4%)、子蓑菌纲(82.8%)和担子菌纲(13.8%),其中主要优势菌属为念珠菌属(Candida spp.)、未能培养真菌(uncultured fungus)、酵母菌属(Saccharomyces spp.),分别占克隆文库的29.2%、15.9%、15.0%.乙肝肝硬化患者组、慢性乙型肝炎患者组、HBV携带者组和健康志愿者组的肠道真菌菌群分别存在有20、16、12、14个OTUs.结论 人类肠道中存在较为丰富的真菌类群,慢性HBV感染者肠道真菌菌群分子生态结构发生明显改变,提示肠道真菌菌群生态结构改变与乙肝发展历程相关.     

Navigating the structure–function–evolutionary relationship of CsaA chaperone in archaea

CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea. The study of phylogenetic distribution of CsaA among prokaryotes suggests that it is present only in few archaeal organisms, mainly species of Thermoplasmatales and Halobacteriales. Interestingly, the CsaA protein from these two archaeal orders cluster separately on the phylogenetic tree with CsaA from Gram-positive and Gram-negative bacteria. It, thus, appears that this protein might have been acquired in these archaeal organisms through independent horizontal gene transfer (HGT) events from different bacteria. In this review, we summarize the earlier biochemical, structural, and functional characterization studies of CsaA. We draw new insights into the evolutionary history of this protein through phylogenetic and structural comparison of bacterial CsaA with modelled archaeal CsaA from Picrophilus torridus and Natrialba magadii.     

Limited selection of sodium channel blocking toxin-producing bacteria from paralytic shellfish toxin-contaminated mussels (Aulacomya ater)

Paralytic shellfish toxins (PSTs) are sodium channel blocking (SCB) toxins, produced by cyanobacteria, as well as by marine dinoflagellates and their associated bacteria, and cause serious health and economic concern worldwide. In a previous study, approximately 70% of the bacteria enriched from PST-contaminated shellfish tissue and isolated on marine agar medium were observed to produce SCB toxins. In the study reported here, the high percentage of cultivable toxigenic bacteria is demonstrated to be obtained through a marked selection on marine agar medium. The cultivable as well as the total bacterial diversity associated with PST-contaminated shellfish collected from the Magallanes region in the south of Chile has been analysed. Approximately 80% of bacterial isolates, analysed by restriction analysis of PCR amplified ribosomal DNA (i.e., ARDRA fingerprinting), were limited to only two genotypic OTUs (operational taxonomic unit). Sequence determination and analysis of the 16S rDNA from representative isolates of both OTUs established them to be closely related to species of the Psychrobacter genus of the gamma-subclass of the Proteobacteria. The total bacterial diversity in the shellfish was further analysed, using a cultivation-independent strategy of extraction of total DNA from contaminated tissue, PCR-amplification of bacterial 16S rRNA genes, cloning of the PCR products and analysis of the cloned 16S rDNA sequence types by fingerprinting and sequencing. Only 2% of the cloned sequence types corresponded to species of the Psychrobacter genus. The 16S rDNA sequence types detected clustered with species of the y-Proteobacteria subclass, the Cytophaga-Flexibacter-Bacteroides (CFB), the Fusobacteria and the Firmicutes phyla. The level of diversity observed within the libraries of cloned 16S rDNA was markedly greater than that observed among isolates obtained through marine agar enrichment cultures from the same shellfish tissue. Additionally the predominant cloned 16S rDNA sequence types detected from samples of the surrounding seawater demonstrated no correlation with those observed in the PST-contaminated mussels.     

怀有先天性心脏病胎儿的孕妇与正常孕妇肠道菌群的高通量测序分析

目的:分析怀有先天性心脏病胎儿的孕妇(PW组)与正常孕妇(NW组)的肠道菌群特征。方法:对可能引起个体肠道菌群差异的因素加以控制,2013年6月18号~2013年12月17号收集15例正常孕妇和17例异常孕妇的粪便样本,提取细菌基因组DNA,用PCR方法扩增16S r DNA,进行二代Illumina测序。测序数据应用运算分类单位(operational taxonomic unit,OTU)聚类分析、多样性分析和分类学分析等生物信息技术分析2类孕妇肠道菌群的结构、多样性和丰度。结果:2类孕妇肠道菌群的高通量测序分析分别得到2 696 276(NW组)条和2 445 530(PW组)条优化序列,测序覆盖深度97%。经过97%相似度归并后分别得到77 243个(NW组)和75 600个OTUs(PW组);菌群多样性分析显示正常孕妇肠道菌群的Chao 1指数和Shannon指数均高于异常孕妇。在最佳分类水平上,正常孕妇肠道菌群由38个科的细菌构成,归属于14个门,以厚壁菌门(Firmicutes)为主,其次为变形菌门(Proteobacteria)、放线菌门(Actinobacteria)等。怀有先心胎儿孕妇肠道菌群构成与正常孕妇相似,最佳分类水平上由33个科的细菌构成,归属于9个门,其中Firmicutes为(75.7±15.8)%,Proteobacteria为(21.1±17.0)%,Actinobacteria为(2.0±2.1)%。在最佳分类水平上,方差分析显示两者的双歧杆菌科(Bifidobacteriaceae)和红蝽杆菌科(Coriobacteriaceae)菌种丰度有明显差异。结论:PW组孕妇与NW组孕妇相比,整体肠道菌群含量明显下降,提示PW组孕妇有更恶劣的肠道环境,其中部分菌群含量存在明显差异。先天性心脏病胎儿的发生可能与孕妇恶劣的肠道微环境有关,其中Bifidobacteriaceae和Coriobacteriaceae在先天性心脏病的预防方面可能有重要作用。     

A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene

The diversity of methanogenic Archaea from the gut of 6 humans was investigated by targeting mcrA, a molecular metabolic marker of methanogenesis. Three operational taxonomic units (OTUs) were recovered from about 400 clones analyzed, two of which were attributed to the expected Methanobacteriales Methanobrevibacter smithii (4 volunteers) and Methanosphaera stadtmanae (1 volunteer). The third OTU (1 volunteer) corresponded to a distant phylotype that does not cluster with any of the five methanogenic orders. This result, also supported by 16S archaeal sequences retrieved from the same volunteer, strongly suggests there may be a sixth order and hence potential underestimation of the role of methanogens in gut physiology.     

Faecal microbiome in new-onset juvenile idiopathic arthritis

Alterations in the intestinal microbial flora have been linked with autoimmune diseases. Our objective was to analyse the composition of the faecal microbiome of children with new-onset juvenile idiopathic arthritis (JIA) compared to healthy controls, and to identify specific gut bacteria associated with JIA. Stool samples from patients were taken at the time of diagnosis of JIA. The microbiome profiles of samples of 30 children with JIA (mean age 6.2 years, 22 girls) were analysed with 16S region-based sequencing profiling and compared to the stool samples of healthy controls (n?=?27, mean age 5.4 years, 18 girls). The proportion of bacteria belonging to the phylum Firmicutes was significantly lower in children with JIA [21 % (95 % confident interval [CI]: 17–25 %)] compared to controls [33 % (95 % CI: 26–41 %), p?=?0.009]. Bacteria belonging to Bacteroidetes were significantly more abundant in JIA [78 % (95 % CI: 74–82 %)] than in control samples [65 % (95 % CI: 57–73 %), p?=?0.008]. Shared operational taxonomic units (OTUs) between the groups revealed that genera Actinobacteria and Fusobacteria were present only in JIA patients and Lentisphaerae only in controls. In summary, faecal flora in JIA is characterised by a low level of Firmicutes and an abundance of Bacteroidetes, resembling the aberration reported in type 1 diabetes. We suggest that alterations in the intestinal microbial flora may challenge the mucosal immune system of genetically susceptible subjects predisposing to local proinflammatory cascades, thus contributing to the development of JIA.     

Magnetic resonance spectroscopy of the occipital cortex and the cerebellar vermis distinguishes individual cats affected with alpha‐mannosidosis from normal cats

A genetic deficiency of lysosomal alpha‐mannosidase causes the lysosomal storage disease alpha‐mannosidosis (AMD), in which oligosaccharide accumulation occurs in neurons and glia. The purpose of this study was to evaluate the role of magnetic resonance spectroscopy (MRS) in detecting the oligosaccharide accumulation in AMD. Five cats with AMD and eight age‐matched normal cats underwent in vivo MRS studies with a single voxel short echo time (20 ms) STEAM spectroscopy sequence on a 4.7T magnet. Two voxels were studied in each cat, from the cerebellar vermis and the occipital cortex. Metabolites of brain samples from these regions were extracted with perchloric acid and analyzed by high resolution NMR spectroscopy. A significantly elevated unresolved resonance signal between 3.4 and 4. ppm was observed in the cerebellar vermis and occipital cortex of all AMD cats, which was absent in normal cats. This resonance was shown to be from carbohydrate moieties by high resolution NMR of tissue extracts. Resonances from the Glc‐NAc group (1.8–2.2 ppm) along with anomeric proton signals (4.6–5.4 ppm) from undigested oligosaccharides were also observed in the extract spectra from AMD cats. This MRS spectral pattern may be a useful biomarker for AMD diagnosis as well as for assessing responses to therapy. Copyright © 2009 John Wiley & Sons, Ltd.     

High genetic diversity among Stenotrophomonas maltophilia strains despite their originating at a single hospital

The levels of genetic relatedness of 139 Stenotrophomonas maltophilia strains recovered from 105 hospitalized non-cystic fibrosis patients (51% from medical wards, 35% from intensive care units, and 14% from surgical wards) and 7 environmental sources in the same hospital setting during a 4-year period were typed by the pulsed-field gel electrophoresis (PFGE) technique. A total of 99 well-defined distinct XbaI PFGE patterns were identified (Simpson's discrimination index, 0.996). The dendrogram showed a Dice similarity coefficient ranging from 28 to 80%. Two major clusters (I and II), three minor clusters (III, IV, and V), and two independent branches were observed when using a 36% Dice coefficient, indicating a high diversity of genetic relatedness. It is of note that 84% of strains were grouped within two major clonal lineages. No special cluster gathering was found among strains belonging to the same sample type specimen, patients' infection or colonization status, and ward of precedence. Despite this fact, three different clones (A, B, and C) recovered from respiratory samples from six, three, and two patients, respectively, and two clones, D and E, in two bacteremic patients each, were identified. Isolation of an S. maltophilia strain belonging to the clone A profile in a bronchoscope demonstrated a common source from this clone. This study revealed a high genetic diversity of S. maltophilia isolates despite their origin from a single hospital, which may be related to the wide environmental distribution of this pathogen. However, few clones could be transmitted among different patients, yielding outbreak situations.     

Recognition of two novel phenons of the genus Acinetobacter among non-glucose-acidifying isolates from human specimens

Genomic species diversity among 147 Acinetobacter clinical isolates not belonging to the A. calcoaceticus- A. baumannii (ACB) complex was investigated by phenotypic and genotypic identification methods. The isolates were obtained between 1991 and 1999 from numerous diagnostic laboratories in the Czech Republic and were studied by numerical probabilistic identification using two biochemical frequency matrices and amplified rDNA restriction analysis (ARDRA). Their final identification was derived from the combined phenotypic and ARDRA results. In total, 102 isolates were unambiguously (n = 89) or presumptively (n = 13) identified as A. lwoffii (n = 63), genomic species 13BJ/14TU (n = 9), A. johnsonii (n = 7), A. haemolyticus (n = 6), A. junii (n = 5), and other genomic species (n < 5 isolates each). Forty-five isolates could not be identified as belonging to any described species. Among the unidentified isolates two large groups of non-glucose-acidifying, nonhemolytic, and non-gelatinase-producing isolates were distinguished. These groups, designated phenon 1 (n = 17) and phenon 2 (n = 15), had distinctive phenotypic features and novel ARDRA profiles, which suggests that they represent hitherto undescribed Acinetobacter species. Phenon 2 included mainly clinically insignificant isolates from outpatients, while phenon 1 comprised clinically relevant isolates mostly from the blood of hospitalized patients, and its precise taxonomic definition may therefore be of medical importance. Overall, the development of practical methods for identification required for the elucidation of the biological significance of the (genomic) species within the genus Acinetobacter remains a challenging task.     

Hyperploidy induced by drugs that inhibit formation of microtubule promotes chromosome instability

BACKGROUND: Antimicrotubule drugs (AMDs), such as taxol and vincristine, are the most important addition to the chemotherapeutic armamentarium against human cancers. It has been shown that prolonged AMD treatment induces hyperploidy in G1-checkpoint-defective cancer cells and that these hyperploid cells subsequently undergo apoptosis. However, a fraction of these hyperploid cells are able to survive the prolonged mitotic stress and resume cell-cycle progression. RESULTS: We established hyperploid clones that escaped from cell death after AMD treatment from two glioma cell lines, U251MG and U87MG. Subtractive comparative genomic hybridization (CGH) analysis revealed that clones derived from U87MG mainly had chromosome number changes, but that those from U251MG showed both numerical and structural chromosomal changes. Furthermore, numerous aberrations identified in U251MG clones were remarkably chromosome-specific, which may have been due to clonal selection for cells that have an advantage in growth and/or survival. All clones derived from both cell lines had abnormalities in chromosome segregation, and karyotypes of clones were more heterogeneous than those of parental cells, suggesting that cells having a higher chromosome number are subject to asymmetric chromosome segregation, resulting in a heterogeneous karyotype. All clones derived from U87MG and U251MG increased both centric and acentromeric micronuclei, suggesting the presence of chromosome structural abnormality. CONCLUSIONS: AMD treatment induces hyperploid formation and chromosome instability in checkpoint-deficient cancer cells.     

Clonal dissemination of two clusters of Acinetobacter baumannii producing OXA-23 or OXA-58 in Rome, Italy

Thirty consecutive Acinetobacter baumannii isolates producing carbapenem-hydrolysing oxacillinases, OXA-23 or OXA-58, were recovered from patients hospitalized in Rome, Italy, between January and November 2007. Among these isolates, two clones not associated with the European clones I or II were observed. The oxacillinase-encoding genes were plasmid- or chromosome-borne. This study reports the dissemination of carbapenem-resistant A. baumannii belonging to two clones among several units in a single hospital and emphasizes the ability of A. baumannii to cause epidemic/endemic outbreaks and also to acquire various resistance genes circulating in the hospital environment.     

Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor

Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system.     

Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis.

A total of 53 field and reference strains, including the type strains of the seven named species (nomenspecies) and belonging to the 18 described genomic species (DNA groups) of the genus Acinetobacter, were studied by amplified ribosomal DNA restriction analysis (ARDRA). Restriction analysis with the enzymes AluI, CfoI, MboI, RsaI, and MspI of the enzymatically amplified 16S rRNA genes allowed us to identify all species except the genomic species 4 (Acinetobacter haemolyticus) and 7 (A. johnsonii), 5 (A. junii) and 17, and 10 and 11, which clustered pairwise in three respective groups. Further analysis with the enzyme HaeIII, HinfI, NciI, ScrFI, or TaqI did not allow us to differentiate the species within these three clusters. However, use of a few additional simple phenotypic tests (hemolysis, growth at 37 degrees C, production of acid from glucose, and gelatin hydrolysis) can be used to differentiate between the species within these clusters. ARDRA proved to be a rapid and reliable method for the identification of most of the Acinetobacter genomic species, including the closely related DNA groups 1 (A. calcoaceticus), 2 (A. baumannii), 3, and 13. The results of this study suggest that ARDRA can be used for the identification of Acinetobacter species and as such may help to elucidate the ecology and clinical significance of the different species of this genus. Since ARDRA uses universal 16S rRNA gene primers, it is expected to be applicable to the identification of most bacterial species. Furthermore, ARDRA is less prone to contamination problems than PCR for detection, since the use of cultured organisms results in a large initial quantity of target DNA.     

Comprehensive Analysis of the Effect of Probiotic Intake by the Mother on Human Breast Milk and Infant Fecal Microbiota

BackgroundHuman breast milk (HBM) contains optimal nutrients for infant growth. Probiotics are used to prevent disease and, when taken by the mother, they may affect infant microbiome as well as HBM. However, few studies have specifically investigated the effect of probiotic intake by the mother on HBM and infant microbiota at genus/species level. Therefore, we present a comprehensive analysis of paired HBM and infant feces (IF) microbiome samples before and after probiotic intake by HBM-producing mothers.MethodsLactating mothers were administered with Lactobacillus rhamnosus (n = 9) or Saccharomyces boulardii capsules (n = 9), for 2 months; or no probiotic (n = 7). Paired HBM and IF samples were collected before and after treatment and analyzed by next-generation sequencing.ResultsForty-three HBM and 49 IF samples were collected and sequenced. Overall, in 43 HBM samples, 1,190 microbial species belonging to 684 genera, 245 families, 117 orders, and 56 classes were detected. In 49 IF samples, 372 microbial species belonging to 195 genera, 79 families, 42 orders, and 18 classes were identified. Eight of 20 most abundant genera in both HBM and IF samples overlapped: Streptococcus (14.42%), Lactobacillus, Staphylococcus, and Veillonella, which were highly abundant in the HBM samples; and Bifidobacterium (27.397%), Bacteroides, and Faecalibacterium, which were highly abundant in the IF samples. Several major bacterial genera and species were detected in the HBM and IF samples after probiotic treatment, illustrating complex changes in the microbiomes upon treatment.ConclusionThis is the first Korean microbiome study in which the effect of different probiotic intake by the mother on the microbiota in HBM and IF samples was investigated. This study provides a cornerstone to further the understanding of the effect of probiotics on the mother and infant microbiomes.     

Isolation and identification of a Candida digboiensis strain from an extreme acid mine drainage of the Lignite Mine,Gujarat

An extremely acidic mine drainage (AMD) water sample was collected in 1998 and 2008 from Panandhro lignite mine, Gujarat, India. The yeast isolated from this sample was identified using mini API identification system, as a member of genus Candida. The major cellular fatty acids detected by FAME from the isolate are C_16:0 and C_{18:2 cis 9,12}/C_18:0α as 25.23 and 19.5%, respectively. The isolate was identified as Candida digboiensis by 18S rRNA gene sequence analysis and designated as Candida digboiensis SRDyeast1. Phylogenetic analysis using D1/D2 variable domains showed that the closest relative of this strain is Candida blankii with 3% divergence. This organism has been reported for the first time from the lignite mine AMD sample, and for cellular fatty acid analysis. This yeast is able to survive in the AMD sample preserved at 10–42 °C temperature since last 10 years along with iron oxidizing microorganisms. It can grow in the presence of 40% glucose, 10% NaCl and in the pH range of 1 to 10. The isolate is capable of producing enzymes like protease and lipase. This isolate differs from the type strain Candida digboiensis in as many as six physiological and metabolic characteristics. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Isolation, identification and seasonal distribution of soilborne fungi in tea growing areas of Iyidere-Ikizdere vicinity (Rize-Turkey)

This study involves the isolation and identification of soil borne fungi from different altitudes of Iyidere-Ikizdere vicinity in Rize, Turkey. The qualitative and quantitative fungal composition of the soil of Iyidere-Ikizdere vicinity was surveyed seasonally during a year (between summer 2003 and spring 2004). The soil samples were collected from 10 different locations. Some physical and chemical properties of the soil samples were studied. Soil samples were observed to have the proper pH levels (pH 4.00-6.75) for the growth of microfungi. By using a soil dilution technique, the mycological analysis of 40 soil samples were studied at 25 cm depth. The number of microfungi ranged from 2,000-160,000 CFU g(-1). 249 different microfungi belonging to 15 genera were isolated. 45 of the isolates were Mycelia Sterilia. Penicillium, Aspergillus, Trichoderma and Fusarium were the most abundant genera (26.8%, 14.8%, 9.6% and 8.4%, respectively). Penicillium phialosporum, Penicillium trzebinskianum and Gliocladium virens were reported for the first time in Turkey.