Culture-independent analysis of the soil bacterial assemblage at the Great Salt Plains of Oklahoma

The Great Salt Plains (GSP) of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described GSP bacterial assemblages through the phylogenetic and phenetic characterization of 105 isolates from 46 phylotypes. The current report describes the same bacterial assemblages through culture-independent 16S rRNA gene clone libraries. Although from similar hypersaline mud flats, the bacterial libraries from two sites, WP3 and WP6, were quite different. The WP3 library was dominated by cyanobacteria, mainly Cyanothece and Euhalothece. The WP6 library was rich in anaerobic sulfur-cycle organisms, including abundant Desulfuromonas. This pattern likely reflects differences in abiotic factors, such as frequency of flooding and hydrologic push. While more than 100 OTUs were identified, the assemblages were not as diverse, based on Shannon indexes, as bacterial communities from oligohaline soils. Since natural inland hypersaline soils are relatively unstudied, it was not clear what kind of bacteria would be present. The bacterial assemblage is predominantly genera typically found in hypersaline systems, although some were relatives of microbes common in oligohaline and marine environments. The bacterial clones did not reflect wide functional diversity, beyond phototrophs, sulfur metabolizers, and numerous heterotrophs.     

Infectivity of soilborne Frankia and mycorrhizae in Discaria trinervis along a vegetation gradient in Patagonian soil

The infective capacities of the nitrogen fixing Actinomycete Frankia and arbuscular mycorrhizal fungi from soils near watercourses, along a vegetation gradient, were studied using plant bioassays. Frankia and arbuscular mycorrhizas capable of infecting Discaria trinervis were found at seventeen sites sampled. More specific enumeration of the infective capacities of both microorganisms in relation to environmental factors was performed in seven representative soils of the analysed vegetation zones (rainforest, xeric forest and steppe) using the most probable number method. The highest nodulation capacities ranged from 340 infective units g(-1 )soil, in a steppe marsh devoid of actinorhizas, to 61 in a coastal actinorhizal scrub (in xeric forest). The highest number of infective mycorrhizal units--also found in marsh--was 145. In general, rainforest soils had the lowest values for both microorganisms. Infective units of Frankia and arbuscular mycorrhizal fungi in soil were positively correlated (r = 0.89, P < 0.05). Both soilborne symbionts showed the highest infective capacity in semi-arid conditions nearby watercourse and at the valley bottom location. Tripartite symbiosis was effective in plants inoculated with steppe and xeric forest soils and plants inoculated with Frankia BCU110501 and Glomus mosseae. Interaction between both symbionts and influence of environmental conditions, in general, would contribute to define comparable trends of their infective capacities.     

Characterization by culture and molecular analysis of the microbial diversity of a deep subsurface gas storage aquifer

The bacterial diversity of a subsurface water sample collected from a gas storage aquifer in an Upper Jurassic calcareous formation was investigated by culture of microorganisms and construction of a 16S rRNA gene library. Both culture and molecular techniques showed that members of the phyla Firmicutes and class δ-proteobacteria dominated the bacterial community. The presence of hydrogen-utilizing autotrophic bacteria including sulfate reducers (e.g. Desulfovibrio aespoeensis) and homoacetogens (e.g. Acetobacterium carbinolicum) suggested that CO₂ and H₂ are the main carbon and energy sources sustaining a nutrient-limited subsurface lithoautotrophic microbial ecosystem (SLiME). Gram-positive SRB belonging to the genus Desulfotomaculum, frequently observed in subsurface environments, represented 25% of the clone library and 4 distinct phylotypes. No Archaea were detected by both experimental approaches.Water samples were collected in an area of the rauracian geological formation located outside the maximum seasonal extension of underground gas storage. Considering the observed microbial diversity, there is no evidence of any influence on the microbial ecology of the aquifer in the surroundings of maximum extension reached by the gas bubble of the underground storage, which should have resulted from the introduction of exogenous carbon and energy sources in a nutrient-limited ecosystem.     

Study on the correlation between soil microbial diversity and ambient environmental factors influencing the safflower distribution in Xinjiang

The effects of soil microbial properties and physiographical factors on safflower distributions in the main safflower plantations of Xinjiang province in China were studied. This study may help determine the basis of the environmental factors for evaluating the geoherbalism of this medicinal plant. The soil microbial biodiversity in the bulk soil and rhizosphere of safflower at different growth stages and from different sampling plots were characterized by analyzing the environmental DNAs in the samples. With general primers targeting the 16S ribosomal DNA for bacteria and the internal transcribed spacer 1 gene for fungi, the study was performed using marker gene amplification coupled with Illumina HiSeq high-throughput sequencing technologies. Correlation analysis and a distance-based redundancy analysis were performed to determine the dominant factors affecting the distribution of the microorganism in safflower soils. A total of 16517 bacterial operational taxonomic units (OTUs) were obtained from all the 108 soil samples of nine safflower sampling plots. At the phylum level, 48 phyla have been identified with Actinobacteria (32.9%) and proteobacteria (28.7%) being predominant. For fungi, 8746 OTUs were obtained, which belonged to seven phyla with Ascomycota overwhelmingly superior in relative abundance. A significant positive correlation was found between soil microbe quantity and ASL (above sea level). Safflower was sensitive to changes in elevation, growing more abundantly in the mountainous regions at heights of around 1,200 m above sea level. It is concluded that the dominant factors affecting the distribution of microorganisms in safflower soils were soil moisture, available N, and ASL.     

Impact of salinity-tolerant MCM6 transgenic tobacco on soil enzymatic activities and the functional diversity of rhizosphere microbial communities

The development of genetically modified plants for agriculture has provided numerous economic benefits, but has also raised concern over the potential impact of transgenic plants upon the environment. The rhizosphere is the soil compartment that is directly under the influence of living roots; it constitutes a complex niche likely to be exploited by a wide variety of bacteria potentially influenced by the introduction of transgenes in genetically modified plants. In the present study, the impact of overexpression of the salinity stress-tolerant minichromosome maintenance complex subunit 6 (MCM6) gene upon functional diversity and soil enzymatic activity in the rhizosphere of transgenic tobacco in the presence and absence of salt stress was examined. The diversity of culturable bacterial communities and soil enzymes, namely, dehydrogenases and acid phosphatases, was assessed and revealed no significant (or only minor) alterations due to transgenes in the rhizosphere soil of tobacco plants. Patterns in principal components analysis showed clustering of transgenic and non-transgenic tobacco plants according to the fingerprint of their associated bacterial communities. However, the presence of MCM6 tobacco did not cause changes in microbial populations, soil enzymatic activities or the functional diversity of the rhizosphere soil microbial community.     

Phototactic responses along a gradient of light intensities for the sibling speciesDrosophila melanogaster andDrosophila simulans

The phototactic responses of four recently collected isofemale strains ofDrosophila melanogaster andDrosophila simulans were measured in a light gradient from 590 to 10 lux. High light intensities were preferred by most flies, but a small proportion of flies preferred the lowest light intensity. Based on the strains tested,D. simulans showed greater phototaxis thanD. melanogaster, and within each species variability was found. The niche breadth ofD. melanogaster appears likely to be greater than that ofD. simulans for phototaxis in the light gradient. These results are in general qualitative agreement with earlier results published on dispersal activities from the same populations.     

Influence of high-carbon basal fertiliser on the structure and composition of a soil microbial community under tobacco cultivation

Soil microorganisms play a crucial role in cycling soil nutrients and providing organic nutrients for plant growth and development. Fertilisation balances soil fertility and quality, and affects soil microbial communities. Fertilisation is a frontier subject in agricultural and environmental sciences. Here we showed that the application of high-carbon basal fertiliser treatment could improve the tobacco yield and quality when compared to chemical fertiliser, high-carbon basal fertiliser and mixed high-carbon chemical fertiliser. The potential reason is that different fertiliser treatments influence soil fertility, such as nitrogen, phosphorus, and other contents, besides soil organic matter. Further experiments revealed that populations of bacteria, fungi and actinomycetes fluctuated during tobacco development under different fertilisation treatments. Then we performed high-throughput sequencing of the 16S rRNA gene, and the results showed that the fertilisation treatments had significant effects on the microbial community, particularly within the finer taxonomic divisions or non-dominant taxa. Moreover, proteobacteria and fungal genera had significantly different relative abundances during tobacco growth under various tobacco developmental stages and fertilisation treatments. These results indicated that mixed high-carbon chemical fertiliser could improve soil fertility by influencing the soil microorganism, and that the fertilisation treatments impacted on the structure and composition of the microbial community, and especially the diversity of non-dominant taxa. However, more studies are needed to confirm their reliability.     

Ecology and evolution in microbial systems: the generation and maintenance of diversity in phage-host interactions

Insights gained from studying the interactions between viruses and bacteria have important implications for the ecology and evolution of virus–host interactions in many environments and for pathogen–host and predator–prey interactions in general. Here, we focus on the generation and maintenance of diversity, highlighting recent laboratory and field experiments with microorganisms.     

Molecular and culture-based assessment of the microbial diversity of diabetic chronic foot wounds and contralateral skin sites

Wound debridement samples and contralateral (healthy) skin swabs acquired from 26 patients attending a specialist foot clinic were analyzed by differential isolation and eubacterium-specific PCR-denaturing gradient gel electrophoresis (DGGE) in conjunction with DNA sequencing. Thirteen of 26 wounds harbored pathogens according to culture analyses, with Staphylococcus aureus being the most common (13/13). Candida (1/13), pseudomonas (1/13), and streptococcus (7/13) were less prevalent. Contralateral skin was associated with comparatively low densities of bacteria, and overt pathogens were not detected. According to DGGE analyses, all wounds contained significantly greater eubacterial diversity than contralateral skin (P < 0.05), although no significant difference in total eubacterial diversity was detected between wounds from which known pathogens had been isolated and those that were putatively uninfected. DGGE amplicons with homology to Staphylococcus sp. (8/13) and S. aureus (2/13) were detected in putatively infected wound samples, while Staphylococcus sp. amplicons were detected in 11/13 noninfected wounds; S. aureus was not detected in these samples. While a majority of skin-derived DGGE consortial fingerprints could be differentiated from wound profiles through principal component analysis (PCA), a large minority could not. Furthermore, wounds from which pathogens had been isolated could not be distinguished from putatively uninfected wounds on this basis. In conclusion, while chronic wounds generally harbored greater eubacterial diversity than healthy skin, the isolation of known pathogens was not associated with qualitatively distinct consortial profiles or otherwise altered diversity. The data generated support the utility of both culture and DGGE for the microbial characterization of chronic wounds.     

Effects of long-term fertilization on the diversity of bacterial mercuric reductase gene in a Chinese upland soil

Soil mercury (Hg) pollution has received considerable attention due to its neurotoxin effects and its potential risk to food safety. The microbial transformation of Hg plays a key role in reducing Hg toxicity by the mercuric reductase (MerA) conferred by genes arranged in the mer operon. This study investigated the effects of long‐term fertilization on the diversity of bacterial mercuric reductase gene (merA), which specify the reduction of ionic Hg²⁺ to the volatile elemental form Hg⁰, in an agricultural soil with relatively high Hg content. The soil samples were collected from different treatments, including control without fertilizer (CK), fertilizer nitrogen (N), combined fertilizers (NPK) of N, phosphorus (P) and potassium (K), and NPK plus organic manure (NPK + OM). The merA gene diversity patterns were analyzed based on the merA clone libraries and sequencing measurements. Results showed that the merA gene diversity was influenced by soil variables depending on the fertilization practices. In particular, NH₄⁺ and NO₃^– contents had strong effect on the merA gene diversity pattern both in the N and NPK treatments, whereas the merA gene diversity pattern in NPK + OM treatment was distinctly influenced by the contents of organic matter, available P and K. These results suggested that long‐term fertilization had significant influences on merA gene diversity, which could be helpful to understand the Hg reduction process and potentially serve microbial remediation of Hg contaminated soil. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Differential expression of RARbeta isoforms in the mouse striatum during development: a gradient of RARbeta2 expression along the rostrocaudal axis.

The retinoic acid receptor RARbeta is highly expressed in the striatum of the ventral telencephalon. We studied the expression pattern of different RARbeta isoforms in the developing mouse striatum by in situ hybridization. We found a differential ontogeny of RARbeta2 and RARbeta1/3 in embryonic day (E) 13.5 lateral ganglionic eminence (striatal primordium). RARbeta2 mRNA was detected primarily in the rostral and ventromedial domains, whereas RARbeta1/3 mRNAs were enriched in the caudal and dorsolateral domains. Notably, by E16.5, a prominent decreasing gradient of RARbeta2 mRNA was present in the developing striatum along the rostrocaudal axis, i.e., RARbeta2 was expressed at higher levels in the rostral than the caudal striatum. No such gradient was found for RARbeta1/3 and RARbeta3 mRNAs. The rostrocaudal RARbeta2 gradient gradually disappeared postnatally and was absent in the adult striatum. The differential expression pattern of RARbeta isoforms in the developing striatum may provide an anatomical basis for differential gene regulation by RARbeta signaling.     

Phenology of Ixodes ricinus and infection with Borrelia burgdorferi sensu lato along a north- and south-facing altitudinal gradient on Chaumont Mountain, Switzerland

Questing Ixodes ricinus L. ticks were collected monthly from 2003 to 2005 on the north- and south-facing slopes of Chaumont Mountain in Neuchatel, Switzerland, at altitudes varying from 620 to 1,070 m. On the south-facing slope, questing tick density was higher than on the north-facing slope, and it decreased with altitude. Density tended to increase with altitude on the north-facing slope. Saturation deficit values higher than 10 mmHg and lasting for >2 mo were often recorded on the south-facing slope, explaining seasonal patterns of questing tick activity. The overall prevalence of Borrelia burgdorferi sensu lato was 22.4%, and prevalence differed according to exposure and among years. No difference was noticed between nymphs and adults. Four Borrelia species were identified. Mixed infections were detected in 52 ticks, B. garinii and B. valaisiana (n = 21) and B. afzelii and B. burgdorferi s.s. (n = 20) were the most frequent associations observed. The density of infected ticks varied from 3.6 to 78.7 infected nymphs per 100 m2 and from 0.6 to 16.9 infected adults per 100 m2, both slopes combined. The study on the south-facing slope was a follow-up of a previous study carried out at the same location during 1999-2001. Comparison of climatic data between the two periods showed a marked increase in saturation deficit. Substantial differences in density and phenology of ticks also were observed. At high elevations, ticks were significantly more abundant during the current study. This can be explained by rising temperatures recorded during summer at altitude, reaching values similar to those registered in the first study beneath. At the lowest altitude, adults were significantly less abundant, probably due to long-lasting high saturation deficits that impaired nymphal survival. The density of Borrelia-infected ticks was higher than in the previous study.     

Extended gene diversity at the FMR1 locus and neighbouring CA repeats in a sub-Saharan population

We report on the allele distributions in a normal black African population at two microsatellite loci neighbouring the FRAXA locus and at the CGG repeat in the 5′ end of the FMR-1 gene, which causes the fragile X syndrome. The CGG repeat distribution was found to be similar to that of other ethnic groups, as well as to that of other nonhuman primates, possibly predicting a comparable prevalence of fragile X in Africa. Significant linkage disequilibrium has been observed between fragile X mutations and alleles of the DXS548 and FRAXAC1 loci in European and Asian populations, and some founder chromosomes may be extremely old. Those associated with FRAXAC1-A and DXS548-2 alleles are not present in the Asian fragile X samples. We searched for these alleles and their frequency in the well defined Bamileke population of Cameroon. All previously described alleles and some new ones were found in this sample, supporting the hypothesis of their pre-existence and subsequent loss in Asian populations. Finally, the heterozygosity of the Bamileke sample was significantly higher at both marker loci and comparable to that of Europeans at the CGG repeat, confirming the notion that genetic diversity is greater in Africans than in other groups and supporting the view that evolution of modern man started in Africa. © 1996 Wiley-Liss, Inc.     

Molecular analysis reveals a genetic basis for the phenotypic diversity of metaplastic breast carcinomas

Cancers may be composed of multiple populations of submodal clones sharing the same initiating genetic lesions, followed by the acquisition of divergent genetic hits. Intra‐tumour genetic heterogeneity has profound implications for cancer clinical management. To determine the extent of intra‐tumour genetic heterogeneity in breast cancers, and whether the morphological diversity of breast cancers is underpinned by divergent genetic aberrations, we analysed the genomic profiles of microdissected, morphologically distinct components of six metaplastic breast carcinomas, tumours characterized by the presence of morphological areas with divergent differentiation. Each morphologically distinct component was separately microdissected and subjected to high‐resolution microarray‐based comparative genomic hybridization. Each component was also analysed by immunohistochemistry and in situ hybridization. Clonal relationship between the distinct components was tested by TP53 sequencing and human androgen receptor (HUMARA) X‐chromosome inactivation assay. In the majority of cases, all morphologically distinct components from each case were clonal and displayed remarkably similar genetic profiles. In two cases, however, morphologically distinct components harboured specific genetic aberrations. In an adenosquamous carcinoma, the differences were such that only 20% of the genome harboured similar copy number changes. The squamous component displayed EGFR gene amplification, EGFR over‐expression and lack of expression of hormone receptors, whereas the lobular component displayed the reverse pattern. The components of a biphasic spindle cell carcinoma harboured similar gains, losses, amplifications of 9p23 and 17q12 (HER2) and identical TP53 mutations, suggesting that these were relatively early events in the development of this tumour; however, each component displayed divergent focal amplifications. Importantly, the metastatic deposit of this case, despite harbouring a TP53 mutation identical to that found in the primary tumour, harboured additional specific focal amplifications. This proof‐of‐principle study provides direct evidence of intra‐tumour genetic heterogeneity in breast cancers, and shows that in some cases morphological diversity may be underpinned by distinct genetic aberrations. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.     

Consider the advantages and disadvantages of microbial examinations in a hospital, and ideal microbial laboratory

The main benefit of carrying out microbial examinations in a hospital is that it rapidly yields information on infectious diseases. Microbiology technicians can easily communicate with the physicians and can carry out precise analyses. The disadvantages are the high costs of microbiological examinations, and the need for long training times for microbial laboratory technicians because of the highly technical nature of their duties. In-hospital microbial inspections will lead to: 1)improved rapid diagnostic tests for infectious diseases and evaluation of antibiotic treatment in the early stages of disease; 2) detection of the precise origin of microbes and confirmation of etiological factors; 3) antibiotic susceptibility testing and evaluation of combined effects of antibiotics against multiple drug-resistant bacteria; and 4)genetic analysis and epidemiological statistical analysis for the purpose of infection control in a hospital and surrounding areas.     

Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area

The prokaryotic diversity associated with an Indian soda lake (Lonar Crater Lake) located in a basaltic soil area was investigated using a culture-independent approach. Community DNA was extracted directly from four sediment samples obtained by coring to depths of 10-20 cm. Small subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific to the domains Bacteria and Archaea. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 500 clones were randomly selected for further analysis. After restriction fragment length polymorphism (RFLP) analysis and subsequent sequencing, a total of 44 unique phylotypes were obtained. These phylotypes spanned a wide range within the domain Bacteria, occupying eight major lineages/phyla. 34% of the clones were classified as firmicutes. The other clones were grouped into proteobacteria (29.5%), actinobacteria (6.8%), deinococcus-thermus (4.5%), cytophages-flavobacterium-bacteroidetes (13.3%), planctomycetes (6.8%), cyanobacteria (4.5%) and spirochetes (2.27%). In the case of the archaeal 16S rDNA library, analysis of 250 randomly selected clones revealed the presence of 13 distinct phylotypes; 5 phylotypes were associated with Crenarchaeota and 8 with Euryarchaeota. Most of the euryarchaeota sequences were related to methanogens. Findings from this molecular study of a site investigated for the first time have revealed the presence of a highly diverse bacterial population and a comparatively less diverse archaeal population. The majority ( approximately 80%) of the cloned sequences show little affiliation with known taxa (<97% sequence similarity) and may represent novel taxa/sequences and organisms specifically adapted to this basaltic soda lake environment. Diversity analyses demonstrate greater diversity and evenness of bacterial species compared to a skewed representation of species for Archaea.