Molecular characterisation of Halobacillus strains isolated from different medieval wall paintings and building materials in Austria

We previously reported on the detection and isolation of an indigenous population of Halobacillus from salt-damaged medieval wall paintings and building materials of Herberstein castle in St. Johann bei Herberstein in Styria, Austria. Several moderately halophilic, Gram-positive, endospore-forming Halobacillus-like bacteria could be again isolated by conventional enrichment from salt efflorescences collected in the medieval St. Virgil's chapel in Vienna. Comparative 16S rDNA sequence analyses showed that the St. Virgil isolates are most closely related (>98.5% sequence similarity) to Halobacillus trueperi, Halobacillus litoralis, and to our previous halobacilli strains obtained from the castle Herberstein. Based on 16S rDNA sequence analysis, the strains could be clustered in three different groups. Group I: St. Virgil strains S3, S4, S21, and S22 (99.8–100% sequence similarity); group II: Herberstein strains K3-1, I7, and the St. Virgil strain S20 (99.3–99.7% sequence similarity); and group III: Herberstein strains I3, I3A, and I3R (100% sequence similarity). Molecular typing by denaturing gradient gel electrophoresis (DGGE), random amplified polymorphic DNA (RAPD-PCR), and internal transcribed spacer-homoduplex–heteroduplex polymorphism (ITS-HHP) fingerprinting showed that all isolates are typeable by each of the methods. RAPD was the most discriminatory method. With respect to their physiological characteristics—i.e., growth in the presence of 5–20% (w/v) NaCl, no growth in the absence of NaCl, optimum growth at 37 °C in media containing 5–10% (w/v) NaCl, and optimum pH around 7.5–8.0—the St. Virgil isolates resembled our previously isolated strains. However, the St. Virgil strains showed some differences in their biochemical properties. St. Virgil isolates hydrolysed Tween 80, two isolates reduced nitrate, and no isolate liquefied gelatine. The recurrent isolation of halobacilli from salt efflorescences on historic buildings and monuments at two different geographical locations may indicate that this group of bacteria is common in salt-affected ruins.     

岩画和壁画类文物微生物病害研究进展

古代岩画和壁画是人类文明发展历史进程的重要记录,具有极高的历史价值、艺术价值及科学价值,但他们无时无刻不受到环境因素引起的物理、化学及生物的劣化作用。近年,有关微生物对古代岩/壁画的危害逐渐受到关注。阐述了世界一些著名的岩/壁画文物的微生物的研究进展,如法国拉斯科洞穴岩画(Lascaux Cave)、西班牙阿尔塔米拉洞穴岩画(Altamira Cave)、敦煌石窟壁画、嘉峪关魏晋墓壁画以及我国东北地区公元5世纪的墓葬壁画等。通过对以上所述岩画和壁画微生物群落的分析比较,发现主要的细菌群落是变形菌门和放线菌门,放线菌门以假诺卡氏菌为主。真菌群落主要以虫生真菌为主。进一步分析了岩画和壁画微生物病害的共性和区别,揭示了洞穴、墓室等特殊环境下的微生物群落特点,为防治古代岩/壁画微生物病害提供了以下借鉴。     

Molecular characterisation of Halobacillus strains isolated from different medieval wall paintings and building materials in Austria

We previously reported on the detection and isolation of an indigenous population of Halobacillus from salt-damaged medieval wall paintings and building materials of Herberstein castle in St. Johann bei Herberstein in Styria, Austria. Several moderately halophilic, Gram-positive, endospore-forming Halobacillus-like bacteria could be again isolated by conventional enrichment from salt efflorescences collected in the medieval St. Virgil's chapel in Vienna. Comparative 16S rDNA sequence analyses showed that the St. Virgil isolates are most closely related (>98.5% sequence similarity) to Halobacillus trueperi, Halobacillus litoralis, and to our previous halobacilli strains obtained from the castle Herberstein. Based on 16S rDNA sequence analysis, the strains could be clustered in three different groups. Group I: St. Virgil strains S3, S4, S21, and S22 (99.8–100% sequence similarity); group II: Herberstein strains K3-1, I7, and the St. Virgil strain S20 (99.3–99.7% sequence similarity); and group III: Herberstein strains I3, I3A, and I3R (100% sequence similarity). Molecular typing by denaturing gradient gel electrophoresis (DGGE), random amplified polymorphic DNA (RAPD-PCR), and internal transcribed spacer-homoduplex–heteroduplex polymorphism (ITS-HHP) fingerprinting showed that all isolates are typeable by each of the methods. RAPD was the most discriminatory method. With respect to their physiological characteristics—i.e., growth in the presence of 5–20% (w/v) NaCl, no growth in the absence of NaCl, optimum growth at 37 °C in media containing 5–10% (w/v) NaCl, and optimum pH around 7.5–8.0—the St. Virgil isolates resembled our previously isolated strains. However, the St. Virgil strains showed some differences in their biochemical properties. St. Virgil isolates hydrolysed Tween 80, two isolates reduced nitrate, and no isolate liquefied gelatine. The recurrent isolation of halobacilli from salt efflorescences on historic buildings and monuments at two different geographical locations may indicate that this group of bacteria is common in salt-affected ruins.     

Life and death in ancient populations: Bones of contention in paleodemography

In a recent articleBocquet-Appel & Masset (1985) renew their criticism of paleodemography and criticizeVan Gerven & Armelagos' (1983) defense of paleodemographic methods. In the present analysis we respond toBocquet-Appel andMasset's criticisms ofVan Gerven andArmelagos and then address the question of whether paleodemographic methods are capable of producing plausible results based on what is known about contemporary human populations. This is done by expanding the life tables previously analysed byVan Gerven and co-workers for the Medieval Christian site of Kulubnarti in Nubia'sBatn el Hajar. The expanded results are then compared to data obtained from contemporary human populations as well as interpreted in light of Nubian culture history.     

Detection of Indigenous Halobacillus Populations in Damaged Ancient Wall Paintings and Building Materials: Molecular Monitoring and Cultivation

Several moderately halophilic gram-positive, spore-forming bacteria have been isolated by conventional enrichment cultures from damaged medieval wall paintings and building materials. Enrichment and isolation were monitored by denaturing gradient gel electrophoresis and fluorescent in situ hybridization. 16S ribosomal DNA analysis showed that the bacteria are most closely related to Halobacillus litoralis. DNA-DNA reassociation experiments identified the isolates as a population of hitherto unknown Halobacillus species.     

Detection of representatives of the Planctomycetes in Sphagnum peat bogs by molecular and cultivation approaches

By means of fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes (FISH), it has been shown that members of the phylum Planctomycetes represent a numerically significant bacterial group in boreal Sphagnum peat bogs. The population size of planctomycetes in oxic layers of the peat bog profile was in the range of 0.4–2.0 × 10⁷ cells per g of wet peat, comprising 4 to 13% of the total bacterial cell number. A novel effective approach that combined a traditional cultivation technique with FISH-mediated monitoring of the target organism during the isolation procedure has been developed for the isolation of planctomycetes. Using this approach, we succeeded in isolating several peat-inhabiting planctomycetes in a pure culture. Sequencing of the 16S rRNA genes from two of these isolates, strains A10 and MPL7, showed that they belonged to the planctomycete lineages defined by the genera Gemmata and Planctomyces, respectively. The 16S rRNA gene sequence similarity between strains A10 and MPL7 and the phylogenetically closest organisms, namely, Gemmata obscuriglobus and Planctomyces limnophilus, was only 90%. These results suggest that the indigenous planctomycetes inhabiting Sphagnum peat bogs are so far unknown organisms.     

Detection of representatives of the Planctomycetes in Sphagnum peat bogs by molecular and cultivation methods

By means of fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes (FISH), it has been shown that members of the phylum Planctomycetes represent a numerically significant bacterial group in boreal Sphagnum peat bogs. The population size of planctomycetes in oxic layers of the peat bog profile was in the range of 0.4-2.0 x 10(7) cells per g of wet peat, comprising 4 to 13% of the total bacterial cell number. A novel effective approach that combined a traditional cultivation technique with FISH-mediated monitoring of the target organism during the isolation procedure has been developed for the isolation of planctomycetes. Using this approach, we succeeded in isolating several peat-inhabiting planctomycetes in a pure culture. Sequencing of the 16S rRNA genes from two of these isolates, strains A10 and MPL7, showed that they belonged to the planctomycete lineages defined by the genera Gemmata and Planctomyces, respectively. The 16S rRNA gene sequence similarity between strains A10 and MPL7 and the phylogenetically closest organisms, namely, Gemmata obscuriglobus and Planctomyces limnophilus, was only 90%. These results suggest that the indigenous planctomycetes inhabiting Sphagnum peat bogs are so far unknown organisms.     

Nursing biocrusts: isolation,cultivation, and fitness test of indigenous cyanobacteria

Biological soil crusts (biocrust) are microbial communities that develop at the soil surface of drylands and play an important role in erosion control and fertility. Soil surface disturbance from a broad range of natural and human processes (e.g. fire, livestock grazing, off‐road traffic) cause significant losses in biocrust cover and associated ecosystems services. Hence, biocrust restoration is emerging as an important intervention strategy to rehabilitate degraded dryland soils. In a multistep process, we designed protocols for the establishment of “microbial nurseries” to produce photosynthetic cyanobacterial inoculum for biocrust seeding at scale. We first report on the strategy for isolation, directly from the target site, of a large culture collection of cyanobacteria that included multiple representatives of the five most common biocrust taxa. After genetic pedigreeing of these isolates, we could select those that best matched field populations genetically for scale‐up cultivation. We then developed protocols for effective cyanobacterial biomass production to obtain sufficient inoculum. This was followed by conditioning treatments (hardening off) to preacclimate this inoculum to the stressful conditions expected in the field. Finally, we show that the inoculum obtained was fit to thrive in its original soil under natural outdoor conditions if sufficient water was available. We repeated this process successfully for four sites, two in the hot Chihuanuan desert and two in the cooler Great Basin Desert, and on two textural types of soils in each. The cyanobacterial biocrust nursery approach represents a versatile, viable, and safe tool for the rehabilitation of dryland soils.     

Hemoglobins, haptoglobins, and transferrins in indigenous populations of Kenya

Hemoglobin, haptoglobin, and transferrin phenotypes were determined by means of starch-gel electrophoresis for a sample of 226 Kenya hospital patients. Allele frequencies were: Hb_β^S=0.081; Hp¹=0.057; Tf^D=0.038. Hemoglobin S was the only aberrant hemoglobin found in this sample. Transferrins C and D were the only transferrins found. Hemoglobin and transferrin phenotypes were also determined for a sample of 201 newborn Kenya infants. One of these infants had hemoglobins F, S, and C, eight had hemoglobins A, F, and S, and the remainder had hemoglobins A and F. Transferrins C, B, and D were found in this sample. Allele frequencies were: Tf^B=0.008; Tf^D=0.019.     

Adaptive molecular evolution of MC1R gene reveals the evidence for positive diversifying selection in indigenous goat populations

Detecting signatures of selection can provide a new insight into the mechanism of contemporary breeding and artificial selection and further reveal the causal genes associated to the phenotypic variation. However, the signatures of selection on genes entailing for profitable traits between Chinese commercial and indigenous goats have been poorly interpreted. We noticed footprints of positive selection at MC 1R gene containing SNP s genotyped in five Chinese native goat breeds. An experimental distribution of F _ST was built based on approximations of F _ST for each SNP across five breeds. We identified selection using the high F _ST outlier method and found that MC 1R candidate gene show evidence of positive selection. Furthermore, adaptive selection pressure on specific codons was determined using different codon based on maximum‐likelihood methods; signature of positive selection in mammalian MC 1R was explored in individual codons. Evolutionary analyses were inferred under maximum likelihood models, the HyPhy package implemented in the DATAMONKEY Web Server. The results of codon selection displayed positive diversifying selection at the sites were mainly involved in development of genetic variations in coat color in various mammalian species. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat MC 1R provides new insights that the gene evolution may have been modulated by domestication events in goats.     

Dental polymorphism of the raccoon dog in indigenous and invasive populations: internal and external causation

In total, 721 specimens from eight populations of the raccoon dog Nyctereutes procyonoides across native and colonized areas have been studied. The most polymorphic populations inhabit the European part of Russia and a part of the native area. The raccoon dog from Eastern Poland and the Primorie Far East is characterized by low intrapopulational variability. Quantitative genetic variations in the studied populations indicate a relatively higher level in the population from the Primorie Far East compared to the Southern Vologda and Eastern Poland. The pattern of morphological variability in the raccoon dog is shaped by such factors as the latest phylogenetic history of the species and the structure of the morphotype frequency in the time of the divergence of the populations on both micro-and macro-geographic levels. The influence of geographic and climatic factors forms a well-pronounced trend towards diversification in tooth morphology, which is most probably the consequence of adaptations to changes in the food niche.     

Biodegradation of trichloroethylene and toluene by indigenous microbial populations in vadose sediments

The unsaturated subsurface (vadose zone) receives significant amounts of hazardous chemicals, yet little is known about its microbial communities and their capacity to biodegrade pollutants. Trichloroethylene (TCE) biodegradation occurs readily in surface soils; however, the process usually requires enzyme induction by aromatic compounds, methane, or other cosubstrates. The aerobic biodegradation of toluene and TCE by indigenous microbial populations was measured in samples collected from the vadose zone at unpolluted and gasoline-contaminated sites. Incubation at field moisture levels showed little activity on either TCE or toluene, so samples were tested in soil suspensions. No degradation occurred in samples suspended in water or phosphate buffer solution; however, both toluene and TCE were degraded in samples suspended in mineral salts medium. TCE degradation depended on toluene degradation, and little loss occurred under sterile conditions. Studies with specific nutrients showed that addition of ammonium sulfate was essential for degradation, and addition of other mineral nutrients further enhanced the rate. Additional studies with vadose sediments amended with nutrients showed similar trends to those observed in sediment suspensions. Initial rates of biodegradation in suspensions were faster in uncontaminated samples than in gasolinecontaminated samples, but the same percentages of chemicals were degraded. Biodegradation was slower and less extensive in shallower samples than deeper samples from the uncontaminated site. Two toluene-degrading organisms isolated from a gasoline-contaminated sample were identified as Corynebacterium variabilis SVB74 and Acinetobacter radioresistens SVB65. Inoculation with 10⁶ cells of C. variabilis ml^–1 of soil solution did not enhance the rate of degradation above that of the indigenous population. These results indicate that mineral nutrients limited the rate of TCE and toluene degradation by indigenous populations and that no additional benefit was derived from inoculation with a toluene-degrading bacterial strain. Correspondence to: K.M. Scow     

Biodegradation of trichloroethylene and toluene by indigenous microbial populations in soil.

The biodegradation of trichloroethylene (TCE) and toluene, incubated separately and in combination, by indigenous microbial populations was measured in three unsaturated soils incubated under aerobic conditions. Sorption and desorption of TCE (0.1 to 10 micrograms ml-1) and toluene (1.0 to 20 micrograms ml-1) were measured in two soils and followed a reversible linear isotherm. At a concentration of 1 micrograms ml-1, TCE was not degraded in the absence of toluene in any of the soils. In combination, both 1 microgram of TCE ml-1 and 20 micrograms of toluene ml-1 were degraded simultaneously after a lag period of approximately 60 to 80 h, and the period of degradation lasted from 70 to 90 h. Usually 60 to 75% of the initial 1 microgram of TCE ml-1 was degraded, whereas 100% of the toluene disappeared. A second addition of 20 micrograms of toluene ml-1 to a flask with residual TCE resulted in another 10 to 20% removal of the chemical. Initial rates of degradation of toluene and TCE were similar at 32, 25, and 18 degrees C; however, the lag period increased with decreasing temperature. There was little difference in degradation of toluene and TCE at soil moisture contents of 16, 25, and 30%, whereas there was no detectable degradation at 5 and 2.5% moisture. The addition of phenol, but not benzoate, stimulated the degradation of TCE in Rindge and Yolo silt loam soils, methanol and ethylene slightly stimulated TCE degradation in Rindge soil, glucose had no effect in either soil, and dissolved organic carbon extracted from soil strongly sorbed TCE but did not affect its rate of biodegradation.     

Assessing and monitoring bird populations in Africa: an overview

Bennun, L. 2000. Assessing and monitoring bird populations in Africa: an overview. Ostrich 71 (1 & 2): 214–215.

Access to reliable population data is crucial for effective conservation and management of birds. So far, relatively little attention has been paid to assessing and monitoring bird populations in Africa. This is beginning to change. Regional meetings, for example in East Africa, are discussing and defining standard methodologies, and making technical information more widely available. Researchers are using these methods to access the populations of threatened species, or those of economic value. Projects involving long-term monitoring, particularly of waterbirds, are beginning to yield results that are useful for management. Some challenges that remain include: securing institutional and financial support for long-term monitoring work; integrating monitoring efforts (especially of migratory species) across borders; understanding the ecological significance of population trends; finding robust and reliable methods to census economically important species, such as game-birds; and making accurate global assessments of the populations of threatened species.     

Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

Admixture between wild and captive populations is an increasing concern in conservation biology. Understanding the extent of admixture and the processes involved requires identification of admixed and non-admixed individuals. This can be achieved by statistical methods employing Bayesian clustering, but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943–1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pairwise F_ST of 0.047 and 0.053). By analysing a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor rescuing a part of the indigenous population from introgression.     

Detection of abundant sulphate-reducing bacteria in marine oxic sediment layers by a combined cultivation and molecular approach

The depth distribution and diversity of sulphate-reducing bacteria (SRB) was analysed in the upper intertidal zone of a sandy marine sediment of the Dutch island Schiermonnikoog. The upper centimetre of the sediment included the oxic-anoxic interface and was cut into five slices. With each slice, most probable number (MPN) dilution series were set up in microtitre plates using five different substrates. In the deeper sediment layers, up to 1 x 10(8) cm(-3) lactate-utilizing SRB were counted, corresponding to 23% of the total bacterial count. From the highest positive dilutions of the MPN series, 27 strains of SRB were isolated in pure culture. Sequencing of a 580 bp fragment of the 16S rDNA revealed that 21 isolates had identical sequences, also identical with that of the previously described species Desulfomicrobium apsheronum. However, the diversity of the isolates was higher with respect to their physiological properties: a total of 11 different phenotypes could be distinguished. Genomic fingerprinting by enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR) revealed an even higher diversity of 22 different genotypes. A culture-independent analysis by PCR and denaturing-gradient gel electrophoresis (DGGE) revealed that the partial 16S rDNA sequence of the isolated D. apsheronum strains constituted a significant fraction of the Desulfovibrionaceae. The high subspecies diversity suggests that this abundant aggregate-forming species may have evolved adaptations to different ecological niches in the oxic sediment layers.     

Comparison of lactase persistence polymorphism in ancient and present-day Hungarian populations

The prevalence of adult-type hypolactasia varies ethnically and geographically among populations. A C/T-13910 single nucleotide polymorphism (SNP) upstream of the lactase gene is known to be associated with lactase non-persistence in Europeans. The aim of this study was to determine the prevalence of lactase persistent and non-persistent genotypes in current Hungarian-speaking populations and in ancient bone samples of classical conquerors and commoners from the 10th-11th centuries from the Carpathian basin; 181 present-day Hungarian, 65 present-day Sekler, and 23 ancient samples were successfully genotyped for the C/T-13910 SNP by the dCAPS PCR-RFLP method. Additional mitochondrial DNA testing was also carried out. In ancient Hungarians, the T-13910 allele was present only in 11% of the population, and exclusively in commoners of European mitochondrial haplogroups who may have been of pre-Hungarian indigenous ancestry. This is despite animal domestication and dairy products having been introduced into the Carpathian basin early in the Neolithic Age. This anomaly may be explained by the Hungarian use of fermented milk products, their greater consumption of ruminant meat than milk, cultural differences, or by their having other lactase-regulating genetic polymorphisms than C/T-13910. The low prevalence of lactase persistence provides additional information on the Asian origin of Hungarians. Present-day Hungarians have been assimilated with the surrounding European populations, since they do not differ significantly from the neighboring populations in their possession of mtDNA and C/T-13910 variants.