The occurrence of herbs and woody juveniles in a hardwood floodplain forest in relation to flooding and light

Abstract. A study of the distribution of herbs, seedlings and vegetative propagules of woody species in a hardwood flood-plain forest along the Upper Rhine in France revealed that the occurrence of most species is significantly correlated to elevation above river level and light transmission in summer. Species confined to higher-lying sites which are only occasionally and briefly flooded in the growing season show most damage upon flooding. Tall herb species occur on sites where more than 5% daylight reaches the herb layer and they only reach a dense cover where flooding is occasional. The occurrence of woody juveniles is negatively correlated with tall herb cover and largely confined to more shaded sites or more frequently flooded sites. The results indicate that both shading and flooding are important for regeneration of woody species and for maintaining species diversity in hardwood flood-plain forests.     

Occurrence of natural tularemia foci in Kamchatka

The focus of tularemia in the Ust-Kamchatsky region belongs probably to the flood-plain and swamp type with muskrats and tundra voles being the main carriers. In autumn 1980 for the first time three cultures were isolated in this region: 1 from a tundra vole and 2 from muskrats. The presence of antibodies to tularemia antigen in Norway rats was revealed in the passive hemagglutination test.     

Key variables controlling the vegetation of a cool-temperate mire in northern Japan

Abstract. In the cool-temperate Bibi Mire, Hokkaido, Japan, valley fens and flood-plain fens have quite different vegetation. The main variables controlling the vegetation were all hydrological: mean water level, water level fluctuation and surface water flow. Chemical factors such as electrical conductivity, dissolved oxygen and related peat decomposition were less important. The pH was about neutral and has little effect. The flood-plain fen developed under fluctuating water table conditions. The dominant species are Calamagrostis langsdotffii and Carex pseudocuraica. When temporal inundation occurs in the rainy or typhoon seasons, the submergence stimulates bud germination of the stoloniferous C. pseudocuraica, which can rapidly elongate its stolons upward. Some large floating peat mats occurred in the flood-plain fen zone. On these mats some Alnus japonica saplings establish and patches of alder forest can arise. Here the water level was higher than in the peripheral alder forest zone. The valley fen is dominated by Carex lasiocarpa var. occultans and/or C. limosa. It is formed under stable water table conditions in the inundated parts of the mire -where the non-inundated wet areas are dominated by alder trees. In the area where the surface water is flowing, these two fen sedges grow in deeper water since the high oxygen content is considered to compensate the flooding stress.     

Bacterial diversity in microcosms of soils with various humidity]

The succession analysis of bacterial diversity in the A horizons (rich in organic matter) of three contrasting types of soil--burozem, soddy gley soil, and chernozem--showed that the bacterial diversity of soil microcosms in humid regions can be adequately evaluated only if soil samples are incubated at different soil moisture contents. A complete account of actinobacteria and proteobacteria requires the levels of soil moisture corresponding to the maximum capillary-sorption moisture and capillary moisture, respectively. The bacterial diversity, whose value was maximum on the 40th day of succession, was higher in soddy gley soil than in burozem. The taxonomic structures of the bacterial communities of these two types of soil were different. After wetting chernozem samples from arid regions, the soil bacterial community changed insignificantly with time and drastically differed from that of soils from humid regions. The difference in the bacterial diversity of soils was the most distinct when it was evaluated by measuring the proportion between proteobacteria and actino-bacteria.     

Adaptation of the photosynthetic apparatus of the immature broadleaf trees to the flood-plain conditions

We studied the mechanisms of adaptation of immature broadleaf trees to natural placor and flood-plain conditions. Changes in the anatomical and physiological features of plants inhabiting different ecotops are considered an adaptive response of the photosynthetic apparatus.     

Evaluation of Bacterial Diversity in Soil Microcosms at Different Moisture Contents

The succession analysis of bacterial diversity in the A horizons (rich in organic matter) of three contrasting types of soil—burozem, soddy gley soil, and chernozem—showed that the bacterial diversity of soil microcosms in humid regions can be adequately evaluated only if soil samples are incubated at different soil moisture contents. A complete account of actinobacteria and proteobacteria requires the levels of soil moisture corresponding to the maximum capillary–sorption moisture and capillary moisture, respectively. The bacterial diversity, whose value was maximum on the 40th day of succession, was higher in soddy gley soil than in burozem. The taxonomic structures of the bacterial communities of these two types of soil were different. After wetting chernozem samples from arid regions, the soil bacterial community changed insignificantly with time and drastically differed from that of soils from humid regions. The difference in the bacterial diversity of soils was the most distinct when it was evaluated by measuring the proportion between proteobacteria and actinobacteria.     

Vaginal epithelial cells regulate membrane adhesiveness to co‐ordinate bacterial adhesion

Vaginal epithelium is colonized by different bacterial strains and species. The bacterial composition of vaginal biofilms controls the balance between health and disease. Little is known about the relative contribution of the epithelial and bacterial cell surfaces to bacterial adhesion and whether and how adhesion is regulated over cell membrane regions. Here, we show that bacterial adhesion forces with cell membrane regions not located above the nucleus are stronger than with regions above the nucleus both for vaginal pathogens and different commensal and probiotic lactobacillus strains involved in health. Importantly, adhesion force ratios over membrane regions away from and above the nucleus coincided with the ratios between numbers of adhering bacteria over both regions. Bacterial adhesion forces were dramatically decreased by depleting the epithelial cell membrane of cholesterol or sub‐membrane cortical actin. Thus, epithelial cells can regulate membrane regions to which bacterial adhesion is discouraged, possibly to protect the nucleus.     

The Structure of Bacterial Complexes in the Protva River Floodplain

The synecological analysis of bacterial communities from the Protva River floodplain biogeocenosis showed that all of their horizons contain spirilla, which are typical hydrobionts, and pigmented coryneform bacteria associated with the herbaceous plants of the floodplain meadows. The alluvial meadow soils of the inundated regions of the floodplain differ from the unflooded regions of the floodplain in that they have a more diverse bacterial population that is continuously distributed over the soil profile.     

Classification of Bacteria Based on the Biases of Terminal Amino Acid Residues

The frequencies of amino acid residues are known to be biased at both terminal regions of amino acid sequences deduced from bacterial genomic DNA. To investigate whether or not the features of biases of amino acid residues at the terminal regions are related to the bacterial phylogeny, we calculated the normalized amino acid compositions at both terminal regions, and used these compositions to classify 144 bacteria by hierarchical clustering analysis. Our results showed that most of these bacteria were classified into taxonomic classes by the hierarchical clustering analysis that was based on the normalized amino acid compositions at the N-terminal region. Therefore, we concluded that the features of biases of the N-terminal amino acid residues were related to the bacterial phylogeny.     

Mallomonas parana (Synurophyceae, Synurales), a new chrysophyte species from a river flood-plain lake of the Parana River system, Argentina

Mallomonas parana sp. nov. (Synurophyceae, Synurales) was found in a river flood-plain lake of the Paraná River system, Santa Fe Province, Argentina. Transmission and scanning electron microscopic observations were made. The new taxon is referred to the series Allorgei of the section Quadratae, and biogeographical aspects of this series are dicusssed.     

Bacterial populations in samples of bioleached copper ore as revealed by analysis of DNA obtained before and after cultivation.

The composition of bacterial populations in copper bioleaching systems was investigated by analysis of DNA obtained either directly from ores or leaching solutions or after laboratory cultures. This analysis consisted of the characterization of the spacer regions between the 16 and 23S genes in the bacterial rRNA genetic loci after PCR amplification. The sizes of the spacer regions, amplified from DNAs obtained from samples, were compared with the sizes of those obtained from cultures of the main bacterial species isolated from bioleaching systems. This allowed a preliminary assessment of the bacterial species present in the samples. Identification of the bacteria was achieved by partial sequencing of the 16S rRNA genes adjacent to the spacer regions. The spacer regions observed in DNA from columns leached at different iron concentrations indicated the presence of a mixture of different bacteria. The spacer region corresponding to Thiobacillus ferrooxidans was the main product observed at high ferrous iron concentration. At low ferrous iron concentration, spacer regions of different lengths, corresponding to Thiobacillus thiooxidans and "Leptospirillum ferrooxidans" were observed. However, T. ferrooxidans appeared to predominate after culture of these samples in medium containing ferrous iron as energy source. Although some of these strains contained singular spacer regions, they belonged within previously described groups of T. ferrooxidans according to the nucleotide sequence of the neighbor 16S rRNA. These results illustrate the bacterial diversity in bioleaching systems and the selective pressure generated by different growth conditions.     

水稻种子的细菌含量和群落结构及其影响因素分析

【目的】种子是植物微生物群代际传递的重要途径，但种子携带的微生物群落尚缺乏系统的研究。本研究以水稻种子为模型，定量分析种子的细菌含量、测定种子的细菌群落结构、探究地域与品种对细菌含量及群落结构的影响和鉴定水稻种子的核心菌群。【方法】选取18个水稻品种，每个品种分别来自中国海南和天津2个地域，共36组样本。每组样本包含5或10个DNA样本，每个DNA样本由3粒种子提取的总DNA构成。使用细菌特异性16S rDNA介导的荧光定量PCR技术测定种子的细菌含量，并分析影响因素；使用16S rDNA扩增子测序技术测定种子的细菌群落结构，并用生物信息学方法分析了影响因素和核心菌群。【结果】本研究测定了1 080粒水稻种子的细菌含量，发现经过表面除菌的水稻种子内部存在共栖细菌，平均每克种子的细菌含量为1.53×10⁶。水稻品种对种子的细菌含量有显著影响，而地域无影响。测定180个扩增子文库的细菌群落结构，发现水稻种子的菌群与水稻植株有相似之处，均以变形菌门为主要的细菌门类；地域对水稻种子的细菌群落结构有重要影响，不同地域的水稻种子在主坐标分析(principal co-ordinate analysis, PCoA)中有明显分离；而粳稻和籼稻之间无显著差异。还发现水稻种子存在核心菌群，且相对丰度高达总菌群的85.56%。【结论】本研究系统地揭示了水稻种子的细菌含量、群落结构及其影响因素，为利用种传微生物促进水稻健康提供了数据和方法支持。     

DNA substrate specificity of reverse gyrase from extremely thermophilic archaebacteria

It has been shown earlier that eukaryotic type I DNA topoisomerases act on duplex DNA regions, while eubacterial type I topoisomerases require single-stranded regions. The present paper demonstrates that the type I topoisomerase from extremely thermophilic archaebacteria, reverse gyrase, winds DNA by binding to single-stranded DNA regions. Thus, type I topoisomerases, both relaxing one in eubacteria and reverse gyrase in extremely thermophilic archaebacteria share a substrate specificity to melted DNA regions. The important consequence of this specificity is that the cellular DNA superhelical stress actively controlled by bacterial topoisomerases is confined to a narrow range characterized by a low stability of the double helix. Hence we suppose that bacterial topoisomerase systems control duplex stability near its minimum, for which purpose they create an appropriate negative superhelicity at moderate temperatures or a positive one at extremely high temperatures, the feedback being ensured by the aforesaid specificity of type I bacterial topoisomerases.     

Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes

The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that could be recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to see the generality of this pattern, we have analyzed 43 additional genomes belonging to most established bacterial phyla. Differential densities between regulatory and nonregulatory regions are detectable in most of the analyzed genomes, with the exception of those that have evolved toward extreme genome reduction. Thus, presence of this pattern follows that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is an outcome of the process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely related bacterial genomes.     

Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes

The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that could be recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to see the generality of this pattern, we have analyzed 43 additional genomes belonging to most established bacterial phyla. Differential densities between regulatory and nonregulatory regions are detectable in most of the analyzed genomes, with the exception of those that have evolved toward extreme genome reduction. Thus, presence of this pattern follows that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is an outcome of the process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely related bacterial genomes.     

The ecology of the Kafue lechwe population of Zambia before the operation of hydro-electric dams on the Kafue River

Aerial surveys from 1970 onwards suggest a stable Kafue lechwe population of 94 000±9% on the Kafue Flats. The present distribution shows a contraction in dry and wet season range in comparison with 1953/54. Sex ratios of populations on both the North and South banks of the Kafue river do not differ significantly from unity. North bank males have a higher survival rate than South bank males. Survival curves for males and females on the South bank show the same pattern. For both the 1971 and 1972 breeding seasons 73% of South bank females older than 1½ years are expected to have bred successfully. The peaks of conceptions for both seasons are from mid-December to mid-March, suggesting a main lambing period from mid-July until mid-October. Present sex ratio, age structure, reproductive status and the reproductive cycle have been compared with 1961/62 data. Variation in physical condition, based on monthly measurements of the kidney fat percentage, dressing-out percentage and live weight, although influenced by the physiological demands of rut and pregnancy, is correlated with the availability of flood-plain grazing. The lowest values of condition parameters are found during the period of maximum flood, after the end of the rains (April/May), until the receding flood makes flood-plain grazing available, usually in early June. A high level of tuberculosis, lungworm infection and many other pathogens amongst the South bank population are reported. Animals from the North bank are thought to be in better physical condition. The Kafue Gorge dam, completed in 1971, and the Iteshi-teshi dam, at present under construction, will prolong the high flood period in wet years and prevent most flooding in dry years, both of these effects will reduce the carrying capacity of the flood plain for lechwe and a large reduction of the size of the population is expected to result from the operation of the dams.     

Transduction of bacteriophage Mu by bacteriophage T1.

Phage T1 transduces phage Mu PFU from Mu-lysogenic donor cells to sensitive recipient cells. The efficiency of transduction depends on the chromosomal location of the Mu prophage. T1, therefore, appears to package different regions of the bacterial chromosome with different efficiencies. Although T1 transduces bacterial markers with different efficiencies, there is no direct correlation between the efficiency of transduction of a bacterial marker and the efficiency of transduction of Mu PFU from donor cells with the Mu prophage located in that marker.     

Identification of a Core Bacterial Community within the Large Intestine of the Horse

The horse has a rich and complex microbial community within its gastrointestinal tract that plays a central role in both health and disease. The horse receives much of its dietary energy through microbial hydrolysis and fermentation of fiber predominantly in the large intestine/hindgut. The presence of a possible core bacterial community in the equine large intestine was investigated in this study. Samples were taken from the terminal ileum and 7 regions of the large intestine from ten animals, DNA extracted and the V1-V2 regions of 16SrDNA 454-pyrosequenced. A specific group of OTUs clustered in all ileal samples and a distinct and different signature existed for the proximal regions of the large intestine and the distal regions. A core group of bacterial families were identified in all gut regions with clear differences shown between the ileum and the various large intestine regions. The core in the ileum accounted for 32% of all sequences and comprised of only seven OTUs of varying abundance; the core in the large intestine was much smaller (5-15% of all sequences) with a much larger number of OTUs present but in low abundance. The most abundant member of the core community in the ileum was Lactobacillaceae, in the proximal large intestine the Lachnospiraceae and in the distal large intestine the Prevotellaceae. In conclusion, the presence of a core bacterial community in the large intestine of the horse that is made up of many low abundance OTUs may explain in part the susceptibility of horses to digestive upset.     

Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences

Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A search of 302 complete bacterial genomes predicted 403 putative prophage regions, accounting for 2.7% of the total bacterial DNA. Analysis of the 285 putative attachment sites revealed tRNAs are targets for integration slightly more frequently (33%) than intergenic (31%) or intragenic (28%) regions, while tmRNAs were targeted in 8% of the regions. The most popular tRNA targets were Arg, Leu, Ser and Thr. Mapping of the insertion point on a consensus tRNA molecule revealed novel insertion points on the 5' side of the D loop, the 3' side of the anticodon loop and the anticodon. A novel method of constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of the phage/prophage proteomes. This method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes.