Comparative analysis of the composition of two chlorophyll-b-containing light-harvesting complexes

The major light-harvesting complexes from Mantoniella squamata (Prasinophyceae) and from Chlorella fusca (Chlorophyceae) were analyzed with respect to polypeptide composition and pigmentation. It was found that the polypeptides of Mantoniella are smaller than those of Chlorella and bind twice the amount of pigment. We assume that the amount of pigment per polypeptide is of ecological as well as of taxonomical importance.Abbreviations Chl chlorophyll - LHC light-harvesting complex - Xan xanthophyll We thank the support by the Deutsche Forschungsgemeinschaft.     

Comparative phylogenetic analysis of microbial communities in pristine and hydrocarbon-contaminated Alpine soils

A molecular characterization of pristine and petroleum hydrocarbon-contaminated Alpine soils sampled in Tyrol (Austria) was performed. To identify predominant bacteria, PCR-amplified 16S rRNA gene fragments from five pristine and nine contaminated soils were analysed using denaturing gradient gel electrophoresis (DGGE). Sequencing and phylogenetic analyses demonstrated that the majority of the DGGE bands represented bacteria in the Actinobacteria and Proteobacteria phyla: 18 and 73%, respectively, in pristine soils, compared with 20 and 76%, respectively, in contaminated soils. A different distribution pattern of bacterial classes in the Proteobacteria was observed between pristine and contaminated soils. The relative proportion of microorganisms belonging to the Alphaproteobacteria was larger in pristine (46%) than in contaminated (24%) soils, while Betaproteobacteria and Gammaproteobacteria were detected only in the hydrocarbon-contaminated soils. This result compared favourably with earlier work in which hydrocarbon-degradation genotypes, largely pseudomonads and Acinetobacter, belonging to the Gammaproteobacteria, were enriched following oil hydrocarbon contamination. In contrast, members of the Actinobacteria phylum, represented by Rhodococcus and Mycobacterium, were found in pristine soils where contamination events had not occurred. The results demonstrate a significant shift in the microbial community structure in Alpine soils following contamination. Furthermore, more potentially novel phylotypes were found in the pristine soils than in the contaminated soils.     

Use of carbon isotope composition for characterization of microbial activity in arable soils

The effect of glucose on microbial mineralization of soil organic matter (SOM) was studied in arable soil specimens. The flows of carbon dioxide generated during this degradation were deduced from differences in the carbon isotope ratios of glucose (delta13C = -11.4 per mil) and SOM (delta13C = -27.01 per mil). The priming effect of glucose and respiratory quotient (RQ) were taken as indices of activation of SOM-consuming microbiota. The data on microbial mineralization of organic matter in soil, obtained in this study, show that addition of a readily consumable substance (glucose) to soil favors SOM degradation and increases the release of carbon dioxide from soil to atmosphere.     

Molecular analysis of the hydrolytic component of petroleum-contaminated soils and of soils remediated with chitin

Molecular genetic techniques (FISH and metagenomic analysis) were used to investigate prokaryotic complexes in native soils (gray forest soil and urbostratozema typical), soils contaminated by petroleum products (gasoline or diesel fuel), and soils subject to remediation by addition of a nitrogen-containing polysaccharide biopolymer chitin. The share of metabolically active prokaryotic cells in the hydrolytic complex of soil microcosms was determined, as well as their biomass and biodiversity. Compared to the control, in the pollutant-containing experimental microcosms, a decrease in the share of metabolically active prokaryotic cells was observed, as well as changes of the hydrolytic complex structure, such as an increase in the share of the phylum Actinobacteria (specifically of the genera Galiella and Nocardioides in the samples contaminated with gasoline and diesel fuel, respectively). Supplementing the hydrocarbon-contaminated system the biopolymer chitin resulted in processing of mixed-minerals with an increase in the number of layers of the smectite type and, as a result, in formation of aggregates and improved aeration. An increase in the number of metabolically active prokaryotic cells and decreased diversity of the soil prokaryotic complex were observed, which were probably associated with the development of a selective group of the hydrolytic complex of chitindegrading microorganisms.     

Testing the functional significance of microbial composition in natural communities

Ecologists have long studied the relationship between biotic composition and ecosystem functioning in larger organisms; however, only recently has this relationship been investigated widely in microorganisms. Recent studies are reviewed within a framework of three experimental approaches that are often used to study larger organisms: environmental treatment, common garden, and reciprocal transplant experiments. Although the composition of microorganisms cannot be easily manipulated in the field, applying these approaches to intact microbial communities can begin to tease apart the effects of microbial composition from environmental parameters on ecosystem functioning. The challenges in applying these approaches to microorganisms are highlighted and it is discussed how the experimental approach and duration affects a study's interpretation. In general, long-term environmental treatment experiments identify correlative relationships between microbial composition and ecosystem functioning, whereas short-term common garden experiments demonstrate that microbial composition influences ecosystem functioning. Finally, reciprocal transplants simultaneously test for interactive effects of the environment and composition on functioning. The studies reviewed provide evidence that, at least in some cases, microbial composition influences ecosystem functioning. It is concluded that whole-community experiments offer a way to test whether information about microbial composition will help predict ecosystem responses to global change.     

Distribution of carbon isotope composition of modern soils on the Qinghai-Tibetan Plateau

This paper presents a large data set on carbon isotope composition (¹³C) of modern soils which were collected under the main vegetation communities along an altitude of 1250–5500m above sea level in the Qinghai-Tibetan Plateau. The ¹³C values of 198 samples range from –28.6 to –15.1 versus PDB and exhibit a clean relation to different vegetation communities from forest (–25.9±1.2) to shrub (–24.7±1.4), steppe (–23.1±1.3), alpine meadow (–23.6±0.7), alpine desert steppe (–21.3±1.6), and alpine desert (–18.9±2.5). We attributed the observed variability in ¹³C values to that the mean annual precipitation (MAP) and the mean annual temperature (MAT) are the main factors controlling the distribution of vegetation types in the Tibetan Plateau, which causes the change in carbon isotope composition of modern soils at any given altitude. The result of both linear and nonlinear regression analyses also confirms that MAP and MAT are the major factors affecting the ¹³C values of surface soils. In the absence of favorable moisture and temperature conditions, low pCO₂ alone is not sufficient to cause the distinct changes in carbon isotope composition of modern soils in the Tibetan Plateau. This study provides some fundamental information on the carbon isotope composition of terrestrial carbon pools and bears some practical significance for the use of carbon isotope data to document vegetation changes and environmental conditions of the high plateau in the past.     

The functional significance of the microbial biomass in organic and conventionally managed soils

In order to achieve sustainability in managed ecosystems we must understand management impacts on soil processes and clarify the regulatory role of the microbial community on these processes. Crop rotation and organic management practices are thought to have positive impacts on the microbial biomass; however, the specific impacts of crop rotation organic management on soil microbial ecology are largely unknown. The effect of organic management on soil microbial ecology was investigated using soils collected from the Rodale Institute Research Center's long-term Farming Systems Trial (FST) experiment. The FST, begun in 1981, included a manured and a cover cropped organic rotation and a conventionally managed grain based rotation. Soil respiration rates and¹³C-isotope fate in a companion study suggest that the biomass characteristics of the FST treatment soils were different in November 1991. However, direct measurement of the microbial community at this time using Phospholipid Fatty Acid Analysis (PLFA) did not identify statistically significant treatment based differences in soil biomass characteristics. Variability among the PLFA profiles of treatment replicates was as great as variability between farming systems. Treatment based trends were observed among selected PLFAs, particularly those present in large amounts, that were consistent with indirect biomass and biomass-dependent measures. Overall, PLFA profiles, soil respiration rates and¹³C-cycling suggested that the organic cover cropped soil had the Largest and most heterogeneous microbial population while the biomass of the organic-manure amended soil was the least heterogeneous, and the most metabolically active. Present address: University of Illinois, 11025. Goodwin ave. Urbana, IL 61801, USA     

Comparative study of the elemental composition of vegetative and dormant microbial cells

X-ray microanalysis showed that vegetative cells, viable resting forms, and nonviable forms (micromummies) of the bacteria Bacillus cereus and Micrococcus luteus and the yeast Saccharomyces cerevisiae differ in the contents of bioelements S, P, Ca, and K and the Ca/K and P/S ratios. Viable resting forms (cystlike refractory cells and bacillar endospores) had more calcium and less phosphorus and potassium than vegetative cells, the difference being higher for bacilli than for micrococci and yeasts. The distinctive feature of all viable resting microbial forms was their low P/S ratios and high Ca/K ratios. The differences revealed in the cellular content and ratios of bioelements probably reflect changes in ionic homeostasis accompanying the transition of vegetative microbial cells to the dormant state. Relevant potassium parameters indicate that the membranes of viable resting forms retain their barrier function. At the same time, the nonviable forms, even morphologically intact, of B. cereus and S. cerevisiae exhibited an anomalously low content of potassium, while those of M. luteus had an anomalously high content of this element. This suggests that the cellular membranes of micromummies lose their barrier function, which results in a free diffusion of potassium ions across the membranes. The possibility of using the elemental composition parameters for quick analysis of the physiological state of microorganisms in natural environments is discussed.     

Effect of glyphosate on the microbial activity of two Romanian soils

Glyphosate applied to soils potentially affect microbial activity. A series of field and laboratory experiments assessed the effect of this herbicide on soil microorganisms. The aim of experiments was to evaluate the effect of glyphosate application on the soil microbial community structure, function and their activity. We studied "in vitro", changes in the microbial activity of typical Chernozem and Gleysol soils, with and without applied glyphosate. The herbicide was applied at a rate of 2, respectively 4 mg kg(-1) of soil and microbial activity were measured by fluorescein diacetate (FDA) hydrolysis. We found an increase of 9 to 13% in FDA hydrolyses in the presence of glyphosate in rate of 2 mg kg (-1) compared with the same type of soil which had never received herbicide. The double quantity of glyphosate decrease soil microbial activity; the amount of hydrolyzed fluorescein is lower than the addition of 2 ppm. The greater decrease was observed in the Gleysol type where the fluorescein hydrolyzed is with 4, 85% lower than version control without glyphosate. Chemical characters of soil, influence soil biological activity when herbicide is added. In Chemozem case, rich in humus, whose predominant micro flora is represented by actinomycetes through glyphosate treatment these organisms growths of as major producers of antibiotics actinomycetes determine an inhibitory effect on eubacteria and micromycetes growth, which is highlighted by estimating a relatively small number of them. After 10 days, once with decreasing of glyphosate content in soil, decreases the number of active actinomycetes, therefore we are witnessing to a numerical growth of bacterial population. In Gleysol type the indigenous micro flora is represented by eubacteria, so when the glyphosate is added it was registered a high growth of these organisms fraction.     

The species composition and ecological characteristics of trematodes from reptiles in the Volga delta

In the result of parasitological researches of reptiles of the Volga delta, 17 species of trematodes belonging to 10 families and 5 orders have been recovered. The dynamics of trematodes in reptiles is regulated by transformations of biocenoses of the delta depending on fluctuations of the Caspian sea level.     

Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears

The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C.?perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.     

Insights into the effect of imidazolium-based ionic liquids on chemical structure and hydrolytic activity of microbial lipase

Bioprocess and Biosystems Engineering - This work studied the effect of the cation alkyl chain length of 1-alkyl-n-methylimidazolium chloride ([Cnmim]Cl)-based ILs on the activity of Aspergillus...     

Comparative analysis of pregnancy proteins and regulation of the functional activity of T-suppressors in pregnancy

The relationship between the pregnancy specific proteins (SP1, SP3) and the functional activity of ConA-induced T-suppressors has been studied during normal gestation. There were a positive correlation between the activity of T-suppressors and the level of SP1 during 8-28 weeks of gestation; between the activity of T-suppressors and the level of SP3 during 8-36 weeks, especially during 29-36 weeks of gestation. It was shown that a progressive accumulation of these proteins apparently necessary for the formation a suppression's dominant in the condition of the immunoregulatory branches during gestation. These findings suggest that SP1 and SP3 as a natural endogenous immunoregulators may play an important role in reproductive strategy of human gestation.     

Post-fire transformation of microbial communities and invertebrate complexes in the pine forest soils,Central Siberia

We studied post-fire transformations in functional characteristics of soil microbial communities and invertebrate complexes in the central-taiga pine forests of Central Siberia. The study revealed that fires of any severity reduce the density and diversity of soil invertebrates and adversely affect the structure and functioning of the sandy podzol microbial complexes. Post-fire recovery of the density and structure of soil invertebrate complexes and the functioning of sandy podzol microbial communities depend on fire duration and severity, as well as dynamics of hydrothermal and trophic properties of the pine forest soils.     

Comparative functional analysis of the Rac GTPases

Small GTPases of the Rho family including Rac, Rho and Cdc42 regulate different cellular processes like reorganization of the actin cytoskeleton by acting as molecular switches. The three distinct mammalian Rac proteins share very high sequence identity but how their specificity is achieved is hitherto unknown. Here we show that Rac1 and Rac3 are very closely related concerning their biochemical properties, such as effector interaction, nucleotide binding and hydrolysis. In contrast, Rac2 displays a slower nucleotide association and is more efficiently activated by the Rac-GEF Tiam1. Modeling and normal mode analysis support the idea that altered dynamics of Rac2 at the switch I region may be responsible for different biochemical properties. These results provide insight into the individual functionalities of the Rac isoforms.     

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper‐arid polar desert

Permafrost in the high elevation McMurdo Dry Valleys of Antarctica ranks among the driest and coldest on Earth. Permafrost soils appear to be largely inhospitable to active microbial life, but sandstone lithic microhabitats contain a trophically simple but functional cryptoendolithic community. We used metagenomic sequencing and activity assays to examine the functional capacity of permafrost soils and cryptoendolithic communities in University Valley, one of the most extreme regions in the Dry Valleys. We found metagenomic evidence that cryptoendolithic microorganisms are adapted to the harsh environment and capable of metabolic activity at in situ temperatures, possessing a suite of stress response and nutrient cycling genes to fix carbon under the fluctuating conditions that the sandstone rock would experience during the summer months. We additionally identified genes involved in microbial competition and cooperation within the cryptoendolithic habitat. In contrast, permafrost soils have a lower richness of stress response genes, and instead the metagenome is enriched in genes involved with dormancy and sporulation. The permafrost soils also have a large presence of phage genes and genes involved in the recycling of cellular material. Our results underlie two different habitability conditions under extreme cold and dryness: the permafrost soil which is enriched in traits which emphasize survival and dormancy, rather than growth and activity; and the cryptoendolithic environment that selects for organisms capable of growth under extremely oligotrophic, arid and cold conditions. This study represents the first metagenomic interrogation of Antarctic permafrost and polar cryptoendolithic microbial communities.     

Genetic variance in the composition of two functional groups (diazotrophs and cyanobacteria) from a hypersaline microbial mat

Examination of variation in ecological communities can lead to an understanding of the forces that structure communities, the consequences of change at the ecosystem level, and the relevant scales involved. This study details spatial and seasonal variability in the composition of nitrogen-fixing and cyanobacterial (i.e., oxygenic photosynthetic) functional groups of a benthic, hypersaline microbial mat from Salt Pond, San Salvador Island, Bahamas. This system shows extreme annual variability in the salinity of the overlying water and the extent of water coverage. Analysis of molecular variance and F(ST) tests of genetic differentiation of nifH and cyanobacterial 16S rRNA gene clone libraries allowed for changes at multiple taxonomic levels (i.e., above, below, and at the species level) to inform the conclusions regarding these functional groups. Composition of the nitrogen-fixing community showed significant seasonal changes related to salinity, while cyanobacterial composition showed no consistent seasonal pattern. Both functional groups exhibited significant spatial variation, changing with depth in the mat and horizontally with distance from the shoreline. The patterns of change suggest that cyanobacterial composition was more insensitive to water stress, and consequently, cyanobacteria dominated the nitrogen-fixing community during dry months but gave way to a more diverse community of diazotrophs in wet months. This seasonal pattern may allow the mat community to respond quickly to water-freshening events after prolonged dry conditions (system recovery) and maintain ecosystem function in the face of disturbance during the wet season (system resilience).     

Mutational analysis of the hydrolytic activity of yeast RNA polymerase III.

For 25 mutant alleles of ret1, encoding the second largest subunit of yeast RNA polymerase III, we have studied the polymerase III nuclease activity, measuring both the total yield and dinucleotide product composition. Mutations affecting amino acids 309-325 gave slightly elevated nuclease activity. In region 367-376, two mutations gave 12-15-fold increased nuclease activity. Our results do not support the catalytic role in nuclease activity proposed for the conserved DDRD motif in this region (Shirai, T., and Go, M. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 9056-9060). Mutations centered on a basic region from amino acids 480 to 490, which aligns with Escherichia coli beta-subunit sequences between Rif(r) clusters I and II, produce changes in the relative yields of A- and G-containing dinucleotides. Four such mutant polymerases pause during elongation at GPy sequences and, in addition, have a reduced frequency of termination at T(5) terminator sequences. We propose that the side chains of these mutationally altered amino acids are in direct contact with bases in the RNA-DNA hybrid very near the growing 3'-end. Two mutations in domain I near the C terminus produced very large increases in exonuclease activity and strongly increased termination, suggesting that this region also contacts the nascent RNA in the hybrid region.     

Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens

In 1993, the WHO declared tuberculosis a global emergency on the basis that there are 8 million new cases per year. The complete genome of the strain H37Rv of the causative microorganism, Mycobacterium tuberculosis, comprising 3924 genes has been sequenced. We compared the proteomes of two non-virulent vaccine strains of M. bovis BCG (Chicago and Copenhagen) with two virulent strains of M. tuberculosis (H37Rv and Erdman) to identify protein candidates of value for the development of vaccines, diagnostics and therapeutics. The mycobacterial strains were analysed by two-dimensional electrophoresis (2-DE) combining non-equilibrium pH gradient electrophoresis (NEPHGE) with SDS-PAGE. Distinct and characteristic proteins were identified by mass spectrometry and introduced into a dynamic 2-DE database (http://www.mpiib-berlin.mpg.de/2D-PAGE). Silver-stained 2-DE patterns of mycobacterial cell proteins or culture supernatants contained 1800 or 800 spots, respectively, from which 263 were identified. Of these, 54 belong to the culture supernatant. Sixteen and 25 proteins differing in intensity or position between M. tuberculosis H37Rv and Erdman, and H37Rv and M. bovis BCG Chicago, respectively, were identified and categorized into protein classes. It is to be hoped that the availability of the mycobacterial proteome will facilitate the design of novel measures for prevention and therapy of one of the great health threats, tuberculosis.