Heterotrophic microbial communities use ancient carbon following glacial retreat

When glaciers retreat they expose barren substrates that become colonized by organisms, beginning the process of primary succession. Recent studies reveal that heterotrophic microbial communities occur in newly exposed glacial substrates before autotrophic succession begins. This raises questions about how heterotrophic microbial communities function in the absence of carbon inputs from autotrophs. We measured patterns of soil organic matter development and changes in microbial community composition and carbon use along a 150-year chronosequence of a retreating glacier in the Austrian Alps. We found that soil microbial communities of recently deglaciated terrain differed markedly from those of later successional stages, being of lower biomass and higher abundance of bacteria relative to fungi. Moreover, we found that these initial microbial communities used ancient and recalcitrant carbon as an energy source, along with modern carbon. Only after more than 50 years of organic matter accumulation did the soil microbial community change to one supported primarily by modern carbon, most likely from recent plant production. Our findings suggest the existence of an initial stage of heterotrophic microbial community development that precedes autotrophic community assembly and is sustained, in part, by ancient carbon.     

Microbial population dynamics on seeds during drum and steeping priming

In the UK, seeds are primed commercially via drum or steeping priming processes to improve seed germination and seedling establishment but the microbial population dynamics occurring during these processes are unknown. Consequently, changes in culturable bacterial and fungal populations that occurred during laboratory and commercial scale drum priming of carrot, leek and parsnip seed and during laboratory scale and commercial scale steeping priming of carrot and sugar beet seed were investigated. Populations of bacteria and pseudomonads increased by 2 and 4 log₁₀ cfu g^–1 seed during priming to reach between 7 and 10 log₁₀ cfu g^–1 seed with less than 1 log₁₀ cfu g^–1 seed decrease after redrying, irrespective of seed type or priming process. Pseudomonads represented approximately 10% of the culturable bacterial population. Fungal populations also increased by between 1 and 3 log₁₀ cfu g^–1 seed during priming of carrot, leek and parsnip seed and were little affected by redrying. Addition of a tefluthrin coating (a standard commercial insecticide treatment) during the drying stage of commercial scale drum priming had little effect on microbial populations. During steeping priming, populations of bacteria and pseudomonads on sugar beet also increased by 2 and 4 log₁₀ cfu g^–1 seed with less than 1 log₁₀ cfu g^–1 seed decrease after redrying. However, fungi did not increase in the same manner on sugar beet, suggesting that the sugar beet seed itself may have an inhibitory effect on fungal growth. The presence of thiram in the steeping liquid (a standard commercial fungicide treatment) inhibited fungal proliferation on carrot and sugar beet seed. Spore forming bacteria generally occurred at low levels on all seeds (between 2 and 5 log₁₀ cfu g^–1seed) and did not exhibit any characteristic population changes during priming or redrying. Clearly some culturable populations of microorganisms can increase reproducibly during these priming processes and survive the redrying procedure, thereby demonstrating the potential for a novel method of introducing microbial inoculants onto seed.     

Bacterial communities of some brown and red algae from Peter the Great Bay, the Sea of Japan

The structure of microbial communities of brown algae, red algae, and of the red alga Gracilaria verrucosa, healthy and affected with thallus rot, were comparatively investigated; 61 strains of heterotrophic bacteria were isolated and characterized. Most of them were identified to the genus level, some Vibrio spp., to the species level according to their phenotypic properties and the fatty acid composition of cellular lipids. The composition of the microflora of two species of brown algae was different. In Chordaria flagelliphormis, Pseudomonas spp. prevailed, and in Desmarestia viridis, Bacillus spp. The composition of the microflora of two red algae, G. verrucosa and Camphylaephora hyphaeoides, differed mainly in the ratio of prevailing groups of bacteria. The most abundant were bacteria of the CFB cluster and pseudoalteromonads. In addition, the following bacteria were found on the surface of the algae: Sulfitobacter spp., Halomonas spp., Acinetobacter sp., Planococcus sp., Arthrobacter sp., and Agromyces sp. From tissues of the affected G. verrucosa, only vibrios were isolated, both agarolytic and nonagarolytic. The existence of specific bacterial communities characteristic of different species of algae is suggested and the relation of Vibrio sp. to the pathological process in the tissues of G. verrucosa is supposed.     

The use of protein characteristics to assess the retrievability of ancient DNA from ancient bones

The ability to retrieve DNA from ancient specimens has been one of the greatest achievements of the past decade, and has opened a totally new field of research with applications in seemingly distant domains such as archeobotany, the molecular phylogeny of extinct genomes, human paleopathology and the genetic of ancient human populations. However, extraction of ancient DNA has often a very low rate of success, prompting researchers to develop screening methods for the selection of promising specimens. With this goal in mind, we studied the amino acid content of nine human bones of ancient origin. We demonstrate that a single HPLC chromatogram is indicative of the integrity of ancient bone proteins. Among five specimens containing amplifiable DNA, four exhibited a protein content similar to that of contemporary bone protein content. Three of the four specimens, from which we were unable to extract any amplifiable DNA, had an amino acid content strikingly different from that of contem-porary bone. A non-parametric statistical test, Kendall's tau, was used to show that protein content and PCR products, are probably correlated (at a 95% confidence level). In addition, the D/L Asp and D/L Glu racemization ratios obtained are indicative of the presence of ancient organic compounds. We propose that protein analysis should be systematically performed in studies where there are many samples in order to select the specimens that are most likely to contain retrievable ancient DNA.     

Characterisation by molecular hybridization of RNA fragments isolated from ancient (1400 B.C.) seeds

Summary The analysis of cress seeds from Thebes dated approximately 1400 years B.C. showed that fragments of RNA up to 10 bases in length were still present in the ancient seeds. After having been made radioactive at the 5OH terminus, the RNA fragments were used as probes in a spot hybridization experiment. They were shown to hybridize to cress DNA and, to a lesser extent, to that of phylogenetically distant species. When fixed onto nitrocellulose and probed with different cloned genes, the RNA fragments were shown to originate from breakage of the 25 and 18s cytoplasmic rRNA.     

Spatial distribution of microbial communities in the cystic fibrosis lung

Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from microbial infections of the lungs. Culture-independent studies of CF-associated microbial communities have indicated that microbial diversity in the CF airways is much higher than suggested by culturing alone. However, these studies have relied on indirect methods to sample the CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the diversity of microbial communities in tissue sections from anatomically distinct regions of the CF lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly between different areas of the lungs, and few taxa were common to microbial communities in all anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial, but also spatially heterogeneous suggesting that treatment regimes tailored to dominant populations in sputum or BAL samples may be ineffective against infections in some areas of the lung.     

Microbial communities involved in anaerobic degradation of alkanes

Saturated hydrocarbons are quantitatively the most abundant fraction among all petroleum hydrocarbons. Significant advances have been made in the understanding of the anaerobic biodegradability of alkanes in terms of the microorganisms involved and the biochemical pathways over the past two decades. They can be used as carbon and energy sources by diverse physiological groups of microorganisms (isolates or consortia) grown under chlorate-reducing, nitrate-reducing, sufidogenic or methanogenic conditions. Two general biochemical mechanisms have been proposed for the initial activation of alkanes including addition of fumarate and carboxylation. However, glycyl radical enzymes dependent fumarate addition which yields alkyl-substituted succinate appear to be the most commonly shared mechanism for the anaerobic attack of alkanes under various redox conditions by phylogenetically diverse microorganisms. The genes encoding the candidate alkylsuccinate synthase have been recently described in alkane-degrading sulfate- and nitrate-reducers as well as in hydrocarbon-rich environments. Alternative mechanisms may also be available depending on the alkane-degrading microbial community and electron acceptors utilized.     

Benthic macrofauna communities of the submersed Pleistocene Elbe valley in the southern North Sea

Macrozoobenthic community structure was studied in two surveys along a transect of 13 stations following the submersed Pleistocene Elbe valley in the south-eastern North Sea during May to June 2000 and March 2001. Two replicates of bottom samples were taken with a van Veen grab of 0.1 m² sampling size. In order to analyse the benthic macrofauna communities, the animals obtained were identified and counted, and MDS and cluster analysis were performed. Out of 200 taxa identified, 84 were polychaetes, 46 molluscs, 40 crustaceans, 15 echinoderms, and 15 belonged to other groups. Mean abundance was 4,860 individuals per m², mean biomass 32.9 g ash free dry mass per m². Mean diversity was 1.76 and mean evenness 0.54. The macrofauna of the Pleistocene Elbe valley is composed of three associations according to the cluster analysis. Each association is described by a combination of characterizing and discriminating species. An Amphiura-brachiata―Tellimya-ferruginosa-association was found in the south-eastern part of the depression, whereas a transitional association with elements of both assemblages lead to an Amphiura-filiformis―Galathowenia-oculata―Nuculoma-tenuis-association in the north-western part of the valley. In the context of the entire southern North Sea, both associations are small-scale substructures, and as such are contained in the Nucula-nitidosa-community and the Amphiura-filiformis-community, respectively. A north-westward shift of the community of the southern Elbe valley was found and discussed as a possible consequence of warm winters of the last decades.     

Microbial consortia involved in the anaerobicdegradation of hydrocarbons

In this review, we examine the energetics of well-characterized biodegradation pathways and explore the possibilities for these to support growth of multiple organisms interacting in consortia. The relevant phenotypic and/or phylogenetic characteristics of isolates and consortia mediating hydrocarbon degradation coupled with different terminal electron-acceptingprocesses (TEAP) are also reviewed. While the information on metabolic pathways has been gained from the analysis of individual isolates, the energetic framework presented here demonstrates that microbial consortia could be readily postulated for hydrocarbon degradation coupled to any TEAP. Several specialized reactions occur within these pathways, and the organisms mediating these are likely to play a key role in defining the hydrocarbon degradation characteristics of the community under a given TEAP. Comparing these processes within and between TEAPs reveals biological unity in that divergent phylotypes display similar degradation mechanisms and biological diversity in that hydrocarbon-degraders closely related as phylotypes differ in the type and variety of hydrocarbon degradation pathways they possess. Analysis of microcosms and of field samples suggests that we have only begun to reveal the diversity of organisms mediating anaerobic hydrocarbon degradation. Advancements in the understanding of how hydrocarbon-degrading communities function will be significantly affected by the extent to which organisms mediating specialized reactions can be identified, and tools developed to allow their study in situ.     

Microbial quality of soil from the Pampa biome in response to different grazing pressures

The aim of this study was to evaluate the impact of different grazing pressures on the activity and diversity of soil bacteria. We performed a long-term experiment in Eldorado do Sul, southern Brazil, that assessed three levels of grazing pressure: high pressure (HP), with 4% herbage allowance (HA), moderate pressure (MP), with 12% HA, and low pressure (LP), with 16% HA. Two reference areas were also assessed, one of never-grazed native vegetation (NG) and another of regenerated vegetation after two years of grazing (RG). Soil samples were evaluated for microbial biomass and enzymatic (β-glucosidase, arylsulfatase and urease) activities. The structure of the bacterial community and the population of diazotrophic bacteria were evaluated by RFLP of the 16S rRNA and nifH genes, respectively. The diversity of diazotrophic bacteria was assessed by partial sequencing of the 16S rDNA gene. The presence of grazing animals increased soil microbial biomass in MP and HP. The structures of the bacterial community and the populations of diazotrophic bacteria were altered by the different grazing managements, with a greater diversity of diazotrophic bacteria in the LP treatment. Based on the characteristics evaluated, the MP treatment was the most appropriate for animal production and conservation of the Pampa biome.     

The in vitro effect of hydrogen peroxide on vaginal microbial communities

This study presents a series of experiments carried out in order to elucidate the role of H2O2 in antimicrobial activity of lactobacilli. Vaginal swabs were collected from 60 premenopausal women and checked for pH and Nugent score, and Lactobacillus species were cultured, phenotyped and genotyped. The main outcome measures involved: (1) species of vaginal lactobacilli most effective in liberating H2O2, (2) minimal microbicidal concentrations of added H2O2, (3) kinetics of H2O2 liberation in relation to oxygen tension, (4) antimicrobial activity of pure H2O2 versus one produced by selected vaginal lactobacilli and the total activity of their culture supernatants. Results showed that H2O2 was liberated especially by: Lactobacillus delbrueckii, Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus johnsonii and L. gasseri. Hydrogen peroxide reached concentrations from 0.05 to 1.0 mM, which under intensive aeration increased even up to 1.8 mM. Microorganisms related to vaginal pathologies show varied resistance to the action of pure H2O2. Most potent inhibitory activity against bacteria and yeasts was presented by Lactobacillus culture supernate producing H2O2, followed by the nonproducing strain and pure H2O2. To conclude - the antimicrobial activity of lactobacilli is a summation of various inhibitory mechanisms in which H2O2 plays some but not a crucial role, in addition to other substances.     

Effects of soybean oligosaccharides on intestinal microbial communities and immune modulation in mice

BackgroundSoybean oligosaccharides (SBOSs) are potential prebiotics that may be used to improve immune function. Here, we investigated the effects of intragastric administration of SBOSs in mice to determine the effects on autochthonous intestinal microbial communities and immunological parameters. Results E: After 22-day administration, 4.0 g kg body weight (BW)⁻¹ SBOSs significantly enhanced the proliferation of bifidobacteria and lactic acid bacteria (LAB) as compared to the control. This dose of SBOSs also significantly increased numbers of enterococci and decreased numbers of Clostridium perfringens. Treatment with 4.0 g kg BW⁻¹ SBOSs also significantly increased the percentage of T-lymphocytes and lymphocyte proliferation as compared to the control, suggesting that SBOSs promoted cellular immunity in mice. Additionally, 4.0 g kg BW⁻¹ SBOSs induced significant differences in hemolysin production, natural killer (NK) cell activity, phagocytic activity, cytokine production, and immunoglobulin levels compared to the control. Conclusion: Our data demonstrated that intragastric administration of SBOSs at a dose of 4.0 g kg BW⁻¹ improved the numbers of beneficial intestinal microbes and enhanced immunological function of mice. Therefore, these data supported that SBOSs may have applications as a prebiotic to improve immune responses in humans. Further studies are warranted.     

Prenylated flavonoids from seeds of Calopogonium mucunoides

The seeds of Calopogonium mucunoides furnished 7-O-γ,γ-dimethylallyl-8-methoxy-3′,4′-dioxymethylene-isoflavone, 7-O-γ,γ-dimethylallyl-3′-hydroxy-4′-methoxyisoflavone, 7-O-γ,γ-dimethylallyl-3′,4′-dimethoxyisoflavone and 2S-di[6′',6′'-dimethylpyrano (2′',3′':7,8;2′',3′':4′,3′)]-flavanone whose structures were established by spectroscopic means involving the use of 400 MHz ¹H NMR with double irradiation and INDOR techniques.     

Methanotrophs of the Psychrophilic Microbial Community of the Russian Arctic Tundra

In tundra, at a low temperature, there exists a slowly developing methanotrophic community. Methane-oxidizing bacteria are associated with plants growing at high humidity, such as sedge and sphagnum; no methanotrophs were found in polytrichous and aulacomnious mosses and lichens, typical of more arid areas. The methanotrophic bacterial community inhabits definite soil horizons, from moss dust to peat formed from it. The potential ability of the methanotrophic community to oxidize methane at 5°C enhances with the depth of the soil profile in spite of the decreasing soil temperature. The methanotrophic community was found to gradually adapt to various temperatures due to the presence of different methane-oxidizing bacteria in its composition. Depending on the temperature and pH, different methanotrophs occupy different econiches. Within a temperature range from 5 to 15°C, three morphologically distinct groups of methanotrophs could be distinguished. At pH 5–7 and 5–15°C, forms morphologically similar to Methylobacter psychrophilus predominated, whereas at the acidic pH 4–6 and 10–15°C, bipolar cells typical of Methylocella palustris were mostly found. The third group of methanotrophic bacteria growing at pH 5–7 and 5–10°C was represented by a novel methanotroph whose large coccoid cells had a thick mucous capsule.     

Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere

The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.     

The pattern of recovery of disturbed microbial communities inhabiting hard substrates

The recovery of microbial communities removed from hard substrates was studied in the laboratory and on microepiphyton in the White Sea, in St. Petersburg, and in Karelija. The removal of these communities from hard substrates destroyed their spatial structure. Recovery was allowed to proceed from the suspension on a horizontal substrate in stagnant water at low temperature. The sequence of colonization in the laboratory was the same as that in the field. Laboratory recovery was complete in 12–24 h and did not depend on the age of the natural community. From the comparison between laboratory and field data on such mechanical disturbance, a pattern of recovery, termed ‘self-assembly’, is proposed. This revised version was published online in September 2006 with corrections to the Cover Date.