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PubMed2004

Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils.

The diversity and composition of soil bacterial communities were compared among six Austrian natural forests, including oak-hornbeam, spruce-fir-beech, and Austrian pine forests, using terminal restriction fragment length polymorphism (T-RFLP, or TRF) analysis and sequence analysis of 16S rRNA genes. The forests studied differ greatly in soil chemical characteristics, microbial biomass, and nutrient turnover rates. The aim of this study was to relate these differences to the composition of the bacterial communities inhabiting the individual forest soils. Both TRF profiling and clone sequence analysis revealed that the bacterial communities in soils under Austrian pine forests, representing azonal forest types, were distinct from those in soils under zonal oak-hornbeam and spruce-fir-beech forests, which were more similar in community composition. Clones derived from an Austrian pine forest soil were mostly affiliated with high-G+C gram-positive bacteria (49%), followed by members of the alpha-Proteobacteria (20%) and the Holophaga/Acidobacterium group (12%). Clones in libraries from oak-hornbeam and spruce-fir-beech forest soils were mainly related to the Holophaga/Acidobacterium group (28 and 35%), followed by members of the Verrucomicrobia (24%) and the alpha-Proteobacteria (27%), respectively. The soil bacterial communities in forests with distinct vegetational and soil chemical properties appeared to be well differentiated based on 16S rRNA gene phylogeny. In particular, the outstanding position of the Austrian pine forests, which are determined by specific soil conditions, was reflected in the bacterial community composition.

Bacteria↗
PubMed2006

Concentration-dependent patterns of leucine incorporation by coastal picoplankton.

Coastal pelagic environments are believed to feature concentration gradients of dissolved organic carbon at a microscale, and they are characterized by pronounced seasonal differences in substrate availability for the heterotrophic picoplankton. Microbial taxa that coexist in such habitats might thus differ in their ability to incorporate substrates at various concentrations. We investigated the incorporation patterns of leucine in four microbial lineages from the coastal North Sea at concentrations between 0.1 and 100 nM before and during a spring phytoplankton bloom. Community bulk incorporation rates and the fraction of leucine-incorporating cells in the different populations were analyzed. Significantly fewer bacterial cells incorporated the amino acid before (13 to 35%) than during (23 to 47%) the bloom at all but the highest concentration. The incorporation rate per active cell in the prebloom situation was constant above 0.1 nM added leucine, whereas it increased steeply with substrate concentration during the bloom. At both time points, a high proportion of members of the Roseobacter clade incorporated leucine at all concentrations (55 to 80% and 86 to 94%, respectively). In contrast, the fractions of leucine-incorporating cells increased substantially with substrate availability in bacteria from the SAR86 clade (8 to 31%) and from DE cluster 2 of the Flavobacteria-Sphingobacteria (14 to 33%). The incorporation patterns of marine Euryarchaeota were between these extremes (30 to 56% and 48 to 70%, respectively). Our results suggest that the contribution of microbial taxa to the turnover of particular substrates may be concentration dependent. This may help us to understand the specific niches of coexisting populations that appear to compete for the same resources.

Animals↗
PubMed2001

Evidence for anaerobic syntrophic acetate oxidation during methane production in the profundal sediment of subtropical Lake Kinneret (Israel).

Methane production was measured in samples of the profundal sediment from Lake Kinneret. Production rates of CH(4) were higher at 30 degrees C than at the in situ temperature of 15 degrees C and were higher in the top 5 cm layer than below. Turnover of [2-(14)C]-acetate resulted in the production of (14)CH(4) and (14)CO(2) with turnover times of < 42 min. However, < 30% of the added radioactivity was converted to gaseous products, indicating that only part of the acetate pool was microbially available. The calculated acetate turnover rates were sufficient to account for total CH(4) production, indicating that CH(4) was produced exclusively from acetate. This conclusion was confirmed by inhibition of methanogens with chloroform, which resulted in an almost stoichiometric accumulation of acetate. However, a large percentage (30-60%) of [2-(14)C]-acetate was converted to (14)CO(2), despite lack of reducible sulphate or other oxidants in the sediment. Anoxic preincubation of the sediment did not result in reduced production of (14)CO(2). Therefore, part of the acetate must have been oxidized rather than methanogenically cleaved. Conversion of [(14)C]-bicarbonate to (14)CH(4) indicated that 30-50% of total CH(4) production originated from reduction of CO(2). To reconcile the relatively high contribution of H(2)/CO(2)-dependent methanogenesis with the relatively high oxidative conversion of acetate, we assume that part of the acetate was used syntrophically by consortia of acetate-oxidizing bacteria and H(2)/CO(2)-using methanogens. This conclusion is supported by favourable thermodynamic conditions for syntrophic acetate oxidation under in situ conditions and complete inhibition of [2-(14)C]-acetate turnover at high H(2) partial pressures. Further evidence to support this conclusion comes from the analysis of the structure of the archaeal community. Terminal restriction fragment length polymorphism (T-RFLP) and partial sequence analysis of the SSU rRNA genes amplified from DNA extracts of the sediment showed Methanomicrobiaceae as the dominant methanogenic group, whereas acetoclastic methanogens could not be detected.

Acetates↗
PubMed2005

Structural stability and prebiotic properties of resistant starch type 3 increase bile acid turnover and lower secondary bile acid formation.

Microbial metabolism is essential in maintaining a healthy mucosa in the large bowel, preferentially through butyrate specific mechanisms. This system depends on starch supply. Two structurally different resistant starches type 3 (RS3) have been investigated with respect to their resistance to digestion, fermentability, and their effects on the composition and turnover of bile acids in rats. RSA (a mixture of retrograded maltodextrins and branched high molecular weight polymers), which is more resistant than RSB (a retrograded potato starch), increased the rate of fermentation accompanied by a decrease of pH in cecum, colon, and feces. Because they were bound to RS3, less bile acids were reabsorbed, resulting in a higher turnover through the large bowel. Because of the rise of volume, the bile acid level was unchanged and the formation of secondary bile acids was partly suppressed. The results proved a strong relation between RS3, short chain fatty acid production, and microflora. However, butyrate specific benefits are only achieved by an intake of RS3 that result in good fermentation properties, which depend on the kind of the resistant starch structures.

Animals↗
PubMed2003

Structural and functional approach to studying pesticide side-effects on specific soil functions.

The microbial communities in the soil are responsible for material cycling and thus also for maintaining the fertility of agricultural soils. In order to assess pesticide side effects on the soil processes, detailed knowledge is required about the structure and function of the soil microflora. Therefore, the degradation and humification of 14C-labeled maize straw was studied in process-oriented microcosms. Apart from a native orthic luvisol, a heat-treated soil was used that has been freed from organic carbon by incineration at 600 degrees C. Microbial communities involved in the turnover of the crop residues were investigated using denaturing gradient gel electrophoresis (DGGE) of 16S rDNA sequences. Both 13C-nuclear magnetic resonance (NMR) spectroscopy and gel permeation chromatography were used to analyze humic acids produced in the microcosms. To evaluate the sensitivity of the microcosms, the influence of the fungicide dithianon was used in a case study at a concentration of 50 mg/kg. Microbial activity was reduced because of the application of the pesticide, especially in the native soils, while mineralization of 14C-labeled maize straw was only slightly affected. The buildup of fungal biomass was inhibited for at least three weeks. Despite these effects on the microbial communities, no significant differences in the humification products after 26 weeks of incubation were observed.

Anthraquinones↗
PubMed2006

Microbial degradation and impact of Bracken toxin ptaquiloside on microbial communities in soil.

The carcinogenic and toxic ptaquiloside (PTA) is a major secondary metabolite in Bracken fern (Pteridium aquilinum (L.) Kuhn) and was hypothesized to influence microbial communities in soil below Bracken stands. Soil and Bracken tissue were sampled at field sites in Denmark (DK) and New Zealand (NZ). PTA contents of 2.1 +/- 0.5 mg g(-1) and 37.0 +/- 8.7 mg g(-1) tissue were measured in Bracken fronds from DK and NZ, respectively. In the two soils the PTA levels were similar (0-5 microg g(-1) soil); a decrease with depth could be discerned in the deeper B and C horizons of the DK soil (weak acid sandy Spodosol), but not in the NZ soil (weak acid loamy Entisol). In the DK soil PTA turnover was predominantly due to microbial degradation (biodegradation); chemical hydrolysis was occurring mainly in the uppermost A horizon where pH was very low (3.4). Microbial activity (basal respiration) and growth ([3H]leucine incorporation assay) increased after PTA exposure, indicating that the Bracken toxin served as a C substrate for the organotrophic microorganisms. On the other hand, there was no apparent impact of PTA on community size as measured by substrate-induced respiration or composition as indicated by community-level physiological profiles. Our results demonstrate that PTA stimulates microbial activity and that microorganisms play a predominant role for rapid PTA degradation in Bracken-impacted soils.

Biodegradation, Environmental↗
PubMed1998

Effect of a Saccharomyces cerevisiae culture on nutrient digestion in lactating dairy cows.

The digestive effects of a Saccharomyces cerevisiae culture were investigated. Four cows in early lactation that were fitted with ruminal and duodenal cannulas were used in a crossover design. The diet, which consisted of 60% corn silage and 40% concentrates, was supplemented or not supplemented with a daily dose of 50 g of premix containing 0.5 g of S. cerevisiae (6 x 10(8) cfu/g of premix). Total and ruminal digestibilities of organic matter, duodenal flows of nonmicrobial and microbial N, solid and liquid turnover rates, ruminal protozoal numbers, pH, ammonia N and volatile fatty acid concentrations, and concentrations of some plasma metabolites were not modified by the addition of S. cerevisiae. Ruminal dry matter content increased when S. cerevisiae was supplemented to the diet. In situ ruminal degradabilities of dry matter and neutral detergent fiber from corn stalk and of N from soybean meal were not modified; degradability of acid detergent fiber from corn stalk increased (32.5% vs. 26.3%) with the addition of S. cerevisiae. A short-term increase in N degradation was observed after 4 and 8 h of incubation. This experiment showed no effect of S. cerevisiae on most quantitative digestive events; however, a positive transitory postprandial effect on some parameters of microbial activity was observed.

Ammonia↗
PubMed1995

Molecular characterization of plasminogen activators in human gingival crevicular fluid.

Plasminogen activators (PAs), a family of serine proteases, and their inhibitors (PAIs) are important in fibrinolysis, wound healing and tissue remodelling. Previous studies revealed differences in the localization of PA activity between healthy and diseased gingival tissues, suggesting that PAs and PAIs could play a part in periodontal homeostasis and disease. PAs and PAIs are synthesized by most of the cells types making up the periodontium and can be identified in gingival crevicular fluid (GCF). These studies sought to characterize the molecular species of PAs and their inhibitors in GCF collected from clinically healthy sites. PA enzymatic activity in GCF samples demonstrated by fibrin zymography revealed the presence of only tissue-type PA (tPA) activity. No urokinase-type PA (uPA) enzymatic activity was detected. tPA enzymatic activity appeared predominantly as an uncomplexed 70-kDa species, although some samples contained enzyme-inhibitor complexes. Quantitation of total tPA by enzyme immunoassay showed a mean concentration of 1.6 ng/microl. Analysis of GCF samples for uPA by immunoblotting and enzyme immunoassay disclosed the presence of small amounts of uPA (0.2 ng/microl), which were present predominantly in activator-inhibitor complexes. Immunoblotting showed specific PAI-2 immunoreactivity bands in high molecular-weight complexes and low molecular-weight degradation products, but less than nanogram amounts of free PAI-2 molecules. Enzyme immunoassay revealed that PAI-2 was present in an at least a seven times greater amount than PAI-1. These observations support the hypothesis that PA-generated proteolysis and its regulation by endogenous inhibitors has a role in the diverse biochemical mechanisms underlying periodontal physiology and pathology including host-microbial interaction, polymorphonuclear leucocyte infiltration, turnover and migration of epithelial cells, connective tissue degradation and remodelling, fibrinolysis and wound healing.

Adult↗
PubMed2002

Marine environmental pollution stress detection through direct viable counts of bacteria.

Direct viable counts (DVC) of bacteria were quantified from polluted and relatively less/non-polluted coastal locations during different seasons to assess whether they can be routinely monitored for an understanding of environmental stress(es) that may impede the full functioning of bacterial communities in situ. Most notably, DVC were quite low during pre-monsoon (March-May) in pollution-affected locations when compared to relatively less/non-polluted ones. In contrast, their abundance was significantly higher (up to or > 10%) suggesting a substantially higher microbial activity (thus, a larger turnover of organic matter) during monsoon (June-September) and post-monsoon (October-February) even in pollution-affected locations. The ease of reliably measuring DVC was useful in realising decreased metabolic functioning of bacteria during pre-monsoon, a season where dispersion of land discharges/effluents is much lower. From laboratory and field analyses of this study it is ascertained that DVC are direct indices of potential bacterial metabolic activity, reliable for sensing metabolic stress experienced by bacterial communities in situ and can be useful for evaluating risks in marine environment through human (industrial) activities.

Bacteria↗
PubMedDate not supplied

Combining mixing regimes for optimized anaerobic wastewater treatment.

Operational practice of high-rate anaerobic bioreactors such as upflow anaerobic sludge bed (UASB) reactors is generally based on maximization of the biomass concentration and, in the case of more than one reactor compartment, operation in parallel. In this article, a modeling approach is used to postulate that the treatment performance of anaerobic bioreactors can be improved by simple operational measures. To achieve minimized effluent soluble substrate concentrations, operation of two reactors in series combined with active exchange of biomass between both reactors is suggested. In this way, substrate concentrations lower than the minimum achievable concentration in a completely mixed reactor can be achieved. It is furthermore suggested that maximized biomass concentrations (and solid retention times [SRTs]) do not necessarily lead to minimized effluent concentrations of organic material. At elevated SRTs, the soluble microbial products resulting from biomass turnover are shown to represent the main fraction of soluble organic material in the effluent of the reactor, limiting treatment efficiency.

Bacteria, Anaerobic↗
PubMed2006

Infection paradox: high abundance but low impact of freshwater benthic viruses.

The discovery of an abundant and diverse virus community in oceans and lakes has profoundly reshaped ideas about global carbon and nutrient fluxes, food web dynamics, and maintenance of microbial biodiversity. These roles are exerted through massive viral impact on the population dynamics of heterotrophic bacterioplankton and primary producers. We took advantage of a shallow wetland system with contrasting microhabitats in close proximity to demonstrate that in marked contrast to pelagic systems, viral infection, determined directly by transmission electron microscopy, and consequently mortality of prokaryotes were surprisingly low in benthic habitats in all seasons. This was true even though free viruses were abundant throughout the year and bacterial infection and mortality rates were high in surrounding water. The habitats in which we found this pattern include sediment, decomposing plant litter, and biofilms on aquatic vegetation. Overall, we detected viruses in only 4 of a total of approximately 15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of approximately 5,000 cells suspended in the water column were infected. The strikingly low incidence of impact of phages in the benthos may have important implications, since a major portion of microbial biodiversity and global carbon and nutrient turnover are associated with surfaces. Therefore, if failure to infect benthic bacteria is a widespread phenomenon, then the global role of viruses in controlling microbial diversity, food web dynamics, and biogeochemical cycles would be greatly diminished compared to predictions based on data from planktonic environments.

Bacteria↗
PubMedDate not supplied

Dioxin cycling in aquatic sediments: the Passaic River Estuary.

The contribution of dechlorination reactions to the transformation of dioxins in river sediments was evaluated under a range of geochemical conditions mimicking freshwater, estuarine and marine environments, and interpreted in the light of recent evidence for their accumulation at the air-water interface. The yield of dechlorinated products increased with salinity, but never exceeded 20% of the initial dioxins present. Among the homologue groups in saline conditions, diCDDs were dominant at 32-47 mol% (8-16 nM). The production of 2,3,7,8-TCDD increased with decreasing salinity and in the presence of dissolved organic matter, exhibiting a maximum ratio (2,3,7,8-TCDD:non-2,3,7,8-TCDD) of 0.5. These differences in patterns may be related to the dominant microbial respiratory processes responsible for carbon turnover under the imposed conditions, and are strongly affected by the presence of organic matter. Based on these results, a conceptual dechlorination and carbon turnover model is proposed to help explain the likely reactivity of dioxins in the Passaic River Estuary.

Carbon↗
PubMed1993

[Effect of the vegetative cover on the biological activity of the soil of Chaco Arido].

Vegetation plays a primal role in arid ecosystems, since it creates microclimate conditions that moderate the characteristics of the region whereby the rational use of vegetal resources is fundamental. Felling, clearing and overgrazing lead to decrease in organic contribution and stimulate soil compaction, causing an alteration of microbial activity, with losses in nutrient turnover. The global biological activity is a soil parameter easy to obtain and indicates the presence and diversity of soil life as well as substrate availability and is useful in order to characterize soil potential fertility. This work was carried out in Natural Forest Reserve Chancaní, Province of Córdoba (Argentina), which is representative of Argentine Dry Chaco. Dominant tree species are: Prosopis flexuosa and Aspidosperma quebracho blanco. The global biological activity (GBA) was measured along one year, under trees, under shrubs and in interspaces. Soil samples were taken monthly from plots with four management systems: 1) forest, ii) selective clearing (only dominant species remain), iii) bush (clearing invaded by Larrea sp) and iv) grazing (cleared area, neither trees nor shrubs). GBA was evaluated using the CO2 release method, after ten days of incubation. It is concluded that in the plots with grasses and under the trees GBA was higher than with other treatments. The lesser GBA was detected in bushes and interspaces. All differences were more prominent during extreme temperature months. No significant difference between both species of dominant trees was observed.

Animal Husbandry↗
PubMed2003

Large-scale spatial distribution of virioplankton in the Adriatic Sea: testing the trophic state control hypothesis.

Little is known concerning environmental factors that may control the distribution of virioplankton on large spatial scales. In previous studies workers reported high viral levels in eutrophic systems and suggested that the trophic state is a possible driving force controlling the spatial distribution of viruses. In order to test this hypothesis, we determined the distribution of viral abundance and bacterial abundance and the virus-to-bacterium ratio in a wide area covering the entire Adriatic basin (Mediterranean Sea). To gather additional information on factors controlling viral distribution on a large scale, functional microbial parameters (exoenzymatic activities, bacterial production and turnover) were related to trophic gradients. At large spatial scales, viral distribution was independent of autotrophic biomass and all other environmental parameters. We concluded that in contrast to what was previously hypothesized, changing trophic conditions do not directly affect virioplankton distribution. Since virus distribution was coupled with bacterial turnover times, our results suggest that viral abundance depends on bacterial activity and on host cell abundance.

Bacteria↗
PubMed2004

RNA fingerprinting--a new method to screen for differences in plant litter degrading microbial communities.

Microbial activities are essential for the nutrient turnover processes in soil and play an important role in the degradation of complex organic material, for example, plant leaf litter. However, very little is known about the microorganisms and their genes involved during the course of leaf litter decomposition. In the present study, we describe the non-radioactive application of RNA arbitrarily primed-PCR (RAP-PCR) protocol in combination with the classic litter bag technique to investigate the metabolic profiles of microbial community involved in leaf litter degradation after 2 and 8 weeks of degradation in four different soil sites, without using selective primer systems for PCR. Due to the significantly reduced target sites for PCR primers, compared to the published papers about RAP fingerprinting of more complex microbial communities based on DNA analysis (only transcripts from microbes on the litter material were analysed), the patterns of parallel samples were highly reproducible (>95%). Shifts in microbial community structure and function were observed during the course of degradation. Each litter sample had its unique metabolic profile and both soil effects and litter quality effects were evident. RAP-PCR products were also cloned to generate libraries. Clone libraries were screened by restriction fragment length polymorphism (RFLP) and representative samples sequenced to identify the inserts. Both mRNA and rRNA transcripts were obtained confirming the presence of mRNA in total RNA preparations. Hence, the described protocol is a good screening method to find similarities or differences in the structure and function of microbial communities involved in litter degradation, which may be the basis for more detailed studies by cloning and sequencing approaches.

Electrophoresis, Polyacrylamide Gel↗
PubMed2003

The telltale structures of epoxide hydrolases.

Traditionally, epoxide hydrolases (EH) have been regarded as xenobiotic-metabolizing enzymes implicated in the detoxification of foreign compounds. They are known to play a key role in the control of potentially genotoxic epoxides that arise during metabolism of many lipophilic compounds. Although this is apparently the main function for the mammalian microsomal epoxide hydrolase (mEH), evidence is now accumulating that the mammalian soluble epoxide hydrolase (sEH), despite its proven role in xenobiotic metabolism, also has a central role in the formation and breakdown of physiological signaling molecules. In addition, a certain class of microbial epoxide hydrolases has recently been identified that is an integral part of a catabolic pathway, allowing the use of specific terpens as sole carbon sources. The recently available x-ray structures of a number of EHs mirror their respective functions: the microbial terpen EH differs in its fold from the canonical alpha/beta hydrolase fold of the xenobiotic-metabolizing mammalian EHs. It appears that the latter fold is the perfect solution for the efficient detoxification of a large variety of structurally different epoxides by a single enzyme, whereas the smaller microbial EH, which has a particularly high turnover number with its prefered substrate, seems to be the better solution for the hydrolysis of one specific substrate. The structure of the sEH also includes an additional catalytic domain that has recently been shown to possess phosphatase activity. Although the physiological substrate for this second active site has not been identified so far, the majority of known phosphatases are involved in signaling processes, suggesting that the sEH phosphatase domain also has a role in the regulation of physiological functions.

Animals↗
PubMed1971

Microbial assimilation of hydrocarbons: phospholipid metabolism.

An analysis of the turnover of the major phospholipids of Micrococcus cerificans growing or nongrowing cultures. The turnover rates of (14)C-PE and (14)C-PE were 61.5% of the total phospholipid, exhibited no significant rate of turnover in either growing or nongrowing cultures. The turnover rates of PE-(14)C and PE-(32)P were 3.2% per hr and 1.2% per hr, respectively. Phosphatidylglycerol (PG) exhibited a turnover rate of 11% and 7.7% per hr for (14)C and (32)P, respectively, indicating an extremely slow metabolism. PG metabolism was examined in greater detail, and the data indicated a preferential 75% incorporation of glycerol-1,3-(14)C into the unacylated portion of the PG molecule. The turnover of cardiolipin (CL) was extremely slow in growing cells whereas nongrowing cells exhibited a 30% and 36% increase per hr for (14)C-Cl and (14)C-CL, respectively. Glycerol-1,3-(14)C was not converted to phospholipid fatty acid carbon; all radioactivity appeared only in the water-soluble backbone of the phospholipids. The kinetics of assimilation of hexadecane-1-(14)C into cellular lipids is presented. Radioactivity in neutral lipid increased approximately sevenfold over the growth cycle, whereas radioactivity in phospholipid increased 50-fold during the same time period. The incorporation of radioactive fatty acids derived from the direct oxidation of hexadecane-1-(14)C demonstrated differential kinetics of assimilation into PE, PG, and CL. The results indicated a rapid turnover of phospholipid fatty acids in M. cerificans growing at the expense of hexadecane.

Alkanes↗
PubMed2002

Developmental kinetics and lifespan of dendritic cells in mouse lymphoid organs.

The labeling kinetics of 5 dendritic cell (DC) subtypes within the lymphoid organs of healthy laboratory mice during continuous administration of bromodeoxyuridine (BrdU) was determined to investigate developmental relationships and determine turnover rates. Individual DC subtypes behaved as products of separate developmental streams, at least as far back as their dividing precursors. The rate of labeling varied with the lymphoid organ and the DC subtype. Labeling was faster overall in spleen and mesenteric lymph nodes (LNs) and slower in thymus and skin-draining LNs. The CD8(+) DC subtype displayed the most rapid turnover, with a uniformly short (3-day) lifespan in spleen but with distinct short-lived and longer-lived subgroups in thymus. All the skin-derived DCs in LNs showed delayed and slow BrdU labeling, indicating a long overall lifespan; however, this was shown to reflect a long residence time in skin rather than a long-duration presenting antigen in the draining LN. Epidermal-derived Langerhans DCs displayed longer BrdU labeling lag and slower overall turnover than the dermal-derived DCs, and the movement of fluorescent Langerhans DC from skin to LN was slower than that of dermal DCs following skin painting with a fluorescent dye. However, once they arrived in lymphoid organs, all DCs present in healthy, uninfected mice displayed a rapid turnover, and this turnover was even faster after antigenic or microbial product stimulation.

Animals↗