Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients

Stable isotope probing (SIP) of nucleic acids allows the detection and identification of active members of natural microbial populations that are involved in the assimilation of an isotopically labelled compound into nucleic acids. SIP is based on the separation of isotopically labelled DNA or rRNA by isopycnic density gradient centrifugation. We have developed a highly sensitive protocol for the detection of 'light' and 'heavy' nucleic acids in fractions of centrifugation gradients. It involves the fluorometric quantification of total DNA or rRNA, and the quantification of either 16S rRNA genes or 16S rRNA in gradient fractions by real-time PCR with domain-specific primers. Using this approach, we found that fully 13C-labelled DNA or rRNA of Methylobacterium extorquens was quantitatively resolved from unlabelled DNA or rRNA of Methanosarcina barkeri by cesium chloride or cesium trifluoroacetate density gradient centrifugation respectively. However, a constant low background of unspecific nucleic acids was detected in all DNA or rRNA gradient fractions, which is important for the interpretation of environmental SIP results. Consequently, quantitative analysis of gradient fractions provides a higher precision and finer resolution for retrieval of isotopically enriched nucleic acids than possible using ethidium bromide or gradient fractionation combined with fingerprinting analyses. This is a prerequisite for the fine-scale tracing of microbial populations metabolizing 13C-labelled compounds in natural ecosystems.     

Sarcocystis muris--a rare case in laboratory mice

In a lifespan transgeneration study under standard laboratory conditions using a total of 4682 CBA/J mice, unusual intramuscular inclusions were found in the diaphragm, heart and skeletal muscle of one mouse using light microscopy. Located within the myocytes, they caused no visible tissue reaction. Cross-sections of these spherical and cystic lesions showed numerous banana-shaped structures, identified as permanent parasitic bradyzoites, which permitted these infections to be diagnosed microscopically as sarcocystosis.     

Isolation and characterization of new strains of methanogens from cold terrestrial habitats

Five strains of methanogenic archaea (MT, MS, MM, MSP, ZB) were isolated from permanently and periodically cold terrestrial habitats. Physiological and morphological studies, as well as phylogenetic analyses of the new isolates were performed. Based on sequences of the 16S rRNA and methyl-coenzyme M reductase a-subunit (mcrA) genes all new isolates are closely related to known mesophilic and psychrotolerant methanogens. Both, phylogenetic analyses and phenotypic properties allow to classify strains MT, MS, and MM as members of the genus Methanosarcina. Strain MT is a new ecotype of Methanosarcina mazei, whereas strains MM and MS are very similar to each other and can be assigned to the recently described psychrotolerant species Methanosarcina lacustris. The hydrogenotrophic strain MSP is a new ecotype of the genus Methanocorpusculum. The obligately methylotrophic strain ZB is closely related to Methanomethylovorans hollandica and can be classified as new ecotype of this species. All new isolates, including the strains from permanently cold environments, are not true psychrophiles according to their growth temperature characteristics. In spite of the ability of all isolates to grow at temperatures as low as 1-5 degrees C, all of them have their growth optima in the range of moderate temperatures (25-35 degrees C). Thus, they can be regarded as psychrotolerant organisms. Psychrotolerant methanogens are thought to play an important role in methane production in both, habitats under seasonal temperature variations or from permanently cold areas.     

Effects of Amendment with Ferrihydrite and Gypsum on the Structure and Activity of Methanogenic Populations in Rice Field Soil

Methane emission from paddy fields may be reduced by the addition of electron acceptors to stimulate microbial populations competitive to methanogens. We have studied the effects of ferrihydrite and gypsum (CaSO₄·2H₂O) amendment on methanogenesis and population dynamics of methanogens after flooding of Italian rice field soil slurries. Changes in methanogen community structure were followed by archaeal small subunit (SSU) ribosomal DNA (rDNA)- and rRNA-based terminal restriction fragment length polymorphism analysis and by quantitative SSU rRNA hybridization probing. Under ferrihydrite amendment, acetate was consumed efficiently (<60 μM) and a rapid but incomplete inhibition of methanogenesis occurred after 3 days. In contrast to unamended controls, the dynamics of Methanosarcina populations were largely suppressed as indicated by rDNA and rRNA analysis. However, the low acetate availability was still sufficient for activation of Methanosaeta spp., as indicated by a strong increase of SSU rRNA but not of relative rDNA frequencies. Unexpectedly, rRNA amounts of the novel rice cluster I (RC-I) methanogens increased significantly, while methanogenesis was low, which may be indicative of transient energy conservation coupled to Fe(III) reduction by these methanogens. Under gypsum addition, hydrogen was rapidly consumed to low levels (~0.4 Pa), indicating the presence of a competitive population of hydrogenotrophic sulfate-reducing bacteria (SRB). This was paralleled by a suppressed activity of the hydrogenotrophic RC-I methanogens as indicated by the lowest SSU rRNA quantities detected in all experiments. Full inhibition of methanogenesis only became apparent when acetate was depleted to nonpermissive thresholds (<5 μM) after 10 days. Apparently, a competitive, acetotrophic population of SRB was not present initially, and hence, acetotrophic methanosarcinal populations were less suppressed than under ferrihydrite amendment. In conclusion, although methane production was inhibited effectively under both mitigation regimens, different methanogenic populations were either suppressed or stimulated, which demonstrates that functionally similar disturbances of an ecosystem may result in distinct responses of the populations involved.     

Interactions between planktonic microalgae and protozoan grazers

For an algal bloom to develop, the growth rate of the bloom-forming species must exceed the sum of all loss processes. Among these loss processes, grazing is generally believed to be one of the more important factors. Based on numerous field studies, it is now recognized that microzooplankton are dominant consumers of phytoplankton in both open ocean and coastal waters. Heterotrophic protists, a major component of microzooplankton communities, constitute a vast complex of diverse feeding strategies and behavior which allow them access to even the larger phytoplankton species. A number of laboratory studies have shown the capability of different protistan species to feed and grow on bloom-forming algal species. Because of short generation times, their ability for fast reaction to short-term variation in food conditions enables phagotrophic protists to fulfill the function of a heterotrophic buffer, which might balance the flow of matter in case of phytoplankton blooms. The importance of grazing as a control of microalgae becomes most apparent by its failure; if community grazing controls initial stages of bloom development, there simply is no bloom. However, if a certain algal species is difficult to graze, e.g. due to specific defense mechanisms, reduced grazing pressure will certainly favor bloom development. The present contribution will provide a general overview on the interactions between planktonic microalgae and protozoan grazers with special emphasis on species-specific interactions and algal defense strategies against protozoan grazers.     

Planktonic primary production in the German Wadden Sea

By combining weekly data of irradiance, attenuation and chlorophylla concentrations with photosynthesis (P) versus light intensity(E) curve characteristics, the annual cycle of planktonic primaryproduction in the estuarine part of the Northfrisian WaddenSea was computed for a 2 year period. Daily water column particulategross production ranged from 5 to 2200 mg C m^–2 day^–1and showed a seasonal pattern similar to chlorophyll a. Budgetcalculation yielded annual gross particulate primary productionsof 124 and 176 g C m^–2 year^–1 in 1995 and 1996,respectively. Annual amounts of phytoplankton respiration, calculatedaccording to a two-compartment model of Langdon [in Li,W.K.W.and Maestrini,S.Y. (eds), Measurement of Primary Productionfrom the Molecular to the Global Scale. International Councilfor the Exploration of the Sea, Copenhagen, 1993, pp. 20–36],and dissolved production in 1996, were both in the range of24–39 g C m^–2 year^–1. Annual total net productionwas thus very similar to particulate gross production (127 and177 g C m^–2 year^–1 in 1995 and 1996, respectively).Phytoplankton growth was low or even negative in winter. Inspring and summer, production/biomass (Pr/B) ratios varied from0.2 up to 1.7. Phytoplankton growth during the growth seasonalways surpassed average flushing time in the area, thus underliningthe potential of local phytoplankton bloom development in thispart of the Wadden Sea. The chlorophyll-specific maximum photosyntheticrate (P^B_max) ranged from 0.8 to 9.9 mg C mg^–1 Chl h^–1and was strongly correlated with water temperature (r² = 0.67).By contrast, there was no clear seasonal cycle in ^B, which rangedfrom 0.007 to 0.039 mg C mg^–1 Chl h^–1 (µmolphotons m^–2 s^–1)^–1. Its variability was muchless than P^B_max and independent of temperature. The magnitudeand part of the variability of P^B_max and ^B are presumably causedby changes in species composition, as evidenced from the rangeof these parameters found among 10 predominant diatom speciesisolated from the Wadden Sea. The ratio of average light conditionsin the water column (E_av) to the light saturation parameterE_k indicates that primary production in the Wadden Sea regionunder study is predominantly controlled by light limitationand that nutrient limitation was likely to occur for a few hoursper day only during 5 (dissolved inorganic nitrogen) to 10 (PO₄,Si) weeks in the 2 year period investigated.     

On the allelochemical potency of the marine dinoflagellate Alexandrium ostenfeldii against heterotrophic and autotrophic protists

Three strains of the marine dinoflagellate Alexandrium ostenfeldiiof different geographic origin were tested for their short-termdeleterious effects on a diversity of marine protists. All A.ostenfeldii strains were capable of eliciting an apparent allelochemicalresponse, but the various protistan target species were differentiallyaffected. Protists that were negatively affected by exposureto cells of A. ostenfeldii and associated extracellular metabolitescomprised both autotrophs (Rhodomonas sp., Dunaliella salina,Thalassiosira weissflogii) and heterotrophs (Oxyrrhis marina,Amphidinium crassum, Rimostrombidium caudatum). Observed effectsincluded immobilisation (e.g. of O. marina), morphological changes(e.g. in D. salina) and/or aberrant behaviour (e.g. of R. caudatum),mainly as preliminary stages of cell lysis. Immobilization andlytic effects against O. marina were strongly dependent on A.ostenfeldii cell concentrations. Effects also differed substantiallyamong strains and different batch cultures of the same strain.Values of EC₅₀, defined as the A. ostenfeldii cell concentrationcausing lysis of 50% of O. marina cells, ranged from 0.3 to1.9 x 10³ mL^–1, depending on the A. ostenfeldii strain.The autotrophic dinoflagellate Scrippsiella trochoidea reactedto exposure to A. ostenfeldii cells by formation of temporary(ecdysal) cysts, whereas, in contrast, the flagellates Emilianiahuxleyi and Prymnesium parvum and the ciliate Strombidium sp.were relatively refractory or even unaffected. As long as cellsdid not lyse, the fluorescence yield of target autotrophs, estimatedby pulse-amplitude modulation fluorometry, did not significantlychange during the first 3 h of incubation, suggesting that allelochemicalsproduced by A. ostenfeldii caused no short-term negative effectson the photosynthetic apparatus. Overall, the allelochemicalresponses of target species showed no obvious relationship tocell quota or extracellular concentrations of either toxic macrocyclicimines (spirolides) or tetrahydropurine neurotoxins (saxitoxinand analogues) produced by various strains of A. ostenfeldii.Instead, the potency of A. ostenfeldii, eliciting immobilizationand lytic species-specific responses in potential predatorsand competitors, is consistent with the existence of an allelochemicalmechanism unrelated to the bioactivity of known phycotoxinsof the genus Alexandrium.     

Diffusion Regulation in the Vitreous Humor

The efficient treatment of many ocular diseases depends on the rapid diffusive distribution of solutes such as drugs or drug delivery vehicles through the vitreous humor. However, this multicomponent hydrogel possesses selective permeability properties, which allow for the diffusion of certain molecules and particles, whereas others are immobilized. In this study, we perform an interspecies comparison showing that the selective permeability properties of the vitreous are conserved across several mammalian species. We identify the polyanionic glycosaminoglycans hyaluronic acid and heparan sulfate as two key macromolecules that establish this selective permeability. We show that electrostatic interactions between the polyanionic macromolecules and diffusing solutes can be weakened by charge screening or enzymatic glycosaminoglycan digestion. Furthermore, molecule penetration into the vitreous is also charge-dependent and only efficient as long as the net charge of the molecule does not exceed a certain threshold.     

Contribution of Fdh3 and Glr1 to Glutathione Redox State,Stress Adaptation and Virulence in Candida albicans

The major fungal pathogen of humans, Candida albicans, is exposed to reactive nitrogen and oxygen species following phagocytosis by host immune cells. In response to these toxins, this fungus activates potent anti-stress responses that include scavenging of reactive nitrosative and oxidative species via the glutathione system. Here we examine the differential roles of two glutathione recycling enzymes in redox homeostasis, stress adaptation and virulence in C. albicans: glutathione reductase (Glr1) and the S-nitrosoglutathione reductase (GSNOR), Fdh3. We show that the NADPH-dependent Glr1 recycles GSSG to GSH, is induced in response to oxidative stress and is required for resistance to macrophage killing. GLR1 deletion increases the sensitivity of C. albicans cells to H₂O₂, but not to formaldehyde or NO. In contrast, Fdh3 detoxifies GSNO to GSSG and NH₃, and FDH3 inactivation delays NO adaptation and increases NO sensitivity. C. albicans fdh3⎔ cells are also sensitive to formaldehyde, suggesting that Fdh3 also contributes to formaldehyde detoxification. FDH3 is induced in response to nitrosative, oxidative and formaldehyde stress, and fdh3Δ cells are more sensitive to killing by macrophages. Both Glr1 and Fdh3 contribute to virulence in the Galleria mellonella and mouse models of systemic infection. We conclude that Glr1 and Fdh3 play differential roles during the adaptation of C. albicans cells to oxidative, nitrosative and formaldehyde stress, and hence during the colonisation of the host. Our findings emphasise the importance of the glutathione system and the maintenance of intracellular redox homeostasis in this major pathogen.