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PubMed2002

Occurrence of nitrifying bacteria and nitrification in Finnish drinking water distribution systems.

Microbiological nitrification process may lead to chemical, microbiological and technical problems in drinking water distribution systems. Nitrification activity is regulated by several physical, and chemical, and operational factors. However, the factors affecting nitrification in the distribution systems in boreal region, having its specific environmental characteristics, are poorly known. We studied the occurrence and activity of nitrifying bacteria in 15 drinking water networks distributing water with very different origin and treatment practices. The waters included chloraminated surface water, chlorinated surface water, and non-disinfected groundwater. The networks were located in eight towns in different parts of Finland. Our results showed that nitrifying bacteria are common in boreal drinking water distribution systems despite their low temperature. Surprisingly high numbers and activities of nitrifiers were detected in pipeline sediment samples. The numbers of ammonia-oxidizing bacteria and their oxidation potentials were highest in chloraminated drinking water delivering networks, whereas the nitrite-oxidizing bacteria were present in the greatest numbers in those networks that used non-disinfected groundwater. The occurrence of nitrifying bacteria in drinking water samples correlated positively with the numbers of heterotrophic bacteria and turbidity, and negatively with the content of total chlorine. Although nitrifying bacteria grew well in drinking water distribution systems, the problems with nitrite accumulation are rare in Finland.

Ammonia↗
PubMed2004

Assessment of the microbial integrity, sensu G.S. Wilson, of piped and bottled drinking water in the condition as ingested.

The second half of the 20th century witnessed substantial progress in the assurance and verification of microbiological integrity, i.e., safety and sensory quality, of drinking water. Enteropathogenic agents, such as particular viruses and protozoa, not previously identified as transmitted by industrially provided water supplies, were demonstrated to cause disease outbreaks, when ingested with piped water. The potential harm posed by carry-over of orally toxic metabolites of organisms, producing 'algal' (cyanophytic) blooms, was considered. In addition, earlier observations on the colonization of attenuated drinking water bodies by a variety of oligotrophic Gram-negative bacteria were confirmed and extended. This new evidence called for updating both water purification technologies and analytical methodology, serving to verify that goals had been attained. For the former purpose, the hazard analysis empowering control of critical practices (HACCP) strategy, introduced about 1960 in industrial food processing, was successfully adopted. Elimination, devitalization or barrier technologies for the more recently identified water-borne pathogens were elaborated, taking account of the hazard of production of chlorinated compounds with alleged adverse health effects. Biofilm formation throughout water distribution networks was brought under control by strict limitation of concentrations of compounds, assimilable by oligotrophic bacteria. Upon acknowledging that direct detection tests for pathogens were futile, because of their most sporadic and erratic distribution, Schardinger's marker organism concept was anew embraced, rigorously revised and substantially enlarged. Misleading designations, like searches for 'faecal coliforms' were replaced by boundary testing for Escherichia coli and appropriate Enterococcus spp. In addition, though still to be perfected, detection protocols for relevant bacteriophages or index viruses and, to a certain extent, also for spores of aerobic and anaerobic sporing rods were also elaborated. In all monitoring account was taken of sublethally injured target organisms, surviving purification technologies, though not deprived of their ecological significance. A need remains for a rigorously standardized operating procedure (SOP) for colony counts of psychrotrophic, oligotrophic Gram-negative rod-shaped bacteria ('heterotrophic plate count'), which constitute a useful criterion of indicator value. As in the contemporary HACCP approach to food safety, guidelines for assessing success or failure in control of integrity (Water Safety Objectives) were empirically elaborated. These rely on surveys on water samples, originating from drinking water supplies, previously verified as complying with longitudinally integrated HACCP-based purification technologies. Structured Academic dissemination of these innovations, through professional microbiologists to operator and executive levels, is recommended. Web based Distance Learning MSc Programmes, like the one, since the academic year 2003-2004, offered by the University of Hertfordshire, Hatfield, UK, may contribute to such endeavours. Though the complete Course is centered around Food Safety, the Modules in-Residence Practicals and Science and Technology of Drinking Water can be studied as an entity while being employed.

Bacteria↗
PubMed2001

Transcriptional responses in the hemiparasitic plant Triphysaria versicolor to host plant signals.

Parasitic plants in the Scrophulariaceae use chemicals released by host plant roots to signal developmental processes critical for heterotrophy. Haustoria, parasitic plant structures that attach to and invade host roots, develop on roots of the hemiparasitic plant Triphysaria versicolor within a few hours of exposure to either maize (Zea mays) root exudate or purified haustoria-inducing factors. We prepared a normalized, subtractive cDNA library enriched for transcripts differentially abundant in T. versicolor root tips treated with the allelopathic quinone 2,6-dimethoxybenzoquinone (DMBQ). Northern analyses estimated that about 10% of the cDNAs represent transcripts strongly up-regulated in roots exposed to DMBQ. Northern and reverse northern analyses demonstrated that most DMBQ-responsive messages were similarly up-regulated in T. versicolor roots exposed to maize root exudates. From the cDNA sequences we assembled a unigene set of 137 distinct transcripts and assigned functions by homology comparisons. Many of the proteins encoded by the transcripts are predicted to function in quinone detoxification, whereas others are more likely associated with haustorium development. The identification of genes transcriptionally regulated by haustorium-inducing factors provides a framework for dissecting genetic pathways recruited by parasitic plants during the transition to heterotrophic growth.

Benzoquinones↗
PubMed1984

Effect of organic contamination upon microbial distributions and heterotrophic uptake in a Cape Cod, Mass., aquifer.

Bacterial abundance, distribution, and heterotrophic uptake in a freshwater aquifer contaminated by treated sewage were determined from analyses of groundwater and sediment-core samples. The number of free-living (unattached) bacteria in contaminated groundwater declined steadily with increasing distance from the source of sewage infiltration, from 1.94 (+/- 0.20) X 10(6) ml-1 at 0.21 km to 0.25 (+/- 0.02) X 10(6) ml-1 at 0.97 km. Bacterial abundance in groundwater sampled at 0.31 km correlated strongly with specific conductance and increased sharply from 4.0 (+/- 0.3) X 10(4) ml-1 at a depth of 6 m to 1.58 (+/- 0.12) X 10(6) ml-1 at 14 m, then declined at 20 and 31 m to 1.29 (+/- 0.12) X 10(6) and 0.96 (+/- 0.12) X 10(6) ml-1, respectively. A majority of the bacteria in contaminated and uncontaminated zones of the aquifer were bound to the surfaces of particulates, less than 60 micron in diameter. The glucose uptake rate, assayed at in situ and 5 microM concentrations, declined steadily in contaminated groundwater sampled along a transect. A preparative wet-sieving technique for use in processing core samples for bacterial enumeration is described and evaluated.

Bacteria↗
PubMed1997

Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation.

The plastid genomes of some nonphotosynthetic parasitic plants have experienced an extreme reduction in gene content and an increase in evolutionary rate of remaining genes. Nothing is known of the dynamics of these events or whether either is a direct outcome of the loss of photosynthesis. The parasitic Scrophulariaceae and Orobanchaceae, representing a continuum of heterotrophic ability ranging from photosynthetic hemiparasites to nonphotosynthetic holoparasites, are used to investigate these issues. We present a phylogenetic hypothesis for parasitic Scrophulariaceae and Orobanchaceae based on sequences of the plastid gene rps2, encoding the S2 subunit of the plastid ribosome. Parasitic Scrophulariaceae and Orobanchaceae form a monophyletic group in which parasitism can be inferred to have evolved once. Holoparasitism has evolved independently at least five times, with certain holoparasitic lineages representing single species, genera, and collections of nonphotosynthetic genera. Evolutionary loss of the photosynthetic gene rbcL is limited to a subset of holoparasitic lineages, with several holoparasites retaining a full length rbcL sequence. In contrast, the translational gene rps2 is retained in all plants investigated but has experienced rate accelerations in several hemi- as well as holoparasitic lineages, suggesting that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis. Independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages. Parasitic Scrophulariaceae (including the traditional Orobanchaceae) provide a rich platform for the investigation of molecular evolutionary process, gene function, and the evolution of parasitism.

Arabidopsis Proteins↗
PubMed2001

Kinetic model of autotrophic denitrification in sulphur packed-bed reactors.

Autotrophic denitrification of synthetic wastewater by Thiobacillus denitrificans in upflow sulphur packed-bed reactors was studied in order to establish the process kinetics for prediction of effluent concentration. Elemental sulphur particles of different size served as energy substrate as well as the physical support for the microbial biofilm. Experiments were performed under operating conditions of (i) different flow rates at constant influent nitrate concentration; and (ii) different influent nitrate concentrations at constant flow rate. The experimental results show that autotrophic denitrification rates in upflow sulphur packed-bed reactors can be described by a half-order kinetic model for biofilms. It was found that the half-order kinetic constants of upflow packed-bed reactors are 2.94-3.60, 1.47-2.04, and 1.12-1.29 mg1/2/L1/2 h for sulphur particle sizes of 2.8-5.6, 5.6-11.2, and 11.2-16 mm, respectively. The half-order kinetic constants could be related to the specific surface area of the reactor media by a simple equation. Successful application of the half-order reaction rate model was demonstrated for an actual wastewater (nitrified leachate). A comparison with the literature showed that the half-order reaction rate constants for autotrophic denitrification using elemental sulphur are approximately one order of magnitude lower than those of heterotrophic denitrification. An improved stoichiometric equation for autotrophic denitrification using elemental sulphur as electronic donor is also proposed.

Biodegradation, Environmental↗
PubMed2000

Origin and evolution of the mitochondrial proteome.

The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria or bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome or in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast, there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of the ancestral host of the alpha-proteobacterial endosymbiont is unclear, but there is no indication that it was an autotroph. There are no indications of a specific alpha-proteobacterial origin to genes for glycolysis. In the absence of data to the contrary, it is assumed that the ancestral host cell was a heterotroph.

Alphaproteobacteria↗
PubMedDate not supplied

High-yield production of lutein by the green microalga Chlorella protothecoides in heterotrophic fed-batch culture.

The green microalga Chlorella protothecoides was grown heterotrophically in batch mode in a 3.7-L fermenter containing 40 g/L glucose and 3.6 g/L urea. In the late exponential phase, concentrated nutrients containing glucose and urea were fed into the culture, in which the nitrogen source was sufficient compared to carbon source. As a result, a maximum cell dry weight concentration of 48 g/L was achieved. This cell dry weight concentration was 28.4 g/L higher than that obtained in batch culture under the same growth conditions. In another cultivation run, the culture was provided with the same initial concentrations of glucose (40 g/L) and urea (3.6 g/L) as in the batch mode, followed by a relatively reduced supply of nitrogen source in the fed-batch mode to establish a nitrogen-limited culture. Such a modification resulted in an enhanced lutein production without significantly lowering biomass production. The cellular lutein content was 0.27 mg/g higher than that obtained in the N-sufficient culture. The improvements were also reflected by higher maximum lutein yield, lutein productivity, and lutein yield coefficient on glucose. This N-limited fed-batch culture was successfully scaled up from 3.7 L to 30 L, and a three-step cultivation process was developed for the high-yield production of lutein. The maximum cell dry weight concentration (45.8 g/L) achieved in the large fermenter (30 L) was comparable to that in the small one (3.7 L). The maintenance of the culture at a higher temperature (i.e., 32 degrees C) for 84 h resulted in a 19.9% increase in lutein content but a 13.6% decrease in cell dry weight concentration as compared to the fed-batch culture (30 L) without such a treatment. The enhancement of lutein production resulted from the combination of nitrogen limitation and high-temperature stress.

Biomass↗
PubMedDate not supplied

Biotreatment of ammonia from air by an immobilized Arthrobacter oxydans CH8 biofilter.

A heterotrophic Arthrobacter oxydans CH8 that was capable of removing NH3 from NH3 containing gas was isolated from livestock farming wastewater. The A. oxydans CH8 was immobilized with calcium alginate packed into filter column. Metered NH3-containing gas was partially humidified and passed through the glass column. Extensive tests including the removal characteristics, the removal efficiencies, and the metabolic products of NH3 by A. oxydans CH8 were conducted. Additionally, the operation criteria for the biofilter was also established. NH3 removel capacities were elevated by the immobilized-cell (biological conversion) method and the BDST (bed depth service time) method (physical adsorption), respectively. The optium temperature for removing NH3 was 30 degrees C, while the nitrification ability remained 80% at 40 degrees C. The high efficiency (> 97%) in the removal of NH3 was attained at 36 L/h with pH control and was not decreased because of high NH3 inlet concentration. In addition, the high maximum removal rate (1.22 g of N/day (kg of bead)) enhanced the use of the biofilter in industrial-scale NH3(g) pollution control. The ability to remove NH3 at high inlet concentration and temperature suggested that the immobilized A. oxydans CH8 biofilter has potential in processing NH3 gas.

Adsorption↗
PubMed2003

Scanning transmission X-ray, laser scanning, and transmission electron microscopy mapping of the exopolymeric matrix of microbial biofilms.

Confocal laser scanning microscopy (CLSM), transmission electron microscopy (TEM), and soft X-ray scanning transmission X-ray microscopy (STXM) were used to map the distribution of macromolecular subcomponents (e.g., polysaccharides, proteins, lipids, and nucleic acids) of biofilm cells and matrix. The biofilms were developed from river water supplemented with methanol, and although they comprised a complex microbial community, the biofilms were dominated by heterotrophic bacteria. TEM provided the highest-resolution structural imaging, CLSM provided detailed compositional information when used in conjunction with molecular probes, and STXM provided compositional mapping of macromolecule distributions without the addition of probes. By examining exactly the same region of a sample with combinations of these techniques (STXM with CLSM and STXM with TEM), we demonstrate that this combination of multimicroscopy analysis can be used to create a detailed correlative map of biofilm structure and composition. We are using these correlative techniques to improve our understanding of the biochemical basis for biofilm organization and to assist studies intended to investigate and optimize biofilms for environmental remediation applications.

Bacteria↗
PubMed2005

Kinetics of hydrogen-dependent denitrification under varying pH and temperature conditions.

It is important to determine the effect of changing environmental conditions on the microbial kinetics for design and modeling of biological treatment processes. In this research, the kinetics of nitrate and nitrite reduction by autotrophic hydrogen-dependent denitrifying bacteria and the possible role of acetogens were studied in two sequencing batch reactors (SBR) under varying pH and temperature conditions. A zero order kinetic model was proposed for nitrate and nitrite reduction and kinetic coefficients were obtained at two temperatures (25 +/- 1 and 12 +/- 1 degrees C), and pH ranging from 7 to 9.5. Nitrate and nitrite reduction was inhibited at pH of 7 at both temperatures of 12 +/- 1 and 25 +/- 1 degrees C. The optimum pH conditions for nitrate and nitrite reduction were 9.5 at 25 +/- 1 degrees C and 8.5 at 12 +/- 1 degrees C. Nitrate and nitrite reduction rates were compared, when they were used separately as the sole electron acceptor. It was shown that nitrite reduction rates consistently exceeded nitrate reduction rates, regardless of temperature and pH. The observed transitional accumulation of nitrite, when nitrate was used as an electron acceptor, indicated that nitrite reduction was slowed down by the presence of nitrate. No activity of acetogenic bacteria was observed in the hydrogenotrophic biomass and no residual acetate was detected, verifying that the kinetic parameters obtained were not influenced by heterotrophic denitrification and accurately represented autotrophic activity.

Bacteria↗
PubMed2002

Microbially mediated redox processes in natural analogues for radioactive waste.

Natural analogues allow scientists to investigate biogeochemical processes relevant to radioactive waste disposal that occur on time scales longer than those that may be studied by time-limited laboratory experiments. The Palmottu U-Th deposit in Finland and the Bangombé natural nuclear reactor in Gabon involve the study of natural uranium, and are both considered natural analogues for subsurface radioactive waste disposal. The microbial population naturally present in groundwater may affect the redox conditions, and hence, the radionuclide solubility and migration. Therefore, groundwater samples from the two sites were investigated for microbial populations. The total numbers of cells ranged from 10(4) to 10(6) cells ml(-1). Iron-reducing bacteria (IRB) were the largest culturable microbial population in the Palmottu groundwater and were present at up to 1.3 x 10(5) cells ml(-1). Sulfate-reducing bacteria (SRB) and acetogens could also be cultured from the Palmottu groundwater. The numbers of IRB and SRB were largest in groundwater with the lowest uranium concentrations. Removal of dissolved U(VI) from solution was concomitant with the growth of IRB enrichment cultures and the reduction of iron. The redox buffer in the Palmottu groundwater consists of iron and uranium species, both of which are affected by IRB. IRB and aerobic heterotrophs were cultured from the Bangombé groundwater, where redox potentials are buffered by iron and organic carbon species. Microbial populations similar to those found at Palmottu and Bangombé are found throughout the Fennoscandian Shield, a potential host rock for subsurface radioactive waste disposal. These results confirm that microorganisms can be expected to play a role in stabilizing radioactive waste disposed of in the subsurface by lowering redox potential and immobilizing radionuclides.

Bacteria↗
PubMed2003

Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms.

An increasing number of studies shows that the glycogen-accumulating organisms (GAOs) can survive and may indeed proliferate under the alternating anaerobic/aerobic conditions found in EBPR systems, thus forming a strong competitor of the polyphosphate-accumulating organisms (PAOs). Understanding their behaviors in a mixed PAO and GAO culture under various operational conditions is essential for developing operating strategies that disadvantage the growth of this group of unwanted organisms. A model-based data analysis method is developed in this paper for the study of the anaerobic PAO and GAO activities in a mixed PAO and GAO culture. The method primarily makes use of the hydrogen ion production rate and the carbon dioxide transfer rate resulting from the acetate uptake processes by PAOs and GAOs, measured with a recently developed titration and off-gas analysis (TOGA) sensor. The method is demonstrated using the data from a laboratory-scale sequencing batch reactor (SBR) operated under alternating anaerobic and aerobic conditions. The data analysis using the proposed method strongly indicates a coexistence of PAOs and GAOs in the system, which was independently confirmed by fluorescent in situ hybridization (FISH) measurement. The model-based analysis also allowed the identification of the respective acetate uptake rates by PAOs and GAOs, along with a number of kinetic and stoichiometric parameters involved in the PAO and GAO models. The excellent fit between the model predictions and the experimental data not involved in parameter identification shows that the parameter values found are reliable and accurate. It also demonstrates that the current anaerobic PAO and GAO models are able to accurately characterize the PAO/GAO mixed culture obtained in this study. This is of major importance as no pure culture of either PAOs or GAOs has been reported to date, and hence the current PAO and GAO models were developed for the interpretation of experimental results of mixed cultures. The proposed method is readily applicable for detailed investigations of the competition between PAOs and GAOs in enriched cultures. However, the fermentation of organic substrates carried out by ordinary heterotrophs needs to be accounted for when the method is applied to the study of PAO and GAO competition in full-scale sludges.

Acetates↗
PubMed2006

Degradation of xenobiotics originating from the textile preparation, dyeing, and finishing industry using ozonation and advanced oxidation.

Effluents from textile preparation, dyeing, and finishing processes contain high concentrations of biologically difficult-to-degrade or even inert auxiliaries. Under these circumstances, it most often becomes inevitable to apply energy-intense and hence "imperative" treatment technologies (so-called advanced oxidation processes, AOPs) to achieve an acceptable reduction in the organic content of the effluent, thereby improving the biocompatibility of the originally refractory wastewater. The present experimental study focused on three problematic dyehouse effluent streams in order to alleviate the problem of toxicity and recalcitrance arising from the use of certain textile chemicals at source. For that purpose, the textile preparation stage was simulated by a nonionic surfactant (NS), the polyamide dyeing stage by a synthetic tannin (syntan; ST), and an aqueous biocidal finishing (BF) solution was employed to mimic typical textile finishing effluent. Synthetic effluent streams bearing NS, ST, or BF were subjected to treatment with different, well-established AOPs (ozonation at varying pH; advanced oxidation with H(2)O(2)/UV-C at varying H(2)O(2) concentrations) in order to degrade the active ingredients of the auxiliary formulations, thereby eliminating their toxicity and recalcitrance. Baseline experiments were conducted in order to optimize AOP conditions that were consecutively applied to observe changes in the originally poor effluent biodegradability and high toxicity. Obtained experimental findings revealed that (i) the COD content of NS could be reduced by at least 50% after H(2)O(2)/UV-C treatment at pH 9.0 accompanied by a nearly twofold improvement in its already fair biodegradability; (ii) the inhibitory effect of the biochemically reluctant ST on heterotrophic biomass was completely eliminated upon ozonation (dose=900 mg h(-1)) at pH 3.5; and (iii) the microbial toxicity exerted by BF totally disappeared after ozonation (dose=600 mg h(-1)) at pH 7.2. However, the achievement of detoxification and/or biodegradability improvement was accompanied with high electrical energy requirements.

Biodegradation, Environmental↗
PubMed2003

Effects of linear alkylbenzene sulfonates on functional diversity of microbial communities in soil.

Linear alkylbenzene sulfonates (LAS) often occur in sewage sludge that is applied to agricultural soil. Here LAS may affect the microbial activity, which is an important basis for nutrient cycling. Previous studies have shown that single bacterial species and specific soil processes can be very sensitive to LAS. Here we report that two levels of LAS, 22 and 174 mg/kg dry weight soil, had little or no significant influence of the functional diversity of bacteria in a sandy soil, as tested by community-level physiological profiles. Briefly, these profiles are a characterization of the microbial communities based on the pattern of substrate utilization in 96-well microtiter plates (Biolog EcoPlates). Sandy agricultural soil was incubated in duplicate 1-L mesocosms with or without LAS, and bacteria were extracted after one, two, and four weeks. During incubation, more than 98 and 93% of LAS added to 22 and 174 mg/kg dry weight soil was degraded, respectively. The presence of LAS at 174 mg/kg dry weight caused a higher number of bacteria in the soil extracts, maximally corresponding to 2.5 times the numbers in LAS-free soil (1.8 x 10(7) cells/g dry wt soil) after four weeks of incubation. No inhibitory effect of LAS was observed when the substrate utilization data were analyzed for substrate richness and diversity (Shannon-Weaver indices). Principal component analysis, however, showed that the pattern of substrate utilization in soil with the highest LAS content (174 mg/kg dry wt) could be distinguished from control soil and soil with 22 mg LAS/kg dry weight. Yet the overall conclusion was that the functional diversity of the aerobic, heterotrophic bacterial community was rather insensitive to LAS.

Agriculture↗
PubMed2001

Light conditions affect the measurement of oceanic bacterial production via leucine uptake.

The effect of irradiance in the range of 400 to 700 nm or photosynthetically active radiation (PAR) on bacterial heterotrophic production estimated by the incorporation of 3H-leucine (referred to herein as Leu) was investigated in the northwestern Mediterranean Sea and in a coastal North Atlantic site, with Leu uptake rates ranging over 3 orders of magnitude. We performed in situ incubations under natural irradiance levels of Mediterranean samples taken from five depths around solar noon and compared them to incubations in the dark. In two of the three stations large differences were found between light and dark uptake rates for the surface most samples, with dark values being on average 133 and 109% higher than in situ ones. Data obtained in coastal North Atlantic waters confirmed that dark enclosure may increase Leu uptake rates more than threefold. To explain these differences, on-board experiments of Leu uptake versus irradiance were performed with Mediterranean samples from depths of 5 and 40 m. Incubations under a gradient of 12 to 1,731 micromol of photons m(-2) x s(-1) evidenced a significant increase in incorporation rates with increasing PAR in most of the experiments, with dark-incubated samples departing from this pattern. These results were not attributed to inhibition of Leu uptake in the light but to enhanced bacterial response when transferred to dark conditions. The ratio of dark to light uptake rates increased as dissolved inorganic nitrogen concentrations decreased, suggesting that bacterial nutrient deficiency was overcome by some process occurring only in the dark bottles.

Cyanobacteria↗
PubMedDate not supplied

There are high levels of functional and genetic diversity in Oxyrrhis marina.

Oxyrrhis marina, a widely distributed marine protist, is used to model heterotrophic flagellate responses in microbial food webs. Although clonal variability occurs in protists, assessments of intraspecific diversity are rare; such assessments are critical, particularly where species are used as models in ecological studies. To address the extent of intraspecific variation within O. marina, we assessed diversity among 11 strains using 5.8S rDNA and ITS sequences. The 5.8S rDNA and ITS regions revealed high divergence between strains: 63.1% between the most diverse. To compare O. marina diversity relative to other alveolates, 18S rDNA sequences for five strains were analysed with sequences from representatives of the major alveolate groups. 18S rDNA also revealed high divergence in O. marina. Additionally, consistent with phylogenies based on protein coding genes, maximum likelihood analysis indicated that O. marina was monophyletic and ancestral to the dinoflagellates. To assess ecophysiological differences, growth rates of seven O. marina strains were measured at 10 salinities (10-55 per thousand). Two salinity responses occurred: one group achieved highest growth rates at high salinities; the other grew best at low salinities. There was no clear correlation between molecular, ecophysiological, or geographical differences. However, salinity tolerance was associated with habitat type: intertidal strains grew best at high salinities; open-water strains grew best at low salinities. These data indicate the need to examine many strains of a species in both phylogenetic and ecological studies, especially where key-species are used to model ecological processes.

Animals↗
PubMed2004

Identification of archaea and some extremophilic bacteria using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.

Archaea and a number of groups of environmentally important bacteria, e.g., sulfate-reducing bacteria, anoxygenic phototrophs, and some thermophiles, are difficult to characterize using current methods developed for phenotypically differentiating heterotrophic bacteria. We have evaluated matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF-MS) as a rapid method for identifying different groups of extremophilic prokaryotes using a linear mass spectrometer (Micromass, UK). The instrument is designed to acquire mass-spectral patterns from prokaryotic cell-wall components between masses of 500 and 10,000 Da in a statistically robust manner and create a database that can be used for identification. We have tested 28 archaea (10 genera, 20 spp.) and 42 bacteria (25 genera, 37 spp.) and found that all species yield reproducible, unique mass-spectral profiles. As a whole, the profiles for the archaea had fewer peaks and showed less differentiation compared to the bacteria, perhaps reflecting fundamental differences in cell-wall structure. The halophilic archaea all had consistent patterns that showed little differentiation; however, the software was able to consistently distinguish Halobacterium salinarium, Halococcus dombrowski, and Haloarcula marismortui from one another, although it could not always correctly distinguish four strains of Hb. salinarium from one another. The method was able to reliably identify 10(5) cells of either Albidovulum inexpectatum or Thermococcus litoralis and could detect as low as 10(3) cells. We found that the matrix, alpha-cyano-4-hydroxy-cinnamic acid yielded better spectra for archaea than 5-chloro-2-mercapto-benzothiazole. Overall, the method was rapid, required a minimum of sample processing, and was capable of distinguishing and identifying a very diverse group of prokaryotes.

Archaea↗