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[Determination of carbon dioxide released from soil at different humidities].

The detection of soil microorganisms by their evolution of carbon dioxide does not always correlate with the number of microorganisms and the rate of biochemical processes in soil. New microbial populations appear in the incubation chamber as the concentration of carbon dioxide increases; this results in an increase in the activity of such processes as photosynthesis, chemosynthesis and heterotrophic assimilation of carbon dioxide. Life detection on other planets by determining carbon dioxide evolved from the ground may lead to erroneous conclusions on the presence of microorganism in the ground.

Carbon Dioxide↗

Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Soil Columns.

The enhanced mineralization of immobilized nitrogen by bacteriophagous protozoa has been thought to favor the nitrification process in soils in which nitrifying bacteria must compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the flagellate Adriamonas peritocrescens on the competition for ammonium between the chemolithotrophic species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi was studied in soil columns, which were continuously percolated with media containing 5 mM ammonium and different amounts of glucose at a dilution rate of 0.007 h (liquid volumes). A. globiformis won the competition for ammonium. The grazing activities of the flagellates had two prominent effects on the competition between N. europaea and A. globiformis. First, the distribution of ammonium over the profile of the soil columns was more uniform in the presence of flagellates than in their absence. In the absence of flagellates, relatively high amounts of ammonium accumulated in the upper layer (0 to 3 cm), whereas in the underlying layers the ammonium concentrations were low. In the presence of flagellates, however, considerable amounts of ammonium were found in the lower layers, whereas less ammonium accumulated in the upper layer. Second, the potential ammonium-oxidizing activity of N. europaea was stimulated in the presence of flagellates. The numbers of N. europaea at different glucose concentrations in the presence of flagellates were comparable to those in the absence of protozoa. However, in the presence of flagellates, the potential ammonium-oxidizing activities were four to five times greater than those in the absence of protozoa.

Journal Article↗

Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Chemostats.

The enhanced mineralization of organic nitrogen by bacteriophagous protozoa is thought to favor the nitrification process in soils, in which nitrifying bacteria have to compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the bacteriovorous flagellate Adriamonas peritocrescens on the competition for limiting amounts of ammonium between the ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis was studied in the presence of Nitrobacter winogradskyi in continuous cultures at dilution rates of 0.004 and 0.01 h. The ammonium concentration in the reservoir was maintained at 2 mM, whereas the glucose concentration was increased stepwise from 0 to 7 mM. A. globiformis won the competition for limiting amounts of ammonium when the glucose concentration in the reservoirs increased, in agreement with previously described experiments in which the flagellates were not included. The numbers of nitrifying bacteria decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations. Critical C/N ratios, i.e., ratios between glucose and ammonium in the reservoirs at which no nitrate was found in the culture vessels, of 12.5 and 10.5 were determined at dilution rates of 0.004 and 0.01 h, respectively. Below these critical values, coexistence of the competing species was found. The numbers of nitrifying bacteria decreased more in the presence of flagellates than in their absence, presumably by selective predation on the nitrifying bacteria, either in the liquid culture or on the glass wall of the culture vessels. Despite this, the rate of nitrate production did not decrease more in the presence of flagellates than in their absence. This demonstrates that no correlation has to be expected between numbers of nitrifying bacteria and their activity and that a constant nitrification rate per cell cannot be assumed for nitrifying bacteria. Above the critical C/N ratios, low numbers of nitrifying bacteria were still found in the culture vessels, probably because of attachment of the nitrifying bacteria to the glass wall of the culture vessels. Like the numbers of heterotrophic bacteria, the numbers of flagellates increased when the glucose concentrations in the reservoirs increased. Numbers of 2 x 10 and 12 x 10 flagellates ml were found at 7 mM glucose at dilution rates of 0.004 and 0.01 h, respectively. It was concluded that the critical C/N ratios were practically unaffected by the presence of protozoa. Although nitrate production rates were equal in the presence and absence of flagellates, the numbers of nitrifying bacteria decreased more strongly in their presence. This indicates a higher activity per nitrifying cell in the presence of flagellates.

Journal Article↗

State estimation for a biological phosphorus removal process using an asymptotic observer.

This study investigated the use of an asymptotic observer for state estimation in a continuous biological phosphorus removal process. The estimated states are the concentration of heterotrophic, autotrophic and phosphorus accumulating organisms, polyphosphate, glycogen and PHA. The reaction scheme describing the process was simplified from a combined ASM 1-Delft model. Three examples were investigated: operation at steady state, operation at steady state with a random white-noise in the measurements and operation with a ramp disturbance. In each case, the estimation was quite accurate even if the convergence, driven by the dilution rate, was slow (from 15 to 60 days). The propagation of the measurement noise and a bias in the estimation of glycogen and PHA could be the result of the high condition number of one of the matrices used in the algorithm of the asymptotic observer for the aerated tanks.

Air↗

Profiling bacterial survival through a water treatment process and subsequent distribution system.

AIMS: To profile fractions of active bacteria and of bacteria culturable with routine heterotrophic plate count (HPC) methods through a typical water treatment process and subsequent distribution system. In doing so, investigate how water treatment affects both bacterial abundance and diversity, and reveal the identities of active bacteria not detected by traditional HPC culture. METHODS AND RESULTS: Profiling active fractions was performed by flow cytometric cell sorting of either membrane-intact (BacLight kit) or enzymatically active (carboxyfluorescein diacetate, CFDA) bacteria, followed by eubacterial 16S rDNA-directed PCR and denaturing gradient gel electrophoresis (DGGE). Water treatment significantly reduced active bacterial numbers detected by the BacLight kit and CFDA assay by 2.89 and 2.81 log respectively. Bacterial diversity was also reduced from > 20 DGGE bands in the active fractions of reservoir water to only two bands in the active fractions of finished water. These two bands represented Stenotrophomonas maltophila, initially culturable by HPC, and a Burkholderia-related species. Both species maintained measurable traits of physiological activity in distribution system bulk water but were undetected by HPC. CONCLUSIONS: Flow cytometric cell sorting with PCR-DGGE, to assess water treatment efficacy, identified active bacteria from a variety of major phylogenetic groups undetected by routine HPC. Following treatment S. maltophila and a Burkholderia-related species retained activity and entered distribution undetected by HPC. SIGNIFICANCE AND IMPACT OF THE STUDY: Methods used here demonstrate how water treatment operators can better monitor water treatment plant efficacy and assess distribution system instability by the detection and identification of active bacteria recalcitrant to routine HPC culture.

Bacteria↗

Protein transport into secondary plastids and the evolution of primary and secondary plastids.

Chloroplasts are key organelles in algae and plants due to their photosynthetic abilities. They are thought to have evolved from prokaryotic cyanobacteria taken up by a eukaryotic host cell in a process termed primary endocytobiosis. In addition, a variety of organisms have evolved by subsequent secondary endocytobioses, in which a heterotrophic host cell engulfed a eukaryotic alga. Both processes dramatically enhanced the complexity of the resulting cells. Since the first version of the endosymbiotic theory was proposed more than 100 years ago, morphological, physiological, biochemical, and molecular data have been collected substantiating the emerging picture about the origin and the relationship of individual organisms with different primary or secondary chloroplast types. Depending on their origin, plastids in different lineages may have two, three, or four envelope membranes. The evolutionary success of endocytobioses depends, among other factors, on the specific exchange of molecules between the host and endosymbiont. This raises questions concerning how targeting of nucleus-encoded proteins into the different plastid types occurs and how these processes may have developed. Most studies of protein translocation into plastids have been performed on primary plastids, but in recent years more complex protein-translocation systems of secondary plastids have been investigated. Analyses of transport systems in different algal lineages with secondary plastids reveal that during evolution existing translocation machineries were recycled or recombined rather than being developed de novo. This review deals with current knowledge about the evolution and function of primary and secondary plastids and the respective protein-targeting systems.

Endocytosis↗

Heterotrophic bacteria growing in association with Methylococcus capsulatus (Bath) in a single cell protein production process.

The methanotrophic bacterium Methylococcus capsulatus (Bath) grows on pure methane. However, in a single cell protein production process using natural gas as methane source, a bacterial consortium is necessary to support growth over longer periods in continuous cultures. In different bioreactors of Norferm Danmark A/S, three bacteria consistently invaded M. capsulatus cultures growing under semi-sterile conditions in continuous culture. These bacteria have now been identified as a not yet described member of the Aneurinibacillus group, a Brevibacillus agri strain, and an acetate-oxidiser of the genus Ralstonia. The physiological roles of these bacteria in the bioreactor culture growing on natural, non-pure methane gas are discussed. The heterotrophic bacteria do not have the genetic capability to produce either the haemolytic enterotoxin complex HBL or non-haemolytic enterotoxin.

Bacillus↗

Interactions between photolyase and dark repair processes in Chlamydomonas reinhardtii.

The participation of DNA photolyase in dark repair processes has been reported in some heterotrophic organisms. To assess the role of photolyase in dark repair in photoautotrophs, double mutants of Chlamydomonas reinhardtii deficient in dark repair and photoreactivation were constructed and assayed for UV sensitivity in different posttreatment light conditions (with or without subsequent photoreactivation). We found that a functional PHR1 gene enhanced dark survival in the excision deficient (uvs9, uvs12) and in the recombination deficient (uvs10) genetic backgrounds but failed to do so in the strain deficient in a repair pathway other than excision and recombination (uvs13). Therefore we can conclude that photolyase may stimulate dark repair processes in C. reinhardtii also via pathway(s) other than nucleotide excision repair. The fact that some of the double mutants deficient in dark repair and photoreactivation survived better in the light than in the dark supports the idea that additional photorepair might be active and may enhance survival in a specific genetic background.

Animals↗

Microbial diversity in sediments of saline Qinghai Lake, China: linking geochemical controls to microbial ecology.

Saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. The objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from Qinghai Lake. The lake is saline (12.5 g/L salinity) and alkaline (pH 9.4) and is located on the Qinghai-Tibetan Plateau at an altitude of 3196 m above sea level. Pore water chemistry of the core revealed low concentrations of sulfate and iron (<1 mM), but high concentrations of acetate (40-70 mM) and dissolved organic carbon (1596-5443 mg/L). Total organic carbon and total nitrogen contents in the sediments were approximately 2 and <0.5%, respectively. Acridine orange direct count data indicated that cell numbers decreased from 4 x 10(9) cells/g at the water-sediment interface to 6 x 10(7) cells/g wet sediment at the 40-cm depth. This change in biomass was positively correlated with acetate concentration in pore water. Phospholipid fatty acid (PLFA) community structure analyses determined decrease in the proportion of the Proteobacteria and increase in the Firmicutes with increased depth. Characterization of small subunit (SSU) rRNA genes amplified from the sediments indicated a shift in the bacterial community with depth. Whereas the alpha-, beta-, and gamma-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) were dominant at the water-sediment interface, low G + C gram-positive bacteria (a subgroup of Firmicutes) became the predominant group in the anoxic sediments. Both PLFA and the sequence data showed similar trend. The Proteobacteria, CFB, and gram-positive bacteria are present in other saline lakes, but the presence of Actinobacteria and Acidobacteria/Holophaga in significant proportions in the Qinghai Lake sediments appears to be unique. The archaeal diversity was much lower, and clone sequences could be grouped in the Euryarchaeota and Crenarchaeota domains. The archaeal clones were not related to any known cultures but to sequences previously found in methane-rich sediments. Acetate-utilizing methanogens were isolated from sediment incubations, and alpha- and gamma-proteobacterial isolates were obtained from a water sample from the lake-bottom (23 m). Our data collectively showed that the observed diversity and shift in the community structure with depth was correlated with geochemical parameters (the redox state and availability of electron acceptor and donor). Heterotrophic methanogenesis is possibly adominant metabolic process in the Qinghai Lake sediments. These results reinforce the importance of geochemical controls on microbial ecology in saline and alkaline lake environments.

Acridine Orange↗

A new medium for the enumeration and subculture of bacteria from potable water.

Plate count agar is presently the recommended medium for the standard bacterial plate count (35 degrees C, 48-h incubation) of water and wastewater. However, plate count agar does not permit the growth of many bacteria that may be present in treated potable water supplies. A new medium was developed for use in heterotrophic plate count analyses and for subculture of bacteria isolated from potable water samples. The new medium, designated R2A, contains 0.5 g of yeast extract, 0.5 g of Difco Proteose Peptone no. 3 (Difco Laboratories), 0.5 g of Casamino Acids (Difco), 0.5 g of glucose, 0.5 g of soluble starch, 0.3 g of K2HPO4, 0.05 g of MgSO4 X 7H2O, 0.3 g of sodium pyruvate, and 15 g of agar per liter of laboratory quality water. Adjust the pH to 7.2 with crystalline K2HPO4 or KH2PO4 and sterilize at 121 degrees C for 15 min. Results from parallel studies with spread, membrane filter, and pour plate procedures showed that R2A medium yielded significantly higher bacterial counts than did plate count agar. Studies of the effect of incubation temperature showed that the magnitude of the count was inversely proportional to the incubation temperature. Longer incubation time, up to 14 days, yielded higher counts and increased detection of pigmented bacteria. Maximal bacterial counts were obtained after incubation at 20 degrees C for 14 days. As a tool to monitor heterotrophic bacterial populations in water treatment processes and in treated distribution water, R2A spread or membrane filter plates incubated at 28 degrees C for 5 to 7 days is recommended.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteria↗

ANAMMOX and partial denitritation in anaerobic nitrogen removal from piggery waste.

The anaerobic ammonium removal from a piggery waste with high strength (56 g COD/L and 5 g T-N/L) was investigated using a lab-scale upflow anaerobic sludge bed reactor at a mesophilic condition. Based on the nitrogen and carbon balance in the process, the contribution of autotrophic and heterotrophic organisms was also evaluated in terms of the influent NO2-N/NH4-N ratio (1:0.8 and 1:1.2 for Phase 1 and Phase 2, respectively). The result of this research demonstrates that the anaerobic ammonium removal from the piggery waste, using the UASB reactor, can be performed successfully. Furthermore, it appears that by using granular sludge as the seed biomass, the ANAMMOX reaction can start more quickly. Average nitrogen conversion was 0.59 kg T-N/m3 reactor-day (0.06 kg T-N/kg VSS/day) and 0.66 kg T-N/m3 reactor-day (0.08 kg T-N/kg VSS/day) for Phase 1 and Phase 2. The NO2-N/NH4-N removal ratio by the ANAMMOX was 1.48 and 1.79 for Phase 1 and Phase 2. The higher nitrite contents (about 50%) in the substrate resulted in higher nitrite nitrogen removal by the partial denitritation, as well as the ANAMMOX reaction, implying higher potential of partial denitritation. However, the result reveals that the ANAMMOX reaction was influenced less by the degree of partial denitritation, and the ANAMMOX bacteria did not compete with denitritation bacteria. The colour of the biomass at the bottom of the reactor changed from dark gray to dark red, which was accompanied by an increase in cytochrome content. At the end of the experiment, red-coloured granular sludge with diameter of 1-2 mm at the lower part of the reactor was also observed.

Animals↗

Effect of storage upon the toxicity of synfuel process waters to bacteria.

Storage of synfuel process waters at 4 degrees C for 8 years appeared to reduce the toxicity of these waters to indicator bacteria. When these waters were mixed in the amount of 10 percent process waters to 90 percent sewage, heterotrophic bacteria grew which indicate that storage or aeration may improve the treatability of these waters.

Bacteria↗

SecY, an integral subunit of the bacterial preprotein translocase, is encoded by a plastid genome.

Although the paradigm for the acquisition of photosynthetic organelles is the endocytosis of cyanobacteria-like progenitors by heterotrophic protists, details of this evolutionary process are unclear. The small organellar chromosomes are remnants of the larger bacterial genomes with most genes from the endosymbiont's DNA having been either relocated to the protist's nucleus or entirely lost. As a result of those gene transfers, differences exist between plastids from different algal phyla and higher plants. We report here on the retention of a secY gene in cyanelle (= plastid) DNA of the eukaryotic protist Cyanophora paradoxa. This cyanelle secY encodes a functional protein homologous to SecY of Escherichia coli, identified as a subunit of the preprotein translocase complex. Similarity of the cyanelle and E. coli SecY topology, predicted from sequence information, has been confirmed experimentally through SecY-PhoA fusion protein analysis in E. coli. Cyanelle SecY, expressed in an E. coli secY mutant, substituted for the defective prokaryotic SecY. A plastid-encoded gene for a membrane protein functioning in protein transport across plastid membranes is unprecedented in higher plants. From these results we infer that a functional homolog of the prokaryotic preprotein translocation machinery is retained in some plastids.

Adenosine Triphosphatases↗

Removal of cyanobacteria, cyanotoxins, heterotrophic bacteria and endotoxins at an operating surface water treatment plant.

The removal of cyanobacteria, hepatotoxins produced by them (microcystins), phytoplankton, heterotrophic bacteria and endotoxins were monitored at a surface water treatment plant with coagulation, clarification, sand filtration, ozonation, slow sand filtration and chlorination as the treatment process. Coagulation-sand filtration reduced microcystins by 1.2-2.4, and endotoxins by 0.72-2.01 log10 units. Ozonation effectively removed the residual microcystins. The treatment process reduced phytoplankton biomass by 2.2-4.6 and heterotrophic bacteria by 2.0-5.0 log10 units. In treated water, the concentration of microcystins never exceeded the WHO guide value (1 microg/L), but picoplankton and monad cells were often detected in high numbers. The heterotrophic bacterial isolates from the treated waters belonged to genera Sphingomonas, Pseudomonas, Bacillus, Herbaspirillum and Bosea.

Bacteria↗

[Bacterial quantity and microbial reactivity in Tugur bay of the Okhotsk Sea].

The paper presents the results of investigation of the total abundance and the biomass of bacterioplankton, the abundance of heterotrophic bacteria, and the activity of microbiological processes involved in the carbon cycle in the water of the Bay of Tugur of the Sea of Okhotsk. In different regions of the bay, the total abundance of bacterioplankton was found to vary from 0.51 x 10(6) to 2.54 x 10(6) cells/ml; the bacterioplankton biomass, from 8.5 to 46.5 micrograms C/l; the abundance of heterotrophic bacteria, from 0.06 x 10(3) to 2.12 x 10(3) cells/ml; the bacterial assimilation of CO2, glucose, acetate, and protein hydrolysate, from 0.8 to 6.3, from 0.11 to 1.88, from 0.07 to 0.56, and from 0.01 to 0.22 mg C/(m3 day), respectively; the degradation of organic matter ranged from 28 to 221 mg C/(m3 day); and the intensity of methane oxidation, from 0.0005 to 0.17 microliter CH4/l. The spatial pattern and the functional characteristics of bacterioplankton in the Bay of Tugur were found to be dependent on the tidal dynamics.

Acetates↗

[Effect of grazing on microbiological processes of N2O production in grassland soils].

A laboratory incubation study on effect of grazing on microbiological processes of N2O production in Aneurolepidium chinese grassland soils by using the acetylene-inhibition method was firstly conducted and the seasonal variations of related bacteria groups and N2O fluxes were analyzed. Results suggested that grazing behavior altered the soil structure which were benefit to microbiological denitrification so that N2O emission from this steppe soil was reduced. It was the heterotrophic nitrification that is the key microbiological process for N2O production in the non-grazing and grazing semi-arid typical grassland soils in Inner Mongolia. The reasons why N2O flux from Inner Mongolia semi-arid typical grassland soils was lower were also explained in this paper.

Animals↗

Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation.

In many oceanic regions, growth of phytoplankton is nitrogen-limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, and NO3-) by anaerobic microbial processes. Globally, 30-50% of the total nitrogen loss occurs in oxygen-minimum zones (OMZs) and is commonly attributed to denitrification (reduction of nitrate to N2 by heterotrophic bacteria). Here, we show that instead, the anammox process (the anaerobic oxidation of ammonium by nitrite to yield N2) is mainly responsible for nitrogen loss in the OMZ waters of one of the most productive regions of the world ocean, the Benguela upwelling system. Our in situ experiments indicate that nitrate is not directly converted to N2 by heterotrophic denitrification in the suboxic zone. In the Benguela system, nutrient profiles, anammox rates, abundances of anammox cells, and specific biomarker lipids indicate that anammox bacteria are responsible for massive losses of fixed nitrogen. We have identified and directly linked anammox bacteria to the removal of fixed inorganic nitrogen in the OMZ waters of an open-ocean setting. We hypothesize that anammox could also be responsible for substantial nitrogen loss from other OMZ waters of the ocean.

Atlantic Ocean↗