Anaerobic degradation of papermill sludge in a two-phase digester containing rumen microorganisms and colonized polyurethane foam

Summary The use of reticulated polyurethane foam as a support material for the immobilization of methanogenic associations and its application to the anaerobic treatment of fine particulate solid wastes was investigated. The colonization of polyurethane support particles in a continuous upflow reactor fed on a mixture of acetate, propionate and butyrate, was both rapid and dense. The combination of rumen microorganisms and colonized support particles in a two-phase digester resulted in an efficient anaerobic decomposition of papermill sludge.     

Kinetics of nitrite oxidation in two Nitrobacter species grown in nitrite-limited chemostats

The influence of growth rate, the presence of acetate and variation in the dissolved oxygen concentration on the kinetics of nitrite oxidation was studied in suspensions of intact cells of Nitrobacter winogradskyi and Nitrobacter hamburgensis. The cells were grown in nitrite-limited chemostats at different dilution rates under chemolithotrophic and mixotrophic conditions. Growth of N. hamburgensis in continuous culture was dependent on the presence of acetate. Acetate hardly affected the maximal nitrite oxidation rate per cell (V _max), but displayed a distinctly negative effect on the saturation constants for nitrite oxidation (K _m ) of both Nitrobacter species. This effect was reversible; when acetate was removed from the suspensions the K _m -values for nitrite oxidation returned to their original values. A reduction of the dissolved oxygen concentration from 100% to 18% air saturation slightly decreased the V _max of chemolithotrophically grown N. winogradskyi cells, whereas a 2.3 fold increase was observed with mixotrophically grown cells of N. hamburgensis. It is suggested that the large variation in K _m encountered in field samples could be due to this observed phenotypic variability. The V _max per cell is not a constant, but apparently is dependent on growth rate and environmental conditions. This implies that potential nitrite oxidation activity and numbers of cells are not necessarily related. Considering their kinetic characteristics, it is unlikely that N. hamburgensis is able to compete succesfully with N. winogradskyi for limiting amounts of nitrite under mixotrophic conditions. However, at reduced partial oxygen tensions, N. hamburgensis may become the better competitor.     

The effect of acetylene on N transformations in an acid oak-beech soil

The effectiveness of acetylene (C₂H₂) as inhibitor of nitrification was studied in relation to the decomposition of C₂H₂. This was done by examining the effects of single and multiple additions of different C₂H₂ concentrations (10, 100, 1000 Pa) on mineral N and NO₃ ^–-N production in samples of the organic (FH) and upper mineral (Ah) layer of an acid oak-beech forest soil. The decomposition of C₂H₂ was much faster in Ah samples than in FH samples. A single addition of 10 Pa C₂H₂ was not sufficient for complete inhibition of nitrification in the Ah samples. Nitrification was blocked completely by all other C₂H₂ treatments in both FH and Ah samples. Addition of C₂H₂ decreased net mineral N production in Ah samples but not in FH samples. Addition of carboxymethyl-cellulose and chitin to Ah soil had no affect on the rate of decomposition of C₂H₂. Chitin had a negative effect on net NO₃ ^–-N production.     

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats

The absence of nitrification in soils rich in organic matter has often been reported. Therefore, competition for limiting amounts of ammonium between the chemolithotrophic 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⁻¹. Ammonium limitation of A. globiformis was achieved by increasing the glucose concentration in the reservoir stepwise from 0 to 5 mM while maintaining the ammonium concentration at 2 mM. The numbers of N. europaea and N. winogradskyi cells decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations for both dilution rates. Critical carbon-to-nitrogen ratios of 11.6 and 9.6 were determined for the dilution rates of 0.004 and 0.01 h⁻¹, respectively. Below these critical values, coexistence of the competing species was found in steady-state situations. Although the numbers were strongly reduced, the nitrifying bacteria were not fully outcompeted by the heterotrophic bacteria above the critical carbon-to-nitrogen ratios. Nitrifying bacteria could probably maintain themselves in the system above the critical carbon-to-nitrogen ratios because they are attached to the glass wall of the culture vessels. The numbers of N. europaea decreased more than did those of N. winogradskyi. This was assumed to be due to heterotrophic growth of the latter species on organic substrates excreted by the heterotrophic bacteria.     

Growth yield and energy generation in anaerobically-grown Campylobacter spec.

An anaerobic continuous culture study was made with Campylobacter spec. to determine growth yields under various growth conditions. The growth media contained 0.1% (w/v) yeast extract as carbon source. When grown in an aspartate-limited culture Y _asp ^max was 4.6. Inclusion of formate in the culture medium hardly affected the true growth yield. The number of ATP equivalents generated in the fumaratereductase system was 0.66 and the Y _ATP ^max was 7.0. In the nitrate reduction with formate 1.7 ATP equivalents were generated, and a YNO _3- ^max of 12.2 was observed. The true growth yield obtained with a mixture of lactate and aspartate was lower than that found with aspartate alone.     

The effect of genomic information on optimal contribution selection in livestock breeding programs

Background

Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity.

Methods

The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences.

Results

Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data.

Conclusions

The use of genomic estimated breeding values increased genetic gain in optimal contribution selection. Genomic estimated breeding values were more accurate and showed more within-family variation, which led to higher genetic gains for the same restriction on inbreeding. Using genomic relationships to restrict inbreeding provided no additional gain, except in the case of very large full-sib families.     

Response of nitrogen dynamics in semi-natural and agricultural grassland soils to experimental variation in tide and salinity

In the framework of rehabilitation efforts to enhance the ecological value of closed-off estuaries, we studied the effects of restoring a tidal movement and seawater incursion on soil nitrogen conversion rates and vegetation response of semi-natural and agricultural grasslands in an outdoor mesocosm experiment. Intact soil monoliths including vegetation were collected in June 2004 on two locations on the shores of the Haringvliet lagoon in the south-western part of the Netherlands, which used to be a well-developed estuary before closure in 1970. For more than 1 year, soil monoliths were continuously subjected to a full-factorial combination of tidal treatment [stagnant/tidal (0.20 m amplitude)] and water type [(freshwater, oligohaline (salinity = 3)]. Soil, soil moisture and water nitrogen concentrations were monitored for a year, as well as vegetation response and nitrogen conversion rates in the soil. As expected, nitrogen mineralization rates were enhanced by the tidal treatment in comparison with the stagnant treatment. Denitrification rates however, were much less affected by tide and were even lower in the tidal treatments after 3 months in the agricultural grassland soils, implying that in general, soils were more oxic in the tidal treatments. Oligohaline treatments had virtually no effect on soil nitrogen conversion rates compared to freshwater treatments. Vegetation performance, however, was lower under saline conditions, especially in the semi-natural grassland. No further significant differences in response to the tidal and oligohaline treatments were found between the two soils although they differed strongly in soil characteristics. We conclude that if the rehabilitation measures in the former Haringvliet estuary are carried out as planned, drastic changes in soil nitrogen processes and vegetation composition will not occur.     

Effects of substratum on the diversity and stability of ammonia-oxidizing communities in a constructed wetland used for wastewater treatment

AIM: To study the relationship between the nature of the substratum and the diversity and stability of the ammonia-oxidizing microbial community in a constructed wetland for the treatment of wastewaters. METHODS AND RESULTS: Samples have been taken the year around from sections of the wetland filled with different substrata. When present, the root zones of the helophyte Phragmites australis were also sampled. The diversity of the ammonia-oxidizing community was established by a coupled PCR-DGGE method based on the 16s rRNA gene. Averaged over the seasons, no large differences in community composition were observed between the different substrata, although the section with zeolite always showed the highest frequencies of bands belonging to ammonia-oxidizing bacteria of the beta-subclass of the Proteobacteria. Only sequences related to the Nitrosospira lineage were detected. Averaged again over the seasons, the section with zeolite was also most constant with respect to the potential ammonia-oxidizing activity. CONCLUSIONS: Although the ammonia-oxidizing communities did not differ significantly between the different sections of the constructed wetland, the characteristics of zeolite were most appropriate to accommodate a stable and active community of ammonia-oxidizing bacteria. The presence of the helophyte had no effect on the diversity and stability of the ammonia-oxidizing community. SIGNIFICANCE AND IMPACT OF THE STUDY: It has been shown that substrata used in constructed wetlands made no distinction between ammonia-oxidizing strains in relation to attachment. However, zeolite had the best performance with respect to activity over the seasons.     

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

Background  

Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa.