101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.

Fire-induced pine woodland to shrubland transitions in Southern Europe may promote shifts in soil fertility

Since the mid of the last century, fire recurrence has increased in the Iberian Peninsula and in the overall Mediterranean basin due to changes in land use and climate. The warmer and drier climate projected for this region will further increase the risk of wildfire occurrence and recurrence. Although the impact of wildfires on soil nutrient content in this region has been extensively studied, still few works have assessed this impact on the basis of fire recurrence. This study assesses the changes in soil organic C and nutrient status of mineral soils in two Southern European areas, Várzea (Northern Portugal) and Valencia (Eastern Spain), affected by different levels of fire recurrence and where short fire intervals have promoted a transition from pine woodlands to shrublands. At the short-term (<1year), the amount of soil organic matter was higher in burned than in unburned soils while its quality (represented as labile to total organic matter) was actually lower. In any case, total and labile soil organic matter showed decreasing trends with increasing fire recurrence (one to four fires). At the long-term (>5years), a decline in overall soil fertility with fire recurrence was also observed, with a drop between pine woodlands (one fire) and shrublands (two and three fires), particularly in the soil microsites between shrubs. Our results suggest that the current trend of increasing fire recurrence in Southern Europe may result in losses or alterations of soil organic matter, particularly when fire promotes a transition from pine woodland to shrubland. The results also point to labile organic matter fractions in the intershrub spaces as potential early warning indicators for shifts in soil fertility in response to fire recurrence.

Virus safety of plasma products using 20 nm instead of 15 nm filtration as virus removing step

During the manufacture of human plasma derivatives, a series of complementary measures are undertaken to prevent transmission of blood-borne viruses. Virus filtration using 15 nm (Planova15N) filters has successfully been implemented in manufacturing processes for various plasma derivatives primarily because virus filtration is a technique, mild for proteins, that can effectively remove even small non-lipid-enveloped viruses, such as HAV and parvovirus B19. However, the use of 15 nm filters has limitations with regard to protein capacity of the filters and the process flow, resulting in an expensive manufacturing step. Therefore, studies were performed to test whether the use of 20 nm (Planova20N) filters, having different characteristics compared to 15 nm filters, can be an alternative for the use of 15 nm filters. It is shown that 20 nm filtration can be an alternative for 15 nm filtration. However, the virus removal capacity of the 20 nm filters depends on the plasma product that is filtered. Therefore, an optimisation study must be performed with regard to process parameters such as pressure, pH and protein concentration for each plasma product. In this study, using optimised conditions, the virus removal capacity of 20 nm filters appears to be comparable or even better when compared to that of 15 nm filters.

Protozoan grazing and bacterial production in stratified lake vechten estimated with fluorescently labeled bacteria and by thymidine incorporation

In stratified Lake Vechten, The Netherlands, protozoan grazing was estimated on the basis of uptake of fluorescently labeled bacteria and compared with bacterial production estimated on the basis of thymidine incorporation. By using a grazer-free mixed bacterial population from the lake in continuous culture, an empirical relationship between cell production and thymidine incorporation was established. Thymidine incorporation into total cold-trichloroacetic-acid-insoluble macromolecules yielded a relatively constant empirical conversion factor of ca. 10 (range, 0.38 x 10 to 1.42 x 10) bacteria mol of thymidine at specific growth rates (mu) ranging from 0.007 to 0.116 h. Although thymidine incorporation has been assumed to measure DNA synthesis thymidine incorporation appeared to underestimate the independently measured bacterial DNA synthesis by at least 1.5- to 13-fold, even if all incorporated label was assumed to be in DNA. However, incorporation into DNA was found to be insignificant as measured by conventional acid-base hydrolysis. Methodological problems of the thymidine technique are discussed. Like the cultures, Lake Vechten bacteria showed considerable thymidine incorporation into total macromolecules, but no significant incorporation into DNA was found by acid-base hydrolysis. This applied not only to the low-oxygen hypo- and metalimnion but also to the aerobic epilimnion. Thus, the established empirical conversion factor for thymidine incorporation into total macromolecules was used to estimate bacterial production. Maximum production rates (141 x 10 bacteria liter h; mu, 0.012 h) were found in the metalimnion and were 1 order of magnitude higher than in the epi- and hypolimnion. In all three strata, the estimated bacterial production was roughly balanced by the estimated protozoan grazing. Heterotrophic nanoflagellates were the major consumers of the bacterial production and showed maximum numbers (up to 40 x 10 heterotrophic nanoflagellates liter) in the microaerobic metalimnion.

Fixation, counting, and manipulation of heterotrophic nanoflagellates

Quantitative effects of several fixatives on heterotrophic nanoflagellates (HNAN) and phototrophic nanoflagellates (PNAN) were investigated by hemacytometer and epifluorescence counting techniques. Counts of Monas sp. cultures before and after fixation with unbuffered 0.3% glutaraldehyde and 5% formaldehyde showed no loss of cells during fixation, and cell concentrations remained constant for several weeks after fixation. Buffering of fixatives with borax caused severe losses, up to 100% within 2 h. Field samples from Lake Vechten showed no decline of HNAN and total nanoflagellate concentrations for at least 1 week after fixation with 5% formaldehyde and with 1% glutaraldehyde. With 1% glutaraldehyde, the chlorophyll autofluorescence of PNAN was much brighter than with 5% formaldehyde, although it was lost after a few days and thus limited the storage time of samples. However, when primulin-stained slides were prepared soon after fixation and stored at -30 degrees C, the loss of autofluorescence was prevented and PNAN and HNAN concentrations were stable for at least 16 weeks. Effects of filtration and centrifugation on HNAN were also studied. Filtration vacuum could not exceed 3 kPa since 10 kPa already caused losses of 15 to 20%. Similar losses were caused by centrifugation, even at low speed (500 x g).

Protozoan grazing, bacterial activity, and mineralization in two-stage continuous cultures

In two-stage continuous cultures, at bacterial concentrations, biovolumes, and growth rates similar to values found in Lake Vechten, ingestion rates of heterotrophic nanoflagellates (HNAN) increased from 2.3 bacteria HNAN . h at a growth rate of 0.15 day to 9.2 bacteria . HNAN . h at a growth rate of 0.65 day. On a yeast extract medium with a C/N/P ratio of 100:15:1.2 (Redfield ratio), a mixed bacterial population showed a yield of 18% (C/C) and a specific carbon content of 211 fg of C . mum. The HNAN carbon content and yield were estimated at 127 fg of C . mum and 47% (C/C). Although P was not growth limiting, HNAN accelerated the mineralization of PO(4)-P from dissolved organic matter by 600%. The major mechanism of P remineralization appeared to be direct consumption of bacteria by HNAN. N mineralization was performed mainly (70%) by bacteria but was increased 30% by HNAN. HNAN did not enhance the decomposition of the relatively mineral-rich dissolved organic matter. An accelerated decomposition of organic carbon by protozoa may be restricted to mineral-poor substrates and may be explained mainly by protozoan nutrient regeneration. Growth and grazing in the cultures were compared with methods for in situ estimates. Thymidine incorporation by actively growing bacteria yielded an empirical conversion factor of 1.1 x 10 bacteria per mol of thymidine incorporated into DNA. However, nongrowing bacteria also showed considerable incorporation. Protozoan grazing was found to be accurately measured by uptake of fluorescently labeled bacteria, whereas artificial fluorescent microspheres were not ingested, and selective prokaryotic inhibitors blocked not only bacterial growth but also protozoan grazing.

Functional stability of microbial communities in contaminated soils near a zinc smelter (Budel, the Netherlands)

Environmental pollution causes adverse effects on many levels of ecosystem organization; it might affect the use efficiency of available resources which will make the system more sensitive to subsequent stress. Alternatively the development of community tolerance may make the system more resistant to additional stresses. In this study we investigate the functional stability, measured in the terms of resistance and resilience, of microbial populations inhabiting contaminated soils near a zinc smelter. With functional stability we mean that we look at processes rather than at population dynamics. We measure changes in respiration and bacterial growth rate in response to addition of stress (lead, salt) or disturbance (heat). We used soils that differ in the level of pollution with zinc and cadmium originating from an adjacent smelter. Our results showed, with regard to respiration, that the most polluted soils have the lowest stability to salt (stress) and heat (disturbance). This confirms the hypothesis that more stressed systems have less energy to cope with additional stress or disturbance. However, bacterial growth rates were affected in a different way than respiration. There was no difference between the soils in resistance and resilience to addition of lead. In case of salt treatment, the least polluted soils showed highest stability. In contrast, the least polluted soils were the least stable to increased temperature, which supports the hypothesis that more stressed soils are more stable to additional stress/disturbance due to properties they gained when exposed to the first stress (pollution by the smelter). Thus, the responses of microbial processes to stress, their nature and size, depend on the kinds of stress factors, especially whether a subsequent stress is similar to the first stress, in terms of the mechanism with which the organisms deal with the stress.

Within-trophic group interactions of bacterivorous nematode species and their effects on the bacterial community and nitrogen mineralization

Knowledge of the interactions between organisms within trophic groups is important for an understanding of the role of biodiversity in ecosystem functioning. We hypothesised that interactions between bacterivorous nematodes of different life history strategies would affect nematode population development, bacterial community composition and activity, resulting in increased N mineralization. A microcosm experiment was conducted using three nematode species (Bursilla monhystera, Acrobeloides nanus and Plectus parvus). All the nematode species interacted with each other, but the nature and effects of these interactions depended on the specific species combination. The interaction between B. monhystera and A. nanus was asymmetrically competitive (0,-), whereas that between B. monhystera and P. parvus, and also A. nanus and P. parvus was contramensal (+, -). The interaction that affected microcosm properties the most was the interaction between B. monhystera and P. parvus. This interaction affected the bacterial community composition, increased the bacterial biomass and increased soil N mineralization. B. monhystera and P. parvus have the most different life history strategies, whereas A. nanus has a life history strategy intermediate to those of B. monhystera and P. parvus. We suggest that the difference in life history strategies between species of the same trophic group is of importance for their communal effect on soil ecosystem processes. Our results support the idiosyncrasy hypothesis on the role of biodiversity in ecosystem functioning.

Fully automatic determination of soil bacterium numbers, cell volumes, and frequencies of dividing cells by confocal laser scanning microscopy and image analysis

We describe a fully automatic image analysis system capable of measuring cell numbers, volumes, lengths, and widths of bacteria in soil smears. The system also determines the number of cells in agglomerates and thus provides the frequency of dividing cells (FDC). Images are acquired from a confocal laser scanning microscope. The grey images are smoothed by convolution and by morphological erosion and dilation to remove noise. The background is equalized by flooding holes in the image and is then subtracted by two top hat transforms. Finally, the grey image is sharpened by delineation, and all particles above a fixed threshold are detected. The number of cells in each detected particle is determined by counting the number of local grey-level maxima in the particle. Thus, up to 1,500 cells in 10 fields of view in a soil smear are analyzed in 30 min without human intervention. Automatic counts of cell numbers and FDC were similar to visual counts in field samples. In microcosms, automatic measurements showed significant increases in cell numbers, FDC, mean cell volume, and length-to-width ratio after amendment of the soil. Volumes of fluorescent microspheres were measured with good approximation, but the absolute values obtained were strongly affected by the settings of the detector sensitivity. Independent measurements of bacterial cell numbers and volumes by image analysis and of cell carbon by a total organic carbon analyzer yielded an average specific carbon content of 200 fg of C (mu)m(sup-3), which indicates that our volume estimates are reasonable.