Tomasz Oszako

Industrial wastewater as raw material for exopolysaccharide production by Rhizobium leguminosarum

The objective of this study was to evaluate the exopolysaccharide (EPS) production by Rhizobium leguminosarum cultivated in wastewater generated by oil companies (WWOC1 and WWOC2) and fish processing industry (WWFP). The results obtained in Erlenmeyer flasks indicated that the rhizobial strain grew well in industrial wastewater. Generally, wastewater composition affected the growth and the EPS production. WWFP allowed good bacterial growth similar to that obtained with the standard medium (YMB). During growth, various quantities of EPS were produced and yields varied depending on the media. Growing in YMB, EPS production did not exceed 9.7 g/L obtained after 72 h of growth. In wastewater, the maximum EPS value reached 11.1 g/L obtained with the fish processing wastewater, after 72 h of growth. The use of a mixture of the oil company wastewater (WWOC2) and the fish processing wastewater (WWFP) as culture medium affected not only the rhizobial strain growth, but also EPS production. The highest EPS (42.4 g/L, after 96 h of culture) was obtained using a ratio of WWFP and WWOC2 of 50:50 (v:v). Therefore, this work shows the ability of Rhizobium leguminosarum, growing in industrial wastewater as new economic medium, to produce EPS. This biopolymer could be applied in enormous biotechnological areas.

Seven recommendations to make your invasive alien species data more useful

Science-based strategies to tackle biological invasions depend on recent, accurate, well-documented, standardised and openly accessible information on alien species. Currently and historically, biodiversity data are scattered in numerous disconnected data silos that lack interoperability. The situation is no different for alien species data, and this obstructs efficient retrieval, combination, and use of these kinds of information for research and policy-making. Standardization and interoperability are particularly important as many alien species related research and policy activities require pooling data. We describe seven ways that data on alien species can be made more accessible and useful: 1) Create data management plans; 2) Increase interoperability of information sources; 3) Document data through metadata; 4) Format data using existing standards; 5) Adopt controlled vocabularies; 6) Increase data availability; and 7) Ensure long-term data preservation. We identify four properties specific and integral to alien species data (species status, introduction pathway, degree of establishment, and impact mechanism) that are either missing from existing data standards or lack a recommended controlled vocabulary. Improved access to accurate, real-time and historical data will repay the long-term investment in data management infrastructure, by providing more accurate, timely and realistic analyses. If we improve core biodiversity data standards by developing their relevance to alien species, it will allow the automation of common activities regarding data processing in support of environmental policy. Furthermore, we call for considerable effort to maintain, update, standardise, archive, and aggregate datasets, to ensure proper valorisation of alien species data and information before they become obsolete or lost.

Forest Tree Species Traced with a DNA-Based Proof for Illegal Logging Case in Poland

Precise identification of biological samples remains the most important proof in the forensic science. Illegal logging has become the urgent issue in Poland during the last decades, and conventional methods of investigation turn out to be often insufficient. Recently, the DNA-based markers (SSR and cytoplasmic genes) can remarkably help in the forensic botany performed by the Forest Service Guards and the Police investigation in illegal logging of timber. The identification method relies on comparison of the piece of evidence (i.e., stolen wood fragments) with the piece of reference (e.g., tree parts remained in the forest). We present the usefulness of the DNA neutral markers (i.e., microsatellite loci) and cytoplasmic genes in forensic botany based on several case studies of illegal wood identification in Poland, concerning the most economically important coniferous tree species such as Pinus sylvestris L., Picea abies (L.) Karst., Abies alba Mill., and Larix decidua (L.). Thanks to the DNA profiles established on the basis of minimum 4 microsatellite nuclear DNA loci, and at least one cytoplasmic organelle (mitochondrial or chloroplast) DNA marker, the determination of the DNA profiles provided fast and reliable comparison between material of evidence (also wood and needles) and material of reference (first of all tree stumps) in the forest. These data strongly supported the decision taken by several District Courts in Poland, as far as the identification of wood samples was proved with a high probability (approximately 98–99 %). The aim of the below publication is to present Polish case study on DNA use to fight illegal logging which became very successful among foresters.

Slow Sand Filters as a part of integrated protection of seedlings against disease in forest nurseries

Abstract Slow Sand Filters (SSF) are a biological method used to protect nursery plants, from pathogen infections which can cause serious diseases in many forest tree species. Thanks to SSF application the number of phytopathogens in nurseries can be significantly reduced, as demonstrated by many field and greenhouse experiments (e.g. in Polish nurseries, and for horticultural crops in Germany and The Netherlands). In this study, the effect of pollution from fertilizers and fungicides used in agriculture (e.g. PCNB) on the efficiency of SSFs was assessed. A quantitative analysis was performed of the copiotrophic and oligotrophic bacterial composition colonizing SSF biofilms. The efficiency with which selected Oomycete strains belonging to the genus Phytophthora (P. alni, P. cactorum, P. plurivora) were removed from water was determined based on genetic material (DNA of the organisms) found in the SSF filtrate. Specific primers and TaqMan probes (qPCR) appeared to be the most sensitive molecular methods. Moreover, the microbiological analysis of SSF biofilm performed with selective media allowed the growth of copiothrophic and oligothrophic bacteria to be estimated. The influence of fungicide (PCNB) and N-fertilizer on the number of bacteria in each biofilm was also evaluated. The pollution of water with fertilizer (being used for plant irrigation) was demonstrated to reduce the efficiency of filtration more than fungicide addition (the amount of DNA from those investigated pathogens in the water decreased with time). The amount of bacteria in SSF biofilm readily increased after application of N-fertilizer in contrast to fungicide (PCNB) addition.

Comparative genomics of bacillus amyloliquefaciens strains reveals a core genome with traits for habitat adaptation and a secondary metabolites rich accessory genome

The Gram positive, non-pathogenic endospore-forming soil inhabiting prokaryote Bacillus amyloliquefaciens is a plant growth-promoting rhizobacterium. Bacillus amyloliquefaciens processes wide biocontrol abilities and numerous strains have been reported to suppress diverse bacterial, fungal and fungal-like pathogens. Knowledge about strain level biocontrol abilities is warranted to translate this knowledge into developing more efficient biocontrol agents and bio-fertilizers. Ever-expanding genome studies of B. amyloliquefaciens are showing tremendous increase in strain-specific new secondary metabolite clusters which play key roles in the suppression of pathogens and plant growth promotion. In this report, we have used genome mining of all sequenced B. amyloliquefaciens genomes to highlight species boundaries, the diverse strategies used by different strains to promote plant growth and the diversity of their secondary metabolites. Genome composition of the targeted strains suggest regions of genomic plasticity that shape the structure and function of these genomes and govern strain adaptation to different niches. Our results indicated that B. amyloliquefaciens: (i) suffer taxonomic imprecision that blurs the debate over inter-strain genome diversity and dynamics, (ii) have diverse strategies to promote plant growth and development, (iii) have an unlocked, yet to be delimited impressive arsenal of secondary metabolites and products, (iv) have large number of so-called orphan gene clusters, i.e., biosynthetic clusters for which the corresponding metabolites are yet unknown, and (v) have a dynamic pan genome with a secondary metabolite rich accessory genome.

Current possibilities and prospects of using fungicides in forestry

Abstract The possibility of using chemicals in European forestry is extremely limited due to the binding legal regulations and specific conditions concerning the market of plant protection products. This is reflected in the limited availability of active fungicides in forestry. Due to this limitation, practitioners using fungicides in forest nurseries and forest cultivation must have substantial knowledge of the biology of pathogens to ensure satisfactorily effective protection. The work presented here provides an overview of the currently recommended fungicides in Polish forestry as well as the mechanisms of interaction between the active substances and the pathogen, the plant and mycorrhizal fungi. The risk of fungicide resistance, which has been insufficiently explored in the context of forest pathogens, is also discussed in this paper.

Phosphite fertilisers as inhibitors of Hymenoscyphus fraxineus (anamorph Chalara fraxinea) growth in tests in vitro

Abstract This study is designed to test the potential for reducing the growth of the mycelium of the fungus Hymenoscyphus fraxineus (anamorph Chalara fraxinea) by using phosphite preparations at various concentrations in vitro. The study shows that adding pure phosphite to potato dextrose agar media inhibits the development of the fungus, but if the preparation is applied in the form of ammonium phosphite (Actifos), the growth of fungus will be accelerated. Probably the addition of nitrogen contained in the product Actifos has positive effect on the mycelial growth, but pure phosphite restricts its development. These studies are preliminary and only show the potential use of phosphite to reduce the development of H. fraxineus; however, to completely confirm its operation, further research is needed in this area.

The use of phosphates in forestry

Abstract Phosphite preparations are now an important alternative in plant protection against new, invasive pathogens of the genus Phytophthora and/or Pythium. It is crucial to intervene when alien, invasive oomycetes are carried to plantations or forest stands and attack fine roots via zoospores. The aim of this paper was to demonstrate the possibility of phosphite application to induce resistance to tree pathogens. Phosphate-based fertilizers have been used successfully in nurseries, where application is relatively easy by means of foliar sprays. the traditional fungicides, which are effective in combating fungi, however, fail to control oomycetes. Instead, they mask the disease, which, in turn, causes serious damage to seedlings after they have been planted in a suitable environment. Moreover, the number of effective fungicides available for forest plant protection has continued to decrease in the last decade. The effectiveness of the chemicals is reduced due to their frequent use and their similarity in terms of the active compound or the mechanism of action. Given the low diversity of active compounds, it is necessary to monitor the development of resistance of pathogens to fungicides by means of molecular biology (sequencing and quantitative PCR). Minimising the undesired side effects of chemicals on both, mycorrhizal fungi and pathogens can be achieved by strict adherence to rigorous security measures and, where possible, frequently changing the active compounds to alternatives such as phosphites. The significance of phosphate and phosphite uptake by trees is still a matter of debate, especially under field conditions. Nevertheless, phosphites are environmentally friendly compounds, which constitute an alternative or complement to the traditional chemicals (in accordance with the Directive on Integrated Plant management).

Phytophthora quercina infections in elevated CO2 concentrations

Abstract In the last decades, a new wave of oak decline has been observed in Poland. The most important pathogenic organisms involved in this phenomenon are probably soil-borne pathogens Phytophthoragenus, especially P. quercina. In this work, we sought to test the influence of elevated CO2 concentration on the susceptibility of oaks (Quercus robur L.) to infection by P. quercina. In order to test the susceptibility of oak fine roots to infection, we applied phosphite-based fertiliser Actifos in 0.6% concentration. One-year-old oak seedlings were grown for one year in greenhouse with either an ambient atmosphere (400 ppm CO2) or an elevated (800 ppm) concentration of CO2. Oaks grown at the elevated CO2 concentration developed longer shoots as proved by statistically significant differences. However, there was no difference in the development of root systems. The application of Actifos had a positive significant effect on the development of shoots and the surface area of fine roots under the elevated CO2 concentration.

Slow sand filters for plant protection in nurseries

Filtry piaskowe w ochronie roślin przed chorobami w szkółkach Slow sand filters for plant protection in nurseries In some nurseries to irrigate plants water must be taken from natural reservoirs. Rivers and lakes are often polluted with microorganisms and a proportion of these are pathogenic to cultivated forest tree species. To avoid the infection of seedlings due to plant irrigation with contaminated water, a system of Slow Sand Filters (SSF) was designed and installed in the Kiejsze forest nursery (Koło Forest District in central Poland). Tests of slow sand filters efficiency were performed using qPCR to assess their effectiveness in reducing the concentration of bacterial DNA in filtrated water. Measurements after filtration through SSF, revealed a significant reduction in bacterial DNA. After 24 hours, 60% of Rhizobium tumefaciens was eliminated and that progressed to 71% after 48 h. In the case of Pseudomonas syringae, purification of water was even more efficient, 67% after 24 h and 74% after 48 h, and there was a similar reduction for Xanthmonas campestris (71% and 70%, respectively). These data allow us to recommend this approach to water purification as an alternative preventive method for plant protection in nurseries.