Molecular genetic detection and differentiation of <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i>, bacterial leaf streak agents of rice

The genus Xanthomonas comprises phytopathogenic bacteria which infect about 400 host species, including a wide variety of economically important plants. Xanthomonas oryzae pv. oryzicola (Fang et al., 1957) Swings et al., 1990 is the causal agent of bacterial leaf streak (BLS) being one of the most destructive bacterial diseases of rice. BLS symptoms are very similar to those of bacterial blight caused by closely related Xanthomonas oryzae pv. oryzae. X. o. pv. oryzae and X. o. pv. oryzicola and often occur in rice f ields simultaneously, so separate leaves may show symptoms of both diseases. The quarantine status and high severity of the pathogen require a highly eff icient, fast and precise diagnostic method. We have developed an assay for Xanthomonas oryzae pv. oryzicola detection using real-time polymerase chain reaction (qPCR) and PCR amplicon sequencing. The DNA samples of X. o. pv. oryzae and X. o. pv. oryzicola were obtained from the collection of CIRM-CFBR (France). To evaluate the analytical sensitivity of the assay, a vector construct based on the pAL2-T plasmid was created through the insertion of X. o. pv. oryzicola target fragment (290 bp). Primers and a probe for qPCR were selected for the hpa1 gene site. They allowed identifying all the strains the sequences of which had been loaded in the GenBank NCBI Nucleotide database before November 11, 2021. The SeqX.o.all sequencing primers were selected for the hrp gene cluster sequence, namely for the nucleotide sequence encoding the Hpa1 protein, the sequencing of which allows for eff icient differentiation of X. oryzae species. The analytical specif icity of the system was tested using the DNAs of 53 closely related and accompanying microorganisms and comprised 100 % with no false-positive or false-negative results registered. The system’s analytical sensitivity was not less than 25 copies per PCR reaction. Its eff icacy has been conf irmed using f ive different qPCR detection systems from different manufacturers, so it can be recommended for diagnostic and screening studies

Geochemical groundwater peculiarities of Paleogene sediments in S-E Western Siberia artesian basin

The geochemical peculiarities of groundwater in Paleogene deposits in southeastern part of Western Siberia artesian basin are considered in the paper. Landscape, climate, geostructural and hydrogeological conditions define the water composition and quality peculiarities in this region. It has been established that ion-saline composition, mineralization and water quality changes arre governed by the horizontal zonal distribution. Groundwater of taiga landscapes generally is in equilibrium with kaolinite and quartz, mainly involving Ca- and Mg-montmorillonite, illite, carbonate minerals, sometimes barite. Groundwater in woodland grass and grassland, together with previously mentioned minerals, is usually in equilibrium with barite, colestine, and particularly, fluorite and gypsum. As a result, all relevant elements are removed from the groundwater and their accumulation level is restricted

water chemistry are new challenges possible from coda compositional data analysis point of view

John Aitchison died in December 2016 leaving behind an important inheritance: to continue to explore the fascinating world of compositional data. However, notwithstanding the progress that we have made in this field of investigation and the diffusion of the CoDA theory in different researches, a lot of work has still to be done, particularly in geochemistry. In fact most of the papers published in international journals that manage compositional data ignore their nature and their consequent peculiar statistical properties. On the other hand, when CoDA principles are applied, several efforts are often made to continue to consider the log-ratio transformed variables, for example the centered log-ratio ones, as the original ones, demonstrating a sort of resistance to thinking in relative terms. This appears to be a very strange behavior since geochemists are used to ratios and their analysis is the base of the experimental calibration when standards are evolved to set the instruments. In this chapter some challenges are presented by exploring water chemistry data with the aim to invite people to capture the essence of thinking in a relative and multivariate way since this is the path to obtain a description of natural processes as complete as possible

The creative function of water in the formation of the world around us

The article is focused on the evolution mechanism of the ‘inert’ and living world around us, which is determined by the creative function of water. Water and igneous rocks of basic and ultrabasic compositions create an abiogenic dissipative system that never reaches an equilibrium and therefore is capable of maintaining its continuous, strictly directed, geologically long-term development and the formation of numerous new minerals that are paragenetically associated with specific geochemical types of water. This system is equilibrium-nonequilibrium. It develops in a thermodynamic area, far from an equilibrium. It is non-linear, irreversible, and internally contradictory. In this system, water has the creative function: the hydrolysis mechanism continuously dissolves some minerals, with which the system is not in equilibrium, and, at the same time, creates others minerals, with which there is an equilibrium, including the mineral that have been absent on our planet. After the occurrence of photosynthesis, the system was supplemented with organic compounds and developed into the ‘water-rock-gas-organic matter’ system. The mechanisms of this system were generally described by V.I. Vernadsky, and we suggest to name this system after him. The Vernadsky system had not only repeatedly became more and more complicated, but acquired the capability of creating more complex organic compounds from simple carbohydrates, such as proteins, lipids, more complex carbohydrates, hemoglobin etc. With time, these components developed into living organisms. Regardless of the repeated complication of the system, the basic mechanisms of its evolution remain essentially the same, and water has preserved and enhanced its creative function through dissolving simple compounds and creating more complex ones. An important factor in the continuous complication of the system is the natural water cycle