The structure of microbial communities in redoximorphic microsites of Gleysol

Microbial communities were studied in redoximorphic microsites of highly heterogeneous Gleysol at a mm scale using 16S and 18S amplicon sequencing to demonstrate if the composition of soil microbes reflects the differences in ferric and ferrous micro-sites. In both explored gley horizons with redoximorphic features (Bg2 and Cg), ferric mottles were significantly enriched with total P and Fe and depleted of O, Si, Al, K and Ca compared with the adjacent ferrous groundmass (SEM–EDS). Ferric mottles were determined as Fe oxide coatings and hypocoatings. In Bg2, both prokaryotic and micro-eukaryotic communities differed significantly between mottles and groundmass in composition of operational taxonomic units (OTUs) and in proportions of phyla, reflecting heterogeneities in the soil properties there. Mottles in Bg2 were characterized by increased proportion of Proteobacteria, decreased proportion of Acidobacteriota among prokaryotes and by dominance of a single proteobacterial OTU from Anaplasmataceae compared to all other samples. The composition of micro-eukaryotes showed an opposite trend, as micro-eukaryotes of Bg2 groundmass were unique among the other horizons, while micro-eukaryotes of Bg2 mottles had similar composition to neighbouring horizons. Microbial communities of adjacent samples were not more similar to each other than communities of randomly selected ones in Bg2 horizon. That suggests that at mm scale, the sample distance does not represent the driving factor of microbial community composition and that the adjacent samples differ rather due to physicochemical factors. The spatial organization of microbial communities revealed in Bg2 has not reappeared in similarly organized Cg horizon, probably due to other overriding factors. The differences revealed between Bg2 and Cg horizons, including granulometric composition, content of crystalline Fe, exchangeable Al, and organic carbon, as well as exposition to groundwater, were discussed as possible reasons of the distinct organization in Cg. The similarity of pro−/eukaryotic communities of adjacent and non-adjacent couples suggests no distance decay pattern at a mm scale. The agreement between patchiness in soil properties and microbial communities was revealed for the first time and confirms the importance of microscale patterns in soil.     

Comparative Analysis of the Major Metabolites of Ukrainian Saffron Samples by HPLC

Plant Foods for Human Nutrition - Crocus sativus L. is one of the most valuable crops, which stigmas are used as the food supplement and herbal medicine. In Ukraine, the cultivation of C. sativus...     

Soil respiration of karst grasslands subjected to woody‐plant encroachment

The transition of grasslands to forests influences many ecosystem processes, including water and temperature regimes and the cycling of nutrients. Different components of the carbon biogeochemical cycle respond strongly to woody plant encroachment; as a consequence, the carbon balance of the invaded grasslands can change markedly. In our research, we studied the response of soil respiration (R_S) to natural succession of calcareous grassland. We established two research sites, called grassland and invaded site, at each of which eddy flux measurement were also performed. Within these sites, triplicate plots were fenced for soil flux measurements. At the invaded site, measurements were performed for forest patches and grassy spaces separately. Soil respiration was strongly dependent on temperature and reached 8–12 µmol CO₂ m^?2 s^?1 in mid‐summer; it was greater at the grassland than at the invaded site. R_S dependence on temperature and soil water content was similar between the different vegetation covers (grassland, gaps and forest patches). At a reference temperature of 10°C, the average R_S was 2.71 µmol CO₂ m^?2 s^?1. The annual sums of R_S were also similar between years and sites: 1345 ± 47 (2009) and 1150 ± 37 g C m^?2 year^?1 (2010) for grassland and 1324 ± 26 (2009) and 1268 ± 26 g C m^?2 year^?1 (2010) for the invaded site, which is at the upper range of the values reported in the literature. Cumulative R_S peaked in July, with about 200 g C m^?2. Large mid‐summer R_S rates rely on strong biological activity supported by high, but non‐extreme soil temperatures and by regular summer precipitation. A coupling of photosynthesis and R_S was revealed by a 24‐hour measurement, which showed asymmetrical clockwise hysteresis patterns.     

Spatial patterns and temporal changes of heavy metal distributions in river sediments in a region with multiple pollution sources

Purpose

The main purpose of this study was to evaluate temporal and regional variability of contamination by heavy metals (HMs) in river sediments using their enrichment factors (EFs) and benchmarking according to sediment quality guidelines (SQGs). The Zlin region in the Czech Republic (Morava and Drevnice River basins) represents a model area where several regionally specific ecological risk assessment studies have recently been conducted with a focus on organic pollution, eco-toxicity, geological, and geochemical characteristics.

Materials and methods

Four consecutive sediment sampling campaigns were undertaken in spring and autumn 2005–2006. Aqua-regia leachable content of Cd, Co, Cr, Cu, Ni, Pb, Sb, V, and Zn in surface sediments from 14 sites was analyzed using ICP-MS, and Hg content was analyzed using AMA-254 analyzer. EFs were calculated to identify the human impact on pollution in the area. Comparisons to SGQs were conducted to identify the areas and HMs of greatest risk.

Results and discussion

Calculation of EFs contributed to the effective clustering of HMs. Median EFs of Co, Ni, and V ranged from 0.9 to 1.4 at all sites indicating concentrations very close to natural geological background levels. There was greater enrichment at locally polluted sites, the highest in the cases of Cd, Sb, Hg, and Cr. Widespread influence of diffuse HM sources (traffic, agriculture, and urban wastes) was apparent from elevated concentrations of Pb, Cu, and Zn at all sites. EF values also helped to identify the greatest temporal changes and shifts in HMs contamination between adjacent sites caused by 50-year recurrence interval floods in early spring 2006. The impact was most apparent in downstream sites; namely directly below the confluence of the two major rivers.

Conclusions

The overall contamination of HMs in the region was classified as low-to-moderate with significantly contaminated sub-areas. The study showed relatively stable spatial distributions of HMs, indicating potential sources of pollution. Cu was identified as the HM of greatest risk. The study emphasizes the necessity of considering both environmental circumstances and background HM occurrence to prevent misinterpretation of the pollution situation. The use of EFs which include grain size proxy normalization and HM background levels, along with the comparison of the detected concentrations to SQGs, proved an efficient way to identify hazardous contamination from anthropogenic sources.     

Speciation of 90Sr and other metal cations in artificially contaminated soils: the influence of bone sorbent addition

Purpose

The influence of bone sorbent addition onto distribution of ⁹⁰Sr in artificially contaminated soil was preliminary studied to assess the possibility of biogenic apatite utilization for reduction of ⁹⁰Sr mobility and availability. Simultaneously, the disruption of soil micro- (Cd, Zn, Co, Cu, Cr, and Ni,) and macroelements (Al, Fe, Mn, K, Mg, and Ca) upon Sr contamination and sorbent addition was monitored.

Materials and methods

The model soil was contaminated by inactive Sr, in the form of Sr(NO₃)₂ solution. As a soil additive, sorbent obtained by annealing bovine bones at 400 °C (B400) was applied. Both the uncontaminated and Sr-contaminated soils were mixed with 1, 3, 5, and 10 % of sorbent, suspended in distilled water (initial pH?5; solid/solution ratio, 1:2), and equilibrated for 15 days on a rotary shaker. Solid residues were subjected to modified Tessier five-step sequential extraction analysis, and the amounts of chosen metals in each fraction were determined by inductively coupled plasma–optical emission spectroscopy.

Results and discussion

In the original soil, Sr was mainly found in exchangeable (61 %) and carbonate phase (16 %), whereas after contamination, the content of Sr in exchangeable phase raised to 94 %. With the addition of B400, the decrease in Sr amounts in exchangeable fraction was detected, whereas increase occurred mainly in operationally defined carbonate phase and in the residual. High level of Sr contamination caused the increase in Zn, Ni, Co, Cu, Cd, and Mn and decrease in Ca content in exchangeable phase. Sorbent addition resulted in a migration of these cations to less soluble fractions. This effect was observed even for major soil elements such as Fe, Al, and Mn, regardless of the excessive amounts of Sr in the soil.

Conclusions

Mixing the soil with B400 resulted in reduced Sr mobility and bioavailability. B400 acted as a stabilizing agent for heavy metals, as well. Apatite distinguished selectivity towards heavy metals may interfere with the Sr immobilization and disrupt original cation distribution. Further studies should include more realistic (lower) Sr concentrations in the soil, different soil types, pH, and longer incubation times.     

Incidence of eyespot on winter triticale and quantification of Oculimacula spp. population using real-time PCR in Lithuania

The aim of this study was to estimate the incidence of eyespot in winter triticale crops in different agro-ecological zones of Lithuania and to use real-time polymerase chain reaction (Real-time PCR) to determine the dominant Oculimacula fungi populations in winter triticale crops grown in Lithuania, which has not been previously established. Differences in common fungicide usage practices in triticale crops between Lithuanian agro-ecological zones suggest that the composition of Oculimacula fungi differs across the country. From 2008 to 2012, a total of 70 winter triticale fields were reviewed for eyespot incidence, and the presence of eyespot was identified in 93.5% of the fields tested. Over this five-year period, the disease incidence averaged 32%. The highest incidence (34.8%) of eyespot was found in the Middle Lowland zone of Lithuania, the lowest (25.8%) was in the Eastern zone and an intermediate incidence (30.2%) was observed in the Western zone. During the 2010–2012 period, Oculimacula acuformis was the most prevalent Oculimacula spp. in the majority of triticale crops inspected. Only in 3 cases out of 27 was the amount of Oculimacula yallundae DNA higher than that of O. acuformis. According to our results, the incidence of eyespot in triticale varied greatly and could be of economic importance in some fields. The predominance of O. acuformis over O. yallundae is an important consideration in the choice of fungicides for eyespot control.     

Cruciferous plants' use as biofumigants in potato against wireworms

In Slovenia, only tefluthrin is registered for controlling wireworms. In order to investigate the potential alternatives for controlling wireworms in potato, the field experiment was conducted in the period from 2011 (year 1) to 2012 (year 2). As alternatives, different Brassica crops (year 1: rapeseed, oilseed radish and white mustard; year 2: rapeseed, oilseed radish, oilseed rape, kale and white mustard) were tested (fresh foliage was incorporated into the soil by ploughing) for their biofumigant effect. Results of our investigation showed that in both years the potato yield was affected by measures of pest control; however, none of the tested biofumigant plants proved to be a potentially promising candidate in wireworm control. The rapid release of volatiles after plant chopping before and during incorporation into the soil could be the reason of inefficacy in our experiment. In our study, most wireworm damage occurred on biggest potato tubers. Moreover, edge effect of the field played an important role in our experiment in year 1. Treatment (chemical or biological) of wireworms only at the edge part of the field could offer a cost-effective, time-saving and environmentally more friendly way of controlling studied pest organism.     

Chemical Characterization of Sewage Sludges in Chile and Their Potential Utilization as Amendment to Reclaim Soils for Forestation Purposes

Soils open for forestation in Chile are characterized by their very low organic carbon content; therefore, new forest plantations, needed to restore soil ecological equilibria, are scarcely developed. Stabilized sewage sludge contain organic compounds which have been demonstrated can serve as good soil amendments. To evaluate their actual uses in Chile it is necessary to characterize the carbon (C)-distribution pattern of such sludges in order to foresee their potential contribution for soil reclamation and plant growth, acting both as a source of stable C-reservoir and as readily available C-source.

The molecular weight (m.w.) distribution and carbon balance in Chilean sewage sludges are quite similar to soil humus and some woody by-products, as sawdust and bark dust. Total C varies from 30 to 35%, N from 5 to 9%, and P from 10,000 to 12,000 ppm. No significant content was found for heavy metals.

The C-balance indicates that around 70% of total-C is under stabilized forms as humine and humic macromolecule structures. The sewage sludge can be considered as good amendments for forest soils, especially in areas heavily eroded and depleted of natural humus. Their soluble-C fractions (13% of total-C) will serve as good energy starter source to strengthen indigenous soil microbial ecology, while their high m.w. fractions (humic acid-like and humine-like macromolecules) will serve both as good humus reservoir and as microelement frame in soils treated with such sewage sludges.     

RaBoT: a rarefaction-by-bootstrap method to compare genome-wide levels of genetic diversity

Context

No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary.

Aims

We developed a method to compare genome-wide diversity estimates while taking into account—and factoring out—variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels.

Methods

An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers.

Results

RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots.

Conclusion

RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).