Search

Studies on the impact of human agricultural activities on the soil microbiome and soil quality are extremely important, but such studies on floodplains in river valleys are lacking. The aim of this preliminary study was to determine the impact of blackcurrant cultivation on Fluvisols located in the Vistula River valley (Poland). The dehydrogenases (DHa) and phosphatases (acid-AcP, and alkaline-AlP) activities, carbon (MBC) and nitrogen (MBN) contents of the microbial biomass, the metabolic potential of the microbial community (EcoPlate™ Biolog) and taxonomic diversity of the soil microbiome were determined (next-generation sequencing (NGS) of the 16S rRNA gene). Enzymatic activity and metabolic potential and diversity (EcoPlate™) were higher in the soils from meadows, but MBC and MBN and biodiversity indices derived from NGS were higher in the cultivated soils. It can be confirmed that human activities affect the physicochemical, biological and microbiological parameters of Fluvisols. This may indicate that microorganisms are numerically more abundant and taxonomically more diverse in the cultivated soils, but are more active in the soils from meadows.

Deadwood plays an important role in forest ecology; its degradation and, therefore, carbon assimilation is carried out by fungi and bacteria. To quantify the abundance and distribution of microbial taxa inhabiting dead spruce logs fallen over a span of 50 years and the soil beneath, we used taxonomic profiling with NGS sequencing of hypervariable DNA fragments of ITS1 and 16S V3-V4, respectively. The analysis of sequencing data revealed a high level of diversity in microbial communities participating in the degradation of spruce logs. Differences in the relative abundance of microbial taxa between the samples of the wood that died in 1974 and 2014, and of the soil in its immediate vicinity, were visible, especially at the genus level. Based on the Lefse analysis significantly higher numbers of classified bacterial taxa were observed in the wood and soil samples from 2014 (wood: 1974-18 and 2014-28 taxa; soil: 1974-8 and 2014-41 taxa) while the number of classified fungal taxa was significantly higher in the wood and soil samples from 1974 (wood: 1974-17 and 2014-9 taxa; soil: 1974-57 and 2014-28 taxa). Most of the bacterial and fungal amplicon sequence variants (ASVs) unique to wood were found in the samples from 1974, while those unique to soil were detected in the samples from 2014. The ATR-FTIR method supported by CHN analysis revealed physicochemical changes in deadwood induced by the activity of fungal and bacterial organisms.

The isolation of new bacterial strains from the natural environment can lead to the detection of microorganisms of potential practical importance. The characterization of such microorganisms can be carried out using classical microbiological and molecular biology methods. Currently, studies of newly detected microorganisms are based on sequencing techniques. Sequencing of the full genome can provide information about the origin of the strain, its taxonomic status, and phenotypic characteristics. The studies were conducted using the bacteria Achromobacter sp. 77Bb1 isolated from the maize crop rhizosphere. The bacterial genome was sequenced using Illumina 2 × 150 nt technology. The obtained sequences were analyzed using bioinformatics methods, resulting in 57 contigs and genome containing 6,651,432 nt. Phylogenetic analysis based on 16S rRNA gene sequences enabled the assignment of the analyzed bacteria to the genus Achromobacter. The obtained genome contained genes for 4855 proteins with functional assignment. Some of these genes were connected with xenobiotics biodegradation and metabolisms. All genes for aminobenzoate degradation and almost all for benzoate and styrene degradation were found in the analyzed genome, suggesting that the isolated strain has the potential to be used in natural bioremediation methods.

Terrestrial plants act as ecosystem engineers modifying the flow of energy and matter and creating new habitats for other organisms. This vital concept also encompasses plants' effects on landforms and soils, crucial components of forested landscapes worldwide. In the present study, we investigate how trees through their roots and symbiotic organisms influence soil-weathering processes. The aim of the study was to answer one of the big questions in Earth sciences: how do biological agents, including fungi, acting at the critical interface between the biosphere and the abiotic environment, shape soil and landscape evolution? Within the present study we ask what is the level of fungal activity within root systems of trees and how can it influence biological weathering. The area of interest is in the Poprad River gorge in the southern part of the Sącz Beskidy Mountains, the Outer Western Carpathians. We applied the following analyses: 1) determination of the structural diversity of fungi (ITS1) and 2) assessment of the metabolic profile of soils (Biolog FFPlates). The highest average number of classified genera were fungi which simultaneously carried out pathotrophic, saprotrophic and symbiotrophic functions. Boletales, Agaricales, Cantharellales and Archaeorhizomycetales were the most abundant orders, but in one sample we also found a particularly high proportion of the order Mortierellales. The order Boletales and its family Boletaceae were significantly enriched in rock crack samples, whereas the highest number of differentially abundant taxa was observed in reference samples. The most frequently utilised substrates by fungi were: glycyl-L-glutamic acids, L-ornithine, L-phenylalanine, L-proline, D-galacturonic acid, fumaric acids, D-saccharic acids, succinic acids and N-acetyl-D-glucosamine. Our study demonstrates that the fungal community in the root zone is geochemically active and the organic acids secreted by plant roots in oligotrophic conditions and nutrient limitations significantly affect soil weathering.

Fungi from the genus Diaporthe have been reported as plant pathogens, endophytes, and saprophytes on a wide range of host plants worldwide. Their precise identification is problematic since many Diaporthe species can colonize a single host plant, whereas the same Diaporthe species can inhabit many hosts. Recently, Diaporthe has been proven to be a rich source of bioactive secondary metabolites. In our initial study, 40 Diaporthe isolates were analyzed for their metabolite production. A total of 153 compounds were identified based on their spectroscopic properties—Ultraviolet-visible and mass spectrometry. From these, 43 fungal metabolites were recognized as potential chemotaxonomic markers, mostly belonging to the drimane sesquiterpenoid-phthalide hybrid class. This group included mainly phytotoxic compounds such as cyclopaldic acid, altiloxin A, B, and their derivatives. To the best of our knowledge, this is the first report on the metabolomic studies on Diaporthe eres species complex from fruit trees in the South-Eastern Poland. The results from our study may provide the basis for the future research on the isolation of identified metabolites and on their bioactive potential for agricultural applications as biopesticides or biofertilizers.

As the market indicates a growing interest in organically grown fruit, there is a need for biostimulants to counter the adverse effects of pathogenic fungi and fungal-like-pathogens. Four microbial pathogens (Botrytis cinerea, Verticillium sp., Phytophthora sp., and Colletotrichum sp.) which are the most often causes of strawberry diseases were selected. Five kinds of biostimulants (C1, C2, C3, C4, and C5) containing bacterial consortia were developed to combat the pathogens. The antagonistic effect of selected microorganisms against strawberry pathogens was observed. The effectiveness of various beneficial bacteria in combating fungal pathogens of cv. Honeoye strawberries was compared and the impact of their activity on fruit quality was assessed. The most significant effect on the strawberry firmness was found for the C2 consortium, which provided the strawberries infected with the pathogens group (MIX: B. cinerea, Verticillium sp., Phytophthora sp., and Colletotrichum sp.) with a 140% increase in maximum load in a puncture test compared to the positive control (C0). Strawberries contaminated with Phytophthora sp. after the application of Consortium C4 (C4) showed the largest increase (127%) in soluble solid content (SSC) when compared to the C0. Fruit contaminated with Colletotrichum sp. and B. cinerea after the application of C2 and Consortium 5 (C5), respectively, had the highest levels of anthocyanins and total phenolic content, when compared to C0. The largest increase, which reached as high as 25%, in D-galacturonic acid content was observed for the group of pathogens after Consortium 1 (C1) application. The extraction of strawberry pectin allowed for the study of the rheological properties of pectin solutions; on this basis, strawberry pectin from the control (NC) was distinguished as it showed the highest viscosity (0.137–0.415 Pas). Taking into account the individual effects of bacteria on strawberry pathogenic fungi and fungal-like-pathogens, it is possible to reduce the adverse effects of fungal disease and to improve the properties of strawberries by selecting the appropriate bacterial consortium. Interactions between microorganisms are often complex and not fully understood, which suggests the need for further research in this direction.

The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.

Recently, Diaporthe has been considered the most frequently isolated genera of endophytic fungi, having a broad spectrum of host plants and a worldwide distribution. The endophytic Diaporthe strain used in the present work came from the Fungal Collection of Phytopathology and Mycology Subdepartment, University of Life Sciences in Lublin (Poland), and was isolated from healthy Prunus domestica shoots during previous studies. Due to the possibility of using the Diaporthe endophytes as a promising option for plant disease management, the main goal of the research was to study the antagonistic effect of endophytic Diaporthe strain against six phytopathogens: Verticillium dahliae, Botrytis cinerea, Fusarium avenaceum, F. sprotrichioides, Alternaria alternata, and Trichothecium roseum based on the dual culture assay and to determine the catabolic profile of the endophyte by using Biolog FF Plates. The dual-culture test assay revealed the ability of the endophytic Diaporthe to limit the growth of all tested pathogens. The growth inhibition percentage ranged from 20% (V. dahliae) to 40% (T. roseum). A distinct zone of inhibition occurred between the endophytic Diaporthe and the pathogens T. roseum, V. dahliae, and B. cinerea in the co-growth combinations. As for the catabolic profile results, the most intensive utilization of carbon substrates was observed after 168 h of incubation. The growth of the analyzed strain was observed on 79 media containing carbohydrates, carboxylic acids, amino acids, amines and amides, polymers, and others. The most effective decomposition was observed in the polymers group, the least in amines and amides. Molecular identification indicated that this strain was closely related to the Diaporthe eres species complex.

Smelter waste deposits pose environmental and health threats and require remediation actions. Phytostabilisation techniques, based on soil amendments, help to establish plant cover and limit the secondary emission of potentially toxic trace elements. However, methods to optimize their effectiveness are needed. The application of bacterial inoculants in combination with soil amendments in the remediation of soils and wastes contaminated with metals still has not been extensively tested. Therefore, the aim of this study was to determine the effectiveness of indigenous (Streptomyces sp., Pseudomonas sp.) and foreign (Streptomyces costaricanus) strains of bacteria in supporting grass growth on extremely contaminated waste slag. They were applied alone and in combination with compost mixed with phosphate fertilizer or iron oxide. The tested strains improved plant growth and increased plant availability of phosphorus. The interaction of the soil amendments and some bacterial strains also stimulated a decrease in the extractability of metals, likely through the phosphate-induced precipitation of lead. Our data show that the effectiveness of soil amendments in the phytostabilisation of heavily polluted smelter deposits can be enhanced by plant growth-promoting bacteria (PGPB).

As an adaptation to unfavorable conditions, microorganisms may represent different phenotypes. Azolla filiculoides L. is a hyperaccumulator of pollutants, but the functions of its microbiome have not been well recognized to date. We aimed to reveal the potential of the microbiome for degradation of organic compounds, as well as its potential to promote plant growth in the presence of heavy metals. We applied the BiologTM Phenotypic Microarrays platform to study the potential of the microbiome for the degradation of 96 carbon compounds and stress factors and assayed the hydrolytic potential and auxin production by the microorganisms in the presence of Pb, Cd, Cr (VI), Ni, Ag, and Au. We found various phenotype changes depending on the stress factor, suggesting a possible dual function of the studied microorganisms, i.e., in bioremediation and as a biofertilizer for plant growth promotion. Delftia sp., Staphylococcus sp. and Microbacterium sp. exhibited high efficacy in metabolizing organic compounds. Delftia sp., Achromobacter sp. and Agrobacterium sp. were efficient in enzymatic responses and were characterized by metal tolerant. Since each strain exhibited individual phenotype changes due to the studied stresses, they may all be beneficial as both biofertilizers and bioremediation agents, especially when combined in one biopreparation.

The aims of the study were (1) to recognize the structure of bacteria diversity in Technosols developed from mine spoils containing iron (Fe) sulphides with the use of culture-independent technique, and (2) to determine microbial metabolic activities, in the context of their potential to be an adequate indicators of soil properties being the consequence of land reclamation. The study site was located in the vicinity of the abandoned Fe sulphide and uranium mine in Rudki village (Holy Cross Mts., Poland). Three soil profiles with different chemical properties (pH, content of carbonates, soil salinity, content of total organic carbon and total nitrogen) were studied. Biodiversity was determined with the use of meta-barcoding of 16S rRNA community profiling analysis based on the hypervariable V3-V4 region of 16S rRNA gene (MiSeq, Illumina). The catabolic fingerprinting of soil microbial communities was evaluated with the use of Biolog®EcoPlates™ System. It was evidenced that changes in microbial structure and their metabolic activity were the consequence of a combined effect of both the soil depth and soil chemical properties being the final result of reclamation process. Consequently, microbial indicators (from phyla to genera level) indirectly testifying about success or ineffectiveness of reclamation in technogenic soils were recommended. To our best knowledge, the present study is the first insight into Polish Technosols biodiversity and catabolic activity.

The aim of this study was to analyse the genetic and phenotypic differentiation of bacteria isolated from root nodules of Trifolium rubens, a rare clover species. The symbiotic compatibility of selected isolates was investigated using two agronomically important plants, red clover (Trifolium pratense L.) and pea (Pisum sativum L.). A high genetic diversity of analysed strains was shown using the Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) method. Most of the strains showed a high similarity to R. leguminosarum in the 16S rRNA sequence. Two strains were identified as Agrobacterium spp. There was a strong positive correlation between fresh clover weight and the number of root nodules and a statistically significant increase in the number of the root nodules in selected strains compared to the negative control. Phenotypic tests and BIOLOG analysis showed the ability of the analysed strains to grow in different experimental conditions (pH = 6–10, 0.5–3% NaCl, different carbon and nitrogen sources), which makes them suitable for application as an agronomically important factor.