Svornostia abyssi gen. nov., sp. nov. isolated from the world's deepest silver-uranium mine currently devoted to the extraction of radon-saturated water.

A Gram-stain-positive, rod-shaped, aerobic, motile bacterium, J379T, was isolated from radioactive water spring C1, located in a former silver-uranium mine in the Czech Republic. This slow-growing strain exhibited optimal growth at 24-28 °C on solid media with <1 % salt concentration and alkaline pH 8-10. The only respiratory quinone found in strain J379T was MK-7(H4). C18 : 1 ω9c (60.9 %), C18 : 0 (9.4 %), C16 : 0 and alcohol-C18 : 0 (both 6.2 %) were found to be the major fatty acids. The peptidoglycan contained directly cross-linked meso-diaminopimelic acid. Phylogenetic reconstruction based on the 16S rRNA gene sequences and the core-genome analysis revealed that strain J379T forms a separate phylogenetic lineage within the recently amended order Solirubrobacterales. A comparison of the 16S rRNA gene sequences between strain J379T and other members of the order Solirubrobacterales showed <96 % similarity. This analysis revealed that the closest type strains were Parviterribacter kavangonensis D16/0 /H6T (95.2 %), Capillimicrobium parvum 0166_1T (94.9 %) and Conexibacter arvalis KV-962T (94.5 %). Whole-genome analysis showed that the closest type strain was Baekduia soli BR7-21T with an average nucleotide identity of 78 %, average amino acid identity of 63.2 % and percentage of conserved proteins of 48.2 %. The G+C content of the J379T genomic DNA was 71.7 mol%. Based on the phylogenetic and phylogenomic data, as well as its physiological characteristics, strain J379T is proposed to represent a type strain (DSM 113746T=CCM 9300T) of Svornostia abyssi gen. nov. sp. nov. within the family Baekduiaceae.

Species phylogeny, ecology, and root traits as predictors of root exudate composition.

Root traits including root exudates are key factors affecting plant interactions with soil and thus play an important role in determining ecosystem processes. The drivers of their variation, however, remain poorly understood. We determined the relative importance of phylogeny and species ecology in determining root traits and analyzed the extent to which root exudate composition can be predicted by other root traits. We measured different root morphological and biochemical traits (including exudate profiles) of 65 plant species grown in a controlled system. We tested phylogenetic conservatism in traits and disentangled the individual and overlapping effects of phylogeny and species ecology on traits. We also predicted root exudate composition using other root traits. Phylogenetic signal differed greatly among root traits, with the strongest signal in phenol content in plant tissues. Interspecific variation in root traits was partly explained by species ecology, but phylogeny was more important in most cases. Species exudate composition could be partly predicted by specific root length, root dry matter content, root biomass, and root diameter, but a large part of variation remained unexplained. In conclusion, root exudation cannot be easily predicted based on other root traits and more comparative data on root exudation are needed to understand their diversity.

Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant.

An actinobacterial strain, designated A5X3R13T, was isolated from a compost soil suspension supplemented with extracellular material from a Micrococcus luteus-culture supernatant. The strain was cultured on tenfold-diluted reasoner's 2A agar. The cells were ovoid-to-rod shaped, non-motile, Gram-stain-positive, oxidase-negative, catalase-positive and had a width of 0.5 µm and a length of 0.8-1.2 µm. The results of both 16S rRNA-based phylogenetic and whole-genome analyses indicate that A5X3R13T forms a distinct lineage within the family Nocardioidaceae (order Propionibacteriales). On the basis of the 16S rRNA gene sequence, A5X3R13T was closely related to Aeromicrobium terrae CC-CFT486T (96.2 %), Nocardioides iriomotensis IR27-S3T (96.2 %), Nocardioides guangzhouensis 130T (95.6 %), Marmoricola caldifontis YIM 730233T (95.5 %), Aeromicrobium alkaliterrae KSL-107T (95.4 %), Aeromicrobium choanae 9H-4T (95.4 %), Aeromicrobium panaciterrae Gsoil 161T (95.3 %), and Nocardioides jensenii NBRC 14755T (95.2 %). The genome had a length of 4 915 757 bp, and its DNA G+C content was 68.5 mol %. The main fatty acids were 10-methyl C17 : 0, C16 : 0, C15 : 0, C18 : 0, C17 : 0 and iso-C16 : 0. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. MK-9(H4) was the predominant respiratory quinone. The peptidoglycan type was A3γ (A41.1) and contained alanine, glycine, glutamic acid and ll-diaminopimelic acid in a molar ratio of 1.2 : 0.9 : 1.0 : 0.8. On the basis of the results of the phylogenetic and phenotypic analyses and comparisons with other members of the family Nocardioidaceae, strain A5X3R13T is proposed to represent a novel species within a novel genus, for which the name Solicola gregarius gen. nov., sp. nov. is proposed. The type strain is A5X3R13T (=DSM 112953T=NCCB 100840T).

Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden.

A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6T, was classified in the family Chromobacteriaceae, class Betaproteobacteria, and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with Silvimonas terrae (98.20 % similarity) and Silvimonas amylolytica (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69-81 % with the members of genera Silvimonas and Amantichitinum. On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus Silvimonas with the designation Silvimonas soli 17-6T (=DSM 115342T=CCM 9308T).

Plant-soil interactions in the native range of two congeneric species with contrasting invasive success.

The aim of this study was to compare plant-soil interactions in the native range of two congeneric European species differing in their invasive success in the world: a globally invasive Cirsium vulgare and non-invasive C. oleraceum. We assessed changes in soil nutrients and soil biota following soil conditioning by each species and compared performance of plants grown in self-conditioned and unconditioned soil, from which all, some or no biota was excluded. The invasive species depleted more nutrients than the non-invasive species and coped better with altered nutrient levels. The invasive species had higher seedling establishment which benefited from the presence of unconditioned biota transferred by soil filtrate. Biomass of both species increased in soil with self-conditioned soil filtrate and decreased in soil with self-conditioned whole-soil inoculum compared to unconditioned filtrate and inoculum. However, the increase was smaller and the decrease greater for the invasive species. The invasive species allocated less biomass to roots when associated with harmful biota, reducing negative effects of the biota on its performance. The results show that in the native range the invasive species is more limited by self-conditioned pathogens and benefits more from unconditioned mutualists and thus may benefit more from loss of effectively specialized soil biota in a secondary range. Our study highlights the utility of detailed plant-soil feedback research in species native range for understanding factors regulating species performance in their native range and pinpointing the types of biota involved in their regulation.

Arthrobacter polaris sp. nov., a new cold-adapted member of the family Micrococcaceae isolated from Antarctic fellfield soil.

An aerobic, Gram-stain-positive and non-spore-forming strain, designated C1-1T, was isolated from a fellfield soil sample collected from frost-sorted polygons on Jane Col, Signy Island, Maritime Antarctic. Cells with a size of 0.65-0.9×1.2-1.7 µm have a flagellar motile apparatus and exhibit a rod-coccus growth cycle. Optimal growth conditions were observed at 15-20 °C, pH 7.0 and NaCl concentration up to 0.5 % (w/v) in the medium. The 16S rRNA gene sequence of C1-1T showed the highest pairwise similarity of 98.77 % to Arthrobacter glacialis NBRC 113092T. Phylogenetic trees based on the 16S rRNA and whole-genome sequences revealed that strain C1-1T belongs to the genus Arthrobacter and is most closely related to members of the 'Arthrobacter psychrolactophilus group'. The G+C content of genomic DNA was 58.95 mol%. The original and orthologous average nucleotide identities between strain C1-1T and A. glacialis NBRC 113092T were 77.15 % and 77.38 %, respectively. The digital DNA-DNA relatedness values between strain C1-1T and A. glacialis NBRC 113092T was 21.6 %. The polar lipid profile was composed mainly of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The predominant cellular fatty acids were anteiso-C15 : 0 (75 %) and anteiso-C17 : 0 (15.2 %). Menaquinone MK-9(H2) (86.4 %) was the major respiratory quinone in strain C1-1T. The peptidoglycan type was determined as A3α (l-Lys-l-Ala3; A11.6). Based on all described phylogenetic, physiological and chemotaxonomic characteristics, we propose that strain C1-1T (=DSM 112353T=CCM 9148T) is the type strain of a novel species Arthrobacter polaris sp. nov.

Pedomonas mirosovicensis gen. nov., sp. nov., a bacterium isolated from soil with the aid of Micrococcus luteus culture supernatant containing resuscitation-promoting factor.

An orange-golden iridescent culture, designated A1X5R2T, was isolated from a compost soil suspension which was amended with Micrococcus luteus NCTC 2665T culture supernatant. The cells were non-motile, Gram-stain-negative, 0.4-0.5 µm wide and 0.7-1.4 µm long. The 16S rRNA-based phylogenetic and whole-genome analyses revealed that strain A1X5R2T forms a distinct lineage within the family Sphingosinicellaceae and is closely related to members of the genus Sphingoaurantiacus (S. capsulatus, 93.04 % similarity, and S. polygranulatus, 92.77 %). The organism grew at 22-47 °C (optimal at 37 °C), salinity <3 % (optimal at 1.5 %) and at pH 7. The major respiratory quinone was ubiquinone-10, but a small quantity of ubiquinone-9 was also detected The major polyamine was homospermidine, but a small quantity of putrescine was also detected. The strain contained C18  :  1ω7c, C16 : 0, C16 : 1 ω7c and C18 : 0 as the major fatty acids. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, sphingoglycolipid, diphosphatidylglycerol, two unidentified phospholipids and three unidentified amino lipids. The DNA G+C content was 64.9 mol%. According to the results of phylogenetic and phylogenomic analyses, as well as its physiological characteristics, strain A2X5R2T represents the type species of a novel genus within the family Sphingosinicellaceae. The name Pedomonas mirosovicensis gen. nov., sp. nov. is proposed, with the type strain being A1X5R2T (=NCCB 100839T=DSM 112829T).

Key parameter optimization using multivariable linear model for the evaluation of the in vitro estrogenic activity assay in T47D cell lines (CXCL-test).

In comparison with analytical tools, bioassays provide higher sensitivity and more complex evaluation of environmental samples and are indispensable tools for monitoring increasing in anthropogenic pollution. Nevertheless, the disadvantage in cellular assays stems from the material variability used within the assays, and an interlaboratory adaptation does not usually lead to satisfactory test sensitivities. The aim of this study was to evaluate the influence of material variability on CXCL12 secretion by T47D cells, the outcome of the CXCL-test (estrogenic activity assay). For this purpose, the cell line sources, sera suppliers, experimental and seeding media, and the amount of cell/well were tested. The multivariable linear model (MLM), employed as an innovative approach in this field for parameter evaluation, identified that all the tested parameters had significant effects. Knowledge of the contributions of each parameter has permitted step-by-step optimization. The most beneficial approach was seeding 20,000 cells/well directly in treatment medium and using DMEM for the treatment. Great differences in both basal and maximal cytokine secretions among the three tested cell lines and different impacts of each serum were also observed. Altogether, both these biologically based and highly variable inputs were additionally assessed by MLM and a subsequent two-step evaluation, which revealed a lower variability and satisfactory reproducibility of the test. This analysis showed that not only parameter and procedure optimization but also the evaluation methodology must be considered from the perspective of interlaboratory method adaptation. This overall methodology could be applied to all bioanalytical methods for fast multiparameter and accurate analysis.

Separation of regioisomers and enantiomers of triacylglycerols containing branched fatty acids (iso and/or anteiso).

A combination of two chromatographic and one enzymatic methods was used for identification of the molecular species of triacylglycerols (TAGs) from Streptomyces avermitilis. Streptomyces avermitliswas cultured on various carbon sources and the ratio of iso- (i-FAs), anteiso- (ai-FAs), and straight-chain- (n-FAs) fatty acids was modified by precursor-directed biosynthesis. Saturated TAGs were separated from other lipids (including TAGs containing unsaturated FAs) using Ag+ ion cartridges. Analysis of TAGs wereperformed by RP-HPLC/ESI+ tandem mass spectrometry. Both the synthetically prepared sn-TAGs and the natural mixture of TAGmolecular species of wereseparated and identified by tandem MS. The structures of synthetic TAGs werefurther confirmed by pancreatic lipase, which cleaves sn-TAGs into sn-2-monoacylglycerols. The retention times (tR) of the individual regioisomers and enantiomers were found to be depend on the structure of the TAGs. If one branched acyl (iso or anteiso) is present in the TAG molecule, then the elution order is enantiomer (n/n/br), opposite enantiomer (br/n/n), regioisomer (n/br/n). In the case where two branched acyls are in the TAG molecule, the order of the elution is different, that is, br/n/br, n/br/br, br/br/n. In all cases, it was further demonstrated that tandem MS of either synthetically prepared TAGs or TAGs obtained from natural material, that is, n-16:0/ai-15:0/n-16:0 and i-16:0/n-15:0/i-16:0 are identical. Unfortunately, it is not possible to distinguish by ESI+ tandem MS such TAGs, which differ only in the branching of the acyls. The results of our analyses of TAGs are in good agreement with previously published data in other streptomycetes.

Biodegradability of Dental Care Antimicrobial Agents Chlorhexidine and Octenidine by Ligninolytic Fungi.

Chlorhexidine (CHX) and octenidine (OCT), antimicrobial compounds used in oral care products (toothpastes and mouthwashes), were recently revealed to interfere with human sex hormone receptor pathways. Experiments employing model organisms-white-rot fungi Irpex lacteus and Pleurotus ostreatus-were carried out in order to investigate the biodegradability of these endocrine-disrupting compounds and the capability of the fungi and their extracellular enzyme apparatuses to biodegrade CHX and OCT. Up to 70% ± 6% of CHX was eliminated in comparison with a heat-killed control after 21 days of in vivo incubation. An additional in vitro experiment confirmed manganese-dependent peroxidase and laccase are partially responsible for the removal of CHX. Up to 48% ± 7% of OCT was removed in the same in vivo experiment, but the strong sorption of OCT on fungal biomass prevented a clear evaluation of the involvement of the fungi or extracellular enzymes. On the other hand, metabolites indicating the enzymatic transformation of both CHX and OCT were detected and their chemical structures were proposed by means of liquid chromatography-mass spectrometry. Complete biodegradation by the ligninolytic fungi was not achieved for any of the studied analytes, which emphasizes their recalcitrant character with low possibility to be removed from the environment.

Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge.

The creamy white to beige, aerobic, non-motile, ovoid to rod-shaped, Gram-stain-negative strain, Cd-10T, was isolated from heavy-metal-contaminated sludge from a decantation basin of a heavy metal processing factory based on its ability to tolerate CdCl2 in the cultivation medium. In the reconstruction of its phylogeny based on 16S rRNA gene sequences, strain Cd-10T clustered with species of the genera Gemmobacter, Xinfangfangia, Tabrizicola and Rhodobacter within the family Rhodobacteraceae. Its 16S rRNA gene sequence exhibited 96.32 % pairwise similarity to the type strain of Xinfangfangia soli, 95.3 % to that of Gemmobacter intermedius, followed by Tabrizicola fusiformis (95.10 %), Rhodobacter sediminis (94.88 %), Gemmobacter nectariphilus and Rhodobacter capsulatus (both 94.81 %). The major respiratory quinone was Q-10 accompanied by Q-9, the fatty acid profile consisted predominantly of C18 : 1ω7c, C18 : 0, C16 : 0 and C16 : 1ω7c, the major polar lipids were phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and diphosphatidylglycerol. An analysis of the percentage of conserved proteins deduced from draft or complete genomic sequences of strain Cd-10T and representatives of its closest relatives suggested that strain Cd-10T is a member of a novel genus within the Rhodobacteraceae family for which we propose the name Pseudogemmobacter. Strain Cd-10T (=DSM 103618T=NCCB 100645T) is the type strain of Pseudogemmobacter bohemicus gen. nov., sp. nov., the type species of the genus Pseudogemmobacter gen. nov.

Implications of mycoremediated dry olive residue application and arbuscular mycorrhizal fungi inoculation on the microbial community composition and functionality in a metal-polluted soil.

Metal-polluted soils represent hostile environments affecting the composition and functions of soil microbial communities. This study evaluated the implication of combining the mycoremediated dry olive residue (MDOR) amendment application with the inoculation of the arbuscular mycorrhizal fungi (AMF) Funneliformis mosseae in restoring the quality, composition, and functionality of soil microbial communities. To achieve this aim, a mesocosms experiment was set up that included three variations: i) with and without application of Penicillium chrysogenum-10-transformed MDOR (MDOR_Pc), and Chondrosterum purpureum-transformed MDOR (MDOR_Cp) amendments; ii) with and without F. mosseae inoculation; and iii) 30-day and 60-day soil treatment time. As a result of this combined treatment, changes in the soil labile organic C and N fractions were observed throughout the experiment. Increases in the abundance of phospholipid fatty acids (PLFAs) for bacteria, actinobacteria, and Gram- and Gram+ bacteria were also recorded at the end of the experiment. The addition of MDOR amendments boosted fungal and AM fungi communities. AM fungi root and soil colonization was also enhanced as the result of improvement nutrient turnover and spatial conditions caused by adding MDOR in combination with an inoculation of F. mosseae. The composition and functionality of microbial communities seemed to be an important ecological attribute indicating an apparently fully functional restoration of this metal-polluted soil and therefore suggesting the suitability of the combined MDOR and AM fungus treatment as a reclamation practice.

Investigating the coagulation of non-proteinaceous algal organic matter: Optimizing coagulation performance and identification of removal mechanisms.

The removal of algal organic matter (AOM) is a growing concern for the water treatment industry worldwide. The current study investigates coagulation of non-proteinaceous AOM (AOM after protein separation), which has been minimally explored compared with proteinaceous fractions. Jar tests with either aluminum sulphate (alum) or polyaluminium chloride (PACl) were performed at doses of 0.2-3.0 mg Al per 1 mg of dissolved organic carbon in the pH range 3.0-10.5. Additionally, non-proteinaceous matter was characterized in terms of charge, molecular weight and carbohydrate content to assess the treatability of its different fractions. Results showed that only up to 25% of non-proteinaceous AOM can be removed by coagulation under optimized conditions. The optimal coagulation pH (6.6-8.0 for alum and 7.5-9.0 for PACl) and low surface charge of the removed fraction indicated that the prevailing coagulation mechanism was adsorption of non-proteinaceous matter onto aluminum hydroxide precipitates. The lowest residual Al concentrations were achieved in very narrow pH ranges, especially in the case of PACl. High-molecular weight saccharide-like organics were amenable to coagulation compared to low-molecular weight (<3 kDa) substances. Their high content in non-proteinaceous matter (about 67%) was the reason for its low removal. Comparison with our previous studies implies that proteinaceous and non-proteinaceous matter is coagulated under different conditions due to the employment of diverse coagulation mechanisms. The study suggests that further research should focus on the removal of low-molecular weight AOM, reluctant to coagulate, with other treatment processes to minimize its detrimental effect on water safety.

The role of CuZn- and Mn-superoxide dismutases in earthworm Eisenia andrei kept in two distinct field-contaminated soils.

Polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs), together with polycyclic aromatic hydrocarbons (PAHs), represent highly toxic and persistent organic environmental pollutants, especially due to their capability for bioaccumulation in fatty tissues. To observe the environmentally relevant effect of these compounds on earthworms, two soils naturally contaminated with PCDD/Fs and PAHs were used in our experiments. We focused on the role of CuZn- and Mn-superoxide dismutases. We assembled a full-length sequences of these molecules from Eisenia andrei earthworm and confirmed their activity. We demonstrated the significant reduction of CuZn-SOD on both mRNA and enzyme activity levels and increased levels of reactive oxygen species in earthworms kept in PCDD/F-polluted soil, which corresponds to the observed histopathologies of the earthworm intestinal wall and adjacent chloragogenous tissue. The results show an important role of CuZn-SOD in earthworm tissue damage caused by PCDD/Fs present in soil. We did not detect any significant changes in the mRNA expression or activity of Mn-SOD in these earthworms. In earthworms maintained in PAH-polluted soil the activity of both CuZn-SOD and Mn-SOD significantly increased. No histopathological changes were detected in these worms, however significant decrease of coelomocyte viability was observed. This reduced viability was most likely independent of oxidative stress.

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

Real-time PCR quantification of arbuscular mycorrhizal fungi: does the use of nuclear or mitochondrial markers make a difference?

Root colonization by arbuscular mycorrhizal fungi (AMF) can be quantified by different approaches. We compared two approaches that enable discrimination of specific AMF taxa and are therefore emerging as alternative to most commonly performed microscopic quantification of AMF in roots: quantitative real-time PCR (qPCR) using markers in nuclear ribosomal DNA (nrDNA) and mitochondrial ribosomal DNA (mtDNA). In a greenhouse experiment, Medicago truncatula was inoculated with four isolates belonging to different AMF species (Rhizophagus irregularis, Claroideoglomus claroideum, Gigaspora margarita and Funneliformis mosseae). The AMF were quantified in the root samples by qPCR targeted to both markers, microscopy and contents of AMF-specific phospholipid fatty acids (PLFA). Copy numbers of nrDNA and mtDNA were closely related within all isolates; however, the slopes and intercepts of the linear relationships significantly differed among the isolates. Across all isolates, a large proportion of variance in nrDNA copy numbers was explained by root colonization intensity or contents of AMF-specific PLFA, while variance in mtDNA copy numbers was mainly explained by differences among AMF isolates. We propose that the encountered inter-isolate differences in the ratios of mtDNA and nrDNA copy numbers reflect different physiological states of the isolates. Our results suggest that nrDNA is a more suitable marker region than mtDNA for the quantification of multiple AMF taxa as its copy numbers are better related to fungal biomass across taxa than are copy numbers of mtDNA.

Asymmetric response of root-associated fungal communities of an arbuscular mycorrhizal grass and an ectomycorrhizal tree to their coexistence in primary succession.

The arbuscular mycorrhizal (AM) grass Calamagrostis epigejos and predominantly ectomycorrhizal (EcM) tree Salix caprea co-occur at post-mining sites spontaneously colonized by vegetation. During succession, AM herbaceous vegetation is replaced by predominantly EcM woody species. To better understand the interaction of AM and EcM plants during vegetation transition, we studied the reciprocal effects of these species' coexistence on their root-associated fungi (RAF). We collected root and soil samples from three different microenvironments: stand of C. epigejos, under S. caprea canopy, and contact zone where roots of the two species interacted. RAF communities and mycorrhizal colonization were determined in sampled roots, and the soil was tested for EcM and AM inoculation potentials. Although the microenvironment significantly affected composition of the RAF communities in both plant species, the effect was greater in the case of C. epigejos RAF communities than in that of S. caprea RAF communities. The presence of S. caprea also significantly decreased AM fungal abundance in soil as well as AM colonization and richness of AM fungi in C. epigejos roots. Changes observed in the abundance and community composition of AM fungi might constitute an important factor in transition from AM-dominated to EcM-dominated vegetation during succession.

Dynamics of a vertical-flow windrow vermicomposting system.

Large-scale vermicomposting under outdoor conditions may differ from small-scale procedures in the laboratory. The present study evaluated changes in selected properties of a large-scale vertical-flow windrow vermicomposting system with continuous feeding with household biowaste. The windrow profile was divided into five layers of differing thickness and age after more than 12 months of vermicomposting. The top layer (0-30 cm, age <3 months) was characterised by partially decomposed organic matter with a high pH value and an elevated carbon/nitrogen (C/N) ratio. The earthworm biomass was 15 g kg-1 with a population density of 125 earthworms per kilogram predominantly found in clusters. The greatest amount of fungi (3.5 µg g-1 dw) and bacteria (62 µg g-1 dw) (expressed as phospholipid fatty acid analysis) was found in this layer. Thus, the top layer could be used for an additional cycle of windrow vermicomposting and for the preparation of aqueous extracts to protect plants against diseases. The lower layers (graduated by 30 cm and by 3 months of age) were mature as reflected by the low content of ammonia nitrogen, ratio of ammonia to nitrate nitrogen and dissolved organic carbon, and high ion-exchange capacity and its ratio to carbon. These layers were characterised by elevated values for electrical conductivity, total content of nutrients, available magnesium content, and a relatively large bacterial/fungal ratio. On the basis of the observed properties, the bottom layers were predetermined as effective fertilisers.

Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation.

Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55(T), which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55(T) include Bryocella elongata SN10(T) (95.4% identity), Acidicapsa ligni WH120(T) (95.2% identity), and Telmatobacter bradus TPB6017(T) (95.0% identity), revealing that strain S55(T) should be classified within the phylum Acidobacteria, subdivision 1. Strain S55(T) is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55(T) corresponds to a new genus within the phylum Acidobacteria; thus, we propose the name Terracidiphilus gabretensis gen. nov., sp. nov. (strain S55(T) = NBRC 111238(T) = CECT 8791(T)). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55(T) also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55(T) being expressed in the forest soil, especially during winter. Our results suggest an important contribution of T. gabretensis S55(T) in the carbon cycle in the Picea abies coniferous forest.

Source Impact Determination using Airborne and Ground Measurements of Industrial Plumes.

Industrial particulate matter (PM) air pollution exposing nearby residential areas forms several European air pollution hot-spots. One of these hot-spot is the residential district of Ostrava Radvanice-Bartovice with frequent exceedances for PM and benzo[a]pyrene B[a]P, a carcinogenic polycyclic aromatic hydrocarbon (PAH) of MW > 228 amu. Such PAHs are highly bonded to the ultrafine particles (UFPs), the smallest PM size fraction, which deposits most efficiently in the alveolar region of human lungs. Airborne measurements identified UFP point sources in the adjacent metallurgical complex and mapped limited horizontal and vertical dispersion of industrial plumes enriched with UFPs (3.2 × 10(5)cm(-3)). The plumes, episodes of simultaneous peaks of UFPs (1.4 × 10(5)cm(-3)), SO2 (88.2 ppb), and CO (11.3 ppm), were recorded on the ground downwind in the residential district when wind speeds >1 ms(-1). In the plumes, UFPs were mostly 19-44 nm in diameter, enriched with PAHs/B[a]P up to 43.8/3.5 mg·g(-1). Electron microscopy showed that these plume UFPs were mostly agglomerates of spherules of 30-50 nm in diameter. These source impact measurements, that combine airborne and ground-level measurements, are applicable to clearly identify specific industrial air pollution sources and provide information to assess their possible impact to human health in similar hot-spots worldwide.