Bacterial Community Structure Responds to Soil Management in the Rhizosphere of Vine Grape Vineyards.

The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere samples were collected from three neighbouring vineyards with the same time of planting and planting material (rootstock: Teleki 5C; Vitis vinifera: Müller Thurgau). Our objective was to examine the diversity occurring in bacterial community structures in vineyards that differ only in the methods of tillage procedure applied, namely intensive (INT), extensive (EXT), and abandoned (AB). For that we took samples from two depths (10-30 cm (shallow = S) and 30-50 cm (deep = D) of the grape rhizosphere in each vineyard and the laboratory and immediately prepared the slices of the roots for DNA-based analysis of the bacterial communities. Bacterial community structure was assessed by means of PCR-DGGE analysis carried out on the v3 region of 16S rRNA gene. Based on the band composition of the DGGE profiles thus obtained, the diversity of the microbial communities was evaluated and determined by the Shannon-Weaver index (H'). Between the AB and EXT vineyards at the S depth, the similarity of the community structure was 55%; however, the similarity of the D samples was more than 80%, while the difference between the INT samples and the other two was also higher than 80%. Based on our results, we can conclude that intensive cultivation strongly affects the structure and diversity of the bacterial community.

Effectiveness of bio-effectors on maize, wheat and tomato performance and phosphorus acquisition from greenhouse to field scales in Europe and Israel: a meta-analysis.

Biostimulants (Bio-effectors, BEs) comprise plant growth-promoting microorganisms and active natural substances that promote plant nutrient-acquisition, stress resilience, growth, crop quality and yield. Unfortunately, the effectiveness of BEs, particularly under field conditions, appears highly variable and poorly quantified. Using random model meta-analyses tools, we summarize the effects of 107 BE treatments on the performance of major crops, mainly conducted within the EU-funded project BIOFECTOR with a focus on phosphorus (P) nutrition, over five years. Our analyses comprised 94 controlled pot and 47 field experiments under different geoclimatic conditions, with variable stress levels across European countries and Israel. The results show an average growth/yield increase by 9.3% (n=945), with substantial differences between crops (tomato > maize > wheat) and growth conditions (controlled nursery + field (Seed germination and nursery under controlled conditions and young plants transplanted to the field) > controlled > field). Average crop growth responses were independent of BE type, P fertilizer type, soil pH and plant-available soil P (water-P, Olsen-P or Calcium acetate lactate-P). BE effectiveness profited from manure and other organic fertilizers, increasing soil pH and presence of abiotic stresses (cold, drought/heat or salinity). Systematic meta-studies based on published literature commonly face the inherent problem of publication bias where the most suspected form is the selective publication of statistically significant results. In this meta-analysis, however, the results obtained from all experiments within the project are included. Therefore, it is free of publication bias. In contrast to reviews of published literature, our unique study design is based on a common standardized protocol which applies to all experiments conducted within the project to reduce sources of variability. Based on data of crop growth, yield and P acquisition, we conclude that application of BEs can save fertilizer resources in the future, but the efficiency of BE application depends on cropping systems and environments.

Characterisation of Luvisols Based on Wide-Scale Biological Properties in a Long-Term Organic Matter Experiment.

Soil organic matter is a biological system that functions as an integrated whole. These assemblies have different properties, functions, and decomposition times. SOM is one of the main determinants of soil productivity. Our studies were carried out in a temperate deciduous oak forest on Luvisols soil. In the DIRT Project (Detritus Input and Removal Treatments), the following treatments were applied: Double Litter, Double Wood, Control, No Litter, No Root and No Input. Our objective was to compare the effect of withdrawal or doubling of organic matter on the protein pattern of the soil and the biological activity and changes in labile C (permanganate-oxidizable carbon) content in a long-term organic matter manipulation experiment. Patterns of thermostable proteins, soil dehydrogenase enzyme activity, CO2 emission, and POXC content were measured at the most biologically active soil depth of 0-5 cm after 23 years of treatment. Our results show that the enzyme activities of the litter removal treatments were significantly reduced compared to the doubling treatments, as were the values of soil respiration. The same significant difference was also detected in the C content of the soils of the treatments. Based on cluster analysis of the protein profile of the soil samples, the No Litter and No Input treatments were significantly different from the other treatments. This shows that specific organic matter is needed to enhance soil biological activity and the associated POXC content.

Co-Inoculation of Organic Potato with Fungi and Bacteria at High Disease Severity of Rhizoctonia solani and Streptomyces spp. Increases Beneficial Effects.

Rhizobacteria-based technologies may constitute a viable option for biological fertilization and crop protection. The effects of two microbial inoculants (1) PPS: Pseudomonas protegens, P. jessenii and Stenotrophomonas maltophilia biocontrol bacterium strains and (2) TPB: Trichoderma atroviride, Pseudomonas putida, and Bacillus subtilis fungi, bacteria biocontrol, and biofertilizer combinations were examined on potato (Solanum tuberosum L. var. Demon) in three consecutive years in irrigated organic conditions. The number of tubers showing symptoms of Streptomyces sp. and Rhizoctonia sp. was recorded. The severity of symptoms was evaluated based on the damaged tuber surface. There was a large annual variability in both the symptoms caused by soil-borne pathogens, and the effect of bio-inoculants. In the first and second year, with a stronger Rhizoctonia and Streptomyces spp. incidence, the bacterial and fungal combination of TPB inoculums with both the potential plant nutrition and biocontrol ability of the strains seemed to have a better efficiency to control the diseases. This tendency was not supported in the third year, and this may be attributed to the relatively high natural precipitation. Further studies are required to investigate the agronomic benefits of these inoculants and to tailor their application to the soil microbial characteristics and weather conditions.

Toxic metal phytoextraction potential and health-risk parameters of some cultivated plants when grown in metal-contaminated river sediment of Danube, near an industrial town.

Toxic metal phytoextraction potential of some higher plants, the white mustard (Sinapis alba L.), perennial rye grass (Lolium perenne L.) and also two cultivated plants, as green pea (Pisum sativum L. var. Rajnai törpe), radish (Raphanus sativus L. var. Szentesi óriás vaj), was studied in a field experiment, along the river Danube in close vicinity of an industrial town, Dunaújváros, Hungary. Soil/sediment and the various plant organs (leaves, stems and roots) were assessed for the contamination with some potentially toxic elements (PTE), such as the cadmium (Cd), nickel (Ni), copper (Cu), and zinc (Zn). It was found that Cd and Ni concentration was below, while the Cu and Zn elements were above the Hungarian permissible limits in each of the studied soil/sediment samples. Bioconcentration factor (BAF) was less than 1 in the shoot biomass of test plant samples and followed the order of Cu > Zn > Cd and Ni. Phytoremediation potential of selected test plants was found to be rather limited. The translocation factor (TF) was more than 1 for Cu and Zn elements, at each test plants. Cadmium was translocated into the leaves in case of the radish, only. Considering of the potential human daily intake of metals (DIM), it was less than 1 both for the adults and for the children. Health risk index (HRI) values of children, however, were higher than 1 for the Cd in case of radish, and for Zn and Cu in case of the pea. Results suggest that consumption of these plants grown in gardens of contaminated sediments can result in some risks for citizens in the industrial town of Dunaújváros. Further studies are required to identify appropriate plants with greater toxic metal phytoextraction potential.

Time-lapse effect of ancient plant coal biochar on some soil agrochemical parameters and soil characteristics.

Biochar is a solid material obtained from reductive, oxygen-free processes, i.e. the thermo-chemical conversion of biomass in oxygen-limited environment. The obtained products have high carbon sequestration potential and strong nutrient-water absorption capacities because of the enlarged carbon surfaces. It is not yet clear how carbon stimulates agrochemical parameters in soil and how those characteristics are developing as time goes on a long-term basis. Samples of ancient (25, 35, 80 years old) plant coal-affected soils were collected in a temperate deciduous forest site located in the south part of the Bükk Mountains (in North Eastern Hungary). Physical-chemical soil characteristics, such as soil pH, cation exchange capacity (CEC), the organic and inorganic nitrogen (NH4+, NH3-) and the available nutrients (P2O5 and K2O), were estimated beside organic matter (SOM) content, measured by two different methods. Levels of polycyclic aromatic hydrocarbon (PAH) compounds in soil and in various biochar samples were assessed in relation with permissible limit values and potential toxicity. Positive correlation was found between the amount of available nutrients, total organic nitrogen content, cation exchange capacity and the age of plant coal-affected soils. The sample soils were exposed to continuous plant coal biochar effect for 25 years, during which macronutrients absorbed and accumulated in the plant coal surfaces. After this period, the degradation of carbon developed simultaneously with the reduction of the amount of available nutrients, till the end of the studied 80-year-affecting period. Measured CEC level indicated positive correlation with nutrient availability and the age of biochar-affected soils. Our results support the hypothesis that biochar in soil can improve its general agrochemical characteristics in relation with its persistence in a specific soil-plant system. Potential PAH content and toxicity of biochar products are key issues of developing proper application rates in sustainable agricultural practices.

Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and ß-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

Mycorrhizal symbiosis effects on growth of chalk false-brome (Brachypodium pinnatum) are dependent on the environmental light regime.

AMF (arbuscular mycorrhizal fungi) colonization of the grass chalk false-brome (Brachypodium pinnatum (L.) P. B.) was studied in selected habitats under spatially different light regimes: (a) shade condition under oak trees, (b) half shade in a shrubby area and (c) full-sun conditions on unshaded grassland. This study assessed the variations in AMF colonization of the grass dependent on the light supply in field habitats. Soil, root and shoot samples were collected four times during the vegetation period (in June, July, September and October). Root colonization, root and shoot biomass as well as soil water content were determined. The highest rate of AMF colonization was detected in June under half-sun and full-sun conditions, where about 50% of the roots were colonized. The average amount of arbuscules was less than 20% in the roots at the three sites, with the highest number of arbuscules in June, under half-sun and full-sun conditions, however, not under the trees. Overall, best mycorrhizal colonization occurred during summer, and its rate decreased in autumn. This tendency inversely correlated with the amount of precipitation, and thus with the water content of soils. The high colonization rate of the examined root samples, and also its seasonal fluctuation, might reflect the importance of the symbiosis where inorganic nutrients and water are the growth-limiting factors. The marginal AMF colonization of chalk false-brome under shade conditions indicates that plants do not use AMF under all stress conditions. When low light limits photosynthesis and thus growth of the plants, they dispense with the colonization of AMF in order to save the expenditure of organic carbon.

Natural and enhanced biodegradation of propylene glycol in airport soil.

Aircraft de-icing fluids (ADF) are a source of water and soil pollution in airport sites. Propylene glycol (PG) is a main component in several commercial formulations of ADFs. Even though PG is biodegradable in soil, seasonal overloads may result in occasional groundwater contamination. Feasibility studies for the biostimulation of PG degradation in soil have been carried out in soil slurries, soil microcosms and enrichment cultures with and without the addition of nutrients (N and P sources, oligoelements), alternative electron acceptors (nitrate, oxygen releasing compounds) and adsorbents (activated carbon). Soil samples have been taken from the contaminated area of Gardermoen Airport Oslo. Under aerobic conditions and in the absence of added nutrients, no or scarce biomass growth is observed and PG degradation occurs by maintenance metabolism at constant removal rate by the original population of PG degraders. With the addition of nutrient, biomass exponential growth enhances aerobic PG degradation also at low temperatures (4 ° C) that occur at the high season of snowmelt. Anaerobic PG degradation without added nutrients still proceeds at constant rate (i.e. no biomass growth) and gives rise to reduced fermentation product (propionic acid, reduced Fe and Mn, methane). The addition of nitrate does not promote biomass growth but allows full PG mineralization without reduced by-products. Further exploitation on the field is necessary to fully evaluate the effect of oxygen releasing compounds and adsorbents.

Integration of geophysical, geochemical and microbiological data for a comprehensive small-scale characterization of an aged LNAPL-contaminated site.

Characterization of aged hydrocarbon-contaminated sites is often a challenge due to the heterogeneity of subsurface conditions. Geoelectrical methods can aid in the characterization of such sites due to their non-invasive nature, but need to be supported by geochemical and microbiological data. In this study, a combination of respective methods was used to characterize an aged light non-aqueous phase liquid-contaminated site, which was the scene of a crude oil blow-out in 1994. As a consequence, a significant amount of crude oil was released into the subsurface. Complex resistivity has been acquired, both along single boreholes and in cross-hole configuration, in a two-borehole test site addressed with electrodes, to observe the electrical behaviour at the site over a two-year period (2010-2011). Geoelectrical response has been compared to results of the analysis of hydrocarbon contamination in soil and groundwater samples. Geochemical parameters of groundwater have been observed by collecting samples in a continuous multi-channel tubing (CMT) piezometer system. We have also performed a biological characterization on soil samples by drilling new boreholes close to the monitoring wells. Particular attention has been given to the characterization of the smear zone that is the sub-soil zone affected by the seasonal groundwater fluctuations. In the smear zone, trapped hydrocarbons were present, serving as organic substrate for chemical and biological degradation, as was indicated by an increase of microbial biomass and activity as well as ferrogenic-sulfidogenic conditions in the smear zone. The results show a good agreement between the intense electrical anomaly and the peaks of total organic matter and degradation by-products, particularly enhanced in the smear zone.

Endophytic Burkholderia fungorum DBT1 can improve phytoremediation efficiency of polycyclic aromatic hydrocarbons.

Burkholderia fungorum DBT1 is a bacterial strain isolated from an oil refinery discharge and capable of transforming dibenzothiophene, phenanthrene, naphthalene, and fluorene. In order to evaluate the influence of a policyclic aromatic hydrocarbon (PAH)-transforming bacterial strain on the phytoremediation of organic contaminants, B. fungorum DBT1 was inoculated into hybrid poplar (Populus deltoides×Populus nigra). The poplar plants were grown for 18-wk with or without naphthalene, phenanthrene, fluorene and dibenzothiophene (488mgkg(-1) soil each) in non-sterile sand-peat substrate. Evidences were gained that B. fungorum DBT1 was present in high concentration in poplar root tissues (2.9-9.5×10(3)CFUg(-1)), while the strain was not detected in stem, leaves and rhizosphere. When poplar was planted in uncontaminated substrate, the infection caused negative effects on biomass index, leaves and stem dry weight, without showing however any disease symptoms. On the other hand, plants inoculated with the strain DBT1 resulted in better tolerance against the toxic effects of PAHs, in terms of root dry weight. Although the presence of plants acted as the main effective treatment for PAH dissipation (82-87%), the inoculum with DBT1 strain lead to the highest PAH abatement (up to 99%). In the present study, an environmental isolate with proper metabolic features was demonstrated to be possibly suitable as a poplar endophyte for improving microbe-assisted phytoremediation in PAH contaminated matrices.

Emission ((57)Co) Mössbauer spectroscopy as a tool for probing speciation and metabolic transformations of cobalt(II) in bacterial cells.

The emission ((57)Co) variant of Mössbauer spectroscopy, rarely used in biology-related studies, was applied to study binding and possible transformations of (57)Co(II) traces in live and dead (hydrothermally treated) cells of the rhizobacterium Azospirillum brasilense (strain Sp7) at T=80 K in frozen aqueous suspensions and as their dried residues. The Mössbauer parameters calculated from the spectra were compared with the similarly obtained data reported earlier for another A. brasilense strain, Sp245 (which differs from strain Sp7 by the ecological niche occupied in the rhizosphere and was found earlier to exhibit different metabolic responses under similar environmental conditions). Similarly to strain Sp245, live cells of strain Sp7, rapidly frozen 2 min and 1 h after their contact with (57)Co(2+) (measured in frozen suspensions), showed marked differences in their Mössbauer parameters, reflecting metabolic transformations of (57)Co(2+) occurring within an hour. However, the parameters for strains Sp7 (this work) and Sp245 (reported earlier), obtained under similar conditions, were found to significantly differ, implying dissimilarity in their metabolic response to Co(2+). This is in line with their different metabolic responses to several heavy metals, including Co(2+), detected earlier using Fourier transform infrared spectroscopy.

Laboratory-scale evaluation of a combined soil amendment for the enhanced biodegradation of propylene glycol-based aircraft de-icing fluids.

A combined soil amendment was tested in microcosm experiments with an aim to enhance the aerobic biodegradation of propylene glycol (PG)-based aircraft de-icing fluids during and following the infiltration of contaminated snowmelt. A key objective under field conditions is to increase degradation of organic pollutants in the surface soil where higher microbial activity and plant rhizosphere effects may contribute to a more efficient biodegradation of PG, compared to subsoil ground layers, where electron acceptors and nutrients are often depleted. Microcosm experiments were set up in Petri dishes using 50 g of soil mixed with appropriate additives. The samples contained an initial de-icing fluid concentration of 10,000 mg/kg soil. A combined amendment using calcium peroxide, activated carbon and 1 x Hoagland solution resulted in significantly higher degradation rates for PG both at 4 and 22 degrees C. Most probable numbers of bacteria capable of utilizing 10,000 mg/kg de-icing fluid as a sole carbon source were about two orders of magnitude higher in the amended soil samples compared to unamended controls at both temperatures. The elevated numbers of such bacteria in surface soil may be a source of cells transported to the subsoil by snowmelt infiltration. The near-surface application of amendments tested here may enhance the growth of plants and plant roots in the contaminated area, as well as microbes to be found at greater depth, and hence increase the degradation of a contaminant plume present in the ground.

Significance of treated agrowaste residue and autochthonous inoculates (Arbuscular mycorrhizal fungi and Bacillus cereus) on bacterial community structure and phytoextraction to remediate soils contaminated with heavy metals.

In this study, we analyzed the impact of treatments such as Aspergillus niger-treated sugar beet waste (SB), PO4(3-) fertilization and autochthonous inoculants [arbuscular mycorrhizal (AM) fungi and Bacillus cereus], on the bacterial community structure in a soils contaminated with heavy metals as well as, the effectiveness on plant growth (Trifolium repens). The inoculation with AM fungi in SB amended soil, increased plant growth similarly to PO4(3-) addition, and both treatments matched in P acquisition but bacterial biodiversity estimated by denaturing gradient gel electrophoresis of amplified 16S rDNA sequences, was more stimulated by the presence of the AM fungus than by PO4(3-) fertilization. The SB amendment plus AM inoculation increased the microbial diversity by 233% and also changed (by 215%) the structure of the bacterial community. The microbial inoculants and amendment used favoured plant growth and the phytoextraction process and concomitantly modified bacterial community in the rhizosphere; thus they can be used for remediation. Therefore, the understanding of such microbial ecological aspects is important for phytoremediation and the recovery of contaminated soils.

Drought, but not salinity, determines the apparent effectiveness of halophytes colonized by arbuscular mycorrhizal fungi.

The halophytes Plantago maritima, Aster tripolium, Artemisia santonicum, Puccinellia limosa, Festuca pseudovina and Lepidium crassifolium from two different saline soils of the Hungarian steppe were examined for colonization by arbuscular mycorrhizal fungi (AMF). The salt aster (A. tripolium) and the sea plantain (P. maritima) were examined more thoroughly by recording root colonization parameters, the salt content in the soil and monthly precipitations in 2001 and 2002. Mycorrhizal colonization was maximal in late spring to early summer and had a second peak later in the autumn. Arbuscule formation and overall mycorrhizal colonization appeared to be inversely correlated with the intensity of rainfall at the investigated sites. The results suggest that, in addition to seasonality, drought may play an important role in governing mycorrhizal activity in saline habitats. In greenhouse experiments, conditions in which AMF could overcome the inhibitory effects of sodium chloride on establishing plant-mycorrhizal symbiosis were not met.

The arbuscular mycorrhizal fungus Glomus geosporum in European saline, sodic and gypsum soils.

Plants of saline and sodic soils of the Hungarian steppe and of gypsum rock in the German Harz mountains, thus soils of high ionic strength and electric conductivity, were examined for their colonization by arbuscular mycorrhizal fungi (AMF). Roots of several plants of the saline and sodic soils such as Artemisia maritima, Aster tripolium or Plantago maritima are strongly colonized and show typical AMF structures (arbuscules, vesicles) whereas others like the members of the Chenopodiaceae, Salicornia europaea, Suaeda maritima or Camphorosma annua, are not. The vegetation of the gypsum rock is totally different, but several plants are also strongly colonized there. The number of spores in samples from the saline and sodic soils examined is rather variable, but high on average, although with an apparent low species diversity. Spore numbers in the soil adjacent to the roots of plants often, but not always, correlate with the degree of AMF colonization of the plants. As in German salt marshes [Hildebrandt et al. (2001)], the dominant AMF in the Hungarian saline and sodic soils is Glomus geosporum. All these isolates provided nearly identical restriction fragment length polymorphism (RFLP) patterns of the internal transcribed spacer (ITS) region of spore DNA amplified by polymerase chain reaction (PCR). Cloning and sequencing of several PCR products of the ITS regions indicated that ecotypes of the G. geosporum/ Glomus caledonium clade might exist at the different habitats. A phylogenetic dendrogram constructed from the ITS or 5.8S rDNA sequences was nearly identical to the one published for 18S rDNA data (Schwarzott et al. 2001). It is tempting to speculate that specific ecotypes may be particularly adapted to the peculiar saline or sodic conditions in such soils. They could have an enormous potential in conferring salt resistance to plants.