Application of nitrogen-rich sunflower husks biochar promotes methane oxidation and increases abundance of Methylobacter in nitrogen-poor soil

The area of sunflower crops is steadily increasing. A beneficial way of managing sunflower waste biomass could be its use as a feedstock for biochar production. Biochar is currently being considered as an additive for improving soil parameters, including the ability to oxidise methane (CH4) - one of the key greenhouse gases (GHG). Despite the high production of sunflower husk, there is still insufficient information on the impact of sunflower husk biochar on the soil environment, especially on the methanotrophy process. To fill this knowledge gap, an experiment was designed to evaluate the effects of addition of sunflower husk biochar (produced at 450-550 °C) at a wide range of doses (1-100 Mg ha-1) to Haplic Luvisol. In the presented study, the CH4 oxidation potential of soil with and without sunflower husk biochar was investigated at 60 and 100% water holding capacity (WHC), and with the addition of 1% CH4 (v/v). The comprehensive study included GHG exchange (CH4 and CO2), physicochemical properties of soil (pH, soil organic carbon (SOC), dissolved organic carbon (DOC), nitrate nitrogen (NO3--N), WHC), and the structure of soil microbial communities. That study showed that even low biochar doses (5 and 10 Mg ha-1) were sufficient to enhance pH, SOC, DOC and NO3--N content. Importantly, sunflower husk biochar was significant source of NO3--N, which soil concentration increased from 9.40 ± 0.09 mg NO3--N kg-1 for the control to even 19.40 ± 0.26 mg NO3--N kg-1 (for 100 Mg ha-1). Significant improvement of WHC (by 11.0-12.4%) was observed after biochar addition at doses of 60 Mg ha-1 and higher. At 60% WHC, application of biochar at a dose of 40 Mg ha-1 brought significant improvements in CH4 oxidation rate, which was 4.89 ± 0.37 mg CH4-C kg-1 d-1. Higher biochar doses were correlated with further improvement of CH4 oxidation rates, which at 100 Mg ha-1 was seventeen-fold higher (8.36 ± 0.84 mg CH4-C kg-1 d-1) than in the biochar-free control (0.48 ± 0.28 mg CH4-C kg-1 d-1). CO2 emissions were not proportional to biochar doses and only grew circa (ca.) twofold from 3.16 to 6.90 mg CO2-C kg-1 d-1 at 100 Mg ha-1. Above 60 Mg ha-1, the diversity of methanotrophic communities increased, with Methylobacter becoming the most abundant genus, which was as high as 7.45%. This is the first, such advanced and multifaceted study of the wide range of sunflower husk biochar doses on Haplic Luvisol. The positive correlation between soil conditions, methanotroph abundance and CH4 oxidation confirmed the multifaceted, positive effect of sunflower husk biochar on Haplic Luvisol. Sunflower husk biochar can be successfully used for Haplic Luvisol supplementation. This additive facilitates soil protection against degradation and has the potential to mitigate GHG emissions.

Changes in the mycobiome structure in response to reduced nitrogen fertilization in two cropping systems of maize

Nitrogen (N) is an essential element for plant productivity; hence, it is abundantly applied to the soil in the form of organic or chemical fertilizers, which consequently have a negative impact on the environment. Therefore, the main objective of our study was to investigate the structure and richness of the soil mycobiome in response to reduced nitrogen fertilization under two cropping systems: plowing (P) and no-till (NT). Moreover, the scope of the study perfectly falls into the EU "From Field to Table" strategy, which recommends a 20 % reduction of nitrogen fertilization of agricultural soils by 2030. In our study, the samples were collected twice during a single growing season: before maize sowing (without fertilization) and after harvesting the crop (four different fertilization rates). The mycobiome structure was identified based on the next generation sequencing (NGS) technique. Overall, our research has proved that the cropping system is important in terms of the formation of the fungal mycobiome structure and relative abundance. In addition, we confirmed that soil properties have a significant impact on fungal communities. We determined that a 20 % lower nitrogen fertilization rate (92.0 kg N ha-1) had a positive effect on the abundance of fungal communities. Moreover, the highest biodiversity at each of the taxonomic levels tested (phylum, class, genus) in the NT system and at the class and genus levels in the P system was also evidenced at the 20 % lower N fertilization rate. We also recommended potential indicators confirming the positive impact of reduced fertilization in two cropping systems: plowing - Epicoccum, Metarhizium, Mycosphaerella, and Paraconiothyrium and no-till - Peziza, Podospora, Metarhizium, Trechispora, and Umbelopsis.

Weathering and soil production under trees growing on sandstones - The role of tree roots in soil formation

Rock weathering drives both landform formation and soil production/evolution. The less studied biological component of weathering and soil production caused by tree root systems is the main focus of the present study. Weathering by trees, which likely has been important in soil formation since the first trees emerged in the middle and late Devonian, is accomplished through both physical and biological means, like acids excreted by plants and exudates from associated bacterial communities. However, these processes are relatively poorly known. We assessed the impact of tree roots and associated microbiota on the potential level of biological weathering. Three research plots were selected in two sandstone regions in Poland. Two plots were in the Stołowe Mountains (Złotno, Batorów), a tableland built of Cretaceous sandstones. The third plot (Żegiestów) was in the Sącz Beskidy Mountains, the Carpathians. Soil samples were taken from tree root zones of Norway spruces from predefined sampling positions. Soils from non-tree control positions were also sampled. Soil samples were a subject of laboratory analyses which included the content of Fe and Al (amorphous and labile forms), carbon (C), nitrogen (N), and soil pH. The microbial functional diversity of soil microorganisms was determined using the Biolog (EcoPlate) system. Rock fragments were collected for mineralogical and a subject of optical microscopy and cathodoluminescence analyses in order to examine their mineralogical composition. Significant differences (pHolm-corrected < 0.05) between sample locations were found mostly for the Żegiestów plot: Soils at control positions differed from the crack and bulk soil sample positions in terms of C, N, C/N, and pH. Tree roots were able to develop a great variety of sizes and forms by following the existing net of bedrock discontinuities and hillslope microrelief. They developed along the most accessible surfaces, and caused rockcliff retreat and scree slope formation. These two features can be considered as initial stages of soil production. Trees add to the complexity of the soil system and allow formation of rhizospheric soils, and horizons rich in organic matter which are zones of a high microbial activity. However, as our study shows, rock cracks with roots cannot be considered as zones of microbial weathering. In addition, C content and microbial activity decreases with depth but can stay on a high level along living and dead roots. When entering rock fractures, they change the intensity of biomechanical weathering and soil properties. The highest biological activity of microorganisms was found in the control samples. Overall, tree roots do change the pattern of soil formation and explain the existing pattern of soil chemical properties, microbial activity, and potentially biological weathering intensity, and the intensity of those processes in correlation with root presence varies in space.

Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies

The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL-1 day-1.

Metabolic Profiling of Endophytic Bacteria in Relation to Their Potential Application as Components of Multi-Task Biopreparations

Agricultural crops are exposed to various abiotic and biotic stresses that can constrain crop productivity. Focusing on a limited subset of key groups of organisms has the potential to facilitate the monitoring of the functions of human-managed ecosystems. Endophytic bacteria can enhance plant stress resistance and can help plants to cope with the negative impacts of stress factors through the induction of different mechanisms, influencing plant biochemistry and physiology. In this study, we characterise endophytic bacteria isolated from different plants based on their metabolic activity and ability to synthesise 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD), the activity of hydrolytic exoenzymes, the total phenolic compounds (TPC) and iron-complexing compounds (ICC). Test GEN III MicroPlate indicated that the evaluated endophytes are highly metabolically active, and the best used substrates were amino acids, which may be important in selecting potential carrier components for bacteria in biopreparations. The ACCD activity of strain ES2 (Stenotrophomonas maltophilia) was the highest, whereas that of strain ZR5 (Delftia acidovorans) was the lowest. Overall, the obtained results indicated that ∼91.3% of the isolates were capable of producing at least one of the four hydrolytic enzymes. In addition, most of the tested strains produced ICC and TPC, which play a significant role in reducing stress in plants. The results of this study suggest that the tested endophytic bacterial strains can potentially be used to mitigate climate change-associated stresses in plants and to inhibit plant pathogens.

Microbial Community Response to Various Types of Exogenous Organic Matter Applied to Soil

Recycling of solid biowaste and manure would reduce the dependence of agriculture on synthetic products. Most of the available studies on the effects of exogenous organic matter (EOM) application to soil were focused on nutrients and crop yield, with much less attention to microbiological processes in soil, especially using modern molecular methods. The aim of this study was to evaluate the effects of various types of manure, sewage sludge and bottom sediment on the biochemical activity and biodiversity of soil and plant yield in a pot experiment. The soil was treated with a range of EOM types: six types of manure (cattle, pig, goat, poultry, rabbit and horse manure; two bottom sediments (from urban and rural systems); and two types of municipal sewage sludge. All EOMs stimulated dehydrogenases activity at a rate of 20 t ha-1. Alkaline phosphatase was mostly stimulated by poultry manure and one of the sludges. In general, the two-fold greater rate of EOMs did not further accelerate the soil enzymes. The functional diversity of the soil microbiome was stimulated the most by cattle and goat manure. EOMs produce a shift in distribution of the most abundant bacterial phyla and additionally introduce exogenous bacterial genera to soil. Poultry and horse manure introduced the greatest number of new genera that were able to survive the strong competition in soil. EOMs differentiated plant growth in our study, which was correlated to the rate of nitrate release to soil. The detailed impacts of particular amendments were EOM-specific, but in general, no harm for microbial parameters was observed for manure and sludge application, regardless of their type. There was also no proof that the PAH and pesticide contents measured in manure or sludge had any effect on microbial activity and diversity.

Pioneering Metabolomic Studies on Diaporthe eres Species Complex from Fruit Trees in the South-Eastern Poland

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.

Microbial Community, Metabolic Potential and Seasonality of Endosphere Microbiota Associated with Leaves of the Bioenergy Tree Paulownia elongata × fortunei

The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5–V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67–36.18%) and amino acids (23.95–35.66%) were preferred by all by all communities, whereas amines and amides (0.38–9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4–97.1%) and Actinobacteria (2.29–78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations.

Can Model Experiments Give Insight into the Response of the Soil Environment to Flooding? A Comparison of Microcosm and Natural Event

Studies using soil microcosms are very common, but few involve flooded soils, and comparing the results from such an experiment with natural conditions is unheard of. In the present study, we investigated the biological activity of soil (pH value, dehydrogenases and phosphatase activities) and the metabolic potential (EcoPlate™ Biolog®) of soil microorganisms in three fluvisol subjected to flooding under laboratory and natural conditions. The results indicate that soil flooding under both natural and laboratory conditions affected soil pH, enzymatic activity and metabolic potential (AWCD, average well colour development) of soil microorganisms. Changes in these parameters are more pronounced in the microcosmic experiment than in the field conditions. Furthermore, depending on the characteristics of the soil (i.e., its type, structure, vegetation) some of the soil quality parameters may return to their preflood state. Microcosm studies are needed in environmental ecology and microbiology to predict changes due to various factors, but their scale and course must be carefully planned.

Biochar dose determines methane uptake and methanotroph abundance in Haplic Luvisol

Biochar promotes C sequestration and improvement of soil properties. Nevertheless, the effects of biochar addition on soil condition are poorly understood, especially with respect to greenhouse gas (GHG) emissions. A large proportion of GHG emissions derive from agriculture and, thus, recognition of the effect of biochar addition to soil on GHG emissions from terrestrial ecosystems is an important issue. The purpose of our study was to evaluate the short- and long-term effects of biochar application on soil in aspects of: GHG exchange (CH₄ and CO₂), basic physicochemical soil properties and structure of microbial communities in Haplic Luvisol. Soil was collected from fallow fields enriched with three doses of wood offcuts biochar (10, 20 and 30 Mg ha^-1) and incubated at two moisture levels (60 and 100% WHC) with the addition of 1% CH₄. To evaluate the influence of biochar aging in soil, the samples were analysed directly (short-term response) and five years (long-term response) after amendment. Generally, biochar addition increased soil pH, redox potential (Eh), organic carbon (SOC) and dissolved organic carbon (DOC) contents. Under 60% WHC, direct biochar application to the soil resulted in a clear improvement in the CH₄ uptake rate. In contrast to that (at 100% WHC) methane uptake rates were twofold decreased. The positive effect was reduced due to biochar aging in the soil, but five years after application, at 60% WHC and the highest biochar dose (30 Mg ha^-1) still significantly enhanced CH₄ oxidation. From a short-term perspective, biochar application increased CO₂ emissions, but after five years this effect was not observed. Microbial tests confirmed that the improvement in CH₄ oxidation was correlated with methanotroph abundance in the soil. Moreover, an increase of Methylocystis abundance in the soil enriched with biochar along with enhanced CH₄ uptake rates confirm the positive biochar influence on methanotrophic communities.

Fungal Indicators of Sensitivity and Resistance to Long-Term Maize Monoculture: A Culture-Independent Approach

Although fungi are regarded as very important components of soils, the knowledge of their community in agricultural (monocultural) soils is still limited. This indicates that soil fungal communities are investigated less intensively than bacteria. Therefore, the main goal of this paper was to evaluate the fungal mycobiome structure in monoculture soils in a culture-independent approach. Firstly, the study was conducted to identify the core mycobiome composition and its variability at different stages of the maize growing season (spring, summer, and autumn). Secondly, we identified and recommended fungal indicators of both sensitivity and resistance to long-term maize monoculture. Two neighboring fields from the Potulicka Foundation area were selected for the study: K20 sown with a Gorzow mixture (intercropping mixture) to improve soil quality after a maize monoculture in 2020 and K21, where long-term (over 30 years) monoculture cultivation was continued. The basic chemical features [acidity, redox potential, total organic carbon (TOC), and moisture] of soils were determined, fungal genetic diversity was assessed by ITS next generation sequencing (NGS) analyses, and biodiversity indices were calculated. The results of the NGS technique facilitated recognition and classification of the fungal mycobiome to the taxonomic genus level and changes in the fungal structure in the three periods (spring, summer, and autumn) were assessed. It was evidenced that the mycobiome composition was dependent on both the seasons and the agricultural practices. It was also found that even a 1-year break in the monoculture in favor of an intercropping mixture improved soil properties thus contributing to higher biodiversity. Mortierella was recommended as a potential indicator of sensitivity to long-term maize cultivation, whereas Solicoccozyma and Exophiala were proposed as indicators of resistance to long-term maize cultivation. We proved that the precision farming principles applied on the Potulicka Foundation farm had a very positive effect on fungal biodiversity, which was high even in the long-term maize monoculture field. Therefore, the monoculture cultivation carried out in this way does not induce biological degradation of monoculture soils but preserves their good biological quality.

Microbial activity and community level physiological profiles (CLPP) of soil under the cultivation of spring rape with the Roundup 360 SL herbicide

PURPOSE

The use of glyphosate in agriculture raises a lot of controversy because research concerning its impact on the soil provides contradictory information. However, despite these negative opinions, glyphosate is still used in agricultural practice. Therefore, for a more complete assessment, the authors carried out research using traditional microbiological methods and a modern method of metabolic profile analysis in glyphosate-treated soil.

METHODS

The study was carried out on the soil witch was sown with six cultivars of rapeseed. Seven days before harvest, the plants were sprayed with the herbicide. The analyses consisted in determining the number of selected groups of microorganisms, biochemical and enzymatic activity, and differentiation of the catabolic potential of soil microbial communities.

RESULTS

The results showed significant changes in the analyzed parameters. Respiratory activity and ammonification processes were stimulated in the treatments with rapeseed cultivation treated with the herbicide. Changes in the enzymatic activity were generally positive. The EcoPlate assessment of microbial community catabolism showed that the highest activity was recorded in the soil sown with the cultivars Belinda, Tamarin, and Sw svinto. Concurrently, these soils were characterized by the highest correlations between rapeseed cultivar and metabolic activity.

CONCLUSION

Cultivation of specific plant varieties that reduce the negative effect of herbicides used in agriculture may be one of the methods to prevent soil degradation. In our research, Belinda turned out to be a cultivar, under the cultivation of which an increase in the activity of microorganisms was recorded most frequently compared to soil not sown with rapeseed.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-021-00753-3.

The Use of Interactions Between Microorganisms in Strawberry Cultivation (Fragaria x ananassa Duch.)

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.

Phenotype Switching in Metal-Tolerant Bacteria Isolated from a Hyperaccumulator Plant

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 Biolog^TM 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.

Microbial Involvement in Carbon Transformation via CH4 and CO2 in Saline Sedimentary Pool

Simple Summary

Methane and carbon dioxide are commonly found in the environment and are considered the most important greenhouse gases. Transformation of these gases is in large carried by microorganisms, which occur even in extreme environments. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Biological activity (carbon dioxide and methane production or methane oxidation), confirmed by stable isotope indices, occurred in all of the studied Wieliczka rocks. CH₄-utilizing microbes constituted 0.7–3.6% while methanogens (represented by Methanobacterium) only 0.01–0.5% of taxa present in the Wieliczka Salt Mine rocks. Water activity was the key factor regulating microbial activity in saline subsurface sediments. Generally, CO₂ respiration was higher in anaerobic conditions while methanogenic and methanotrophic activities were dependent on the type of rock.

Abstract

Methane and carbon dioxide are one of the most important greenhouse gases and significant components of the carbon cycle. Biogeochemical methane transformation may occur even in the extreme conditions of deep subsurface ecosystems. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Rock samples (W2, W3, and W4) differed in lithology (clayey salt with veins of fibrous salt and lenses of gypsum and anhydrite; siltstone and sandstone; siltstone with veins of fibrous salt and lenses of anhydrite) and the accompanying salt type (spiza salts or green salt). Microbial communities present in the Miocene strata were studied using activity measurements and high throughput sequencing. Biological activity (i.e., carbon dioxide and methane production or methane oxidation) occurred in all of the studied clayey salt and siltstone samples but mainly under water-saturated conditions. Microcosm studies performed at elevated moisture created more convenient conditions for the activity of both methanogenic and methanotrophic microorganisms than the intact sediments. This points to the fact that water activity is an important factor regulating microbial activity in saline subsurface sediments. Generally, respiration was higher in anaerobic conditions and ranged from 36 ± 2 (W2_200%t.w.c) to 48 ± 4 (W3_200%t.w.c) nmol CO₂ gdw⁻¹ day⁻¹. Methanogenic activity was the highest in siltstone and sandstone (W3, 0.025 ± 0.018 nmol CH₄ gdw⁻¹ day⁻¹), while aerobic methanotrophic activity was the highest in siltstone with salt and anhydrite (W4, 220 ± 66 nmol CH₄ gdw⁻¹ day⁻¹). The relative abundance of CH₄-utilizing microorganisms (Methylomicrobium, Methylomonas, Methylocystis) constituted 0.7–3.6% of all taxa. Methanogens were represented by Methanobacterium (0.01–0.5%). The methane-related microbes were accompanied by a significant number of unclassified microorganisms (3–64%) and those of the Bacillus genus (4.5–91%). The stable isotope composition of the CO₂ and CH₄ trapped in the sediments suggests that methane oxidation could have influenced δ¹³C_CH4, especially in W3 and W4.

Influence of pipe material on biofilm microbial communities found in drinking water supply system

The biofilms and water samples from a model installation built of PVC-U, PE-HD and cast iron pipes were investigated using standard heterotrophic plate count and 16S rRNA Next Generation Sequencing. The results of the high throughput identification imply that the construction material strongly influences the microbiome composition. PVC-U and PE-HD pipes were dominated with Proteobacteria (54-60%) while the cast pipe was overgrown by Nitrospirae (64%). It was deduced that the plastic pipes create a more convenient environment for the potentially pathogenic taxa than the cast iron. The 7-year old biofilms were described as complex habitats with sharp oxidation-reduction gradients, where co-existence of methanogenic and methanotrophic microbiota takes place. Furthermore, it was found that the drinking water distribution systems (DWDS) are a useful tool for studying the ecology of rare bacterial phyla. New ecophysiological aspects were described for Aquihabitans, Thermogutta and Vampirovibrio. The discrepancy between identity of HPC-derived bacteria and NGS-revealed composition of biofilm and water microbiomes point to the need of introducing new diagnostical protocols to enable proper assessment of the drinking water safety, especially in DWDSs operating without disinfection.

A Comprehensive Analysis Using Colorimetry, Liquid Chromatography-Tandem Mass Spectrometry and Bioassays for the Assessment of Indole Related Compounds Produced by Endophytes of Selected Wheat Cultivars

Liquid chromatography–tandem mass spectrometry (LC–MS/MS), colorimetry, and bioassays were employed for the evaluation of the ability of endophytic bacterial strains to synthesize indole-related compounds (IRCs) and in particular indole-3-acetic acid (IAA). A total of 54 endophytic strains belonging to seven bacterial genera isolated from tissues of common and spelt wheat cultivars were studied. The endophytic bacteria isolated from different tissues of the tested wheat types were capable of IRCs production, including IAA, which constituted from 1.75% to 52.68% of all IRCs, in in vitro conditions via the tryptophan dependent pathway. The selected post-culture medium was also examined using a plant bioassay. Substantial growth of wheat coleoptile segments treated with the bacterial post-culture medium was observed in several cases. Our data suggest that the studied endophytic bacteria produce auxin-type compounds to support plant development. Summarizing, our approach to use three complementary methods for estimation of IRCs in different endophytic strains provides a comprehensive picture of their effect on wheat growth.

Organic nitrogen modulates not only cadmium toxicity but also microbial activity in plants

It is known that organic nitrogen may modify uptake and toxicity of metals but direct metabolic and microbial comparison of various organic N sources is not available. We therefore studied comparative impact of additional N sources (nitrate, urea or allantoin as 1 mM of N for each compound in addition to 15 mM of inorganic N in the Hoagland solution) on Cd toxicity and microbial activity in common crop cucumber. Organic N significantly elevated the growth, chlorophyll content and photosynthetic activity under Cd excess in comparison with inorganic N though the impact on Cd uptake was negligible. Both organic N compounds also affected accumulation of mineral nutrients, total N, amino acids, and protein content in Cd-stressed plants. Among organic acids, mainly allantoin and partially urea affected accumulation of citrate and tartrate. The most notably, we detected that allantoin was decomposed even within 24 h by microbes into the urea, but it significantly elevated rhizosphere microbial activity. All these data indicate that allantoin is metabolized by plants/microbes into the urea and that it affects microbes mainly in the rhizosphere, which could contribute to amelioration of Cd toxicity.

Fungal Community, Metabolic Diversity, and Glomalin-Related Soil Proteins (GRSP) Content in Soil Contaminated With Crude Oil After Long-Term Natural Bioremediation

Fungi have increased tolerance to environmental stress (also related to the access of pollutants, e.g., trace elements and polycyclic aromatic hydrocarbons PAHs). The aim of the study was to evaluate the mycobiome and functional diversity of fungi in long-term crude-oil contaminated soils as the potential bioremediators of oil contaminated sites. Samples were taken from three historical oil wells (over a century old) at two distances: within a 0.5 m radius of the oil wells (OWP1, OWP2, and OWP3) and within a 3 m radius from the oil wells as the controls (OW1, OW2, and OW3). Next generation sequencing (for the ITS region) was accompanied with determination of the functional fungal community based on Biolog FFPlates, glomalin related soil protein (GRSP) content, trace element and PAHs concentration. The research hypothesis assumed that long-term natural bioremediation of crude oil contaminated soils can contribute to intensive development of a unique fungal community adapted to the contamination conditions. The identification of such fungi can be of particular importance in soil bioremediation. There were significant differences in the fungal community and functional diversity between the soil samples. The soils collected directly from the oil wells were characterized by higher biological activity and higher diversity of PAH-degrading fungal candidates compared to the soils collected within 3 m of the oil wells. The total glomalin-related soil proteins (T-GRSP) and easily-extractable glomalin-related soil proteins (EE-GRSP) contents were lower in soil samples taken directly from the crude oil well. The control soil (OW) subjected to a long-term natural remediation may already have sufficient conditions for the growth and development of mycorrhizal fungi. The mycobiome of the soils collected directly from the oil wells (OWP1, OWP2, and OWP3) was characterized by a 35% share of PAH-degrading candidates, compared to the soil collected at the 3 m distance from the oil wells (OW1, OW2, and OW3) at < 5%. The main PAH-degrading fungal candidates belong to genera Ilyonectria, Chaetomium, Gibberella, Paraphoma, Schizothecium, Pseudorobillarda, Tetracladium, Ganoderma, Cadophora, Exophiala, Knufia, Mycoleptodiscus, Cyphellophora, Fusicolla, Devriesia, Didymella, Plenodomus, Pyrenochaetopsis, Symbiotaphrina, Phallus, Coprinellus, Plectosphaerella, Septoriella, and Hypholoma. The share of three- and four-ringed PAHs in soil was higher as the distance from the oil well increased. These results may indicate that more effective degradation processes occur closer to the oil wells.

Biochar addition reinforces microbial interspecies cooperation in methanation of sugar beet waste (pulp)

Biogas production and microbial community structure were analyzed as an effect of biochar addition to a fermentation sludge containing sugar beet pulp. Positive effects of the treatment including an increase in process efficiency and better biogas quality were noted. The effect of biochar on AD (anaerobic digestion process) microbial communities was investigated after total DNA extraction from biochar-amended fermentation mixtures by PCR amplification of bacterial 16S rRNA gene fragments and Illumina amplicon sequencing. A combination of microbiological and physico-chemical analyses was used to study the mechanism by which biochar influences the process of anaerobic digestion of sugar beep pulp. It was found that the main reason of the changes in biogas production was the reshaping of the microbial communities, in particular enrichment of Bacteroidales and Clostridiales. It was proposed that biochar, in addition to being a conductor for mediating interspecies electron transfer, serves also as a habitat for hydrolytic bacteria. It was elucidated that the main driving force for the preferential colonization of biochar surfaces is its hydrophobicity. The presented research indicates the high potential of biochar to stimulate the methane fermentation process.

Culture-independent analysis of an endophytic core microbiome in two species of wheat: Triticum aestivum L. (cv. 'Hondia') and the first report of microbiota in Triticum spelta L. (cv. 'Rokosz')

The main goal of the study was to determine the structure of endophytic bacteria inhabiting different parts (endosperm, germ, roots, coleoptiles, and leaves) of two wheat species, Triticum aestivum L. (cv. 'Hondia') and Triticum spelta L. (cv. 'Rokosz'), in order to provide new knowledge about the stability and/or changeability of the core microbiome in different plant organs. The endophytic core microbiome is associated with plants throughout their whole life cycle; however, plant organs can determine the actual endophytic community. Therefore, next generation sequencing with MiSeq Illumina technology was applied to identify the endophytic microbiome of T. aestivum and T. spelta. Bioinformatic analyses were performed with the use of the DADA2(1.8) package and R software (3.5.1). It was demonstrated that wheat, which is an important crop plant, was associated with beneficial endophytic bacteria inside the endosperms, germs, roots, leaves, and coleoptiles. Importantly, for the first time, biodiversity was recognized in the coleoptiles of the investigated wheat species. Flavobacterium, Pseudomonas and Janthinobacterium were shown to be common genera for both tested wheat cultivars. Among them, Pseudomonas was found to be the only endophytic genus accompanying both wheat species from the endosperm stage to the development of the leaf. Paenibacillus was recognized as a core genus for the 'Hondia' cv., whereas Pedobacter and Duganella constituted the core microbiome in the 'Rokosz' cv. In addition, the first insight into the unique and yet unrecognized endophytic microbiome of T. spelta is presented.

Role of Festuca rubra and Festuca arundinacea in determinig the functional and genetic diversity of microorganisms and of the enzymatic activity in the soil polluted with diesel oil

The objective of this study was to analyze the effect of two grass species, i.e. red fescue (Festuca rubra) and tall fescue (F. arundinacea), on the functional and genetic diversity of soil-dwelling microorganisms and on the enzymatic activity of soil not polluted and polluted with diesel oil. Grasses were examined for their effectiveness in accelerating degradation of PAHs introduced into soil with diesel oil. A growing experiment was conducted in Kick-Brauckman pots. The soil not polluted and polluted with diesel oil (7 cm3 kg-1 d.m.) was determined for the count of bacteria, colony development index, ecophysiological diversity index, functional diversity (using Biolog system), genetic diversity of bacteria (using NGS), enzymatic activity, and content of hydrocarbons. Study results demonstrated disturbed homeostasis of soil. The toxic effect of diesel oil on grasses alleviate with time since soil pollution. The yield of the first swath of red fescue decreased by 98% and that of tall fescue by 92%, whereas the yields of the second swath decreased by 82% and 89%, and these of the third swath by 50% and 47%, respectively. Diesel oil diminished also the functional and genetic diversity of bacteria. The use of grasses significantly decreased contents of C6-C12 (gasoline total), C12-C35 mineral oils, BTEX (volatile aromatic hydrocarbons), and PAHs in the soil, as well as enabled restoring the microbiological equilibrium in the soil, and increased functional and genetic diversity of bacteria. For this reason, both analyzed grass species, i.e. Festuca rubra and F. arundinacea, may be recommended for the remediation of soil polluted with diesel oil.

Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment

The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m2), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5-21.3 g kg-1). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles.

Genetic and Functional Diversity of Bacterial Microbiome in Soils With Long Term Impacts of Petroleum Hydrocarbons

Soil contamination with petroleum, especially in the area of oil wells, is a serious environmental problem. Restoring soil subjected to long-term pollution to its original state is very difficult. Under such conditions, unique bacterial communities develop in the soil that are adapted to the contaminated conditions. Analysis of the structure and function of these microorganisms can be a source of valuable information with regard to bioremediation. The aim of this study was to evaluate structural and functional diversity of the bacterial communities in soils with long-term impacts from petroleum. Samples were taken from the three oldest oil wells at the Crude Oil Mine site in Węglówka, Poland; the oldest was established in 1888. They were collected at 2 distances: (1) within a radius of 0.5 m from the oil wells, representing soil strongly contaminated with petroleum; and (2) 3 m from the oil wells as the controls. The samples were analyzed by 16S rRNA sequencing and the community level physiological profiling (CLPP) method in order to better understand both the genetic and functional structure of soil collected from under oil wells. Significant differences were found in the soil samples with regard to bacterial communities. The soils taken within 0.5 m of the oil wells were characterized by the highest biodiversity indexes. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria were strongly correlated with biological activity in these soils. Families of Alphaproteobacteria were also dominant, including: Bradyrhizobiaceae, Rhizobiaceae, Rhodobacteraceae, Acetobacteraceae, Hyphomicrobiaceae, and Sphingomonadaceae. The study showed that the long term contamination of soil changes bacterial communities and their metabolic activity. Even so, natural bioremediation leads to the formation of specific groups of bacteria that actively grow at the site of contamination in the soil.

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS), reduced tillage (RT), full tillage (FT), and crop rotation (CR). Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation) and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation). The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895), genus level (P = 0.026, F = 3.313) and on the species level (P = 0.033, F = 2.718). This study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function.

Early differentation of lamellar structure of the intervertebral disc in staged human embryos

Introduction. In the vast literature concerning the development of the intervertebral discs controversies exist as to the period of differentiation and structure of the nucleus pulposus and annulus fibrosus. These controversies result from different determination of age of the investigated embryos. Aim. Using embryos from departmental collection age of which was established according to international Carnegie staging and expressed in postfertilizational days, the differentiation of the intervertebral discs was traced. Material and methods. Study was performed on 34 embryos at developmental stages 13–23 (32–56 days). Embryos were serially sectioned in sagittal, frontal and horizontal planes. Sections were stained with various histological methods and impregnated with silver.Results. Division of sclerotomes into loose cranial and dense caudal zones (sclerotomites) was observed in embryos aged 32 days (stage 13). The intervertebral disc developed from the dense zone of sclerotome and was well recognized in embryos aged 33 days (stage 14). At the end of fifth week (embryos at stage 15, 36 days) the annulus fibrosus and the nucleus pulposus were seen. The annulus fibrosus differentiated into lateral and medial zones. Within the lateral zone cells were arranged into circular rows. These rows were considered as the first stage of laminar structure. In further developmental stages the laminae occupied both zones of the annulus fibrosus.Conclusions. The intervertebral discs develop from the dense zone of the sclerotome which is evident in embryos at stage 13 (32 days). Discs differentiate in embryos aged 33 days, when the nucleus pulposus and annulus fibrosus are recognized. In embryos aged 36 days in the annulus fibrosus circular rows forming laminar arrangement are seen.

Phytoremediation of Polycyclic Aromatic Hydrocarbons in Soils Artificially Polluted Using Plant-Associated-Endophytic Bacteria and Dactylis glomerata as the Bioremediation Plant

The reaction of soil microorganisms to the contamination of soil artificially polluted with polycyclic aromatic hydrocarbons (PAHs) was evaluated in pot experiments. The plant used in the tests was cock’s foot (Dactylis glomerata). Three different soils artificially contaminated with PAHs were applied in the studies. Three selected PAHs (anthracene, phenanthrene, and pyrene) were used at the doses of 100, 500, and 1000 mg/kg d.m. of soil and diesel fuel at the doses of 100, 500, and 1000 mg/kg d.m. of soil. For evaluation of the synergistic effect of nitrogen fixing bacteria, the following strains were selected: associative Azospirillum spp. and Pseudomonas stutzerii. Additionally, in the bioremediation process, the inoculation of plants with a mixture of the bacterial strains in the amount of 1 ml suspension per 500 g of soil was used. Chamber pot-tests were carried out in controlled conditions during four weeks of plant growth period. The basic physical, microbiological and biochemical properties in contaminated soils were determined. The obtained results showed a statistically important increase in the physical properties of soils polluted with PAHs and diesel fuel compared with the control and also an important decrease in the content of PAHs and heavy metals in soils inoculated with Azospirillum spp. and P. stutzeri after cock’s foot grass growth. The bioremediation processes were especially intensive in calcareous rendzina soil artificially polluted with PAHs.