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.

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.

Quantitative and Qualitative Changes in the Genetic Diversity of Bacterial Communities in Anaerobic Bioreactors with the Diatomaceous Earth/Peat Cell Carrier.

This paper analyses the impact of the diatomaceous earth/peat (DEP; 3:1) microbial carrier on changes in the bacterial microbiome and the development of biofilm in the anaerobic digestion (AD) of confectionery waste, combined with digested sewage sludge as inoculum. The physicochemical properties of the carrier material are presented, with particular focus on its morphological and dispersion characteristics, as well as adsorption and thermal properties. In this respect, the DEP system was found to be a suitable carrier for both mesophilic and thermophilic AD. The evaluation of quantitative and qualitative changes in the genetic diversity of bacterial communities, carried out using next-generation sequencing (NGS), showed that the material has a modifying effect on the bacterial microbiome. While Actinobacteria was the most abundant cluster in the WF-control sample (WF-waste wafers), Firmicutes was the dominant cluster in the digested samples without the carrier (WF-dig.; dig.-digested) and with the carrier (WF + DEP). The same was true for the count of Proteobacteria, which decreased twofold during biodegradation in favor of Synergistetes. The Syntrophomonas cluster was identified as the most abundant genus in the two samples, particularly in WF + DEP. This information was supplemented by observations of morphological features of microorganisms carried out using fluorescence microscopy. The biodegradation process itself had a significant impact on changes in the microbiome of samples taken from anaerobic bioreactors, reducing its biodiversity. As demonstrated by the results of this innovative method, namely the BioFlux microfluidic flow system, the decrease in the number of taxa in the digested samples and the addition of DEP contributed to the microbial adhesion in the microfluidic system and the formation of a stable biofilm.

Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming.

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

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.

Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris).

The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon's diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land.

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.

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

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 (W2200%t.w.c) to 48 ± 4 (W3200%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 δ13CCH4, especially in W3 and W4.

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.

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.

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.

Activity and Diversity of Microorganisms in Root Zone of Plant Species Spontaneously Inhabiting Smelter Waste Piles.

The aim was to assess plant driven changes in the activity and diversity of microorganisms in the top layer of the zinc and lead smelter waste piles. The study sites comprised two types (flotation waste-FW and slag waste-SW) of smelter waste deposits in Piekary Slaskie, Poland. Cadmium, zinc, lead, and arsenic contents in these technosols were extremely high. The root zone of 8 spontaneous plant species (FW-Thymus serpyllum, Silene vulgaris, Solidago virgaurea, Echium vulgare, and Rumex acetosa; and SW-Verbascum thapsus; Solidago gigantea, Eupatorium cannabinum) and barren areas of each waste deposit were sampled. We observed a significant difference in microbial characteristics attributed to different plant species. The enzymatic activity was mostly driven by plant-microbial interactions and it was significantly greater in soil affected by plants than in bulk soil. Furthermore, as it was revealed by BIOLOG Ecoplate analysis, microorganisms inhabiting barren areas of the waste piles rely on significantly different sources of carbon than those found in the zone affected by spontaneous plants. Among phyla, Actinobacteriota were the most abundant, contributing to at least 25% of the total abundance. Bacteria belonging to Blastococcus genera were the most abundant with the substantial contribution of Nocardioides and Pseudonocardia, especially in the root zone. The contribution of unclassified bacteria was high-up to 38% of the total abundance. This demonstrates the unique character of bacterial communities in the smelter waste.

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.

The Response of Red Clover (Trifolium pratense L.) to Separate and Mixed Inoculations with Rhizobium leguminosarum and Azospirillum brasilense in Presence of Polycyclic Aromatic Hydrocarbons.

This study aimed to evaluate the impact of co-inoculation Rhizobium sp. and Azospirillum sp. on plant (Trifolium pratense L.) growth in the presence of polycyclic aromatic hydrocarbon (PAH) contamination (anthracene, phenanthrene, and pyrene). Eight strains from the genus Rhizobium leguminosarum bv. trifolii were selected for biotest analysis. Two methods of inoculation were used in the chamber experiment: (1) R. leguminosarum alone and (2) a combined inoculant (R. leguminosarum and Azospirillum brasilense). For comparison, non-contaminated controls were also used. The results demonstrated that co-inoculation of plants with Rhizobium and Azospirillum resulted in more root and shoot biomass than in plants inoculated with R. leguminosarum alone. The results indicated that application of a co-inoculation of bacteria from Rhizobium and Azospirillum species had a positive effect on clover nodulation and growth under the condition of PAH contamination.

New Insight into the Composition of Wheat Seed Microbiota.

Endophytes are associated with host plants throughout their life history from seed germination to fruit development. One of the most important plant organs colonized by endophytic microbiota is the seed. The aim of this study was to determine the structure of the seed core microbiome inhabiting the endosperms and embryos of eight wheat cultivars with the use of a culture-independent technique. The seeds of Triticum aestivum L. cv. Hondia, Wilejka, STH, Opcja, Tybalt, Euforia and Triticum spelta L. cv. Rokosz and Schwabencorn (producer: Plant Breeding Strzelce Sp. z o.o. Group IHAR) were studied. Rokosz and Hondia were cultured in vitro and in vivo to identify obligatory bacterial endophytes. A restrictive analysis of reads originating from the in vitro plants has demonstrated that the bacterial genera Paenibacillus and Propionibacterium inhabiting Rokosz and Hondia plants have a status of obligatory microorganisms. Greater biodiversity of seed-borne endophytes was found in the seed endosperms than in the embryos. The multiple comparison analysis of the OTU abundance indicated that the seed part significantly influenced the relative abundance. The seed-born microbiome is not statistically significantly dependent on the wheat cultivars; however, it cannot be claimed that every wheat seed is the same.

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.

Azolla filiculoides L. as a source of metal-tolerant microorganisms.

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95-105 versus 36-44). In these treatments the share of subdominant Actinobacteria (0.4-0.8%), Firmicutes (0.5-0.9%) and Bacteroidetes (0.2-0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.

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.

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community.

Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO2/H2). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH4 L-1 d-1) was highest in the culture grown with tryptone, yeast extract, and CO2/H2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.

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 Pulawy, 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.