The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng.

• Klíčová slova
• Panax notoginseng, Continuous cropping obstacle, High-throughput sequencing, Total DNA, Total RNA,
• MeSH
• Bacteria * klasifikace   genetika   izolace a purifikace   MeSH
• biodiverzita * MeSH
• DNA bakterií genetika   MeSH
• fylogeneze * MeSH
• kořeny rostlin mikrobiologie   MeSH
• nemoci rostlin mikrobiologie   MeSH
• Panax notoginseng * mikrobiologie   MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• rhizosféra * MeSH
• RNA ribozomální 16S genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA bakterií MeSH
• půda MeSH
• RNA ribozomální 16S MeSH

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

• Klíčová slova
• Arctic biology, TE proliferation, biotrophy–saprotrophy evolution, carbon degradation, fungal genomics, fungal guild, genome size diversity, plant-fungus interactions, root-associations, saprotrophs,
• MeSH
• Agaricales * genetika   MeSH
• fylogeneze MeSH
• genom fungální * genetika   MeSH
• molekulární evoluce MeSH
• přenos genů horizontální MeSH
• rostliny mikrobiologie   genetika   MeSH
• transpozibilní elementy DNA genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• transpozibilní elementy DNA MeSH

Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.

• Klíčová slova
• Biofuel, Cellulases, Cellulose degradation, Lignocellulose,
• Publikační typ
• časopisecké články MeSH

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.

• Klíčová slova
• 16S rRNA, Biolog EcoPlates, biological activity, forest bulk soil, forest ecosystem, next-generation sequencing (NGS), physiological profiles of soil microorganisms,
• MeSH
• Bacteria MeSH
• biodiverzita MeSH
• borovice lesní * MeSH
• bříza MeSH
• ekosystém MeSH
• Ilex * MeSH
• olše * MeSH
• půda chemie   MeSH
• půdní mikrobiologie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• půda MeSH

Arbuscular mycorrhizal fungi (AMF) colonize the roots of numerous aquatic and wetland plants, but the establishment and functioning of mycorrhizal symbiosis in submerged habitats have received only little attention. Three pot experiments were conducted to study the interaction of isoetid plants with native AMF. In the first experiment, arbuscular mycorrhizal (AM) symbiosis did not establish in roots of Isoëtes echinospora and I. lacustris, while Littorella uniflora roots were highly colonized. Shoot and root biomass of L. uniflora were, however, not affected by AMF inoculation, and only one of nine AMF isolates significantly increased shoot P concentration. In the second experiment, we compared colonization by three Glomus tetrastratosum isolates of different cultivation history and origin (aquatic versus terrestrial) and their effects on L. uniflora growth and phosphorus nutrition under submerged versus terrestrial conditions. The submerged cultivation considerably slowed, but did not inhibit mycorrhizal root colonization, regardless of isolate identity. Inoculation with any AMF isolate improved plant growth and P uptake under terrestrial, but not submerged conditions. In the final experiment, we compared the communities of AMF established in two cultivation regimes of trap cultures with lake sediments, either submerged on L. uniflora or terrestrial on Zea mays. After 2-year cultivation, we did not detect a significant effect of cultivation regime on AMF community composition. In summary, although submerged conditions do not preclude the development of functional AM symbiosis, the contribution of these symbiotic fungi to the fitness of their hosts seems to be considerably less than under terrestrial conditions.

• Klíčová slova
• Aquatic plants, Arbuscular mycorrhizal symbiosis, Isoetids, Isoëtes, Littorella uniflora, Submerged roots,
• MeSH
• biomasa MeSH
• Glomeromycota * MeSH
• houby MeSH
• kořeny rostlin MeSH
• mykorhiza * MeSH
• symbióza MeSH
• Publikační typ
• časopisecké články MeSH

The estimation of oral microbiome (OM) taxonomic composition in periodontally healthy individuals can often be biased because the clinically periodontally healthy subjects for evaluation can already experience dysbiosis. Usually, they are included just based on the absence of clinical signs of periodontitis. Additionally, the age of subjects is used to be higher to correspond well with tested groups of patients with chronic periodontitis, a disorder typically associated with aging. However, the dysbiosis of the OM precedes the clinical signs of the disease by many months or even years. The absence of periodontal pockets thus does not necessarily mean also good periodontal health and the obtained image of "healthy OM" can be distorted.To overcome this bias, we taxonomically characterized the OM in almost a hundred young students of dentistry with precise oral hygiene and no signs of periodontal disease. We compared the results with the OM composition of older periodontally healthy individuals and also a group of patients with severe periodontitis (aggressive periodontitis according to former classification system). The clustering analysis revealed not only two compact clearly separated clusters corresponding to each state of health, but also a group of samples forming an overlap between both well-pronounced states. Additionally, in the cluster of periodontally healthy samples, few outliers with atypical OM and two major stomatotypes could be distinguished, differing in the prevalence and relative abundance of two main bacterial genera: Streptococcus and Veillonella. We hypothesize that the two stomatotypes could represent the microbial succession from periodontal health to starting dysbiosis. The old and young periodontally healthy subjects do not cluster separately but a trend of the OM in older subjects to periodontitis is visible. Several bacterial genera were identified to be typically more abundant in older periodontally healthy subjects.

• Klíčová slova
• aging, core microbiome, oral microbiome, periodontal health, periodontitis, stomatotype, taxonomic composition,
• MeSH
• agresivní parodontitida * MeSH
• chronická parodontitida * MeSH
• dysbióza MeSH
• lidé MeSH
• mikrobiota * MeSH
• parodontální chobot MeSH
• senioři MeSH
• Check Tag
• lidé MeSH
• senioři MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The dysbiosis of oral microbiome (OM) precedes the clinical signs of periodontal disease. Its simple measure thus could indicate individuals at risk of periodontitis development; however, such a tool is still missing. Up to now, numerous microbial taxa were associated with periodontal health or periodontitis. The outputs of most studies could, nevertheless, be slightly biased from following two reasons: First, the healthy group is often characterized only by the absence of the disease, but the individuals could already suffer from dysbiosis without any visible signs. Second, the healthy/diseased OM characteristics are frequently determined based on average data obtained for whole groups of periodontally healthy persons versus patients. Especially in smaller sets of tested individuals the typical individual variability can thus complicate the unambiguous assignment of oral taxa to respective state of health. In this work the taxonomic composition of OM was evaluated for 20 periodontally healthy individuals and 15 patients with chronic periodontitis. The narrowed selection set of the most diseased patients (confirmed by clinical parameters) and the most distant group of healthy individuals with the lowest probability of dysbiosis was determined by clustering analysis and used for identification of marker taxa. Based on their representation in each individual oral cavity we proposed the numeric index of periodontal health called R/G value. Its diagnostic potential was further confirmed using independent set of 20 periodontally healthy individuals and 20 patients with periodontitis with 95 percent of samples assigned correctly. We also assessed the individual temporal OM dynamics in periodontal health and we compared it to periodontitis. We revealed that the taxonomic composition of the system changes dynamically but generally it ranges within values typical for periodontal health or transient state, but far from values typical for periodontitis. R/G value tool, formulated from individually evaluated data, allowed us to arrange individual OMs into a continuous series, instead of two distinct groups, thus mimicking the gradual transformation of a virtual person from periodontal health to disease. The application of R/G value index thus represents a very promising diagnostic tool for early prediction of persons at risk of developing periodontal disease.

• Klíčová slova
• core microbiome, diagnosis, oral microbiome, periodontal health, periodontitis, taxonomic composition, temporal dynamics,
• MeSH
• chronická parodontitida * MeSH
• dysbióza MeSH
• lidé MeSH
• mikrobiota * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In temperate forests, climate seasonality restricts the photosynthetic activity of primary producers to the warm season from spring to autumn, while the cold season with temperatures below the freezing point represents a period of strongly reduced plant activity. Although soil microorganisms are active all-year-round, their expressions show seasonal patterns. This is especially visible on the ectomycorrhizal fungi, the most abundant guild of fungi in coniferous forests. We quantified the production of fungal mycelia using ingrowth sandbags in the organic layer of soil in temperate coniferous forest and analysed the composition of fungal communities in four consecutive seasons. We show that fungal biomass production is as low as 0.029 µg g-1 of sand in December-March, while it reaches 0.122 µg g-1 in June-September. The majority of fungi show distinct patterns of seasonal mycelial production, with most ectomycorrhizal fungi colonising ingrowth bags in the spring or summer, while the autumn and winter colonisation was mostly due to moulds. Our results indicate that fungal taxa differ in their seasonal patterns of mycelial production. Although fungal biomass turnover appears all-year-round, its rates are much faster in the period of plant activity than in the cold season.

• Klíčová slova
• Picea abies, ectomycorrhiza, fungal ecology, metabarcoding, mycelial growth, soil fungi, temperate forest,
• Publikační typ
• časopisecké články MeSH

Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.

• MeSH
• Bacteria klasifikace   genetika   MeSH
• Basidiomycota růst a vývoj   MeSH
• Cistus růst a vývoj   mikrobiologie   MeSH
• metagenomika MeSH
• mikrobiální interakce MeSH
• mikrobiota * MeSH
• požáry v divočině prevence a kontrola   MeSH
• půdní mikrobiologie * MeSH
• taxonomické DNA čárové kódování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A robust and widely applicable method for sampling of aquatic microbial biofilm and further sample processing is presented. The method is based on next-generation sequencing of V4-V5 variable regions of 16S rRNA gene and further statistical analysis of sequencing data, which could be useful not only to investigate taxonomic composition of biofilm bacterial consortia but also to assess aquatic ecosystem health. Five artificial materials commonly used for biofilm growth (glass, stainless steel, aluminum, polypropylene, polyethylene) were tested to determine the one giving most robust and reproducible results. The effect of used sampler material on total microbial composition was not statistically significant; however, the non-plastic materials (glass, metal) gave more stable outputs without irregularities among sample parallels. The bias of the method is assessed with respect to the employment of a non-quantitative step (PCR amplification) to obtain quantitative results (relative abundance of identified taxa). This aspect is often overlooked in ecological and medical studies. We document that sequencing of a mixture of three merged primary PCR reactions for each sample and further evaluation of median values from three technical replicates for each sample enables to overcome this bias and gives robust and repeatable results well distinguishing among sampling localities and seasons.

• MeSH
• Bacteria klasifikace   genetika   MeSH
• biofilmy * růst a vývoj   MeSH
• mikrobiologie vody * MeSH
• mikrobiota genetika   MeSH
• monitorování životního prostředí metody   MeSH
• odběr biologického vzorku MeSH
• reprodukovatelnost výsledků MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA * MeSH
• vysoce účinné nukleotidové sekvenování * MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Názvy látek
• RNA ribozomální 16S MeSH