microbial functioning
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The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.
- MeSH
- Bacteria klasifikace enzymologie genetika MeSH
- ekologie MeSH
- ekosystém MeSH
- houby klasifikace enzymologie genetika MeSH
- metabolomika MeSH
- metagenomika MeSH
- mikrobiota genetika MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
The increasing use of silver nanoparticles (AgNPs) due to their well-known antimicrobial activity, has led to their accumulation in soil ecosystems. However, the impact of environmental realistic concentrations of AgNPs on the soil microbial community has been scarcely studied. In this work, we have assessed the impact of AgNPs, that mimic real concentrations in nature, on tropical soils cultivated with Coffea arabica under conventional and organic management systems. We evaluated the biomass, extracellular enzyme activities, and diversity of the soil microbial community, in a microcosm experiment as a function of time. After seven days of incubation, we found an increase in microbial biomass in an AgNPs-concentration-independent manner. In contrast, after 60-day-incubation, there was a decrease in Gram+ and actinobacterial biomass, in both soils and all AgNPs concentrations. Soil physico-chemical properties and enzyme activities were not affected overall by AgNPs. Regarding the microbial community composition, only some differences in the relative abundance at phylum and genus level in the fungal community were observed. Our results suggest that environmental concentrations of AgNPs affected microbial biomass but had little impact on microbial diversity and may have little effects on the soil biogeochemical cycles mediated by extracellular enzyme activities.
- MeSH
- Bacteria klasifikace účinky léků enzymologie genetika MeSH
- bakteriální geny MeSH
- beta-glukosidasa chemie MeSH
- biomasa MeSH
- kovové nanočástice toxicita MeSH
- kyselá fosfatasa chemie MeSH
- látky znečišťující půdu toxicita MeSH
- mikrobiota účinky léků MeSH
- půdní mikrobiologie MeSH
- RNA ribozomální 16S MeSH
- stříbro toxicita MeSH
- ureasa chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Chemical fertilizers have substantially increased crop yields but have also contributed to significant environmental challenges, including soil and water contamination and the emergence of human health issues. As a more sustainable alternative, biofertilizers-comprising beneficial microorganisms such as bacteria-have been promoted as eco-friendly solutions. However, their use may pose risks to soil microbial communities and biodiversity under certain conditions. For instance, horizontal gene transfer among bacteria can convert non-pathogenic strains into pathogenic ones. Additionally, the introduction of microbial inoculants may outcompete native microbial species, potentially disrupting soil microbial balance and impairing ecosystem functioning. The long-term effects of biofertilizers on nutrient cycling and soil biodiversity remain insufficiently studied. To mitigate these risks, it is crucial to establish rigorous production standards, prioritize native microbial strains, continuously monitor soil microbial dynamics, and implement comprehensive regulatory frameworks. Therefore, the adoption of biofertilizers in agricultural practices should be approached cautiously and guided by evidence-based regulations.
One of the universal traits of microorganisms is their ability to form multicellular structures, the cells of which differentiate and communicate via various signaling molecules. Reactive oxygen species (ROS), and hydrogen peroxide in particular, have recently become well-established signaling molecules in higher eukaryotes, but still little is known about the regulatory functions of ROS in microbial structures. Here we summarize current knowledge on the possible roles of ROS during the development of colonies and biofilms, representatives of microbial multicellularity. In Saccharomyces cerevisiae colonies, ROS are predicted to participate in regulatory events involved in the induction of ammonia signaling and later on in programmed cell death in the colony center. While the latter process seems to be induced by the total ROS, the former event is likely to be regulated by ROS-homeostasis, possibly H(2)O(2)-homeostasis between the cytosol and mitochondria. In Candida albicans biofilms, the predicted signaling role of ROS is linked with quorum sensing molecule farnesol that significantly affects biofilm formation. In bacterial biofilms, ROS induce genetic variability, promote cell death in specific biofilm regions, and possibly regulate biofilm development. Thus, the number of examples suggesting ROS as signaling molecules and effectors in the development of microbial multicellularity is rapidly increasing.
Microorganisms do not live alone, but rather they communicate using diverse „languages“. In general, each bacterial species produces and responds to a unique autoinducer signal. Gram-negative bacteria use N-acylated homoserine lactones and gram-positive bacteria use oligopeptides as autoinducers. Function of autoinducer 2 is bacterial interspecies cell-to-cell communication. The structure and function of two main signaling molecules (farnesol and tyrosol) in the C. albicans quorum sensing (QS) system were also already described. Signaling molecules control the behavior of the whole population (especially virulence factors expression). That’s why QS systems represent a new therapeutic target, especially because of an increasing worldwide antibiotic resistance. Quorum sensing inhibitors are a promising direction in the treatment of infection caused by pathogenic micro¬organisms.
- Klíčová slova
- signální molekuly, N-acyl-homoserin lakton, inhibitory quorum sensing,
- MeSH
- antibakteriální látky MeSH
- antiinfekční látky MeSH
- Bacteria genetika klasifikace metabolismus patogenita MeSH
- bakteriální léková rezistence MeSH
- biofilmy MeSH
- Candida albicans patogenita MeSH
- česnek MeSH
- houby metabolismus patogenita MeSH
- kvasinky metabolismus patogenita MeSH
- léčivé rostliny chemie klasifikace MeSH
- mezibuněčná komunikace MeSH
- Pseudomonas aeruginosa patogenita MeSH
- quorum sensing * fyziologie genetika účinky léků MeSH
- signální transdukce MeSH
- Vibrio cholerae patogenita MeSH
- virulence genetika MeSH
- Publikační typ
- přehledy MeSH
Microorganisms and eukaryotic human cells coexist in synergistic relationships in nearly every niche of the human body. The female genital tract consisting of the vagina, uterus with its cervix and endometrium, uterine tubes and ovaries - harbors its own typical microbiota, which accounts for 9 % of the total bacterial population in females. To this organ system, we also assigned the microbiome of the placenta, which has not been studied much until now. Among the spectrum of microbial species, the female genital tract is mainly dominated by Lactobacillus species, which are considered to be one of the simplest yet most important microbial communities. However, this relationship between macro- and micro-organisms seems to have a number of physiological functions, e.g., the vaginal and cervical microbiota have unique impact on reproductive health. The aim of this review was to provide current view on female genital tract microbiota and its role in reproductive health. We describe in detail the association of vaginal or tubal epithelium with microbiota or the role of microbiota in normal placental function.
- MeSH
- lidé MeSH
- mikrobiota * fyziologie MeSH
- placenta MeSH
- těhotenství MeSH
- vagina mikrobiologie MeSH
- vejcovody * mikrobiologie MeSH
- ženské pohlavní orgány MeSH
- Check Tag
- lidé MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
The concept of small-molecule mimicry even of weak microbial metabolites present in rodents and humans, as a means to expand drug repertoires, is new. Hitherto, there are few proof-of-concept papers demonstrating utility of this concept. More recently, papers demonstrating mimicry of intestinal microbial metabolites could expand the drug repertoire for diseases such as inflammatory bowel disease (IBD). We opine that, as more functional metabolite-receptor pairings are discovered, small-molecule metabolite mimicry could be a significant effort in drug discovery.
- MeSH
- lidé MeSH
- mikrobiota * MeSH
- molekulární mimikry * MeSH
- objevování léků * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Soil from Trhové Dušníky (Příbram, Czech Republic) is characterized by its high polymetallic accumulations in Pb-Ag-Zn due to mining and smelting activities. In previous studies performed in our research group, we have evaluated the potential use of amendments that would reduce the mobility and availability of metals such as Hg. We have observed that the application of digestate and fly ash in metal-polluted soil has an impact in immobilizing these metals. However, until now we have lacked information about the effect of these amendments on soil microbial functionality and communities. The multi-contaminated soil was used to grow wheat in a pot experiment to evaluate the impact of digestate and fly ash application in soil microbial communities. Soil samples were collected after 30 and 60 days of treatment. The digestate application improved chemical attributes such as the content in total organic carbon (TOC), water soluble carbon (WSOC), total soluble carbon (C), total soluble nitrogen (N), and inorganic N forms (NO3(-)) as consequence of high content in C and N which is contained in digestate. Likewise, microbial activity was greatly enhanced by digestate application, as was physiological diversity. Bacterial and fungal communities were increased, and the microbial biomass was highly enhanced. These effects were evident after 30 and 60 days of treatment. In contrast, fly ash did not have a remarkable effect when compared to digestate, but soil microbial biomass was positively affected as a consequence of macro- and micro-nutrient sources applied by the addition of fly ash. This study indicates that digestate can be used successfully in the remediation of metal-contaminated soil.
- MeSH
- biomasa MeSH
- dusík analýza MeSH
- hornictví MeSH
- houby fyziologie MeSH
- kovy analýza metabolismus MeSH
- látky znečišťující půdu analýza metabolismus MeSH
- mikrobiální společenstva MeSH
- popel uhelný * MeSH
- pšenice růst a vývoj MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- rtuť analýza metabolismus MeSH
- uhlík analýza chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Peatland vegetation is composed mostly of mosses, graminoids and ericoid shrubs, and these have a distinct impact on peat biogeochemistry. We studied variation in soil microbial communities related to natural peatland microhabitats dominated by Sphagnum, cotton-grass and blueberry. We hypothesized that such microhabitats will be occupied by structurally and functionally different microbial communities, which will vary further during the vegetation season due to changes in temperature and photosynthetic activity of plant dominants. This was addressed using amplicon-based sequencing of prokaryotic and fungal rDNA and qPCR with respect to methane-cycling communities. Fungal communities were highly microhabitat-specific, while prokaryotic communities were additionally directed by soil pH and total N content. Seasonal alternations in microbial community composition were less important; however, they influenced the abundance of methane-cycling communities. Cotton-grass and blueberry bacterial communities contained relatively more α-Proteobacteria but less Chloroflexi, Fibrobacteres, Firmicutes, NC10, OD1 and Spirochaetes than in Sphagnum. Methanogens, syntrophic and anaerobic bacteria (i.e. Clostridiales, Bacteroidales, Opitutae, Chloroflexi and Syntrophorhabdaceae) were suppressed in blueberry indicating greater aeration that enhanced abundance of fungi (mainly Archaeorhizomycetes) and resulted in the highest fungi-to-bacteria ratio. Thus, microhabitats dominated by different vascular plants are inhabited by unique microbial communities, contributing greatly to spatial functional diversity within peatlands.
- MeSH
- Bacteria klasifikace genetika izolace a purifikace metabolismus MeSH
- brusnice s jedlými plody růst a vývoj mikrobiologie MeSH
- houby klasifikace genetika izolace a purifikace metabolismus MeSH
- lipnicovité růst a vývoj mikrobiologie MeSH
- methan metabolismus MeSH
- mikrobiota MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- rašeliníky růst a vývoj mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.
