Microbial community structure
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Forests are essential biomes for global biogeochemical cycles, and belowground microorganisms have a key role in providing relevant ecosystem services. To predict the effects of environmental changes on these ecosystem services requires a comprehensive understanding of how biotic and abiotic factors drive the composition of microbial communities in soil. However, microorganisms are not homogeneously distributed in complex environments such as soil, with different features affecting microbes at different extent depending on the niche they occupy. Indeed, this spatial heterogeneity hampers the extrapolation of microbial diversity study results from particular habitats to the ecosystem level, even if the resolution of the more recent studies has increased significantly after the standardization of high-throughput sequencing techniques. The present work intends to give a comprehensive view of the knowledge accumulated until date defining the more important drivers determining the structure of forest soil microbial communities from fine to continental scales.
- MeSH
- Bacteria MeSH
- ekosystém * MeSH
- lesy * MeSH
- mikrobiota fyziologie MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Feedstock type influences bacterial and methanogenic communities in anaerobic digestion. These two communities work tightly to maintain the stability of anaerobic digestion. How to quick report the changes of microbial community structure especially methanogenesis is the key issue for optimizing anaerobic digestion process. In this study, 13C isotope fractionations of CH4 and CO2 in biogas and microbial community composition were analyzed in 5 different feedstocks. Our results showed that grass silage, maize silage and swine manure fed reactors had similar δ 13C values and methanogenic community composition, dominated by Methanosarcinaceae. The lowest δ 13CH4 values were detected in straw and chicken manure fed reactors, reflecting reduced microbial degradation of material or the presence of toxic components in these feedstocks. The straw fed bioreactor lead to low δ 13CH4 values, probably reflecting relatively high levels of the syntrophic acetate oxidizing bacteria, Synergistaceae and Syntrophaceae, which might work collectively with hydrogenotrophic methanogens, resulting in the low δ 13CH4 values in this bioreactor. Significantly, all core microbes in the 5 different feedstock fed bioreactors were either Clostridia species or related to the Synergistaceae (syntrophic acetate oxidizing bacteria).
- MeSH
- anaerobióza MeSH
- biopaliva * MeSH
- bioreaktory MeSH
- hnůj MeSH
- izotopy MeSH
- methan MeSH
- mikrobiota * MeSH
- prasata MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
V přírodě rostou mikroby většinou v podobě biofilmu. Biofilm je strukturované mikrobiální společenství, uložené v mezibuněčné hmotě a adherující k inertním i živým povrchům. Mikrobiální buňky rostoucí v podobě biofilmu se svými vlastnostmi zásadně liší od volně se vznášejících buněk planktonických, především jsou vysoce odolné k zevním vlivům. Popsán je vývoj biofilmu a jeho architektura. Biofilmy představují vyšší a složitější způsob života mikrobů a jsou analogií tkání vyšších organismů. Vykazují totiž 1. účinnou homeostázu, 2. prvky primitivního oběhového systému, 3. rysy buněčné kooperace a specializace a 4. značný způsob ochrany před antimikrobiálními činiteli.Povědomí o biofilmu proniká do lékařské mikrobiologie pomalu, i když platí, že bakterie v biofilmu jsou až o tři řády odolnější k účinku antibiotik než buňky planktonické. Uvedeny jsou příklady chronických a perzistentních infekcí, v jejichž patogenezi se významně uplatňuje biofilm vznikající jak na přirozeném povrchu tkání, tak na neživém povrchu různých pomůcek a náhrad zaváděných do makroorganismu. Naznačeny jsou cesty k terapeutickému ovlivnění biofilmu a je zdůrazněna prospěšná role biofilmu v ochraně sliznic před patogeny.
In natural environment, microbes grow mostly in the form of a biofilm. Biofilm is a structured microbial community placed in an extracellular matrix and adhering to both inert and live surfaces. Microbial cells growing as a biofilm have qualities fundamentally different from those of freely floating planctonic cells, in the first place they are extremely resistant to outer influences. The development and the architecture of the biofilm are described. Biofilms represent a higher and more complex mode of microbial life and are an analogy of tissues of higher organisms. They are characterised by 1. an effective homeostasis, 2. components of a primitive circulatory system, 3. elements of cellular cooperation and specialization, and 4. a considerable way of protection against antimicrobial agents. The awareness of the biofilm penetrates only slowly into medical microbiology, even though it has been known that bacteria in the biofilm are as much as a thousand timesmore resistant to the effect of antibiotics than planctonic cells. Examples of chronic and persistent infections are given, in the pathogenesis of which a significant role is played by the biofilm, growing both on the natural surface of tissues and on the inert surface of different devices and prostheses inserted into the macrooganism. Possible ways to the therapeutic tampering with the biofilm are foreshadowed and the beneficial role of the biofilm in the protection of mucosal surfaces against pathogens is emphasized.
- MeSH
- antibiotická rezistence MeSH
- bakteriální adheze MeSH
- biofilmy mikrobiologie MeSH
- Publikační typ
- přehledy MeSH
In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.
- MeSH
- Bacteria klasifikace genetika izolace a purifikace MeSH
- biodiverzita * MeSH
- fylogeneze MeSH
- klimatické změny MeSH
- lesy MeSH
- nadmořská výška MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- roční období MeSH
- teplota MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Itálie MeSH
Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.
- MeSH
- analýza moči MeSH
- biodiverzita * MeSH
- komorbidita MeSH
- lidé středního věku MeSH
- lidé MeSH
- metagenomika metody MeSH
- mikrobiota * MeSH
- močové ústrojí mikrobiologie MeSH
- senioři MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Current models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition (16S rRNA gene sequencing) to physicochemical parameters (e.g. dissolved oxygen and nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: (i) glacial rivers; (ii) active layer thaw-fed streams and waterbodies and (iii) Lake Hazen, into which (i) and (ii) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial communities were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that these communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.
- MeSH
- ekosystém MeSH
- jezera mikrobiologie MeSH
- klimatické změny MeSH
- mikrobiologie vody * MeSH
- mikrobiota * MeSH
- půda MeSH
- půdní mikrobiologie MeSH
- řeky mikrobiologie MeSH
- RNA ribozomální 16S MeSH
- roční období MeSH
- sladká voda mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Arktida MeSH
- Nunavut MeSH
We studied the differences in a microbial community structure with respect to the water pollution level and seasonal changes. The determination of phylogenetic groups of Bacteria and Archaea was done using fluorescent in situ hybridization (FISH). The total number of microorganisms was determined by direct counting of DAPI (4',6-diamidino-2-phenylindole) stained samples using a fluorescence microscope. Our results showed that the microbial community structure was significantly dependent on the level of water pollution, both in absolute microbial counts and in relative abundance of phylogenetic groups. For surface water with anthropogenic pollution, the microbial community with significant proportion of Betaproteobacteria and Cytophaga-Flavobacterium was characteristic. Gammaproteobacteria were significant in municipal waste water. In microbial communities with low numbers of microorganisms (e.g. non-polluted water and some industrial waste water) represented the significant component groups Alphaproteobacteria and Archaea. The impact of seasonal changes on the microbial distribution was not significant.
- MeSH
- Archaea klasifikace účinky léků genetika MeSH
- Bacteria klasifikace účinky léků genetika MeSH
- hybridizace in situ fluorescenční MeSH
- látky znečišťující vodu toxicita MeSH
- mikrobiologie vody MeSH
- monitorování životního prostředí MeSH
- roční období MeSH
- znečištění vody škodlivé účinky analýza MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Forests are recognised as spatially heterogeneous ecosystems. However, knowledge of the small-scale spatial variation in microbial abundance, community composition and activity is limited. Here, we aimed to describe the heterogeneity of environmental properties, namely vegetation, soil chemical composition, fungal and bacterial abundance and community composition, and enzymatic activity, in the topsoil in a small area (36 m(2)) of a highly heterogeneous regenerating temperate natural forest, and to explore the relationships among these variables. The results demonstrated a high level of spatial heterogeneity in all properties and revealed differences between litter and soil. Fungal communities had substantially higher beta-diversity than bacterial communities, which were more uniform and less spatially autocorrelated. In litter, fungal communities were affected by vegetation and appeared to be more involved in decomposition. In the soil, chemical composition affected both microbial abundance and the rates of decomposition, whereas the effect of vegetation was small. Importantly, decomposition appeared to be concentrated in hotspots with increased activity of multiple enzymes. Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments.
Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material.
- MeSH
- aktivace enzymů MeSH
- dusík metabolismus MeSH
- enzymy metabolismus MeSH
- hydrolýza MeSH
- mikrobiota * MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- uhlík metabolismus MeSH
- zeměpis MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Arktida MeSH
- Sibiř MeSH
Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.
