Phylogenetic structure of microbial communities
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The phylogenetic composition, bacterial biomass, and biovolume of both planktonic and biofilm communities were studied in a low-order Bystřice stream near Olomouc City, in the Czech Republic. The aim of the study was to compare the microbial communities colonizing different biofilm substrata (stream aggregates, stream sediment, underwater tree roots, stream stones, and aquatic macrophytes) to those of free-living bacteria. The phylogenetic composition was analyzed using fluorescence in situ hybridization for main phylogenetic groups. All phylogenetic groups studied were detected in all sample types. The stream stone was the substratum where nearly all phylogenetic groups were the most abundant, while the lowest proportion to the DAPI-stained cells was found for free-living bacteria. The probe specific for the domain Bacteria detected 20.6 to 45.8 % of DAPI-stained cells while the probe specific for the domain Archaea detected 4.3 to 17.9 %. The most abundant group of Proteobacteria was Alphaproteobacteria with a mean of 14.2 %, and the least abundant was Betaproteobacteria with a mean of 11.4 %. The average value of the Cytophaga-Flavobacteria group was 10.5 %. Total cell numbers and bacterial biomass were highest in sediment and root biofilm. The value of cell biovolume was highest in stone biofilm and lowest in sediment. Overall, this study revealed relevant differences in phylogenetic composition, bacterial biomass, and biovolume between different stream biofilms and free-living bacteria.
- MeSH
- Archaea klasifikace genetika izolace a purifikace MeSH
- Bacteria klasifikace genetika izolace a purifikace MeSH
- biofilmy * MeSH
- biomasa MeSH
- chemické jevy MeSH
- fylogeneze * MeSH
- geologické sedimenty mikrobiologie MeSH
- hybridizace in situ fluorescenční MeSH
- řeky mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Geografické názvy
- Česká republika MeSH
The potential for comparing microbial community population structures has been greatly enhanced by developments in next generation sequencing methods that can generate hundreds of thousands to millions of reads in a single run. Conversely, many microbial community comparisons have been published with no more than 1,000 sequences per sample. These studies have presented data on levels of shared operational taxonomic units (OTUs) between communities. Due to lack of coverage, that approach might compromise the conclusions about microbial diversity and the degree of difference between environments. In this study, we present data from recent studies that highlight this problem. Also, we analyzed datasets of 16 rRNA sequences with small and high sequence coverage from different environments to demonstrate that the level of sequencing effort used for analyzing microbial communities biases the results. We randomly sampled pyrosequencing-generated 16S rRNA gene libraries with increasing sequence effort. Sequences were used to calculate Good's coverage, the percentage of shared OTUs, and phylogenetic distance measures. Our data showed that simple counts of presence/absence of taxonomic unities do not reflect the real similarity in membership and structure of the bacterial communities and that community comparisons based on phylogenetic tests provide a way to test statistically significant differences between two or more environments without need an exhaustive sampling effort.
- MeSH
- Bacteria klasifikace genetika izolace a purifikace MeSH
- biodiverzita MeSH
- DNA bakterií genetika MeSH
- fylogeneze MeSH
- mikrobiologie životního prostředí MeSH
- RNA ribozomální 16S genetika MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
Shark Bay, Western Australia is a World Heritage area with extensive microbial mats and stromatolites. Microbial communities that comprise these mats have developed a range of mitigation strategies against changing levels of photosynthetically active and ultraviolet radiation, including the ability to biosynthesise the UV-absorbing natural products scytonemin and mycosporine-like amino acids (MAAs). To this end, the distribution of photoprotective pigments within Shark Bay microbial mats was delineated in the present study. This involved amplicon sequencing of bacterial 16S rDNA from communities at the surface and subsurface in three distinct mat types (smooth, pustular and tufted), and correlating this data with the chemical and molecular distribution of scytonemin and MAAs. Employing UV spectroscopy and MS/MS fragmentation, mycosporine-glycine, asterina and an unknown MAA were identified based on typical fragmentation patterns. Marker genes for scytonemin and MAA production (scyC and mysC) were amplified from microbial mat DNA and placed into phylogenetic context against a broad screen throughout 363 cyanobacterial genomes. Results indicate that occurrence of UV screening compounds is associated with the upper layer of Shark Bay microbial mats, and the occurrence of scytonemin is closely dependent on the abundance of cyanobacteria.
- MeSH
- aminokyseliny metabolismus MeSH
- fenoly metabolismus MeSH
- fotosyntéza MeSH
- fylogeneze * MeSH
- glycin metabolismus MeSH
- indoly metabolismus MeSH
- mikrobiota účinky záření MeSH
- sinice klasifikace genetika izolace a purifikace metabolismus MeSH
- tandemová hmotnostní spektrometrie MeSH
- ultrafialové záření MeSH
- výpočetní biologie MeSH
- zátoky mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Austrálie MeSH
Phylogenetic analysis was conducted to examine ruminal bacteria in two ruminal fractions (adherent fraction vs. liquid fraction) collected from cattle fed with two different diets: forage alone vs. forage plus concentrate. One hundred forty-four 16S rRNA gene (rrs) sequences were obtained from clone libraries constructed from the four samples. These rrs sequences were assigned to 116 different operational taxonomic units (OTUs) defined at 0.03 phylogenetic distance. Most of these OTUs could not be assigned to any known genus. The phylum Firmicutes was represented by approximately 70% of all the sequences. By comparing to the OTUs already documented in the rumen, 52 new OTUs were identified. UniFrac, SONS, and denaturing gradient gel electrophoresis analyses revealed difference in diversity between the two fractions and between the two diets. This study showed that rrs sequences recovered from small clone libraries can still help identify novel species-level OTUs.
- MeSH
- bachor mikrobiologie MeSH
- Bacteria klasifikace genetika izolace a purifikace MeSH
- biodiverzita MeSH
- fylogeneze MeSH
- genomová knihovna MeSH
- krmivo pro zvířata mikrobiologie MeSH
- mikrobiální společenstva genetika MeSH
- polymorfismus délky restrikčních fragmentů MeSH
- ribotypizace MeSH
- RNA ribozomální 16S analýza MeSH
- sekvenční analýza DNA MeSH
- skot MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.
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
To investigate the link between the functionality and the diversity of microbial communities under strong selective pressure from pollutants, two types of mesocosms that simulate natural attenuation and phytoremediation were generated using soil from a site highly contaminated with jet fuel and under air-sparging treatment. An increase in the petroleum hydrocarbon concentration from 4900 to 18,500 mg kg(-1) dw soil simulated a pollutant rebound (postremediation pollutant reversal due to residual contamination). Analysis of soil bacterial communities by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments showed stronger changes and selection for a phylogenetically diverse microbial population in the mesocosms with pollutant-tolerant willow trees. Enumeration of the main subfamilies of catabolic genes characteristic to the site detected a rapid increase in the degradation potential of both systems. A marked increase in the abundance of genes encoding extradiol dioxygenases with a high affinity towards various catecholic substrates was found in the planted mesocosms. The observed adaptive response to the simulated pollutant rebound, characterized by increased catabolic gene abundance, but with different changes in the microbial structure, can be explained by functional redundancy in biodegrading microbial communities.
- MeSH
- Bacteria klasifikace genetika metabolismus MeSH
- biodegradace MeSH
- fylogeneze MeSH
- fyziologická adaptace MeSH
- látky znečišťující půdu metabolismus toxicita MeSH
- molekulární sekvence - údaje MeSH
- oxygenasy genetika metabolismus MeSH
- půda chemie MeSH
- půdní mikrobiologie MeSH
- ropa metabolismus toxicita MeSH
- sekvence nukleotidů MeSH
- uhlovodíky metabolismus toxicita MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Phylogenetic distances of coexisting species differ greatly within plant communities, but their consequences for decomposers and decomposition remain unknown. We hypothesized that large phylogenetic distance of leaf litter mixtures increases differences of their litter traits, which may, in turn, result in increased resource complementarity or decreased resource concentration for decomposers and hence increased or decreased chemical transformation and reduction of litter. We conducted a litter mixture experiment including 12 common temperate tree species (evolutionarily separated by up to 106 Myr), and sampled after seven months, at which average mass loss was more than 50%. We found no effect of increased phylogenetic distance on litter mass loss or on abundance and diversity of invertebrate decomposers. However, phylogenetic distance decreased microbial biomass and increased carbon/nitrogen (C/N) ratios of litter mixtures. Consistently, four litter traits showed (marginally) significant phylogenetic signal and in three of these traits increasing trait difference decreased microbial biomass and increased C/N. We suggest that phylogenetic proximity of litter favours microbial decomposers and chemical transformation of litter owing to a resource concentration effect. This leads to a new hypothesis: closely related plant species occurring in the same niche should promote and profit from increased nutrient availability.
- MeSH
- bezobratlí fyziologie MeSH
- biodegradace MeSH
- biomasa MeSH
- dusík analýza MeSH
- fylogeneze MeSH
- lesy MeSH
- listy rostlin chemie klasifikace MeSH
- Magnoliopsida klasifikace fyziologie MeSH
- mikrobiota fyziologie MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- stromy klasifikace fyziologie MeSH
- uhlík analýza MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Francie MeSH
Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated by erm resistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.
- MeSH
- Bacteria klasifikace genetika izolace a purifikace MeSH
- bakteriální nálož MeSH
- biodiverzita MeSH
- DNA bakterií chemie genetika MeSH
- dusík analýza MeSH
- fylogeneze MeSH
- houby klasifikace genetika izolace a purifikace MeSH
- koncentrace vodíkových iontů MeSH
- methyltransferasy genetika MeSH
- molekulární sekvence - údaje MeSH
- organické látky analýza MeSH
- počet mikrobiálních kolonií MeSH
- polymorfismus délky restrikčních fragmentů MeSH
- půda chemie MeSH
- půdní mikrobiologie MeSH
- rostliny mikrobiologie MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- uhlík analýza MeSH
- vysokoúčinná kapalinová chromatografie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Ecosystems worldwide are exposed to pollutants connected to the industrial production of pharmaceuticals. The objective of this study was to study the composition and characteristics of the soil microbial communities that had been exposed to long-term selection pressure caused by the industrial production of penicillin G. Soil samples from four sites among the penicillin G production plant were analysed using 16S rRNA profiling via Illumina MiSeq platform and were compared with the control samples from four sites outside the plant. Total metagenomic DNA from the impacted soil was also used for the preparation of E. coli T1R-based fosmid library which was consequently qualitatively tested for the presence of penicillin G acylase (PGA)-encoding genes using the method of sequence homology. Analyses of alpha diversity revealed that the long-term antibiotic presence in the soil significantly increased the microbial diversity and richness in terms of Shannon diversity index (p = 0.002) and Chao estimates (p = 0.004). Principal component analysis showed that the two types of communities (on-site and control) could be separated at the phylum, class and genus level. The on-site soil was enriched in Betaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetia, while a significant decrease in Actinobacteria was observed. Metagenomic fosmid library revealed high hit rates in identifying PGAs (14 different genes identified) and confirmed the biotechnological potential of soils impacted by anthropogenic activity. This study offers new insights into the changes in microbial communities of soils exposed to anthropogenic activity as well as indicates that those soils may represent a hotspot for biotechnologically interesting targets.
- MeSH
- antibakteriální látky biosyntéza MeSH
- Bacteria klasifikace genetika izolace a purifikace metabolismus MeSH
- biodiverzita MeSH
- DNA bakterií genetika MeSH
- Escherichia coli genetika MeSH
- fylogeneze MeSH
- látky znečišťující půdu MeSH
- metagenom MeSH
- metagenomika MeSH
- mikrobiota * genetika MeSH
- průmyslová mikrobiologie MeSH
- půda MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S genetika MeSH
- Publikační typ
- časopisecké články MeSH
