Recognition of the environmental role of photoheterotrophic bacteria has been one of the main themes of aquatic microbiology over the last 15 years. Aside from cyanobacteria and proteorhodopsin-containing bacteria, aerobic anoxygenic phototrophic (AAP) bacteria are the third most numerous group of phototrophic prokaryotes in the ocean. This functional group represents a diverse assembly of species which taxonomically belong to various subgroups of Alpha-, Beta- and Gammaproteobacteria. AAP bacteria are facultative photoheterotrophs which use bacteriochlorophyll-containing reaction centers to harvest light energy. The light-derived energy increases their bacterial growth efficiency, which provides a competitive advantage over heterotrophic species. Thanks to their enzymatic machinery AAP bacteria are active, rapidly growing organisms which contribute significantly to the recycling of organic matter. This chapter summarizes the current knowledge of the ecology of AAP bacteria in aquatic environments, implying their specific role in the microbial loop.

• MeSH
• aerobní bakterie fyziologie   MeSH
• biodiverzita MeSH
• ekologie MeSH
• fototrofní procesy fyziologie   MeSH
• mikrobiologie vody * MeSH
• oceány a moře MeSH
• potravní řetězec MeSH
• vodní organismy fyziologie   MeSH
• životní prostředí * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Geografické názvy
• oceány a moře 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

Trap fluid of aquatic carnivorous plants of the genus Utricularia hosts specific microbiomes consisting of commensal pro- and eukaryotes of largely unknown ecology. We examined the characteristics and dynamics of bacteria and the three dominant eukaryotes, i.e. the algae-bearing ciliate Tetrahymena utriculariae (Ciliophora), a green flagellate Euglena agilis (Euglenophyta), and the alga Scenedesmus alternans (Chlorophyta), associated with the traps of Utricularia reflexa. Our study focused on ecological traits and life strategies of the highly abundant ciliate whose biomass by far exceeds that of other eukaryotes and bacteria independent of the trap age. The ciliate was the only bacterivore in the traps, driving rapid turnover of bacterial standing stock. However, given the large size of the ciliate and the cell-specific uptake rates of bacteria we estimated that bacterivory alone would likely be insufficient to support its apparent rapid growth in traps. We suggest that mixotrophy based on algal symbionts contributes significantly to the diet and survival strategy of the ciliate in the extreme (anaerobic, low pH) trap-fluid environment. We propose a revised concept of major microbial interactions in the trap fluid where ciliate bacterivory plays a central role in regeneration of nutrients bound in rapidly growing bacterial biomass.

• MeSH
• anaerobióza MeSH
• Bacteria MeSH
• biomasa MeSH
• Chlorophyta MeSH
• Ciliophora fyziologie   MeSH
• ekologie * MeSH
• koncentrace vodíkových iontů MeSH
• Magnoliopsida chemie   růst a vývoj   mikrobiologie   parazitologie   MeSH
• mikrobiální společenstva MeSH
• stadia vývoje MeSH
• symbióza fyziologie   MeSH
• Tetrahymena růst a vývoj   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND AND AIMS: Rootless carnivorous plants of the genus Utricularia are important components of many standing waters worldwide, as well as suitable model organisms for studying plant-microbe interactions. In this study, an investigation was made of the importance of microbial dinitrogen (N2) fixation in the N acquisition of four aquatic Utricularia species and another aquatic carnivorous plant, Aldrovanda vesiculosa. METHODS: 16S rRNA amplicon sequencing was used to assess the presence of micro-organisms with known ability to fix N2. Next-generation sequencing provided information on the expression of N2 fixation-associated genes. N2 fixation rates were measured following (15)N2-labelling and were used to calculate the plant assimilation rate of microbially fixed N2. KEY RESULTS: Utricularia traps were confirmed as primary sites of N2 fixation, with up to 16 % of the plant-associated microbial community consisting of bacteria capable of fixing N2. Of these, rhizobia were the most abundant group. Nitrogen fixation rates increased with increasing shoot age, but never exceeded 1·3 μmol N g(-1) d. mass d(-1). Plant assimilation rates of fixed N2 were detectable and significant, but this fraction formed less than 1 % of daily plant N gain. Although trap fluid provides conditions favourable for microbial N2 fixation, levels of nif gene transcription comprised <0·01 % of the total prokaryotic transcripts. CONCLUSIONS: It is hypothesized that the reason for limited N2 fixation in aquatic Utricularia, despite the large potential capacity, is the high concentration of NH4-N (2·0-4·3 mg L(-1)) in the trap fluid. Resulting from fast turnover of organic detritus, it probably inhibits N2 fixation in most of the microorganisms present. Nitrogen fixation is not expected to contribute significantly to N nutrition of aquatic carnivorous plants under their typical growth conditions; however, on an annual basis the plant-microbe system can supply nitrogen in the order of hundreds of mg m(-2) into the nutrient-limited littoral zone, where it may thus represent an important N source.

• MeSH
• amoniové sloučeniny analýza   MeSH
• Bacteria genetika   izolace a purifikace   metabolismus   MeSH
• bakteriální RNA chemie   genetika   MeSH
• Droseraceae metabolismus   mikrobiologie   MeSH
• dusík metabolismus   MeSH
• ekologie MeSH
• ekosystém MeSH
• fixace dusíku * MeSH
• izotopy dusíku MeSH
• Magnoliopsida metabolismus   mikrobiologie   MeSH
• molekulární sekvence - údaje MeSH
• RNA ribozomální 16S chemie   genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza RNA MeSH
• voda metabolismus   MeSH
• výhonky rostlin metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.

• MeSH
• Bacteria metabolismus   MeSH
• Eukaryota MeSH
• mikrobiologie vody * MeSH
• mikrobiota * MeSH
• potravní řetězec * MeSH
• predátorské chování * MeSH
• řeky MeSH
• Tetrahymena fyziologie   MeSH
• uhlík metabolismus   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• audiovizuální média MeSH
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

Litter decomposition is a vital part of the global carbon cycle as it determines not only the amount of carbon to be sequestered, but also how fast carbon re-enters the cycle. Freshwater systems play an active role in the carbon cycle as it receives, and decomposes, terrestrial litter material alongside decomposing aquatic plant litter. Decomposition of organic matter in the aquatic environment is directly controlled by water temperature and nutrient availability, which are continuously affected by global change. We adapted the Tea Bag Index (TBI), a highly standardized methodology for determining soil decomposition, for lakes by incorporating a leaching factor. By placing Lipton pyramid tea bags in the aquatic environment for 3 h, we quantified the period of intense leaching which usually takes place prior to litter (tea) decomposition. Standard TBI methodology was followed after this step to determine how fast decomposition takes place (decomposition rate, k1) and how much of the material cannot be broken down and is thus sequestered (stabilization factor, S). A Citizen Science project was organized to test the aquatic TBI in 40 European lakes located in four climate zones, ranging from oligotrophic to hypereutrophic systems. We expected that warmer and/or eutrophic lakes would have a higher decomposition rate and a more efficient microbial community resulting in less tea material to be sequestered. The overall high decomposition rates (k1) found confirm the active role lakes play in the global carbon cycle. Across climate regions the lakes in the warmer temperate zone displayed a higher decomposition rate (k1) compared to the colder lakes in the continental and polar zones. Across trophic states, decomposition rates were higher in eutrophic lakes compared to oligotrophic lakes. Additionally, the eutrophic lakes showed a higher stabilization (S), thus a less efficient microbial community, compared to the oligotrophic lakes, although the variation within this group was high. Our results clearly show that the TBI can be used to adequately assess the decomposition process in aquatic systems. Using "alien standard litter" such as tea provides a powerful way to compare decomposition across climates, trophic states and ecosystems. By providing standardized protocols, a website, as well as face to face meetings, we also showed that collecting scientifically relevant data can go hand in hand with increasing scientific and environmental literacy in participants. Gathering process-based information about lake ecosystems gives managers the best tools to anticipate and react to future global change. Furthermore, combining this process-based information with citizen science, thus outreach, is in complete agreement with the Water Framework Directive goals as set in 2010.

• MeSH
• čaj MeSH
• ekosystém * MeSH
• jezera * MeSH
• podnebí MeSH
• uhlík MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups, it is advisable to combine HTS with quantification using microscopy and/or the addition of internal standards.IMPORTANCE High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

• MeSH
• Bacteria klasifikace   MeSH
• Eukaryota klasifikace   MeSH
• fluorescenční mikroskopie MeSH
• fylogeneze MeSH
• mikrobiota * MeSH
• mořská voda mikrobiologie   MeSH
• reprodukovatelnost výsledků MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• statistické modely MeSH
• vysoce účinné nukleotidové sekvenování * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Microbial mats are abundant in many alpine and polar aquatic ecosystems. With warmer temperatures, new hydrologic pathways are developing in these regions and increasing dissolved nutrient fluxes. In the McMurdo Dry Valleys, thermokarsting may release both nutrients and sediment, and has the potential to influence mats in glacial meltwater streams. To test the role of nutrient inputs on community structure, we created nutrient diffusing substrata (NDS) with agar enriched in N, P and N + P, with controls, and deployed them into two Dry Valley streams. We found N amendments (N and N + P) to have greater chlorophyll-a concentrations, total algal biovolume, more fine filamentous cyanobacteria and a higher proportion of live diatoms than other treatments. Furthermore, N treatments were substantially elevated in Bacteroidetes and the small diatom, Fistulifera pelliculosa. On the other hand, species richness was almost double in P and N + P treatments over others, and coccoid green algae and Proteobacteria were more abundant in both streams. Collectively, these data suggest that nutrients have the potential to stimulate growth and alter community structure in glacial meltwater stream microbial mats, and the recent erosion of permafrost and accelerated glacial melt will likely impact resident biota in polar lotic systems here and elsewhere.

• MeSH
• chlorofyl analýza   MeSH
• Chlorophyta metabolismus   MeSH
• dusík analýza   MeSH
• ekosystém MeSH
• fosfor analýza   MeSH
• ledový příkrov mikrobiologie   MeSH
• Proteobacteria izolace a purifikace   metabolismus   MeSH
• řeky mikrobiologie   MeSH
• rozsivky izolace a purifikace   metabolismus   MeSH
• sinice izolace a purifikace   metabolismus   MeSH
• společenstvo MeSH
• teplota MeSH
• Publikační typ
• časopisecké články MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Geografické názvy
• Antarktida MeSH

As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of eukaryotic genomes from metagenomes. This study assessed the reconstruction of microbial eukaryotic genomes using 6000 metagenomes from terrestrial and some transition environments using the EukRep pipeline. Only 215 metagenomic libraries yielded eukaryotic bins. From a total of 447 eukaryotic bins recovered 197 were classified at the phylum level. Streptophytes and fungi were the most represented clades with 83 and 73 bins, respectively. More than 78% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic, and anthropogenic terrestrial. However, only 93 bins were taxonomically assigned at the genus level and 17 bins at the species level. Completeness and contamination estimates were obtained for a total of 193 bins and consisted of 44.64% (σ = 27.41%) and 3.97% (σ = 6.53%), respectively. Micromonas commoda was the most frequent taxon found while Saccharomyces cerevisiae presented the highest completeness, probably because more reference genomes are available. Current measures of completeness are based on the presence of single-copy genes. However, mapping of the contigs from the recovered eukaryotic bins to the chromosomes of the reference genomes showed many gaps, suggesting that completeness measures should also include chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, development of tools for dealing with repeat-rich genomes, and improved reference genomes databases.

• MeSH
• ekosystém MeSH
• Eukaryota * genetika   MeSH
• genom mikrobiální MeSH
• houby genetika   MeSH
• metagenom * MeSH
• metagenomika MeSH
• Publikační typ
• časopisecké články MeSH

Taxa of microbial eukaryotes defined on morphological basis display a large degree of genetic diversity, implying the existence of numerous cryptic species. However, it has been postulated that genetic diversity merely mirrors accumulation of neutral mutations. As a case taxon to study cryptic diversity in protists, we used a widely distributed filamentous genus, Klebsormidium, specifically the lineage E (K. flaccidum/K. nitens complex) containing a number of morphologically similar strains. Fourteen clades were recognized in the phylogenetic analysis based on a concatenated ITS rDNA + rbcL data set of more than 70 strains. The results of inferred character evolution indicated the existence of phylogenetic signal in at least two phenotypic characters (production of hydro-repellent filaments and morphology of zoosporangia). Moreover, the lineages recovered exhibited strong ecological preferences to one of the three habitat types: natural subaerial substrata, artificial subaerial substrata, and aquatic habitats. We interpret these results as evidence of existence of a high number of cryptic species within the single morphospecies. We consider that the permanent existence of genetically and ecologically well-defined cryptic species is enabled by the mechanism of selective sweep.

• MeSH
• ekologie * MeSH
• fylogeneze MeSH
• genetická variace genetika   MeSH
• ribozomální DNA genetika   MeSH
• Streptophyta klasifikace   genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH