Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions.IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.

• Klíčová slova
• AAP community composition, aerobic anoxygenic phototrophic bacteria, bacterial community composition, phytoplankton-bacteria coupling,
• MeSH
• aerobní bakterie růst a vývoj   metabolismus   MeSH
• ekosystém * MeSH
• fotosyntéza MeSH
• fototrofní procesy * MeSH
• fyziologie bakterií MeSH
• mikrobiota * MeSH
• mořská voda mikrobiologie   MeSH
• sladká voda mikrobiologie   MeSH
• světlo MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.

• Klíčová slova
• Algerian soils, Bacterial community, Cellulases, Decomposition, Hemicellulases, Lignocellulose,
• MeSH
• Bacteria klasifikace   enzymologie   genetika   izolace a purifikace   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• celulasa genetika   metabolismus   MeSH
• ekosystém MeSH
• fylogeneze MeSH
• glykosidhydrolasy genetika   metabolismus   MeSH
• lesy MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Alžírsko MeSH
• Názvy látek
• bakteriální proteiny MeSH
• celulasa MeSH
• glykosidhydrolasy MeSH
• hemicellulase MeSH Prohlížeč
• půda MeSH

Combining a minimum food web model with Arctic microbial community dynamics, we have suggested that top-down control by copepods can affect the food web down to bacterial consumption of organic carbon. Pursuing this hypothesis further, we used the minimum model to design and analyse a mesocosm experiment, studying the effect of high (+Z) and low (-Z) copepod density on resource allocation, along an organic-C addition gradient. In the Arctic, both effects are plausible due to changes in advection patterns (affecting copepods) and meltwater inputs (affecting carbon). The model predicts a trophic cascade from copepods via ciliates to flagellates, which was confirmed experimentally. Auto- and heterotrophic flagellates affect bacterial growth rate and abundance via competition for mineral nutrients and predation, respectively. In +Z, the model predicts low bacterial abundance and activity, and little response to glucose; as opposed to clear glucose consumption effects in -Z. We observed a more resilient bacterial response to high copepods and demonstrate this was due to changes in bacterial community equitability. Species able to use glucose to improve their competitive and/or defensive properties, became predominant. The observed shift from a SAR11-to a Psychromonodaceae - dominated community suggests the latter was pivotal in this modification of ecosystem function. We argue that this group used glucose to improve its defensive or its competitive abilities (or both). Adding such flexibility in bacterial traits to the model, we show how it creates the observed resilience to top-down manipulations observed in our experiment.

• MeSH
• autotrofní procesy MeSH
• Bacteria růst a vývoj   izolace a purifikace   metabolismus   MeSH
• Ciliophora fyziologie   MeSH
• Copepoda fyziologie   MeSH
• fyziologie bakterií * MeSH
• glukosa metabolismus   MeSH
• heterotrofní procesy MeSH
• mikrobiota MeSH
• potravní řetězec * MeSH
• uhlík metabolismus   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Arktida MeSH
• Názvy látek
• glukosa MeSH
• uhlík MeSH

Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood's properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood.IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.

• Klíčová slova
• HMSC, biotic interactions, co-occurrence, conditional cross-validation, cross-validation, fungal-bacterial interactions, joint species distribution modeling,
• Publikační typ
• časopisecké články MeSH

Invasive plants often impact soil conditions, notably through changes in soil chemistry and microbial community composition, potentially leading to altered soil functionality. We determine the impacts of invasive nitrogen-fixing Australian Acacia trees on soil chemistry and function (carbon, nitrogen, and phosphorus cycling) in South Africa's Core Cape Subregion, and whether any differences in soil function are linked to differences in soil chemical properties and bacterial community composition between neighbouring acacia-invaded and uninvaded sites. We do so by using Illumina MiSeq sequencing data together with soil chemistry and soil enzyme activity profiles. Acacias significantly increased levels of soil nitrogen (NO3-, NH4+, and total N), C, and pH. Although we did not find evidence that acacias affected soil bacterial community diversity, we did find them to alter bacterial community composition. Acacias also significantly elevated microbial phosphatase activity, but not β-glucosidase, whilst having contrasting effects on urease. Changes in soil chemical properties under acacia invasion were found to correlate with changes in enzyme activities for urease and phosphatase. Similarly, changes in soil bacterial community composition were correlated to changes in phosphatase enzymatic activity levels under acacia invasion. Whilst we found evidence for acacias altering soil function by changing soil chemical properties and bacterial community composition, these impacts appear to be specific to local site conditions.

• Klíčová slova
• 16S rDNA, Australian acacias, Enzyme activities, Fynbos, Invasion, Soil function, Soil microbial ecology,
• MeSH
• akácie * MeSH
• mikrobiota * MeSH
• půda MeSH
• půdní mikrobiologie MeSH
• živiny MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Austrálie MeSH
• Názvy látek
• půda MeSH

Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4-6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (delta BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing to production rate over periods of 48-72 h and A BCC showed that delta BCC was positively and tightly correlated (r2 = 0.784) with shifts in the ratio of grazing mortality to cell production. While the nature of a shift in BCC is unpredictable, the magnitude of the change can be related to changes in the balance between bacterial production and protistan grazing. bacterial community composition

• MeSH
• Bacteria genetika   růst a vývoj   MeSH
• Ciliophora fyziologie   MeSH
• ekosystém * MeSH
• Eukaryota fyziologie   MeSH
• hybridizace in situ fluorescenční MeSH
• kultivační média MeSH
• sladká voda mikrobiologie   parazitologie   MeSH
• stravovací zvyklosti * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kultivační média MeSH

The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across the GrIS, using sequence analysis and quantitative PCR of 16S rRNA genes from co-extracted DNA and RNA. Communities were found to differ across the ice sheet, with 82.8% of the total calculated variation attributed to spatial distribution on a scale of tens of kilometers separation. Amplicons related to Sphingobacteriaceae, Pseudanabaenaceae and WPS-2 accounted for the greatest portion of calculated dissimilarities. The bacterial communities of ice and cryoconite were moderately similar (global R = 0.360, P = 0.002) and the sampled surface type (ice versus cryoconite) did not contribute heavily towards community dissimilarities (2.3% of total variability calculated). The majority of dissimilarities found between cryoconite 16S rRNA gene amplicons from DNA and RNA was calculated to be the result of changes in three taxa, Pseudanabaenaceae, Sphingobacteriaceae and WPS-2, which together contributed towards 80.8 ± 12.6% of dissimilarities between samples. Bacterial communities across the GrIS are spatially variable active communities that are likely influenced by localized biological inputs and physicochemical conditions.

• Klíčová slova
• Greenland, bacteria, biogeography, cryoconite, diversity, ice,
• MeSH
• biodiverzita MeSH
• DNA bakterií genetika   MeSH
• ledový příkrov mikrobiologie   MeSH
• mikrobiota genetika   MeSH
• polymerázová řetězová reakce MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• Sphingobacterium genetika   izolace a purifikace   MeSH
• Synechococcus genetika   izolace a purifikace   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Grónsko MeSH
• Názvy látek
• DNA bakterií MeSH
• RNA ribozomální 16S MeSH

To study the various processes in the rumen the in vitro techniques are widely used to realize more controlled and reproducible conditions compared to in vivo experiments. Mostly, only the parameters like pH changes, volatile fatty acids content or metabolite production are monitored. In this study we examine the bacterial community dynamics of rumen fluid in course of ten day cultivation realize under standard conditions described in the literature. Whereas the pH values, total VFA content and A/P ratio in bioreactor were consistent with natural conditions in the rumen, the mean redox-potential values of -251 and -243mV were much more negative. For culture-independent assessment of bacterial community composition, the Illumina MiSeq results indicated that the community contained 292 bacterial genera. In course of ten days cultivation a significant changes in the microbial community were measured when Bacteroidetes to Firmicutes ratio changed from 3.2 to 1.2 and phyla Proteobacteria and Actinobacteria represented by genus Bifidobacterium and Olsenella significantly increased. The main responsible factor of these changes seems to be very low redox potential in bioreactor together with accumulation of simple carbohydrates in milieu as a result of limited excretion of fermented feed and absence of nutrient absorbing mechanisms.

• Klíčová slova
• 16S rDNA, Bioreactor, Microbiome analysis, Redox potential, Rumen fluid,
• MeSH
• bachor metabolismus   mikrobiologie   MeSH
• Bacteria klasifikace   genetika   růst a vývoj   izolace a purifikace   MeSH
• Bacteroidetes genetika   růst a vývoj   izolace a purifikace   MeSH
• bioreaktory mikrobiologie   MeSH
• DNA bakterií MeSH
• fermentace MeSH
• Firmicutes genetika   růst a vývoj   izolace a purifikace   MeSH
• kyseliny mastné těkavé metabolismus   MeSH
• mikrobiota * genetika   MeSH
• oxidace-redukce MeSH
• Proteobacteria genetika   růst a vývoj   izolace a purifikace   MeSH
• RNA ribozomální 16S genetika   MeSH
• skot MeSH
• zvířata MeSH
• Check Tag
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA bakterií MeSH
• kyseliny mastné těkavé MeSH
• RNA ribozomální 16S MeSH

The digestive tract of medicinal leeches from commercial suppliers has been investigated previously and comprises of a relatively simple bacterial community. However, the microbiome of medicinal leeches collected directly from the natural habitat has not been examined. In this study, we characterized the bacterial community in the digestive tract (anterior crop, posterior crop, and intestine) of the European medicinal leech, Hirudo verbana, collected from the Danube river using culture-independent and culture-dependent approaches. Culture-independent approach confirmed that the digestive tract of H. verbana carries a relatively simple bacterial community with species richness in the individual samples ranging from 43 to164. The dominant bacterial taxon was Mucinivorans sp. (49.7% of total reads), followed by Aeromonas sp. (18.7% of total reads). Several low abundance taxa, new for H. verbana, such as Phreatobacter, Taibaiella, Fluviicola, Aquabacterium, Burkholderia, Hydrogenophaga, Wolinella, and unidentified Chitinophagia, were also detected. The aerobic culturing approach showed Aeromonas veronii (Proteobacteria), the known leech symbiont, as the most dominant taxon followed by several Pseudomonas and Acidovorax spp. No significant differences in the bacterial community composition were detected among different parts of the digestive tract of individual leeches. However, the overall composition of the bacterial community among individual specimen varied significantly and this is possibly due to differences in leech age, feeding status, and blood source. Our results showed that the core bacterial community of H. verbana collected from the natural habitat is similar to that reported from the digestive tract of commercially supplied leeches maintained in the laboratory.

• Klíčová slova
• 16S rDNA, Bacterial community, Digestive tract, Hirudo verbana, Medicinal leech,
• MeSH
• Bacteria klasifikace   genetika   MeSH
• bakteriální RNA analýza   MeSH
• gastrointestinální trakt mikrobiologie   MeSH
• pijavice mikrobiologie   MeSH
• řeky MeSH
• RNA ribozomální 16S analýza   MeSH
• střevní mikroflóra * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Rumunsko MeSH
• Názvy látek
• bakteriální RNA MeSH
• RNA ribozomální 16S MeSH

The high boron (B) content in desalinated seawater is a concern for crop development. However, in spite of the importance of the soil microbial community in soil fertility, the below-ground impacts of B are still unknown. Here, in a soil-ryegrass model system, the activity, biomass and diversity of the soil microbial community were evaluated in response to irrigation with: i) 0.3 mg B L-1; ii) 1 mg B L-1; and iii) 50 mg B L-1. We assessed two different compounds of boron: boric acid (H3BO3) and disodium tetraborate decahydrate (Na2B4O7·10H2O). Overall, the 1 mg B L-1 dose was identified as the threshold limit that did not irreversibly harm soil sustainability. In contrast, the highest B dose had a noticeable impact on the nitrogen (N) cycle of the soil, as demonstrated by an increase in the water-soluble N content and a decrease in urease activity. Analysis of the phospholipid fatty acids (PLFAs) revealed that the effect of B on the soil microbial biomass was dependent on the chemical form used. High B doses reduced soil microbial respiration and influenced the composition of the bacterial and fungal communities, with fungal diversity being diminished, as revealed by sequencing approaches.

• Klíčová slova
• Boron, Desalinated seawater, Diversity, Enzyme activities, Semi-arid soil, Soil microbial community,
• MeSH
• biodiverzita MeSH
• biomasa MeSH
• bor analýza   toxicita   MeSH
• látky znečišťující půdu analýza   toxicita   MeSH
• mikrobiota * MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bor MeSH
• látky znečišťující půdu MeSH
• půda MeSH