River systems are exposed to anthropogenic disturbances, including chemical pollution and eutrophication. They may affect a structure and diversity of microbial communities in river sediment. The aim ...of the study was to describe diversity and structure of a bacterial community in the Kamniška Bistrica river sediment using culture-dependent and molecular methods. Sediment samples were collected from three sampling stations along the Kamniška Bistrica river: upstream (Kamniška Bistrica), midstream (Vir) and downstream (Bišče), and physico-chemical analysis was conducted on-site. Isolates were recovered from three different agar plate media (LB, NB in R2A) and micro- as well as macromorphologically described. DNA was extracted from pure cultures and directly from sediment samples, and 16S rRNA gene segments were PCR amplified using universal bacterial primers. The PCR products were subjected to denaturing gradient gel electrophoresis (DGGE). The results showed that the DGGE was an appropriate method for monitoring the changes in the community structure of the river sediment and allows to determine the impact of environmental factors on bacterial diversity. The comparative analysis of the DGGE profiles from isolates and sediment samples showed that the DGGE banding patterns revealed different bacterial community structures for all three sampling stations, while the DGGE profiles of isolates did not represent dominant bacterial populations of the sediment. On the bases of the DGGE profiles, 25 isolates were chosen and their 16S rRNA genes were amplified and sequenced. All partial nucleotide sequences of 16S rRNA genes were preleminary taxonomically identified by using BLAST. The majority of sequenced isolates belonged to bacteria normally present in aquatic environments.
Anaerobic digestion, despite its preferable use as a treatment for high organic matter polluted waste streams, is susceptible to inhibitors, salt included. Therefore, two different experiments were ...conducted to observe the responses of bacterial and archaeal communities to hypersaline environments. In the first experiment, salt was added gradually, while in the second experiment, salt was added rapidly (so-called salt shocks were performed). The results of the gradual addition of salt showed a recovery of methane production after the salt concentration decreased. The NaCl concentration of 28.2 g/L seems to be the limit between stable operation and occurrence inhibition. The specific biogas production varied between 0.490 and 0.562 m3/kgtCOD during the stepwise salt addition, depending on the salt concentration, while the maximal achieved COD removal was 79.8%. The results of the rapid salt addition showed good recovery of the bacterial community, while a reduction of salt-sensitive species was observed in the archaeal community. The trend of specific biogas production during rapid salt addition was stable with an average value of 0.590 m3/kgtCOD, and it was observed that higher concentrations of up to 39.4 g/L of NaCl were tolerated. The maximum COD removal achieved during rapid salt addition was 83.1%. In conclusion, certain bacterial and archaeal communities were well-adapted to the hypersaline environment and remained active during the anaerobic digestion of substrates with high salt concentration.
Five strictly anaerobic Gram-negative bacterial strains, P4-65, P4-76ᵀ, P5-60, P5-119, and P5-125, presumably belonging to the genus Prevotella were isolated from pig fecal samples. Strains were ...tested for various phenotypic traits and nearcomplete genome sequences were obtained and analyzed. Phylogenetic analysis based on 16S rRNA gene sequences and multilocus sequence analysis based on five conserved genes confirmed that the strains belong to the genus Prevotella, revealing that they represent a novel and discrete lineage distinct from other known species of this genus. The size of the genome of the isolated strains is 3–3.3 Mbp, and the DNA G+C content is 47.5–48.1 mol%. The isolates are strictly anaerobic, rod-shaped with rounded ends, non-motile and non-spore-forming. The main fermentation products are succinate and acetate, with minor concentrations of isovalerate, propionate and isobutyrate. Hydrogen is also produced. Major cellular fatty acids consist of anteiso-C₁₅:₀ and iso-C₁₅:₀, and a number of additional acids are present in lower concentrations. A substantial portion of genes involved in carbohydrate utilization is devoted to pectin degradation and utilization, while those supporting growth on xylan in ruminal Prevotella could not have been revealed. On the basis of the presented results, a novel species, Prevotella pectinovora sp. nov. is proposed. The type strain is P4-76ᵀ (=DSM 29996ᵀ =ZIM B1020ᵀ).
Microalgae biomass has a great potential in search for new alternative energy sources. They can be used as a substrate for the biogas production in anaerobic digestion. When using microalgae, the ...efficiency of this process is hampered due to the resistant cell wall. In order to accelerate the hydrolysis of cell wall and increase the efficiency of biogas production we applied two different pretreatments - biological and thermal under mesophilic and thermophilic conditions. During biological pretreatment we incubated microalgae with anaerobic hydrolytic bacteria Pseudobutyrivibrio xylanivorans Mz5T. In thermal pretreatment we incubated microalgae at 90 °C. We also tested a combined thermal and biological pretreatment in which we incubated P. xylanivorans Mz5T with thermally pretreated microalgae. Thermal pretreatment in mesophilic and thermophilic process has increased methane production by 21% and 6%, respectively. Biological pretreatment of microalgae has increased methane production by 13%, but only under thermophilic conditions (pretreatment under mesophilic conditions showed no effect on methane production). Thermal-biological pretreatment increased methane production by 12% under thermophilic conditions and by 6% under mesophilic conditions.
•The impact of bioaugmentation on methane production from spent grain was examined.•Methane production elevated for 17.8% with P. xylanivorans Mz5T bioaugmentation.•Bioaugmentation enhances the ...hydrolysis of brewery spent grain.•Changes in bacterial and archaeal communities were detected during biogas process.•Bioaugmentation enables successful biogas production from brewery spent grain.
Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate. Ruminococcus flavefaciens 007C, Pseudobutyrivibrio xylanivorans Mz5T, Fibrobacter succinogenes S85 and Clostridium cellulovorans as pure and mixed cultures were used to enhance the lignocellulose degradation and elevate the biogas production. P. xylanivorans Mz5T was the most successful in elevating methane production (+17.8%), followed by the coculture of P. xylanivorans Mz5T and F. succinogenes S85 (+6.9%) and the coculture of C. cellulovorans and F. succinogenes S85 (+4.9%). Changes in microbial community structure were detected by fingerprinting techniques.
Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors ...Komagataeibacter maltaceti LMG 1529T and Gluconacetobacter entanii LTH 4560T. Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S–23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus. Average nucleotide identity of T5K1 and AV446 draft genome sequences compared to other Komagataeibacter type strains was below 94% and at the same time, in-silico DNA–DNA hybridization was below 70%. Both strains on the other hand showed approximately 98% (average nucleotide identity) and 87% (in silico DNA–DNA hybridization) similarity to each other. Strains T5K1 and AV446 can be differentiated from other Komagataeibacter type strains based on their ability to produce 2-keto-d-gluconic acid and at the same time inability to produce 5-keto-d-gluconic acid. Furthermore, strains of the new species do not grow on Asai medium supplemented with d-glucose or d-mannitol. The growth is also absent (T5K1) or weak (AV446) on Hoyer–Frateur medium supplemented with afore mentioned sugars. Both strains produce cellulose. In addition, draft genome analysis revealed that strains T5K1 and AV446 possess genes involved in the synthesis of acetan-like extracellular heteropolysaccharide. We propose the name Komagataeibacter pomaceti sp. nov. for the new species with LMG 30150T =CCM 8723T=ZIM B1029T as the type strain. Data collected in this study and in a previous study also revealed that Komagataeibacter kombuchae is a later heterotypic synonym of Komagataeibacter hansenii.
Anaerobic digestion of brewery spent grain as a mono-substrate was studied. Brewery spent grain is a substrate consisting largely of cellulose, hemicellulose and lignin, which are difficult to ...degrade anaerobically, mostly due to the presence of degradation products, such as phenolic compounds, which cause process inhibition. Therefore, a two-stage system was used for anaerobic digestion. Anaerobic digestion was phase separated in a solid-state anaerobic digestion reactor, where microbiological hydrolysis and acidogenesis occurred and in a granular biomass reactor where mostly methanogenesis was performed. The overall process exhibited total solids degradation efficiency between 75.9 and 83.0%. Average specific biogas production was 414 ± 32 L/kg, whereas biomethane production was 224 ± 34 L/kg of added total solids. Granular biomass after adaptation exhibited stable operation at substrate C/N ratios in range 0.16–4.68. p-cresol was present in concentrations up to 45 mg/L and during the process was successfully degraded by granular biomass. The excellent adaptability of granular biomass was confirmed by 68.2% shift in bacterial and a 31.8% shift in archaeal community structure in a granular biomass reactor. The structure of the bacterial community from granular biomass reactor and solid-state anaerobic digestion reactor remained 79.4% similar at the end of the experiment, whereas archaeal community was only 31.6% similar. The process exhibited stable operation for 198 days, which shows that brewery spent grain can be successfully anaerobically digested and used for biogas production.
•Long–term and stable biogas production from brewery spent grain is possible.•Up to 472 L of biogas per kg of brewery spent grain total solids can be produced.•The granular biomass is able to operate at very low C/N ratios between 0.16 and 4.68.•p-cresol as inhibitory intermediate degradation product is successfully degraded.•Bacterial and archaeal microbial communities adapted successfully to BSG substrate.
27 strains representing eight new Prevotella species were isolated from rumen of a single sheep in eight weeks interval. One of the putative species encompassing the highest number of isolated ...strains which also exhibited some genetic variability in preliminary data, was then selected for description of a novel species. We examined six strains in genomic and phenotypic detail, two of which may actually be the same strain isolated nearly three weeks apart. Other strains formed clearly diverged intraspecies lineages as evidenced by core genome phylogeny and phenotypic differences. Strains of the proposed new Prevotella species are strictly saccharolytic as is usual for rumen Prevotella, and use plant cell-wall xylans and pectins for growth. However, the range of cell-wall polysaccharides utilised for growth is rather limited compared to rumen generalists such as Prevotella bryantii or Prevotella ruminicola and this extends also to the inability to utilise starch, which is unexpected for the members of the genus Prevotella. Based on the data obtained, we propose Prevotella communis sp. nov. to accommodate strain E1-9T as well as other strains with the similar properties. The proposed species is widespread: two other strains were previously isolated from sheep in Japan and is also common in metagenomic data of cattle and sheep rumen samples from Scotland and New Zealand. It was also found in a collection of metagenome-assembled genomes originating from cattle in Scotland. Thus, it is a ubiquitous bacterium of domesticated ruminants specialising in degradation of a somewhat restricted set of plant cell wall components.
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