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SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at −20 °C led to a significant reduction in gene copy numbers.

Purpose Biovalorization of lignin-derived aromatic monomers such as ferulic acid (FA) has attracted considerable interest. The cold-adapted strain Paraburkholderia aromaticivorans AR20-38 converts FA to the value-added product vanillic acid (VA), without further VA degradation. The efficiency of the bioconversion of FA to VA was optimized by studying culture conditions. Methods Various cultivation parameters (agitation, temperature, FA concentration, nutrient supplementation) were assessed to increase biomass production and shorten the cultivation time, while obtaining high VA production yields. The fate of the intermediate vanillin was also studied. Lignin monomers and degradation products (FA, vanillin, VA) were quantified via UV/Vis-HPLC. Result Full bioconversion of 5 mM FA occurred over a broad temperature range of 5–30 °C. Concentrations up 30 mM FA were utilized as the sole carbon source at 20 °C. Molar VA yields (> 90%) produced from 5 to 12.5 mM FA and from 15 to 17.5 mM FA (82–87%) were not significantly different at 10 °C and 20 °C. The supplementation of the mineral medium with monosaccharides (glucose, fructose, mannose) and/or N-rich complex compounds (yeast extract, casamino acids) resulted in high biomass production, accelerated FA bioconversion, and high molar yields (96–100%). The presence of the N-rich compounds alone or in combination with glucose reduced the incubation time necessary to convert FA to VA. Vanillin, formed as an intermediate during FA degradation, was consumed and converted to VA before FA metabolization, when added in combination with FA. Vanillin bioconversion was significantly accelerated in the presence of glucose. Conclusion The variation of culture conditions improved the efficiency of the studied strain to convert FA via vanillin to VA and demonstrated remarkable FA bioconversion under varying environmental conditions, especially temperature, substrate concentration, and nutrient availability, which is of importance for potential future application.

pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0–8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.

Substrates with high sulfate levels pose problems for biogas production as they allow sulfate reducing bacteria to compete with syntrophic and methanogenic members of the community. In addition, the end product of sulfate reduction, hydrogen sulfide, is toxic and corrosive. Here we show how sulfate addition affects physiological processes in a thermophilic methanogenic system by analyzing the carbon flow and the microbial community with quantitative PCR and amplicon sequencing of the 16s rRNA gene. A sulfate addition of 0.5 to 3 g/L caused a decline in methane production by 73–92%, while higher sulfate concentrations had no additional inhibitory effect. Generally, sulfate addition induced a shift in the composition of the microbial community towards a higher dominance of Firmicutes and decreasing abundances of Bacteroidetes and Euryarchaeota. The abundance of methanogens (e.g., Methanoculleus and Methanosarcina) was reduced, while sulfate reducing bacteria (especially Candidatus Desulforudis and Desulfotomaculum) increased significantly in presence of sulfate. The sulfate addition had a significant impact on the carbon flow within the system, shifting the end product from methane and carbon dioxide to acetate and carbon dioxide. Interestingly, methane production quickly resumed, when sulfate was no longer present in the system. Despite the strong impact of sulfate addition on the carbon flow and the microbial community structure during thermophilic biogas production, short-term process disturbances caused by unexpected introduction of sulfate may be overcome due to the high resilience of the engaged microorganisms.

Lignin bio-valorization is an emerging field of applied biotechnology and has not yet been studied at low temperatures. Paraburkholderia aromaticivorans AR20-38 was examined for its potential to degrade six selected lignin monomers (syringic acid, p-coumaric acid, 4-hydroxybenzoic acid, ferulic acid, vanillic acid, benzoic acid) from different upper funneling aromatic pathways. The strain degraded four of these compounds at 10°C, 20°C, and 30°C; syringic acid and vanillic acid were not utilized as sole carbon source. The degradation of 5 mM and 10 mM ferulic acid was accompanied by the stable accumulation of high amounts of the value-added product vanillic acid (85–89% molar yield; 760 and 1540 mg l−1, respectively) over the whole temperature range tested. The presence of essential genes required for reactions in the upper funneling pathways was confirmed in the genome. This is the first report on biodegradation of lignin monomers and the stable vanillic acid production at low and moderate temperatures by P. aromaticivorans.Key points• Paraburkholderia aromaticivorans AR20-38 successfully degrades four lignin monomers.• Successful degradation study at low (10°C) and moderate temperatures (20–30°C).• Biotechnological value: high yield of vanillic acid produced from ferulic acid.

Aims The objectives of this study were to investigate the influence of plants on net methane flux from forest and grassland soils depending on bedrock, temperature, and plant species, and to determine the abundance of methanogenic and methanotrophic microorganisms. Methods Lab-scale gas measurements with forest and grassland soils and different site-specific plants were performed. Next-generation sequencing was conducted to characterize the archaeal community structure and the abundance of methanotrophic bacteria was determined via quantitative PCR. Results Forest and grassland soils had a high potential to consume methane under ambient conditions. Irrespective of bedrock and plant species, a highly significant influence of temperature was established. The studied site-specific grassland plants Plantago lanceolata and Poa pratensis significantly increased methane balance with varying extent depending on temperature. In contrast, the studied forest plants Picea abies and especially Larix decidua significantly boosted methane consumption. The flux measurements pointed to higher net methane consumption rates on limestone compared to siliceous bedrock. The proportion of Euryarchaeota - including methanogens-increased in rhizosphere soil of grassland plants compared to bulk soil whereas methanotrophic abundances did not differ between bulk and rhizosphere soil. Conclusions Results highlight that the methane fluxes in uplands soils are altered depending on plant species, temperature, and vegetation type and emphasize the need to better resolve the influence of plants on the methane cycle and the involved microorganisms.

In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.

Methanogens and methanotrophs play unique roles as producers and consumers of the greenhouse gas methane (CH4) in soils, respectively. Here, we aimed to reveal whether and to which extent methane-cyclers occur in high-alpine soils, and to assess their spatial distribution along an altitudinal gradient (2700–3500 m) in the Austrian Alps at sites located within the alpine (2700–2900 m), the alpine-nival (3000–3100 m) and the nival belts (3200–3500 m). Methanococcales and Methanocella spp. were most abundant among all quantified methanogenic guilds, whereas Methanosarcinales were not detected in the studied soil. The detected methanogens seem to be capable of persisting despite a highly oxic low-temperature environment. Methanogenic and methanotrophic activities and abundances of methanotrophs, Methanococcales and Methanocella spp. declined with altitude. Methanogenic and methanotrophic abundances were best explained by mean annual soil temperature and dissolved organic carbon, respectively. Alpine belt soils harbored significantly more methane-cyclers than those of the nival belt, indicating some influence of plant cover. Our results show that methanogens are capable of persisting in high-alpine cold soils and might help to understand future changes of these environments caused by climate warming. Methanogenic archaea and methanotrophic bacteria were discovered in aerated high-alpine soils, indicating their ability to withstand low temperatures. Graphical Abstract Figure. Methanogenic archaea and methanotrophic bacteria were discovered in aerated high-alpine soils, indicating their ability to withstand low temperatures.

Although methanogens were recently discovered to occur in aerated soils, alpine regions have not been extensively studied for their presence so far. Here, the abundance of archaea and the methanogenic guilds Methanosarcinales, Methanococcales, Methanobacteriales, Methanomicrobiales and Methanocella spp. was studied at 16 coniferous forest and 14 grassland sites located at the montane and subalpine belts of the Northern Limestone Alps (calcareous) and the Austrian Central Alps (siliceous) using quantitative real-time PCR. Abundance of archaea, methanogens and the methanogenic potentials were significantly higher in grasslands than in forests. Furthermore, methanogenic potentials of calcareous soils were higher due to pH. Methanococcales, Methanomicrobiales and Methanocella spp. were detected in all collected samples, which indicates that they are autochthonous, while Methanobacteriales were absent from 4 out of 16 forest soils. Methanosarcinales were absent from 10 out of 16 forest soils and 2 out of 14 grassland soils. Nevertheless, together with Methanococcales they represented the majority of the 16S rRNA gene copies quantified from the grassland soils. Contrarily, forest soils were clearly dominated by Methanococcales. Our results indicate a higher diversity of methanogens in well-aerated soils than previously believed and that pH mainly influences their abundances and activities. Various methanogenic guilds were found to be present in aerated forest and grassland soils located at the montane and subalpine belts of the European Alps. Graphical Abstract Figure. Various methanogenic guilds were found to be present in aerated forest and grassland soils located at the montane and subalpine belts of the European Alps.

We isolated a filamentous, thermophilic, and first anaerobic representative of the genus Thermoactinomyces, designated strain AMNI-1T, from a biogas plant in Tyrol, Austria and report the results of a phenotypic, genetic, and phylogenetic investigation. Strain AMNI-1T was observed to form a white branching mycelium that aggregates into pellets when grown in liquid medium. Cells could primarily utilize lactose, glucose, and mannose as carbon and energy sources, with acetate accelerating and yeast extract being mandatory for growth. The optimum growth temperature and pH turned out to be 55 °C and pH 7.0, respectively, with an optimum NaCl concentration of 0–2% (w/v). 16S rRNA gene sequence comparison indicated that the genetic relatedness between strain AMNI-1T and Thermoactinomyces intermedius, Thermoactinomyces khenchelensis, and Thermoactinomyces vulgaris was less than 97%. The G + C content of the genomic DNA was 44.7 mol%. The data obtained suggest that the isolate represents a novel and first anaerobic species of the genus Thermoactinomyces, for which the name Thermoactinomyces mirandus is proposed. The type strain is AMNI-1T (= DSM 110094T = LMG 31503T). The description of the genus Thermoactinomyces is emended accordingly.