Gasification chars and activated carbon: Systematic physico-chemical characterization and effect on biogas production.

Gasification residues/chars (GR) and activated carbon (AC) are added to wastewater treatment processes mainly as a fourth purification stage, e.g., to adsorb heavy metals or pharmaceutical residues. However, the effects of GR or AC, which are transferred to the anaerobic digestion (AD) via the sludge, are not yet fully understood. Although, the positive effect of char addition on AD has been demonstrated in several investigations, systematic studies with chemically well described chars are still missing. Therefore, in this study, different chars were characterized in detail, subjected to AD in different concentrations, and their effect on methane production investigated. GR of a gasification plant with a floating fixed bed technology, carbon made by chemical impregnation with ZnCl2 from waste-wood, carbon produced by thermochemical activation with CO2 from GR and commercial powdered AC were used for the experiments. Among others, thermogravimetric analysis, physisorption, pH, and conductivity analysis were used to characterize the chars. Mesophilic AD batch tests with different concentrations (0.025, 0.05, 0.5, 1.0, 7.0, 14.0 gL-1) of all chars (GR and ACs, respectively) were performed with digester sludge from a wastewater treatment plant for a period of 47 d. Volatile fatty acids (VFA) as well as biogas production and CH4 concentrations were monitored. It could be shown, that concentrations below 1.0 g char L-1 did not result in significant effects on CH4 and/or VFA production, whereas high concentrations of GR and AC influenced both, the CH4 yield and kinetics. Depending on the production process and the characteristics of the chars, the effect on AD varied, whereby both, positive and negative effects on biogas yield and methane production were observed. This study provides the first systematic evaluation of char application to AD processes, and therefore allows for better predictions of char applicability and effect.

Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils.

BACKGROUND: In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover. RESULTS: The overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover. CONCLUSION: This is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.

Revised taxon definition in European Cortinarius subgenus Dermocybe based on phylogeny, chemotaxonomy, and morphology.

Cortinarius (Fr.) Fr. is one of the most species-rich genera in the Agaricales (Basidiomycota). Cortinarius subgen. Dermocybe (Fr.) Trog includes brightly coloured Cortinarii with anthraquinone pigments. The chemotaxonomic approach has always been as important as classical methods for species definition of Dermocybe and helped to improve overall species concepts. However, some species concepts within this group remain unclear. We therefore address this topic based on a combined phylogenetic, morphological, and pigment-chemical approach. For this, sequence data, HPLC-MS pigment profiles and spore sizes were included were included to obtain a better resolution of taxa. The study was based on 173 recent collections and 12 type specimens. A total of 117 rDNA ITS sequences were produced from the collections in this study, 102 sequences were retrieved from databases. We could detect and clearly delimit 19 Dermocybe species occurring in central European habitats, from which 16 are discussed in detail. Additionally, we grouped the detected anthraquinone pigments into four groups. This detailed analysis of dermocyboid Cortinarius species occurring in a restricted number of habitat types confirmed our hypothesis that species diversity is much higher than currently assumed. This high diversity is blurred by too wide and incorrect species concepts of several classical species like C. croceus and C. cinnamomeus. Molecular and chemotaxonomical studies carried out together with careful phenotypical analyses resulted in a good differentiation of species. A key is presented for these taxa to allow a better identification of Cortinarius subgenus Dermocybe spp. occurring in Central Europe mainly in the alpine range. Supplementary Information: The online version contains supplementary material available at 10.1007/s11557-024-01959-z.

Co-cultivation of Mortierellaceae with Pseudomonas helmanticensis affects both their growth and volatilome.

Volatile organic compounds (VOCs) might mediate microbial interactions, especially in spatially structured environments, such as soil. However, the variety and specificity of VOC production are poorly understood. Here, we studied 25 Mortierellaceae strains belonging to the genera Linnemannia and Entomortierella in both pure and co-culture with Pseudomonas helmanticensis under laboratory conditions. We analysed both the fungal growth depending on co-cultivation and the cultures' volatilomes applying proton-transfer-reaction time-of-flight and gas chromatography-mass spectrometry (PTR-ToF-MS and GC-MS). In a strain-specific manner, we found the fungi's radial growth rate and colony morphology affected by the presence of P. helmanticensis. The fungus seemed to generally reduce the bacterial growth. The volatilomes of the fungal and bacterial pure and co-cultures were diverse. While the fungi frequently consumed VOCs, P. helmanticensis produced a higher diversity and amount of VOCs than any fungal strain. Our results support that both the pure and co-culture volatilomes are taxonomically conserved. Taken together, our data supports the relevance of VOCs in Mortierellaceae-P. helmanticensis interaction. We also discuss individual VOCs that appear relevant in the interaction.

Mammalian gut metabolomes mirror microbiome composition and host phylogeny.

In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.

Effect of biomass fly ashes from fast pyrolysis bio-oil production on soil properties and plant yield.

A globally increased demand for fuels and environmental concerns regarding fossil sources call for sustainable alternatives. Fast pyrolysis is a promising approach for converting different types of biomass to renewable Fast Pyrolysis Bio-Oil (FPBO) that can be used for heating, power generation and mobility. Side-products emerging from the process include low calorific gases and charcoal. Both are further combusted to generate energy for the process. From the charcoal, the process leaves behind fly ashes (FAs) that contain macro- and micronutrients. In this regard, FPBO-FAs might present valuable soil fertilizers, but also bear the risk of soil heavy metal (HM) contamination. In this study, the risk and potential benefit of FPBO-FAs derived from three different biomass sources (bark, forest residue and Miscanthus sp.) as soil amendments was tested. Twice, in autumn 2017 and 2018, FPBO-FAs were applied to the field (500 kg ash ha-1 y-1) in a grassland experiment. Neither physico-chemical and microbiological soil properties nor plant yield were affected following FPBO-FAs application. Seasonal differences and changes from year to year, however, were evident, both for some soil and plant properties. The lack of effects on (i) plant yield, (ii) soil microbiological and physicochemical properties, (iii) heavy metal concentrations in soil and plant suggest that the product may safely be applied. The fact that these field-trial results are in discordance with previous greenhouse trials suggest, however, that long-term trials would be needed.

Habitat, Snow-Cover and Soil pH, Affect the Distribution and Diversity of Mortierellaceae Species and Their Associations to Bacteria.

Mortierellaceae species are among the most frequent and globally distributed soil fungi. However, the factors shaping their diversity and distribution remain obscure. Several species have been reported to be associated to bacteria, but the kind and frequency of such associations were not addressed up to now. We hypothesized that such associations could be important for Mortierellaceae ecology. Therefore, our aim was to understand the driving factors responsible for the Mortierellaceae diversity, community composition and bacterial associations in alpine and subalpine habitats. For answering our question, we collected both snow-free and snow-covered soil at sampling sites from different habitats: bare alpine soil in a glacier forefield, alpine dwarf-willow habitats, and high-altitude Pinus cembra forests. The isolations were carried out by direct cultivation without any antibiotics to the isolation media. Altogether, we obtained 389 Mortierellaceae isolates representing 29 operational taxonomic units (OTUs). Many OTUs could be placed to the genera Mortierella sensu stricto, Dissophora, Entomortierella, Gamsiella, Linnemannia, and Podila, but others could not unambiguously be assigned to a genus. Our results demonstrate that both, the distribution as well as the diversity of the Mortierellaceae species, were significantly influenced by habitat, soil pH, and snow-cover. We noticed that >30% of our isolates were associated to a non-contaminant bacterium. The bacteria associated to our Mortierellaceae isolates belonged to seven different genera. Pseudomonas was the most frequently detected genus associated to the isolated Mortierellaceae species and it was found to be species-specific. Mortierellaceae-bacteria pairs, including those with Pseudomonas, were influenced by location, habitat, and snow-cover. The majority of the fungus-bacterium associations were potentially epihyphal, but we also detected potential endohyphal bacterial species belonging to Mycoavidus, Burkholderiaceae, and Paraburkholderia. Taken together, the non-random associations we detected suggest that fungus-bacterium associations are ecologically meaningful - an interesting path that needs to be investigated further.

SCAPP: an algorithm for improved plasmid assembly in metagenomes.

BACKGROUND: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. RESULTS: We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)-an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. CONCLUSIONS: SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP . Video abstract.

The Molecular Information About Deadwood Bacteriomes Partly Depends on the Targeted Environmental DNA.

Microbiome studies mostly rely on total DNA extracts obtained directly from environmental samples. The total DNA consists of both intra- and extracellular DNA, which differ in terms of their ecological interpretation. In the present study, we have investigated for the first time the differences among the three DNA types using microbiome sequencing of Picea abies deadwood logs (Hunter decay classes I, III, and V). While the bacterial compositions of all DNA types were comparable in terms of more abundant organisms and mainly depended on the decay class, we found substantial differences between DNA types with regard to less abundant amplicon sequence variants (ASVs). The analysis of the sequentially extracted intra- and extracellular DNA fraction, respectively, increased the ecological depth of analysis compared to the directly extracted total DNA pool. Both DNA fractions were comparable in proportions and the extracellular DNA appeared to persist in the P. abies deadwood logs, thereby causing its masking effect. Indeed, the extracellular DNA masked the compositional dynamics of intact cells in the total DNA pool. Our results provide evidence that the choice of DNA type for analysis might benefit a study's answer to its respective ecological question. In the deadwood environment researched here, the differential analysis of the DNA types underlined the relevance of Burkholderiales, Rhizobiales and other taxa for P. abies deadwood decomposition and revealed that the role of Acidobacteriota under this scenario might be underestimated, especially compared to Actinobacteriota.

High-Throughput Volatilome Fingerprint Using PTR-ToF-MS Shows Species-Specific Patterns in Mortierella and Closely Related Genera.

In ecology, Volatile Organic Compounds (VOCs) have a high bioactive and signaling potential. VOCs are not only metabolic products, but are also relevant in microbial cross talk and plant interaction. Here, we report the first large-scale VOC study of 13 different species of Mortierella sensu lato (s. l.) isolated from a range of different alpine environments. Proton Transfer Reaction-Time-of-Flight Mass Spectrometry (PTR-ToF-MS) was applied for a rapid, high-throughput and non-invasive VOC fingerprinting of 72 Mortierella s. l. isolates growing under standardized conditions. Overall, we detected 139 mass peaks in the headspaces of all 13 Mortierella s. l. species studied here. Thus, Mortierella s. l. species generally produce a high number of different VOCs. Mortierella species could clearly be discriminated based on their volatilomes, even if only high-concentration mass peaks were considered. The volatilomes were partially phylogenetically conserved. There were no VOCs produced by only one species, but the relative concentrations of VOCs differed between species. From a univariate perspective, we detected mass peaks with distinctively high concentrations in single species. Here, we provide initial evidence that VOCs may provide a competitive advantage and modulate Mortierella s. l. species distribution on a global scale.

Publisher Correction: Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood.

Deadwood decomposition is relevant in nature and wood inhabiting fungi (WIF) are its main decomposers. However, climate influence on WIF community and their interactions with bacteria are poorly understood. Therefore, we set up an in-field mesocosm experiment in the Italian Alps and monitored the effect of slope exposure (north- vs. south-facing slope) on the decomposition of Picea abies wood blocks and their microbiome over two years. Unlike fungal richness and diversity, we observed compositional and functional differences in the WIF communities as a function of exposure. Wood-degrading operational taxonomic units (OTUs) such as Mycena, and mycorrhizal and endophytic OTUs were characteristic of the south-facing slope. On the north-facing one, Mucoromycota, primarily Mucor, were abundant and mixotrophic basidiomycetes with limited lignin-degrading capacities had a higher prevalence compared to the southern slope. The colder, more humid conditions and prolonged snow-coverage at north exposure likely influenced the development of the wood-degrading microbial communities. Networks between WIF and N2-fixing bacteria were composed of higher numbers of interacting microbial units and showed denser connections at the south-facing slope. The association of WIF to N2-fixing Burkholderiales and Rhizobiales could have provided additional competitive advantages, especially for early wood colonization.

Insights Into Culturomics of the Rumen Microbiome.

Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort.

Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories.

Deadwood decay employs a complex metabolism and provides carbon and nutrients for soils. Although being highly diverse, the contribution of the bacterial deadwood colonizing community is underexplored compared with the fungal one. Therefore, we performed an in-field mesocosm study and monitored the bacterial communities in decaying experimental Picea abies wood blocks and their underlying soil on north- and south- exposed slopes in the Italian Alps over a 2-year period. The faster deadwood decay at the south-facing slope was associated with a higher bacterial richness and a higher number of specialist operational taxonomic units (OTUs) which were more strongly correlated to environmental parameters than other bacterial community members. With progressing decay, the wood and soil bacterial communities became more similar in terms of richness, diversity and evenness and especially at the south-facing slope, they also became more similar in terms of community composition. Exposure-specific OTUs suggest wood-soil interaction. However, despite the strong influence of exposure on the soil bacterial communities, the P. abies wood blocks shared a comparably high number of OTUs with the soil irrespective of the slope. At finer taxonomic scale, we identified Pseudomonas, Microbacteria, Sphingomonas, Xanthomonas, Methylovirgula and Burkholderia as decay associated, although their functional role needs further studies.

Microbiota in a cooling-lubrication circuit and an option for controlling triethanolamine biodegradation.

Cooling and lubrication agents like triethanolamine (TEA) are essential for many purposes in industry. Due to biodegradation, they need continuous replacement, and byproducts of degradation may be toxic. This study investigates an industrial (1,200 m³) cooling-lubrication circuit (CLC) that has been in operation for 20 years and is supposedly in an ecological equilibrium, thus offering a unique habitat. Next-generation (Illumina Miseq 16S rRNA amplicon) sequencing was used to profile the CLC-based microbiota and relate it to TEA and bicine dynamics at the sampling sites, influent, machine rooms, biofilms and effluent. Pseudomonas pseudoalcaligenes dominated the effluent and influent sites, while Alcaligenes faecalis dominated biofilms, and both species were identified as the major TEA degrading bacteria. It was shown that a 15 min heat treatment at 50°C was able to slow down the growth of both species, a promising option to control TEA degradation at large scale.

Biotic and abiotic dynamics of a high solid-state anaerobic digestion box-type container system.

A solid-state anaerobic digestion box-type container system for biomethane production was observed in 12 three-week batch fermentations. Reactor performance was monitored using physico-chemical analysis and the methanogenic community was identified using ANAEROCHIP-microarrays and quantitative PCR. A resilient community was found in all batches, despite variations in inoculum to substrate ratio, feedstock quality, and fluctuating reactor conditions. The consortia were dominated by mixotrophic Methanosarcina that were accompanied by hydrogenotrophic Methanobacterium, Methanoculleus, and Methanocorpusculum. The relationship between biotic and abiotic variables was investigated using bivariate correlation analysis and univariate analysis of variance. High amounts of biogas were produced in batches with high copy numbers of Methanosarcina. High copy numbers of Methanocorpusculum and extensive percolation, however, were found to negatively correlate with biogas production. Supporting these findings, a negative correlation was detected between Methanocorpusculum and Methanosarcina. Based on these results, this study suggests Methanosarcina as an indicator for well-functioning reactor performance.

End-product inhibition and acidification limit biowaste fermentation efficiency.

Converting waste to resource may mitigate environmental pollution and global resource limitation. The platform chemical lactic acid can be produced from biowaste and its liquid fraction after solid-liquid separation. A fermentation step for lactic acid production prior to the conversion of biowaste to methane and organic fertilizer would increase the biowaste's value. Despite the huge potential and promising results of the treatment procedure, the reasons for efficiency loss observed previously need to be addressed in order to pave the way for an up-scaling of the fermentation process. Therefore, biowaste was fermented applying pH control, acid extraction and glucose addition in order to counteract reasons such as acidification, end-product inhibition and carbon limitation, respectively. The fermentation was competitive compared to other renewable lactic acid production substrates and reached a maximum productivity of >5 g Clactic acidg(-1)Ch(-1) and a concentration exceeding 30 g L(-1). A combination of acidification and end-product inhibition was identified as major obstacle. Lactobacillus crispatus and its closest relatives were identified as key lactic acid producers within the process using Miseq Illumina sequencing.

Demand-driven energy supply from stored biowaste for biomethanisation.

Energy supply is a global hot topic. The social and political pressure forces a higher percentage of energy supplied by renewable resources. The production of renewable energy in form of biomethane can be increased by co-substrates such as municipal biowaste. However, a demand-driven energy production or its storage needs optimisation, the option to store the substrate with its inherent energy is investigated in this study. The calorific content of biowaste was found unchanged after 45 d of storage (19.9±0.19 kJ g(-1) total solids), and the methane yield obtained from stored biowaste was comparable to fresh biowaste or even higher (approx. 400 m(3) Mg(-1) volatile solids). Our results show that the storage supports the hydrolysis of the co-substrate via acidification and production of volatile fatty acids. The data indicate that storage of biowaste is an efficient way to produce bioenergy on demand. This could in strengthen the role of biomethane plants for electricity supply the future.

Lactic acid fermentation within a cascading approach for biowaste treatment.

Limited availability of resources and increased amounts of waste coupled with an ever-increasing demand for raw materials are typical characteristics of our times. As such, there is an urgent need to accordingly update waste treatment technology. The aim of this study was to determine whether a separate treatment of the liquid and the solid fraction of biowaste could enhance overall efficiency. Liquid fractions obtained from two different separation procedures were fermented at a pH of 5 and uncontrolled pH conditions for 72 h. The fermentation conditions leading to highest lactic acid productivity and yield were evaluated. The substrates gained by both separation procedures showed efficient lactic acid production up to <25 g L(-1). The pH control increased lactic acid concentration by about 27 %. Furthermore, quantitative real-time PCR analyses revealed stronger Lactobacilli growth in these fermentations. As identified via Illumina sequencing Lactobacillus delbrueckii and its closest relatives seemed to drive the fermentation independent of the substrate. These results could help to improve today's resourcing concept by providing a separate treatment of the liquid and solid biowaste fraction.