The use of extracellular DNA as a proxy for specific microbial activity

The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly gaining importance in many fields of application such as medicine and environmental microbiology. Although sources and types of exDNA are manifold, ratios of specific DNA-molecules inside and outside of living cells can give reliable information about the activity of entire systems and of specific microbial groups or species. Here, we introduce a method to discriminate between internal (iDNA), as well as bound and free exDNA, and evaluate various DNA fractions and related ratios (ex:iDNA) regarding their applicability to be used as a fast, convenient, and reliable alternative to more tedious RNA-based activity measurements. In order to deal with microbial consortia that can be regulated regarding their activity, we tested and evaluated the proposed method in comparison to sophisticated dehydrogenase- and RNA-based activity measurements with two anaerobic microbial consortia (anaerobic fungi and syntrophic archaea and a microbial rumen consortium) and three levels of resolution (overall activity, total bacteria, methanogenic archaea). Furthermore, we introduce a 28S rRNA gene-specific primer set and qPCR protocol, targeting anaerobic fungi (Neocallimastigomycota). Our findings show that the amount of actively released free exDNA (fDNA) strongly correlates with different activity measurements and is thus suggested to serve as a proxy for microbial activity.publishersversionPeer reviewe

The potential of calcium hydroxide to reduce storage losses: A four months monitoring study of spruce wood chip piles at industrial scale

The objective of this study was to investigate the effect of an alkaline additive on the storage of wood chips from Norway spruce forest residues. Piles of untreated and calcium hydroxide treated wood chips (250 m3) were set up and investigated for four months. It was demonstrated that adding Ca(OH)2 to moist wood chips decreased the dry matter loss by 6%. This was attributed to the increase of the pH to a level of 8, rendering the habitat less suitable for fungal colonisation. The results suggest the set-up storage strategy as a potential alternative method for preserving wood chips when long term storage is required

Phlorizin released by apple root debris is related to apple replant disease

Autotoxic compounds are likely to be among the causes of apple replant disease, but their secretion is low during plant life. Using targeted metabolomics, the changes in soil phenolic profile were analyzed after the addition of apple roots, and their potential autotoxicity was assessed on apple seedlings. The addition of apple roots severely damaged the plants, attributed to autotoxic action of the phenolic compound phlorizin. Prolonged residence time of the roots in the soil before planting reduced their negative action, probably due to the degradation of phlorizin

The effect of calcium hydroxide on the storage behaviour of poplar wood chips in open-air piles

Biomass degradation by microorganisms may cause major losses during the storage of wood chips for energy production. Poplar wood chips from short rotation coppices are especially prone to degradation with dry matter losses (DML) of up to 25% within a storage period, emphasizing the need for countermeasures. Therefore, we investigated the potential of the addition of alkaline Ca(OH)2 to the wet biomass of poplar wood chips and hypothesised that the establishment of an alkaline environment would reduce the activity of fungi, the primary wood degraders. Three industrial-scale piles (250 m³) with 0, 1.5 and 3% Ca(OH)2 were installed in Güssing, Austria and for four months (April–August 2019) the pile temperature, pH, moisture content, gas evolution (O2, CO2, H2, H2S, CH4) as well as DML were monitored. Ca(OH)2 altered the physicochemical properties of the wood chips but did not prevent biomass losses. However, as compared to literature, the DML were, compared to earlier investigations, also low in the control. In addition, cultivation methods were performed to evaluate the diversity of thermophilic microbes throughout the storage. Numerous filamentous fungi belonging to the phyla Ascomycota and Mucoromycota were isolated, being Rhizomucor pusillus, Aspergillus fumigatus, Thermomyces lanuginosa and Thermoascus aurantiacus the dominant species. Only minor differences in the fungal composition were detected as a result of Ca(OH)2 addition. Instead, clear shifts in colony forming units (CFUs) were detected as a function of progressing storage time, with a decrease of the number of propagules after four months

Soil carbonyl sulfide exchange in relation to microbial community composition: Insights from a managed grassland soil amendment experiment

The viability of carbonyl sulfide (COS) measurements for partitioning ecosystem-scale net carbon dioxide (CO2) fluxes into photosynthesis and respiration critically depends on our knowledge of non-leaf sinks and sources of COS in ecosystems. We combined soil gas exchange measurements of COS and CO2 with next-generation sequencing technology (NGS) to investigate the role of soil microbiota for soil COS exchange. We applied different treatments (litter and glucose addition, enzyme inhibition and gamma sterilization) to soil samples from a temperate grassland to manipulate microbial composition and activity. While untreated soil was characterized by consistent COS uptake, other treatments reduced COS uptake and even turned the soil into a net COS source. Removing biotic processes through sterilization led to positive or zero fluxes. We used NGS to link changes in the COS response to alterations in the microbial community composition, with bacterial data having a higher explanatory power for the measured COS fluxes than fungal data. We found that the genera Arthrobacter and Streptomyces were particularly abundant in samples exhibiting high COS emissions. Our results indicate cooccurring abiotic production and biotic consumption of COS in untreated soil, the latter linked to carbonic anhydrase activity, and a strong dependency of the COS flux on the activity, identity, abundance of and substrate available to microorganisms.Austrian National Science Fund (FWF) | Ref. P27176-B16Tyrolean Science Fund (TWF) | Ref. UNI-0404/1801Ministerio de Economía y Competitividad | Ref. RYC-2016-2123