Judith Ascher-Jenull

Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps

Due to their sensitivity to changing environmental conditions sub- and alpine soils are often monitored in the context of climate change, usually, however, neglecting slope exposure. Therefore, we set up a climosequence-approach to study the effect of exposure and, in general, climate, on the microbial biomass and microbial diversity and activity, comprising five pairs of north (N)- and south (S)-facing sites along an altitudinal gradient ranging from 1200 to 2400m a.s.l. in the Italian Alps (Trentino Alto Adige, Italy). Soil physico-chemical properties were related to microbiological properties (microbial biomass: double strand DNA yield vs. substrate-induced respiration; diversity of bacterial, fungal and archaeal communities: genetic fingerprinting DGGE vs. real-time PCR; microbial activity: basal respiration vs. multiple hydrolytic enzyme assays) to monitor shifts in the diversity and activity of microbial communities as a function of slope exposure and to evaluate the most determinant chemical parameters shaping the soil microbiota. The exposure-effect on several hydrolytic key-enzymes was enzyme-specific: e.g. acid phosphomonoesterase potential activity was more pronounced at the N-facing slope while the activities of alkaline phosphomonoesterase, pyrophosphate-phosphodiesterase and arylsulfatase were higher at the S-facing slope. Furthermore, this exposure-effect was domain-specific: bacteria (S>N, altitude-independent); fungi (N~S); and archaea (N>S; altitude-dependent). Additionally, the abiotic parameters shaping the community composition were in general depending on soil depth. Our multidisciplinary approach allowed us to survey the exposure and altitudinal effects on soil physico-chemical and microbiological properties and thus unravel the complex multiple edaphic factor-effects on soil microbiota in mountain ecosystems.

Soil attributes and microclimate are important drivers of initial deadwood decay in sub-alpine Norway spruce forests.

Deadwood is known to significantly contribute to global terrestrial carbon stocks and carbon cycling, but its decay dynamics are still not thoroughly understood. Although the chemistry of deadwood has been studied as a function of decay stage in temperate to subalpine environments, it has generally not been related to time. We therefore studied the decay (mass of deadwood, cellulose and lignin) of equal-sized blocks of Picea abies wood in soil-mesocosms over two years in the Italian Alps. The 8 sites selected were along an altitudinal sequence, reflecting different climate zones. In addition, the effect of exposure (north- and south-facing slopes) was taken into account. The decay dynamics of the mass of deadwood, cellulose and lignin were related to soil parameters (pH, soil texture, moisture, temperature) and climatic data. The decay rate constants of Picea abies deadwood were low (on average between 0.039 and 0.040y(-1)) and of lignin close to zero (or not detectable), while cellulose reacted much faster with average decay rate constants between 0.110 and 0.117y(-1). Our field experiments showed that local scale factors, such as soil parameters and topographic properties, influenced the decay process: higher soil moisture and clay content along with a lower pH seemed to accelerate wood decay. Interestingly, air temperature negatively correlated with decay rates or positively with the amount of wood components on south-facing sites. It exerted its influence rather on moisture availability, i.e. the lower the temperature the higher the moisture availability. Topographic features were also relevant with generally slower decay processes on south-facing sites than on north-facing sites owing to the drier conditions, the higher pH and the lower weathering state of the soils (less clay minerals). This study highlights the importance of a multifactorial consideration of edaphic parameters to unravel the complex dynamics of initial wood decay.

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.

Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories: Decaying spruce bacteria depend on time and slope

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.

Chemical and microbiological changes in Norway spruce deadwood during the early stage of decomposition as a function of exposure in an alpine setting

ABSTRACT Alpine ecosystems are vulnerable to ever-changing environmental conditions, leading to shifts in vegetation distribution and composition with implications on soil functionality and carbon (C) turnover. Although deadwood represents an important global C stock, scarce information is available on how slope exposure influences the wood-inhabiting microbiota throughout the decomposition process in an Alpine setting. We therefore evaluated the impact of slope exposure (north- vs. south-facing sites) on physicochemical and microbiological properties (microbial abundance based on real-time PCR: fungal 18S rRNA, dinitrogen reductase [nifH]; microbial biomass: double strand DNA; and microbial activity: hydrolytic enzyme activities of the main nutrient cycles) of Picea abies wood blocks and the underlying soil in a field experiment in the Italian Alps during a three-year period. Overall, a higher abundance of fungi and nitrogen-fixing bacteria was recorded in the soil at the north-facing site where cooler and moister conditions were observed. In contrast, no exposure effects were found for these two microbial groups in the wood blocks, while their abundance increased over time, accompanied by more acidic conditions with progressing decay. The impact of exposure was also enzyme specific and time dependent for both the P. abies wood blocks and the underlying soil.

Recycling of Organic Wastes to Soil and Its Effect on Soil Organic Carbon Status

Abstract Organic residues of various kinds should be considered an abundant source of carbon and nutrients able to contribute to the maintenance of soil fertility. This chapter gives some examples of the past, showing the necessity of considerate utilization of organic wastes. The authors give an overview on the various kinds of organic wastes from agriculture, forestry, households, and the industrial sector and discuss some pretreatment options. It is also emphasized to take the necessary care for quality control, both of the input and output material of treatment operations. Last but not least, global change aspects of organic waste management are addressed.

Humusica: Soil biodiversity and global change

Abstract Born in Trento (Italy, 2003) for the purpose of standardising vocabulary and units of humus form classification, after publishing a first synthetic classification e-book (Zanella et al. 2011) they do not cover all site conditions in the European area. Although having basic concepts and general lines, the European (and North American, Canadian, the Humus group decided to use its classification for handling global change (Zanella and Ascher-Jenull 2018). The process is detailed in many scientific articles published in three Special Issues (Humusica 1, 2 and 3) of the journal Applied Soil Ecology. Conceptually, the whole of Humusica answers three crucial questions: A) What is soil? Soil is a biological ecosystem. It recycles dead structures and implements mineral material, furnishing more or less re-elaborated organic, mineral and organic-mineral elements to support living organisms. Article chapters: 1. Essential vocabulary; 2. Soil covers all the Earth’s surfaces (soil as the seat of processes of organic matter storage and recycling); 3. Soil may be involved in the process of natural evolution (through organisms’ process of recycling biomass after death). B) If soil has a biogenic essence, how should it be classified to serve such managerial purposes as landscape exploitation or protection? A useful classification of soil should consider and propose useful references to biologically discriminate soil features. Article chapters: 4. Soil corresponds to a biogenic structure; 5. TerrHum, an App for classifying forest humipedons worldwide (a first attempt to use a smartphone as a field manual for humus form classification). C) How can this soil classification be used for handling the current global change? Using the collected knowledge about the biodiversity and functioning of natural (or semi-natural) soil for reconstructing the lost biodiversity/functioning of heavily exploited or degraded soils. Article chapters: 6. Agricultural soils correspond to simplified natural soils (comparison between natural and agricultural soils); 7. Organic waste and agricultural soils; 8. Is traditional agriculture economically sustainable? Comparing past traditional farm practices (in 1947) and contemporary intensive farm practices in the Venice province of Italy.

Extracellular DNA in natural environments: features, relevance and applications

Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.