The effect of silvicultural systems on soil function depends on bedrock geology and altitude.

Soil quality and function in forest environments are influenced by the interaction of soil-forming parameters and silvicultural systems. Hyrcanian forests were recently accepted as a UNESCO World Heritage Site, which extends across an area of approximately 1.8 million hectares and ascend to an elevation of 2800 m above sea level (m.a.s.l). In these woodlands, Oriental Beech (Fagus orientalis Lipsky) is the predominant tree species and could be observed at 700-1500 m.a.s.l., and occur on different parent rocks. Shelterwood and single-tree selection techniques have been the primary management methods for beech forests for the past forty years. Studies investigating the impacts of silvicultural systems have not yet been done on soil and forest floor features on different bedrock geology and altitudes. Therefore, in this study, we examined the influence of single-tree selection and shelterwood methods, 25 years after employing those methods, on soil quality and function compared to control areas (intact forests) in Hyrcanian beech stands. For this purpose, 15 forest floor (30 × 30 cm) and topsoil (0-10 cm depth) samples in each silvicultural systems (i.e., single-tree selection and shelterwood methods and control zones) × 4 regions (including Rasht, Nowshahr, Sari and Gorgan) × 4 altitude levels (with averages of 800, 1000, 1200 and 1400 m.a.s.l.) were considered. According to our findings, the investigated forest regions, forest floor and soil characteristics across various locations spots could be separated by principal component analysis output, and more than 85% of the variance was explained by the first and second axes. The structural equation model showed that the region, altitude and silvicultural systems had an effective role in the changes in soil biological activities by influencing the forest floor, and the soil physicochemical features. Based upon the network model, the C/N ratio, the sand content, the soil aggregate stability, the available K, the fulvic acid, and the Acarina density were found to be prominent factors with regard to soil function. In the control sites, increased soil organic material fractions, microbial/enzyme and biota activities were detected, particularly at the lower altitudes of the Nowshahr site, which had geological formations of dolomite and calcic layers. Taken together, it seems that the single-tree method, commonly referred to as the close-to-nature technique produces more suitable conditions for soil functioning compared to the shelterwood management approach. Silvicultural systems, bedrock geology and altitude can have major detrimental effects on soil function and fertility, over the long-term, impacts may increase with harvest intensity.

Influence of earthworms on the microbial properties and extracellular enzyme activities during vermicomposting of raw and distilled grape marc.

The treatment of winery wastes by using appropriate management technologies is of utmost need in order to reduce to a minimum their disposal and avoid negative environmental impacts. This is of particular interest for grape marc, the main solid by-product of the winery industry. However, comparative studies on a pilot-scale dealing with the impact of earthworms on marc derived from both red and white grape varieties during vermicomposting are still scarce. The present study sought to evaluate the changes in the biochemical and microbiological properties of red and white raw marc in the presence and the absence of the earthworm species Eisenia andrei. The distilled marc obtained through distillation of the red grape marc was also considered under this scenario. Samples were taken after 14, 28, 42, and 63 days of vermicomposting. On day 14 earthworms led to a pronounced increase in most of the enzymatic activities, but only in those vermireactors fed with raw marc from the red grape variety. Alfa- and beta-glucosidase as well as chitinase and leucine-aminopeptidase activities were between 3 to 5-times higher relative to the control, while alkaline phosphomonoesterase was even up to 14-fold higher with earthworm presence. From day 28 onwards the magnitude of earthworms' effect on the studied enzymes was also dependent on the type of grape marc. Reduced values of basal respiration, ranging between 200 and 350 mg CO2 kg OM h-1 and indicative of stabilized materials were found in the resulting vermicomposts. Moreover, the content of macro- and micronutrients in the end products matched with those considered to have the quality criteria of a good vermicompost. Altogether, these findings reinforce the effectiveness of vermicomposting for the biological stabilization of grape marc with the dual purpose of fertilizer production and environmental protection.

Microbial response on the first full-scale DEMON® biomass transfer for mainstream deammonification.

Sidestream partial nitritation and deammonification (pN/A) of high-strength ammonia wastewater is a well-established technology. Its expansion to the mainstream is, however mainly impeded by poor retention of anaerobic ammonia oxidizing bacteria (AnAOB), insufficient repression of nitrite oxidizing bacteria (NOB) and difficult control of soluble chemical oxygen demand and nitrite levels. At the municipal wastewater treatment plant in Strass (Austria) the microbial consortium was exhaustively monitored at full-scale over one and a half year with regular transfer of sidestream DEMON® biomass and further retention and enrichment of granular anammox biomass via hydrocyclone operation. Routine process parameters were surveyed and the response and evolution of the microbiota was followed by molecular tools, ex-situ activity tests and further, AnAOB quantification through particle tracking and heme measurement. After eight months of operation, the first anaerobic, simultaneous depletion of ammonia and nitrite was observed ex-situ, together with a direction to higher nitrite generation (68% of total NOx-N) as compared to nitrate under aerobic conditions. Our dissolved oxygen (DO) scheme allowed for transient anoxic conditions and had a strong influence on nitrite levels and the NOB community, where Nitrobacter eventually dominated Nitrospira. The establishment of a minor but stable AnAOB biomass was accompanied by the rise of Chloroflexi and distinct emergence of Chlorobi, a trend not seen in the sidestream system. Interestingly, the most pronounced switch in the microbial community and noticeable NOB repression occurred during unfavorable conditions, i.e. the cold winter season and high organic load. Further abatement of NOB was achieved through bioaugmentation of aerobic ammonia oxidizing bacteria (AerAOB) from the sidestream-DEMON® tank. Performance of the sidestream pN/A was not impaired by this operational scheme and the average volumetric nitrogen removal rate of the mainstream even doubled in the second half of the monitoring campaign. We conclude that a combination of both, regular sidestream-DEMON® biomass transfer and granular SRT increase via hydrocyclone operation was crucial for AnAOB establishment within the mainstream.

Changes in the nutrient dynamics and microbiological properties of grape marc in a continuous-feeding vermicomposting system.

Finding strategies to reuse and treat organic wastes is of utmost need. Biological processes offer the possibility to transform them into safer end products with benefits for both agriculture and the environment. Moreover, it represents an ecologically-sound and economically attractive alternative to landfill disposal and incineration. In this work, we evaluated the feasibility of vermicomposting to treat and process grape marc, the main solid by-product of the wine industry. The long-term changes in grape marc derived from both white and red winemaking processes were assessed throughout the process of vermicomposting from a physico-chemical and microbiological perspective. New layers of fresh marc were added sequentially in the presence and absence of earthworms (Eisenia andrei) forming an age gradient during a 42-week period. An optimal moisture level of 70% was maintained over the course of the process. The pH fell within weak-alkaline levels through the layers profile and the electrical conductivity was between 200 and 300 µS cm-1, providing optimum conditions for earthworm growth. The mass loss caused by earthworm activity led to an increased content of macro- and micronutrients at the end of the trial. An overall decrease in microbial biomass and its activity, indicative of a stabilised material, was also recorded with depth of layer. Altogether, this points to vermicomposting as a suitable management system for processing grape marc with a dual purpose, that is fertilizer production and environment protection. This is especially relevant in the current attempts to reach a fully circular economy.

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.

Special Issue "Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management".

Anthropogenic activity generates huge amounts of solid organic wastes [...].

Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review.

Organic wastes have the potential to be used as soil organic amendments after undergoing a process of stabilization such as composting or as a resource of renewable energy by anaerobic digestion (AD). Both composting and AD are well-known, eco-friendly approaches to eliminate and recycle massive amounts of wastes. Likewise, the application of compost amendments and digestate (the by-product resulting from AD) has been proposed as an effective way of improving soil fertility. The study of microbial communities involved in these waste treatment processes, as well as in organically amended soils, is key in promoting waste resource efficiency and deciphering the features that characterize microbial communities under improved soil fertility conditions. To move beyond the classical analyses of metataxonomic data, the application of co-occurrence network approaches has shown to be useful to gain insights into the interactions among the members of a microbial community, to identify its keystone members and modelling the environmental factors that drive microbial network patterns. Here, we provide an overview of essential concepts for the interpretation and construction of co-occurrence networks and review the features of microbial co-occurrence networks during the processes of composting and AD and following the application of the respective end products (compost and digestate) into soil.

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.

CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis.

In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce "CoMA-Comparative Microbiome Analysis" as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.

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.

Temporal Dynamics of Bacterial Communities in a Pilot-Scale Vermireactor Fed with Distilled Grape Marc.

Vermicomposting has been found as a profitable approach to dispose of and treat large quantities of raw grape marc. However, less information is available with regard to its efficiency for treating distillery winery byproducts, even though distillation has been widely used as a way to economically valorize grape marc. As such, we sought to characterize the compositional and functional changes in bacterial communities during vermicomposting of distilled grape marc by using 16S rRNA high-throughput sequencing. Samples were collected at the initiation of vermicomposting and at days 14, 21, 28, 35 and 42. There were significant changes (p < 0.0001) in the bacterial community composition of distilled grape marc after 14 days of vermicomposting that were accompanied by twofold increases in bacterial richness and diversity from a taxonomic and phylogenetic perspective. This was followed by significant increases in functional diversity of the bacterial community, including metabolic capacity, lignin and cellulose metabolism, and salicylic acid synthesis. These findings indicate that the most striking compositional and functional bacterial community changes took place during the active phase of the process. They also pinpoint functional attributes that may be related to the potential beneficial effects of distilled grape marc vermicompost when applied on soil and plants.

Effectiveness of vermicomposting for bioconversion of grape marc derived from red winemaking into a value-added product.

Grape marc, the main solid by-product of the wine industry, can be used as a nutrient-rich organic amendment if treated appropriately before its application into soil. In this study, we evaluated the potential of vermicomposting to process grape marc derived from the red winemaking of Mencía grapes in order to yield a high-quality, polyphenol-free organic vermicompost that could be used as an environmentally friendly fertiliser. We observed that the grape marc from this cultivar appears to be an optimum substrate for feeding earthworms providing optimum conditions for growth and reproduction, and sufficient energy to sustain large populations. Moreover, earthworm activity favoured the stabilisation of the grape marc resulting in a final vermicompost characterised by a higher concentration of macro- and micro-nutrients and a reduced polyphenol content after 112 days of vermicomposting. Lower values of microbial activity, indicative of stabilised materials, were recorded at the end of the process. These findings highlight vermicomposting as an environmentally sound management system for processing grape marc that could easily be scaled up for industrial application.

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 co-occurring 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.

Rapid Bacterial Community Changes during Vermicomposting of Grape Marc Derived from Red Winemaking.

Previous studies dealing with changes in microbial communities during vermicomposting were mostly performed at lab-scale conditions and by using low-throughput techniques. Therefore, we sought to characterize the bacterial succession during the vermicomposting of grape marc over a period of 91 days in a pilot-scale vermireactor. Samples were taken at the initiation of vermicomposting, and days 14, 28, 42, and 91, representing both active and mature stages of vermicomposting. By using 16S rRNA high-throughput sequencing, significant changes in the bacterial community composition of grape marc were found after 14 days and throughout the process (p < 0.0001). There was also an increase in bacterial diversity, both taxonomic and phylogenetic, from day 14 until the end of the trial. We found the main core microbiome comprised of twelve bacterial taxa (~16.25% of the total sequences) known to be capable of nitrogen fixation and to confer plant-disease suppression. Accordingly, functional diversity included increases in specific genes related to nitrogen fixation and synthesis of plant hormones (salicylic acid) after 91 days. Together, the findings support the use of grape marc vermicompost for sustainable practices in the wine industry by disposing of this high-volume winery by-product and capturing its value to improve soil fertility.

Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment.

Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a litter transplantation experiment from oak forests (home site) to two away sites without oak in South Tyrol (Italy). We aimed to produce an in-depth analysis of the fungal and bacterial decomposer communities using Illumina sequencing and qPCR, to understand whether local adaptation occurs and whether this was associated with litter mass loss dynamics. Temporal shifts in the decomposer community occurred, reflecting changes in litter chemistry over time. Fungal community composition was site dependent, while bacterial composition did not differ across sites. Total litter mass loss and rates of litter decomposition did not change across sites. Litter quality influenced the microbial community through the availability of different carbon sources. Additively, our results do not support the hypothesis that locally adapted microbial decomposers lead to a greater or faster mass loss. It is likely that high functional redundancy within decomposer communities regulated the decomposition, and thus greater future research attention should be given to trophic guilds rather than taxonomic composition.

Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost.

Vermicomposting is the process by which organic waste is broken down through the synergistic actions of earthworms and microbial communities. Although vermicomposting has been shown to effectively reduce organic biomass and generate high-quality fertilizer for plants, little is known about the bacterial communities that are involved in this decomposition process. Since optimization of vermicomposting for commercial use necessitates additional knowledge of the underlying biological processes, this study sought to characterize the bacterial succession involved in the vermicomposting of Scotch broom (Cytisus scoparius), a leguminous shrub that has become invasive around the world with consequences for the dynamics and productivity of the ecosystems they occupy. Scotch broom was processed in a pilot-scale vermireactor for 91 days with the earthworm species Eisenia andrei. Samples were taken at the initiation of vermicomposting, and days 14, 42 and 91, representing both active and mature stages of vermicomposting. Significant changes (P < 0.0001) in the bacterial community composition (richness and evenness) were observed throughout the process. Increases in taxonomic diversity were accompanied by increases in functional diversity of the bacterial community, including metabolic capacity, streptomycin and salicylic acid synthesis, and nitrification. These results highlight the role of bacterial succession during the vermicomposting process and provide evidence of microbial functions that may explain the beneficial effects of vermicompost on soil and plants.

Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño.

Winemaking produces millions of tons of grape marc, a byproduct of grape pressing, each year. Grape marc is made up of the skins, stalks, and seeds remaining after pressing. Raw grape marc can be hazardous to the environment due to its low pH and high polyphenol content, but previous work has shown that grape marc can be stabilized via vermicomposting to produce organic fertilizer. Here, we utilize 16S rRNA high-throughput sequencing to characterize the bacterial community composition, diversity and metabolic function during vermicomposting of the white grape marc Vitis vinifera v. Albariño for 91 days. Large, significant changes in the bacterial community composition of grape marc vermicompost were observed by day 7 of vermicomposting and throughout the duration of the experiment until day 91. Similarly, taxonomic and phylogenetic α-diversity increased throughout the experiment and estimates of ß-diversity differed significantly between time points. Functional diversity also changed during vermicomposting, including increases in cellulose metabolism, plant hormone synthesis, and antibiotic synthesis. Thus, vermicomposting of white grape marc resulted in a rich, stable bacterial community with functional properties that may aid plant growth. These results support the use of grape marc vermicompost for sustainable agricultural practices in the wine industry.

Strategies for recycling and valorization of grape marc.

Grapes are one of the most cultivated fruit crops worldwide. Either for wine or juice production, grape processing generates a large amount of residues that must be treated, disposed of or reused properly to reduce their pollution load before being applied to the soil. In this review, a special focus is given to the treatment and valorization of the winemaking by-product like grape marc via anaerobic digestion, composting and vermicomposting at laboratory, pilot, and industrial scales. The impact of the final products (digestates, composts, and vermicomposts) on soil properties is briefly addressed. Moreover, the role of grape marc and seeds as a valuable source of natural phytochemicals that include polyphenols and other bioactive compounds of interest for pharmaceutical, cosmetic, and food industries is also discussed. This is of paramount importance given the fact that sustainability requires the use of management and valorization strategies that allow the recovery of valuable compounds (e.g. antioxidants) with minimum disposal of waste streams.