Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting.

Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w).

Learning vs. understanding: When does artificial intelligence outperform process-based modeling in soil organic carbon prediction?

In recent years, machine learning (ML) algorithms have gained substantial recognition for ecological modeling across various temporal and spatial scales. However, little evaluation has been conducted for the prediction of soil organic carbon (SOC) on small data sets commonly inherent to long-term soil ecological research. In this context, the performance of ML algorithms for SOC prediction has never been tested against traditional process-based modeling approaches.

Soil quality increases with long-term chabazite-zeolite tuff amendments in arable and perennial cropping systems.

The application of natural zeolites to improve soil quality and functioning has become highly popular, but we still miss information about the long-term effects on the soil due to its application. This study assesses the soil quality index (SQI) of three distinct agricultural soil systems 6-10 years after a single application of natural chabazite zeolite as a soil amendment. These soils exhibit different management practices: intensive arable (cereals), intensive perennial (pear) and organic perennial (olive).

Carbon isotope effects in the sorption of chlorinated ethenes on biochar and activated carbon.

As an alternative to activated carbon, biochar is a promising, environmentally friendly sorbent that can be used to remove organic groundwater pollutants, such as chlorinated ethenes (CEs). Stable isotope fractionation in biofilters is used to quantify pollutant degradation and to distinguish degradation from pollutant sorption on e.g.

Meta-analysis protocol on the effects of cover crops on pool specific soil organic carbon.

Soil organic carbon (SOC) plays an important role in agricultural soils, as it contributes to overall soil health as well as climate change mitigation and adaptation. By conducting a meta-analysis, we aim to quantitatively summarize research studying the effects of cover crops (CC) on SOC pools throughout soil depths in arable cropland. We included global studies located in the climatic zones present in Europe.

AI for life: Trends in artificial intelligence for biotechnology.

Due to popular successes (e.g., ChatGPT) Artificial Intelligence (AI) is on everyone's lips today.

Recycling nitrogen from liquid digestate via novel reactive struvite and zeolite minerals to mitigate agricultural pollution.

Recycling nutrients is of paramount importance. For this reason, struvite and nitrogen enriched zeolite fertilizers produced from wastewater treatments are receiving growing attention in European markets. However, their effects on agricultural soils are far from certain, especially struvite, which only recently was implemented in EU Fertilizing Product Regulations.

Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau.

Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau's agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa.

Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking.

Molecular diagnostic methods are increasingly applied for food and environmental analysis. Since several steps are involved in sample processing which can affect the outcome (e.g.

Cadmium retention and microbial response in volcanic soils along gradients of soil age and climate on the Galápagos Islands.

The behavior of trace metals may vary strongly in the course of volcanic soil development. Cadmium retention in soils is specifically important for some Galápagos islands where agriculture is leading to anthropogenic Cd contamination. To assess the influence of soil development factors on soil Cd retention and toxicity, we performed Cd sorption-desorption experiments with volcanic topsoils from the Galápagos Islands sampled along gradients of (a) substrate age (chronosequence, 1.

Effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N-turnover, the NO reductase-gene nosZ and NO:N partitioning from agricultural soils.

Nitrification inhibitors (NIs) have been shown to reduce emissions of the greenhouse gas nitrous oxide (NO) from agricultural soils. However, their NO reduction efficacy varies widely across different agro-ecosystems, and underlying mechanisms remain poorly understood. To investigate effects of the NI 3,4-dimethylpyrazole-phosphate (DMPP) on N-turnover from a pasture and a horticultural soil, we combined the quantification of N and NO emissions with N tracing analysis and the quantification of the NO-reductase gene (nosZ) in a soil microcosm study.

Does Soil Contribute to the Human Gut Microbiome?

Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with the modern lifestyle. We tracked relationships between the soil microbiome and the human intestinal microbiome. We propose a novel environmental microbiome hypothesis, which implies that a close linkage between the soil microbiome and the human intestinal microbiome has evolved during evolution and is still developing.

Fungicide application increased copper-bioavailability and impaired nitrogen fixation through reduced root nodule formation on alfalfa.

Copper-based fungicides have been used for a long time in viticulture and have accumulated in many vineyard soils. In this study, incrementing Cu(OH)-based fungicide application from 0.05 to 5 g Cu kg on two agricultural soils (an acidic sandy loam (L, pH 4.

Response of Microbial Communities and Their Metabolic Functions to Drying⁻Rewetting Stress in a Temperate Forest Soil.

Global climate change is predicted to alter drought-precipitation patterns, which will likely affect soil microbial communities and their functions, ultimately shifting microbially-mediated biogeochemical cycles. The present study aims to investigate the simultaneous variation of microbial community compositions and functions in response to drought and following rewetting events, using a soil metaproteomics approach. For this, an established field experiment located in an Austrian forest with two levels (moderate and severe stress) of precipitation manipulation was evaluated.

Sample Preparation for Metaproteome Analyses of Soil and Leaf Litter.

Soil and litter metaproteomics, assigning soil and litter proteins to specific phylogenetic and functional groups, has a great potential to shed light on the impact of microbial diversity on soil ecosystem functioning. However, metaproteomic analysis of soil and litter is often hampered by the enormous heterogeneity of the soil matrix and high concentrations of humic acids. To circumvent these challenges, sophisticated protocols for sample preparation have to be applied.

Biochar application increases sorption of nitrification inhibitor 3,4-dimethylpyrazole phosphate in soil.

Biochar (BC) application to soils is of growing interest as a strategy to improve soil fertility and mitigate climate change. However, BC-induced alterations in the soil N cycle are currently under debate. BC has recently been shown to accelerate the emissions of NO via the biotic ammonium oxidation pathway, which results in lower nitrogen use efficiency and environmentally harmful losses of NO and/ or NO.

Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure.

Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community.

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events.

Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling.

Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.

The increasing application of soil metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies.

Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling.

Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization.

A closeup study of early beech litter decomposition: potential drivers and microbial interactions on a changing substrate.

Aims: Litter decomposition and subsequent nutrient release play a major role in forest carbon and nutrient cycling. To elucidate how soluble or bulk nutrient ratios affect the decomposition process of beech ( L.) litter, we conducted a microcosm experiment over an 8 week period.

Soil metaproteomics - Comparative evaluation of protein extraction protocols.

Metaproteomics and its potential applications are very promising to study microbial activity in environmental samples and to obtain a deeper understanding of microbial interactions. However, due to the complexity of soil samples the exhaustive extraction of proteins is a major challenge. We compared soil protein extraction protocols in terms of their protein extraction efficiency for two different soil types.

Influence of litter chemistry and stoichiometry on glucan depolymerization during decomposition of beech (Fagus sylvatica L.) litter.

Glucans like cellulose and starch are a major source of carbon for decomposer food webs, especially during early- and intermediate-stages of decomposition. Litter quality has previously been suggested to notably influence decomposition processes as it determines the decomposability of organic material and the nutrient availability to the decomposer community. To study the impact of chemical and elemental composition of resources on glucan decomposition, a laboratory experiment was carried out using beech (Fagus sylvatica, L.

Stoichiometric controls of nitrogen and phosphorus cycling in decomposing beech leaf litter.

Resource stoichiometry (C:N:P) is an important determinant of litter decomposition. However, the effect of elemental stoichiometry on the gross rates of microbial N and P cycling processes during litter decomposition is unknown. In a mesocosm experiment, beech (Fagus sylvatica L.

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions.

Leaf-litter decomposition is a central process in carbon cycling; however, our knowledge about the microbial regulation of this process is still scarce. Metaproteomics allows us to link the abundance and activity of enzymes during nutrient cycling to their phylogenetic origin based on proteins, the 'active building blocks' in the system. Moreover, we employed metaproteomics to investigate the influence of environmental factors and nutrients on the decomposer structure and function during beech litter decomposition.