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Publications (47)
Background. Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of mic...
Aims
Cropland agroforestry systems are land-use systems with numerous environmental advantages over monoculture croplands including promotion of soil life. This study aimed to investigate tree-species and tree-distance effects on soil biota in a temperate agroforestry system.
Methods
Our study was conducted at a paired alley-cropping and monocultu...
Aims
Incorporation of flower strips is an agricultural measure to increase aboveground biodiversity and ecosystem services. Although soil communities are key components of terrestrial biodiversity and drive important ecosystem services, their abundance, diversity, and composition in flower strips remain largely unexplored. Here, we shed light on ea...
Flower strips are a prominent agri‐environmental scheme with the central objective to promote biodiversity and maintain associated ecosystem services. The promotion of natural enemies by increasing resource availability through flower strips is a promising approach for integrated pest management.
In a 3‐year field study, two annual and two perennia...
The loss of soil biodiversity through agricultural intensification is a major contributor to the collapse of ecosystem services. Despite their wide application to promote biodiversity, the impact of flower strips on soil organisms is largely unknown. Here, we studied the effects of perennial flower strips on earthworm communities at 46 sites with p...
Agroforestry systems are multifunctional land-use systems that promote soil life. Despite their large potential spatio-temporal complexity, the majority of studies that investigated soil organisms in temperate cropland agroforestry systems focused on rather non-complex systems. Here, we investigated the topsoil and subsoil microbiome of two complex...
Intensive agricultural land use negatively impacts biodiversity, including arthropod predator diversity and their pest control potential. Alley‐cropping agroforestry systems (integration of tree rows into arable land) are increasingly considered an economically viable alternative for more sustainable and biodiversity‐friendly agriculture. However,...
Background
Extreme rainfall and flooding events are projected to increase in frequency and disturb biogeochemi-cal cycles such as the nitrogen (N) cycle. By combining trees and grasses, silvopastoral agroforestry is expected to increase the stability of this cycle in response to flooding. However, little is known about the response of nitrifica-tio...
In addition to the removal of excess mineral nitrogen (N) via root uptake, trees in agroforestry systems may mitigate negative effects of high N fertilization of adjacent crops by enhancing complete denitrification of excess mineral N aside from root uptake. Presently, little is known about the potential for NO3⁻ reduction through denitrification (...
Information on microbial biomass carbon (MBC) is crucial to assess their stocks and role for plant nutrient release in soil. Next to fumigation-extraction, molecular methods are routinely used to estimate the contribution of fungi, bacteria, and archaea to the soil microbial community. However, more information on the links between these different...
Background and aims
Agroforestry, whereby trees are associated with crops and/or livestock, is expected to mitigate nitrogen (N) losses from agriculture. However , little is known about how nitrification potential, an important process that drives N losses, is affected by agroforestry systems. This study aimed to investigate the effect of different...
Intensively managed open croplands are highly productive but often have deleterious environmental impacts. Temperate agroforestry potentially improves ecosystem functions, although comprehensive analysis is lacking. Here, we measured primary data on 47 indicators of seven ecosystem functions in croplands and 16 indicators of four ecosystem function...
Flower strips are a common agricultural practice to increase aboveground biodiversity and beneficial ecosystem services. Although soil communities are a key component of terrestrial biodiversity and drive important ecosystem services, their abundance, diversity, and composition in flower strips remain largely unexplored. Here, we shed light on eart...
Incorporation of crop residues into agricultural soils is a common practice that can improve soil quality. However, the impact of different straw incorporation techniques on soil bacteria and their functions is still not well understood, especially across soil depths. Here, we investigated the impact of three maize straw management methods (straw r...
Aims
Temperate alley-cropping agroforestry systems maintain agricultural production while offering several environmental benefits. Central benefits of agroforestry systems such as the ‘safety-net’-role of the trees for leached nutrients are mainly due to processes occurring below the soil surface: the subsoil. Microorganisms in the subsoil may play...
Taxonomic marker gene analysis allows uncovering taxonomic profiles of microbial communities at low cost, making it omnipresent in microbiome research. There is an ever-expanding set of tools to extract further biological information from this kind of data. In this perspective, we enunciate several concerns regarding the biological validity of pred...
Fusarium culmorum is a major pathogen of grain crops. Infected plants accumulate deox-ynivalenol (DON), 3-acetyl-deoxynivalenol (3-ADON), or nivalenol (NIV), which are mycotoxins of the trichothecene B group. These toxins are also produced by F. graminearum species complex. New trichothecenes structurally similar to trichothecenes B but lacking the...
Background
Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the mos...
Fusarium culmorum is a major pathogen of grain crops. Infected plants accumulate deoxynivalenol (DON), 3-acetyl-deoxynivalenol (3-ADON), or nivalenol (NIV), which are mycotoxins of the trichothecene B group. These toxins are also produced by F. graminearum species complex. New trichothecenes structurally similar to trichothecenes B but lacking the...
Fusarium culmorum is a major pathogen of grain crops. Infected plants accumulate deoxynivalenol (DON), 3-acetyl-deoxynivalenol (3-ADON), or nivalenol (NIV), which are mycotox-ins of the trichothecene B group. These toxins are also produced by F. graminearum species complex. New trichothecenes structurally similar to trichothecenes B but lacking the...
Fusarium culmorum is a major pathogen of grain crops. Infected plants accumulate deoxynivalenol (DON), 3-acetyl-deoxynivalenol (3-ADON), or nivalenol (NIV), which are mycotoxins of the trichothecene B group. These toxins are also produced by F. graminearum species complex. New trichothecenes structurally similar to trichothecenes B but lacking the...
Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capaci...
Modern temperate alley-cropping systems combine rows of trees with rows of crops (agroforestry), which allows for diverse interspecific interactions such as the complementary and competitive use of resources. The complementary use of resources between trees and crops is considered the main advantage of these multifunctional land use systems over cr...
Conversion of monoculture to agroforestry (integrating trees with crops) is promoted as a promising management in reducing N2O emissions from croplands. How agroforestry influences gross N2O emission (N2O + N2 from N2O reduction) and uptake (N2O reduced to N2) compared to monoculture is unknown. We used the ¹⁵N2O pool dilution technique to quantify...
Incorporating legumes is one option for improving pasture fertility, sustainability, and biodiversity. Diazotrophic microorganisms, including rhizobia that form symbioses with legumes, represent a small fraction of the total soil microbial community. Yet, they can offset nitrogen (N) fertilizer inputs through their ability to convert atmospheric N2...
Several ecological data types, especially microbiome count data, are commonly sample-wise normalized before analysis to correct for sampling bias and other technical artifacts. Recently, we developed an algorithm for the normalization of ecological count data called ‘scaling with ranked subsampling (SRS)’, which surpasses the widely adopted ‘rarefy...
Background: Alley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of...
Increased global production of animal-based protein results in high greenhouse gas (GHG) emissions and other adverse consequences for human and planetary health. Recently, commercial insect rearing has been claimed a more sustainable source of animal protein. However, this system also leaves residues called frass, which—depending on the insect diet...
Faeces from cows with different milk yield and non-lactating cows were applied to soil to investigate whether soil N 2 O efflux is related to feeding-induced differences in faecal microbiome and abundances of nitrification and denitrification genes. Fungal 18S-rRNA gene abundance was the highest in the faeces of the non-lactating group. The 18S-rRN...
Plant production systems that are more sustainable than conventional monoculture croplands are the vision of future agriculture. With numerous environmental benefits, agroforestry is among the most promising alternatives. Although soil fungi are key drivers of plant productivity and ecosystem processes, investigations of these microorganisms in tem...
Background
Tree-based intercropping (agroforestry) has been advocated to reduce adverse environmental impacts of conventional arable cropping. Modern agroforestry systems in the temperate zone are alley-cropping systems that combine rows of fast-growing trees with rows of arable crops. Soil microbial communities in these systems have been investig...
Nitrogen (N) fertilization is the major contributor to nitrous oxide (N2O) emissions from agricultural soil, especially in post‐harvest seasons. This study was carried out to investigate whether ryegrass serving as cover crop affects soil N2O emissions and denitrifier community size. A microcosm experiment was conducted with soil planted with peren...
Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is a popular method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, res...
Supplementary file 1 from Microorganisms 2020, 8(4), 532; https://doi.org/10.3390/microorganisms8040532
As our understanding of soil biology deepens, there is a growing demand for investigations addressing microbial processes in the earth beneath the topsoil layer, called subsoil. High clay content in subsoils often hinders the recovery of sufficient quantities of DNA as clay particles bind nucleic acids. Here, an efficient and reproducible DNA extra...
Maize plants are often infected with fungal pathogens of the genus Fusarium. Taxonomic characterization of these species by microscopic examination of pure cultures or assignment to mating populations is time-consuming and requires specific expertise. Reliable taxonomic assignment may be strengthened by the analysis of DNA sequences. Species-specif...
Agroforestry, which is the integration of trees into monoculture cropland, can alter soil properties and nutrient cycling. Temperate agroforestry practices have been shown to affect soil microbial communities as indicated by changes in enzyme activities, substrate-induced respiration, and microbial biomass. Research exploring soil microbial communi...
Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in pai...
Background
Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as micr...
Background: Temperate agroforestry is regarded as a sustainable alternative to monoculture agriculture due to enhanced provisioning of ecosystem services. Plant health and food safety are crucial requirements for sustainable agriculture; however, studies of fungal diseases and mycotoxin contamination of crops grown under temperate agroforestry are...
Outbreaks of defoliating insects may affect microbial populations in forests and thereby mass balances and ecosystem functioning. Here, we investigated the microbial dynamics in Scots pine (Pinus sylvestris L.) forests during outbreaks of the nun moth (Lymantria monacha L.) and the pine-tree lappet (Dendrolimus pini L.). We used real-time PCR (poly...
Outbreaks of forest pests increase with climate change, and thereby may affect microbial communities and ecosystem functioning. We investigated the structure of phyllosphere and soil microbial communities during defoliation by the nun moth (Lymantria monacha L.) (80% defoliation) and the pine tree lappet (Dendrolimus pini L.) (50% defoliation) in S...
Nanomaterials enter the terrestrial environment via the repeated application of sludge to soils over many years. The goal of this investigation was to compare the effects of CuO and Ag nanomaterials on soil microorganisms after a single application and after repeated applications ultimately resulting in the same test concentrations. The effect on s...
