Michael Schloter

Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) | HZM · Research Unit Environmental Genomics

1 3,6 4 5 2 Microbiome in pre-alpine grasslands ▪ Pre-Alpine grassland soils are exposed to decreasing summer precipitation and rising temperatures, twice as high as the global average. 1 ▪ Microorganisms are considered as architects of soil quality 2,3,4 and drive nutrient turnover in soil, but at the same time are strongly affected by climate cha...

The global decline in biodiversity and insect populations highlights the urgent to conserve ecosystem functions, such as plant pollination by solitary bees. Human activities, particularly agricultural intensification, pose significant threats to these essential services. Changes in land use alter resource and nest site availability, pesticide expos...

Background Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with antibiotics. Seed endophyte composition can be influenced by pollination, plant cultivar, and soil physicochemical conditions. Howeve...

The GHG (CO2, CH4, N2O) emission potential along a chronosequence of former agricultural soils abandoned for 9 to 32 years were compared to an actively managed (on-going) agricultural soil (reference). The soils were incubated in mesocosms with and without manure amendment, and microbial functional groups involved in nitrous oxide emission were qua...

For the prediction of permafrost nitrogen (N) climate feedbacks, a better process-based understanding of the N cycle in permafrost ecosystems is urgently needed. Therefore, we characterized and quantified soil organic matter, gross soil microbial ammonification and nitrification and soil-atmosphere exchange of nitrous oxide (N2O) of boreal permafro...

Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for access...

Zusammenfassung Die in den letzten Jahrzehnten beobachtete Aufgabe der Almbewirtschaftung ist der größte Landnutzungswandel im Alpenraum und führt zu einem Verlust von Jahrhunderte bis Jahrtausende alter Kulturlandschaft mit ihren Bodenfunktionen, ihrer Artenvielfalt und ihrer touristischen Attraktivität. Die 1955 aufgelassene Brunnenkopfalm im Amm...

Soil P pools are strongly driven by microbial activities, and vice versa, P pools shape bacterial communities and their functional potential. Biological soil crusts (biocrusts) represent a microbial hotspot for nutrient turnover. We compared biocrusts and bulk soil samples from different temperate beech (Fagus sylvatica L.) forests representing a g...

A 2-year outdoor mesocosm experiment was carried out to determine the effects of high C amendments (HCAs; wheat straw and sawdust) compared to a control with no addition of HCAs (no-HCA) and 2 different crop rotation systems (spring barley/winter barley and faba bean/winter barley) on soil bacterial communities using a molecular barcoding approach....

Nutrient imbalances cause the deterioration of tree health in European forests, but the underlying physiological mechanisms are unknown. Here, we investigated the consequences of decreasing root carbohydrate reserves for phosphorus (P) mobilisation and uptake by forest trees. In P‐rich and P‐poor beech (Fagus sylvatica) forests, naturally grown, yo...

Abstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbi...

Apple replant disease (ARD) occurs when apple is repeatedly planted at the same site, leading to growth reductions and losses in fruit yield and quality. Up to now, the etiology has been poorly understood; however, soil (micro)biota are known to be involved. Because endophytes often colonize plants via the rhizosphere, this study aimed at comparing...

Microbiome research has consistently been placed in the spotlight over the past two decades, and has shown tremendous promise in the fields of medicine, environmental science, food production, and agriculture. Life on Earth does not exist without microbes, and we may benefit from learning more about them. Yet, there is no common understanding among...

Microbiomes are complex microbial communities, with manifold interactions in a given ecosystem. They are characterized by defined functional properties and pattern of activities. Microbiomes play an important role as parts of “holobionts” and strongly drive the health of their particular hosts. The article describes challenges and chances of recent...

Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive...

Short-lived pulses of soil nitrous oxide (N2O) emissions during freeze-thaw periods can dominate annual cumulative N2O fluxes from temperate managed and natural soils. However, the effects of freeze thaw cycles (FTCs) on dinitrogen (N2) emissions, i.e., the dominant terminal product of the denitrification process, and ratios of N2/N2O emissions hav...

Sulfate-reducing microorganisms (SRMs) often compete with methanogens for common substrates. Due to thermodynamic reasons, SRMs should outcompete methanogens in the presence of sulfate. However, many studies have documented coexistence of these microbial groups in natural environments, suggesting that thermodynamics alone cannot explain the interac...

Mechanisms used by plants to respond to water limitation have been extensively studied. However, even though the inoculation of beneficial microbes has been shown to improve plant performance under drought stress, the inherent role of soil microbes on plant response has been less considered. In the present work, we assessed the importance of the so...

Grazed alpine pastures have shaped landscapes of the European Alps for millennia, but have partially been abandoned since the 1950s. Re-grazing of abandoned pastures could preserve this cultural landscape with its high species diversity, but also alter soil carbon and nitrogen cycles, as well as microbial communities, potentially affecting ecosyste...

An amendment to this paper has been published and can be accessed via the original article.

The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.

Bronchopulmonary dysplasia (BPD) is a multifactorial disease mainly provoked by pre-and postnatal infections, mechanical ventilation, and oxygen toxicity. In severely affected premature infants requiring mechanical ventilation, association of bacterial colonization of the lung and BPD was recently disclosed. To analyze the impact of bacterial colon...

Opencast mining for lignite continuously creates areas of land that require restoration. Here we applied a chronosequence approach to investigate the development of soil bacterial communities during 52 years as influenced by the restoration process and subsequent changes in soil physico-chemical conditions starting from the initial reclamation of t...

The genus Paraburkholderia includes a variety of species with promising features for sustainable biotechnological solutions in agriculture through increasing crop productivity. Here, we present a novel Paraburkholderia isolate, a permanent and predominant member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) phyllosphere, making up to 25%...

Agro-ecosystems experience huge losses of land every year due to soil erosion induced by poor agricultural practices such as intensive tillage. Erosion can be minimized by the presence of stable soil aggregates, the formation of which can be promoted by bacteria. Some of these microorganisms have the ability to produce exopolysaccharides and lipopo...

Worldwide bees decline put in danger human food supply, since most of the pollination is done by bees. Previous data show that changes in the gut microbiome disturb the nutrition and make bees more likely to get infected by opportunistic pathogens. Several recent studies have used next generation sequencing (mainly 16s amplicon libraries) to unders...

Agricultural management is a key force affecting soil processes and functions. Triggered by biophysical constraints as well as rapid structural and technological developments, new management practices are emerging with largely unknown impacts on soil processes and functions. This impedes assessments of the potential of such emerging practices for s...

Some temperate tree species are associated with very low soil nitrification rates, with important implications for forest N dynamics, presumably due to their potential for biological nitrification inhibition (BNI). However, evidence for BNI in forest ecosystems is scarce so far and the nitrifier groups controlled by BNI‐tree species have not been i...

Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and li...

Soil biodiversity is threatened by intensification of land use. The consequences of different land use on belowground biodiversity remain insufficiently explored for soil protists. Alongside being abundant and extremely diverse in soil, protists provide many ecosystem services: key players in the microbial loop, turnover of organic matter and stimu...

Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for...

Warming occurs in the Arctic twice as fast as the global average, which in turn leads to a large enhancement in terpenoid emissions from vegetation. Volatile terpenoids are the main class of biogenic volatile organic compounds (VOCs) that play crucial roles in atmospheric chemistry and climate. However, the biochemical mechanisms behind the tempera...

Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post‐mining area. We collected soi...

Background: Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death. Results: Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tr...

Background Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear. Results As expected, th...

Environmental discharges of very high (mg/L) antibiotic levels from pharmaceutical production contributed to the selection, spread and persistence of antibiotic resistance. However, the effects of less antibiotic-polluted effluents (μg/L) from drug-formulation on exposed aquatic microbial communities are still scarce. Here we analyzed formulation e...

Following publication of the original article [1], the authors advised that their article had published with an error in the title.

In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types...

Rhodococcus qingshengii RL1 was isolated from surface-sterilized leaves of Eruca sativa Mill. and shows plant growth-promoting (PGP) properties. The de novo genome assembly consists of one chromosome with 6,253,838 bp and two plasmids with 144,038 bp and 448,745 bp. Many genes could be identified reflecting its PGP potential.

Bacterial communities associated with the ripening process in artisanal wild boar and deer meat sausages were investigated by molecular barcoding using the 16S rRNA gene as a marker. A core microbiota shared by 83.54% of the samples indicated remarkable level of Lactobacillus sakei and Lactobacillus curvatus, accounting for 20.55% in initial and 70...

Climate change affects all seasons, but warming is more pronounced in winter than summer at mid- and high latitudes. Winter warming can have profound ecological effects, which are rarely compared to the effects of summer warming, and causal explanations are not well established. We compared mild aboveground infrared warming in winter to warming in...

The functioning and service provisioning of ecosystems in the face of anthropogenic environmental and biodiversity change is a cornerstone of ecological research. The last three decades of biodiversity–ecosystem functioning (BEF) research have provided compelling evidence for the significant positive role of biodiversity in the functioning of many...

While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the associ...

Miscanthus x giganteus is a high biomass producing plant with tolerance to heavy metals. This makes Miscanthus interesting to be used for phytoremediation of heavy metal contaminated areas coupled with energy production. Since plant performance in metal polluted areas is impaired, their growth and phytoremediation effect can be improved with bacter...

The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mot...

Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major...

Submerged rice cultivation is characterized by redox fluctuations and results in the formation of paddy soils, often accompanied by soil organic carbon (SOC) accumulation. The impact of redox fluctuations and the underlying soil type on the fate of organic carbon (OC) in paddy soils are unknown. Hence, we mimicked paddy soil development in the labo...

The persisting dogma that the healthy human lung is sterile led to neglect of the lung microbiome for a long time and it is only recently that it has been acknowledged as an issue. Culture-independent methods have shown that a diverse microbial community is present in the lung of healthy individuals and that it harbours important functional traits....

Background: Stable soil aggregates are essential for optimal crop growth and preventing soil erosion. However, tillage is often used in agriculture to loosen the soil, which disrupts the integrity of these aggregates. Soil aggregation can be enhanced by bacteria through their ability to produce exopolysaccharides and lipopolysaccharides. These com...

The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and...

Background: Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fis...

Effluents from antibiotic manufacturing may contain high concentrations of antibiotics, which are the main driving force behind the selection and spread of antibiotic resistance genes in the environment. However, our knowledge about the impact of such effluent discharges on the antibiotic resistome and bacterial communities is still limited. To gai...

Magnitude and timing of precipitation events within the growing season might be decisive for alterations in potential extracellular enzyme activity (PEEA), with consequences for nutrient cycle, and carbon storage in grassland ecosystems. Pattern of PEEA catalyzing major steps of the carbon cycle (β-glucosidase (β-gls), cellobiohydrolase (cel), gluc...

High-elevation ecosystems will experience increasing periods of above-average warmth and altered precipitation changes because of climate change. This causes uncertainties for community properties such as productivity and biodiversity. Increasing temperature may increase productivity by increasing growing season length and metabolic rate or decreas...

Chemical-structural composition of young and old SOM in Russia’s chernozems: information from solid-state 13C-NMR study of recent soils and paleosols I. Yevdokimov1, A. Larionova1, B. Zolotareva1, Yu. Kolyagin2, F. Buegger3, M. Schloter3 1) Institute of Physicochemical and Biological Problems in Soil Science, RAS, Pushchino, Moscow Region, Russ...