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38
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Introduction
Additional affiliations
August 2014 - April 2018
April 2014 - present
January 2012 - present
Publications
Publications (38)
To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impac...
Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have...
Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and pro...
Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diver...
Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories....
Aims
Visualization of enzymatic activity links microbial functioning to localization in heterogeneous soil habitats. To assess enzymatic reactions in soil thin layer at the microscopic level, we developed a micro-zymography approach and tested it by visualization of the potential activity of phosphomonoesterase for aggregates collected from the rhi...
Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant–microbe-soil interface and aim to link this kn...
Arbuscular mycorrhizal fungi (AMF) form obligate mutualistic associations with the roots of most plant families, providing nutrients for their host plants and receiving carbon in return. Soil nutrient availability is known to affect AMF abundance and community composition. For example, excessive phosphorus (P) fertilization decreases AM fungal root...
Enzymes are secreted by microbial cells into the soil to catalyze the acquisition of carbon or nutrients like nitrogen and phosphorus from soil organic matter. Apart from microorganisms and soil fauna, roots also secrete enzymes to mobilize nutrients from the soil nutrient pool. Thus, living plants and microorganisms are considered the main sources...
This study evaluates the performance of the antigen-based anterior nasal screening programme implemented in all Austrian schools to detect SARS-CoV-2 infections. We combined nationwide antigen-based screening data obtained in March 2021 from 5,370 schools (Grade 1–8) with an RT-qPCR-based prospective cohort study comprising a representative sample...
Background
The role of schools in the SARS-CoV-2 pandemic is much debated. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription quantitative polymerase-chain-reaction (RT-qPCR).
Methods
This nationwide prospective cohort study monitors a representative sample of pupils (grade 1–8) and...
Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing studies in soil and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil an...
Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relat...
Background
Thee is much debate about the role of schools and children in the SARS-CoV-2 pandemic. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription polymerase-chain-reaction (RT-PCR).
Methods
This nationwide prospective cohort study monitors a representative sample of pupils (grade...
Letter to the Editor of the European Journal of Soil Science as a reaction to the Russell Review by Phillipe Baveye “Bypass and hyperbole in soil research: worrisome practices critically reviewed through examples” and to his follow‐up Invited Opinion paper “Bypass and hyperbole in soil research: a personal view on plausible causes and possible reme...
Enzymes are produced by microorganisms either intracellularly in cell's cytoplasm and periplasm or extracellularly either as attached to outer surface of cell membranes or released to the soil microhabitats. The distribution of microhabitats in soil is highly heterogeneous with high abundance of microorganisms in the small volume of soil hotspots,...
Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and pro...
Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont n...
Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of...
Root surfaces are major sites of interactions between plants and associated microorganisms. Here, plants and microbes communicate via signaling molecules, compete for nutrients, and release substrates that may have beneficial or harmful effects on each other. Whilst the body of knowledge on the abundance and diversity of microbial communities at ro...
Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I–IV) and is widely used as a marker gene for N2 fixation, permitting investigators to stu...
Understanding interactions of microorganisms with their habitat has recently become an important topic in (environmental) microbiology. In this context phylogenetic identification via in situ hybridization and specific detection and visualization of single microbial cells on resolutions beyond light microscopy is a promising approach. Here we descr...
Plants shape distinct, species-specific microbiomes in their rhizospheres. A main premise for evaluating microbial communities associated with root-soil compartments is their successful separation into the rhizosphere (soil-root interface), the rhizoplane (root surface), and the endosphere (inside roots). We evaluated different approaches (washing,...
Root-triggered processes (growth, uptake and release of solutes) vary in space and time, and interact with heterogeneous soil microenvironments that provide habitats for (micro)biota on various scales. Despite tremendous progress in method development in the past decades, finding a suitable experimental set-up to investigate processes occurring at...
The advent of new sophisticated spectroscopic and tomographic techniques arise interest in the study of environmental conditions within microbial habitats on a submicroscopic level. These methods are based on electromagnetic radiation and result in either elemental characterization or structure visualization. Both aspects are relevant for the inves...
The puddled layer of paddy soils represents a highly dynamic environment regarding the spatio-temporal variability of biogeochemical conditions. To study these effects on the abundance and community structure of microbial populations, a rhizotron experiment was conducted throughout an entire growing season of wetland rice. Soil samples were taken f...
Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was applied to detect microbial cells on the rhizoplane of wetland rice (Oryza sativa L.). Fluorescent signals of high intensity and specificity allowed for a reliable quantification of selected microbial phyla. Absolute cell numbers of archaea and bacteria were observed t...
The objective of this study was to compare the extraction efficiency of commercial DNA kits by evaluating the quantity and purity of DNA extracts obtained from paddy soils. DNA was extracted from three paddy soils using the FastDNA® SPIN kit for soil (FD), the innuSPEED soil DNA kit (INS) and the NucleoSpin® soil kit (NSP). DNA extracts were analys...
Several tyramide solutions were evaluated for the application of fluorescence in situ hybridization with catalyzed reporter deposition (CARD-FISH) in soil. Fluorescently labeled tyramide solutions were synthesized and compared to commercially available tyramides for the detection and quantification of single microbial cells. Among the tyramide solu...
The root-zone of wetland rice was monitored in a paddy soil throughout a vegetation period with the aid of a rhizotron experiment.
For this purpose (a) digital images of the root-zone were taken daily, and (b) the redox potential was measured in situ every
day. The images were processed by image analysis in order to display areas of oxidation and r...
Projects
Projects (6)
In this multidisciplinary Townhall session, we will discuss the current challenges of the publication system, and explore some of the emerging opportunities which aim to render it more open and fair. This event follows a series of engaging articles published in the European Journal of Soil Science in late 2020, initiated by Professor Philippe Baveye from Saint Loup Research Institute in France, on the issues of bypass and hyperbole. A response authored by an international network of early career soil scientists also showcased the difficulties faced by reviewers, as well as the opportunities provided by open access publishing. These likely represent challenges faced across a broad array of geoscience disciplines. The goal of this Townhall is to bring together participants from all EGU divisions to share their perspectives on the limitations of the current publication system, and the emerging possibilities to make it more open and fair to all.
A diverse and international panel comprising both an early career and an established scientist, together with representatives from journal publishing platforms with varying open access options, will present their own perspectives on the challenges and new opportunities in publication practices, which will be followed by an open discussion by all interested conference participants.
This project aims at studying interactions between microbial cells and how space can alter them
We are pleased to invite you to contribute to the session ‘Plant-Microorganism-Soil interactions in the rhizosphere: from chemical, biological, and physical perspectives to an interlinked understanding of processes’ (https://meetingorganizer.copernicus.org/EGU2020/session/35040) at the EGU General Assembly 2020 (03-08 May, Vienna, Austria).
The rhizosphere is regarded as the soil compartment with the highest level of nutrient flux through a multitude of interactions between plants, soil, and (micro)biota. Roots and associated (micro)organisms interact with heterogeneous soil environments that provide habitats for biota on various scales. High metabolic activity and nutrient cycling can be observed from single root tips to whole root systems which makes the rhizosphere of central importance for ecosystem functioning.
The main knowledge-gaps in rhizosphere research are related to the difficulty in mechanistically linking the physical, chemical and biological processes, taking place at different scales (nm to cm) in the rhizosphere and to the challenge of upscaling these processes to the scale of the root system and the soil profile. The key for overcoming these knowledge gaps is to understand rates of matter flux, and to link the spatial arrangement of the different interconnected components of the rhizosphere with their temporal dynamics. This requires concerted efforts to combine methods from different disciplines like plant genomics, imaging, soil physics, chemistry and microbiology.
We welcome experimental and modelling studies on rhizosphere functioning that aim at revealing spatial gradients of e.g. functional biodiversity of microorganisms, uptake and release patterns by roots, soil structure modification by root growth (and vice versa) as well as feedbacks between those processes in order to improve our mechanistic understanding of emerging properties like water acquisition, nutrient cycling, plant health, soil structure development and feedbacks among them.
Solicited speakers: Tiina Roose (University of Southhampton) and Kristian Thorup-Kristensen (University of Copenhagen)
Please submit your abstract until January 15, 2020. Financial support for traveling can be granted until December 1, 2019.
Do not hesitate to contact us in case of any questions. We are looking forward to meeting you in Vienna.
Hannes, Carste, Steffen, Evgenia
