Stefan Geisen

• PhD
• Professor (Assistant) at Wageningen University & Research

Soil fungi, protists, and animals (i.e., the eukaryome) play a critical role in key ecosystem functions in terrestrial ecosystems. Yet, we lack a holistic understanding of the processes shaping the global distribution of the eukaryome. We conducted a molecular analysis of 193 composite soil samples spanning the world's major biomes. Our analysis sh...

The soil microbiome regulates vital ecosystem functions ranging from primary production to soil carbon sequestration. Yet, we have only begun to understand the factors regulating the soil microbiome. While the importance of abiotic factors is increasingly recognized, the roles of trophic regulations in driving the structure and function of the soil...

Biodiversity on Earth is strongly affected by human alterations to the environment. The majority of studies have considered aboveground biodiversity, yet little is known about whether biodiversity changes belowground follow the same patterns as those observed aboveground. It is now established that communities of soil biota have been substantially...

Soil bacteria and fungi are key drivers of carbon released from soils to the atmosphere through decomposition of plant-derived organic carbon sources. This process has important consequences for the global climate. While global change factors, such as increased temperature, are known to affect bacterial- and fungal-mediated decomposition rates, the...

Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists, and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea...

Disease suppressiveness is a complex phenomenon that is assumed to be the resultant of actions of local microbial antagonists in soil environments. Exploitation of disease suppressiveness as a tool to manage pathogens is hindered by our poor understanding of this phenomenon. Here we investigated soil microbiome-based suppression of potato cyst nema...

Trophic interactions in micro‐food webs, such as those between nematodes and their bacterial prey, affect nitrogen cycling in soils, potentially changing nitrous oxide (N2O) production and consumption. However, how nematode‐mediated changes in soil bacterial community composition affect soil N2O emissions is largely unknown. Here, microcosm experim...

Background Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are a...

Plant performance is impacted by rhizosphere bacteria. These bacteria are subjected to both bottom-up control by root exudates as well as top-down control by predators, particularly protists. Protists stimulate plant growth-promoting microbes resulting in improved plant performance. However, knowledge of the mechanisms that determine the interconne...

Potato cyst nematodes (PCNs) are notorious pathogens in all major potato production areas worldwide. Mainly due to the low mobility of this soil pathogen, PCN infestations are mostly observed as patches (“foci”) that only cover a fraction of the acreage. In-field presymptomatic localization of these pathogens is valuable, as it would allow for the...

Arbuscular mycorrhizal (AM) fungi not only play a crucial role in acquiring nutrients for plants but also serve as a habitat for soil microbes. Recent studies observed that AM fungal hyphae are colonized by specific bacterial communities. However, so far it has not been explored whether fungal hyphae and mycorrhizal networks also harbor specific co...

Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings,...

Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database E...

Highly diverse and abundant organisms coexist in soils. However, the contribution of biotic interactions between soil organisms to microbial community assembly remains to be explored. Here, we assess the extent to which soil fauna can shape microbial community assembly using an exclusion experiment in a grassland field to sort soil biota based on b...

Anthropogenic activities such as long-term fertilizer application are known to lead to losses in above and belowground biodiversity, thereby negatively impacting ecosystem function. However, our understanding of the relative sensitivity of different soil organisms groups to increasing fertilizer application levels remains largely unknown. To addres...

Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional...

Crop-specific cultivation practices including crop rotation, cover cropping, and fertilisation are key measures for sustainable farming, for which soil microorganisms are important components. This study aims at identifying links between agronomic practices, potato yield and quality as well as soil microorganisms. We analysed the roles of cover cro...

Fusarium wilt disease of bananas, caused by the soil-borne pathogen Fusarium oxysporum, threatens banana production. Intercropping, cultivation of more than one crop simultaneously on the same field, has emerged as efficient and sustainable land management for suppressing Fusarium wilt disease. Although previous studies have proven the changes in s...

Traditional rice production is often reliant on the unsustainable practice of utilizing intensive inputs in monoculture cropping systems. Alternatives fallow cover cropping and rice–fish coculture (RFC) offer promising solutions. However, the potential of fallow cover cropping in RFC remains underexplored, and its impact on soil microbes is poorly...

Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic...

Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three...

Despite the importance of healthy soils for human livelihood, wellbeing, and safety, current gaps in our knowledge and understanding of biodiversity in soil are numerous, undermining conservation efforts. These gaps are particularly wide in mountain regions where healthy soils are especially important for human safety and yet evidence is accumulati...

Soil ecologists and zoologists often argue about the functional importance of their beloved organisms. However, quantification of the functional impact of a certain group of organisms is not trivial in the opaque and complex soil environment, where myriads of these organisms interact. Soil food webs are a conceptual representation of soil life that...

Aim Soils harbour a large number of unicellular eukaryotic parasites of metazoans, particularly Apicomplexa. Apicomplexan distribution, their associations with hosts, and impacts of human‐dominated land use are little studied. We aimed to fill this gap by a biodiversity survey across large spatial scales. Location China. Time period May to Septem...

The soil microbiome is dynamically structured at the local soil aggregate level by a combination of bottom-up and top-down processes. The soil microbiome is structured at the local soil aggregate scale by a dynamic interplay of bottom-up and top-down processes, yet less attention has been given to the latter (e.g., predation). We aimed to identify...

Urbanization negatively impacts aboveground biodiversity, such as bird and insect communities. City parks can reduce these negative impacts by providing important habitat. However, it remains poorly understood how the degree of urbanization and vegetation types within city parks (e.g., lawns, woodland) impact soil biodiversity. Here we investigated...

Microbiome predators shape the soil microbiome and thereby soil functions. However, this knowledge has been obtained from small-scale observations in fundamental rather than applied settings and has focused on a few species under ambient conditions. Therefore, there are several unaddressed questions on soil microbiome predators: (1) What is the rol...

Across the tree of life, organismal functional strategies form a continuum from slow-to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, the synchronization of these strategies at the entire community level is untested. We combine trait data for >2800 above-and belowground taxa from 14 tr...

Soil food webs are at the nexus of soil biodiversity, functioning, and stability. With a research history of over 35 years, soil food-web research remains a challenging and relatively specialised field. Initially receiving wide attention after the general model of William H. Hunt and colleagues in 1987, the field diversified over the last two decad...

Aboveground, large and higher trophic-level organisms often respond more strongly to environmental changes than small and lower trophic-level organisms. However, whether this trophic or size-dependent sensitivity also applies to the most abundant animals, microscopic soil-borne nematodes, remains largely unknown. Here, we sampled an altitudinal tra...

Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conc...

Drought events are increasingly affecting the planet’s biodiversity. While shrinking body size in response to drought has been observed in many vertebrate animals, whether this rule applies to microscopic animals and the mechanisms during this process remains largely unknown. To address this knowledge gap, we conducted a regional-scale investigatio...

Background For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organis...

The clubroot pathogen Plasmodiophora brassicae is a major and growing problem for the cultivation of Brassica crops. As conventional control disease management methods are ineffective or prohibited due to their ecological impact, and crop resistance is frequently broken, biological control of the pathogen has become a key focus for the development...

Plant–nematode interactions are mainly considered from the negative aspect with a focus on plant‐parasitic nematodes (PPNs), which is justified considering the agronomic losses caused by PPNs. Despite the fact that PPNs are outnumbered by nonparasitic free‐living nematodes (FLNs), the functional importance of FLNs, especially with regard to plant p...

Host‐associated fungi can help protect plants from pathogens, and empirical evidence suggests that such microorganisms can be manipulated by introducing probiotic to increase disease suppression. However, we still generally lack the mechanistic knowledge of what determines the success of probiotic application, hampering the development of reliable...

The physiological performance of organisms depends on their environmental context, resulting in performance–response curves along environmental gradients. Parasite performance–response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental con...

Climate change is affecting how energy and matter flow through ecosystems, thereby altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate...

Extreme droughts can weaken the biotic resistance of native plant communities against the establishment of invading plants. However, we know little about the underlying mechanisms. Using a plant-soil feedback approach, we tested how an extreme drought event alters the soil-mediated biotic resistance of resident native plant communities against inva...

Biodiversity is widely linked to human health, however, connections between human health and soil biodiversity in urban environments remain poorly understood. Here, we stress that reductions in urban soil biodiversity elevate risks to human health, but soil biodiversity can improve human health through pathways including suppressing pathogens, reme...

There have been major developments in the molecular characterization of soil protist and micrometazoan diversity, leading to a better understanding of these minute soil eukaryotes. Like in all newly developing research fields, several approaches are currently used in parallel to study these organisms. Here, we synthesize these various approaches an...

Soils harbor a large number of unicellular eukaryotic parasites. These parasites, such as Apicomplexa, inhabit a wide range of soil metazoans. However, the distribution of these apicomplexan parasites, their links with hosts and the impact of human-dominated land use remain unknown across larger spatial scales. In this study, we used metabarcoding...

Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much is unknown about how soil biodiversity and function will change in the future in response to simultaneous alterations in climate and land use, as well as other environmental drivers. It is crucial to understand the direct, indirect and intera...

Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack a sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with co...

Biodiversity, both aboveground and belowground, is negatively affected by global changes such as drought or warming. This loss of biodiversity impacts Earth's ecosystems, as there is a positive relationship between biodiversity and ecosystem functioning (BEF). Even though soils host a large fraction of biodiversity that underlies major ecosystem fu...

Global warming and precipitation extremes (drought or increased precipitation) strongly affect plant primary production and thereby terrestrial ecosystem functioning. Recent syntheses show that combined effects of warming and precipitation extremes on plant biomass are generally additive, while individual experiments often show interactive effects,...

Climate change is affecting how energy and matter flow within ecosystems, altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses...

As important ecosystem engineers in soils, earthworms strongly influence carbon cycling through their burrowing and feeding activities. Earthworms do not perform these roles in isolation, because their intestines create a special habitat favorable for complex bacterial communities. However, how the ecological functioning of these earthworm-microbe...

Beyond interacting with neighboring plants, crop performance is affected by the microbiome that includes pathogens and mutualists. While the importance of plant–plant interactions in explaining overyielding in intercropping is well known, the role of the microbiome, in particular how the presence of microbes from heterospecific crop species inhibit...

High-throughput sequencing technology is increasingly used in the study of nematode biodiversity. However, the annotation difference of commonly used primers and reference databases on nematode community is still unclear. We compared two pairs of primers (3NDf/C_1132rmod, NF1F/18Sr2bR) and three databases (NT_v20200604, SILVA138/18s Eukaryota and P...

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-sca...

To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have negative consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we investigated the diversity and community compositions...

Introduction The soil bacterial microbiome plays a crucial role in ecosystem functioning. The composition and functioning of the microbiome are tightly controlled by the physicochemical surrounding. Therefore, the microbiome is responsive to management, such as fertilization, and to climate change, such as extreme drought. It remains a challenge to...

It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally manage...

Anthropogenic land use is threatening global biodiversity. As one of the most abundant animals on Earth, nematodes occupy several key positions in belowground food webs and contribute to many ecosystem functions and services. However, the effects of land use on nematode abundance and its determinants remain poorly understood at a global scale. To c...

Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance,...

Nematode predation plays an essential role in determining the rhizosphere microbiome. In doing so, predation dynamically affects the soil nutrient cycling, for instance, by shifting the availability of phosphorus (P) for plant uptake.

Here we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, consumption of dead organic matter, and interactions with microbial and plant com...

The health and functioning of soil ecosystems are the foundation of sustainable food production and land management. Of key importance in achieving sustainability, is the frequent measurement of soil health, and indices based on the community structure of nematodes are amongst the most widely used toolsets by soil ecologists. Thirty years after the...

Plant health is strongly impacted by beneficial and pathogenic plant microbes, which are themselves structured by resource inputs. Organic fertilizer inputs may thus offer a means of steering soil-borne microbes, thereby affecting plant health. Concurrently, soil microbes are subject to top-down control by predators, particularly protists. However,...

Heterolobosea is one of the major protist groups in soils. While an increasing number of soil heterolobosean species has been described, we have likely only scratched the surface of heterolobosean diversity in soils. Here, we expand this knowledge by morphologically and molecularly classifying four novel strains. One was identified as Naegleria cla...

Pedogenesis determines soil physicochemical properties and many biodiversity facets, including belowground microbial bacteria and fungi. At the local scale, top-down predation by microbial protists regulates the soil microbiome, while the microbiome also affects protistan communities. However, it remains unknown how pedogenesis affects protistan co...

Soil photoautotrophic prokaryotes and micro‐eukaryotes – known as soil algae – are, together with heterotrophic microorganisms, a constitutive part of the microbiome in surface soils. Similar to plants, they fix atmospheric carbon (C) through photosynthesis for their own growth, yet their contribution to global and regional biogeochemical C cycling...

Soil organisms drive major ecosystem functions by mineralising carbon and releasing nutrients during decomposition processes, which supports plant growth, aboveground biodiversity and, ultimately, human nutrition. Soil ecologists often operate with functional groups to infer the effects of individual taxa on ecosystem functions and services. Simult...

Here we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, direct consumption of dead organic matter, and interactions with microbial and pl...

Protists are the most abundant and diverse eukaryotes that inhabit virtually all soils. They are active players in soil food webs as phototrophic algae, plant and animal parasites, and microbiome predators. As predators, protists lead to modification of their prey community composition typically promoting functions linked to (plant-)pathogen suppre...

Arbuscular mycorrhizal (AM) fungi and terrestrial plants form one of the most important and ubiquitous symbioses on the planet. Although the central role of AM fungi in rhizosphere processes is well established, the extent of their influence on the development of the whole soil microbial community is less well characterized. We assessed the tempora...

There are millions of species living in soils. Most of this biodiversity is made up of bacteria and fungi, tiny organisms that make up what is called the soil microbiome. The size and composition of the soil microbiome is mainly controlled by two groups of predators: protists and nematodes. Protists are tiny single-celled organisms, while nematodes...

Climate warming will likely disrupt the flow of matter and energy within ecosystems, threatening the global carbon balance. Microorganisms are fundamental components of carbon cycling and are thus integral to ecosystem climate responses. However, ecosystem responses to warming are uncertain due to the functional and trophic complexity of microbial...

Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have unti...

Microbes dominate the planet’s biodiversity in terms of species number and by driving essential Earth system functions such as the carbon cycle. Soils contain most of this microbial biodiversity. Only recently, we have started to better understand the diversity of bacteria and fungi at the global scale. Here, I list my views on some shortcomings of...

Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth–defence relationships...

We have profound knowledge on biodiversity on Earth including plants and animals. In the recent decade, we have also increased our understanding on microorganisms in different hosts and the environment. However, biodiversity is not equally well studied among different biodiversity groups and Earth's systems with eukaryotes in freshwater sediments b...

Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study...