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Geisen, S.

Publications and source records attributed to Geisen, S..

11 recordsLinked to original sources

Top predators in soil food webs increase carbon cycling efficiency

Soil microbes are considered central in litter decomposition and soil carbon formation. Microbial activity and abundance are controlled by microbivores, which are themselves preyed upon by top predators. However, the role of top predators in carbon cycling is rarely studied, especially in bacterivore-dominated food webs. Here we tested how trophic cascades, consisting of microbes, microbivores (bacterivore-dominated nematode communities) and top predators (nematode-feeding mites) impact carbon cycling and associated microbial pools and processes. We found that our model top predator decreased the abundance of fungivorous nematodes and had cascading effects on microbiome composition, notably increasing Gram-positive bacterial biomass, thus promoting the bacterial energy channel. These trophic cascades propagated to carbon cycling, decreasing heterotrophic respiration by 10 % while maintaining litter decomposition rates. Taken together, our results suggest that top predators increase carbon cycling efficiency and highlight the importance of complex trophic interactions, including trophic cascades, in determining soil carbon cycling.

ecology↗

Quantitative stable isotope probing to measure in situ growth of protist populations

Soil protists shape microbial food webs and nutrient cycling, yet methods for measuring their population growth in soil have lagged behind the taxonomic resolution available from 18S rRNA gene sequencing. Microscopy-based approaches can estimate abundance and growth, but with limited taxonomic resolution. Here, we tested whether quantitative stable isotope probing (qSIP) can provide reproducible, sequencing-resolved growth measurements for soil protists. We incubated soil with natural-abundance or {superscript 1} O-labeled water and measured taxon-specific 18O enrichment in DNA using three common 18S rRNA gene primer sets. 18O enrichment values were positively correlated across datasets, with relationships closest to 1:1 after poorly resolved taxonomic assignments were excluded, indicating that qSIP provides reproducible population-level growth signals across marker choices. We then compared 18S amplicon profiles from unfractionated DNA with qSIP-derived growth measurements across a soil moisture gradient. Amplicon profiles showed small shifts in relative abundances of major protist groups, whereas qSIP revealed a large moisture response in the growing community: 7 ASVs were growing at 20% field capacity compared with 143 at 80% field capacity, representing 1.6% and 63.3% of total protist relative abundance, respectively. Average growth was <1% day{square}1 in the two driest treatments, increasing to 2.1% day{square}1 at 60% and 5.6% day{square}1 at 80% field capacity; among growing taxa, rates averaged 8.7% and 8.3% day{square}1 in the two wetter treatments. By pairing taxonomic resolution with isotope-based growth estimates, qSIP with 18O-H2O moves soil protist ecology toward quantitative population dynamics: identifying which taxa grow, how fast, and how growth responds to the environment.

microbiology↗

Soil microbiome predator diversity outperforms nitrogen addition in boosting plant biomass via bacterial community shifts

Nitrogen (N) is crucial for plant growth, but its overuse harms biodiversity. Increasing soil biodiversity might provide the means to reduce N inputs, but experimental evidence for this paradigm-shift is limited. Using microbiome predators (protists and nematodes) that shape microbiome composition and release N, we examined how interactions between their diversity and N addition affect Cannabis sativa growth. Microbiome predator addition overall boosted plant biomass by up to 53%, particularly under low N conditions, primarily by altering bacterial community composition and enriching functions related to carbon and N cycling. In turn, microbiome predator diversity had the strongest effect on biomass production, while N levels played a greater role in determining plant nutrient content. These findings suggest that increased microbiome predator diversity can reduce the plants dependency on added N, showing the pivotal role of soil biodiversity in enhancing plant performance and serving as tools to mitigate N inputs.

ecology↗

Fantastic Antagonists and Where to Find Them: The Global Distribution of Nematode-Antagonistic Fungi

Plant-parasitic nematodes can be suppressed by antagonistic members of the local soil microbiome. Compared to bacterial antagonists, considerably more attention has been paid to nematode-suppressing fungi. However, little is known about their global distribution. As their biogeography matters from both a fundamental and an applied perspective, we set out to mine the GlobalFungi database. After filtering on sample type, biome relevance and sequencing depth, we retained approximately 28,000 samples from 484 studies. An overview of fungal nematode antagonists was generated, and subsequent analyses revealed that 82.6% of the soil samples comprised [&ge;]1 nematode antagonist. Most of these antagonists are not obligatory nematode parasites; they switch between trophic lifestyles including saprophytism. Nematode antagonists are frequently found across most biomes; the detection probability was highest in croplands (88% of samples), woodlands (82%), and grasslands (76%). Most of the common nematode antagonists are present on all continents and across multiple climate zones underlining their enormous ecological flexibility. With one exception, the most frequently detected antagonistic fungi belonged to the fungal order Hypocreales whose members are known to parasitize insects and fungi as well. Analysis of the impact of temperature and precipitation on common antagonists in croplands revealed mostly non-linear responses. Among a selection of six soil properties, pH was the most informative predictor for the abundance of antagonists in croplands. Insights into the prevalence and the distribution of nematode antagonists at a global scale contribute to the exploration of the nematode-suppressive potential, which appears to be more common and widespread than often assumed.

ecology↗

Patchy distribution of potato cyst nematodes within single arable fields reveals local disease suppressiveness mediated by disparate microbialcommunities

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 nematodes (PCN), and, to this end, four apparently homogeneous potato fields with an unexplained non-homogeneous PCN distribution were selected. We hypothesized that this patchy PCN distribution resulted from local variation in disease suppressiveness. Under controlled greenhouse conditions, we confirmed the suppressiveness of these soils vis-a-vis PCN and soils were gamma-irradiated to corroborate the biotic origin of this suppression. Subsequent DNA-based analysis of the microbial community in the potato rhizosphere revealed suppressiveness-related contrasts in community composition between suppressive and conducive patches. Elevated abundances of fungal (e.g., Metacordyceps chlamydosporia) and bacterial (e.g., Pseudomonas fluorescens) nematode antagonists were positively correlated with PCN suppressive patches. Distinct sets of antagonists were found to be associated with PCN suppression despite of the geographical closeness of the locations under investigation. Our findings confirm the biotic origin of local PCN suppressiveness and reveal that it should be regarded as a superficially similar resultant of a biologically diverse phenomenon.

ecology↗

Biodiversity in mountain soils above the treeline

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 accumulating of ongoing degradation, posing significant threats to ecosystem functioning and human settlements. To analyse these gaps in detail, we synthesise current research on the global diversity of microorganisms, cryptogams, and invertebrates in mountain soils above the treeline. This synthesis is based on a semi-quantitative survey of the literature and an expert-based analysis. Our work reveals not only deficiencies in geographic cover but also significant gaps in taxonomic coverage, particularly among soil protists and invertebrates, and a lack of (functional and ecological) description of the uncultivated majority of prokaryotes, fungi, and protists. We subsequently build on this overview to highlight opportunities for research on mountain soils as systems of co-occurring species that interact in complex environmental matrices to fulfil critical functions and make essential contributions to life on land. Closing gaps in biodiversity research in mountain soil is crucial to enhance our understanding and to promote laws and guidelines advancing international soil biodiversity conservation targets in mountains. Addressing sparse and biased data, recognizing the impact of environmental changes on mountain ecosystems, and advocating dedicated policies are essential strategies to safeguard mountain soils and their biodiversity. GLOSSARY O_TBL View this table: org.highwire.dtl.DTLVardef@16682fdorg.highwire.dtl.DTLVardef@121b9feorg.highwire.dtl.DTLVardef@139eadeorg.highwire.dtl.DTLVardef@16abd74org.highwire.dtl.DTLVardef@bc3da9_HPS_FORMAT_FIGEXP M_TBL C_TBL

ecology↗

A fast-slow trait continuum at the level of entire communities

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 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. Most guilds consistently respond to these drivers through both direct and trophically-mediated effects, resulting in a slow-fast axis at the level of the entire community. Fast trait communities were also associated with faster rates of whole ecosystem functioning. These findings demonstrate that slow and fast strategies can be manifested at the level of whole ecosystems, opening new avenues of ecosystem-level functional classification.

ecology↗

Soil legacies of extreme droughts enhance the performance of invading plants

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 invading plant species from native and non-native ranges, namely non-resident natives, native range-expanders, and alien plants. We show that all three types of invading plants performed better in soils with a legacy of extreme drought independent of resident native plant diversity. Path models revealed that extreme drought effects on non-resident natives were mediated by the root biomass of resident native plants and endophytic fungal pathogens during drought, whereas alien plant performance was mediated only via the root biomass of resident native plants also during drought. Our results highlight that the performance of resident native plants during extreme drought and subsequent effects on soil fungi determine the performance of invading plants from native and non-native origins after extreme droughts.

ecology↗

Global monitoring of soil animal communities using a common methodology

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 plant communities. Soil animal effects on ecosystem functions have been demonstrated by correlative analyses as well as in laboratory and field experiments, but these studies typically focus on selected animal groups or species at one or few sites with limited variation in environmental conditions. The lack of comprehensive harmonised large-scale soil animal community data including microfauna, mesofauna, and macrofauna, in conjunction with related soil functions, limits our understanding of biological interactions in soil communities and how these interactions affect ecosystem functioning. To provide such data, the Soil BON Foodweb Team invites researchers worldwide to use a common methodology to address six long-term goals: (1) to collect globally representative harmonised data on soil micro-, meso-, and macrofauna communities; (2) to describe key environmental drivers of soil animal communities and food webs; (3) to assess the efficiency of conservation approaches for the protection of soil animal communities; (4) to describe soil food webs and their association with soil functioning globally; (5) to establish a global research network for soil biodiversity monitoring and collaborative projects in related topics; (6) to reinforce local collaboration networks and expertise and support capacity building for soil animal research around the world. In this paper, we describe the vision of the global research network and the common sampling protocol to assess soil animal communities and advocate for the use of standard methodologies across observational and experimental soil animal studies. We will use this protocol to conduct soil animal assessments and reconstruct soil food webs on the sites included in the global soil biodiversity monitoring network, Soil BON, allowing us to assess linkages among soil biodiversity, vegetation, soil physico-chemical properties, and ecosystem functions. In the present paper, we call for researchers especially from countries and ecoregions that remain underrepresented in the majority of soil biodiversity assessments to join us. Together we will be able to provide science-based evidence to support soil biodiversity conservation and functioning of terrestrial ecosystems.

ecology↗

pr2-primers: an 18S rRNA primer database for protists

Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost uniquely 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 system, a wise primer choice is needed as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few on-line resources available to list existing primers. We built a database listing 179 primers and 76 primer pairs that have been used for eukaryotic 18S rRNA metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 for eukaryotes and a subset of Silva for prokaryotes. This allowed to determine the taxonomic specificity of primer pairs, the location of mismatches as well as amplicon size. We developed a R-based web application that allows to browse the database, visualize the taxonomic distribution of the amplified sequences with the number of mismatches, and to test any user-defined primer set (https://app.pr2-primers.org). This tool will provide the basis for guided primer choices that will help a wide range of ecologists to implement protists as part of their investigations.

ecology↗

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses

Protists - all eukaryotes besides fungi, animals, and plants - represent a major part of the taxonomic and functional diversity of eukaryotic life on the planet and drive many ecosystem processes. However, knowledge of protist communities and their diversity lags behind that of most other groups of organisms, largely due to methodological constraints. While protist communities differ markedly between habitats and biomes, they can be studied in very similar ways. Here we provide a guide to current molecular approaches used for studying protist diversity, with a particular focus on amplicon-based high-throughput sequencing (metabarcoding). We highlight that the choice of suitable primers artificially alters community profiles observed in metabarcoding studies. While there are no true universal primers to target all protist taxa as a whole, we identify some primer combinations with a wide taxonomic coverage and provide detailed information on their properties. Although environmental protistan ecological research will probably shift towards PCR-free metagenomics or/and transcriptomic approaches in a near future, metabarcoding will remain the method of choice for in-depth community analyses and taxon inventories in biodiversity surveys and ecological studies, due its great cost-efficiency, sensitivity, and throughput. In this paper we provide a guide for scientists from a broad range of disciplines to implement protists in their ecological analyses.

microbiology↗