Toward DNA-based taxonomy of prokaryotes and microeukaryotes.

The current nomenclatural rules regulating the naming of microorganisms are too conservative from the perspective of recent developments in molecular genetics tools and organism discovery. The taxonomy of microorganisms would greatly benefit from a conceptual shift toward DNA-based approaches. Current informal practices of DNA-based taxonomy include the use of DNA sequences for species description and type material.

Fungal Assemblages in Northern Elms-Impacts of Host Identity and Health, Growth Environment, and Presence of Dutch Elm Disease.

Dutch elm disease (DED), caused by the pathogenic ascomycete Ophiostoma novo-ulmi, has devastated natural elm (Ulmus spp.) populations in Europe and North America. Elm species vary in their susceptibility to this vascular disease, which may partly reflect differences in their associated mycobiomes.

Global hotspots of mycorrhizal fungal richness are poorly protected.

Mycorrhizal fungi are ecosystem engineers that sustain plant life and help regulate Earth's biogeochemical cycles. However, in contrast to plants and animals, the global distribution of mycorrhizal fungal biodiversity is largely unknown, which limits our ability to monitor and protect key underground ecosystems. Here we trained machine-learning algorithms on a global dataset of 25,000 geolocated soil samples comprising >2.

Shifting community assembly mechanisms in soil eukaryotes over successional time and their implications for restoration.

Integration of soil biodiversity restoration into reforestation strategies is important to accelerate the restoration process given the interplay between belowground and plant community dynamics. Research on the mechanisms underlying the temporal changes that occur in soil communities has been limited, and this is especially true for eukaryotes. Understanding these processes can help us to manipulate soil communities in a way that promotes recovery and stability.

Human contributions to global soundscapes are less predictable than the acoustic rhythms of wildlife.

Across the world, human (anthropophonic) sounds add to sounds of biological (biophonic) and geophysical (geophonic) origin, with human contributions including both speech and technophony (sounds of technological devices). To characterize society's contribution to the global soundscapes, we used passive acoustic recorders at 139 sites across 6 continents, sampling both urban green spaces and nearby pristine sites continuously for 3 years in a paired design. Recordings were characterized by bird species richness and by 14 complementary acoustic indices.

Balancing biodiversity, carbon, and profit with pathogen risk: Effects of felling age and thinning in spruce forests.

Global forestry is balancing multiple societal needs, including carbon sequestration and biodiversity conservation, in addition to timber production. We aim to guide decision-making in managed forests by providing a test case that navigates the trade-offs between these objectives in clear-cut oriented boreal forests. We measured timber yield, biodiversity-critical habitats, aboveground tree carbon and fungal pathogen pressure in 66 thinned (from below) and unthinned Norway spruce dominated stands spanning 40 to >100 years in hemiboreal Estonia.

Land Use Interacts With Climate to Influence Microbial Diversity-To-Biomass Ratios Across Europe via Soil Organic Carbon and Nitrogen.

Ecosystem functioning is potentially dependent on the relationships between soil microbial diversity and biomass. Yet, it remains unclear how land use and climate influence these relationships. Here, we (i) analysed relationships and ratios between richness and biomass of bacteria and fungi in ~500 soils across Europe, including three land-use types (woodlands, grasslands and croplands) and climates (cold, temperate and arid) and (ii) identified the driving factors of changes in richness:biomass (R:B) ratios.

Soil and its microbiome in translocated meadows in the context of habitats in the receptor area.

Turf translocation, which is undertaken to mitigate the destruction of valuable habitats, can challenge the soil biota. We investigated translocated protected Molinion meadows in the context of the surrounding environments. Soil and soil microorganisms were examined in meadows translocated four years earlier to a habitat garden in recycled land.

EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.

The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists.

Decoupling Responses of Phyllosphere and Rhizosphere Bacterial Communities to Spatiotemporal Environmental Changes.

Understanding and predicting how plant-associated microbes respond to environmental changes is of key importance to understanding future plant performance. Yet, how aboveground and belowground plant-associated microbial communities, which may interactively affect plant performance, simultaneously respond to environmental changes, remains unknown. To fill this gap, we monitored temporal changes of phyllosphere and rhizosphere bacterial communities of three perennial species at 18 sites spanning a 1500 m elevational gradient.

Soil moisture and microbiome explain greenhouse gas exchange in global peatlands.

Earth's climate is tightly connected to carbon and nitrogen exchange between the atmosphere and ecosystems. Wet peatland ecosystems take up carbon dioxide in plants and accumulate organic carbon in soil but release methane. Man-made drainage releases carbon dioxide and nitrous oxide from peat soils.

Soil Microbiome Inoculation for Resilient and Multifunctional New Forests in Post-Agricultural Landscapes.

Afforestation is increasingly recognized as a critical strategy to restore ecosystems and enhance biodiversity on post-agricultural landscapes. However, agricultural legacies, such as altered soil structure, nutrient imbalances, and depleted microbial diversity, can slow down forest establishment or cause ecosystems to deviate from expected successional trajectories. In this opinion paper, we explore the potential of soil inoculations as a tool to overcome these challenges by introducing beneficial microbial communities that can accelerate ecosystem recovery and forest development.

Unveiling root nodulation in Tribulus terrestris and Roystonea regia via metagenomics analysis.

Root nodule symbiosis is traditionally recognized in the Fabales, Fagales, Cucurbitales, and Rosales orders within the Rosid I clade of angiosperms. However, ambiguous root nodule formation has been reported in Zygophyllaceae and Roystonea regia (Arecaceae), although a detailed analysis has yet to be conducted. We aimed to perform morphological analyses of root structures in these plants and utilize metagenomic techniques to identify and characterize the bacterial populations within the nodule-like structures.

Toward harnessing biodiversity-ecosystem function relationships in fungi.

Fungi are crucial for terrestrial ecosystems, yet the role of fungal diversity in ecosystem functions remains unclear. We synthesize fungal biodiversity and ecosystem function (BEF) relationships, focusing on plant biomass production, carbon storage, decomposition, and pathogen or parasite resistance. The observed BEF relationships for these ecosystem functions vary in strength and direction, complicating generalizations.

Phylogenetic classification of arbuscular mycorrhizal fungi: new species and higher-ranking taxa in Glomeromycota and Mucoromycota (class Endogonomycetes).

Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based on eDNA samples and long reads as type materials, we describe 15 new species and corresponding genera (, , , , , , , , , , , , , and ), the genus as well as 19 families (Pseudoentrophosporaceae, Hoforsaceae, Kahvenaceae, Kelottijaerviaceae, Kungsaengenaceae, Langduoaceae, Lehetuaceae, Lokrumaceae, Moosteaceae, Nikkaluoktaceae, Parniguaceae, Riederbergaceae, Ruuaceae, Tammsaareaceae, Unemaeeaceae, Bifigurataceae, Planticonsortiaceae, Jimgerdemanniaceae and Vinositunicaceae) and 17 orders (Hoforsales, Kahvenales, Kelottijaerviales, Kungsaengenales, Langduoales, Lehetuales, Lokrumales, Moosteales, Nikkaluoktales, Parniguales, Riederbergales, Ruuales, Tammsaareales, Unemaeeales, Bifiguratales and Densosporales), and propose six combinations (, , , , and ) based on phylogenetic evidence.

Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores.

A trait-based root acquisition-defence-decomposition framework in angiosperm tree species.

To adapt to the complex belowground environment, plants make trade-offs between root resource acquisition and defence ability. This includes forming partnerships with different types of root associating microorganisms, such as arbuscular mycorrhizal and ectomycorrhizal fungi. These trade-offs, by mediating root chemistry, exert legacy effects on nutrient release during decomposition, which may, in turn, affect the ability of new roots to re-acquire resources, thereby generating a feedback loop.

EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.

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 EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants.

Variation of carbon, nitrogen and phosphorus content in fungi reflects their ecology and phylogeny.

Fungi are an integral part of the nitrogen and phosphorus cycling in trophic networks, as they participate in biomass decomposition and facilitate plant nutrition through root symbioses. Nutrient content varies considerably between the main fungal habitats, such as soil, plant litter or decomposing dead wood, but there are also large differences within habitats. While some soils are heavily loaded with N, others are limited by N or P.

Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA.

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world.