Do fungal pathogens drive density-dependent mortality in established seedlings of two dominant African rain-forest trees?

Where one or a few tree species reach local high abundance, different ecological factors may variously facilitate or hinder their regeneration. Plant pathogens are thought to be one of those possible agents which drive intraspecific density-dependent mortality of tree seedlings in tropical forests. Experimental evidence for this is scarce, however. In an African rain forest at Korup, we manipulated the density of recently established seedlings (~5-8 wk old; low vs. high-density) of two dominant species of contrasting recruitment potential, and altered their exposure to pathogens using a broad-spectrum fungicide. Seedling mortality of the abundantly recruiting subcanopy tree Oubanguia alata was strongly density-dependent after 7 mo, yet fungicide-treated seedlings had slightly higher mortality than controls. By contrast, seedling mortality of the poorly recruiting large canopy-emergent tree Microberlinia bisulcata was unaffected by density or fungicide. Ectomycorrhizal colonization of M. bisulcata was not affected by density or fungicide either. For O. alata, adverse effects of fungicide on its vesicular arbuscular mycorrhizas may have offset any possible benefit of pathogen removal. We tentatively conclude that fungal pathogens are not a likely major cause of density dependence in O. alata, or of early post-establishment mortality in M. bisulcata. They do not explain the latter's currently very low recruitment rate at Koru

Greenhouse gas balance of open peatlands is globally governed by soil water content and archaeal abundance : EGU21-8969

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The endangered northern bettong, Bettongia tropica, performs a unique and potentially irreplaceable dispersal role for truffle ectomycorrhizal fungi

Organisms that are highly connected in food webs often perform unique and vital functions within ecosystems. Understanding the unique ecological roles played by highly connected organisms and the consequences of their loss requires a comprehensive understanding of the functional redundancy among organisms. One important, yet poorly understood, food web is that between truffle‐forming ectomycorrhizal fungi and their mammalian consumers and dispersers. Mammalian fungal specialists rely on fungi as a food source, and they consume and disperse a higher diversity and abundance of fungi than do mycophagous mammals with generalist diets. Therefore, we hypothesise that mammalian fungal specialists are functionally distinct because they disperse a set of fungal taxa not fully nested within the set consumed by the combined generalist mammalian community (i.e. functional redundancy of fungal dispersal is limited). Using high‐throughput sequencing, we compared the fungal composition of 93 scats from the endangered fungal specialist northern bettong (Bettongia tropica) and 120 scats from nine co‐occurring generalist mammal species across three sites and three seasons. Compared with other generalist mammals, B. tropica consumed a more diverse fungal diet with more unique taxa. This aligns with our hypothesis that B. tropica performs a unique dispersal function for ectomycorrhizal truffle fungi. Additionally, modelling of mammalian extinctions predicted rapid loss of food web connections which could result in loss of gene flow for truffle taxa. Our results suggest that this system is sensitive to the extinction of highly connected specialist species like B. tropica and their loss could have consequences for ectomycorrhizal truffle fungal diversity. This suggests that the conservation of fungal specialists is imperative to maintaining ectomycorrhizal fungal diversity and healthy plant‐mycorrhizal relationships

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic

Source:DOI: 10.1002/mbo3.375Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for subsurface temperature and moisture conditions, community structure, and nutrient mobilization through microbial belowground processes. Here, we address the effect of increased snow depth on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid- July to mid- September in both control and deep snow plots. Richness of ECM fungi was lower, while saprotrophic fungi was higher in increased snow depth plots relative to controls. [Correction added on 23 September 2016 after first online publication: In the preceding sentence, the richness of ECM and saprotrophic fungi were wrongly interchanged and have been fixed in this current version.] ECM fungal richness was related to soil NO3- N, NH4- N, and K; and saprotrophic fungi to NO3-N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results suggest that some fungal species are favored, while others are disfavored resulting in their local extinction due to long- term changes in snow amount. Shifts in species composition of fungal functional groups are likely to affect nutrient cycling, ecosystem respira- tion, and stored permafrost carbon

Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Incorporating molecular data in fungal systematics: a guide for aspiring researchers

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology - comments most welcom

Impacts of wildfire on soil microbiome in Boreal environments

The temperature changes for the future climate are predicted to be the most pronounced in boreal and arctic regions, affecting the stability of permafrost and fire dynamics of these areas. Fires can affect soil microbiome (archaea, bacteria, fungi, and protists) directly via generated heat, whereas fire-altered soil properties have an indirect effect on soil microbiome. Fires usually decrease microbial biomass and alter microbial community composition. These changes can take decades to recover to prefire states. As the fire occurrence times are expected to change in the future, and the fire return intervals, intensity, and severity are expected to increase in boreal environments, the fire-related changes in the soil microbiome, including its recovery and resilience, are inevitable.Peer reviewe

Data sharing practices and data availability upon request differ across scientific disciplines

Data sharing is one of the cornerstones of modern science that enables large-scale analyses and reproducibility. We evaluated data availability in research articles across nine disciplines in Nature and Science magazines and recorded corresponding authors' concerns, requests and reasons for declining data sharing. Although data sharing has improved in the last decade and particularly in recent years, data availability and willingness to share data still differ greatly among disciplines. We observed that statements of data availability upon (reasonable) request are inefficient and should not be allowed by journals. To improve data sharing at the time of manuscript acceptance, researchers should be better motivated to release their data with real benefits such as recognition, or bonus points in grant and job applications. We recommend that data management costs should be covered by funding agencies; publicly available research data ought to be included in the evaluation of applications; and surveillance of data sharing should be enforced by both academic publishers and funders. These cross-discipline survey data are available from the plutoF repository.Peer reviewe

Acclimation of Fine Root Systems to Soil Warming: Comparison of an Experimental Setup and a Natural Soil Temperature Gradient

Global warming is predicted to impact high-latitude and high-altitude forests severely, jeopardizing their overall functioning and carbon storage, both of which depend on the warming response of tree fine root systems. This paper investigates the effect of soil warming on the biomass, morphology and colonizing ectomycorrhizal community of spruce fine and absorptive fine roots. We compare the responses of spruce roots growing at a man-made long-term soil warming (+ 4°C) experiment to results obtained from a geothermal soil temperature gradient (+ 1 to + 14°C) extending to the forest die-off edge, to shed light on the generalizability of the warming response and reveal any thresholds in acclimation ability. Trees in warmer soils formed longer and less-branched absorptive roots with higher specific root length and area, and lower root tissue density in both spruce stands, irrespective of warming method and location. Soil warming at the experimental warming site also supported the occurrence of a more varied EcM community and an increase in the abundance of Tomentella spp., indicating a shift in nutrient foraging. Fine and absorptive fine root biomass decreased toward warmer soil, with a sharp reduction occurring between + 4 and + 6°C from the ambient and leading to the collapse of the fine root system at the geothermal gradient. At the experimental warming site, the applied + 4°C warming had no effect on fine and absorptive fine root biomass. The similar fine root responses at the two warming sites suggest that the observations possibly reflect general acclimation patterns in spruce forests to global warming.We thank Krista Lõhmus for valuable discussions, Kessy Abarenkov for guidance with uploading the EcM fungal sequences, and Aale Puri, Aulis Puri, Laura Soon and Marta Arula for assistance in the laboratory. We acknowledge the EU through the European Regional Development Fund (Center of Excellence ENVIRON and EcolChange), the Estonian Ministry of Education, Research projects IUT2-16, IUT34-9 and Lydia and Felix Krabi Scholarship Fund for financial support. We are very grateful to ExpeER for financing the field work of Kaarin Parts and analyses of EcM fungal community samples at the Achenkirch experimental area. This work contributes to the Icelandic ForHot-Forest Project (IRF Fund, No. 163272-051), the CAR-ES Nordic Network, the ClimMani (ES1308) and the Biolink COST Actions (FP1305).Peer Reviewe