Fungi and global change
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Analyses of Sporocarps, Morphotyped Ectomycorrhizae, Environmental ITS and LSU Sequences Identify Common Genera that Occur at a Periglacial Site

Analyses of Sporocarps, Morphotyped Ectomycorrhizae, Environmental ITS and LSU Sequences Identify Common Genera that Occur at a Periglacial Site | Fungi and global change | Scoop.it
Periglacial substrates exposed by retreating glaciers represent extreme and sensitive environments defined by a variety of abiotic stressors that challenge organismal establishment and survival. The simple communities often residing at these sites enable their analyses in depth. We utilized existing data and mined published sporocarp, morphotyped ectomycorrhizae (ECM), as well as environmental sequence data of internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal RNA gene to identify taxa that occur at a glacier forefront in the North Cascades Mountains in Washington State in the USA. The discrete data types consistently identified several common and widely distributed genera, perhaps best exemplified by Inocybe and Laccaria. Although we expected low diversity and richness, our environmental sequence data included 37 ITS and 26 LSU operational taxonomic units (OTUs) that likely form ECM. While environmental surveys of metabarcode markers detected large numbers of targeted ECM taxa, both the fruiting body and the morphotype datasets included genera that were undetected in either of the metabarcode datasets. These included hypogeous (Hymenogaster) and epigeous (Lactarius) taxa, some of which may produce large sporocarps but may possess small and/or spatially patchy genets. We highlight the importance of combining various data types to provide a comprehensive view of a fungal community, even in an environment assumed to host communities of low species richness and diversity.

Via Jean-Michel Ané
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Pet Peeves - Fierer Lab

Papers using 16S rRNA gene sequencing to characterize bacterial communities are now a dime a dozen. Every day a new ‘microbiome’ is described using these methods and microbiologists like to view themselves as Indiana Jones hacking through the jungle of microbial diversity wielding sequencers for machetes.

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Consequences for ectomycorrhizal fungi of the selective loss or gain of pine across landscapes

Altered disturbance regimes and novel introductions are causing rapid shifts in the distribution of pines (Pinus L.). The functionally obligate symbiosis between pines and ectomycorrhizal (EM) fungi dictates that shifts in the distribution of one partner will affect the distribution of the other. In this review, we examine evidence for three hypotheses. (1) The loss of photosynthates through stress or tree mortality decreases the abundance of EM fungi and selects for less carbon-demanding species. (2) Pine introductions initiate establishment of novel EM fungal communities. (3) The extent of shifts in EM fungal abundance and community composition is mediated by surrounding vegetation. We find support for these hypotheses though changes in EM fungal abundance are variable and context-dependent. We posit that the consequences of shifts in EM fungal abundance and community composition extend beyond the individual tree to the landscape; these changes may affect population dynamics of both symbionts, ecosystem processes, and the conservation and evolution of fungi. In addition to conducting baseline surveys to assess the distribution of EM fungi, increasing our understanding of their function, morphology, propagation, and controls on host-specificity, and shifts would also assist in predicting the trajectory of ecosystems following the loss or gain of pine.

Via Jean-Michel Ané
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Climate Change Responses

Climate Change Responses is an open access interdisciplinary journal dedicated to publishing exceptional research on ecological and evolutionary responses to climate change. The journal is especially interested in publishing ground-breaking work linking responses to environmental change across levels of biological organization, from individuals to ecosystems, and with an emphasis on species interactions.

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Oikos - Volume 124, Issue 1 - January 2015 - Wiley Online Library

Free special issue on phenology

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Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

Functional identity and diversity of animals predict ecosystem functioning better than species-based indices | Fungi and global change | Scoop.it

Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se.

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Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities

Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities | Fungi and global change | Scoop.it

We conclude that, although atmospheric change may significantly alter AM fungal communities, this effect may be masked by the influences of natural changes and successional patterns through time. We suggest that changes in carbon availability are important determinants of the community dynamics of AM fungi.

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The ISME Journal - Dynamics in microbial communities: unraveling mechanisms to identify principles

The ISME Journal - Dynamics in microbial communities: unraveling mechanisms to identify principles | Fungi and global change | Scoop.it
Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this ‘system’ that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

Via Francis Martin
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Forest stand growth dynamics in Central Europe have accelerated since 1870

Forest stand growth dynamics in Central Europe have accelerated since 1870 | Fungi and global change | Scoop.it
Forest ecosystems have been exposed to climate change for more than 100 years, whereas the consequences on forest growth remain elusive. Based on the oldest existing experimental forest plots in Central Europe, we show that, currently, the dominant tree species Norway spruce and European beech exhibit significantly faster tree growth (+32 to 77%), stand volume growth (+10 to 30%) and standing stock accumulation (+6 to 7%) than in 1960. Stands still follow similar general allometric rules, but proceed more rapidly through usual trajectories. As forest stands develop faster, tree numbers are currently 17–20% lower than in past same-aged stands. Self-thinning lines remain constant, while growth rates increase indicating the stock of resources have not changed, while growth velocity and turnover have altered. Statistical analyses of the experimental plots, and application of an ecophysiological model, suggest that mainly the rise in temperature and extended growing seasons contribute to increased growth acceleration, particularly on fertile sites.

Via Francis Martin
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Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars

Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars | Fungi and global change | Scoop.it

 The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High latitude warming decreased microbiome diversity in comparison to natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low-latitude, and high latitude natural communities, and increased the abundance of plausible pathogens.

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New Phytol: Temporal variation in mycorrhizal diversity and carbon and nitrogen stable isotope abundance in the wintergreen meadow orchid Anacamptis morio

New Phytol: Temporal variation in mycorrhizal diversity and carbon and nitrogen stable isotope abundance in the wintergreen meadow orchid Anacamptis morio | Fungi and global change | Scoop.it

Many adult orchids, especially photoautotrophic species, associate with a diverse range of mycorrhizal fungi, but little is known about the temporal changes that might occur in the diversity and functioning of orchid mycorrhiza during vegetative and reproductive plant growth.
Temporal variations in the spectrum of mycorrhizal fungi and in stable isotope natural abundance were investigated in adult plants of Anacamptis morio, a wintergreen meadow orchid.
Anacamptis morio associated with mycorrhizal fungi belonging to Tulasnella, Ceratobasidium and a clade of Pezizaceae (Ascomycetes). When a complete growing season was investigated, multivariate analyses indicated significant differences in the mycorrhizal fungal community. Among fungi identified from manually isolated pelotons, Tulasnella was more common in autumn and winter, the pezizacean clade was very frequent in spring, and Ceratobasidium was more frequent in summer. By contrast, relatively small variations were found in carbon (C) and nitrogen (N) stable isotope natural abundance, A. morio samples showing similar 15N enrichment and 13C depletion at the different sampling times.
These observations suggest that, irrespective of differences in the seasonal environmental conditions, the plant phenological stages and the associated fungi, the isotopic content in mycorrhizal A. morio remains fairly constant over time.


Via Stéphane Hacquard
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Ectomycorrhizal impacts on plant nitrogen nutrition: emerging isotopic patterns, latitudinal variation and hidden mechanisms

Ectomycorrhizal impacts on plant nitrogen nutrition: emerging isotopic patterns, latitudinal variation and hidden mechanisms | Fungi and global change | Scoop.it

Understanding the role of mycorrhizae in global N cycles will require reevaluation of high-latitude perspectives on fractionation sources that structure ecosystem δ15N patterns, as well as better integration of EcM function with biogeochemical theories pertaining to climate-nutrient cycling relationships.

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New Phytologist: Root structural and functional dynamics in terrestrial biosphere models – evaluation and recommendations

New Phytologist: Root structural and functional dynamics in terrestrial biosphere models – evaluation and recommendations | Fungi and global change | Scoop.it

There is wide breadth of root function within ecosystems that should be considered when modeling the terrestrial biosphere. Root structure and function are closely associated with control of plant water and nutrient uptake from the soil, plant carbon (C) assimilation, partitioning and release to the soils, and control of biogeochemical cycles through interactions within the rhizosphere. Root function is extremely dynamic and dependent on internal plant signals, root traits and morphology, and the physical, chemical and biotic soil environment. While plant roots have significant structural and functional plasticity to changing environmental conditions, their dynamics are noticeably absent from the land component of process-based Earth system models used to simulate global biogeochemical cycling. Their dynamic represen- tation in large-scale models should improve model veracity. Here, we describe current root inclusion in models across scales, ranging from mechanistic processes of single roots to parameterized root processes operating at the landscape scale. With this foundation we discuss how existing and future root functional knowledge, new data compilation efforts, and novel modeling platforms can be leveraged to enhance root functionality in large-scale terrestrial biosphere models by improving parameterization within models, and introducing new components such as dynamic root distribution and root functional traits linked to resource extraction.


Via Stéphane Hacquard
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Biotic interactions mediate soil microbial feedbacks to climate change

We explore the potential of soil animals to mediate microbial responses to warming and nitrogen enrichment within a long-term, field-based global change study. The combination of global change factors alleviated the bottom-up limitations on fungal growth, stimulating enzyme production and decomposition rates in the absence of soil animals. However, increased fungal biomass also stimulated consumption rates by soil invertebrates, restoring microbial process rates to levels observed under ambient conditions. Our results support the contemporary theory that top-down control in soil food webs is apparent only in the absence of bottom-up limitation. As such, when global change factors alleviate the bottom-up limitations on microbial activity, top-down control becomes an increasingly important regulatory force with the capacity to dampen the strength of positive carbon cycle–climate feedbacks.

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Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees | Fungi and global change | Scoop.it

• Forest trees affect community composition of bacteria and fungi in soil and litter.
• More fungi than bacteria are tree-specific, especially in the litter.
• Effects of trees on bacteria are likely mediated by litter or soil pH.
• Both root-symbiotic and saprotrophic fungi are tree-specific.
• Litter and soils under different trees are dominated by different fungi.


Via Francis Martin
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Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains

Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains | Fungi and global change | Scoop.it
Separating the effects of environmental factors and spatial distance on microbial composition is difficult when these factors covary. We examined the composition of ectomycorrhizal (EM) fungi along elevation gradients on geographically distant mountains to clarify the effect of climate at the regional scale. Soil cores were collected from various forest types along an elevation gradient in southwestern Japan. Fungal species were identified by the internal transcribed spacer regions of the rDNA using direct sequencing. The occurrence of fungal species in this study was compared with a previous study conducted on a mountain separated by ~550 km. In total, we recorded 454 EM fungi from 330 of 350 soil cores. Forty-seven fungal species (~20% of the total excluding singletons) were shared between two mountains, mostly between similar forest types on both mountains. Variation partitioning in redundancy analysis revealed that climate explained the largest variance in EM fungal composition. The similarity of forest tree composition, which is usually determined by climatic conditions, was positively correlated with the similarity of the EM fungal composition. However, the lack of large host effects implied that communities of forest trees and EM fungi may be determined independently by climate. Our data provide important insights that host plants and mutualistic fungi may respond to climate change idiosyncratically, potentially altering carbon and nutrient cycles in relation to the plant–fungus associations.

Via Francis Martin
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Beyond seasonal climate: statistical estimation of phenological responses to weather

Beyond seasonal climate: statistical estimation of phenological responses to weather | Fungi and global change | Scoop.it
Here, we use a novel statistical approach to estimate the combined effects of multiple variables, including local weather events, on the phenology of several taxa (a tree, an insect, and a fungus). We found that thermal forcing had a significant positive effect on each species, frost events delayed the phenology of the tree and butterfly, and precipitation had a positive effect on fungal fruiting. Using data from sites across latitudinal gradients, we found that these effects are remarkably consistent across sites once latitude and other site effects are accounted for. This consistency suggests an underlying biological response to these variables that is not commonly estimated using data from field observations. This approach's flexibility will be useful for forecasting ongoing phenological responses to changes in climate variability in addition to seasonal trends.


Read More: http://www.esajournals.org/doi/abs/10.1890/13-1533.1
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Where Next for Microbiome Research?

Where Next for Microbiome Research? | Fungi and global change | Scoop.it

.......Overall, future microbiome research regarding the molecules and mechanisms mediating interactions between members of microbial communities and their hosts should lead to discovery of exciting new biology and transformative therapeutics.

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Climate-related range shifts – a global multidimensional synthesis and new research directions

Climate-related range shifts – a global multidimensional synthesis and new research directions | Fungi and global change | Scoop.it

We outline a comprehensive framework for assessing multidimensional changes in species distributions, which should then be contrasted with expectations based on climate change indices, such as velocity measures accounting for complex local climate changes. Finally, we propose a unified classification of geographical patterns of species range shifts, arranged in a bi-dimensional space defined by species’ persistence and movement rates. Placing the observed and expected shifts into this bi-dimensional space should lead to more informed assessments of extinction risks.

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The ISME Journal - Dynamics in microbial communities: unraveling mechanisms to identify principles

The ISME Journal - Dynamics in microbial communities: unraveling mechanisms to identify principles | Fungi and global change | Scoop.it
Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this ‘system’ that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

Via Francis Martin
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Ectomycorrhizal fungi – potential organic matter decomposers, yet not saprotrophs

Ectomycorrhizal fungi – potential organic matter decomposers, yet not saprotrophs | Fungi and global change | Scoop.it
Although hypothesized for many years, the involvement of ectomycorrhizal fungi in decomposition of soil organic matter remains controversial and has not yet been fully acknowledged as an important factor in the regulation of soil carbon (C) storage. Here, we review recent findings, which support the view that some ectomycorrhizal fungi have the capacity to oxidize organic matter, either by ‘brown-rot’ Fenton chemistry or using ‘white-rot’ peroxidases. We propose that ectomycorrhizal fungi benefit from organic matter decomposition primarily through increased nitrogen mobilization rather than through release of metabolic C and question the view that ectomycorrhizal fungi may act as facultative saprotrophs. Finally, we discuss how mycorrhizal decomposition may influence organic matter storage in soils and mediate responses of ecosystem C sequestration to environmental changes.

Via Jean-Michel Ané, Francis Martin
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Nature Climate change: Soil carbon: Microbes, roots and global carbon

Interactions between soil microbes, the physical soil environment and vegetation will determine the magnitude of the terrestrial carbon sink under climate change.


Via Stéphane Hacquard
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Reagent contamination can critically impact sequence-based microbiome analyses

Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples is strongly advised.

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Molecular tools for functional genomics in filamentous fungi: Recent advances and new strategies

Molecular tools for functional genomics in filamentous fungi: Recent advances and new strategies | Fungi and global change | Scoop.it

(Jiang et al, 2013)

In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway.

 

 


Via dromius, Guogen Yang
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Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014)

Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014) | Fungi and global change | Scoop.it

Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.


Via Kamoun Lab @ TSL, Francis Martin
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Arjen ten Have's curator insight, April 10, 2017 6:22 PM
Sharing stuff is key yo any interaction. The higher the mutual dependency, the more partners will share. What I do not have clear yet is whether pathogenic relationships will differ substantially from mutualistic ones. miRNA has been shown in plant pathogen relationships, but I can also envisage these in a mutualistic symbiosis. Quite a conundrum. But that' s what  plant-pathogen relations are about anyway.