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41 results for “Fungal community composition”
Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs
<p>Datasets describing the fungal species diversity, microbial density and acidity of French sourdoughs, phenotypic variation of Kazachstania bulderi and Kazachstania humilis strains as well as the diversity of bread-making practices of 40 bakers and farmers-bakers.The data were collected, analyzed, and reported within the following publication :</p> <p>Elisa Michel, Estelle Masson, Sandrine Bubbendorf, Léocadie Lapicque, Thibault Nidelet, Diego Segond, Stéphane Guézenec, Thérèse Marlin, Hugo deVillers, Olivier Rué, Bernard Onno, Judith Legrand, Delphine Sicard and the participating bakers: <strong>Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs</strong>. PCI Evol. Biol.</p> <p> </p>
Data from: Fungal communities are important determinants of bacterial community composition in deadwood
<p>Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns and little is known about the directionality of such interactions. Here we apply joint species distribution modelling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e. dead wood's properties), or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we test the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e. some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment, as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood.</p> <p><b>Importance</b></p> <p>Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modelling to high throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that non-random fungal-bacterial associations derive from shared habitat use, as well as (potentially) biotic interactions. Importantly,<i> </i>the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modelling approach may help gaining insight into the directionality of interactions between different components of the microbiome in other environments.</p>
Fungal community composition and genetic potential regulate fine root decay in northern temperate forests
<p>Understanding how genetic differences among soil microorganisms regulate spatial patterns in litter decay remains a persistent challenge in ecology. Despite fine root litter accounting for ~50% of total litter production in forest ecosystems, far less is known about the microbial decay of fine roots relative to aboveground litter. Here, we evaluated whether fine root decay occurred more rapidly where fungal communities have a greater genetic potential for litter decay. Additionally, we tested if linkages between decay and fungal genes can be adequately captured by delineating saprotrophic and ectomycorrhizal fungal functional groups based on whether they have genes encoding certain ligninolytic class II peroxidase enzymes, which oxidize lignin and polyphenolic compounds. To address these ideas, we used a litterbag study paired with fungal DNA barcoding to characterize fine root decay rates and fungal community composition at the landscape scale in northern temperate forests, and we estimated the genetic potential of fungal communities for litter decay using publicly available genomes. Fine root decay occurred more rapidly where fungal communities had a greater genetic potential for decay, especially of cellulose and hemicellulose. Fine root decay was positively correlated with ligninolytic saprotrophic fungi and negatively correlated with ECM fungi with ligninolytic peroxidases, likely because these saprotrophic and ectomycorrhizal functional groups had the highest and lowest genetic potentials for plant cell wall degradation, respectively. These fungal variables overwhelmed direct environmental controls, suggesting fungal community composition and genetic variation are primary controls over fine root decay in temperate forests at regional scales.</p>
Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
<p><strong><span>Aim</span></strong></p> <p><span>How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge for microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, its most influential drivers and their spatial scale dependence. </span></p> <p><strong><span>Location</span></strong></p> <p><span>Czech Republic.</span></p> <p><strong><span>Time period</span></strong></p> <p><span>Present.</span></p> <p><strong><span>Taxa studied</span></strong></p> <p><span>Fungi.</span></p> <p><strong><span>Methods</span></strong></p> <p><span>We analyzed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition, climate) in fungi, using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.</span></p> <p><strong><span>Results</span></strong></p> <p><span>We found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance-decay relationships</span><span>,</span><span> and their community composition was driven mainly by vegetation and dispersal at local scales, but at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.</span></p> <p><strong><span>Main conclusions</span></strong></p> <p><span>Our results underscore the remarkable variation in the community ecology of fungi, which seems to range well-known patterns both from the macro- and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro- and macroorganisms. </span></p>
Raw data of the microarthropods and decomposition from: Effects of microarthropod density on soil fungal community composition in nutrient-poor ecosystems
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Data from: Fungal communities are important determinants of bacterial community composition in deadwood
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Fungal community composition and genetic potential regulate fine root decay in northern temperate forests
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Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
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Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay
<p>Dead trees are vital structural elements in forests playing key roles in the carbon and nutrient cycle. Stem traits and fungal community composition are both important drivers of stem decay, and thereby affect ecosystem functioning, but their relative importance for stem decomposition over time remains unclear.</p> <p>To address this issue, we used a common garden decomposition experiment in a Dutch larch forest hosting fresh logs from 13 common temperate tree species. In total 25 fresh wood and bark traits were measured as indicators of wood accessibility for decomposers, nutritional quality, and chemical or physical defense mechanisms. After one and four years of decay, we assessed the richness and composition of wood-inhabiting fungi using amplicon sequencing and determined the proportional wood density loss.</p> <p>Average proportional wood density loss for the first year was 18.5%, with further decomposition occurring at a rate of 4.3% yr<sup>-1</sup> for the subsequent three years across tree species. Proportional wood density loss varied widely across tree species in the first year (8.7-24.8% yr<sup>-1</sup>) and subsequent years (0-11.3% yr<sup>-</sup><sup>1</sup>). The variation was directly driven by initial wood traits during the first decay year, then later directly driven by bark traits and fungal community composition. Moreover, bark traits affected the composition of wood-inhabiting fungi and thereby indirectly affected decomposition rates. Specifically, traits promoting resource acquisition of the living tree, such as wide conduits that increase accessibility and high nutrient concentration, increased initial wood decomposition rates. Fungal community composition, but not fungal richness explained differences in wood decomposition after four years of exposure in the field, where fungal communities dominated by brown-rot and white-rot Basidiomycetes were linked to higher wood decomposition rate.</p> <p><em>Synthesis.</em> Understanding what drives deadwood decomposition through time is important to understand the dynamics of carbon stocks. Here, using a tailor-made experimental design in a temperate forest setting, we have shown that stem trait variation is key to understanding the roles of these drivers; Initially, wood traits explained decomposition rates while subsequently, bark traits and fungal decomposer composition drove decomposition rates. These findings inform forest management with a view to selecting tree species to promote carbon storage.</p>
Data for the article: Coupling of leaf elemental traits with root fungal community composition reveals a plant resource acquisition strategy in a desert ecosystem
<p><em>Purpose</em>: Plant-associated microbes enhance nutrient access and stress tolerance of the host species, and therefore, are crucial for plant traits and resource strategies. However, the links between aboveground plant traits and belowground microbes related to plant resource strategies under stressful conditions remain poorly understood.</p> <p><em>Methods</em>: We tested the relationships between leaf traits linked to water (carbon isotopic composition, δ<sup>13</sup>C) and nutrient use (elemental concentrations and stoichiometry) with microbial compositions in roots and rhizospheres of two dominant species (<em>Artemisia ordosica</em> and <em>Leymus secalinus</em>) in the Mu Us Desert, northern China.</p> <p><em>Results</em>: <em>L. secalinus</em> exhibited higher Mg and Mn concentrations, N:P ratios, stoichiometric flexibility, and root fungi:bacteria ratios, but lower foliar K and Ca concentrations and δ<sup>13</sup>C values than <em>A. ordosica</em>. The leaf N:P of <em>L. secalinus</em> increased with the root fungi:bacteria ratios, whereas the leaf N:P of <em>A. ordosica</em> decreased with the root fungi:bacteria ratios. The plant elemental levels (P, N, K, Ca, Mn, and δ<sup>13</sup>C) of <em>L. secalinus</em> but not <em>A. ordosica</em> were significantly related to their root fungal composition. Additionally, the random forest model identified four key fungal families in predicting leaf elemental traits for both plant species.</p> <p><em>Conclusion</em>: The results suggested tight coupling and coordination between leaf elemental traits and root microbial compositions (especially fungal communities) related to plant resource acquisition strategies. By regulating aboveground and belowground feedback loops through trait flexibility and root microbial compositions, the studied plant species can sustain their resource strategies under stressful environmental conditions.</p>
eDNA metabarcoding reveals high soil fungal diversity and variation in community composition among Spanish cliffs
<p><span>Environments characterized by physical extremes harbor unique species diversity with particular adaptations. Cliffs are harsh environments for organisms but host a great diversity of specialized plants with many endemics, rare and even endangered species. It is, however, less known which fungal diversity the cliff habitats contain and whether it differs among different cliff locations. We thus sampled soil from three separate cliff locations in the North, Centre and South of Spain and used eDNA metabarcoding to determine fungal diversity. To better understand whether cliff specialist plants may promote particular fungal communities, we have sampled soil from crevices with cliff specialist plants and no apparent plants as controls. Major lifestyles found in cliff soils were saprotrophs, and major fungal orders were Dothideomycetes, Sordariomycetes, and Eurotiomycetes, while the amount of symbiotrophic fungi was relatively low. We found no significant differences in fungal amplicon sequence variant (ASV) richness among the three sampled locations, but the sites were significantly different in their community composition and their main indicator species. Overall, there were no significant differences in fungal ASV richness or composition between soils from cliff specialist plants and soils without plants, suggesting a unique fungal diversity in cliff soils independent from specialized plants. However, preliminary findings on soils of the specialist cliff plant Sedum dasyphyllum against control soils suggest that the presence of a specialist plant may be a relevant factor affecting the specificity of the fungal community in cliff soils. Our results indicate the existence of particular cliff fungal communities in each location, and that, despite limited and poorly developed soils and harsh conditions, cliffs can harbor a great diversity of fungal species, comparable to other ecosystems of Spain. This study points out that some fungi may be cliff-specific, shaping particular communities that mediate plant adaptations to cliffs' extreme conditions.</span></p>
Soil amendment with biochar and manure alters wood stake decomposition and fungal community composition
<p><span>Biochar and manure can be used for </span>sustainable land management<span>. However, little is known about how soil amendments might affect surface- and below-ground microbial processes and subsequent wood decomposition</span>. In a split-split-split plot design, we amended soil with two rates of manure (whole plot; 0 and 9 Mg ha<sup>-1</sup>) and biochar (split-plot; 0 and 10 Mg ha<sup>-1</sup>). <span>Wood stakes of three species (hybrid poplar, triploid<em> Populus tomentosa</em> Carr.; aspen, <em>Populus tremuloides</em> Michx.; and pine, <em>Pinus taeda</em> L.) were placed in two positions (horizontally on the soil surface, and inserted vertically in the mineral soil), which served as </span>a substrate for fungal growth<span>. In 3 years, the decomposition rate (mass loss), moisture content, and fungal community (via high-throughput sequencing methods) of stakes were evaluated. Results indicated</span> that <span>biochar and/or manure increased the wood stake decomposition rates, moisture content, and operational taxonomic unit (OTU) abundance. However, the richness and diversity of fungi </span>were<span> dependent on wood stake position (surface > mineral), species (pine > the two <em>Populus</em>), and sample dates. This study highlights that soil amendment with biochar and/or manure can alter the fungal community, which in turn can enhance an important soil process (i.e., decomposition). </span></p>
Data for the article: Coupling of leaf elemental traits with root fungal community composition reveals a plant resource acquisition strategy in a desert ecosystem
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Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites
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Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay
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Warming and reduced rainfall alter fungal necromass decomposition rates and associated microbial community composition and functioning at a temperate-boreal forest ecotone
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Soil amendment with biochar and manure alters wood stake decomposition and fungal community composition
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eDNA metabarcoding reveals high soil fungal diversity and variation in community composition among Spanish cliffs
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Data from: Contrasting effects of host identity, plant community, and local species pool on the composition and colonisation levels of arbuscular mycorrhizal fungal community in a temperate grassland
Arbuscular mycorrhizal fungi (AMF) are important plant symbionts, but we know little about the effects of plant taxonomic identity or functional group on the AMF community composition. To examine effects of the surrounding plant community, of host, and of the AMF pool on the AMF community in plant roots, we manipulated plant community composition in a long-term field experiment. Within four types of manipulated grassland plots, seedlings of eight grassland plant species were planted for 12 weeks, and AMF in their roots were quantified. Additionally, we characterised the AMF community of individual plots (as their AMF pool) and quantified plot abiotic conditions. The largest determinant of AMF community composition was the pool of available AMF, varying at metre scale due to changing soil conditions. The second strongest predictor was the host functional group. The differences between grasses and dicotyledonous forbs in AMF community variation and diversity were much larger than the differences among species within those groups. High cover of forbs in the surrounding plant community had a strong positive effect on AMF colonisation intensity in grass hosts. Using a manipulative field experiment enabled us to demonstrate direct causal effects of plant host and surrounding vegetation.
Data from: Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests
Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free‐living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale‐explicit sampling strategy to examine soil N cycling at scales ranging from the microsite to ecosystem level. We measured fungal community composition, total and inorganic N pools, gross proteolytic rate, net N mineralization and microbial extracellular enzyme activity at multiple locations within 18 permanent plots that span dramatic gradients of soil N concentration, stand age and forest composition. The ratio of inorganic to organic N cycling was correlated with variation in fungal community structure, consistent with a strong influence of ectomycorrhiza on ecosystem‐scale N cycling. However, on average, > 61% of the variation in soil biogeochemistry occurred within plots, and the effects of forest composition were mediated by this local‐scale heterogeneity in total soil N concentrations. These cross‐scale interactions demonstrate the importance of a spatially explicit approach towards an understanding of controls on element cycling.
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