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30 results for “fungal and bacterial communities”
Tree-Associated Fungal and Bacterial Communities at Harvard Forest 2021
Cities are investing in tree-planting initiatives to protect their citizens from climate change-related heat and pollution exposure, yet Boston’s street trees are growing nearly four times as fast and dying twice as young as Massachusetts’ rural forest trees. Our research aims to characterize the belowground variables and microbial community composition that might explain the differences in growth and mortality rates observed between urban and rural trees. In 2021, soil, leaf, and root samples were taken from 25 trees in Harvard Forest to use as a rural comparison to Boston’s street trees and trees in other forests along an urban-to-rural gradient from Boston into Western Massachusetts. At each tree, three 12” deep, 2.4-centimeter radius soil cores were taken within the drip line, and soil cores were divided into the top 6” and lower 6” of soil. Fine roots were picked from each soil core. Six leaf samples were taken from the mid-canopy of each tree, where possible. Soil variables including temperature, moisture, percent organic matter, soluble nitrogen availability, bulk density, and root biomass were measured. Thus far, we have found that urban trees have fewer roots than Harvard Forest trees (F1,252) = 10.88, p = 0.0011), and that urban trees establish more root biomass deeper into the soil than Harvard Forest trees (p = 4.84e-5).
Data from: Shift of bacterial and fungal communities upon soil amelioration is driven by carbon degradability of organic amendments
<p>Microbial communities of bacteria and fungi have been analyzed in soil. Agricultural soil was amended with different organic amendments including straw, compost, biogas residues, and biochar, and incubated in the lab. After 6 months, DNA extracted from soil samples was analyzed via Illumia MiSeq DNA sequencing (16S V3V4 for bacteria, ITS1 for fungi) to evaluate changes to the microbial community structure.</p> <p>For details, please see the respective publication (DOI: 10.1007/s44378-024-00012-5).</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>
Different facets of bacterial and fungal communities drive soil multifunctionality in grasslands spanning a 3,500 km transect
<p>1. Soil microbial communities are essential in regulating ecosystem functions and services. However, the importance of bacterial and fungal communities as predictors of multiple soil functions (i.e., soil multifunctionality) in grassland ecosystems has not been studied systematically.</p> <p>2. Here, we measured soil microbial diversity, community composition, biomass, and multiple soil functions of 41 sites in five grassland ecosystems spanning a 3,500 km northeast–southwest transect. The random forest algorithm was adopted to determine the importance of geographical location, climatic, altitude, edaphic, plant, and microbial predictors in driving a proxy of soil multifunctionality (seven soil functions in this study). Moreover, structural equation models (SEMs) were employed to examine the direct and indirect effects of those predictors on soil multifunctionality.</p> <p>3. Our results demonstrated that soil multifunctionality was positively driven by soil fungal diversity but not by bacterial diversity. Fungal phylogenetic diversity (presence of different evolutionary lineages) showed stronger positive relationships with soil multifunctionality than taxonomic diversity (richness of species). Dominant bacterial taxa, particularly of phyla Actinobacteria and Proteobacteria, were positively associated with soil multifunctionality, while none of the fungal taxa were found to regulate soil multifunctionality. Furthermore, both fungal and bacterial biomass had significant effects on soil multifunctionality, while the effect of microbial biomass was weaker than that of fungal diversity and bacterial taxa. Importantly, the direct positive effects of soil fungal diversity, dominant bacterial taxa, and fungal and bacterial biomass were maintained after accounting for multiple predictors in grassland ecosystems.</p> <p>4. This study provided strong empirical evidence that soil multifunctionality was driven by different facets of the bacterial and fungal communities in the grassland ecosystems. Our results also highlighted that any loss of fungal diversity, dominant bacterial taxa and microbial biomass might reduce soil multifunctionality, exacerbating ecosystem functions and services such as soil fertility, primary production, and climate mitigation in grassland ecosystems. </p>
Different facets of bacterial and fungal communities drive soil multifunctionality in grasslands spanning a 3,500 km transect
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Data from: Fungal communities are important determinants of bacterial community composition in deadwood
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Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards
<p>Pesticides can have unintentional effects on non-target organisms and change biotic communities. Such changes might be particularly important in soil microbial communities which drive many ecosystem functions and may affect crop quality. Here, we investigated, in a 3-year study, how vegetation control (by herbicide application) and soil copper content (from long-term copper-based fungicide application), affect biodiversity and the community structure of soil bacteria, fungi and protists and associated soil functions (respiration, decomposition) in Swiss vineyards. Furthermore, we determined the effects of these two management practices on grape quality as the most direct ecosystem service to farmers. Across all study years, the community composition of microorganisms was affected by herbicide application, however, a significant loss of operational taxonomic units (OTUs) was only observed in fungi and protists. Soil copper content reduced OTU richness of bacteria and protists in some years but had no significant effect on fungal richness. Copper changed the community composition in all three groups of soil microorganisms. While we found no effect of copper on soil functions, herbicide application reduced microbial respiration and biomass by about 39% and 45% respectively. However, decomposition rates remained virtually unchanged by any pesticide. Yeast assimilable nitrogen (YAN) levels in grape must were below the critical threshold of 140 mg/L in 40% of the vineyards without herbicide application and the variety Chasselas , whereas in vineyards with herbicide application it was only 20%. Synthesis and applications: Application of pesticides led to changes in richness and composition of soil microbial communities and directly reduced some soil functions (microbial biomass and respiration), but not all (decomposition). Some grape quality parameters can be indirectly enhanced by pesticide application, highlighting the trade-off between the interests of nature conservation and the interests of the farmer. Balancing these two diverging interests requires the establishment of alternative vineyard management allowing reduced pesticide application.</p>
Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas
<p>These data are the DNA sequences obtained from samples of house plaster with chromatic alteration facies. Three areas (VA1, VA3 and VNA6) of the wall were sampled. the DNA was extracted using the Spin Kit For Soil MPBio. </p> <p>The DNA extracts were sequenced by NGS using Illumina MiSeq</p> <p>Two regions were selected V3V5 16S for Bacteria and ITS1 ITS for Fungi. </p>
Interactions between belowground traits and rhizosheath fungal and bacterial communities for phosphorus acquisition
<p>1. Plant-soil microbes interactions play a central role in plant nutrient acquisition and thus ecosystem functioning and nutrient availability in agroecosystems. Adjustments in root morphology, root exudation and associations with microorganisms such as arbuscular mychorrizal fungi are common for phosphorus acquisition. Yet how plant belowground functional traits interact with microbial communities for P-acquisition remains largely unknown, limiting our understanding of phosphorus availability in agroecosystems.</p> <p>2. Interactions between belowground functional traits and rhizosheath soil microbial communities for P-acquisition were investigated across eight herbaceous species with contrasting root traits. Root morphological and physiological traits involved in P-acquisition were quantified simultaneously with PLFA (phospholipid fatty acid) and NLFA (neutral lipid fatty acid) microbial bioindicators.</p> <p>3. Multiple correlations were observed between root morphology, root exudates and rhizosheath fungal and bacterial communities. Root exudates and in particular release of malate and malonate were strongly linked with indicators of Gram-negative bacteria, which were correlated with changes in rhizosheath soil P concentration and plant P content.</p> <p>4. Our results suggest that root exudation of carboxylates may play an important role in plant-soil microorganism interactions for P-acquisition, underlining their likely role in shaping microbial communities. Incorporating these interactions in biogeochemical models would lead to better predicting power and understanding of P cycling and ecosystem functioning.</p>
Slow soil enzyme recovery following invasive tree removal through gradual changes in bacterial and fungal communities
<p><span>Biological invasions of plants have profound effects on ecosystem functioning by directly and indirectly altering soil microbiota, especially when invasive plants co-invade with their associated microbiomes. Ecosystem functions may recover slowly following invader removal, with implications for restoration. </span></p> <p><span>We investigated the recovery of soil ecosystem function (measured as soil enzymes) following the removal, at different densities and times, of invasive <em>Pinus</em> spp. in New Zealand, and how different enzymatic activities responded to pine legacies. </span></p> <p><span>Enzymatic activities were driven by pine legacies via both abiotic (soil nutrients) and biotic (fungi and bacteria) soil properties, with different enzymes showing distinct patterns. The activity of the enzymes cellobiohydrolase (cellulose degrading), β-glucosidase (cellulose degrading), N-acetyl-glucosaminidase (chitin degrading), laccase (lignin oxidising) and acid phosphatase (organic phosphate hydrolysing) were influenced by time since pine removal and by pine density at removal via effects on biotic communities. In comparison, Mn-peroxidase (lignin oxidising) was positively correlated with density of pines at removal and was negatively correlated with time since removal and was only influenced by fungal communities. </span></p> <p><em><span>Synthesis</span></em><span>. The recovery of soil enzymatic function following invasive species removal is slow, and dependent on pine legacies through the gradual changes in fungal and bacterial communities. The cascading effects of these changes suggest potential implications for the success of future plant establishment and restoration of co-invaded ecosystems.</span></p>
Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards
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Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas
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Soil properties and plant functional traits have different importance in shaping rhizosphere soil bacterial and fungal communities in a meadow steppe
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Contrasting early successional dynamics of bacterial and fungal communities in recently deglaciated soils of the maritime Antarctic
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Slow soil enzyme recovery following invasive tree removal through gradual changes in bacterial and fungal communities
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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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Interactions between belowground traits and rhizosheath fungal and bacterial communities for phosphorus acquisition
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Data from: Unearthing carrion beetles' microbiome: characterization of bacterial and fungal hindgut communities across the Silphidae
Carrion beetles (Coleoptera, Silphidae) are well known for their behaviour of exploiting vertebrate carcasses for nutrition. While species in the subfamily Silphinae feed on large carcasses and on larvae of competing scavengers, the Nicrophorinae are unique in monopolizing, burying and defending small carrion, and providing extensive biparental care. As a first step towards investigating whether microbial symbionts may aid in carcass utilization or defence, we characterized the microbial hindgut communities of six Nicrophorinae (Nicrophorus spp.) and two Silphinae species (Oiceoptoma noveboracense and Necrophila americana) by deep ribosomal RNA amplicon sequencing. Across all species, bacteria in the family Xanthomonadaceae, related to Ignatzschineriao larvae, were consistently common, and several other taxa were present in lower abundance (Enterobacteriales, Burkholderiales, Bacilli, Clostridiales and Bacteroidales). Additionally, the Nicrophorinae showed high numbers of unusual Clostridiales, while the Silphinae were characterized by Flavobacteriales and Rhizobiales (Bartonella sp.). In addition to the complex community of bacterial symbionts, each species of carrion beetle harboured a diversity of ascomycetous yeasts closely related to Yarrowia lipolytica. Despite the high degree of consistency in microbial communities across the Silphidae—specifically within the Nicrophorinae—both the fungal symbiont phylogeny and distance-based bacterial community clustering showed higher congruence with sampling locality than host phylogeny. Thus, despite the possibility for vertical transmission via anal secretions, the distinct hindgut microbiota of the Silphidae appears to be shaped by frequent horizontal exchange or environmental uptake of symbionts. The microbial community profiles, together with information on host ecology and the metabolic potential of related microorganisms, allow us to propose hypotheses on putative roles of the symbionts in carcass degradation, detoxification and defence.
Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities
Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near-pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near-pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near-pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near-pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near-pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche-based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β-diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.
Dataset of manuscript "Divergent responses of soil bacterial and fungal communities to climate warming in an alpine tundra ecosystem"
<p>Our study conducts a translocation experiment in the alpine tundra of the Changbai Mountains to explore how climate warming will affect soil bacterial and fungal communities in the alpine tundra and what are the underlying ecological mechanisms for their potential community changes. Soil samples (n = 24) were respectively collected during the early growing season (June 5, EGS), peak growing season (July 30, PGS), and late growing season (September 20, LGS) of 2021. The uploaded data contains the soil properties and OTU abundance measurements for these soil samples, as well as air and soil temperature from June 1, 2020 to September 15, 2021. </p>
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Allen Brain Atlas
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OpenNeuro
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