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opencc-by-4.0Jan 2020View details →

Linking potential greenhouse gas and nitric oxide fluxes to soil microbial communities in incubation experiments with soil from the SAFE landscape

Description: Controlled lab experiment to measure potential GHG emissions and associated parameters from SAFE soil. Soil taken Nov 2016, lab experiment carried out Apr-May 2017. Day 0 is before fertilisation, day 1 application of NH4NO3 solution to simulate N deposition of approx. 5 kg N ha-1 y-1 . Day 15 for (OP2,OP7 and RR) application of NH4NO3 solution to simulate N deposition of approx 50 kg N ha-1 y-1.Project: This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/126">Characterising soil microbial communities and measuring associated biogeochemical fluxes</a>Funding: These data were collected as part of research funded by: <ul><li>NERC HMTF (Research Programme, (NE/K016091/1), <a href=" http://lombok.nerc-hmtf.info/"> http://lombok.nerc-hmtf.info/</a>)</li></ul>This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.Permits: These data were collected under permit from the following authorities:<ul><li>Sabah Biodiversity Centre (Research licence JKM/MBS.1000-2/3 JLD.2 (115))</li></ul>XML metadata: GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=3897394">here</a>Files: This consists of 1 file: Lab_experiment_Melissa_corrected.xlsxLab_experiment_Melissa_corrected.xlsxThis file contains dataset metadata and 2 data tables:<ol><li>parameters_repeated_measures (described in worksheet parameters_repeated_measures)Description: soil characteristicsNumber of fields: 16Number of data rows: 207Fields: <ul><li>core_id: Location measurement was taken (Field type: id)</li><li>site: Location measurement was taken (Field type: location)</li><li>landuse: Land use of location (Field type: categorical)</li><li>day_of_exp: day number (Field type: numeric)</li><li>flux_CH4: Soil CH4 flux (Field type: numeric)</li><li>flux_CO2: Soil CO2 flux (Field type: numeric)</li><li>flux_N2O-N: Soil N2O flux (Field type: numeric)</li><li>flux_NO: Soil NO flux (Field type: numeric)</li><li>NH4-N: Soil NH4 concentration (Field type: numeric)</li><li>NO3-N: Soil NO3 concentration (Field type: numeric)</li><li>soil_moisture: Soil moisture around the flux chamber (Field type: numeric)</li><li>archaeal amoA: Gene transcript abundance (Field type: numeric)</li><li>Proteobacteria_nirS: Gene transcript abundance (Field type: numeric)</li><li>AniA_nirK: Gene transcript abundance (Field type: numeric)</li><li>nosZ-I: Gene transcript abundance (Field type: numeric)</li><li>nosZ-II: Gene transcript abundance (Field type: numeric)</li></ul></li><li>parameters_one_off (described in worksheet parameters_one_off)Description: soil pH and densityNumber of fields: 5Number of data rows: 18Fields: <ul><li>core id: Location measurement was taken (Field type: id)</li><li>site: Location measurement was taken (Field type: location)</li><li>landuse: Land use of location (Field type: categorical)</li><li>pH: Soil pH (Field type: numeric)</li><li>bulk_density: dry weight of soil (Field type: numeric)</li></ul></li></ol>Date range: 2016-11-01 to 2017-05-30Latitudinal extent: 4.5000 to 5.0700Longitudinal extent: 116.7500 to 117.8200

opencc-zeroAug 2020View details →

Soil properties and N-cycling community data for 324 samples

Soil microbial communities, key players of many crucial ecosystem functions, are prone to degradation due to intensified environmental perturbations. However, few ecological concepts and practices have been developed for rescuing these degraded microbial communities. Here, we carried out a pot experiment (totally 324 pots) with or without arbuscular mycorrhizal fungi (AMF) inoculation and at three levels (one, three and six species) of plant diversity to disentangle how the AMF and vegetation rescue the soil nitrogen (N) -cycling microbial loop. Our results provide strong evidence that AMF inoculation improved the restoration of soil N-cycling microbial communities. This improved restoration is related to the role of AMF in enhancing interactions within the N-cycling microbial loop. Furthermore, increased plant diversity strengthened the role of AMF in rescuing degraded N-cycling microbial communities. Our findings provide novel insights into the roles of AMF and plant diversity in facilitating the rescue of microbial communities in degraded terrestrial ecosystems.

opencc-zeroAug 2020View details →

The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding

Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. However, our knowledge on spatial structure and underlying processes of community assembly for soil arthropods is scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput-sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multi-hierarchical approach was performed using haplotype-level-COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1000 co-distributed species and nearly 3000 haplotypes. Local assemblages were highly distinctive between grasslands and forests, and within each of them showed strong spatial structures and high endemicity at the scale of a few kilometres or less. The local distance-decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was very similar in all three regions, pointing to a significant role of dispersal limitation driving the local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod-diversity on Earth.

opencc-by-4.0Aug 2020View details →

Dataset_2020_Biogeosciences_Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer - prey systems

Dataset associated to the publication: Erktan, A., Rillig, M.C., Carminati, A., Jousset, A., Scheu, S. (2020) Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer - prey systems, Biogeosciences, accepted the 27/08/2020.

opencc-zeroDec 2019View details →

An invasive plant rapidly increased the similarity of soil fungal pathogen communities

Background and Aims: Plant invasions can change soil microbial communities and affect subsequent invasions directly or indirectly via foliar herbivory. It has been proposed that invaders promote uniform biotic communities that displace diverse, spatially variable communities ("Biotic Homogenization Hypothesis") but this has not been experimentally tested for soil microbial communities, so the underlying mechanisms and dynamics are unclear. Here, we compared density-dependent impacts of the invasive plant Alternanthera philoxeroides and its native congener A.sessilis on soil fungal communities, and their feedback effects on plants and a foliar beetle. Methods: We conducted a plant-soil feedback (PSF) experiment and a lab bioassay to examine PSFs associated with the native and invasive plants and a beetle feeding on them. We also characterized the soil fungal community using high-throughput sequencing. Key Results: We found locally differentiated soil fungal pathogen assemblages associated with high densities of the native plant Alternanthera sessilis but little variation in those associated with the invasive congener A. philoxeroides regardless of plant density. In contrast, AM fungal assemblages associated with high densities of the invasive plant were more variable. Soil biota decreased plant shoot mass but their effect was weak for the invasive plant growing in native plant conditioned soils. PSFs increased the larval biomass of a beetle reared on leaves of the native plant only. Moreover, PSFs on plant shoot, root and beetle mass were predicted by different pathogen taxa in a plant species-specific manner. Conclusion: Our results suggest that plant invasions can rapidly increase the similarity of soil pathogen assemblages even at low plant densities leading to taxonomically and functionally homogeneous soil communities that may limit negative soil effects on invasive plants.

opencc-zeroJan 2021View details →

Anthropogenic disturbance impacts ectomycorrhizal communities and abiotic soil properties: implications for an endemic forest disease

In forest ecosystems, habitat fragmentation negatively impacts stand structure and biodiversity; the resulting fragmented patches of forest have distinct, disturbed edge habitats that experience different environmental conditions than the interiors of the fragments. In southwest Western Australia, there is a large-scale decline of the keystone tree species Corymbia calophylla following fragmentation and land use change. These changes have altered stand structure and increased their susceptibility to an endemic fungal pathogen, Quambalaria coyrecup, which causes chronic canker disease especially along disturbed forest habitats. However, the impacts of fragmentation on belowground processes in this system are not well understood. We examined the effects of fragmentation on abiotic soil properties and ectomycorrhizal (ECM) and arbuscular mycorrhizal fungal (AMF) communities, and whether these belowground changes were drivers of disease incidence. We collected soil from 17 sites across the distribution range of C. calophylla. Soils were collected across a gradient from disturbed, diseased areas to undisturbed, disease-free areas. We analysed soil nutrients and grew C. calophylla plants as a bioassay host. Seedlings were harvested and roots collected after six months of growth. DNA was extracted from the roots, amplified using fungal specific primers and sequenced using Illumina MiSeq. Concentrations of key soil nutrients such as nitrogen, phosphorus and potassium were much higher along the disturbed, diseased edges in comparison to undisturbed areas. Disturbance altered the community composition of ECM and AMF; however, only ECM communities had lower rarefied richness and diversity along the disturbed, diseased areas compared to undisturbed areas. Accounting for effects of disturbance, ECM diversity and leaf litter depth were highly correlated with increased disease incidence in C. calophylla. In the face of global change, increased virulence of an endemic pathogen has emerged in this Mediterranean-type forest.

opencc-zeroDec 2014View details →

Data from: Complementarity and selection effects in early and mid-successional plant communities are differentially affected by plant-soil feedback

1. Many studies that provided evidence for a positive relationship between plant diversity and productivity have proposed that this effect may be explained by complementarity among species in resources utilization, or selection of particularly productive species in high-diversity plant communities. Recent studies have related the higher productivity in diverse plant communities to suppression of pathogenic soil biota. If soil biota plays a role in diversity–productivity relationships, the question remains about how they may influence complementarity and selection effects. 2. Here we examine how complementarity and selection effects may depend on soil biota using a plant–soil feedback approach. We used monocultures and mixtures of early successional plant species, which are known to have mostly negative plant–soil feedback effects, and mid-successional plant species, which generally have neutral plant–soil feedback. 3. We found that plant–soil feedback effects differed between monocultures and mixed plant communities, as well as between early and mid-successional plants. This resulted in a significant interaction effect between diversity and successional stage. In monocultures, plant–soil feedback tended to be negative for early and positive for mid-successional plant species. Interestingly, the community feedback responses of the mixed communities were opposite, being positive for early and negative for mid-successional community. 4. Plant–soil feedback differentially affected complementarity and selection effects of early and mid-successional plant communities: it enhanced complementarity effects of early and decreased selection effects of mid-successional species. 5. Synthesis. Soil biota that drive plant–soil feedback effects can influence the diversity–productivity relationship not only through decreased biomass production in monocultures compared to mixtures, but also through influencing complementarity and selection effects among species in mixed plant communities. Our results reveal that biodiversity–productivity relationships depend on plant–soil feedback interactions, which depend on the successional position of the plant. We propose that including successional position and trait-based analyses of plant–soil feedback in diversity-functioning studies will enhance understanding consequences of biodiversity loss for productivity and other ecosystem processes.

opencc-zeroMay 2020View details →

Data from: Effects of aridity on soil microbial communities and functions across soil depths on the Mongolian Plateau

1. Arid and semi-arid grassland ecosystems cover about 15% of the global land surface and provide vital soil carbon (C) and nitrogen (N) sequestration. Although half of the soil C and N is stored in deep soils (below 30 cm), no regional-scale study of microbial properties and their functions through the soil profile has been conducted in these drylands. 2. To explore the distribution and determinants of microbial properties and C and N mineralization rates through soil profile along aridity gradient at a regional scale, we investigated these variables for four soil layers (0-20, 20-40, 40-60, and 60-100 cm) in 132 plots on the Mongolia Plateau. 3. Soil microbial properties (biomass and bacteria:fungi ratio) and C and N mineralization rates decreased with increasing soil depth and aridity at the regional scale. Aridity-induced declines in soil microbial properties mainly resulted from the negative effects of aridity on ANPP/root biomass and soil organic C (SOC) in the surface soil layers (0-20 and 20-40 cm) but from the direct and indirect (via SOC and soil C/N) negative effects of aridity in the deep soil layers (40-60 and 60-100 cm). 4. Aridity-induced declines in soil C mineralization rates mainly resulted from the negative indirect effect of aridity on SOC and microbial properties in each soil layer, with weaker effects of SOC and stronger effects of soil microbes in the deep soil layers. Aridity-induced declines in soil N mineralization rates mainly resulted from the negative indirect effect of aridity on SOC in the three soil layers above 60 cm and mainly resulted from the negative direct effect of aridity in the 60-100 cm soil layer. 5. Aridity via direct or indirect effects strongly determined the patterns of soil microbial properties and C and N mineralization throughout soil profiles on the Mongolian Plateau. These findings suggest that the increases in aridity are likely to induce changes in soil microorganisms and their associated functions across soil depths of semi-arid grasslands, and future models should consider the dynamic interactions between substrates and microbial properties across soil depths in global drylands.

opencc-zeroDec 2018View details →

Data from: Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: is disturbance an alternative explanation?

1. Bacterial endophytes may be fairly host specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community-wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity. 2. We tested the following four non-mutually exclusive hypotheses: 1. The Host Identity Hypothesis: endophytes vary substantially among different host plant species. 2. The Core Microbiome Hypothesis: a subset of microbial taxa will be shared among all host plant species. 3. The Soil Resource Supply Hypothesis: endophytes vary substantially among habitats with experimentally elevated levels of macronutrients. 4. The Disturbance-Disruption Hypothesis: disturbances created by the periodic application of antibiotics structure bacterial endophyte communities. 3. We tested these hypotheses by characterizing endophytes using high-throughput sequencing among seedlings of five phylogenetically diverse tree species nested within a long-term, full factorial nitrogen, phosphorus, and potassium soil fertilization experiment. We artificially disturbed one of our focal species by applying antibiotics every 10-14 days for 29 months within the soil (N,P,K) fertilization experiment. 4. While we detected a significant effect of host identity and soil nutrient additions, together they explained little variation in endophyte community composition (< 10%). We found unequivocal evidence for a core microbiome shared by all species. Specifically, we found nine OTUs were present among 95% or more of all control saplings, representing a third of the total reads. These bacterial taxa belonged to the Actinobacteria. 5. In contrast, disturbance (antibiotics) explained more endophyte variation than all nutrient addition combinations combined and twice the variation explained by host identity for all five tree species. Synthesis: Our results challenge the idea that host identity is a primary filter shaping bacterial endophyte communities; this suggests that many of the same bacterial taxa occur inside plant hosts even if those host plants are phylogenetically diverse. Moreover, we documented a distinct core microbiome shared among our five focal tree species. Finally, we found that disturbance was an important driver of microbial community composition, which parallels the importance of disturbance in other areas of community ecology.

opencc-zeroDec 2017View details →

Data from: When mutualisms matter: Rhizobia effects on plant communities depend on host plant population and soil nitrogen availability

1.Mutualistic interactions, such as the relationship between legumes and rhizobia, can affect community properties, yet there needs to be greater understanding of when these interactions may be most important to communities. Resource mutualism theory provides predictions based on variation in abiotic and biotic factors. First, there is substantial intraspecific genetic variation in how legumes interact with rhizobia, including variation in legume growth response to rhizobia, number of rhizobia-housing nodules, and nitrogen fixation. Rhizobia likely have greater community impacts when associating with hosts that benefit greatly from rhizobia, produce many nodules, and fix a lot of nitrogen. Second, increased soil nutrient availability typically reduces the partner benefits of legume-rhizobium interactions. As a result, the legume-rhizobium resource mutualism may have greater effects on communities in low nitrogen environments. 2.We first conducted a common garden study of the annual legume Chamaecrista fasciculata to explore intraspecific variation in focal traits related to competition and mutualistic interactions with rhizobia. Then, we manipulated the presence of rhizobia, nitrogen fertilization, and population identity of C. fasciculata in mesocosms simulating native plant communities. We measured plant diversity, assessed changes in community composition, and measured soil nutrient availability. 3.We detected significant genetically-based intraspecific variation in growth and mutualism related traits across C. fasciculata populations. From the experimental mesocosms, we found that although rhizobia consistently reduced diversity, rhizobia most strongly reduced diversity when associating with C. fasciculata populations that were highly dependent on rhizobia and when nitrogen was most limiting. We also detected greater variation among populations in their effects on communities in the absence of rhizobia; the presence of rhizobia dramatically minimized effects of population identity on the surrounding community. 4.Synthesis. These findings show that abiotic environmental factors and intraspecific variation in a dominant host plant can influence the magnitude of mutualism effects on communities and, reciprocally, how the presence of key mutualists can influence the importance of genetically-based variation among populations to community outcomes. While prior studies have detected both strong and weak effects of mutualism on plant communities, our study illustrates that mutualism theory may predict when strong mutualism effects are most likely to occur and also shows how theories developed for particular species interactions may make studies investigating the ecological impacts of genetic variation a more predictive science.

opencc-zeroDec 2013View details →

Data from: Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities

1. It is well-known that vascular plants have species-specific effects on soil properties. However, little is known on how individual species forming biocrusts, communities dominated by lichens, mosses and cyanobacteria that are prevalent in many ecosystems world-wide, affect microbial communities and soil variables related to nutrient cycling. 2. We evaluated the relationship of six biocrust-forming lichens (Buellia epipolia, Diploschistes diacapsis, Fulgensia subbracteata, Psora decipiens, Squamarina cartilaginea and Squamarina lentigera) with microbial abundance and multiple variables associated with soil nitrogen (N), carbon (C) and phosphorus (P) cycling and storage. We also evaluated whether the composition of lichen tissues (contents in C, N, P and polyphenols) is related to the C, N, P availability and microbial abundance in soils. Finally, we assessed what lichen species positively and negatively relate to soil fertility compared to bare ground areas without biocrusts. 3. We found contrasted C, N, P availability and soil microbial abundance under the different biocrust-forming lichens. Interestingly, inorganic P and amino acids were the most important factors differentiating lichen microsites. These differences in nutrient availability seem to be related to the C, N and P composition of the lichen tissues. For example, soils under D. diacapsis and P. decipiens, which had the lowest and highest C, N and P contents in their tissues, respectively, had the lowest and highest nutrient availability, respectively. We also found contrasted soil microbes abundance under the different soil lichens. For instance, F. subbracteata and D. diacapsis were negatively related to the abundance of bacteria compared to bare ground areas. 4. Our results support the idea that, as found with vascular plants, biocrust-forming lichens have species-specific effects on soil microbial communities and C, N and P cycling. Thus, continuing considering biocrusts as a unique entity will only add confusion to our knowledge of how they control nutrient availability and microbial abundance in the ecosystems where this key community is prevalent.

opencc-zeroDec 2010View details →

Data from: Resource heterogeneity, soil fertility, and species diversity: effects of clonal species on plant communities

Spatial heterogeneity in soil resources is widely thought to promote plant species coexistence, and this mechanism figures prominently in resource-ratio models of competition. However, most experimental studies have found that nutrient enhancements depress diversity regardless of whether nutrients are uniformly or heterogeneously applied. This mismatch between theory and empirical pattern is potentially due to an interaction between plant size and the scale of resource heterogeneity. Clonal plants that spread vegetatively via rhizomes or stolons can grow large and may integrate across resource patches, thus reducing the positive effect of small-scale resource heterogeneity on plant species richness. Many rhizomatous clonal species respond strongly to increased soil fertility, and they have been hypothesized to drive the descending arm of the hump-shaped productivity-diversity relationship in grasslands. We tested whether clonals reduce species richness in a grassland community by manipulating nutrient heterogeneity, soil fertility, and the presence of rhizomatous clonal species in a 6-year field experiment. We found strong and consistent negative effects of clonals on species richness. These effects were greatest at high fertility and when soil resources were applied at a scale at which rhizomatous clonals could integrate across resource patches. Thus, we find support for the hypothesis that plant size and resource heterogeneity interact to determine species diversity.

Supplementary material 3 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249

Datafile 3

Supplementary material 1 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249

Datafile 1

Supplementary material 2 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249

Datafile 2

Supplementary material 5 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249

Table S1 and Figs S1–S4

Supplementary material 4 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249

Datafile 4

opencc-by-4.0Jun 2021View details →

Figure 6 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249

Figure 6 Taxonomic composition to family level of ECM fungi in gallery forest and woodlands. Abundance measured as fraction of reads (A) and richness measured as fraction of species hypotheses (SH) (B).

opencc-by-4.0Jun 2021View details →

Figure 3 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249

Figure 3 Species accumulation curves for each plot. Curves are based on SHs, by sequencing depth (A) and number of trees sampled (B), presented separately for three gallery forest sites (left panels) and six woodland sites (right panels). Points represent the observed species richness at the actual sequencing depth and trees sampled in A, B respectively. Thin lines represent the accumulation curve calculated by rarefaction (darker) and extrapolation (lighter); shaded regions represent the associated 95% confidence intervals. Dotted lines represent the asymptotic estimate for each site.