Find research datasets worth reusing

opencc-zeroDec 2014View details →

Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.

opencc-zeroDec 2021View details →

Long-term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

The coastal wetland is easily invaded by alien species due to its location in the land and sea transitional area. As a potential driving regeneration force, the soil seed bank is vital to community restoration and species diversity protection. To reveal the long-term S. alterniflora invasion impact on the soil seed banks and regenerated communities, we investigated the seed banks under the different vegetation types (S. alterniflora, Phragmites australis, Scirpus mariquete, ruderal and unvegetated site) and soil depths (0–5 cm and 5–10 cm) in the Chongming island coastal salt marsh wetland. The results showed that the soil seed bank richness and species density under different vegetation types were higher than aboveground vegetation, and those of 0–5 cm seed banks were higher than 5–10 cm, except for the unvegetated site. The species richness and the S. alterniflora seed proportion in the seed banks under the S. alterniflora communities (S.AS) were lower and larger, respectively, than other sites. The species composition between S.AS and the aboveground communities showed high similarity with aggregation phylogenetic structures in two soil depths. The seed bank variations at 0–5 cm and 5–10 cm depths were interpreted 3.03% and 2.25% by aboveground communities, while 4.92% and 5.55% were interpreted by soil microbial biomass. The SEM model explained 98.1% and 91.8% of the seed banks' richness at the 0–5 cm depth and 5–10 cm depth, respectively, and explained 98.8% and 46.1% of the seed banks' species density at the 0–5 cm depth and 5–10 cm depth, respectively. The aboveground vegetation biomass and abundance directly affected the 0–5 cm seed banks' richness and species density, while its height and biomass only affected the 5–10 cm seed banks' species density. The microbial biomass of the 0–10 cm soil depth indirectly affected the richness and species density of the 0-5 cm seed bank, and only affected the richness of the 5–10 cm seed bank. Soil physical and chemical properties only indirectly affected the 0–5 cm seed banks' species density. The results provided a reference for the ecological evaluation of the impacts of S. alterniflora invasion into the coastal salt marsh wetland of eastern China and guidance for the protection and restoration of the native plant communities.

opencc-zeroOct 2022View details →

Microbial community dynamics during decomposition of insect exuviae and frass in soil

As the mass-rearing industry of insects for food and feed is expected to grow, residual streams associated with this activity will become increasingly available. Before these residues can be used as organic amendments, more knowledge on the decomposition and dynamics of the involved microbial communities is needed. This study investigated decomposition, N-mineralization, and fungal/bacterial community composition during 16 weeks of incubation of exuviae and frass of black soldier fly, mealworm, and house cricket in arable soil. Decomposition of insect residues in litterbags was rapid, with more than 50% weight loss in 2 weeks. Accumulation of mineral-N from insect materials distributed in the soil was also highest during the first 2 weeks, but it was more profound for exuviae than their frass counterparts. Soil amendment with insect residues enriched soil microbial inhabitants belonging to Gammaproteobacteria, Bacilli, Actinobacteria, and Mortierellomycetes. Comparison of microbial community composition in soil amended with sterilized and nonsterilized mealworm exuviae indicated that the presence of microbial propagules in the exuviae had no significant influence on the composition of bacterial decomposers and a minor, but significant impact on fungal community composition. Overall, our results reveal a good prospect of using insect residual streams as soil amendment.

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".

opencc-by-4.0Jul 2024View details →

Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils.

This repository holds the final data products from metagenomics processing of bacteria and viruses from the article : "Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils" Contents:  <ul> <li>LU_metadata.csv: information on the samples</li> <li>soil_chemistry.txt: physicochemical information on samples</li> <li>*_len.csv: tables containing the length information for annotated genes, divided by database. These are used to calculate RPKM abundances from count tables. </li> <li>BACTERIA</li> <li>ko_table, ko_unknown, ko2level, ko_description: count table of KEGG annotations, total counts for unnanotated genes, match of ko number to level and description</li> <li>all_bracken.csv: count table of taxonomic bacterial annotations using kraken2 and bracken</li> <li>mags_tax.csv: taxonomy assignments to MAGs (metagenome assembled genomes)</li> <li>mags_count_table.csv: abundante table of MAGs in counts</li> <li>ags_result, gc_mean, gc_variance: functional traits results, average genome size, and gc content</li> <li>lu_c_count, lu_n_count, card_d0, metals_count_table: abundance tables of genes annotated with Cazy (carbon), Ncydb (nitrogen), CARD (antibiotic resistance genes), and Bacmet (heavy metal resistance genes)</li> <li>VIRUS</li> <li>amg_summary.csv: results from AMG annotation with DRAM-V, filtered to keep genes of interest</li> <li>genomad_virus_summary.tsv: viral taxonomy annotations with geNomad</li> <li>virus_len.txt: length of inferred viruses (used for calculation of RPKM from count tables)</li> <li>all_host_prediction_to_genus.csv: virus host annotation with IPhop</li> <li>final_checkv.tsv: table of final viral inferences with quality estimates</li> <li>viral_species_count_table.txt: abundance table of infered viral contigs in counts</li> </ul>

opencc-by-4.0Aug 2024View details →

Impact of transgenic maize Ruifeng125 on diversity and dy-namics of bacterial community in rhizosphere soil

With the development of commercialized planting of genetically modified crops, their ecological security risks remain a hot topic of public concern. Insect-resistant genetically modified maize Ruifeng125 which expressing a fusion Bt protein (Cry1Ab-Cry2Aj) has obtained the application safety certificate issued by the Chinese government. To determine the effects of Ruifeng125 on the diversity and dynamics of bacterial communities, the accumulation and degradation pattern of the fusion Bt protein in the rhizosphere soil of transgenic maize were detected firstly. Results showed that the contents of Bt protein varied significantly at different developmental stages, but after straw returning to the field, over 97% of Bt proteins has been degraded quickly at the early stages (≤ 10 d) and then they were degraded at a relative slow rate. In addition, the variations of bacterial community diversity in the rhizosphere soil were detected by 16S ribosomal RNA (Rrna) high-throughput sequencing technology. A total of 44 phyla, 435 families and 842 genera were obtained by 16S rRNA sequencing, among which Proteobacteria, Actinobacia, Acidobacter Acidobacterium and Chloroflexi were the dominant taxa. At the same developmental stage, no significant differences in soil bacterial diversity were detected between Ruifeng125 and its non-transgenic control variety. Further analysis revealed that developmental stage, rather than the transgenic event, made the greatest contribution for the changes in soil microbial diversity. This research provides important information for evaluating the impacts of Bt crops on the soil microbiome and establish a theoretical foundation for their environmental safety assessment.

opencc-by-4.0Oct 2024View details →

From soil to sediment: Bedform migration shapes microbial communities from eroding bank soil during terrestrial-aquatic regime shift [dataset]

This dataset contains raw data of metabolism measurements, microbial abundance, and nutrients that were assessed for the research paper entitled "From soil to sediment: Bedform migration shapes microbial communities from eroding bank soil during terrestrial-aquatic regime shift," which has been submitted to the Journal of Geophysics: Biogeosciences on October 19, 2024. Please note that raw sequencing data were already submitted to the NCBI library and are accessible via https://www.ncbi.nlm.nih.gov./sra/PRJNA1154565. The excel sheet (.xlsx) contains all relevant parameters that were used to detect the influence of environmental parameters on the microbial community structure, e.g. bacterial, fungal and algal abundance, nutrient concentrations, and final NCP and CR rates. The .zip archive contains all raw metabolism measurements during our experimental duration.

opencc-by-4.0Nov 2024View details →

Plant community composition and traits modulate the impacts of drought intensity on soil microbial community composition and function

Terrestrial ecosystems are increasingly threatened by extreme drought events. Soil microbial communities are central to terrestrial ecosystem function via their role in regulating biogeochemical cycling. Consequently, the impact of increasingly intense drought events on soil microbial communities will have knock-on effects for how ecosystems cope with climate change. In an outdoor grassland mesocosm experiment, we determined how increasing drought intensity affects bacterial and fungal community composition, and functioning, during and after drought. We also tested whether plant community resource acquisition strategy (fast- versus slow-strategy plant communities), plant community composition, and plant functional traits mediate soil microbial responses to increasing drought intensity. We found that increasing drought intensity markedly shifted bacterial and fungal community composition, and these effects persisted until the end of the experiment (two months after re-wetting). Bacterial and fungal communities that experienced severe droughts did not return to baseline composition, while those that experienced a mild drought did. Microbial community functioning (potential extracellular enzyme activity) was reduced at peak drought and shortly after re-wetting. While drought intensity effects on bacterial or fungal communities were insensitive to plant community resource acquisition strategy, functional group abundance (aboveground biomass of grass or forb plant species) composition (grass:forb ratio) and leaf traits (leaf dry matter content and leaf nitrogen concentration) explained significant variation in bacterial and fungal community composition during and after drought. Notably, plant community leaf dry matter content and soil nitrogen were the key factors mediating the effect of increasing drought intensity on microbial indicator taxa (ASVs). We conclude that increasing drought intensity affects grassland soil microbial communities during and after drought, and this impact is influenced by plant community composition and functional traits.

opencc-zeroDec 2015View details →

Data from: Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea

Plant–soil interactions are increasingly recognized to play a major role in terrestrial ecosystems functioning. However, few studies to date have focused on slow dynamic ecosystems such as forests. As they are vertically stratified by multiple vegetation strata, canopy tree removal by thinning operations could alter forest plant community through tree canopy opening. Very little is known about cascading effects on soil biodiversity. We conducted a large-scale, multi-site assessment of collembolan assemblage response to long-term canopy tree removal in sessile oak Quercus petraea temperate forests. A total of 33 experimental plots were studied covering a large gradient of canopy tree basal area, stand age and local abiotic contexts. Collembolan abundance strongly declined with canopy tree removal in early forest successional stage and this was mediated by negative effect of understory plant community composition changes, i.e. shift from moss and forb to tree seedling, fern, shrub and grass species. Negative effect of this composition shift on collembolan species richness was largely offset by positive effect of the increase in understory plant species richness. This gives support to both the plant mass-ratio and functional diversity hypotheses. Collembolan functional groups had contrasting response patterns, which were mediated by different ecological factors. Epedaphic (r-strategist) abundance and species richness increased with canopy tree removal in relation with the increase in understory plant species richness. In contrast, euedaphic (K-strategist) abundance and species richness declined with canopy tree removal in early forest successional stage in relation with changes in understory plant community composition and species richness, as well as microclimatic conditions. Overall, our study provides experimental evidence that forest plant community can be a strong driver of collembolan assemblages. It also emphasizes the role of trees as foundation species of forest ecosystems that can shape soil biodiversity through their regulation of understory plant community and ecosystem abiotic conditions.

opencc-zeroDec 2014View details →

Data from: Temporal dynamics of plant-soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant

1. Pathogens can accumulate on invasive plants over time, which could lead to population declines. The time required for these dynamics to occur is unknown and seldom addressed. Furthermore, no study has assessed plant-soil feedback while characterising plant pathogen and mutualist root fungal communities in the context of invasion time. 2. We used a plant-soil feedback study and 454 pyrosequencing to investigate pathogen accumulation over 100 years on a highly invasive plant in eastern North America that shows localised declines, Vincetoxicum rossicum (Apocynaceae). 3. We collected soil from five sites representing each of four invasion periods of V. rossicum across Ontario, Canada (old, ~100 years; intermediate, 50-60 years; young, <12 years; and uninvaded), and grew V. rossicum in these soils in a glasshouse study. Our hypothesis was that plants grown in soils invaded for longer periods of time would experience less positive feedbacks compared to those grown in more recently invaded or uninvaded soils. We collected roots of V. rossicum from the invasion periods and performed 454 pyrosequencing targeting fungi. We hypothesised that the abundance and richness of fungi that are known plant pathogens would be higher in roots from older invasions compared to more recent invasions. 4. Contrasting with our hypothesis, V. rossicum experienced overall growth promotion due to soil biota, regardless of invasion period. Vincetoxicum rossicum roots were colonised by a large number of fungal taxa, including many known plant pathogens or mutualistic arbuscular mycorrhizal fungi. However, we found no evidence of pathogen accumulation in older invaded sites in terms of species composition, richness or abundance. 5. Synthesis: Our consistent results in the glasshouse and the field highlight the strength of combining high-throughput sequencing data with plant-soil feedback experiments. We showed that the roots of Vincetoxicum rossicum (Apocynaceae) were colonised by many fungal taxa, but found no evidence for changes in plant growth or accumulation of fungal pathogens with longer invasion time. High pathogen loads may not lead to concurrent declines in invasive plants. Plant invasions, as demonstrated by V. rossicum, may be unpredictable in their ability to accumulate pathogens capable of leading to population declines.

opencc-zeroDec 2014View details →

Data from: Reducing soil erosion by improving community functional diversity in semi-arid grasslands

1. Great efforts have been made to control soil erosion by restoring plant communities in degraded ecosystems world-wide. However, soil erosion has not been substantially reduced mainly because current restoration strategies lead to large areas of mono-specific vegetation, which are inefficient in reducing soil erosion because of their simple canopy and root structure. Therefore, an advanced understanding of how community functional composition affects soil erosion processes, as well as an improved restoration scheme to reduce soil erosion, is urgently needed. 2. We investigated the effect of community functional composition on soil erosion in restored semi-arid grasslands on the Loess Plateau of China. Community functional composition of 16 restored grasslands was quantified by community-weighted mean (CWM) and functional diversity (FD) trait values, which were calculated from nine plant functional traits of thirteen locally dominant plant species. Species richness and evenness were also measured. Soil erosion rates were measured using standard erosion plots. The multimodel inference approach was used to estimate the direction and the relative importance of these biodiversity indices in reducing soil erosion. 3. A robust and strong negative effect of functional divergence (FDiv) on soil erosion was found. The prevalence of particular trait combinations can also decrease soil erosion. The greatest control over soil erosion was exerted when the community mean root diameter was small and the root tensile strength was great. 4. Synthesis and applications: These findings imply that community functional diversity plays an important role in reducing soil erosion in semi-arid restored grasslands. This means that current restoration strategies can be greatly improved by incorporating community functional diversity into restoration design. We propose a trait-based restoration framework for reducing soil erosion, termed 'SSM' (Screening–Simulating–Maintaining). SSM aims to translate the target of community functional diversity into community assemblages that can be manipulated by practitioners. Based on this framework, a comprehensive procedure, highlighting functional diversity as the primary concern in determining optimal community assemblages, was developed to meet the pressing need for more effective restoration strategies to reduce soil erosion.

opencc-zeroJul 2021View details →

Drivers of soil microbial community assembly during recovery from selective logging and clear cutting

Despite important progress in understanding the impacts of forest clearing and logging on aboveground communities, how these disturbances affect soil microbial β-diversity and the ecological processes driving microbial assemblages are poorly understood. Further, whether and how the microbial shifts affect vegetation composition and diversity during recovery of post-logged forests remain elusive. 2. Using a spatial grid experiment design in a primary tropical forest intermixed with post-logged patches naturally recovered for half century in Hainan Island, China, we characterized and explained the distance-decay relationships of soil microbial similarities in primary, selectively logged and clear cut forests. 3. Selectively logged sites showed a lower spatial turnover rate of bacterial assemblages based on phylogenetic and taxonomic β-diversity, but a higher spatial turnover rate of fungal assemblages based on phylogenetic β-diversity, suggesting a higher level of phylogenetic variability in fungal composition. Clear cut sites showed lower spatial turnover for both bacterial and fungal assemblages based on the two β-diversity, indicating community homogenization. Main drivers of microbial assemblages shifted from soil properties in primary forest to tree composition in selectively logged sites, whereas microbial-tree associations declined in clear cut sites, leading to stochastically organized microbial assemblages. 4. Synthesis and applications. The increased fungal phylogenetic turnover with tree turnover following selective logging promotes unassisted recovery of plant diversity. In contrast, the decoupling of tree and microbial turnover following clear-cutting suggests restoration approaches based on tree planting, and tree species that have strong associations with bulk soil microbial community should be considered. Our findings advance the understanding of spatial patterns, processes, and drivers of soil microbial assemblages in parallel with tree community recovery during regeneration of post-logged tropical forests, and highlight the importance of coupling assemblage patterns between tree and soil fungal communities for conserving tropical forest biodiversity.12-Jul-2021 --

opencc-zeroJul 2022View details →

Data from: An inventory of the foliar, soil, and dung arthropod communities in pastures of the Southeastern United States

Grassland systems constitute a significant portion of the land area in the U.S. and as a result harbors significant arthropod biodiversity. During this time of biodiversity loss around the world, bioinventories of ecologically important habitats serve as important indicators for the effectiveness of conservation efforts. We conducted a bioinventory of the foliar, soil, and dung arthropod communities in 10 cattle pastures located in the southeastern U.S. during the 2018 grazing season. In sum, 126,251 arthropod specimens were collected. From the foliar community, 13 arthropod orders were observed, with the greatest species richness found in Hymenoptera, Diptera, and Hemiptera. The soil-dwelling arthropod community contained 18 orders. The three orders comprising the highest species richness were Coleoptera, Diptera, and Hymenoptera. Lastly, 12 arthropod orders were collected from cattle dung, with the greatest species richness found in Coleoptera, Diptera, and Hymenoptera. Herbivores were the most abundant functional guild found in the foliar community, and predators were most abundant in the soil and dung communities. Arthropod pests constituted a small portion of the pasture arthropod communities, with 1.01%, 0.34%, and 0.46% pests found in the foliar, soil, and dung communities, respectively. While bioinventories demand considerable time, energy, and resources to accomplish, the information from these inventories has many uses for conservation efforts, land management recommendations, and the direction of climate change science.

opencc-zeroSep 2021View details →

Unaltered soil microbial community composition, but decreased metabolic activity in a semi-arid grassland after two years of passive experimental warming

Soil microbial communities regulate soil carbon feedbacks to climate warming through microbial respiration (i.e. metabolic rate). A thorough understanding of the responses of composition, biomass and metabolic rate of soil microbial community to warming is crucial to predict soil carbon stocks in a future warmer climate. Therefore, we conducted a field manipulative experiment in a semi-arid grassland on the Loess Plateau of China to evaluate the responses of the soil microbial community to increased temperature from April 2015 to December 2017. Soil temperature was 2.0 oC higher relative to the ambient when open-top chambers (OTCs) were used. Warming did not affect microbial biomass or the composition of microbial functional groups. However, warming significantly decreased microbial respiration, directly resulting from soil pH decrease driven by the co-mediation of aboveground biomass increase, inorganic nitrogen increase and moisture decrease. These findings highlight that the soil microbial community structure of semi-arid grasslands resisted the short-term warming by 2 oC, although its metabolic rate declined.

opencc-zeroOct 2021View details →

Is the age of plant communities predicted by the age, stability and soil composition of the underlying landscapes? An investigation of OCBILs

Old, climatically buffered, infertile landscapes (OCBILs) have been hypothesized to harbour an elevated number of persistent plant lineages and are predicted to occur across different parts of the globe, interspersed with other types of landscapes. We tested whether the mean age of a plant community is associated with occurrence on OCBILs, as predicted by climatic stability and poor soil environments. Using digitized occurrence data for seed plants occurring in Australia (7033 species), sub-Saharan Africa (3990 species) and South America (44 482 species), regions that comprise commonly investigated OCBILs (Southwestern Australian Floristic Region, Greater Cape Floristic Region and campos rupestres), and phylogenies pruned to match the species occurrences, we tested for associations between environmental data (current climate, soil composition, elevation and climatic stability) and two novel metrics developed here that capture the age of a community (mean tip length and mean node height). Our results indicate that plant community ages are influenced by a combination of multiple environmental predictors that vary globally; we did not find statistically strong associations between the environments of OCBIL areas and community age, in contrast to the prediction for these landscapes. The Cape Floristic Region was the only OCBIL that showed a significant, although not strong, overlap with old communities.

opencc-zeroOct 2021View details →

Data for: Plant-soil biota interactions explain shifts in plant community composition under global change

1. Plant-soil biota interactions play a crucial role in the assembly of plant communities and the maintenance of plant species diversity. However, few studies have tested how the effect of soil biota on plant species and communities depend on environmental context and whether shifts in plant community composition caused by environmental change are associated with variation in plant-soil biota interactions. 2. We combined a field experiment in a Tibetan alpine meadow and a greenhouse experiment with factorial combinations of nitrogen (N) enrichment and warming to examine the role of plant-soil biota interactions in plant community dynamics. 3. The results showed that plant relative abundances were negatively correlated with the net effects of soil biota on plant growth but only under ambient field conditions. Warming and N-enrichment alleviated the negative soil biota effects in the greenhouse, and changed plant community composition and reduced species diversity in the field. Importantly, changes in soil biota effects on plant growth were positively correlated with changes in plant relative abundances caused by warming and N-enrichment in field. In a parallel field experiment, the diversity of mycorrhizal fungi increased while the diversity of fungal pathogens remained unchanged under warming and N-enrichment, indicating that soil biodiversity may play a critical role in plant responses to environmental change. 4. This study empirically demonstrates that altered plant-soil biota interactions explain shifts in plant community composition under global change, providing new insights into the mechanisms of diversity loss in a changing world.