Analysis of complex trophic networks reveals the signature of land-use intensification on soil communities in agroecosystems.
Ontology highlight
ABSTRACT:
SUBMITTER: Bloor JMG
PROVIDER: S-EPMC8440573 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.
| S-EPMC6399230 | biostudies-literature
Project description:Soil viruses remain understudied when compared to virus found in aquatic ecosystems. Here, we investigate the ecological patterns of soil viral communities across various land use types encompassing forest, agricultural, and urban soil in Xiamen, China. We recovered 59,626 viral operational taxonomic units (vOTUs) via size-fractioned viromic approach with additional mitomycin C treatment to induce virus release from bacterial fraction. Our results show that viral communities are significantly different amongst the land use types considered. A microdiversity analysis indicates that selection act on soil vOTUs, resulting in disparities between land use associated viral communities. Soil pH is one of the major determinants of viral community structure, associated with changes of in-silico predicted host compositions of soil vOTUs. Habitat disturbance and variation of soil moisture potentially contribute to the dynamics of putative lysogenic vOTUs. These findings provide mechanistic understandings of the ecology and evolution of soil viral communities in changing environments.
| S-EPMC9556555 | biostudies-literature
Project description:Land-use intensification is a major driver of local species extinction and homogenization. Temperate grasslands, managed at low intensities over centuries harbored a high species diversity, which is increasingly threatened by the management intensification over the last decades. This includes key taxa like ants. However, the underlying mechanisms leading to a decrease in ant abundance and species richness as well as changes in functional community composition are not well understood. We sampled ants on 110 grassland plots in three regions in Germany. The sampled grasslands are used as meadows or pastures, being mown, grazed or fertilized at different intensities. We analyzed the effect of the different aspects of land use on ant species richness, functional trait spaces, and community composition by using a multimodel inference approach and structural equation models. Overall, we found 31 ant species belonging to 8 genera, mostly open habitat specialists. Ant species richness, functional trait space of communities, and abundance of nests decreased with increasing land-use intensity. The land-use practice most harmful to ants was mowing, followed by heavy grazing by cattle. Fertilization did not strongly affect ant species richness. Grazing by sheep increased the ant species richness. The effect of mowing differed between species and was strongly negative for Formica species while Myrmica and common Lasius species were less affected. Rare species occurred mainly in plots managed at low intensity. Our results show that mowing less often or later in the season would retain a higher ant species richness-similarly to most other grassland taxa. The transformation from (sheep) pastures to intensively managed meadows and especially mowing directly affects ants via the destruction of nests and indirectly via loss of grassland heterogeneity (reduced plant species richness) and increased soil moisture by shading of fast-growing plant species.
| S-EPMC6468076 | biostudies-literature
Project description:The interactions between soil invertebrates and land use and management are fundamental for soil quality assessment but remain largely unaddressed. The aim of this study was to evaluate the changes in soil arthropod community of an entisol brought about by different land use systems under semiarid climate in Pernambuco State, Brazil. The soil invertebrate community was sampled using pitfall traps from areas with eight vegetation types by the end of the austral winter. The land uses studied were native thorn forest plus seven agricultural fields planted with elephant grass, apple guava, passion fruit, carrot, maize, tomato, and green pepper. Native vegetation was considered as a reference, whereas the agricultural fields showed a range of soil use intensities. The abundance of organisms, the total and average richness, Shannon's diversity index, and the Pielou uniformity index were determined, and all of these were affected by several crop and soil management practices such as residue cover, weed control, and pesticide application. Our study found differences in community assemblages and composition under different land use systems, but no single taxa could be used as indicator of soil use intensity.
| S-EPMC4241259 | biostudies-other
Project description:Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. ?-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in ?-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing ?-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.
| S-EPMC3721119 | biostudies-literature
Project description:BACKGROUND: Fungi strongly influence ecosystem structure and functioning, playing a key role in many ecological services as decomposers, plant mutualists and pathogens. The Mediterranean area is a biodiversity hotspot that is increasingly threatened by intense land use. Therefore, to achieve a balance between conservation and human development, a better understanding of the impact of land use on the underlying fungal communities is needed. METHODOLOGY/PRINCIPAL FINDINGS: We used parallel pyrosequencing of the nuclear ribosomal its regions to characterize the fungal communities in five soils subjected to different anthropogenic impact in a typical mediterranean landscape: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards. Marked differences in the distribution of taxon assemblages among the different sites and communities were found. Data analyses consistently indicated a sharp distinction of the fungal community of the cork oak forest soil from those described in the other soils. Each soil showed features of the fungal assemblages retrieved which can be easily related to the above-ground settings: ectomycorrhizal phylotypes were numerous in natural sites covered by trees, but were nearly completely missing from the anthropogenic and grass-covered sites; similarly, coprophilous fungi were common in grazed sites. CONCLUSIONS/SIGNIFICANCE: Data suggest that investigation on the below-ground fungal community may provide useful elements on the above-ground features such as vegetation coverage and agronomic procedures, allowing to assess the cost of anthropogenic land use to hidden diversity in soil. Datasets provided in this study may contribute to future searches for fungal bio-indicators as biodiversity markers of a specific site or a land-use degree.
| S-EPMC3335027 | biostudies-literature
Project description:BackgroundSoil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks.ResultsWe showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses.ConclusionsOur findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.
| S-EPMC8740439 | biostudies-literature
Project description:Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.
| S-EPMC7562711 | biostudies-literature
Project description:To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
| S-EPMC6345909 | biostudies-literature
Project description:BackgroundChange in land use and management can impact massively on soil ecosystems. Ecosystem engineers and other functional biodiversity in soils can be influenced directly by such change and this in turn can affect key soil functions. Here, we employ meta-analysis to provide a quantitative assessment of the effects of changes in land use and land management across a range of successional/extensification transitions (conventional arable → no or reduced tillage → grassland → wooded land) on community metrics for two functionally important soil taxa, earthworms and fungi. An analysis of the relationships between community change and soil structural properties was also included.ResultsMeta-analysis highlighted a consistent trend of increased earthworm and fungal community abundances and complexity following transitions to lower intensity and later successional land uses. The greatest changes were seen for early stage transitions, such as introduction of reduced tillage regimes and conversion to grassland from arable land. Not all changes, however, result in positive effects on the assessed community metrics. For example, whether woodland conversion positively or negatively affects community size and complexity depends on woodland type and, potentially, the changes in soil properties, such as pH, that may occur during conversion. Alterations in soil communities tended to facilitate subsequent changes in soil structure and hydrology. For example, increasing earthworm abundances and functional group composition were shown to be positively correlated with water infiltration rate (dependent on tillage regime and habitat characteristics); while positive changes in fungal biomass measures were positively associated with soil microaggregate stability.ConclusionsThese findings raise the potential to manage landscapes to increase ecosystem service provision from soil biota in relation to regulation of soil structure and water flow.
| S-EPMC4219611 | biostudies-literature