Generalist taxa shape fungal ecological networks in cropping systems
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32542 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3349220_1.fastq.gz | Fastqsanger.gz | |||
| ERR3349220_2.fastq.gz | Fastqsanger.gz | |||
| ERR3349230_1.fastq.gz | Fastqsanger.gz | |||
| ERR3349230_2.fastq.gz | Fastqsanger.gz | |||
| ERR3349240_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 424 |
Similar Datasets
Project description:Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5-17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.
| S-EPMC8299105 | biostudies-literature
Project description:A major challenge for agriculture is to enhance productivity with minimum impact on the environment. Several studies indicate that cover crops could replace anthropogenic inputs and enhance crop productivity. However, so far, it is unclear if cover crop effects vary between different cropping systems, and direct comparisons among major arable production systems are rare. Here we compared the short-term effects of various cover crops on crop yield, nitrogen uptake, and weed infestation in four arable production systems (conventional cropping with intensive tillage and no-tillage; organic cropping with intensive tillage and reduced tillage). We hypothesized that cover cropping effects increase with decreasing management intensity. Our study demonstrated that cover crop effects on crop yield were highest in the organic system with reduced tillage (+24%), intermediate in the organic system with tillage (+13%) and in the conventional system with no tillage (+8%) and lowest in the conventional system with tillage (+2%). Our results indicate that cover crops are essential to maintaining a certain yield level when soil tillage intensity is reduced (e.g. under conservation agriculture), or when production is converted to organic agriculture. Thus, the inclusion of cover crops provides additional opportunities to increase the yield of lower intensity production systems and contribute to ecological intensification.
| S-EPMC5291223 | biostudies-literature
Project description:The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
| S-EPMC9133800 | biostudies-literature
Project description:In the dryland Pacific Northwest wheat cropping systems, no-till is becoming more prevalent as a way to reduce soil erosion and fuel inputs. Tillage can have a profound effect on microbial communities and soilborne fungal pathogens, such as Rhizoctonia. We compared the fungal communities in long-term no-till (NT) plots adjacent to conventionally tilled (CT) plots, over three years at two locations in Washington state and one location in Idaho, US. We used pyrosequencing of the fungal ITS gene and identified 422 OTUs after rarefication. Fungal richness was higher in NT compared to CT, in two of the locations. Humicola nigrescens, Cryptococcus terreus, Cadophora spp. Hydnodontaceae spp., and Exophiala spp. were more abundant in NT, while species of Glarea, Coniochaetales, Mycosphaerella tassiana, Cryptococcus bhutanensis, Chaetomium perlucidum, and Ulocladium chartarum were more abundant in CT in most locations. Other abundant groups that did not show any trends were Fusarium, Mortierella, Penicillium, Aspergillus, and Macroventuria. Plant pathogens such as Rhizoctonia (Ceratobasidiaceae) were not abundant enough to see tillage differences, but Microdochium bolleyi, a weak root pathogen, was more abundant in NT. Our results suggest that NT fungi are better adapted at utilizing intact, decaying roots as a food source and may exist as root endophytes. CT fungi can utilize mature plant residues that are turned into the soil with tillage as pioneer colonizers, and then produce large numbers of conidia. But a larger proportion of the fungal community is not affected by tillage and may be niche generalists.
| S-EPMC5595340 | biostudies-literature
Project description:Dennert et al. 2018 Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance
| PRJEB20139 | ENA
Project description:Our understanding regarding the influence of intensive agricultural practices, including cover cropping and tillage, on communities of arbuscular mycorrhizal fungi (AMF) is lacking. This would prove to be an obstacle in the improvement of current maize (Zea mays L.) production. Therefore, using amplicon sequencing, we aimed to clarify how AMF communities and their diversity in maize roots vary under different cover cropping systems and two types of tillage (rotary and no tillage). Two kinds of cover crops (hairy vetch and brown mustard) and fallow treatments were established with rotary or no tillage in rotation with maize crops. Tillage and no tillage yielded a set of relatively common AMF operational taxonomic units (OTUs) in the maize crops, representing 78.3% of the total OTUs. The percentage of maize crop OTUs that were specific to only tillage and no tillage were 9.6% and 12.0%, respectively. We found that tillage system significantly altered the AMF communities in maize roots. However, the AMF communities of maize crops among cover cropping treatments did not vary considerably. Our findings indicate that compared with cover cropping, tillage may shape AMF communities in maize more strongly.
| S-EPMC7125109 | biostudies-literature
Project description:Generalist species commonly have a fundamental role in ecosystems as they can integrate spatially distinct habitats and food-web compartments, as well as control the composition, abundance and behavior of organisms at different trophic levels. Generalist populations typically consist of specialized individuals, but the potential for and hence degree of individual niche variation can be largely determined by habitat complexity. We compared individual niche variation within three generalist fishes between two comparable lakes in the Czech Republic differing in macrophyte cover, i.e. macrophyte-rich Milada and macrophyte-poor Most. We tested the hypothesis that large individual niche variation among generalist fishes is facilitated by the presence of macrophytes, which provides niches and predation shelter for fish and their prey items. Based on results from stable nitrogen (δ15N) and carbon (δ13C) isotopic mixing models, perch (Perca fluviatilis L.) and rudd (Scardinius erythrophthalmus (L.)) showed larger individual variation (i.e., variance) in trophic position in Milada as compared to Most, whereas no significant between-lake differences were observed for roach (Rutilus rutilus (L.)). Contrary to our hypothesis, all the three species showed significantly lower individual variation in the relative reliance on littoral food resources in Milada than in Most. Rudd relied significantly more whereas perch and roach relied less on littoral food resources in Milada than in Most, likely due to prevalent herbivory by rudd and prevalent zooplanktivory by perch and roach in the macrophyte-rich Milada as compared to macrophyte-poor Most. Our study demonstrates how the succession of macrophyte vegetation, via its effects on the physical and biological complexity of the littoral zone and on the availability of small prey fish and zooplankton, can strongly influence individual niche variation among generalist fishes with different ontogenetic trajectories, and hence the overall food-web structures in lake ecosystems.
| S-EPMC5423621 | biostudies-literature
Project description:Multiple cropping, defined as harvesting more than once a year, is a widespread land management strategy in tropical and subtropical agriculture. It is a way of intensifying agricultural production and diversifying the crop mix for economic and environmental benefits. Here we present the first global gridded data set of multiple cropping systems and quantify the physical area of more than 200 systems, the global multiple cropping area and the potential for increasing cropping intensity. We use national and sub-national data on monthly crop-specific growing areas around the year 2000 (1998-2002) for 26 crop groups, global cropland extent and crop harvested areas to identify sequential cropping systems of two or three crops with non-overlapping growing seasons. We find multiple cropping systems on 135 million hectares (12% of global cropland) with 85 million hectares in irrigated agriculture. 34%, 13% and 10% of the rice, wheat and maize area, respectively are under multiple cropping, demonstrating the importance of such cropping systems for cereal production. Harvesting currently single cropped areas a second time could increase global harvested areas by 87-395 million hectares, which is about 45% lower than previous estimates. Some scenarios of intensification indicate that it could be enough land to avoid expanding physical cropland into other land uses but attainable intensification will depend on the local context and the crop yields attainable in the second cycle and its related environmental costs.
| S-EPMC7737095 | biostudies-literature
Project description:Insects use sensitive olfactory systems to detect relevant host volatiles and avoid unsuitable hosts in a complex environmental odor landscape. Insects with short lifespans, such as gall midges (Diptera: Cecidomyiidae), are under strong selection pressure to detect and locate suitable hosts for their offspring in a short period of time. Ephemeral gall midges constitute excellent models for investigating the role of olfaction in host choice, host shift, and speciation. Midges mate near their site of emergence and females migrate in order to locate hosts for oviposition, thus females are expected to be more responsive to olfactory cues emitted by the host compared to males. In this study, we explored the correlation between host choice and the function of the peripheral olfactory system in 12 species of gall midges, including species with close phylogenetic relationships that use widely different host plants and more distantly related gall midge species that use similar hosts. We tested the antennal responses of males and females of the 12 species to a blend of 45 known insect attractants using coupled gas chromatographic-electroantennographic detection. When the species-specific response profiles of the gall midges were compared to a newly generated molecular-based phylogeny, we found they responded to the compounds in a sex- and species-specific manner. We found the physiological response profiles of species that use annual host plants, and thus have to locate their host every season, are similar for species with similar hosts despite large phylogenetic distances. In addition, we found closely related species with perennial hosts demonstrated odor response profiles that were consistent with their phylogenetic history. The ecology of the gall midges affects the tuning of the peripheral olfactory system, which in turn demonstrates a correlation between olfaction and speciation in the context of host use.
| S-EPMC5891623 | biostudies-literature
Project description:IntroductionModern agriculture emphasizes the design of cropping systems using ecological function and production services to achieve sustainability. The functional characteristics of plants (grasses vs. legumes) affect changes in soil microbial communities that drive agroecosystem services. Information on the relationship between legume-grass mixtures and soil microorganisms in different ecological zones guides decision-making toward eco-friendly and sustainable forage production. However, it is still poorly understood how cropping patterns affect soil microbial diversity in alpine grasslands and whether this effect varies with altitude.MethodsTo fill this gap in knowledge, we conducted a field study to investigate the effects of growing oats (Avena sativa L.), forage peas (Pisum sativum L.), common cornflower (Vicia sativa L.), and fava beans (Vicia faba L.) in monocultures and mixtures on the soil microbial communities in three ecological zones of the high alpine zone.ResultsWe found that the fungal and bacterial community structure differed among the cropping patterns, particularly the community structure of the legume mixed cropping pattern was very different from that of monocropped oats. In all ecological zones, mixed cropping significantly (p < 0.05) increased the α-diversity of the soil bacteria and fungi compared to oat monoculture. The α-diversity of the soil bacteria tended to increase with increasing elevation (MY [2,513 m] < HZ [2,661 m] < GN [3,203 m]), while the opposite was true for fungi (except for the Chao1 index in HZ, which was the lowest). Mixed cropping increased the abundance of soil fungi and bacteria across ecological zones, particularly the relative abundances of Nitrospira, Nitrososphaera, Phytophthora, and Acari. Factors affecting the bacterial community structure included the cropping pattern, the ecological zone, water content, nitrate-nitrogen, nitrate reductase, and soil capacity, whereas factors affecting fungal community structure included the cropping pattern, the ecological zone, water content, pH, microbial biomass nitrogen, and catalase.DiscussionOur study highlights the variation in soil microbial communities among different in alpine ecological regions and their resilience to cropping systems. Our results also underscore that mixed legume planting is a sustainable and effective forage management practice for the Tibetan Plateau.
| S-EPMC10978683 | biostudies-literature