Nematode metabarcoding of apple orchards
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB55597 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13031600_1.fastq.gz | Fastqsanger.gz | |||
| ERR13031600_2.fastq.gz | Fastqsanger.gz | |||
| ERR13031601_1.fastq.gz | Fastqsanger.gz | |||
| ERR13031601_2.fastq.gz | Fastqsanger.gz | |||
| ERR13031602_1.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundDNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples.MethodsThe Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE).ResultsThese platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H') showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67-0.68; BC = 0.19-0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.
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Project description:Birds active in apple orchards in south-eastern Australia can contribute positively (e.g., control crop pests) or negatively (e.g., crop damage) to crop yields. Our study is the first to identify net outcomes of these activities, using six apple orchards, varying in management intensity, in south-eastern Australia as a study system. We also conducted a predation experiment using real and artificial codling moth (Cydia pomonella) larvae (a major pest in apple crops). We found that: (1) excluding birds from branches of apple trees resulted in an average of 12.8% more apples damaged by insects; (2) bird damage to apples was low (1.9% of apples); and (3) when trading off the potential benefits (biological control) with costs (bird damage to apples), birds provided an overall net benefit to orchard growers. We found that predation of real codling moth larvae was higher than for plasticine larvae, suggesting that plasticine prey models are not useful for inferring actual predation levels. Our study shows how complex ecological interactions between birds and invertebrates affect crop yield in apples, and provides practical strategies for improving the sustainability of orchard systems.
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Project description:The microbial communities in two apple orchards were characterised using amplicon-based metabarcoding. Samples were taken from tree station locations along a linear transect and from adjacent grass aisles, at both orchards. Comparison was made between the communities occurring at tree station locations and the grass aisles, and between orchards. Further discussion of these datasets is given in https://doi.org/10.1016/j.apsoil.2018.05.015 (Deakin et al., 2018).
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Project description:Characterising spatial microbial community structure is important to understand and explain the consequences of continuous plantation of one crop species on the performance of subsequent crops, especially where this leads to reduced growth vigour and crop yield. We investigated the spatial structure, specifically distance-decay of similarity, of soil bacterial and fungal communities in two long-established orchards with contrasting agronomic characteristics. A spatially explicit sampling strategy was used to collect soil from under recently grubbed rows of apple trees and under the grassed aisles. Amplicon-based metabarcoding technology was used to characterise the soil microbial communities. The results suggested that (1) most of the differences in soil microbial community structure were due to large-scale differences (i.e. between orchards), (2) within-orchard, small-scale (1-5 m) spatial variability was also present, but spatial relationships in microbial community structure differed between orchards and were not predictable, and (3) vegetation type (i.e. trees or grass and their associated management) can significantly alter the structure of soil microbial communities, affecting a large proportion of microbial groups. The discontinuous nature of soil microbial community structure in the tree stations and neighbouring grass aisles within an orchard illustrate the importance of vegetation type and allied weed and nutrient management on soil microbial community structure.
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Project description:Agricultural production in the Weibei rainfed highland, Northwest China, is challenged by severe drought and water shortages. While the land use pattern has shifted gradually from crop production to orchard farming in Weibei, little is known about the influence of fruit industry development on regional water resources and the rationality of planting orchards. Here, we characterized soil water depletion patterns in rainfed orchards and farmlands to evaluate the occurrence of soil desiccation under land use conversion from farmlands to orchards in Weibei. Soil moisture dynamics were monitored in the 0-150 cm soil profiles of different aged Red Fuji apple orchards (young: 7 years, mature: 13 years, old: 22 years) and long-term cultivated winter wheat fields. We measured soil moisture content by oven-drying method in the middle of each month during the growing season of apple trees (March-September 2019). The over-depletion and depletion of soil water were analyzed to evaluate water stress and differential water depletion by distinct vegetation, respectively. The soil desiccation index was used to determine the occurrence of dry soil layers. Water stress was only observed at the 0-70-cm soil depths in the old orchards (mid-June) and farmlands (mid-May-mid-July). Water depletion took place at deeper depths for longer periods in the older orchards than in the younger orchards. Soil desiccation was absent in the young orchards, with mild desiccation at the 0-80-cm soil depths in the mature and old orchards in mid-June. The desiccation intensity was mild at the 0-60-cm soil depths in mid-April-mid-May, intense at the 0-150-cm soil depths in mid-June, and moderate at the 20-150-cm soil depths in mid-July. Results of this study demonstrate the mitigation of water stress and soil desiccation following conversion from wheat fields to apple orchards, which verifies the rationality of planting orchards in the rainfed highland area. Our findings provide strong support for developing a novel model of agro-industrial development, ecological construction, and sustainable economy in the vast arid and semi-arid areas of Northwest China.
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Project description:Apples depend on insect pollination but intensification of agriculture jeopardizes pollination services in agroecosystems. Concerns about the dependency of crop pollination exclusively on honey bees increase the interest in agricultural practices that safeguard wild pollinators in agroecosystems. The purpose of the study was to assess the potential of floral resource provision in apple orchards to enhance the conservation of hymenopterous pollinating insects and potentially the pollination service to the crop. For this reason, flowering plant mixtures sown in patches inside apple orchards were tested against wild plant patches. Pollinator taxa recorded on the sown and wild plant patches were honey bees, wild bees (Andrena, Anthophora, Eucera, Halictus, Lasioglossum, Megachilidae on both; Systropha only on wild plants; Bombus, Hylaeus, Sphecodes, Nomada, Xylocopa only on sown mixture), syrphids, bee flies. The most abundant pollinator of apple was A. mellifera but wild bees were also recorded (Andrena, Anthophora, Bombus, Xylocopa, Lasioglossum, Megachilidae). The sown mixture attracted a more diverse taxa of pollinators and in greater numbers compared to the weed flora, but it did not have an effect on pollinators visiting apple flowers. Groundcover management with patches of suitable flowering mixtures can enhance pollinator conservation in apple orchards.
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