Dataset Information

Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time.

ABSTRACT:

Background

Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited number incorporating temporal monitoring. We used 16S rRNA gene amplicon sequencing to investigate bacterial community temporal dynamics and community assembly processes on the leaves and fruit, and in the soil of 12 kiwifruit orchards across a cropping season in New Zealand.

Results

Community composition significantly differed (P < 0.001) among the three sample types. However, the communities in the phyllosphere substrates more closely resembled each other, relative to the communities in the soil. There was more temporal stability in the soil bacterial community composition, relative to the communities residing on the leaves and fruit, and low similarity between the belowground and aboveground communities. Bacteria in the soil were more influenced by deterministic processes, while stochastic processes were more important for community assembly in the phyllosphere.

Conclusions

The higher temporal variability and the stochastic nature of the community assembly processes observed in the phyllosphere communities highlights why predicting the responsiveness of phyllosphere communities to environmental change, or the likelihood of pathogen invasion, can be challenging. The relative temporal stability and the influence of deterministic selection on soil microbial communities suggests a greater potential for their prediction and reliable manipulation.

SUBMITTER: Louisson Z

PROVIDER: S-EPMC10463660 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Publications

Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time.

Louisson Ziva Z Ranjard Louis L Buckley Hannah L HL Case Bradley S BS Lear Gavin G

Environmental microbiome 20230824 1

<h4>Background</h4>Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited number incorporating temporal monitoring. We used 16S rRNA gene amplicon sequencing to investigate bacterial community temporal dynamics and community assembly processes on the leaves and fruit, and in the soil of 12 kiwifruit orchards across a cropping season in New Zealand.< ...[more]

PMID: 37620948

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Project description:The phyllosphere and soil are dynamic habitats for microbial communities. Non-pathogenic microbiota, including leaf and soil beneficial bacteria, plays a crucial role in plant growth and health, as well as in soil fertility and organic matter production. In sustainable agriculture, it is important to understand the composition of these bacterial communities, their changes in response to disturbances, and their resilience to agricultural practices. Widespread pesticide application may have had non-target impacts on these beneficial microorganisms. Neonicotinoids are a family of systemic insecticides being vastly used to control soil and foliar pests in recent decades. A few studies have demonstrated the long-term and non-target effects of neonicotinoids on agroecosystem microbiota, but the generality of these findings remains unclear. In this study, we used 16S rRNA gene amplicon sequencing to characterize the effects of neonicotinoid seed treatment on soil and phyllosphere bacterial community diversity, composition and temporal dynamics in a 3-year soybean/corn rotation in Quebec, Canada. We found that habitat, host species and time are stronger drivers of variation in bacterial composition than neonicotinoid application. They, respectively, explained 37.3, 3.2, and 2.9% of the community variation. However, neonicotinoids did have an impact on bacterial community structure, especially on the taxonomic composition of soil communities (2.6%) and over time (2.4%). They also caused a decrease in soil alpha diversity in the middle of the growing season. While the neonicotinoid treatment favored some bacterial genera known as neonicotinoid biodegraders, there was a decline in the relative abundance of some potentially beneficial soil bacteria in response to the pesticide application. Some of these bacteria, such as the plant growth-promoting rhizobacteria and the bacteria involved in the nitrogen cycle, are vital for plant growth and improve soil fertility. Overall, our results indicate that neonicotinoids have non-target effects on phyllosphere and soil bacterial communities in a soybean-corn agroecosystem. Exploring the interactions among bacteria and other organisms, as well as the bacterial functional responses to the pesticide treatment, may enhance our understanding of these non-target effects and help us adapt agricultural practices to control these impacts.

Project description:Living cover is an important management measure for orchards in China, and has certain influences on soil properties, microorganisms, and the micro-ecological environment. However, there are few studies on the effects of living cover on the soil changes in hazelnut orchards. In this study, we compared the soils of living cover treatments with Vulpia myuros and the soils of no cover treatments, and analyzed the observed changes in soil properties, microorganisms, and microbial functions by using high-throughput ITS rDNA and 16S rRNA gene Illumina sequencing. The results demonstrated that the total organic carbon content in the 20-40 cm deep soils under the living cover treatments increased by 32.87 and 14.82% in May and July, respectively, compared with those under the no cover treatments. The living cover treatment with V. myuros also significantly increased the contents of total phosphorus (TP), total nitrogen (TN), available phosphorus (AP), and available potassium (AK) in the soil samples. Moreover, the influence of seasons was not as significant as that of soil depth. The living cover treatment also significantly improved the soil enzyme activity levels. The results demonstrated that Ascomycota, Mortierellomycota and Basidiomycota were the dominant fungal phyla in all samples, while Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, and Chloroflexi were the dominant bacterial phyla, but the different treatments impacted the compositions of fungal and bacterial communities. Principal component analysis (PCA) showed that living cover with V. myuros significantly changed the soil fungal community structures whereas the bacterial community structures may be more sensitive to seasonal changes. At the microbial functional level, the living cover treatment increased the fungal operational taxonomic units (OTUs) of symbiotrophs and decreased that of pathotrophs. According to this study, we believe that the application of a living cover with V. myuros has a favorable regulating influence on soil properties, microbial communities and microbial function. This treatment can also reduce the use of herbicides, reduce the cost of orchard management, and store more carbon underground to achieve sustainable intensification of production in hazelnut orchards, so it can be considered as a management measure for hazelnut orchards.

Dataset Information

Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time.

Background

Results

Conclusions

Publications

Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time.

Similar Datasets

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