Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth

Manching, Heather C.; Carlson, Kara B; Kosowsky, Sean; Smitherman, C. Tyler; Stapleton, Ann E.

doi:10.12688/f1000research.12490.3

Cited by 13 publications

(6 citation statements)

References 60 publications

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“…The moderate but significant effect of management regime on soil prokaryotic communities was consistent with results of a previous study that compared organic and conventional management systems . As with fungal communities, changes in aboveground and root prokaryotic communities based on plant growth stage and sampling timepoint are consistent with the results of previous studies on maize and rice (Manching et al, 2017;Edwards et al, 2018). Differences in assembly between above and belowground tissues may alter the community's ability to respond to agricultural management and plant growth.…”

Section: Discussionsupporting

confidence: 86%

Crop Management Impacts the Soybean (Glycine max) Microbiome

et al. 2020

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Soybean (Glycine max) is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop. Various benefits have been demonstrated for alternative management systems, but their effects on soybean-associated microbial communities are not well-understood. In order to better understand the impact of crop management systems on the soybean-associated microbiome, we employed DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) region and 16S rRNA genes to analyze fungal and prokaryotic communities associated with soil, roots, stems, and leaves. Soybean plants were sampled from replicated fields under long-term conventional, no-till, and organic management systems at three time points throughout the growing season. Results indicated that sample origin was the main driver of beta diversity in soybean-associated microbial communities, but management regime and plant growth stage were also significant factors. Similarly, differences in alpha diversity are driven by compartment and sample origin. Overall, the organic management system had lower fungal and bacterial Shannon diversity. In prokaryotic communities, aboveground tissues were dominated by Sphingomonas and Methylobacterium while belowground samples were dominated by Bradyrhizobium and Sphingomonas. Aboveground fungal communities were dominated by Davidiella across all management systems, while belowground samples were dominated by Fusarium and Mortierella. Specific taxa including potential plant beneficials such as Mortierella were indicator species of the conventional and organic management systems. No-till management increased the abundance of groups known to contain plant beneficial organisms such as Bradyrhizobium and Glomeromycotina. Network analyses show different highly connected hub taxa were present in each management system. Overall, this research demonstrates how specific long-term cropping management systems alter microbial communities and how those communities change throughout the growth of soybean.

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Section: Discussionsupporting

confidence: 86%

Crop Management Impacts the Soybean (Glycine max) Microbiome

et al. 2020

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“…In particular, we have shown a role for temporal variation, alone and in interaction with habitat and host species, as an important driver of bacterial community composition variation, especially in the phyllosphere. While succession of microbial communities in the phyllosphere has been documented previously ( Redford and Fierer, 2009 ; Wagner et al, 2016 ; Manching et al, 2017 ), here we have shown that even in a rotation of annual crops, the patterns of bacterial succession within and among years are an important driver of community structure.…”

Section: Discussionsupporting

confidence: 65%

Neonicotinoid Seed Treatments Have Significant Non-target Effects on Phyllosphere and Soil Bacterial Communities

2021

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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.

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“…After their arrival on the leaf, microorganisms face host and environmental factors that can act as an assembly filter by either supporting or preventing establishment (Figure 1). Such filtering is consistent with communities that track leaf traits over time, as well as with repeated associations of microorganisms across host replicates and seasons (40,89). Host filtering may be passive, with microbial taxa succeeding or failing based on the suitability of leaf conditions or ability to handle the host immune system.…”

Section: Introduction 1foliar Microbiomes As Extended Plant Phenotype...mentioning

confidence: 53%

Extension of Plant Phenotypes by the Foliar Microbiome

Hawkes

Kjøller

Raaijmakers

et al. 2021

Annu. Rev. Plant Biol.

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The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.

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Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth

Cited by 13 publications

References 60 publications

Crop Management Impacts the Soybean (Glycine max) Microbiome

Crop Management Impacts the Soybean (Glycine max) Microbiome

Neonicotinoid Seed Treatments Have Significant Non-target Effects on Phyllosphere and Soil Bacterial Communities

Extension of Plant Phenotypes by the Foliar Microbiome

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