Effect of Fungicide Application on Lowbush Blueberries Soil Microbiome (original) (raw)
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Phytobiomes
We examined the differences between bacterial and eukaryotic soil communities associated with natural and managed habitats of wild blueberry, Vaccinium angustifolium. In total, 138 bacterial and 130 eukaryotic soil and rhizosphere communities across seven blueberry fields, all established at least 30 years ago and from two forest areas adjacent to some of these fields, were analyzed. We analyzed correlations between soil chemical factors and the structure of eukaryotic and bacterial communities, including differences in the microbiome between bulk and rhizosphere soils, and between rhizospheres of plants growing in natural and managed habitats. Characterization of a broad selection of fields across the province of Nova Scotia, Canada, allowed us to tentatively identify specific signatures from several distinct soil niches. Our data indicate that bacterial and eukaryotic communities differ in how they correlate with soil chemical properties. Also, while eukaryotic communities correla...
Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome
Frontiers in Microbiology
A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to hostplant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plantmicrobe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.
Horticulture Research, 2015
A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils, which was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. Amplicon-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline. A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies; two of the four sites had a yield-decline problem, the other two did not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative abundance of individual OTUs was statistically compared for differences between samples from sites with or without yield decline. A total of 721 individual comparisons were statistically significant-involving 366 unique bacterial and 44 unique fungal OTUs. Based on further selection criteria, we focused on 34 bacterial and 17 fungal OTUs and found that yield decline resulted probably from one or more of the following four factors: (1) low abundance of Bacillus and Pseudomonas populations, which are well known for their ability of supressing pathogen development and/or promoting plant growth; (2) lack of the nematophagous fungus (Paecilomyces species); (3) a high level of two non-specific fungal root rot pathogens; and (4) wet soil conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes.
Agronomy, 2022
Decline disease causes serious damage to bayberry, but the reasons behind this disease are not completely understood, although fungal pathogenicity factors have been proposed. Our past studies have identified that the adversity of this disease is linked to the application of soil fungicide. The objective of this study is to explore the mechanism and alleviation effect of the use of the fungicide prochloraz in this disease by investigating the plant and soil parameters. The results of the current study reveal that the application of prochloraz could improve the tree vigor and fruit quality of decline-diseased bayberry. The beneficial effect of prochloraz on plant growth and fruit quality may be associated with its influence on the rhizosphere soil properties and soil microbiota. Indeed, the application of prochloraz was shown to significantly affect the relative abundance and diversity of the rhizosphere soil microbiota, with it having a greater effect on bacteria than on fungi. Furt...
Scientific Reports
Despite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect....
Frontiers in Microbiology
IntroductionThe multifunctionality of microorganisms, including entomopathogenic fungi, represents a feature that could be exploited to support the development, marketing, and application of microbial-based products for plant protection. However, it is likely that this feature could affect the composition and dynamics of the resident soil microorganisms, possibly over a longer period. Therefore, the methodology utilized to evaluate such impact is critical for a reliable assessment. The present study was performed to evaluate the impact of strains of Beauveria brongniartii and Beauveria bassiana on soil bacterial and fungal communities using an approach based on the terminal restriction fragment polymorphism (T-RFLP) analysis.Materials and methodsSoil samples in the vicinity of the root system were collected during a 3-year period, before and after the bioinocula application, in two organic strawberry plantations. Specific primers were used for the amplification of the bacterial 16S ...
Fungicide impacts on microbial communities in soils with contrasting management histories
Chemosphere, 2007
The impacts of the fungicides azoxystrobin, tebuconazole and chlorothalonil on microbial properties were investigated in soils with identical mineralogical composition, but possessing contrasting microbial populations and organic matter contents arising from different management histories. Degradation of all pesticides was fastest in the high OM/biomass soil, with tebuconazole the most persistent compound, and chlorothalonil the most readily degraded. Pesticide sorption distribution coefficient (K d ) did not differ significantly between the soils. Chlorothalonil had the highest K d (97.3) but K d for azoxystrobin and tebuconazole were similar (13.9 and 12.4, respectively). None of the fungicides affected microbial biomass in either soil. However, all fungicides significantly reduced dehydrogenase activity to varying extents in the low OM/biomass soil, but not in the high OM/biomass soil. The mineralization of subsequent applications of herbicides, which represents a narrow niche soil process was generally reduced in both soils by azoxystrobin and chlorothalonil. 16S rRNA-PCR denaturing gradient gel electrophoresis (DGGE) indicated that none of the fungicides affected bacterial community structure. 18S rRNA PCR-DGGE analysis revealed that a small number of eukaryote bands were absent in certain fungicide treatments, with each band being specific to a single fungicide-soil combination. Sequencing indicated these represented protozoa and fungi. Impacts on the specific eukaryote DGGE bands showed no relationship to the extent to which pesticides impacted dehydrogenase or catabolism of herbicides.
Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing
PLoS ONE, 2014
Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ,994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and nonsuppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.
Agriculture, Ecosystems & Environment, 2009
Cabbage seedpod weevil (Ceutorhynchus obstricus (Marsham)) has become a major pest of canola (Brassica spp.) in western Canada (Dosdall et al., 2002), often warranting chemical control (Cá rcamo et al., 2005). Two insecticides that are registered for use to control this pest in Canada are l-cyhalothrin (Matador 1) and deltamethrin (Decis 5EC 1). The same insecticidal compounds can be applied to control other damaging insect pest infestations in canola, including lygus bugs (Lygus spp.), bertha armyworm (Mamestra configurata (Walker), and diamondback moth (Plutella xylostella (L.)) (Anonymous, 2008). Scelerotinia stem rot (caused by Sclerotinia sclerotiorum (Lib) de Bary) is a major canola disease in western Canada (Turkington and Morrall, 1993; Bailey et al., 2003). Because cultural control measures such as crop rotation and sanitization are relatively ineffective (Williams and Stelfox, 1980), and management by canola host resistance has been difficult (Morrall and Dueck, 1982), effective stem rot control has been achieved by application of fungicides such as vinclozolin (Ronilan 1) and iprodione (Rovral Flo 1) (Anonymous, 2008). These fungicides also control alternaria blackspot, which is also an important disease affecting yield, pod shattering and green seed counts (Bailey et al., 2003) and is caused by Alternaria brassicae (Berk.) Sacc., A. brassicicola (Schwein.) Wiltshire, and A. raphani (Groves and Skolko). Information regarding non-target effects of these insecticides and fungicides on soil microorganisms in western Canada is required. Most field studies on fungicide or insecticide effects indicate that when they are applied at recommended rates, they usually have no significant effects or have transitory effects on soil microbial characteristics (Ahtiainen et al., 2003; Griffiths et al., 2006; Vig et al., 2008). In a study of the effects of 19 years of cumulative annual field applications of five pesticides, either singly or in combination at recommended or slightly above recommended rates, Hart and Brookes (1996) reported no measurable harmful effects on soil microbial biomass or its activity (C or N