699 research outputs found
Coming of age for <i>Microbiome </i>gene breeding in plants
No full textThe plant microbiota can complement host functioning, leading to improved growth and health under unfavorable conditions. Microbiome engineering could therefore become a transformative technique for crop production. Microbiome genes, abbreviated as M genes, provide valuable targets for shaping plant-associated microbial communities.</p
Native fungal community remains resilient during bioremediation of DBP pollution by exogenous Gordonia phthalatica QH-11T
No full textMicrobial bioremediation is a highly effective method to degrade phthalates in the environment. However, the response of native microbial communities to the exogenously introduced microorganism remains unknown. In this study, the native fungal community was monitored by amplicon sequencing of the fungal ITS region during the restoration process of the di-n-butyl phthalate (DBP)-contaminated soils with Gordonia phthalatica QH-11T. Our results showed that the diversity, composition, and structure of the fungal community in the bioremediation treatment did not differ from the control, and no significant correlations were found between number of Gordonia and variation of fungal community. It was also observed that DBP pollution initially increased the relative abundance of plant pathogens and soil saprotrophs first, but their proportions returned to the initial level. Molecular ecological network analysis showed that DBP pollution increased the network complexity, while the network was not significantly altered by bioremediation. Overall, the introduction of Gordonia was shown to not have a long-term impact on the native soil fungal community. Therefore, this restoration method can be considered safe in terms of soil ecosystem stability. The present study provides a deeper insight into the effect of bioremediation on fungal communities and provides an extended basis to further explore the ecological risks of introducing exogenous microorganisms
Rhizosphere bacteria show a stronger response to antibiotic-based biopesticide than to conventional pesticides
No full textThe plant microbiota can substantially contribute to various functions related to host health, fitness, and productivity. Therefore, maintaining the integrity of the microbiota is beginning to be seen as a crucial factor in modern agriculture. Here, we evaluated the effects of two chemical pesticides (azoxystrobin and carbendazim) and an antibiotic-based biopesticide (wuyiencin) on the rhizosphere microbiome of tomato plants. It was found that all treatments resulted in changes in the bacterial community structure to varying degrees. The most pronounced changes were observed with the biopesticide, which resulted in an enrichment of Streptomyces in the microbiome. In contrast, the relative abundance of Actinobacteria decreased in samples that were treated with low and high dosages of carbendazim. Clostridia were enriched after the applications of azoxystrobin and wuyiencin. When functioning of the microbiome was assessed, it was shown that genes encoding multidrug efflux pumps and ABC transporters related to nutrient uptake were enriched. This enrichment is likely to overcome potentially negative effects linked to the exposure to the employed substances. The study provides new insights into the potential of different pesticides to modulate native plant microbiomes, and thus highlights the importance to include such evaluations when new active agents are developed
Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance
No full textBackground:
Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant’s defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland.
Results:
The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants.
Conclusion:
Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering
Microbiome succession during apple fruit development: healthy and pathological microbial assemblages
No full textThe surface and internal tissues of fruits host diverse microbial communities but the functional role of this microflora, outside of pathogenic species, in fruit health and quality are largely unknown. The recent use of universal primer sets and advanced sequencing technologies, however, has greatly increased our understanding of these microbial communities without the need to culture them. This is fostering a paradigm shift that views an organism and its microbiota as a single entity (metaorganism). We present our current understanding of the microbiome assembly in apple fruit and its implication on postharvest pathology. We first describe the initial microbial colonization and establishment in flowers, as well as the spatial and temporal community dynamics during fruit development. We then elucidate the patterns of succession that take place in the fruit microbiome as it develops and matures in the field, and subsequently after harvest and during cold storage. Next, we discuss the crucial need to identify species comprising the core microbiome and the need to conduct functional analysis of networks and the cross-talk between microbial components. We then discuss the utilization of this information for the practical development of targeted and precise biological control strategies against postharvest diseases and highlight the opportunities and challenges that exist for designing and manipulating the fruit microbiome. Lastly, topics of research that will enable a paradigm shift in fruit management are discussed in which a fruit and its dynamic microbiota are viewed as one biological entity
Wild again: recovery of a beneficial <i>Cannabis </i>seed endophyte from low domestication genotypes
No full textBackground: beyond carrying the plant embryo, seeds harbour intricate microbial communities whose transmission across successive plant generations can significantly influence the ecological and evolutionary dynamics of plant–microbe symbioses. The process of plant domestication has potential repercussions in genes involved in plant-microbiome interactions. However, the extent to which breeding can impact the seed microbiome is sparsely explored. Cannabis is a high-value crop but sparsely subjected to agricultural innovations established in other crop species during the last century. Here, we conduct a large-scale analysis of the bacterial seed microbiome of Cannabis across different domestication grades and investigate the potential of seed-associated endophytes as plant growth-promoting agents under both controlled and field conditions.Results: analysis of Cannabis seed endophyte composition and diversity across 46 plant genotypes revealed 813 different bacterial genera with a predominance of Gammaproteobacteria, Bacilli, Actinobacteria and Alphaproteobacteria but a genotype-specific microbiome. The assessment of domestication and breeding on microbial assembly revealed a higher bacterial diversity in low domestication genotypes (Shannon index, H′: 1.21 vs. 1.05) and a higher homogeneity in bacterial composition caused by line development. Further, a seed bacterial isolate (Bacillus frigoritolerans C1141) associated with low domestication genotypes, and with genes associated with bio-fertilization, bioremediation and phytohormone production, increased plant growth by 42.3% at the time of harvest, under field conditions.Conclusion: this study addresses critical knowledge gaps related to the assembly of the Cannabis seed-endophytic microbiome. It reveals that Cannabis breeding is linked to alterations of seed microbial communities, which potentially led to the loss of bacteria with functional significance. These results highlight the importance of preserving seed microbiomes in plant breeding to support sustainable plant health and growth enhancement in Cannabis.<br/
Occurrence of green mold disease on Dictyophora rubrovolvata caused by Trichoderma koningiopsis
No full textFG-UNet: fine-grained feature-guided UNet for segmentation of weeds and crops in UAV images
No full textBackground: semantic segmentation of weed and crop images is a key component and prerequisite for automated weed management. For weeds in unmanned aerial vehicle (UAV) images, which are usually characterized by small size and easily confused with crops at early growth stages, existing semantic segmentation models have difficulties to extract sufficiently fine features. This leads to their limited performance in weed and crop segmentation of UAV images. Results: we proposed a fine-grained feature-guided UNet, named FG-UNet, for weed and crop segmentation in UAV images. Specifically, there are two branches in FG-UNet, namely the fine-grained feature branch and the UNet branch. In the fine-grained feature branch, a fine feature-aware (FFA) module was designed to mine fine features in order to enhance the model's ability to segment small objects. In the UNet branch, we used an encoder–decoder structure to realize high-level semantic feature extraction in images. In addition, a contextual feature fusion (CFF) module was designed for the fusion of the fine features and high-level semantic features, thus enhancing the feature discrimination capability of the model. The experimental results showed that our proposed FG-UNet, achieved state-of-the-art performance compared to other semantic segmentation models, with mean intersection over union (MIOU) and mean pixel accuracy (MPA) of 88.06% and 92.37%, respectively. Conclusion: the proposed method in this study lays a solid foundation for accurate detection and intelligent management of weeds. It will have a positive impact on the development of smart agriculture.</p
Novel insight into the mechanisms of neurotoxicity induced by type I and type II pyrethroids via disrupting the gut-brain axis in lizards
No full textType I and type II pyrethroids are widely used and frequently detected in agricultural environments. The neurotoxic effects and underlying mechanisms of pyrethroids in native animal populations, including lizards as common farmland inhabitants, remain unclear. This study exposed male lizards (Eremias argus) to type I bifenthrin (BF) and type II fluvalinate (FA) pyrethroids for 28 days, resulting in abnormal behaviors. Targeted analyses indicated that neurotransmitters, including dopamine, GABA, acetylcholine, and choline in lizard plasma, were significantly decreased with alterations in the cholinergic synapse, dopaminergic synapse, and cAMP signaling pathway in the brain after BF and FA treatment. Nervous system-related genes such as CACNA1A, CACNA1B, and CACNA1C were significantly down-regulated and highly correlated with arachidonic acid metabolism pathway-related metabolites in lizard gut. A notable decrease in metabolites within the arachidonic acid metabolism pathway and alterations in the gut microbiome were indicative for anti-inflammatory responses and neurotoxic effects. Interestingly, increased type I BF bioaccumulation in lizard intestines induced a higher abundance of Akkermansia, which resulted in reduced inflammation in the gut and lower neurotoxic effects compared to the low-dose BF exposure group. This study reveals contrasting dose-responses between pyrethroid types and suggests gut-brain axis-regulated neurotoxicity in lizards.</p
Impact of pyroxasulfone on sugarcane rhizosphere microbiome and functioning during field degradation
No full textPyroxasulfone (PYR) is a widely used herbicide, but its effects on non-target organisms, particularly microorganisms, are largely unknown. Herein, we investigated the effects of various doses of PYR on the sugarcane rhizosphere microbiome by using amplicon sequencing of rRNA genes and quantitative PCR techniques. Correlation analyses indicated that several bacterial phyla (Verrucomicrobia and Rhodothermaeota) and genera (Streptomyces and Ignavibacteria) strongly responded to PYR application. Additionally, we found that both bacterial diversity and composition were significantly altered after 30 days, indicating a prolonged effect of the herbicide. Moreover, co-occurrence analyses of the bacterial community showed that the network complexity was significantly decreased by PYR at day 45. Furthermore, FAPROTAX analysis suggested that some functions with implications for carbon cycling groups were significantly altered after 30 days. Overall, we provide the first indications that PYR may not pose a significant risk for altering microbial communities in the short term (less than 30 days). However, its potential negative effects on bacterial communities in the middle and late stages of degradation deserve further attention. To our knowledge, this is the first study to provide insight into the effects of PYR on the rhizosphere microbiome, providing an extended basis for future risk assessments
- …
