Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum

Aqueel, Rhea; Badar, Ayesha; Roy, Nazish; Mushtaq, Qandeel; Ali, Aimen Fatima; Bashir, Aftab; Ijaz, Umer Zeeshan; Malik, Kauser Abdulla

doi:10.1038/s41522-023-00470-9

Cited by 8 publications

(3 citation statements)

References 54 publications

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“…In the resistant variety, the phyllosphere is home to the most influential nodes present in the network. The leaf epiphytic region is dominated by the top influencers, which is in accordance with our previous findings, where the SA-producing bacteria isolated from the phyllosphere of the FDH-228 variety conferred disease resistance against CLCuD in the susceptible variety ( Aqueel et al, 2023 ). The phyllosphere microbiota are the most selected microbes and partake in nutrient cycling due to their specialized adaptations to climate change ( Dorokhov et al, 2018 ; Cavicchioli et al, 2019 ; Koskella, 2020 ).…”

Section: Discussionsupporting

confidence: 92%

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Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective

Aqueel,

Badar,

Ijaz

et al. 2024

Front. Microbiol.

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Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant’s ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant’s response to viral disease, which may be microbially mediated.

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Section: Discussionsupporting

confidence: 92%

“…The 16S rRNA sequences were processed with the QIIME2 pipeline with the dataset given by Aqueel et al (2023) and revisited in this study. In brief, the Deblur algorithm ( Amir et al, 2017 ) within the QIIME2 platform (version 2019.7.0) was used to recover 38,120 amplicon sequence variants (ASVs).…”

Section: Methodsmentioning

confidence: 99%

Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective

Aqueel,

Badar,

Ijaz

et al. 2024

Front. Microbiol.

Self Cite

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show abstract

“…In the resistant variety, the phyllosphere is home to the most influential nodes present in the network. The leaf epiphytic region is dominated by the top influencers, which is in accordance with our previous findings, where the SA-producing bacteria isolated from the phyllosphere of the FDH-228 variety conferred disease resistance against CLCuD in the susceptible variety (Aqueel et al, 2023). The phyllosphere microbiota are the most selected microbes and partake in nutrient cycling due to their specialized adaptations to climate change (Dorokhov et al, 2018;Cavicchioli et al, 2019;Koskella, 2020).…”

Section: Discussionsupporting

confidence: 89%

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Disease Resistance Correlates with Core Microbiome Diversity in Cotton

Aqueel,

Badar,

Roy

et al. 2024

Curr Microbiol

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Understanding the resident microbial communities and their above and below ground interactions with plants will provide necessary information for crop disease protection and stress management. In this study, we show how diversity of core microbiome varies with disease susceptibility of a crop. To test this hypothesis, we have focused on identifying the core microbial species of cotton leaf curl disease (CLCuD) susceptible Gossypium hirsutum and CLCuD resistant Gossypium arboreum under viral infestation. Derivation of core membership is challenging as it depends on an occupancy threshold of microbial species in a sampling pool, whilst accounting for different plant compartments. We have used an abundance–occupancy distribution approach where we dynamically assess the threshold for core membership, whilst marginalizing for occupancy in four compartments of the cotton plant, namely, leaf epiphyte, leaf endophyte, rhizosphere, and root endophyte. Additionally, we also fit a neutral model to the returned core species to split them into three groups, those that are neutral, those that are selected by the plant environment, and finally those that are dispersal limited. We have found strong inverse relationship between diversity of core microbiome and disease susceptibility with the resistant variety, G. arboreum, possessing higher diversity of microbiota. A deeper understanding of this association will aid in the development of biocontrol agents for improving plant immunity against biotrophic pathogens.

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Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum

Cited by 8 publications

References 54 publications

Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective

Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective

Data_Sheet_1.zip

Disease Resistance Correlates with Core Microbiome Diversity in Cotton

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