Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions

Puri, Ramesh Raj; Adachi, Fumihiko; Omichi, Masayuki; Saeki, Yuichi; Yamamoto, Akihiro; Hayashi, Shinobu; Ali, Md. Arshad; Itoh, Kazuhito

doi:10.1007/s11274-019-2754-2

Cited by 21 publications

(7 citation statements)

References 36 publications

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“…Additionally, the effect of different agricultural practices and climatic conditions have been reported to influence the distribution of endophytic bacteria communities in the root endosphere. 52 Interestingly, the difference observed in the bacterial community in the root and stem of sunflower at the growing stage in Lichtenburg compared to the stem of sunflower at the growing stage in Itsoseng validate the hypothesis of this study on the effect of crop rotational and mixed farming system on the bacterial diversity under different agricultural practices.…”

Section: Discussionsupporting

confidence: 72%

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Adeleke

Babalola

2021

Plant Signaling & Behavior

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Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga , and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces . The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.

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Section: Discussionsupporting

confidence: 72%

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Adeleke

Babalola

2021

Plant Signaling & Behavior

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“…Normally, endophytes are isolated from surface-sterilized plant tissue and subsequently cultivated in proper medium [2]. However, in recent years, with the development of metagenomics studies, many endophyte communities have been studied through culture-independent approaches such as the sequencing of the 16S rRNA gene and internal transcribed spacer regions (ITS1 and ITS2), the whole genome sequencing, or through shotgun metagenomics studies [3][4][5].…”

Section: Introductionmentioning

confidence: 99%

Bacterial Endophytes: The Hidden Actor in Plant Immune Responses against Biotic Stress

Oukala

Aissat

Pastor

2021

Plants

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Bacterial endophytes constitute an essential part of the plant microbiome and are described to promote plant health by different mechanisms. The close interaction with the host leads to important changes in the physiology of the plant. Although beneficial bacteria use the same entrance strategies as bacterial pathogens to colonize and enter the inner plant tissues, the host develops strategies to select and allow the entrance to specific genera of bacteria. In addition, endophytes may modify their own genome to adapt or avoid the defense machinery of the host. The present review gives an overview about bacterial endophytes inhabiting the phytosphere, their diversity, and the interaction with the host. Direct and indirect defenses promoted by the plant–endophyte symbiont exert an important role in controlling plant defenses against different stresses, and here, more specifically, is discussed the role against biotic stress. Defenses that should be considered are the emission of volatiles or antibiotic compounds, but also the induction of basal defenses and boosting plant immunity by priming defenses. The primed defenses may encompass pathogenesis-related protein genes (PR family), antioxidant enzymes, or changes in the secondary metabolism.

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“…Results presented in this work showed differences at the genus level for the symptomless sample K3 in terms of the higher presence of Pseudomonas, Arthrobacter, Chryseobacterium, Bacillus, and Exiguobacterium. All of them possess antimicrobial activities (Foldes et al 2000;Dardanelli et al 2010;Vacheron et al 2013;Chauhan et al 2015;Mashiane et al 2017;Puri et al 2019;Yadav 2020) and perhaps their higher abundance could be the reason for decay symptom absence. The Pseudomonas species are important members of the rhizosphere and their colonization of the root surface prevents colonization of plant pathogens (Vacheron et al 2013).…”

Section: Discussionmentioning

confidence: 99%

The Potential use of Bacterial Diversity Analysis of Soft Rotted Potato Tubers and Their Geocaulospheres

Marković¹,

Popović²,

Berić³

et al. 2021

Preprint

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The soft rot caused by Pectobacterium and Dickeya spp. is among the most important potato disease, responsible for outbreaks worldwide. In 2018, potato tubers (cultivar Lady Claire) with and without visible soft rot symptom, together with their geocaulospheres were sampled from the field in Bačka region (Serbia). The 16S rRNA Next Generation Sequencing (NGS) of tubers with and without soft rot symptom and their corresponding soils was performed to detect differences in microbial diversity and, using this data to predict causal agent(s) of disease and which samples are potentially best for isolating biocontrol strains. The ubiquitous soil bacteria from the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were dominant in all samples. The sequences identified as Pectobacterium aroidearum, P. carotovorum, and P. polaris were present in all tested samples and it can be hypothesized that they caused soft rot. The K3 sample showed the presence of genera with potential antimicrobial activity (Pseudomonas, Arthrobacter, Chryseobacterium, Bacillus, and Exiguobacterium). This result shows that diversity analysis could be used for checking for the presence of potential antagonistic bacteria at infected sites. Also, following the presence or absence of particular taxa could point out a capacity of soil to endure a growth season without an outbreak of soft or to maintain it without significant losses. This is a new approach to interpreting the results of the diversity of bacterial communities of tubers and can be useful for screening the health status of the soil.

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Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions

Cited by 21 publications

References 36 publications

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Bacterial Endophytes: The Hidden Actor in Plant Immune Responses against Biotic Stress

The Potential use of Bacterial Diversity Analysis of Soft Rotted Potato Tubers and Their Geocaulospheres

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