Whole-Genome Sequencing of Bacterial Endophytes From Fresh and Preserved Plant Specimens

Danneels, Bram; Carlier, Aurélien

doi:10.1007/978-1-0716-2871-3_7

Cited by 5 publications

(3 citation statements)

References 42 publications

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“…Further work is needed to identify the species of bacterium that produces the nodules in Keetia. This can be done by genomic studies of dried leaf material (Danneels & Carlier 2023). The symbiont is almost certain to be a Paraburkholderia, given that all other leaf nodule forming endosymbionts of Rubiaceae belong to this genus, and that the non BLN endophytic bacteria recorded in Vanguerieae are also this genus (Verstraete et al 2017).…”

Section: Nigeria South-easternmentioning

confidence: 99%

Keetia nodulosa sp. nov. (Rubiaceae - Vanguerieae) of West-Central Africa: bacterial leaf nodulation discovered in a fourth genus and tribe of Rubiaceae

Cheek,

Onana

2024

webbia

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Keetia nodulosa Cheek, a cloud forest climber nearly endemic to Cameroon, with a single record from Nigeria, is described and illustrated. It is remarkable as the first known species to be recorded with bacterial leaf nodules (BLN) in the genus Keetia, and also, in the tribe Vanguerieae. Other genera in Rubiaceae with BLN are Psychotria (Psychotrieae-Rubioideae), Sericanthe (Coffeeae) and Pavetta (Pavetteae), both Ixoroideae/Dialypetalanthoideae. The BLN in Keetia (Vanguerieae) are illustrated for the first time here. The characteristics and significance of bacterial leaf nodulation in Keetia nodulosa are discussed in the context of rapidly growing knowledge on the subject in flowering plants. Keetia nodulosa is provisionally assessed using the 2012 IUCN standard as Endangered (EN B2ab(iii)). The importance of its conservation, and options for achieving this are discussed in the context of recent extinctions of other plant species in Cameroon. This discovery of a new cloud forest species is discussed in relation to other cloud forest plant species described in the last twenty years which are also distributed over the highlands of the western half of Cameroon.

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Section: Nigeria South-easternmentioning

confidence: 99%

Keetia nodulosa sp. nov. (Rubiaceae - Vanguerieae) of West-Central Africa: bacterial leaf nodulation discovered in a fourth genus and tribe of Rubiaceae

Cheek,

Onana

2024

webbia

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“…Establishing a systematic approach that integrates plant breeding, precision farming, agricultural management, and rhizobacteria research provides a robust strategy for improving sustainable crop production. 18 Challenges to bacterial culturability generally include the following factors: (i) different species require different growth media and/or growth conditions; 37 (ii) certain microorganisms, being obligate endophytes, require a host for survival; 38 (iii) fastgrowing or antagonistic microorganisms can limit or inhibit the growth of slow-growing bacteria; 39 (iv) the growth or dominance of some species depends on the presence of other species; 40,41 and (v) some hard-to-cultivate bacteria exist in low abundance in the environment, rendering it difficult to detect them using metagenomics and speculate on the conditions required for their growth. 42…”

Section: Challenges In Rhizobacteria Culturementioning

confidence: 99%

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Ji,

Guo,

et al. 2024

J. Agric. Food Chem.

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Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.

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“…We previously developed Autometa, an automated binning pipeline that is able to effectively recover genomes from highly convoluted environmental and non-model host-associated microbial communities (3). This tool has seen widespread use in environments ranging from marine, freshwater and terrestrial samples, including corals (4), red algae (5), kinetoplastids (6), deep sea geothermal vents (7)(8)(9), sponges (10)(11)(12), coastal sediments (13), stromatolites (14), seaweeds (15), shipworms (16), plateau lakes (17,18), hot springs (19,20), contaminated rivers (21), beetles (22)(23)(24)(25), Kickxellomycotina fungi (26), Ensifera insects (27), fermented agave (28,29), a marsh orchid rhizobiome (30), domesticated cattle (31,32), mice (33) and human gut (34), periodontal (35) as well as urinary tract (36) microbiomes. As a consequence of Autometa's widespread use, both non-technical and technical researchers alike have communicated their frustrations regarding the ease of installation as well as the efficiency and robustness throughout the various stages of the Autometa workflow.…”

Section: Introductionmentioning

confidence: 99%

Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities

Rees,

Uppal,

Clark

et al. 2023

Preprint

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In 2019, we developed Autometa, an automated binning pipeline that is able to effectively recover metagenome-assembled genomes from complex environmental and non-model host-associated microbial communities. Autometa has gained widespread use in a variety of environments and has been applied in multiple research projects. However, the genome-binning workflow was at times overly complex and computationally demanding. As a consequence of Autometa's diverse application, non-technical and technical researchers alike have noted its burdensome installation and inefficient as well as error-prone processes. Moreover its taxon-binning and genome-binning behaviors have remained obscure. For these reasons we set out to improve its accessibility, efficiency and efficacy to further enable the research community during their exploration of Earth's environments. The highly augmented Autometa 2 release, which we present here, has vastly simplified installation, a graphical user interface and a refactored workflow for transparency and reproducibility. Furthermore, we conducted a parameter sweep on standardized community datasets to show that it is possible for Autometa to achieve better performance than any other binning pipeline, as judged by Adjusted Rand Index. Improvements in Autometa 2 enhance its accessibility for non-bioinformatic oriented researchers, scalability for large-scale and highly-complex samples and interpretation of recovered microbial communities.

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Whole-Genome Sequencing of Bacterial Endophytes From Fresh and Preserved Plant Specimens

Cited by 5 publications

References 42 publications

Keetia nodulosa sp. nov. (Rubiaceae - Vanguerieae) of West-Central Africa: bacterial leaf nodulation discovered in a fourth genus and tribe of Rubiaceae

Keetia nodulosa sp. nov. (Rubiaceae - Vanguerieae) of West-Central Africa: bacterial leaf nodulation discovered in a fourth genus and tribe of Rubiaceae

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities

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