Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2

Tharek, Munirah; Sim, Kee-Shin; Khairuddin, Dzulaikha; Ghazali, Amir Hamzah Ahmad; Najimudin, Nazalan

doi:10.1128/genomea.00305-17

Cited by 8 publications

(10 citation statements)

References 7 publications

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“…The isolate, which was initially identified as an Enterobacter species, was shown to be able to infect and establish an endophytic relationship in rice seedlings Oryza sativa variety MR220 ( Tharek et al 2011 ). However, based on more in-depth molecular identification analysis via polymerase chain reaction (PCR) and amplification of full length 16S rRNA gene fragment (~1.4 kb), the isolate was re-identified as a plant-associated E. coli USML2 ( Tharek et al 2017 ). The genome sequence data was deposited to NCBI with GenBank accession number of CP011124.…”

Section: Methodsmentioning

confidence: 99%

“…This strain was deposited at the Microbial Culture Collection Unit, Institute of Bioscience, Universiti Putra Malaysia, with the accession number of UPMC432. The whole genome shotgun project has been deposited at DDBJ/EMBL/Genbank under the accession number CP011124 ( Tharek et al . 2017 ).…”

Section: Methodsmentioning

confidence: 99%

“…The genome sequence data of E. coli USML2 with GenBank Accession Number CP011124 was used to annotate and predict genes which are related to colonisation and plant growth promotion abilities ( Tharek et al 2017 ). These genes involved in metabolic pathways were generated by Kyoto Encyclopaedia of Genes and Genomes (KEGG) embedded in RAST server ( Kanehisa et al 2016 ; Aziz et al 2008 ; Overbeek et al 2014 ).…”

Section: Methodsmentioning

confidence: 99%

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Plant Growth Promoting Potentials of Beneficial Endophytic Escherichia coli USML2 in Association with Rice Seedlings

Tharek

Khairuddin

Najimudin

et al. 2021

TLSR

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An endophytic Escherichia coli USML2 originally isolated from the inner part of an oil palm (Elaeis guineensis Jacq.) leaf tissue was inoculated to rice seedlings to investigate its ability in colonising plant inner tissues and promoting growth. Infection of E. coli USML2 was initiated by colonisation on the root surface, invasion of the interior root system followed by endophytic spreading. Inoculation of E. coli USML2 in the rice rhizosphere zone resulted in a significant increase in leaf numbers (33.3%), chlorophyll content (33.3%), shoot height (34.8%) and plant dry weight (90.4%) of 42 days old rice seedlings as compared to the control. These findings also demonstrated the ability of E. coli USML2 to spread endophytically which serves as a beneficial strategy for the bacterium to colonise the host plant and gain protection against adverse soil conditions. The genome of E. coli USML2 had also revealed predicted genes essential for endophytic bacterial colonisation and plant growth promotion which further proven potentials of E. coli USML2 as Plant Growth Promoting Endophyte (PGPE).

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Plant Growth Promoting Potentials of Beneficial Endophytic Escherichia coli USML2 in Association with Rice Seedlings

Tharek

Khairuddin

Najimudin

et al. 2021

TLSR

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“…The hybrid assembled complete genomes were obtained after closing the gaps in TGS-Gapfiller using the ONT reads (stLFR + ONT genomes). Finally, the complete reference genomes were assembled based on the Nanopore and NGS data using Unicycler, except for the downloaded NCBI reference genome CP011124.1, which was assembled from PacBio long sequencing reads as the representative complete genome of E. coli K-12 ( Table 1 ) ( Tharek et al., 2017 ). For comparison, we assembled the complete genome in Canu, using only ONT reads.…”

Section: Resultsmentioning

confidence: 99%

Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

Zhang

Liu²,

Chen

et al. 2021

iScience

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Summary In this study, six bacterial isolates with variable GC, including Escherichia coli as mesophilic reference strain, were selected to compare hybrid assembly strategies based on next-generation sequencing (NGS) of short reads, single-tube long-fragment reads (stLFR) sequencing, and Oxford Nanopore Technologies (ONT) sequencing platforms. We obtained the complete genomes using the hybrid assembler Unicycler based on the NGS and ONT reads; others were de novo assembled using NGS, stLFR, and ONT reads by using different strategies. The contiguity, accuracy, completeness, sequencing costs, and DNA material requirements of the investigated strategies were compared systematically. Although all sequencing data could be assembled into accurate whole-genome sequences, the stLFR sequencing data yield a scaffold with more contiguity with more completeness of gene function than NGS sequencing assemblies. Our research provides a low-cost chromosome-level genome assembly strategy for large-scale sequencing of extremophile genomes with different GC contents.

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“…In fact, plants exert niche‐specific selection pressure on the organisms associated with them; for example, strains of E. coli associated with plants are a distinct phenotype and make an independent phylogroup different from that purified from mammalian hosts (Méric, Kemsley, Falush, Saggers, & Lucchini, ). E. coli strain USML2 has been shown to be a growth‐promoting endophyte in leaves of the oil palm ( Elaeis guineensis ; Tharek, Sim, Khairuddin, Ghazali, & Najimudin, ). Different species of Enterobacter have been reported as rhizobacteria associated with different plant species ( E. sakazakii and E. agglomerans with soybean; E. cloacae with citrus, maize, and soybean; and E. asburiae with sweet potato).…”

Section: Filamentous Phages To Boost Environmental Competitiveness Ofmentioning

confidence: 99%

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

Sharma

Karmakar

Kumar

et al. 2019

Ecology and Evolution

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Theories in soil biology, such as plant–microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below‐ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above‐ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost‐effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature‐based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.

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Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2

Cited by 8 publications

References 7 publications

Plant Growth Promoting Potentials of Beneficial Endophytic Escherichia coli USML2 in Association with Rice Seedlings

Plant Growth Promoting Potentials of Beneficial Endophytic Escherichia coli USML2 in Association with Rice Seedlings

Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

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