Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala

Menon, Rahul R.; Kumari, Saroj; Viver, Tomeu; Rameshkumar, N.

doi:10.1016/j.micres.2020.126533

Cited by 21 publications

(6 citation statements)

References 28 publications

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“…The phenotypic characteristics such as cell morphology, motility, anaerobic growth, reduction of nitrate, production of indole, Methyl red and Voges Proskauer (MR-VP), hydrolysis of starch, xylan, carboxymethyl cellulose, esculin, casein, urea, and DNA, and the ability to grow in different standard heterotrophic media, including Luria Bertani (LB), nutrient agar, and trypticase soya agar were performed using methods as described by Rameshkumar et al, 2016 [ 10 ]. The growth at varying temperatures and pH ranges was assayed using the procedure described by Rameshkumar et al, 2016 [ 11 ], with modifications specified by Menon et al, 2020 [ 15 ]. The assimilation of different substrates was determined using an API 20NE strip as per the instructions provided by the manufacturer, and the results were noted after 48 h of incubation at 30 °C.…”

Section: Methodsmentioning

confidence: 99%

“…To achieve this, we cultured the rhizosphere samples of different pokkali rice varieties collected from various sites using different minimal media compositions that contained ACC as the sole nitrogen source and different sugars or organic acids as the carbon source, and 50% natural or 50% artificial seawater (Himedia, India) to mimic brackish environmental conditions. This investigation resulted in the isolation of several potential ACC deaminase-producing indigenous rhizobacterial strains, including the genera Burkholderia , Herbaspirillum , and Rhizobium , and a few unclassified strains that are characterized as novel bacterial taxa; Vogesella oryzae L3B39 T [ 10 ], Arthrobacter pokkalii P3B162 T [ 11 ], Novosphingobium pokkalii L3E4 T [ 12 ], Pokkaliibacter plantistimulans L1E11 T [ 13 ], Sphingomonas pokkalii L3B27 T [ 14 ], and Flavobacterium pokkalii L1I52 T [ 15 ], and functionally some are shown to possess plant growth-promoting abilities [ 13 , 15 ]. Additionally, Rhodoplanes pokkaliisoli JA415 T , a novel phototrophic alphaproteobacterium, was reported from a pokkali paddy field by Lakshmi et al [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

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Characterization of a novel root-associated diazotrophic rare PGPR taxa, Aquabacter pokkalii sp. nov., isolated from pokkali rice: new insights into the plant-associated lifestyle and brackish adaptation

Sunithakumari,

Menon,

Suresh

et al. 2024

BMC Genomics

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Salinity impacts crop growth and productivity and lowers the activities of rhizosphere microbiota. The identification and utilization of habitat-specific salinity-adapted plant growth-promoting rhizobacteria (PGPR) are considered alternative strategies to improve the growth and yields of crops in salinity-affected coastal agricultural fields. In this study, we characterize strain L1I39T, the first Aquabacter species with PGPR traits isolated from a salt-tolerant pokkali rice cultivated in brackish environments. L1I39T is positive for 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation and can promote pokkali rice growth by supplying fixed nitrogen under a nitrogen-deficient seawater condition. Importantly, enhanced plant growth and efficient root colonization were evident in L1I39T-inoculated plants grown under 20% seawater but not in zero-seawater conditions, identifying brackish conditions as a key local environmental factor critical for L1I39T-pokkali rice symbiosis. Detailed physiological studies revealed that L1I39T is well-adapted to brackish environments. In-depth genome analysis of L1I39T identified multiple gene systems contributing to its plant-associated lifestyle and brackish adaptations. The 16S rRNA-based metagenomic study identified L1I39T as an important rare PGPR taxon. Based on the polyphasic taxonomy analysis, we established strain L1I39T as a novel Aquabacter species and proposed Aquabacter pokkalii sp nov. Overall, this study provides a better understanding of a marine-adapted PGPR strain L1I39T that may perform a substantial role in host growth and health in nitrogen-poor brackish environments.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Characterization of a novel root-associated diazotrophic rare PGPR taxa, Aquabacter pokkalii sp. nov., isolated from pokkali rice: new insights into the plant-associated lifestyle and brackish adaptation

Sunithakumari,

Menon,

Suresh

et al. 2024

BMC Genomics

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“…Macro-and micronutrient sources. Several plantassociated bacteria, including Flavobacterium species, provide the macro-and micronutrient resources to host plants (Carrión et al, 2019;Choi et al, 2023;Kraut-Cohen et al, 2021;Menon et al, 2020;Tilak et al, 2005;Youseif, 2018;Zhang et al, 2021) (Fig. 2B).…”

Section: Determinants Produced By Flavobacterium For Improving Plant ...mentioning

confidence: 99%

“…Flavobacterium species have been studied as biostimulants in diverse monocot and dicot plants ( Choi et al, 2023 ; Kwak et al, 2018 ; Menon et al, 2020 ; Samad et al, 2017 ; Yakubovskaya et al, 2019 ; Youseif, 2018 ; Zhang et al, 2021 ) ( Fig. 2 ).…”

Section: Functional Roles Of Flavobacterium In Pla...mentioning

confidence: 99%

The Plant-Associated Flavobacterium: A Hidden Helper for Improving Plant Health

Seo,

Kim,

Lee

et al. 2024

Plant Pathol J

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Flavobacterium is a genus within the phylum Bacteroidota that remains relatively unexplored. Recent analyses of plant microbiota have identified the phylum Bacteroidota as a major bacterial group in the plant rhizosphere. While Flavobacterium species within the phylum Bacteroidota have been recognized as pathogens in the aquatic habitats, microbiome analysis and the characterization of novel Flavobacterium species have indicated the great diversity and potential of their presence in various environments. Many Flavobacterium species have positively contribute to plant health and development, including growth promotion, disease control, and tolerance to abiotic stress. Despite the well-described beneficial interactions of the Flavobacterium species with plants, the molecular mechanisms and bacterial determinants underlying these interactions remain unclear. To broaden our understanding of the genus Flavobacterium’s role in plant health, we review the recent studies focusing on their ecological niche, functional roles, and determinants in plant-beneficial interactions. Additionally, this review discusses putative mechanisms explaining the interactions between plants and Flavobacterium. We have also introduced the importance of future research on Flavobacterium spp. and its potential applications in agriculture.

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“…Flavobacterium is widely distributed in the environment, including activated sludge [ 6 ], stream sediment [ 7 ], glacier [ 8 ], and rhizosphere [ 9 ]. Flavobacterium not only has a wide range of habitats but also has a wide range of characteristics, such as pathogenicity, which causes fatal damage to both wild and cultured fish, and plant growth-promoting properties [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

The Role of Flavobacterium enshiense R6S-5-6 in the Wetland Ecosystem Revealed by Whole-Genome Analysis

Choi¹,

Cha

Lee

et al. 2023

Curr Microbiol

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The wetland is an important ecosystem for purifying pollutants and circulating nutrients. Numerous microorganisms contribute to maintaining this function. We obtained Flavobacterium enshiense R6S-5-6 which was isolated from Ungok (Ramsar) Wetland and conducted whole-genome sequencing to investigate what contribution R6S-5-6 could make to the wetland community. The complete genome sequence of R6S-5-6 has a size of 3,251,289 bp with 37.68% of GC content. Gene annotation revealed that R6S-5-6 has several pathways to break down pollutants, including denitrification, assimilatory sulfate reduction (ASR), and polyphosphate-accumulating process. Furthermore, R6S-5-6 has genes that can have a positive effect on plants living in wetlands, such as storing essential nutrients, promoting plant growth, and protecting plants against pathogens.

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Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala

Cited by 21 publications

References 28 publications

Characterization of a novel root-associated diazotrophic rare PGPR taxa, Aquabacter pokkalii sp. nov., isolated from pokkali rice: new insights into the plant-associated lifestyle and brackish adaptation

Characterization of a novel root-associated diazotrophic rare PGPR taxa, Aquabacter pokkalii sp. nov., isolated from pokkali rice: new insights into the plant-associated lifestyle and brackish adaptation

The Plant-Associated Flavobacterium: A Hidden Helper for Improving Plant Health

The Role of Flavobacterium enshiense R6S-5-6 in the Wetland Ecosystem Revealed by Whole-Genome Analysis

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