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.

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.

External limiting membrane angle as a composite predictive index for post-operative ELM closure in full thickness macular holes.

AIM: To evaluate pre-operative qualitative and quantitative parameters of external limiting membranes (ELM) and other associated full thickness macular holes (FTMH) features and their predictive values for post-operative anatomical and functional outcomes. METHODS: This was a retrospective study of 48 eyes that underwent vitrectomy with internal limiting membrane (ILM) peeling for FTMH and had type 1 closure. All subjects underwent optical coherence tomography (SDOCT, Heidelberg, Spectralis), and the eyes were divided into complete ELM closure (CEC) and incomplete ELM closure (IEC) groups based on the post-operative OCTs within 2 months, and ROC curves were used to estimate which of the pre-operative parameters could best predict eyes falling in the CEC group. RESULTS: The mean pre-op ELM defect was smaller in CEC group (594 µm vs 1126 µm, p < 0.001) and so was the pre-op EZ defect (770 µm vs 1186 µm, p = 0.001). The mean ELM angle also was smaller in the CEC group (51.6° vs 102.5°, p < 0.001) and so was the mean hole inlet distance (353 µm vs 596 µm, p < 0.001). The post-operative ELM defect showed a significant negative correlation with visual acuity (r = - 0.319; p = 0.027). The ELM angle was most predictive with an AUROC of 0.958, and a cut-off of 68.3° had a sensitivity of 90% and a specificity of 89%. CONCLUSION: Our study introduces a novel parameter called the ELM angle and proves that it has a high sensitivity and specificity in predicting complete ELM reformation post-surgery in the short term as well as the long term.

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.

Nine plant-associated bacterial strains designated as L1I52T, NRK F1, NRK F15, NRK F16, NRK F41, NRK F42, NRK F47, NRK F49, and NRK F50 originating from the roots and rhizosphere region of a coastal saline tolerant pokkali rice were taxonomically characterized in this study. Genomic fingerprinting using Enterobacterial Repetitive Intergenic Consensus (ERIC) primers discriminated the nine strains based on the DNA fingerprint patterns indicating that they were not clonal in origin. Phylogenetic analysis using 16S rRNA and other five housekeeping genes (gyrB, glyA, atpA, dnaK and murG) revealed that the novel strains constituted a single novel species within the genus Flavobacterium. In all tree construction methods, the novel strains formed a distinct phylogenetic branch, with Flavobacterium daejeonense GH1-10T, F. sufflavum BBQ-12T, and F. glycines Gm-149T as their nearest phylogenetic neighbours. However, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) comparison between the draft genomes of L1I52T (representative isolate) and it's nearest phylogenetic neighbours were well below the proposed threshold values (<95 % and <70 %) used for species discrimination. Thus, based on the phenotypic, genotypic and chemotaxonomic data obtained in this study, we describe a novel Flavobacterium species for which we propose the name Flavobacterium pokkalii sp.nov., with strain L1I52T (=MTCC 12454T=KCTC 42429T) as the type strain. In addition, L1I52T is a potential plant growth promoting rhizobacteria as they can promote pokkali rice growth and we identified several plant associated gene features in the genome of L1I52T that are potentially involved in plant microbe interactions.

Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis.

Three strains L3B27T, 3CNBAF, L1A4 isolated from a brackish cultivated pokkali rice rhizosphere were characterised using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA and recA gene sequences revealed that these strains were highly similar among each other and formed a separate monophyletic cluster within the genus Sphingomonas with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens DSM 18530T and Sphingomonas trueperi DSM 7225T as their closest relatives sharing 97.9-98.3% 16S rRNA similarity and 91.3-94.0% recA similarity values, respectively. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) values between L3B27T (representative of the novel strains) and its phylogenetically closest Sphingomonas species were well below the established cut-off <94% (ANI/AAI) and <70% (dDDH) for species delineation. Further, the novel strains can be distinguished from its closest relatives based on several phenotypic traits. Thus, based on the polyphasic approach, we describe a novel Sphingomonas species for which the name Sphingomonas pokkalii sp. nov (type strain L3B27T=KCTC 42098T=MCC 3001T) is proposed. In addition, the novel strains were characterised for their plant associated properties and found to possess several phenotypic traits which probably explain its plant associated lifestyle. This was further confirmed by the presence of several plant associated gene features in the genome of L3B27T. Also, we could identify gene features which may likely involve in brackish water adaptation. Thus, this study provides first insights into the plant associated lifestyle, genome and taxonomy of a novel brackish adapted plant associated Sphingomonas.

Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice.

Pokkali rice varieties are known for their saline tolerance when specifically grown in coastal saline affected agri-fields of southern Kerala. These fields are prone to seawater intrusion. During characterization of phytobeneficial rhizobacteria from this pokkali rice, L3E4T was isolated. This strain showed some plant growth-promoting functions (production of indole acetic acid (IAA), acetoin, and siderophore), biofilm formation and capacity to use a wide range of plant-derived organic compounds. In planta assay under axenic conditions showed a positive effect of L3E4T on pokkali rice growth; importantly, it was able to attach and colonize pokkali rice roots in the presence of natural seawater, a key adaptation required for survival in pokkali rice fields. Phylogenetic analysis using 16S rRNA, recA, and gyrB gene sequences showed that strain L3E4T belongs to the genus Novosphingobium, with Novosphingobium capsulatum GIFU 11526T and Novosphingobium rhizosphaerae JM.1T being the nearest phylogenetic relatives. In addition, DNA-DNA hybridization analysis and phenotypic traits established that this strain belongs to a novel Novosphingobium species, for which we propose the name Novosphingobium pokkalii sp. nov. The type strain is represented by strain L3E4T (=MTCC 12357T = KCTC 42224T).