Draft Genome Sequence of Phosphate-Solubilizing Chryseobacterium sp. Strain ISE14, a Biocontrol and Plant Growth-Promoting Rhizobacterium Isolated from Cucumber

Chryseobacterium gotjawalense sp. nov. Isolated from Soil in the Volcanic Forest Gotjawal, Jeju Island

Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.

Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities

Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.

Global Role of Crop Genomics in the Face of Climate Change

The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.

Phylogenetic insights into the diversity of Chryseobacterium species

The genus Chryseobacterium was formally established in 1994 and contains 112 species with validly published names. Most of these species are yellow or orange coloured, and contain a flexirubin-type pigment. The genomes of 83 of these 112 species have been sequenced in view of their importance in clinical microbiology and potential applications in biotechnology. The National Center for Biotechnology Information taxonomy browser lists 1415 strains as members of the genus Chryseobacterium, of which the genomes of 94 strains have been sequenced. In this study, by comparing the 16S rDNA and the deduced proteome sequences, at least 20 of these strains have been proposed to represent novel species of the genus Chryseobacterium. Furthermore, a yellow-coloured bacterium isolated from dry soil in the USA (and identified as Flavobacterium sp. strain B-14859) has also been reconciled as a novel member of the genus Chryseobacterium based on the analysis of 16S rDNA sequences and the presence of flexirubin. Yet another bacterium (isolated from a water sample collected in the Western Ghats of India and identified as Chryseobacterium sp. strain WG4) was also found to represent a novel species. These proposals need to be validated using polyphasic taxonomic approaches.

Chryseobacterium phosphatilyticum sp. nov., a phosphate-solubilizing endophyte isolated from cucumber (Cucumis sativus L.) root

A bacterial strain, designated as ISE14^T, with Gram-stain-negative and non-motile rod-shaped cells, was isolated from the root of a cucumber plant collected in a field in Iksan, Republic of Korea and was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISE14^T represented a member of the genus Chryseobacterium and was closely related to Chryseobacterium viscerum 687B-08^T (16S rRNA gene sequence similarity of 98.50 %), Chryseobacterium lactis NCTC 11390^T (98.49 %), Chryseobacterium ureilyticum F-Fue-04IIIaaaa^T (98.49 %) and Chryseobacterium oncorhynchi 701B-08^T (98.04 %). Average nucleotide identity values between genome sequences of strain ISE14^T and the closely related species ranged from 81.44 to 83.15 %, which were lower than the threshold of 95 % (corresponding to a DNA-DNA hybridization value of 70 %). The DNA G+C content of strain ISE14^T was 36.3 mol%. The dominant fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and eight unidentified lipids; the predominant respiratory quinone was MK-6. On the basis of the evidence presented in this study, strain ISE14^T can be distinguished from closely related species belonging to the genus Chryseobacterium. Thus, strain ISE14^T is a novel species of the genus Chryseobacterium, for which the name Chryseobacteriumphosphatilyticum sp. nov. is proposed. The type strain is ISE14^T (=KACC 19820^T=JCM 32876^T).

Draft Genome Sequences of Chryseobacterium lactis NCTC11390T Isolated from Milk, Chryseobacterium oncorhynchi 701B-08T from Rainbow Trout, and Chryseobacterium viscerum 687B-08T from Diseased Fish

The genus Chryseobacterium, belonging to the family Flavobacteriaceae, contains Gram-negative, yellow-pigmented, rod-shaped, and non-spore-forming bacterial species, which may be free living or parasitic. Here, we report draft genome sequences of type strains of three species of Chryseobacterium containing genes related to biological control and plant growth promotion.

The genus Chryseobacterium, belonging to the family Flavobacteriaceae, contains Gram-negative, yellow-pigmented, rod-shaped, and non-spore-forming bacterial species, which may be free living or parasitic. Here, we report draft genome sequences of type strains of three species of Chryseobacterium containing genes related to biological control and plant growth promotion.