Pantoea endophytica sp. nov., novel endophytic bacteria isolated from maize planting in different geographic regions of northern China

The Microbiome of Fertilization-Stage Maize Silks (Style) Encodes Genes and Expresses Traits That Potentially Promote Survival in Pollen/Style Niches and Host Reproduction

Within flowers, the style channel receives pollen and transmits male gametes inside elongating pollen tubes to ovules. The styles of maize/corn are called silks. Fertilization-stage silks possess complex microbiomes, which may partially derive from pollen. These microbiomes lack functional analysis. We hypothesize that fertilization-stage silk microbiomes promote host fertilization to ensure their own vertical transmission. We further hypothesize that these microbes encode traits to survive stresses within the silk (water/nitrogen limitation) and pollen (dehydration/aluminum) habitats. Here, bacteria cultured from fertilization-stage silks of 14 North American maize genotypes underwent genome mining and functional testing, which revealed osmoprotection, nitrogen-fixation, and aluminum-tolerance traits. Bacteria contained auxin biosynthesis genes, and testing confirmed indole compound secretion, which is relevant, since pollen delivers auxin to silks to stimulate egg cell maturation. Some isolates encoded biosynthetic/transport compounds known to regulate pollen tube guidance/growth. The isolates encoded ACC deaminase, which degrades the precursor for ethylene that otherwise accelerates silk senescence. The findings suggest that members of the microbiome of fertilization-stage silks encode adaptations to survive the stress conditions of silk/pollen and have the potential to express signaling compounds known to impact reproduction. Overall, whereas these microbial traits have traditionally been assumed to primarily promote vegetative plant growth, this study proposes they may also play selfish roles during host reproduction.

Draft Genome Sequence of Pantoea sp. Strain MHSD4, a Bacterial Endophyte With Bioremediation Potential

Pantoea sp. strain MHSD4 is a bacterial endophyte isolated from the leaves of the medicinal plant Pellaea calomelanos. Here, we report on strain MHSD4 draft whole genome sequence and annotation. The draft genome size of Pantoea sp. strain MHSD4 is 4 647 677 bp with a G+C content of 54.2% and 41 contigs. The National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline tool predicted a total of 4395 genes inclusive of 4235 protein-coding genes, 87 total RNA genes, 14 non-coding (nc) RNAs and 70 tRNAs, and 73 pseudogenes. Biosynthesis pathways for naphthalene and anthracene degradation were identified. Putative genes involved in bioremediation such as copA, copD, cueO, cueR, glnGm, and trxC were identified. Putative genes involved in copper homeostasis and tolerance were identified which may suggest that Pantoea sp. strain MHSD4 has biotechnological potential for bioremediation of heavy metals.

Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production

Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. KEY POINTS: • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation.

Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules

A novel bacterium, designated strain MMK2T, was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2T and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2T strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2T and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2T (= DSM 115063T = LMG 33049T).

Insights into the Potential Role of Plasmids in the Versatility of the Genus Pantoea

In the past two decades, 25 different species of the genus Pantoea within the Enterobacteriaceae family, have been isolated from different environmental niches. These species have a wide range of biological roles. Versatility in functions and hosts indicate that this genus has undergone extensive genetic diversification, which can be attributed to the different extra-chromosomal genetic elements or plasmids found across this genus. We have analyzed the functions of these plasmids and categorized them into four major groups for a better understanding of their future applications. The first and second group includes plasmids that contribute to genetic diversification and pathogenicity, respectively. The third group comprises cryptic plasmids of Pantoea. The last group includes plasmids that play a role in the metabolic versatility of the genus Pantoea. We have analyzed the data available up to May 2023 from two databases (viz; NCBI and PLSDB). In our analysis we have found a vast gap in knowledge. Complete gene annotations are available for only a few of the plasmids. This review highlights these challenges as an avenue for future research.

Genomic delineation and description of species and within-species lineages in the genus Pantoea

As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

Diversity of endophytic bacteria in hybrid maize seeds and Bacillus mojavensis J2416-7 may be capable of vertical transmission

The diversity of endophytic bacteria in the progeny is related to the parental lines. In this study, the traditional separation method was used to study the dominant endophytic bacteria of the shared paternal line and its pollen, different maternal lines and their F1 progeny. And the results showed that the dominant endophytic bacteria in maize seeds and the pollen were Bacillus and Pantoea. The Bacillus diversity of the progeny JMC121 and JN728 were the same as both the paternal line and the maternal line, including Bacillus subtilis, Bacillus velezensis, Bacillus mojavensis, and Bacillus licheniformis. The Bacillus subtilis and Bacillus velezensis in JN828 were the same as both the paternal line and the maternal line, while Bacillus licheniformis was only the same as the paternal line. Through the RAPD molecular typing, there was the same strain of Bacillus mojavensis existed in the paternal line J2416, the pollen and the progeny JN728; this meant that the paternal line passed its dominant endophytic bacteria to the progeny through pollen in vertical transmission. This study showed that the dominant endophytic bacteria in maize seeds and the pollen were Bacillus, and the diversity of F1 progeny was related to both the paternal line and the maternal line.

Arthrobacter wenxiniae sp. nov., a novel plant growth-promoting rhizobacteria species harbouring a carotenoids biosynthetic gene cluster

A bacterial strain, designated AETb3-4^T was isolated from the rhizosphere of lily. Comparison of 16S rRNA gene sequences showed that the sequence from strain AETb3-4^T exhibits high sequence similarity with those of Arthrobacter silviterrae KIS14-16^T (97.9%), Arthrobacter livingstonensis LI2^T (97.2%) and Arthrobacter stackebrandtii CCM 2783^T (97.0%). Whole genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values between strain AETb3-4T and the reference strains A. silviterrae DSM 27180^T, A. livingstonensis L12^T and A. stackebrandtii DSM 16005^T were below 83.6% and 27.7%, respectively, values which are considerably below the proposed thresholds for the species delineation, consistent with the proposal that strain AETb3-4^T represents a novel species. The genome size of strain AETb3-4^T is 4.33 Mb and the genomic DNA G + C content is 67.3%. The main polar lipids were identified as phosphatidylglycerol, diphosphatidylglycero, phosphatidylinositol and an unidentified glycolipid. The major fatty acids (> 10%) were identified as anteiso-C_{15: 0} and anteiso-C_{17: 0}. The predominant menaquinone was found to be menaquinone 9 (MK-9) (H₂) (82.2%). Phenotypic tests allowed the strain to be differentiated from its close phylogenetic neighbors. Based on the results obtained, it is proposed that the strain AETb3-4^T (= CFCC 16390^T = LMG 31708^T) represents a novel species in the genus Arthrobacter, for which the names Arthrobacter wenxiniae sp. nov. is proposed. In addition, the novel strain AETb3-4^T has multiple plant growth-promoting characters including ACC-deaminase activity and production of IAA. Furthermore, the genome contains secondary metabolite biosynthesis gene clusters, including a carotenoid biosynthetic gene cluster, suggesting potential capacities for secondary metabolite synthesis. These data suggest that strain AETb3-4^T may have potential applications both in medicine and sustainable agriculture.

Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov

To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.

First Report of Bacterial Rot Caused by Pantoea endophytica on Tobacco in Liuyang, China

Tobacco, Nicotiana tabacum L., is produced largely in China (~1/3 of the global market). In the monsoon summer of 2020, tobacco plant petioles, where axillary buds were removed, became black-rotten, and thick ooze appeared, when squeezed. Lesions encompassed more than half of petiole circumference. Ten tobacco fields (100 plant/field) were investigated in Liuyang, China and 5% disease severity founded in each infected field (Fig. 1A, B, C). Six infected stalks leave of different tobacco were sampled from severe field in Liuyang (N28°21', E113°52') and were surface sterilized (1% sodium hypochlorite for 3 min.), rinsed thrice in sterile distilled water, grounded, and streaked on Luria Bertani agar (LBA). After 24 hours at 28ºC, circular and convex colonies appeared. Hundred colony from ten plates were picked, amplified, and sequenced with the primer 16S-27F/16S-1492R by colony PCR (Lane et al. 1991). 16S rRNA sequence from 100 colony were assembled and fell into two sequences, either similar to Leclercia sp. (86%), or Pantoea sp. (14%). Identification and homology search was done by BLASTn analysis against NCBI and the EzBio Cloud database (Yoon et al. 2017). The Pantoea isolate HN-23 (1,408 bp, MW405831) and the other 16S sequence of 13 Pantoea showed 99.57% identity to the type strain P. endophyitca 596T (PJRT0100022) based on the EzBio Cloud database to identify novel bacteria. Colonies of HN-23 were smooth, translucent, convex with entire margin on LBA, and 1mm and 3mm (diameter), white to yellow, after 24h and 48h (Fig.1 H, I), respectively but white (Fig.1 J, K) on Nutrient Agar (NA). Phenotype of HN-23 (S-1) was performed using API 20E and API ZYM system (bioMérieux, France) and found identical to P. endophytica 596T (Gao et al. 2019). Draft genome of HN-23 (size 4.96Mbp, total Scaffold 79, Scaf N50 218,098bp and Scaf N90 61,041bp) was studied by Illumina sequencing (JAFLWX000000000) and was found to have 98.24% nucleotide identity with the genome of P. endophytica type strain 596. Average nucleotide identity (ANI) values were calculated using Ortho ANIu algorithm (Yoon et al 2017a). HN-23 had 83.89% and 83.65% ANI with P. rodasii LMG26273T and P. dispersa CCUG25232T, respectively (S-2). Six tobacco seedlings (cultivar K326, 30cm height plants grown at greenhouse at 28℃ and 70-80% humidity) were injected by 20μl of culture (109 CFU/ml) of HN-23 and three with dominant species Leclercia sp. HN-7, and reisolated from infected tissues. Pathogenic tissue extract and sterile water were also used as positive and negative control, respectively and experiments were performed in triplicate. After 20h, symptoms of water-soaked decay appeared in the injected leaf axils (Fig. 1D). After 2 days, a severe rot is developed (Fig.1 E). Though, the controls were symptomless (Fig.1 F, G). The bacterium was then isolated from the rotten tissues and identity was confirmed by 16S rDNA sequencing, thus fulfilling Koch's postulates. This species was also reported as endophytes to be isolated from root, stem and leaf of maize planted in diverse parts of China and identified as P. endophytica. To our knowledge, this is the first report of P. endophytica as a plant pathogen, which was firstly isolated from Tobacco planted in southern China.

Variovorax beijingensis sp. nov., a novel plant-associated bacterial species with plant growth-promoting potential isolated from different geographic regions of Beijing, China

Two plant-associated bacterial strains were isolated from Beijing, China. The two strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 99.4% and 94.7%, respectively, suggesting that they belonged to the same species. The 16S rRNA gene phylogeny analysis indicated that the two strains belonged to the genus Variovorax and were closely related to V. paradoxus NBRC 15149^T and V. boronicumulans BAM-48^T. Their phylogenetic relationship were confirmed in both phylogenetic trees constructed with house-keeping gene sequences and concatenated core genes of the genome. The ANI and dDDH comparisons among 502^T and the most related type strains showed values below the accepted threshold for species discrimination. The genome sizes of strains 502^T and T529 were 6.76 and 6.69 Mbp, respectively. The strain 502^T had 6,227 predicted genes with DNA G+C content of 67.4 %. The respiratory quinone was ubiquinone-8 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphospatidylglycerol. The major fatty acids of strain 502^T were C_{10: 0}3-OH (26.2%), C_16:0 (12.9%), C_17:0 cyclo (14.5%) and summed feature 3 (21.4%). Furthermore, both strains showed the potential of plant growth promotion. Based on these results, the two isolates could be considered to represent a novel species of the genus Variovorax, for which the name Variovorax beijingensis sp. nov., is proposed, with 502^T (= DSM 106862^T = CGMCC 1.16560^T) as the type strain.