A Methyl-Accepting Chemotaxis Protein MCP-5685 Associated with Indole Synthesis in Pantoea ananatis YJ76 Influences its Plant Growth-Promoting Potential and Adaptability to Stress Conditions

Pantoea ananatis YJ76 is a predominant endophytic diazotrophic bacterium isolated from rice, which can produce indole as a signal to improve stress resistance, colonization, and growth-promoting effect on the host. Methyl-accepting chemotaxis proteins (MCPs) are the main chemoreceptor in bacteria and participate in regulating various cellular activities. By constructing an mTn5 transposon mutant library of YJ76, we screened out a mutant with decreased indole production. And its ability to resist stresses and starvation, as well as colonizing and growth-promoting effect on host rice plants, was inhibited. Using the hiTAIL-PCR technique combined the genome re-sequencing, the mutation site was identified as the mcp-5685 gene with a length of 1545 bp. Bioinformatics analysis and chemotaxis experiments showed that the MCP encoded by mcp-5685 had L-serine chemotaxis functions, revealing the mechanism of the gene encoding protein to drive L-serine uptake, a key component for tryptophan synthesis, and thus promote indole synthesis in the regulatory pathways for indole synthesis. Starting from the upstream regulation direction of indole synthesis, this study breaks through the previous researching limitation of focusing only on the downstream physiological function regulation of indole and provides new ideas for studying the indole signal.

Indole-3-acetic acid (IAA) protects Azospirillum brasilense from indole-induced stress

Azospirillum brasilense is plant-growth promoting rhizobacteria that produces the phytohormone indole-3-acetic acid (IAA) to induce changes in plant root architecture. The major pathway for IAA biosynthesis in A. brasilense converts tryptophan into indole-3-pyruvic acid (I3P) and then, through the rate-limiting enzyme, indole-3-pyruvate decarboxylase (IpdC), into IAA. Here, we characterize the potential role for IAA biosynthesis in the physiology of these bacteria by characterizing the expression pattern of the ipdC promoter, analyzing an A. brasilense ipdC mutant using multiple physiological assays and characterizing the effect of I3P, which likely accumulates in the absence of ipdC and affects bacterial physiology. We found that the ipdC mutant derivative has a reduced growth rate and an altered physiology, including reduced translation activity as well as a more depolarized membrane potential compared to the parent strain. Similar effects could be recapitulated in the parent strain by exposing these cells to increasing concentrations of I3P, as well as other indole intermediates of IAA biosynthesis. Our results also indicate a protective role for IAA against the harmful effects of indole derivatives, with exogenous IAA restoring the membrane potential of cells exposed to indole derivatives for prolonged periods. These protective effects appeared to restore cell physiology, including in the wheat rhizosphere. Together, our data suggest that the IAA biosynthesis pathway plays a major role in A. brasilense physiology by maintaining membrane potential homeostasis and regulating translation, likely to mitigate the potential membrane-damaging effects of indoles that accumulate during growth under stressful conditions.IMPORTANCEIAA is widely synthesized in bacteria, particularly in soil and rhizosphere bacteria, where it functions as a phytohormone to modulate plant root architecture. IAA as a secondary metabolite has been shown to serve as a signaling molecule in several bacterial species, but the role of IAA biosynthesis in the physiology of the producing bacterium remains seldom explored. Results obtained here suggest that IAA serves to protect A. brasilense from the toxic effect of indoles, including metabolite biosynthetic precursors of IAA, on membrane potential homeostasis. Given the widespread production of IAA in soil bacteria, this protective effect of IAA may be conserved in diverse soil bacteria.

Identification of Pantoea ananatis strain BCA19 as a potential biological control agent against Erwinia amylovora

In this study, we aimed to screen potential antagonistic microorganisms against Erwinia amylovora, the causal agent of fire blight. From 127 unknown bacterial isolates tested, 2 bacterial strains (BCA3 and BCA19) were identified to show distinct antagonistic activity against E. amylovora in agar plate assay. Phylogenetic analysis of the 16s rRNA sequence identified both BCA3 and BCA19 as Pantoea ananatis. Among these BCA19 showed 13.9% stronger antagonistic activity than BCA3. Thus we further characterized antagonistic activity of BCA19. Culture filtrates (CF) of BCA19 significantly inhibited the swimming and swarming motility of E. amylovora. Ethyl acetate and n-butanol extracts of CF of BCA19 exhibited antibacterial activity in disk diffusion assay. Furthermore, gas chromatography-mass spectrometry analysis of ethyl acetate and n-butanol extracts of CF of BCA19 identified antibacterial compounds, including indole and hexahydropyrrolo[1,2-a]pyrazine-1,4-dione. Importantly, indole inhibited growth of E. amylovora with IC50 value of 0.109 ± 0.02 mg/mL (~930.4 μM). Whole genome sequence analysis of BCA 19 revealed gene clusters related with siderphore, andrimid, arylpolyene and carotenoid-type terpene production. This study indicates that BCA19 can be used as a potential biological control agent against Erwinia amylovora.

Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)

Background

This paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth.

Methods

P. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out.

Results and discussion

The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.

A new l-serine binding orphan SerBP affects indole synthesis in Pantoea ananatis

Indole is traditionally known as a metabolite of l-tryptophan and now as an important signaling molecule in bacteria, however, the understanding of its upstream synthesis regulation is very limited. Pantoea ananatis YJ76, a predominant diazotrophic endophyte isolated from rice (Oryza sativa), can produce indole to regulate various physiological and biochemical behaviors. We constructed a mutant library of YJ76 using the mTn5 transposon insertion mutation method, from which an indole-deficient mutant was screened out. Via high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR), the transposon was determined to be inserted in a gene (RefSeq: WP014605468.1) of unknown function that is highly conserved at the intraspecific level. Bioinformatics analysis implied that the protein (Protein ID: WP089517194.1) encoded by the mutant gene is most likely to be a new orphan substrate-binding protein (SBP) for amino acid ABC transporters. Amino acid supplement cultivation experiments and surface plasmon resonance revealed that the protein could bind to l-serine (KD  = 6.149 × 10-5  M). Therefore, the SBP was named as SerBP. This is the first case that a SBP responds to l-serine ABC transports. As a precursor of indole synthesis, the transmembrane transported l-serine was directly correlated with indole signal production and the mutation of serBP gene weakened the resistance of YJ76 to antibiotics, alkali, heavy metals, and starvation. This study provided a new paradigm for exploring the upstream regulatory pathway for indole synthesis of bacteria.

Some like it cold: The cellular organization and physiological limits of cold-tolerant nitrite-oxidizing Nitrotoga

Chemolithoautotrophic production of nitrate is accomplished by the polyphyletic functional group of nitrite-oxidizing bacteria (NOB). A widely distributed and important NOB clade in nitrogen removal processes at low temperatures is Nitrotoga, which however remains understudied due to the scarcity of cultivated representatives. Here, we present physiological, ultrastructural and genomic features of Nitrotoga strains from various habitats, including the first marine species enriched from an aquaculture system. Immunocytochemical analyses localized the nitrite-oxidizing enzyme machinery in the wide irregularly shaped periplasm, apparently without contact to the cytoplasmic membrane, confirming previous genomic data suggesting a soluble nature. Interestingly, in two strains we also observed multicellular complexes with a shared periplasmic space, which seem to form through incomplete cell division and might enhance fitness or survival. Physiological tests revealed differing tolerance limits towards dissolved inorganic nitrogen concentrations and confirmed the generally psychrotolerant nature of the genus was. Moreover, comparative analysis of 15 Nitrotoga genomes showed, e.g., a unique gene repertoire of the marine strain that could be advantageous in its natural habitat and confirmed the lack of genes for assimilatory nitrite reduction in a strain found to require ammonium for growth. Overall, these novel insights largely broaden our knowledge of Nitrotoga and elucidate the metabolic variability, physiological limits and thus potential ecological roles of this group of nitrite oxidizers. This article is protected by copyright. All rights reserved.

The cytidine repressor regulates the survival of Pantoea agglomerans YS19 under oxidative stress and sulfur starvation conditions

Pantoea agglomerans YS19 is a dominant endophytic bacterium isolated from rice, which is capable of promoting host plant growth by nitrogen-fixing and phytohormone secreting. We previously found that the cytidine repressor (CytR) protein conducts the regulation of indole signal in YS19. Here, we compared the whole-cell protein of the wild type YS19 and the ΔcytR mutant and subsequently identified one differential protein as alkyl hydroperoxide reductase subunit C related to oxidative stress and sulfur starvation tolerance. It was tested that cytR had a positive effect on the survival of YS19 under the oxidative stress and sulfur starvation conditions and this effect was inhibited by indole. To further understand the functional mode of indole in this regulation, we cloned the cytR promoter region (P_cytR) of YS19 and tested the effect of indole on P_cytR using gfp as a reporter gene. It was found that P_cytR can sense indole and significantly inhibit the expression of the downstream gene. This study provided a deeper understanding of the multiple function of cytR and expanded a new research direction of how indole participates in gene regulation.

Identification of bacterial isolates from commercial poultry feed via 16S rDNA

The study's objective was to identify typical aerobic isolates from commercial, corn-soybean meal poultry diets utilizing 16S rDNA, assign them their corresponding taxonomy, and compare the data with the previously published WGS analysis of these same isolates. Ten grams of a commercial corn-soybean meal poultry diet was homogenized in 100 mL of tryptic soy broth for 2 min, serially diluted, plated onto tryptic soy agar (TSA), and incubated aerobically for 24 h at 37 °C. Subsequently, 20 unique colonies were streaked for isolation on TSA and incubated aerobically for 24 h at 37 °C. This process was repeated three consecutive times for purification of isolates until only 11 morphologically distinct colonies were obtained. DNA was extracted using Qiagen's DNeasey® Blood and Tissue Kit. The 16S rRNA V4 region was targeted using an Illumina MiSeq and analyzed via QIIME2-2020.2. Alpha diversity and Beta diversity metrics were generated, and taxa were aligned using Silva in Qiime2-2020.2. Twenty-five distinct genera were identified within the 11 different colonies. Because 16S rDNA identification can provide an understanding of pathogen associations and microbial niches within an ecosystem, the information may present a potential method to establish and characterize the hygienic indicator microorganisms associated with poultry feed.

Pantoea ananatis, A New Bacterial Pathogen Affecting Wheat Plants (Triticum L.) in Poland

Wheat (Triticum aestivum) is one of the most economically important crops in the world. During the routine monitoring of wheat pest, the cereal leaf beetle (CLB, Oulema melanopus, Coleoptera, Chrysomelidae), in the Greater Poland region, it was observed that some leaves wounded by CLB also displayed brownish lesions with clear margins and yellow halo, disease symptoms resembling a bacterial infection. The aim of this study was therefore to investigate those symptoms to establish a causal agent of the disease. The identification based on the results of the Biolog’s Gen III system, 16S rRNA, and gyrB genes sequencing, revealed the presence of eight strains of Pantoea ananatis bacteria. Four strains were derived from wheat leaves (Ta024, Ta027, Ta030, Ta046), and four from the CLB’s oral secretion (OUC1, OUD2, OUF2, and OUG1). They shared the nucleotide identity ranging from 99 to 100% to P. ananatis strains deposited in the GenBank database. Additionally, the multi-locus sequence analysis (MLSA) of concatenated sequences of partial atpD, fusA, gyrB, rplB, and rpoB genes was performed. All P. ananatis strains isolated in Poland, grouped into one cluster supported with high bootstrap value. Pathogenicity tests performed on four varieties of wheat plants have identified P. ananatis strains as a causal agent of wheat disease. To our knowledge, this is the first report of P. ananatis affecting wheat plants.

Evaluation and improvement of phosphate solubilization by an isolated bacterium Pantoea agglomerans ZB

A phosphate solubilizing bacterium ZB was isolated from the rhizosphere soil of Araucaria, which falls into the species Pantoea agglomerans. Optimization for phosphate solubilization by strain ZB was performed. At optimum culture conditions, the isolate showed great ability of solubilizing different insoluble inorganic phosphate sources viz. Ca₃(PO₄)₂ (TCP), Hydroxyapatite (HP), CaHPO₄, AlPO₄, FePO₄ along with rock phosphates (RPs). Inoculation with planktonic cells was found to enhance dissolved phosphorous as compared to that achieved by symplasma inoculation. Besides inoculation with different status of cells, pre-incubation could also exert a great effect on phosphate solubilization ability of P. agglomerans. When isolate ZB was cultured with glucose as carbon sources, phosphorous was more efficiently dissolved from HP and RP without pre-incubation in comparison to that obtained with pre-cultivation. Pre-cultivation, however, was more suitable for P solubilization than no pre-cultivation when bacteria were grown with xylose. A positive correlation was detected between the production of organic acids and phosphate solubilization. P. agglomerans ZB possessed many plant growth promotion traits such as N₂ fixation and production of indole 3-acetic acid, phytase, alkaline phosphatase. Pot experiment showed inoculation with single isolate ZB or biofertilizer prepared from semi-solid fermentation of isolate ZB with spent mushroom substrate (SMS) compost could enhance plant growth with respect to number of leaves, plant leave area, stem diameter, root length, root dry mass, shoot dry mass and biomass when compared to the abiotic control, revealing strain ZB could be a promising environmental-friendly biofertilizer to apply for agricultural field.

Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges

Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.

Pantoea agglomerans YS19 poly(A) polymerase I gene possesses the indole-sensing sequence in the promoter region

Pantoea agglomerans YS19 is a predominant diazotrophic endophyte with multiple growth-promoting effects on its host plant that was isolated from rice. Indole is confirmed to induce many changes of physiological and biochemical characteristics in bacteria. Although YS19 cannot produce indole, it can sense indole in the environment and be regulated by indole. Here, using gfp as a reporter gene, we constructed a series of recombinant plasmids containing the promoter region of the poly(A) polymerase I gene (pcnB) fused with gfp, and compared the green fluorescence intensity at different concentrations of exogenous indole by a flow cytometer. In this research, we confirmed that exogenous indole significantly inhibited the expression of pcnB by its promoter; the regulation sequence sensitive to indole in the promoter region of the pcnB gene (In-pcnB) was between -129 and -88 bp. In-pcnB is widely distributed and strictly conserved in the same genus. These results suggest novel roles of In-pcnB in P. agglomerans YS19, showing its special relation to the indole regulatory pathway.

Extracellular DNA enhances the formation and stability of symplasmata in Pantoea agglomerans YS19

Extracellular DNA (eDNA) is an important polymeric substance that plays essential roles in cell aggregation and nutrient provision for the sessile bacteria. eDNA in bacterial biofilms was extensively studied. Here we found that eDNA also exists in symplasmata, a bacterial cell aggregate, which is different to a biofilm, in the rice enophyte Pantoea agglomerans YS19. We found that exogenous eDNA enhanced the formation and stability of symplasmata significantly, and that, exogenous eDNA also improved the stress resistance and colonization ability of the bacterium on host rice. These results strongly indicate novel roles of the eDNA in Pantoea agglomerans YS19, showing its special relation to the stress-resistance and endophyte-host association of the strain.

Colony analysis and deep learning uncover 5-hydroxyindole as an inhibitor of gliding motility and iridescence in Cellulophaga lytica

Iridescence is an original type of colouration that is relatively widespread in nature but has been either incompletely described or entirely neglected in prokaryotes. Recently, we reported a brilliant 'pointillistic' iridescence in agar-grown colony biofilms of Cellulophaga lytica and some other marine Flavobacteria that exhibit gliding motility. Bacterial iridescence is created by a unique self-organization of sub-communities of cells, but the mechanisms underlying such living photonic crystals are unknown. In this study, we used Petri dish assays to screen a large panel of potential activators or inhibitors of C. lytica's iridescence. Derivatives potentially interfering with quorum-sensing and other communication or biofilm formation processes were tested, as well as metabolic poisons or algal exoproducts. We identified an indole derivative, 5-hydroxyindole (5HI, 250 µM) which inhibited both gliding and iridescence at the colonial level. 5HI did not affect growth or cell respiration. At the microscopic level, phase-contrast imaging confirmed that 5HI inhibits the gliding motility of cells. Moreover, the lack of iridescence correlated with a perturbation of self-organization of the cell sub-communities in both the WT and a gliding-negative mutant. This effect was proved using recent advances in machine learning (deep neuronal networks). In addition to its effect on colony biofilms, 5HI was found to stimulate biofilm formation in microplates. Our data are compatible with possible roles of 5HI or marine analogues in the eco-biology of iridescent bacteria.

The cytidine repressor participates in the regulatory pathway of indole in Pantoea agglomerans

Indole, an important signal molecule in both intraspecies and interspecies, regulates a variety of bacterial behaviors, but its regulatory mechanism is still unknown. Pantoea agglomerans YS19, a preponderant endophytic bacterium isolated from rice, does not produce indole, yet it senses exogenous indole. In this study, a mutant of YS19-Rp^r whose target gene expression was downregulated by indole was selected through mTn5 transposon mutagenesis. Using the TAIL-PCR technique, the mutation gene was identified as a cytR homologue, which encodes a cytidine repressor (CytR) protein, a bacterial transcription factor involved in a complex regulation scheme. The negative regulation of indole in cytR, which is equivalent to the mutation in cytR, promotes the expression of a downstream gene deoC, which encodes the key enzyme deoxyribose-phosphate aldolase in participating in pentose metabolism. We found that DeoC is one of the regulatory proteins of P. agglomerans that is involved in counteracting starvation. Furthermore, the expression of deoC was induced by starvation conditions, accompanied by a decrease in cytR expression. This finding suggests that the indole signal and the mutation of cytR relieve inhibition of CytR in the transcription of deoC, facilitating better adaptation of the bacterium to the adverse conditions of the environment.

Indole enhances the survival of Pantoea ananatis YJ76 in face of starvation conditions

Pantoea ananatis YJ76 is an indole-producing predominant diazotrophic endophyte isolated from rice having multiple growth-promoting effects on host plant. As a decomposition metabolite of L-tryptophan (L-Trp), indole is confirmed to regulate various physiological processes of bacteria. In this research, we found that indole significantly improves the survival of YJ76 in face of starvation conditions and the promoting effect is related to the glycogen accumulation promoted by indole, which is much more significant in the middle decline phase than in other growth phases. Since carbon storage regulator CsrA is a key inhibiting factor on the storage of glycogen in bacteria, we explored the relation between indole-enhanced glycogen accumulation and csrA expression and found that there is a positive correlation between indole-enhanced glycogen accumulation and the indole-inhibited csrA expression in YJ76, which implies the potential relation between CsrA regulation and indole regulatory pathway.

Poly(A) polymerase I participates in the indole regulatory pathway of Pantoea agglomerans YS19

Pantoea agglomerans YS19 is a preponderant endophytic bacterium isolated from rice. It is characterized by the formation of symplasmata, a type of multicellular aggregate structure, contributing to a strong stress resistance and specific adaptation of YS19 in endophyte-host associations. Indole is an important signal molecule in intra- or interspecies relationships, regulating a variety of bacterial behaviours such as cell aggregation and stress resistance; however, the regulatory mechanism remains an ongoing area of investigation. This study selected YS19 as a model strain to construct a mutant library, utilizing the mTn5 transposon mutagenesis method, thus obtaining a positive mutant with an indole-inhibited mutation gene. Via thermal asymmetric interlaced PCR, the mutational site was identified as the gene of pcnB, which encodes the poly(A) polymerase I to catalyse the polyadenylation of RNAs. The full length of the pcnB sequence was 1332 bp, and phylogenetic analysis revealed that pcnB is extremely conserved among strains of P. agglomerans. The expression of the gene was significantly inhibited (by 36.6 % as detected via quantitative PCR) by indole (0.5 mM). Many physiological behaviours of YS19 were affected by this mutation: the cell decay rate in the post-stationary growth phase was promoted, symplasmata formation and motility were inhibited in the late stationary growth phase and the colonization ability and growth-promoting effect of YS19 on the host plant were also inhibited. This study discusses the indole regulatory pathways from the point of RNA post-transcriptional modification, thus enriching our knowledge of polyadenylation and expanding current research ideas of indole regulation.

D-tyrosine affects aggregation behavior of Pantoea agglomerans

D-amino acids have been proved to disassemble biofilms by disassociating the matrix. Pantoea agglomerans is characterized by the formation of another kind of multicellular structure called symplasmata, which also remains the ability to form biofilms. In this study, a rice diazotrophic endophyte P. agglomerans YS19 was selected as a model strain to explore the effects of D-amino acids on these two kinds of cell aggregate structures. It was discovered that D-tyrosine disassociates biofilm, yet promotes symplasmata formation. D-tyrosine showed no influence on bacterial growth yet promoted the bacterial motility and inhibited the expression of cellular MalE and OmpF proteins, which enriched our knowledge of the biological effect of D-amino acids and expanded the research ideas of symplasmata formation.

Symplasmata are a clonal, conditional, and reversible type of bacterial multicellularity

Microorganisms are capable of remarkable social behaviours, such as forming transient multicellular assemblages with properties and adaptive abilities exceeding those of individual cells. Here, we report on the formation and structure of genets known as symplasmata produced by Pantoea eucalypti bacteria. Each symplasmatum develops clonally and stochastically from a single bacterium into a membrane-delimited, capsule-embedded cluster of progeny cells and with a frequency that depends on temperature, pH, and nutrient availability. Transposon mutagenesis identified several gene products required for symplasmata formation, including master regulator LrhA, replication inhibitor CspD, polysaccharide transporter RfbX3, and autoinducer synthase PhzI. We also show that bacteria inside symplasmata are shaped irregularly with punctuated cell-to-cell contacts, metabolically responsive to environmental stimuli, dispersal-ready, and transcriptionally reprogrammed to anticipate multiple alternative futures in terms of carbon source availability. The structured and conditionable nature of symplasmata offers exciting prospects towards a mechanistic understanding of multicellular behaviours and their ecological significance.