Elevation of three subspecies of Lonsdalea quercina to species level: Lonsdalea britannica sp. nov., Lonsdalea iberica sp. nov. and Lonsdalea populi sp. nov

Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America

Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and diversity of two populations of the bacterial oak pathogen Lonsdalea quercina from western North America (Colorado and California) and compared these populations to other Lonsdalea species found worldwide. Phylogenetic analysis separated Colorado and California populations into two Lonsdalea clades, with genetic divergence near species boundaries, suggesting long isolation and populations that differ in genetic structure and distribution and possibly their polyphyletic origin. Genotypes collected from different host species and habitats were randomly distributed within the California cluster. Most Colorado isolates from introduced planted trees, however, were distinct from three isolates collected from a natural stand of Colorado native Quercus gambelii, indicating cryptic population structure. The California identical core genotypes distribution varied, while Colorado identical core genotypes were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to its long presence in Colorado or due to migrants moving with nursery stock. Overall, results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystems changes. Further studies are warranted to understand evolutionary relationships among L. quercina from different areas, including the red oak native habitat in northeastern USA.

Diversity, antimicrobial production, and seasonal variation of honey bee microbiota isolated from the honey stomachs of the domestic honey bee, Apis mellifera

The antimicrobial nature of honey and its related apiological origins typically focus on basic chemical analysis without attempting to understand the diversity of the microbial component. The antibacterial activity, chemical characterization, and diversity of bacteria isolated from Apis mellifera honey stomachs and hive honey collected throughout the honey production season are presented. After screening >2,000 isolates, 50 isolates were selected and characterized by 16S rRNA gene homology, Gram stain, catalase and protease tests, as well as for antibacterial activity against select indicators. Antibacterial-producing isolates were predominantly from the Pseudomonas, Paenibacillus, Lonsdalea, Serratia, and Bacillus genera. Isolates collected from honey stomachs in April displayed the highest level of activity (27%). While April isolates did not demonstrate activity against the Gram-negative bacteria tested. Whereas 59% of July isolates, 33% of September isolates, and 100% of the honey isolates did. The predominant honey stomach isolates were Pseudomonas spp. (April), Paenibacillus polymyxa (July, Sept.), and Lonsdalea iberica (Sept.). Chemical characterizations of the antimicrobial compounds show most to be antibiotic in nature with the minority being potential bacteriocins. This study offers the first glimpse into the variability and diversity of the bacteria/host interactions found within the honey stomach of the domestic honey bee while revealing a novel source of potentially beneficial antimicrobial compounds.

Beehives possess their own distinct microbiomes

BACKGROUND

Honeybees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. While producing these products, beehives accumulate a considerable number of microbes, including bacteria that derive from plants and different parts of the honeybees' body. Whether bacteria form similar communities amongst beehives, even if located in close proximity, is an ecologically important question that has been addressed in this study. Specific ecological factors such as the surrounding environment and the beekeeping methods used can shape the microbiome of the beehive as a whole, and eventually influence the health of the honeybees and their ecosystem.

RESULTS

We conducted 16S rRNA meta-taxonomic analysis on honey and beebread samples that were collected from 15 apiaries in the southeast of England to quantify the bacteria associated with different beehives. We observed that honeybee products carry a significant variety of bacterial groups that comprise bee commensals, environmental bacteria and symbionts and pathogens of plants and animals. Remarkably, this bacterial diversity differs not only amongst apiaries, but also between the beehives of the same apiary. In particular, the levels of the bee commensals varied significantly, and their fluctuations correlated with the presence of different environmental bacteria and various apiculture practices.

CONCLUSIONS

Our results show that every hive possesses their own distinct microbiome and that this very defined fingerprint is affected by multiple factors such as the nectar and pollen gathered from local plants, the management of the apiaries and the bacterial communities living around the beehives. Based on our findings, we suggest that the microbiome of beehives could be used as a valuable biosensor informing of the health of the honeybees and their surrounding environment.

Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling

Acute Oak Decline (AOD) is complex syndrome affecting Britain’s keystone native oak species, (Quercus robur L. and Q. petraea L. (Matt.) Liebl.), in some cases causing mortality within five years of symptom development. The most distinguishable symptom is weeping stem lesions, from which four species of bacteria have been isolated: Brenneria goodwinii, Gibbsiella quercinecans, Lonsdalea britannica and Rahnella victoriana. We do not yet know where else these bacteria exist, and little is known about the relationship of the wider oak leaf microbiome (phyllosphere) to acute oak decline. Here we investigate whether incidental evidence from a large oak genome re-sequencing dataset could be used to detect these bacteria in oak foliage, and whether bacterial incidence co-varied with AOD status or location. Oak leaves and buds were sampled from 421 trees at five sites in England. Whole genomic DNA from these samples was shot-gun sequenced with short reads. Non-oak reads were extracted from these data and queried to microbial databases. Reads uniquely matching AOD-associated bacterial genomes were found to be present on trees from all five sites and included trees with active lesions, trees with historic lesions and trees without AOD symptoms. The abundance of the AOD-associated bacteria did not differ between tree health categories but did differ among sites. We conclude that the AOD-associated bacteria may be members of the normal oak microbiome, whose presence on a tree is not sufficient to cause AOD symptoms.

Metagenomic Insights Into Functional and Taxonomic Compositions of an Activated Sludge Microbial Community Treating Leachate of a Completed Landfill: A Pathway-Based Analysis

Upcycling wastes into valuable products by mixed microbial communities has recently received considerable attention. Sustainable production of high-value substances from one-carbon (C1) compounds, e.g., methanol supplemented as an external electron donor in bioreactors for wastewater treatment, is a promising application of upcycling. This study undertook a gene-centric approach to screen valuable production potentials from mixed culture biomass, removing organic carbon and nitrogen from landfill leachate. To this end, the microbial community of the activated sludge from a landfill leachate treatment plant and its metabolic potential for the production of seven valuable products were investigated. The DNA extracted from the activated sludge was subjected to shotgun metagenome sequencing to analyze the microbial taxonomy and functions associated with producing the seven products. The functional analysis confirmed that the activated sludge could produce six of the valuable products, ectoine, polyhydroxybutyrate (PHB), zeaxanthin, astaxanthin, acetoin, and 2,3-butanediol. Quantification of the detected functional gene hit numbers for these valuable products as a primary trial identified a potential rate-limiting metabolic pathway, e.g., conversion of L-2,4-diaminobutyrate into N-γ-acetyl-L2,4,-diaminobutyrate during the ectoine biosynthesis. Overall, this study demonstrated that primary screening by the proposed gene-centric approach can be used to evaluate the potential for the production of valuable products using mixed culture or single microbe in engineered systems. The proposed approach can be expanded to sites where water purification is highly required, but resource recovery, or upcycling has not been implemented.

Affinibrenneria salicis gen. nov. sp. nov. isolated from Salix matsudana bark canker

L3-3HA^T, a Gram-negative-staining, facultatively anaerobic, motile bacterial strain, was isolated from the symptomatic bark of Salix matsudana canker in China. 16S rRNA gene analysis revealed that the novel strain shares the highest sequence similarity with Brenneria goodwinii FRB141^T (95.5%). In phylogenetic trees based on four housekeeping genes (gyrB, rpoB, atpD, and infB) and the 16S rRNA gene sequence, the novel strain formed a separate branch from the five genera of the family Pectobacteriaceae (Lonsdalea, Brenneria, Dickeya, Pectobacterium, and Sodalis), suggesting that the novel strain should belong to a novel species of a novel genus within the family Pectobacteriaceae. The result was also supported by phylogenomics, amino acid identity and average nucleotide identity. The major fatty acids were C_14:0, C_16:0, C_17:0 cyclo, and C_19:0 cyclo ɷ8c. Genome analysis showed that the novel strain has a large genome (5.89 Mb) with 5,052 coding genes, including 181 virulence genes by searching the pathogen-host interactions database (PHI-base), indicating that the novel strain is a potential pathogen of plants and animals. Based on phenotypic and genotypic characteristics, the L3-3HA^T strain represents a novel species of a novel genus in the Pectobacteriaceae family, for which the name Affinibrenneria salicis gen nov. sp. nov. is proposed. The strain type is L3-3HA^T (= CFCC 15588^T = LMG 31209^T).

The Two-Component System DcuS-DcuR Is Involved in Virulence and Stress Tolerance in the Poplar Canker Bacterium Lonsdalea populi

The gram-negative bacterium Lonsdalea populi causes an emerging poplar (Populus × euramericana) canker resulting in severe losses to poplar production in China and Europe. Two-component signal transduction systems play important roles in the regulation of virulence and stress responses in phytopathogenic bacteria. We identified a two-component pair (Lqp2625-Lqp2624) in L. populi, highly homologous to DcuS-DcuR of Escherichia coli. Mutants lacking DcuS or DcuR displayed normal growth while their virulence on poplar twigs was impaired. An inability to produce flagella indicated that DcuS and DcuR are involved in biofilm formation and swimming motility. Moreover, the loss of DcuS or DcuR led to increased sensitivity to oxidative stress and chloramphenicol through downregulation of genes associated with catalases and the multidrug efflux pump, suggesting that the two-component pair contributes to cellular adaptation to oxidative and antibiotic stresses. We identified key domains and putative phosphorylation sites important for virulence and stress responses. Our findings reveal the functions of DcuS-DcuR in virulence and stress responses in L. populi and provide increasing evidence that two-component systems are crucial during the infection process and stress adaptation in bacteria.

Stenotrophomonas cyclobalanopsidis sp. nov., isolated from the leaf spot disease of Cyclobalanopsis patelliformis

A Gram-negative, facultatively anaerobic, motile bacterial strain, TPQG1-4^T, was isolated from the leaf of Cyclobalanopsis patelliformis with spot disease. The isolate was investigated using the polyphasic taxonomic approach. 16S rRNA gene sequencing and analyzing revealed that the novel strain shares the highest sequence similarity with Stenotrophomonas lactitubi M15^T (99.6%), Stenotrophomonas indicatrix WS40^T (99.4%), Stenotrophomonas maltophilia IAM 12423^T (99.2%) and Stenotrophomonas pavanii LMG 25348^T (99.0%). In phylogenetic trees based on 16S rRNA gene sequences, the novel strain branched independently from other species of Stenotrophomonas. Average nucleotide identity values between the novel isolate and S. lactitubi M15^T, S. indicatrix WS40^T, S. maltophilia IAM 12423^T, S. pavanii LMG 25348^T, and Pseudomonas geniculata ATCC 19374^T were 87.2%, 87.3%, 86.3%, 88.0%, and 81.3%, respectively, suggesting the isolate was a novel species of the genus Stenotrophomonas. The DNA G + C content of TPQG1-4^T is 67.1 mol%. The major fatty acids were iso-C_15:0 (25.4%) and anteiso-C_15:0 (17.0%). The polar lipids of TPQG1-4^T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, amino phospholipid and phospholipid. Based on phenotypic and genotypic characteristics, the strain represents a novel species in the genus Stenotrophomonas, for which the name Stenotrophomonas cyclobalanopsidis sp. nov. is proposed. The type strain is TPQG1-4^T (= CFCC 15341^T = LMG 31208^T).

Molecular Aspects of an Emerging Poplar Canker Caused by Lonsdalea populi

The Gram-negative bacterium Lonsdalea populi causes a lethal disease known as bark canker on Populus × euramericana in China and Europe. Typical symptoms of bark canker include an abundant white-colored fluid, which oozes from the infected tissues. The availability of the genomic sequence of the bacterium provided the necessary resource to launch genome-scale investigations into the mechanisms fundamental to pathogenesis. Functional analyses of a diverse group of genes encoding virulence factors and components of signaling pathways indicate that successful bark infection depends on specific responses by the pathogen to various stresses, including oxidative stress. Although physiology of resistance is well studied, the molecular processes underlying the defense responses and the genetic basis of resistance to L. populi and in other poplar species remain largely unknown. Control of the disease has relied on chemical measures. Due to the genetic amenability of Lonsdalea and poplar, this pathosystem will become an important model system to unravel molecular mechanisms of bacterial pathogenicity on woody plants. Increased understanding of pathogenesis and signaling in the interaction will facilitate the management of this kind of poplar canker.

Corticimicrobacter populi gen. nov., sp. nov., a member of the family Alcaligenaceae, isolated from symptomatic bark of Populus × euramericana canker

One Gram-negative aerobic bacterial strain was isolated from the bark tissue of Populus × euramericana and investigated using a polyphasic approach including 16S rRNA gene sequencing and both phenotypic and chemotaxonomic assays. The 16S rRNA gene and housekeeping gene phylogenies suggest that the novel isolate is different from the other genera of the family Alcaligenaceae. The G+C content, major fatty acids, physiological and biochemical data supported the distinctiveness of the novel strain from reference species. The major fatty acids detected in the novel isolate were C_16 : 1ω7c and/or C_16 : 1ω6c, C_16 : 0, C_14 : 0 3OH and/or C_16 : 1isoI and C_18 : 1ω7c. The phospholipid profile of strain d3-2-2^T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminolipid, aminophospholipid and an unidentified lipid. The quinone of the novel isolate was Q-8. Therefore, based on the data, the strain constitutes a novel species of a novel genus within the family Alcaligenaceae, for which the name Corticimicrobacter populi gen. nov., sp. nov. is proposed. The type strain is 3d-2-2^T (=CFCC 11891^T=KCTC 52807^T).

Insects Visiting Drippy Blight Diseased Red Oak Trees Are Contaminated with the Pathogenic Bacterium Lonsdalea quercina

The focus of investigation in this study was to consider the potential of arthropods in the dissemination of the bacterium involved in drippy blight disease, Lonsdalea quercina. Arthropod specimens were collected and tested for the presence of the bacterium with molecular markers. The bacterium L. quercina was confirmed on 12 different insect samples from three orders (Coleoptera, Hemiptera, and Hymenoptera) and eight families (Buprestidae, Coccinellidae, Dermestidae, Coreidae, Pentatomidae and/or Miridae, Apidae, Formicidae, and Vespidae). Approximately half of the insects found to carry the bacterium were in the order Hymenoptera. Estimates of the insects that are contaminated with the bacterium, and likely carry it between trees, is conservative because the documented insects represent only a subset of the insect orders that were observed feeding on the bacterium or present on diseased trees yet were not able to be tested. The insects contaminated with L. quercina exhibited diverse life histories, where some had a facultative relationship with the bacterium and others sought it out as a food source. These findings demonstrate that a diverse set of insects naturally occur on diseased trees and may disseminate L. quercina.

Brenneria corticis sp. nov., isolated from symptomatic bark of Populus×euramericana canker

A Gram-stain-negative, facultatively anaerobic, motile bacterial strain, designated gBX10-1-2^T, was isolated from symptomatic bark of Populus×euramericana canker in China. Phylogenetic analysis based on its 16S rRNA gene sequence showed that the novel isolate belonged to the genus Brenneria, and shared the highest sequence similarity to Brenneria nigrifluens LMG 2694^T (98.3 %). In the phylogenetic trees based on the four housekeeping genes sequences, the novel strain formed a separate branch different from B. nigrifluens LMG 2694^T, indicating that the novel strain should be classified as a novel species. The genome sequence-derived average nucleotide identity (ANI) values between the novel isolate and B. nigrifluens LMG 2694^T, Brenneria roseaesubsp. roseae FRB 222^T and Brenneria roseaesubsp. americana FRB 223^T were less than 85 %, lower than the proposed species boundary ANI cut-off value (95-96 %). The DNA G+C content was 56.2 mol%, and the main fatty acids were C16 : 0, C16 : 1ω7c, C18 : 1ω7c and C17 : 0cyclo. Based on the phenotypic and genotypic characteristics, strain gBX10-1-2^T represents a novel species of genus Brenneria, for which the name Brenneria corticis sp. nov. is proposed. The type strain is gBX10-1-2^T (=CFCC 11842^T=KCTC 42840^T).

A Large-Scale Mutational Analysis of Two-Component Signaling Systems of Lonsdalea quercina Revealed that KdpD-KdpE Regulates Bacterial Virulence Against Host Poplar Trees

Poplar, which is a dominant species in plant communities distributed in the northern hemisphere, is commonly used as a model plant in forestry studies. Poplar production can be inhibited by infections caused by bacteria, including Lonsdalea quercina subsp. populi, which is a gram-negative bacterium responsible for bark canker disease. However, the molecular basis of the pathogenesis remains uncharacterized. In this study, we annotated the two-component signal transduction systems (TCSs) encoded by the L. quercina subsp. populi N-5-1 genome and identified 18 putative histidine kinases and 24 response regulators. A large-scale mutational analysis revealed that 19 TCS genes regulated bacterial virulence against poplar trees. Additionally, the deletion of kdpE or overexpression of kdpD resulted in almost complete loss of bacterial virulence. We observed that kdpE and kdpD formed a bi-cistronic operon. KdpD exhibited autokinase activity and could bind to KdpE (K_d = 5.73 ± 0.64 μM). Furthermore, KdpE is an OmpR family response regulator. A chromatin immunoprecipitation sequencing analysis revealed that KdpE binds to an imperfect palindromic sequence within the promoters of 44 genes, including stress response genes Lqp0434, Lqp3037, and Lqp3270. A comprehensive analysis of TCS functions may help to characterize the regulation of poplar bark canker disease.