Multiple horizontal acquisitions of plant genes in the whitefly Bemisia tabaci

The extent to which horizontal gene transfer (HGT) has shaped eukaryote evolution remains an open question. Two recent studies reported four plant-like genes acquired through two HGT events by the whitefly Bemisia tabaci, a major agricultural pest (Lapadula et al. 2020; Xia et al. 2021). Here, we performed a systematic search for plant-to-insect HGT in B. tabaci and uncovered a total of 50 plant-like genes deriving from at least 24 independent HGT events. Most of these genes are present in three cryptic B. tabaci species, show high level of amino-acid identity to plant genes (mean = 64%), are phylogenetically nested within plant sequences, and are expressed and evolve under purifying selection. The predicted functions of these genes suggest that most of them are involved in plant-insect interactions. Thus, substantial plant-to-insect HGT may have facilitated the evolution of B. tabaci towards adaptation to a large host spectrum. Our study shows that eukaryote-to-eukaryote HGT may be relatively common in some lineages and it provides new candidate genes that may be targeted to improve current control strategies against whiteflies.

An NMR fingerprint matching approach for the identification and structural re-evaluation of Pseudomonas lipopeptides.

Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs display diverse structural variations in terms of the number of the amino acid residues, macrocycle size, amino acid identity and stereochemistry (e.g. D- vs. L-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. However, in some cases, the lack of characterization detail threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. The NMR fingerprint matching approach introduced in this work exploits the fact that the 1H and 13C NMR chemical shift fingerprint is sufficiently sensitive to differentiate the diastereomers of a particular CLiP even when they only differ in a single D/L configuration. This provides a means for a fast screening to determine whether an extracted CLiP has been reported before, by simply comparing the fingerprint of a novel CLiP with that of a reference CLiP. Even when the stereochemistry of a particular reference CLiP is unknown, the NMR fingerprint approach still allows to verify whether a CLiP from a novel source is identical to the reference. To facilitate this, we have made a publicly available knowledge base at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. The latter includes a description of the CLiPs original description, molecular mass, three dimensional structures (if available), and a summary of published antimicrobial activities. Moreover, a detailed protocol will be made available for researchers that wish to record NMR data of their newly extracted lipopeptides to compare them to the publicly available reference data.

Rhizobium lacunae sp. nov., Isolated From a Freshwater Pond

Bacterial strain designated CSW-27T was isolated from a freshwater pond in Taiwan. Cells were Gram-stain-negative, aerobic, oxidase-positive, catalase-negative, rod-shaped and motile by flagella. Strain CSW-27T grew at 20-40 oC (optimum, 30-37 oC), at pH 5-9 (optimum, pH 6-7) and in the presence of 0-4% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set revealed that strain CSW-27T was affiliated with species in the genus Rhizobium. Analysis of 16S rRNA gene sequences showed that strain CSW-27T had the highest similarity to Rhizobium straminoryzae CC-LY845T (98.5%) followed by Rhizobium capsici CC-SKC2T (96.9%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CSW-27T and the closely related Rhizobium species were 73.4-86.5, 66.0-88.8 and 13.3-22.1%, respectively. The principal fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized aminophospholipid, three uncharacterized aminolipids and two uncharacterized lipids. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-27T was 63.3%. These polyphasic taxonomic data indicited that strain CSW-27T should be considered as representing a novel species in the genus Rhizobium, for which the name Rhizobium lacunae sp. nov. is proposed with strain CSW-27T (=BCRC 81244T =LMG 31684T) as the type strain.

Genomic Evaluation of the Genus Coltivirus Indicates Genetic Diversity among Colorado Tick Fever Virus Strains and Demarcation of a New Species

The type species of the genus Coltivirus, Colorado tick fever virus (CTFV), was discovered in 1943 and is the most common tick-borne viral infection in the Western US. Despite its long history, very little is known about the molecular diversity of viruses classified within the species Colorado tick fever coltivirus. Previous studies have suggested genetic variants and potential serotypes of CTFV, but limited genetic sequence information is available for CTFV strains. To address this knowledge gap, we report herein the full-length genomes of five strains of CTFV, including Salmon River virus and California hare coltivirus (CTFV-Ca). The sequence from the full-length genome of Salmon River virus identified a high genetic identity to the CTFV prototype strain with >90% amino acid identity in all the segments except segment four, suggesting Salmon River virus is a strain of the species Colorado tick fever coltivirus. Additionally, analysis suggests that segment four has been associated with reassortment in at least one strain. The CTFV-Ca full-length genomic sequence was highly variable from the prototype CTFV in all the segments. The genome of CTFV-Ca was most similar to the Eyach virus, including similar segments six and seven. These data suggest that CTFV-Ca is not a strain of CTFV but a unique species. Additional sequence information of CTFV strains will improve the molecular surveillance tools and provide additional taxonomic resolution to this understudied virus.

Paraneptunicella aestuarii gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from seawater in East China Sea

An aerobic Gram-stain-negative, curved rod-shaped and non-spore-forming bacterial strain (NBU2194T) was isolated from seawater collected in an intertidal zone in Ningbo, Zhejiang Province, PR China. It was motile though a single polar flagellum and grew at 20–42 °C (optimum, 30 °C), in 0–2.0 % NaCl (0 %, w/v) and at pH 5.0–9.0 (pH 6.0–7.0). The sole respiratory quinone was ubiquinone-8. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and/or C16 : 1 ω6c. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and two unidentified aminophosphoglycolipids. A phylogenetic analysis based on 16S rRNA gene sequences and 65 genomic core genes showed that strain NBU2194T formed a distinct lineage in the family Alteromonadaceae . The genome of strain NBU2194T was 4 913 533 bp with a DNA G+C content of 43.9 mol% and coded 3895 genes, 12 rRNA genes and 47 tRNA genes. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values between strain NBU2194T and related species of Alteromonadaceae were below the threshold limit for prokaryotic species delineation. NBU2194T could be distinguished from other genera in the family Alteromonadaceae based on phenotypic, chemotaxonomic and genomic characteristics. On the basis of the polyphasic taxonomic evidence collected in this study, strain NBU2194T is considered to represent a novel genus and species in the family Alteromonadaceae , for which the name Paraneptunicella aestuarii is proposed. The type strain is NBU2194T (=KCTC 82442T=GDMCC 1.2217T).

Roseococcus microcysteis sp. nov., isolated from a Microcystis aeruginosa culture sample

Strain NIBR12T (=KACC 22094T=HAMBI 3739T), a novel Gram-stain-negative, obligate aerobic, non-spore-forming, non-motile and coccobacillus-shaped bacterium, was isolated from a cyanobacterial sample culture (Microcysitis aeruginosa NIBRCYC000000452). The newly identified bacterial strain grew optimally in modified Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5 and 35 °C. Phylogenetic analysis using the 16S rRNA gene sequence confirmed that strain NIBR12T belongs to the genus Roseococcus , with its closest neighbours being Roseococcus suduntuyensis SHETT (98.8%), Roseococcus thiosulfatophilus RB-3T (97.7%), “Sediminicoccus rosea” R-30T (95.7 %) and Rubritepida flocculans H-8T (95.0 %). Genomic comparison of strain NIBR12T with type species in the genus Roseococcus was conducted using digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity analyses, resulting in values of ≤53.7, ≤93.7 and ≤96.1 %, respectively. The genomic DNA G+C content of strain NIBR12T was 70.9 mol%. The major fatty acids of strain NIBR12T were summed feature 8 (C18 : 1 ω7c and/or C18:1 ω6c) and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). Q-9 was its major respiratory quinone. Moreover, the major polar lipids of strain NIBR12T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on our chemotaxonomic, genotypic and phenotype analyses, strain NIBR12T is identified as represeting a novel species of the genus Roseococcus , for which the name Roseococcus microcysteis sp. nov. is proposed.

Mining marine metagenomes revealed a quorum-quenching lactonase with improved biochemical properties that inhibits the food spoilage bacteria Pseudomonas fluorescens

The marine environment presents great potential as a source of microorganisms that possess novel enzymes with unique activities and biochemical properties. Examples of such are the quorum-quenching (QQ) enzymes that hydrolyze bacterial quorum-sensing (QS) signaling molecules, such as N-acyl-homoserine lactones (AHLs). QS is a form of cell-to-cell communication that enables bacteria to synchronize gene expression in correlation with population density. Searching marine metagenomes for sequences homologous to an AHL lactonase from the phosphotriesterase-like lactonase (PLL) family, we identified new putative AHL lactonases (sharing 30-40% amino acid identity to a thermostable PLL member). Phylogenetic analysis indicated that these putative AHL lactonases comprise a new clade of marine enzymes in the PLL family. Following recombinant expression and purification, we verified the AHL lactonase activity for one of these proteins, named marine originated Lactonase Related Protein (moLRP). This enzyme presented greater activity and stability at a broad range of temperatures and pH, and tolerance to high salinity levels (up to 5M NaCl), as well as higher durability in bacterial culture, compared to another PLL member. The addition of purified moLRP to cultures of Pseudomonas fluorescens inhibited its extracellular protease activity, expression of the protease encoding gene, biofilm formation, and the sedimentation process in milk-based medium. These findings suggest that moLRP is adapted to the marine environment, and can potentially serve as an effective QQ enzyme, inhibiting the QS process in gram-negative bacteria involved in food spoilage. Importance Our results emphasize the potential of sequence and structure-based identification of new quorum-quenching (QQ) enzymes from environmental metagenomes, such as from the ocean, with improved stability or activity. The findings also suggest that purified QQ enzymes can present new strategies against food spoilage, in addition to their recognized involvement in inhibiting bacterial pathogen virulence factors. Future studies on the delivery and safety of enzymatic QQ strategy against bacterial food spoilage should be performed.

Isolation and Characterization of Bovine RVA from Northeast China, 2017–2020

Group A rotaviruses (RVAs) are major enteric pathogens causing infections in calves. To investigate the epidemiological characteristics and genetic diversity of bovine rotavirus (BRV), 233 fecal samples were collected from calves with diarrhea in northeast China. The samples were analyzed for sequences encoding the inner capsid protein VP6 (subgroup) and the outer capsid proteins VP7 and VP4 (G and P type, respectively) using RT-PCR. Ten of the 233 samples (4.3%) were identified as BRV positive and were used for virus isolation and sequence analysis, revealing that all strains analyzed were of the G6P[1] genotype. The isolates exhibited high VP6 sequence identity to the USA cow RVA NCDV strain (>99% amino acid identity) and were further shown to be closely related to Japanese cow RVA BRV101 and Israelian human RVA G6P[1] strains, with >99% amino acid identity to VP7 and VP4 proteins, respectively. Comparative analyses of genome-predicted amino acid sequences between the isolates and the NCDV strains indicated that the antigenicity and infectivity of the strains isolated had changed. In this study, BRV genotypes and the genetic diversity among vaccinated cattle herds were monitored to provide epidemiological data and references for early diagnosis, allowing for early detection of new, potentially pathogenic RVA strains.

Xanthobacter dioxanivorans sp. nov., a 1,4-dioxane-degrading bacterium

A Gram-stain-negative bacterium, designated as YN2T, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2T were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2T grew at 10–40 °C (optimum, 30 °C), pH 5.0–8.0 (pH 7.0) and with 0–1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N2 when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2T belongs to the genus Xanthobacter and shares the highest pairwise identity with Xanthobacter autotrophicus 7cT (98.6 %) and Xanthobacter flavus 301T (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C16 : 0, C19 : 0 cyclo ω8c and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA–DNA hybridization estimate values between strain YN2T and X. autotrophicus 7cT, X. flavus 301T and X. tagetidis TagT2CT (the only three species of Xanthobacter with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2T is considered to represent a novel species of the genus Xanthobacter , for which the name Xanthobacter dioxanivorans sp. nov. is proposed. The type strain is YN2T (=CGMCC 1.19031T=JCM 34666T).

Acuticoccus mangrovi sp. nov., with an antibacterial property, isolated from mangrove sediment

A Gram-stain-negative, aerobic, milky white bacterium, designated B2012T, was isolated from mangrove sediment collected at Beibu Gulf, South China Sea. Antimicrobial activity assay revealed that the isolate possesses the capability of producing antibacterial compounds. Strain B2012T shared the highest 16S rRNA gene sequence relatedness (96.9–95.5 %) with members of the genus Acuticoccus . The isolate and all known Acuticoccus species contain Q-10 as the main respiratory quinone and have the same polar lipid components (phosphatidylcholine, unidentified glycolipid, unidentified lipid, unidentified amino lipid and phosphatidylglycerol). However, genomic relatedness referred by values of average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity and the percentage of conserved proteins between strain B2012T and other type strains of the genus Acuticoccus were below the proposed thresholds for species discrimination. The genome of strain B2012T was assembled into 65 scaffolds with an N50 size of 244239 bp, resulting in a 5.5 Mb genome size. Eight secondary metabolite biosynthetic gene clusters were detected in this genome, including three non-ribosomal peptide biosynthetic loci encoding yet unknown natural products. Strain B2012T displayed moderately halophilic and alkaliphilic properties, growing optimally at 2–3 % (w/v) NaCl concentration and at pH 8–9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0, C16 : 0 dimethyl aldehyde (DMA) and C16 : 0. Combined data from phenotypic, genotypic and chemotaxonomic analyses suggested that strain B2012T represents a novel species of the genus Acuticoccus , for which the name Acuticoccus mangrovi sp. nov. is proposed. The type strain of the type species is B2012T (=MCCC 1K04418T=KCTC 72962T).