Draft genome sequence data of Micrococcus yunnanesis strain ORF15-23 from rice rhizosphere soil in Thailand

A Gram-positive bacterium designated as strain ORF15-23 was isolated from a soil sample collected from rainfed organic paddy fields in Roi Et province, Thailand. This strain is previously reported to produce indole-3-acetic acid and 2-acetyl-1-pyrroline (2AP) compound, solubilize potassium feldspar and promote growth of rice seedlings. The genome sequencing was carried out using Illumina MiSeq platform. The draft genome of strain ORF15-23 was 2,562,005 bp in length with 1677 protein coding sequences and an average G + C content of 72.97 mol.%. Phylogenomic tree supports the assignment of strain ORF15-23 as member of the genus Micrococcus. A comparison of average nucleotide identity (ANIb) values revealed that strain ORF15-23 shared 96.95 % identity with the genome of M. yunnanensis DSM 21948T. The draft genome sequence of M. yunnanesis ORF15-23 has been deposited in the DDBJ/EMBL/GenBank databases under the accession number JAZDRZ000000000. This genome sequence data provides insightful information for the taxonomic characterization and further biotechnological exploitation of M. yunnanesis ORF15-23.

DSM 41014 and DSM 41981 from the DSMZ strain collection

Streptomyces sp. DSM 41014, DSM 41527, and DSM 41981 are three strains from the DSMZ strain collection. Here, we present the draft genome sequences of DSM 41014, DSM 41527, and DSM 41981 with a size of 9.09 Mb, 8.45 Mb, and 9.23 Mb, respectively.

Complete genome sequence of Psychrobacter cibarius AOSW16051, a trimeric autotransporter adhesin synthesizing bacterium isolated from the Baltic Sea

Bacteria of the genus Psychrobacter are widely distributed in the global low-temperature marine environment and have been studied for their effects on the settlement and metamorphosis of marine invertebrates. Psychrobacter cibarius AOSW16051 was isolated from the surface water samples of the Baltic Sea on the edge of the Arctic Ocean. Here, we present the complete genome of strain AOSW16051, which consists of a circular chromosome composed of 3,425,040 nucleotides with 42.98% G + C content and a circular plasmid composed of 5846 nucleotides with 38.66% G + C content. The genes predicted in this strain showed its strong outer membrane system, type VI secretion system and adhesion system. Trimeric autotransporter adhesins (TAAs) has been identified in the genome of P. cibarius AOSW16051, which has a variety of biological functions in interacting with host cells. However, there are no reports on TAAs in marine bacteria and aquatic pathogenic bacteria. By analyzing the genomic data, we can gain valuable insights to enhance our understanding of the physiological characteristics of P. cibarius, as well as the biological functions of TAAs and their role in triggering metamorphosis of invertebrate larvae.

lzh-N1 reveals its antagonistic ability

BACKGROUND

Plant diseases caused by pathogenic fungi are devastating. However, commonly used fungicides are harmful to the environment, and some are becoming ineffective due to fungal resistance. Therefore, eco-friendly biological methods to control pathogenic fungi are urgently needed.

RESULTS

In this study, a strain, Paenibacillus sp. lzh-N1, that could inhibit the growth of the pathogenic fungus Mycosphaerella sentina (Fr) Schrorter was isolated from the rhizosphere soil of pear trees, and the complete genome sequence of the strain was obtained, annotated, and analyzed to reveal the genetic foundation of its antagonistic ability. The entire genome of this strain contained a circular chromosome of 5,641,488 bp with a GC content of 45.50%. The results of species identification show that the strain belongs to the same species as P. polymyxa Sb3-1 and P. polymyxa CJX518. Sixteen secondary metabolic biosynthetic gene clusters were predicted by antiSMASH, including those of the antifungal peptides fusaricidin B and paenilarvins. In addition, biofilm formation-related genes containing two potential gene clusters for cyclic lactone autoinducer, a gene encoding S-ribosylhomocysteine lyase (LuxS), and three genes encoding exopolysaccharide biosynthesis protein were identified.

CONCLUSIONS

Antifungal peptides and glucanase biosynthesized by Paenibacillus sp. lzh-N1 may be responsible for its antagonistic effect. Moreover, quorum sensing systems may influence the biocontrol activity of this strain directly or indirectly.

Complete genome sequence of a novel partitivirus with a dsRNA3 segment, isolated from Fusarium commune strain CP-SX-3 causing strawberry root rot

A novel partitivirus, Fusarium commune partitivirus 1 (FcoPV1), was identified in Fusarium commune strain CP-SX-3 isolated from diseased roots of strawberry with symptoms of root rot. The complete genome of FcoPV1 comprises three double-stranded RNAs (dsRNAs): dsRNA1 (1,825 nt), dsRNA2 (1,592 nt), and dsRNA3 (1,421 nt). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), and dsRNA2 contains a single ORF (ORF2) encoding a coat protein (CP). dsRNA3 is a possible satellite RNA that does not appear to encode a known protein. BLASTp analysis revealed that RdRp (86.59%) and CP (74.13%) encoded by the two ORFs (ORF1 and ORF2) had the highest sequence similarity to their counterparts in Fusarium equiseti partitivirus 1 (FePV1). Phylogenetic analysis based on the complete amino acid sequence of RdRp suggested that FcoPV1 should be considered a member of a new species in the proposed genus "Zetapartitivirus" within the family Partitiviridae. To the best of our knowledge, this is the first report of a zetapartitivirus infecting phytopathogenic F. commune.

Identification and functional characterisation of a locus for target site integration in Fusarium graminearum

BACKGROUND

Fusarium Head Blight (FHB) is a destructive floral disease of different cereal crops. The Ascomycete fungus Fusarium graminearum (Fg) is one of the main causal agents of FHB in wheat and barley. The role(s) in virulence of Fg genes include genetic studies that involve the transformation of the fungus with different expression cassettes. We have observed in several studies where Fg genes functions were characterised that integration of expression cassettes occurred randomly. Random insertion of a cassette may disrupt gene expression and/or protein functions and hence the overall conclusion of the study. Target site integration (TSI) is an approach that consists of identifying a chromosomal region where the cassette can be inserted. The identification of a suitable locus for TSI in Fg would avert the potential risks of ectopic integration.

RESULTS

Here, we identified a highly conserved intergenic region on chromosome 1 suitable for TSI. We named this intergenic region TSI locus 1. We developed an efficient cloning vector system based on the Golden Gate method to clone different expression cassettes for use in combination with TSI locus 1. We present evidence that integrations in the TSI locus 1 affects neither fungal virulence nor fungal growth under different stress conditions. Integrations at the TSI locus 1 resulted in the expression of different gene fusions. In addition, the activities of Fg native promoters were not altered by integration into the TSI locus 1. We have developed a bespoke bioinformatic pipeline to analyse the existence of ectopic integrations, cassette truncations and tandem insertions of the cassette that may occurred during the transformation process. Finally, we established a protocol to study protein secretion in wheat coleoptiles using confocal microscopy and the TSI locus 1.

CONCLUSION

The TSI locus 1 can be used in Fg and potentially other cereal infecting Fusarium species for diverse studies including promoter activity analysis, protein secretion, protein localisation studies and gene complementation. The bespoke bioinformatic pipeline developed in this work together with PCR amplification of the insert could be an alternative to Southern blotting, the gold standard technique used to identify ectopic integrations, cassette truncations and tandem insertions in fungal transformation.

Genome analysis of Shewanella putrefaciens 4H revealing the potential mechanisms for the chromium remediation

Microbial remediation of heavy metal polluted environment is ecofriendly and cost effective. Therefore, in the present study, Shewanella putrefaciens stain 4H was previously isolated by our group from the activated sludge of secondary sedimentation tank in a dyeing wastewater treatment plant. The bacterium was able to reduce chromate effectively. The strains showed significant ability to reduce Cr(VI) in the pH range of 8.0 to 10.0 (optimum pH 9.0) and 25-42 ℃ (optimum 30 ℃) and were able to reduce 300 mg/L of Cr(VI) in 72 h under parthenogenetic anaerobic conditions. In this paper, the complete genome sequence was obtained by Nanopore sequencing technology and analyzed chromium metabolism-related genes by comparative genomics The genomic sequence of S. putrefaciens 4H has a length of 4,631,110 bp with a G + C content of 44.66% and contains 4015 protein-coding genes and 3223,  2414, 2343 genes were correspondingly annotated into the COG, KEGG, and GO databases. The qRT-PCR analysis showed that the expression of chrA, mtrC, and undA genes was up-regulated under Cr(VI) stress. This study explores the Chromium Metabolism-Related Genes of S. putrefaciens 4H and will help to deepen our understanding of the mechanisms of Cr(VI) tolerance and reduction in this strain, thus contributing to the better application of S. putrefaciens 4H in the field of remediation of chromium-contaminated environments.

Severe acute respiratory syndrome Coronavirus-2 GenoAnalyzer and mutagenic anomaly detector using FCMFI and NSCE

In order to deepen our understanding of the virus and help guide the creation of efficient therapies, this study uses artificial intelligence tools to thoroughly explore the genetic sequences of the SARS-CoV-2 virus. The process starts by using the Fuzzy Closure Miner for Frequent Itemsets (FCMFI) on a large corpus of SARS-CoV-2 genomic sequences to reveal hidden patterns, including nucleotides base sequences, repeating motifs, and corresponding interchanges. Then, using the Nucleotide Sequence Comprehension Engine (NSCE) technique, we were able to precisely define the genomic areas for mutation analysis. Structured and unstructured proteins are both strongly impacted by virus mutations, with spike proteins that are linked to the severity of COVID-19 pneumonia being particularly affected. Notably, the Mutagenic Anomaly Detector shows a 65 % efficiency boost in computing genome mutation rates compared to conventional point mutation analysis, while GenoAnalyzer offers a remarkable 93.33 % improvement over existing approaches in recognizing common genomic sequence patterns. These results highlight the potential of FCMFI to reveal complex genomic patterns and significant insights in COVID-19 genetic sequences when combined with mutation analysis. The Mutagenic Anomaly Detector and GenoAnalyzer show promise for revealing hidden genomic patterns and precisely estimating the SARS-CoV-2 mutation rate.

Emerging porcine Enterovirus G infections, epidemiological, complete genome sequencing, evolutionary and risk factor analysis in India

The current study reports the in-depth analysis of the epidemiology, risk factors, and molecular characterization of a complete genome of Enterovirus G (EV-G) isolated from Indian pigs. We analysed several genes of EV-G isolates collected from various provinces in India, using phylogenetic analysis, recombination detection, SimPlot, and selection pressure analyses. Our analysis of 534 porcine faecal samples revealed that 11.61% (62/534) of the samples were positive for EV-G. While the G6 genotype was the most predominant, our findings showed that Indian EV-G strains also clustered with EV-G types G1, G6, G8, and G9. Furthermore, Indian EV-G strains exhibited the highest nucleotide similarity with Vietnamese (81.3%) and Chinese EV-G isolates (80.3%). Moreover, we identified a recombinant Indian EV-G strain with a putative origin from a Japanese isolate and South Korean EV-G isolate. In summary, our findings provide significant insights into the epidemiology, genetic diversity, and evolution of EV-G in India.

Genome characteristics and the ODV proteome of a second distinct alphabaculovirus from Spodoptera litura

BACKGROUND

Spodoptera litura is a harmful pest that feeds on more than 80 species of plants, and can be infected and killed by Spodoptera litura nucleopolyhedrovirus (SpltNPV). SpltNPV-C3 is a type C SpltNPV clone, that was observed and collected in Japan. Compared with type A or type B SpltNPVs, SpltNPV-C3 can cause the rapid mortality of S. litura larvae.

METHODS

In this study, occlusion bodies (OBs) and occlusion-derived viruses (ODVs) of SpltNPV-C3 were purified, and OBs were observed by scanning electron microscopy (SEM). ODVs were observed under a transmission electron microscope (TEM).

RESULTS

Both OBs and ODVs exhibit morphological characteristics typical of nucleopolyhedroviruses (NPVs).The genome of SpltNPV-C3 was sequenced and analyzed; the total length was 148,634 bp (GenBank accession 780,426,which was submitted as SpltNPV-II), with a G + C content of 45%. A total of 149 predicted ORFs were found. A phylogenetic tree of 90 baculoviruses was constructed based on core baculovirus genes. LC‒MS/MS was used to analyze the proteins of SpltNPV-C3; 34 proteins were found in the purified ODVs, 15 of which were core proteins. The structure of the complexes formed by per os infectivity factors 1, 2, 3 and 4 (PIF-1, PIF-2, PIF-3 and PIF-4) was predicted with the help of the AlphaFold multimer tool and predicted conserved sequences in PIF-3. SpltNPV-C3 is a valuable species because of its virulence, and the analysis of its genome and proteins in this research will be beneficial for pest control efforts.

Complete mitochondrial genome of Neuroctenus yunnanensis Hsiao, 1964 (Hemiptera: Aradidae: Mezirinae)

The complete Neuroctenus yunnanensis Hsiao, 1964, mitogenome was sequenced using an Illumina NovaSeq platform and submitted to GenBank (accession number: ON507991). The mitochondrial genome is a typical circular DNA molecule of 15,283 bp with 37 genes, including 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes, and a control region. Phylogenetic reconstruction validated the taxonomic status of N. yunnanensis, which was placed in the Mezirinae subfamily (Aradidae) and most closely related to N. parus. The mitochondrial genome data of N. yunnanensis provides a basis for genetic research.

Comparative genomics hints at dispensability of multiple essential genes in two Escherichia coli L-form strains

Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski's long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6-10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.

Exploring objective feature sets in constructing the evolution relationship of animal genome sequences

BACKGROUND

Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences.

RESULT

Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage.

CONCLUSION

Our study provides objective feature sets in constructing evolution relationships at the genomic level.

Complete genome of Rossellomorea sp. DA94, an agarolytic and orange-pigmented bacterium isolated from mangrove sediment of the South China Sea

Rossellomorea sp. DA94, isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an agarolytic and orange-pigmented bacterium. Here, we present the complete genome sequence of strain DA94, which comprises 4.63 Mb sequences with 43.5% GC content. In total, 4589 CDSs, 33 rRNA genes and 110 tRNA genes were obtained. Genomic analysis of strain DA94 revealed that 108 CAZymes were organized in 4578 PULs involved in polysaccharides degradation, transport, and regulation. Further, we performed the diversity of CAZymes and PULs comparison among Rossellomorea strains. Less CAZymes were organized more PULs, indicating highly efficiently polysaccharides utilization in Rossellomorea. Meanwhile, PUL0459, PUL0460 and PUL0316 related to agar degradation, and exolytic beta-agarase GH50, endo-type beta-agarase GH86 and arylsulfatase were identified in the genome of strain DA94. We verified that strain DA94 can degrade agar to form a bright clear zone around the bacterial colonies in the laboratory. Moreover, the carotenoid biosynthetic pathways were proposed, which may be responsible for orange-pigment of Rossellomorea sp. DA94. This study represents a thorough genomic characterization of CAZymes repertoire and carotenoid biosynthetic pathways of Rossellomorea, provides insight into diversity of related enzymes and their potential biotechnological applications.

Ligilactobacillus salivarius 2102-15 complete genome sequence data

The article presents Ligilactobacillus salivarius 2102-15 whole genome sequencing data generated by using Illumina and Oxford Nanopore platforms. The genome of the isolate consists of a chromosome and two plasmids. The data on bacteriocin-encoding genes present in the genome were collected through genome annotation and by using a BAGEL4 tool. The advantages and limitations of the approaches are highlighted. The data indicate the presence of different types of bacteriocin and immunity protein-encoding genes on both the chromosome and one of the plasmids. The data obtained represents interest to researchers working in the areas related to whole genome sequencing and analysis, as well as being useful for the identification of novel probiotic bacteria and their biomedical applications.

AG-A strain SHX-YJLC-1

A novel mycovirus, Ceratobasidium bipartite virus 1 (CBV1), was identified in Ceratobasidium sp. AG-A strain SHX-YJLC-1 isolated from diseased potato stems. The complete genome of CBV1 consists of two double-stranded RNA (dsRNA) segments: dsRNA1 (2311 bp) and dsRNA2 (1761 bp). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), while dsRNA2 contains a single ORF (ORF2) encoding a hypothetical protein (HP) with unknown function. BLASTp analysis revealed that RdRp (75.04%) and HP (61.86%) encoded by the two ORFs have the highest sequence similarity to their counterparts in Rhizoctonia solani dsRNA virus 11 (RsRV11). The genome organization and phylogenetic analysis indicated that the closest relatives to CBV1 are members of the proposed family "Bipartitiviridae". Based on the collective results, CBV1 is inferred to be a new member of the proposed family "Bipartitiviridae". This is the first report on the complete genome sequence of the novel bipartitivirus CBV1, which infects Ceratobasidium sp. AG-A strain SHX-YJLC-1.

Genome analysis of the novel putative rotavirus species K

Rotaviruses are causative agents of diarrhea in humans and animals. Currently, the species rotavirus A-J (RVA-RVJ) and the putative species RVK and RVL are defined, mainly based on their genome sequence identities. RVK strains were first identified in 2019 in common shrews (Sorex aranaeus) in Germany; however, only short sequence fragments were available so far. Here, we analyzed the complete coding regions of strain RVK/shrew-wt/GER/KS14-0241/2013, which showed highest sequence identities with RVC. The amino acid sequence identity of VP6, which is used for rotavirus species definition, reached only 51% with other rotavirus reference strains thus confirming classification of RVK as a separate species. Phylogenetic analyses for the deduced amino acid sequences of all 11 virus proteins showed, that for most of them RVK and RVC formed a common branch within the RVA-like phylogenetic clade. Only the tree for the highly variable NSP4 showed a different branching; however, with very low bootstrap support. Comparison of partial nucleotide sequences of other RVK strains from common shrews of different regions in Germany indicated a high degree of sequence variability (61-97% identity) within the putative species. These RVK strains clustered separately from RVC genotype reference strains in phylogenetic trees indicating diversification of RVK independent from RVC. The results indicate that RVK represents a novel rotavirus species, which is most closely related to RVC.

Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis

Although several species of purple sulfur bacteria inhabit soda lakes, Rhodobaca bogoriensis is the first purple nonsulfur bacterium cultured from such highly alkaline environments. Rhodobaca bogoriensis strain LBB1T was isolated from Lake Bogoria, a soda lake in the African Rift Valley. The phenotype of Rhodobaca bogoriensis is unique among purple bacteria; the organism is alkaliphilic but not halophilic, produces carotenoids absent from other purple nonsulfur bacteria, and is unable to grow autotrophically or fix molecular nitrogen. Here we analyze the draft genome sequence of Rhodobaca bogoriensis to gain further insight into the biology of this extremophilic purple bacterium. The strain LBB1T genome consists of 3.91 Mbp with no plasmids. The genome sequence supports the defining characteristics of strain LBB1T, including its (1) production of a light-harvesting 1-reaction center (LH1-RC) complex but lack of a peripheral (LH2) complex, (2) ability to synthesize unusual carotenoids, (3) capacity for both phototrophic (anoxic/light) and chemotrophic (oxic/dark) energy metabolisms, (4) utilization of a wide variety of organic compounds (including acetate in the absence of a glyoxylate cycle), (5) ability to oxidize both sulfide and thiosulfate despite lacking the capacity for autotrophic growth, and (6) absence of a functional nitrogen-fixation system for diazotrophic growth. The assortment of properties in Rhodobaca bogoriensis has no precedent among phototrophic purple bacteria, and the results are discussed in relation to the organism's soda lake habitat and evolutionary history.

Identification and genome-wide analysis provide insights into the genetic diversity and biotechnological potentials of novel cold-adapted Acinetobacter strain

Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved specialized strategies to survive and function under such harsh conditions. The study aims to identify, sequence the genome, perform genome assembly, and conduct a comparative genome-wide analysis of Acinetobacter sp. strain P1, which was isolated from the Batura glacier regions of Pakistan. A basic local alignment search tool of NCBI using 16 s RNA gene sequence confirmed the strain Acinetobacter following phylogenetic analysis revealed that strain P1 clustered with Acinetobacter sp. strain AcBz01. The high-throughput Genome sequencing was done by the NovaSeq 6000 sequencing system following de novo genome assembly reported 23 contigs, a genome size of 3,732,502 bp containing approximately 3489 genes and 63 RNAs (60 tRNA, 3 rRNA). The comparative genome analysis revealed that Acinetobacter sp. strain P1 exhibited the highest homology with the Acinetobacter baumannii ATCC 17978 genome and encompassed 1668 indispensable genes, 1280 conserved genes 1821 specific genes suggesting high genomic plasticity and evolutionary diversity. The genes with functional assignments include exopolysaccharide phosphotransferase enzyme, cold-shock proteins, T6SS, membrane modifications, antibiotic resistance, and set of genes related to a wide range of metabolic characteristics such as exopolysaccharides were also present. Moreover, the structural prediction analysis of EPS proteins reveals that structural flexibility allows for conformational modifications during catalysis, which boosts or increases the catalytic effectiveness at lower temperatures. Overall, the identification of Acinetobacter, a cold-adapted bacterium, offers promising applications in bioremediation, enzyme production, food preservation, pharmaceutical development, and astrobiology. Further research and exploration of these microorganisms can unlock their full biotechnological potential and contribute to various industries and scientific endeavors.

Lignin-degrading enzymes from a pathogenic canker-rot fungus Inonotus obliquus strain IO-B2

Inonotus obliquus is a pathogenic fungus found in living trees and has been widely used as a traditional medicine for cancer therapy. Although lignocellulose-degrading enzymes are involved in the early stages of host infection, the parasitic life cycle of this fungus has not been fully understood. In this study, we aimed to investigate the activities of laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) from I. obliquus cultivated in Kirk's medium. The fungus was subjected to genome sequencing, and genes related to wood degradation were identified. The draft genome sequence of this fungus comprised 21,203 predicted protein-coding genes, of which 134 were estimated to be related to wood degradation. Among these, 47 genes associated with lignin degradation were found to have the highest number of mnp genes. Furthermore, we cloned the cDNA encoding a putative MnP, referred to as IoMnP1, and characterized its molecular structure. The results show that IoMnP1 has catalytic properties analogous to MnP. Phylogenetic analysis also confirmed that IoMnP1 was closely related to the MnPs from Pyrrhoderma noxium, Fomitiporia mediterranea, and Sanghuangporus baumii, which belong to the same family of Hymenochaetaceae. From the above results, we suggest that IoMnP1 is a member of MnPs.

Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa

OBJECTIVES

Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa.

METHODS

The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees.

RESULTS

Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (blaACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin.

CONCLUSION

The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.

IMCC1007 isolated from maize rhizosphere: A potential strain in fusaric acid mycotoxin biodegradation

Burkholderia sp. IMCC1007 is a gram-negative, aerobic bacterium affiliated with class Betaproteobacteria, which was successfully isolated from maize rhizospheric soil sample in UTM research plot, Pagoh, Malaysia by using enrichment method. Strain IMCC1007 utilized 50 mgL^-1 fusaric acid as its carbon source and degraded it completely within 14 h. Genome sequencing was performed using Illumina NovaSeq platform. The assembled genome was annotated using RAST (Rapid Annotation Subsystem Technology) server. The genome size was approximately 8,568,405 base pairs (bp) in 147 contigs with a G+C content of 66.04%. The genome includes 8,733 coding sequences and 68 RNAs. The genome sequence has been deposited at GenBank with the accession number of JAPVQY000000000. In the pairwise genome-to-genome comparisons, the strain IMCC1007 had an average nucleotide identity (ANI) of 91.9% and digital DNA-DNA hybridization (dDDH) value of 55.2% with Burkholderia anthina DSM 16086^T respectively. Interestingly, fusaric acid resistance gene (fusC) and nicABCDFXT gene clusters (hydroxylation of pyridine compound) were found in the genome. Additionally, preliminary genome annotation analysis of strain IMCC1007 identified tryptophan halogenase (prnA) gene responsible for antifungal pyrrolnitrin biosynthesis. This dataset herein provides further insights into the fusaric acid degradation mechanism of the genus Burkholderia.

Genome features and secondary metabolite potential of the marine symbiont Streptomyces sp. RS2

Streptomyces sp. RS2 was isolated from an unidentified sponge collected around Randayan Island, Indonesia. The genome of Streptomyces sp. RS2 consists of a linear chromosome of 9,391,717 base pairs with 71.9% of G + C content, 8270 protein-coding genes, as well as 18 rRNA and 85 tRNA loci. Twenty-eight putative secondary metabolites biosynthetic gene clusters (BGCs) were identified in the genome sequence. Nine of them have 100% similarity to BGCs for albaflavenone, α-lipomycin, coelibactin, coelichelin, ectoine, geosmin, germicidin, hopene, and lanthionine (SapB). The remaining 19 BGCs have low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. Biological activity assays of extracts from 21 different cultures of the RS2 strain showed that SCB ASW was the best medium for the production of antimicrobial and cytotoxic compounds. Streptomyces sp. RS2 has great potential to be a producer of novel secondary metabolites, particularly those with antimicrobial and antitumor activities.

Thetidibacter halocola gen. nov., sp. nov., a novel member within the family Roseobacteraceae isolated from seawater

A Gram-staining-negative, strictly aerobic, dark beige-colored, rod-shaped, chemoorganoheterotrophic, and catalase- and oxidase-positive bacterium, designated as KMU-90^T, was isolated from coastal seawater in the Republic of Korea, and subjected to a polyphasic study. The novel isolate was able to grow at 0-6.0% NaCl concentrations (w/v), pH 6.5-9.5, and 4-45 °C. The 16S rRNA gene sequences-based phylogeny revealed that the novel marine isolate belongs to the family Roseobacteraceae of class Alphaproteobacteria and that it shared the greatest sequence similarity (97.3%) with Aestuariicoccus marinus NAP41^T. The novel strain could be distinguished phenotypically from related representatives of the family Roseobacteraceae. The major (> 10%) fatty acids of strain KMU-90^T were C_18:1 ω7c and C_18:1 ω7c 11-methyl and the only respiratory quinone was ubiquinone-10 (Q-10). Strain KMU-90^T contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, two unidentified aminolipids, an unidentified phospholipid, and three unidentified glycolipids as polar lipids. The assembled draft genome size of strain KMU-90^T was 4.84 Mbp with a DNA G + C content of 66.5%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between the genomes of strain KMU-90^T and its closely related representatives were 77.0-79.0%, 14.6-20.0%, and 60.0-69.9%, respectively. From the polyphasic taxonomic results obtained, the strain is considered to represent a novel genus and a new species of the family Roseobacteraceae, for which the name Thetidibacter halocola gen. nov., sp. nov. is proposed. The type species is T. halocola, with the type strain KMU-90^T (= KCCM 90287^T = NBRC 113375^T).

canis and Pasteurella multocida Isolated from Humans and Companion Animals

Background

Comparative analysis of virulence factors (VFs) between Pasteurella canis and Pasteurella multocida are lacking, although both cause zoonotic infections. We determined the virulence-associated genome sequence characteristics of P. canis and assessed the toxin gene prevalence unique to P. canis among clinical isolates of P. canis and P. multocida.

Methods

We selected 10 P. canis and 16 P. multocida whole-genome sequences (WGSs) from the National Center for Biotechnology database. The VFanalyzer tool was used to estimate P. canis-characteristic VFs. Amino acid sequences of VFs were compared with multiple-aligned sequences. The genome structure containing P. canis-characteristic and adjacent loci was compared to the corresponding P. multocida genome structure. After designing primer sequences and assessing their accuracy, we examined the gene prevalence of the P. canis-characteristic VFs using PCR among clinical isolates of P. multocida and P. canis.

Results

Using VFanalyzer, we found virulence-associated cytolethal distending toxin (cdt)A-cdtB-cdtC loci common to all P. canis WGSs that were not found in P. multocida WGSs. Similarities in the multiple alignments of CdtA-CdtB-CdtC amino acid sequences were found among the 10 P. canis WGSs. Shared or similar loci around cdtA-cdtB-cdtC were identified between the P. canis and P. multocida genome structures. The PCR-based cdtA-cdtB-cdtC prevalence differed for P. canis and P. multocida clinical isolates.

Conclusions

P. canis-specific cdtA-cdtB-cdtC prevalence was identified among clinical isolates. These three loci may be unique toxin genes and promising targets for the rapid identification of P. canis in clinical settings.

Identification and examination of nitrogen metabolic genes in Lelliottia amnigena PTJIIT1005 for their ability to perform nitrate remediation

Lelliottia amnigena PTJIIT1005 is a bacterium that utilizes nitrate as the sole nitrogen source and can remediate nitrate from media. The annotation was done related to nitrogen metabolic genes using the PATRIC, RAST tools, and PGAP from the genome sequence of this bacterium. Multiple sequence alignments and phylogenetic analysis of respiratory nitrate reductase, assimilatory nitrate reductase, nitrite reductase, glutamine synthetase, hydroxylamine reductase, nitric oxide reductase genes from PTJIIT1005 were done to find out sequence identities with the most similar species. The identification of operon arrangement in bacteria was also identified. The PATRIC KEGG feature mapped the N-metabolic pathway to identify the chemical process, and the 3D structure of representative enzymes was also elucidated. The putative protein 3D structure was analyzed using I-TASSER software. It gave good quality protein models of all nitrogen metabolism genes and showed good sequence identity with reference templates, approximately 81-99%, except for two genes; assimilatory nitrate reductase and nitrite reductase. This study suggested that PTJIIT1005 can remove N-nitrate from water because of having N-assimilation and denitrification genes.

Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations

BACKGROUND

Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood.

RESULTS

We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato.

CONCLUSIONS

Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.

YS9 with five plasmids isolated from red algae

Ruegeria sp. YS9, an aerobic and chemoheterotrophic bacterium belonging to marine Roseobacter lineage, was a putative new species isolated from red algae Eucheuma okamurai in the South China Sea (Beihai, Guangxi province). The complete genome sequence in strain YS9 comprised one circular chromosome with 3,244,635 bp and five circular plasmids ranging from 38,085 to 748,160 bp, with a total length of 4.30 Mb and average GC content of 58.39%. In total, 4129 CDSs, 52 tRNA genes and 9 rRNA genes were obtained. Genomic analysis of strain YS9 revealed that 85 CAZymes were organized in 147 PUL-associated CAZymes involved in polysaccharides metabolism, which were the highest among its two closely related Ruegeria strains. Numerous PULs related to degradation on the cell wall of algae, especially agar, indicated its major player role in the remineralization of algal-derived carbon. Further, the existence of multiple plasmids provided strain YS9 with distinct advantages to facilitate its rapid environmental adaptation, including polysaccharide metabolism, denitrification, resistance to heavy metal stresses such as copper and cobalt, type IV secretion systems and type IV toxin-antitoxin systems, which were obviously different from the two Ruegeria strains. This study provides evidence for polysaccharide metabolic capacity and functions of five plasmids in strain YS9, broadening our understanding of the ecological roles of bacteria in the environment around red algae and the function patterns of plasmids in marine Roseobacter lineage members for environmental adaptation.

Genomic confirmation of Gossypium barbadense introgression into G. hirsutum and a subsequent MAGIC population

Introgression of superior fiber traits from Pima cotton (Gossypium barbadense, GB) into high yield Upland cotton (G. hirsutum) has been a breeding objective for many years in a few breeding programs in the world. However, progress has been very slow due to introgression barriers resulting from whole genome hybridization between the two species. To minimize such barriers, chromosome substitution lines (CS-B) from Pima cotton 3-79 in an Upland cotton cultivar TM-1 were developed. A multiparent advanced generation inter-cross (MAGIC) population consisting of 180 recombinant inbred lines (RILs) was subsequently made using the 18 CS-B lines and three Upland cotton cultivars as parents. In this research, we sequenced the whole genomes of the 21 parents and 180 RILs to examine the G. barbadense introgression. Of the 18 CS-B lines, 11 contained the target GB chromosome or chromosome segment, two contained more than two GB chromosomes, and five did not have the expected introgression. Residual introgression in non-target chromosomes was prevalent in all CS-B lines. A clear structure existed in the MAGIC population and the 180 RILs were distributed into three groups, i.e., high, moderate, and low GB introgression. Large blocks of GB chromosome introgression were still present in some RILs after five cycles of random-mating, an indication of recombination suppression or other unknown reasons present in the population. Identity by descent analysis revealed that the MAGIC RILs contained less introgression than expected. This research presents an insight on understanding the complex problems of introgression between cotton species.

Antibiotic and metal resistance of Stenotrophomonas maltophilia isolates from Eboling permafrost of the Tibetan Plateau

Whole-genome sequencing of pathogenic bacteria Stenotrophomonas maltophilia from a less polluted environment of permafrost can help understand the intrinsic resistome of both antibiotics and metals. This study aimed to examine the maximum minimum inhibitory concentration (MIC) of both antibiotics and metals, as well as antibiotic resistance genes and metal resistance genes annotated from whole-genome sequences. The permafrost S. maltophilia was sensitive to ciprofloxacin, tetracycline, streptomycin, and bacitracin, and resistant to chloramphenicol, trimethoprim-sulfamethoxazole, erythromycin, Zn²⁺, Ni²⁺, Cu²⁺, and Cr⁶⁺, with a lower maximum MIC, compared with clinical S. maltophilia. The former strain belonged to the lower antibiotic resistance gene (ARG) and metal resistance gene (MRG) clusters compared with the latter ones. The permafrost strain contained no or only one kind of ARG or MRG on a single genomic island, which explained the aforementioned lower maximum MIC and less diversity of ARGs or MRGs. The result indicated that the co-occurrence of antibiotic and metal resistance was due to a certain innate ability of S. maltophilia. The continuous human use of antibiotics or metals induced selective pressure, resulting in higher MIC and more diverse ARGs and MRGs in human-impacted environments.

Genomic insights into the metabolic potential of a novel lignin-degrading and polyhydroxyalkanoates producing bacterium Pseudomonas sp. Hu109A

Lignin is the most abundant heterogeneous aromatic polymer present on planet Earth and is recalcitrant to degradation due to its complex structure, therefore, imposing a challenge to biorefinery procedures. Identifying new microbial strains with the potential to valorize lignin into useful compounds is indispensable to achieving green sustainable consumption. In this study, a novel Pseudomonas strain designated as Hu109A was isolated from the termite gut and the genome was sequenced and analyzed further. The genome contains a circular chromosome with the size of 5,131,917 bp having a GC content of 62.6% and 4698 genes. Genome annotation reveals that the strain possesses lignin-oxidizing enzymes such as DyP-type peroxidases, laccase, dioxygenase, and aromatic degradation gene clusters. The genome also contains O-methyltransferases which function in accelerating the lignin degradation by methylating the free hydroxyl phenolic compounds which in high concentration can inhibit the lignin peroxidase. Furthermore, the genome exhibits two gene clusters encoding the enzymes related to polyhydroxyalkanoates (PHA) synthesis. Pseudomonas strains are generally assumed to produce medium chain length PHAs (mcl-PHAs) only, however, strain Hu109A contains both Class II PHA synthase genes involved in mcl-PHAs and Class III PHA synthase gene involved in short-chain length PHAs (scl-PHAs). Gas Chromatography-Mass Spectrometry (GC-MS) analysis showed that using 1 g/L lignin as the sole carbon source, the maximum production of PHA observed was 103.68 mg/L, which increased to 186 mg/L with an increase in lignin concentration to 3 g/L. However, PHA production while using glucose as the sole carbon source was significantly lower than the lignin source, and maximum production was 125.6 mg/L with 3 g/L glucose. The strain Hu109A can tolerate a broad range of solvents including methanol, isopropanol, dimethylformamide, and ethanol, revealing its potential for industrial applications.

Genetic analysis of genome sequence characteristics of two lumpy skin disease viruses isolated from China

BACKGROUND

Lumpy skin disease (LSD) is an acute or subacute infectious disease caused by lumpy skin disease virus (LSDV) of genus Capripoxvirus. The outbreaks of LSD were confirmed in the Yili area of the Xinjiang autonomous region in August 2019 and the Fujian province in June 2020. We detected LSDV in our daily monitoring work, then isolated, identified and sequenced the virus, and analyzed the whole genome characteristics of the isolated strain.

RESULTS

Whole genome sequencing revealed that the strains isolated were all LSDV and were named as LSDV XJ201901 and LSDV FJ2019. The results showed that the identity based on whole genome sequences between LSDV XJ201901 and LSDV FJ2019 was 100% and the identity based on whole genome sequences between the two isolated strains and the global LSDV strains was 97.28%-99.99%, with the strain LSDV72/PrachuapKhiriKhan/Thailand/2021 (99.99%) having the highest sequence identity. Analysis of potential recombination events revealed that a total of 18 potential recombination events were identified in strains LSDV XJ201901 and LSDV FJ2019. The two strains are a recombination of Neethling vaccine LW 1959 (GeneBank: AF409138.1) with KSGP 0240 (GeneBank: KX683219.1). It was observed that Neethling vaccine LW 1959 (11/18) and KSGP 0240 (10/18) are involved in most of the potential recombination events.

CONCLUSIONS

The virus isolate in this study was LSDV and was identified as a vaccine recombinant strain. The most likely potential parent strains of the two strains in this study are Neethling vaccine LW 1959 and KSGP 0240. The strains in this study are very similar to those isolated in East and Southeast Asia since 2019.

Draft genome sequence of Cronobacter sakazakii strain MEZCS99 sequence type 3 isolated from chicken in South Africa

OBJECTIVES

Cronobacter sakazakii is an emerging opportunistic foodborne pathogen that is frequently associated with life-threatening infections such as infantile septicemia, meningitis, and necrotizing enterocolitis. The emergence of antimicrobial-resistant, livestock-associated C. sakazakii is a great public health concern. Here, we report on the first draft genome sequence of C. sakazakii strain MEZCS99 sequence type 3 (ST3) isolated from feces from a healthy chicken in KwaZulu-Natal Province, South Africa.

METHODS

The genomic DNA of C. sakazakii was sequenced using an Illumina MiSeq platform (Illumina Inc., San Diego, CA). Generated reads were trimmed and de novo assembled. The assembled contigs were analyzed for virulence and antimicrobial resistance genes, extra-chromosomal plasmids, and multilocus sequence type (MLST). To compare the sequenced strains to other previously sequenced C. sakazakii strains, available raw read sequences of C. sakazakii were downloaded and all sequence files were treated identically to generate a core genome phylogenetic tree.

RESULTS

Intrinsic beta-lactam resistance gene blaCSA-1 was detected in MEZCS99. No colistin or other antibiotic resistance genes were detected. MEZCS99 belonged to ST3 and harbored an extra-chromosomal plasmid (IncFIB (pCTU3)). The genome of MEZCS99 strain showed two CRISPR/Cas cluster arrays of I-E (n = 1) and I-F (n = 1) type.

CONCLUSION

The genome sequence of strain MEZCS99 will serve as a reference point for molecular epidemiological studies of livestock-associated C. sakazakii in Africa. In addition, this study allows in-depth analysis of the genomic structure and will provide valuable information that helps understand the pathogenesis and antimicrobial resistance of livestock-associated C. sakazakii.

Insights from the genome sequence of Bacillus tropicus EMB20, an efficient β-lactamase-producing bacterium

We report here the whole-genome sequence of β-lactamase-producing bacteria Bacillus tropicus EMB20. The genome sequence of Bacillus tropicus EMB20 has a size of 5.8 Mb (G + C content of 35.52%) with 5593 coding DNA sequences (CDSs), 108 tRNA, and 14 rRNA operons. The bacterium has the unique ability to produce a β-lactamase enzyme with high activity. β-Lactamases are one of the most common causes of antimicrobial resistance as these enzymes inactivate almost all β-lactam antibiotics. The antibiotic susceptibility test showed that the B. tropicus EMB20 is producing β-lactamase and can degrade the β-lactam antibiotics. Further, the antibiotic degradation potential of this bacteria was confirmed by growing the bacteria in the presence of varying concentrations of β-lactam antibiotic, amoxicillin. The bacteria were able to hydrolyze amoxicillin up to 50 mg/L in 4 h. Furthermore, the analyses of the genome revealed the presence of multiple β-lactamase genes, possibly involved in antibiotic degradation. The availability of the genome sequence will provide further insights into the mechanism of antimicrobial resistance by β-lactamase-producing bacteria.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03395-w.

Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment

Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic to lettuce, despite the only described species in this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%, and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.

De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'

The first genome sequence of an interspecific grape hybrid (Vitis labruscana × Vitis vinifera), 'Shine Muscat', an elite table grape cultivar bred in Japan, is presented. The resultant genome assemblies included two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a 'pseudo-haploid' genome. The unphased sequences, assembled to the chromosome level with Hi-C reads, spanned 488.97 Mb in length, 99.1% of the estimated genome size, with 4,595 scaffold sequences and a 23.9-Mb N50 length. The phased sequences had 15,650 scaffolds spanning 1.0 Gb and a 4.2-Mb N50 length. 32,827 high-confidence genes were predicted on the unphased genomes. Clustering analysis of the 'Shine Muscat' gene sequences with three other Vitis species and Arabidopsis indicated that 11,279 orthologous gene clusters were common to Vitis spp. and Arabidopsis, 4,385 were Vitis specific, and 234 were 'Shine Muscat' specific. Whole-genome resequencing was also performed for the parental lines of 'Shine Muscat', Akitsu-21 and 'Hakunan', and parental-specific copy number variations were identified. The obtained genome resources provide new insights that could assist in cultivation and breeding strategies to produce high-quality table grapes.

Possible involvement of extracellular polymeric substrates of Antarctic cyanobacterium Nostoc sp. strain SO-36 in adaptation to harsh environments

Cyanobacteria are some of the primary producers in extremely cold biospheres such as the Arctic, Antarctic, and vast ice sheets. Many genera of cyanobacteria are identified from these harsh environments, but their specific mechanisms for cold adaptation are not fully understood. Nostoc sp. strain SO-36 is a cyanobacterium isolated in Antarctica more than 30 years ago and regarded as a psychrotolelant species. To determine whether the strain is psychrotolelant or psychrophilic, it was first grown at 30 °C and 10 °C. The cells grew exponentially at 30 °C, but their growth stopped at 10 °C, indicating that the strain is only psychrotolerant. Microscopic analysis revealed that the morphology of the cells grown at 30 °C was filamentous and differentiated heterocysts, which are specialized cells for gaseous nitrogen fixation under nitrogen-deprived conditions, indicating that the strain can grow diazotrophically. The cells grown at 10 °C have a smaller size, shortened filament length and decreased chlorophyll content per cell. At 10 °C, the cells are aggregated with extracellular polymeric substrates (EPSs), which is a common mechanism to protect cells from ultraviolet light. These results imply that segmentation into short filaments was induced by photodamage at low temperatures. To fully understand the adaptation mechanisms of Nostoc sp. strain SO-36 for low-temperature conditions, next-generation sequencing analyses were conducted. Complete genome sequence of the strain revealed that it has one main chromosome of approximately 6.8 Mbp with 4 plasmids, including 6855 coding sequences, 48 tRNA genes, 4 copies of rRNA operons, and 5 CRISPR regions. Putative genes for EPS biosynthesis were found to be conserved in Nostocaceae regardless of their habitat. These results provide basic information to understand the adaptation mechanisms at low temperatures, and the strain can be a model organism to analyze adaptation to extreme environments.

Epidemiological and molecular description of nosocomial outbreak of COVID-19 Alpha (B.1.1.7) variant in Saudi Arabia

BACKGROUND

Nosocomial outbreaks frequently occurred during the Coronavirus disease 2019 (COVID-19) pandemic; however, sharing experiences on outbreak containment is vital to reduce the related burden in different locations.

OBJECTIVES

This article aims at sharing a practical experience on COVID-19 outbreak containment, including contact tracing, screening of target population, testing including molecular analysis, and preventive modalities. It also provides an epidemiological and molecular analysis of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‑CoV‑2) infection outbreak in a tertiary care hospital in Saudi Arabia.

METHODS

The outbreak occurred in a non-COVID medical ward at a tertiary care hospital in Jeddah, Saudi Arabia, from 22nd March and 15th April 2021. The multidisciplinary outbreak response team performed clinical and epidemiological investigations. Whole-Genome Sequencing (WGS) was implemented on selected isolates for further molecular characterization.

RESULTS

A total of eight nurses (20 % of the assigned ward nurses) and six patients (16.2 % of the ward admitted patients at the time of the outbreak) tested positive for the SARS-CoV-2 virus based on PCR testing. The outbreak investigation identified strong evidence of an epidemiologic link between the affected cases. WGS revealed a set of spike mutations and deletions specific to the Alpha variant (B.1.1.7 lineage). All the nurses had mild symptoms, and the fatality among the patients was 50 % (three out of the six patients).

CONCLUSIONS

The current nosocomial COVID-19 outbreak, caused by the Alpha variant, revealed multiple breaches in the adherence to the hospital infection control recommended measures. Containment strategies were successful in controlling the outbreak and limiting infection spread. Molecular analysis and genome sequencing are essential tools besides epidemiological investigation to inform appropriate actions, especially with emerging pathogens.

Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination

Background

Equid gammaherpesvirus 2 (EHV2) is a gammaherpesvirus with a widespread distribution in horse populations globally. Although its pathogenic significance can be unclear in most cases of infection, EHV2 infection can cause upper respiratory tract disease in foals. Co-infection of different strains of EHV2 in an individual horse is common. Small regions of the EHV2 genome have shown considerable genetic heterogeneity. This could suggest genomic recombination between different strains of EHV2, similar to the extensive recombination networks that have been demonstrated for some alphaherpesviruses. This study examined natural recombination and genome diversity of EHV2 field isolates.

Results

Whole genome sequencing analysis of 18 EHV2 isolates, along with analysis of two publicly available EHV2 genomes, revealed variation in genomes sizes (from 173.7 to 184.8 kbp), guanine plus cytosine content (from 56.7 to 57.8%) and the size of the terminal repeat regions (from 17,196 to 17,551 bp). The nucleotide sequence identity between the genomes ranged from 86.2 to 99.7%. The estimated average inter-strain nucleotide diversity between the 20 EHV2 genomes was 2.9%. Individual gene sequences showed varying levels of nucleotide diversity and ranged between 0 and 38.1%. The ratio of nonsynonymous substitutions, Ka, to synonymous substitutions, Ks, (Ka/Ks) suggests that over 50% of EHV2 genes are undergoing diversifying selection. Recombination analyses of the 20 EHV2 genome sequences using the recombination detection program (RDP4) and SplitsTree revealed evidence of viral recombination.

Conclusions

Analysis of the 18 new EHV2 genomes alongside the 2 previously sequenced genomes revealed a high degree of genetic diversity and extensive recombination networks. Herpesvirus genome diversification and virus evolution can be driven by recombination, and our findings are consistent with recombination being a key mechanism by which EHV2 genomes may vary and evolve.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08789-x.

Genomic analysis of heavy metal-resistant Halobacterium salinarum isolated from Sfax solar saltern sediments

The draft genome sequences of five archaeal strains, isolated from Sfax solar saltern sediments and affiliated with Halobacterium salinarum, were analyzed in order to reveal their adaptive strategies to live in hypersaline environments polluted with heavy metals. The genomes of the strains (named AS1, AS2, AS8, AS11, and AS19) are found to contain 2,060,688; 2,467,461; 2,236,624; 2,432,692; and 2,428,727 bp respectively, with a G + C content of 65.5, 66.0, 67.0, and 66.2%. The majority of these genes (43.69–55.65%) are annotated as hypothetical proteins. Growth under osmotic stress is possible by genes coding for potassium uptake, sodium efflux, and kinases, as well as stress proteins, DNA repair systems, and proteasomal components. These strains harbor many genes responsible for metal transport/resistance, such as: copper-translocating P-type ATPases, ABC transporter, and cobalt-zinc-cadmium resistance protein. In addition, detoxification enzymes and secondary metabolites are also identified. The results show strain AS1, as compared to the other strains, is more adapted to heavy metals and may be used in the bioremediation of multi-metal contaminated environments. This study highlights the presence of several commercially valuable bioproducts (carotenoids, retinal proteins, exopolysaccharide, stress proteins, squalene, and siderophores) and enzymes (protease, sulfatase, phosphatase, phosphoesterase, and chitinase) that can be used in many industrial applications.

SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing

BACKGROUND

Microbial strain information databases provide valuable data for microbial basic research and applications. However, they rarely contain information on the genetic operating system of microbial strains.

RESULTS

We established a comprehensive microbial strain database, SynBioStrainFinder, by integrating CRISPR/Cas gene-editing system information with cultivation methods, genome sequence data, and compound-related information. It is presented through three modules, Strain2Gms/PredStrain2Gms, Strain2BasicInfo, and Strain2Compd, which combine to form a rapid strain information query system conveniently curated, integrated, and accessible on a single platform. To date, 1426 CRISPR/Cas gene-editing records of 157 microbial strains have been manually extracted from the literature in the Strain2Gms module. For strains without established CRISPR/Cas systems, the PredStrain2Gms module recommends the system of the most closely related strain as a reference to facilitate the construction of a new CRISPR/Cas gene-editing system. The database contains 139,499 records of strain cultivation and genome sequences, and 773,298 records of strain-related compounds. To facilitate simple and intuitive data application, all microbial strains are also labeled with stars based on the order and availability of strain information. SynBioStrainFinder provides a user-friendly interface for querying, browsing, and visualizing detailed information on microbial strains, and it is publicly available at http://design.rxnfinder.org/biosynstrain/ .

CONCLUSION

SynBioStrainFinder is the first microbial strain database with manually curated information on the strain CRISPR/Cas system as well as other microbial strain information. It also provides reference information for the construction of new CRISPR/Cas systems. SynBioStrainFinder will serve as a useful resource to extend microbial strain research and application for biomanufacturing.

Isolation and characterization of SGF3, a novel Microviridae phage infecting Shigella flexneri

In the context of widespread bacterial contamination and the endless emergence of antibiotic-resistant bacteria, more effective ways to control pathogen infection are urgently needed. Phages become potential bactericidal agents due to their bactericidal specificity and not easy resistance to bacteria. But an important factor limiting its development is the lack of phage species. Therefore, the isolation of more new phages and studying their biological and genomic characteristics is of great significance for subsequent applications. So, in this study, SGF3, a Microviridae phage, which has shown lytic activity against Shigella flexneri, was isolated, purified, and characterized. Morphological and phylogenetic analyses identified it as a phiX174 species belonging to the Microviridae family. The latent period of phage SGF3 was 20 min, with an average burst size of approximately 7.1. Host spectrum experiments indicated its strong host specificity. Furthermore, the biofilm removal efficiency was increased by 20%-25% when SGF3 was coupled with other phages. In conclusion, the phage SGF3 found in this study was a lytic phage belonging to the Microviral family, and could be added as an auxiliary material in the phage cocktail. Studies of its characteristics and bactericidal properties had enriched the germplasm resources of microphages, provided more potential material in fighting against emerging and existing multidrug-resistant bacteria.

Spongiibacter thalassae sp. nov., a marine gammaproteobacterium isolated from seawater

A bacterium, designated as KMU-166^T, belonging to the class Gammaproteobacteria, was isolated from seawater collected on the coastline of Dadaepo, Republic of Korea. Strain KMU-166^T was Gram-staining-negative, ovoid-shaped, motile, strictly aerobic, beige-colored, catalase-positive, and oxidase-negative; and had a chemoorganoheterotrophic metabolism. The novel isolate was found to grow at 1-4% NaCl concentrations (w/v), pH 6.5-9.5, and 10-40 °C. The 16S rRNA gene sequence-based phylogeny showed that strain KMU-166^T affiliates to the family Spongiibacteraceae and that it shared the greatest sequence similarity (96.4%) with Spongiibacter marinus HAL40b^T. The main (> 10%) cellular fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c), C17:1ω8c, and C18:1ω7c. The predominant respiratory quinone was ubiquinone-8 (Q-8). Strain KMU-166^T comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The assembled draft genome was 4.40 Mbp in size with a DNA G+C content of 55.7%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values of KMU-166^T and Spongiibacter marinus HAL40b^T, Spongiibacter tropicus CL-CB221^T, and "Spongiibacter pelagi" KMU-158^T were found to be 77.7-79.8%, 13.7-15.4%, and 66.1-70.9%, respectively. From the distinguishable polyphasic taxonomic results obtained, the strain is considered to represent a novel species of the genus Spongiibacter for which the name Spongiibacter thalassae sp. nov. is proposed. The type strain of S. thalassae sp. nov. is KMU-166^T (= KCCM 90449^T = NBRC 114308^T).

N27

Sulfonamide antibiotics (SAs) have been produced and consumed on a large scale over the last few decades. SAs are a typical class of refractory contaminants that are omnipresent in various environments. Although several [phenyl]-SA-degrading bacteria and their corresponding genomes have been documented, limited genetic information is available for the degraders of heterocyclic products (e.g., 3-amino-5-methylisoxazole [3A5MI] produced via sulfamethoxazole [SMX] catabolism). In this study, the previously isolated SMX-mineralizing bacterial partners, Paenarthrobacter sp. P27 (responsible for the initial cleavage of the -C-S-N- bond of SMX and further degradation of [phenyl]-SMX) and Norcardiodes sp. N27 (responsible for 3A5MI catabolism), were further studied and their complete genomes were sequenced. Complete degradation and bacterial growth were verified by pure-culture experiments with SMX or 3A5MI as the sole carbon, nitrogen, and energy source. By cross-feeding strains P27 and N27, complete catabolism of SMX could be achieved over a wide range of initial SMX concentrations. Moreover, strain P27 was capable of transforming the additional nine SA representatives into their corresponding nitrogen-containing heterocyclic products, strongly indicating the broad substrate spectrum and marked bioremediation potential of strain P27. The genome of strain P27 contained the highly homologous monooxygenase gene cluster, sadABC, which initially attacked the sulfonamide molecules. The complete genome sequences of the two important degraders will benefit future research centering on the molecular mechanism underlying advanced SMX mineralization and will aid in further understanding the interspecific interactions and metabolite exchanges for the optimization of artificially constructed synthetic functional microbiomes.

Erythrobacter rubeus sp. nov., a carotenoid-producing alphaproteobacterium isolated from coastal seawater

A study based on a polyphasic taxonomic approach was carried out to identify and classify a novel marine alphaproteobacterium, designated as KMU-140^T, isolated from coastal seawater collected at Jeju Island, Republic of Korea. Cells of strain KMU-140^T were spherical, Gram-stain-negative, reddish-orange colored, strictly aerobic, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate was able to grow at NaCl concentrations of 0-5%, pH 6.0-9.5, and 10-45 °C. A phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KMU-140^T belongs to the family Erythrobacteraceae and was most closely related to Erythrobacter longus OCh101^T (98.7%). Strain KMU-140^T contained ubiquinone-10 (Q-10) as the only respiratory quinone and C18:1 ω7c, iso-C18:0, and C16:0 as the main (> 10%) cellular fatty acids. Strain KMU-140^T produced carotenoid compounds that rendered the cell biomass a reddish-orange color. The assembled draft genome size of strain KMU-140^T was 3.04 Mbp with G + C content of 60.6 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of KMU-140^T and the species of the genus Erythrobacter were found to be 76.6-78.4%, 14.0-18.7%, and 69.6-77.8%, respectively. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, and two unidentified lipids were identified as major polar lipids. On the basis of the polyphasic taxonomic features presented, the strain is considered to represent a novel species of the genus Erythrobacter for which the name Erythrobacter rubeus sp. nov. is proposed. The type strain of E. rubeus sp. nov. is KMU-140^T (= KCCM 90479^T = NBRC 115159^T).

Draft genome sequence of a lipopeptide-producing Bacillus amyloliquefaciens strain isolated from wheat field soil with antagonistic activity against azole-resistant Fusarium graminearum

OBJECTIVES

Lipopeptides have been revealed as good potential biocontrol agents against various pathogenic microbes. In the present work, we report the draft genome sequence of a lipopeptide-producing strain of Bacillus amyloliquefaciens (7D3) that showed good antifungal activity against the azole-resistant pathogenic fungus Fusarium graminearum.

METHODS

Whole-genome sequencing of strain 7D3 was performed on an Illumina MiSeq 300 platform. Raw data were cleaned using Trim Galore v.0.4.0 and were checked for quality using FastQC. De novo assembly was performed using the SOAPdenovo2 package. Genes responsible for the biosynthesis of secondary metabolites were identified using antiSMASH.

RESULTS

Bacillus amyloliquefaciens 7D3 genome assembly resulted in a total genome size of 3 913 220 bp with a G+C content of 46.13%. There were 3998 predicted genes with 72 tRNAs and 9 rRNAs. A total of ten gene clusters were found to be related to secondary metabolite biosynthesis, of which five were identified as lipopeptide synthesis clusters.

CONCLUSION

This study presents the genome sequence of B. amyloliquefaciens 7D3, which exhibited intense antagonistic activity against azole-resistant fungi. The whole genome sequence will help in the search for novel antifungal peptides against drug-resistant pathogens.

Genomic characterization of bacteriophage BI-EHEC infecting strains of Enterohemorrhagic Escherichia coli

OBJECTIVE

The aims of this research were to determine the genomic properties of BI-EHEC to control Enterohemorrhagic Escherichia coli (EHEC), which was isolated from previous study. Genomic analysis of this phage is essential for the assessment of this bacteriophage for further application as food preservatives.

RESULTS

Genome of BI-EHEC was successfully annotated using multiPhATE2. Structural and lytic cycle-related proteins such as head, tail, capsid, and lysozyme (lysin) were annotated. The phylogenetic tree of tail fiber protein and BRIG results showed that BI-EHEC was similar to phages of the same host in the bacteriophage genome database. There were no indications of virulence properties, antibiotic resistance genes and lysogenic protein among annotated genes which implied BI-EHEC followed a lytic life cycle. PHACTS analysis was done to confirm this notion further and yielded a lytic cycle result. Further analysis using CARD found that BI-EHEC does not contain residual ARGs per recommended parameter. Furthermore, BI-EHEC confirmed as lytic bacteriophage, making it a good candidate for biocontrol agent.

Whole genome sequence data of Chromobacterium violaceum WCH4, a human pathogenic strain from Sabah, Malaysia

Chromobacterium violaceum is a gram-negative, facultative anaerobic bacillus which is commonly found in soil. It can cause mild diarrhoea upon infection but can progress, although rarely, to fatal multi-organ failure and death. Here we report the whole genome sequence data of Chromobacterium violaceum WCH4 strain, a pathogenic strain that was obtained from a 78 year old male patient suffering from an eye infection. This is a rare case of human infection of the bacteria. Blood culture report as well as 16S rRNA confirmed the presence of C. violaceum WCH4. DNA sequencing using the Illumina HiSeq 4000 system revealed a genome size of 4,637,406 bp with a GC-content of 64.89%. We identified 4,572 protein coding sequences (CDS), 78 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. The CDS included 1,261 hypothetical proteins and 3,311 proteins with functional assignments. We also identified seven putative genes involved in efflux pump and conferring multidrug antibiotic resistance. The genome data has been deposited at NCBI under the accession number JAFBBB000000000 and consist of full annotated genome and raw sequence data. Our data resource will assist in further downstream analysis and understanding of the mechanism of rare human infection caused by Chromobacterium violaceum WCH4 strain.

Genome mining of secondary metabolites from a marine-derived Aspergillus terreus B12

Owing to the prominent capabilities of bioconversion and biosynthesis, A. terreus has become attractive in biotechnical and pharmaceutical industry. In this work, an Aspergillus strain with potential antibacterial activities, was isolated from sponge in South China Sea. Based on the morphological and phylogenetic analysis, the strain was identified as A. terreus B12. Via the Illumina MiSeq sequencing platform, the complete genome was obtained, showing a genetic richness of biosynthetic gene clusters (BGCs), which might underpin the metabolic plasticity and adaptive resilience for the strain. Genome mining identified 67 BGCs, among which, 6 gene clusters could allocate to known BGCs (100% identity), corresponding to diverse metabolites like clavaric acid, dihydroisoflavipucine/isoflavipucine, dimethylcoprogen, alternariol, aspterric acid, and pyranonigrin E. Moreover, a range of compounds was isolated from B12 fermentation, e.g., terrein, butyrolactone I, terretonin A&E, acoapetaline B, and epi-aszonalenins A. Of note, acoapetaline B and epi-aszonalenins A, which had been respectively reported in plants and A. novofumigatus but with scarce information, was unexpectedly obtained from this species for the first time. The genomic and metabolic heterogeneity observed in strain B12, should be at least partially attributed to the genetic variability and biochemical diversity of A. terreus, which could be an interesting issue open to future efforts.