Expanded microbial genome coverage and improved protein family annotation in the COG database

Taxonomic and genomic attributes of oligotrophic soil bacteria

Not all bacteria are fast growers. In soil as in other environments, bacteria exist along a continuum-from copiotrophs that can grow rapidly under resource-rich conditions to oligotrophs that are adapted to life in the "slow lane." However, the field of microbiology is built almost exclusively on the study of copiotrophs due, in part, to the ease of studying them in vitro. To begin understanding the attributes of soil oligotrophs, we analyzed three independent datasets that represent contrasts in organic carbon availability. These datasets included 185 samples collected from soil profiles across the USA, 950 paired bulk soil and rhizosphere samples collected across Europe, and soils from a microcosm experiment where carbon availability was manipulated directly. Using a combination of marker gene sequencing and targeted genomic analyses, we identified specific oligotrophic taxa that were consistently more abundant in carbon-limited environments (subsurface, bulk, unamended soils) compared to the corresponding carbon-rich environment (surface, rhizosphere, glucose-amended soils), including members of the Dormibacterota and Chloroflexi phyla. In general, putative soil oligotrophs had smaller genomes, slower maximum potential growth rates, and were under-represented in culture collections. The genomes of oligotrophs were more likely to be enriched in pathways that allow oligotrophs to metabolize a range of energy sources and store carbon, while genes associated with energy-intensive functions like chemotaxis and motility were under-represented. However, few genomic attributes were shared, highlighting that oligotrophs likely use a range of different metabolic strategies and regulatory pathways to thrive in resource-limited soils.

Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics

Holosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts.

Microbulbifer bruguierae sp. nov., isolated from sediment of mangrove plant Bruguiera sexangula, and comparative genomic analyses of the genus Microbulbifer

A Gram-negative, non-motile, strictly aerobic, rod-shaped bacterium, designated as H12T, was isolated from the sediments of mangrove plant Bruguiera sexangula taken from Dapeng district, Shenzhen, PR China. The pairwise 16S rRNA gene sequence analysis showed that strain H12T shared high identity levels with species of the genus Microbulbifer, with the highest similarity level of 98.5 % to M. pacificus SPO729T, followed by 98.1 % to M. donghaiensis CN85T. Phylogenetic analysis using core-genome sequences showed that strain H12T formed a cluster with type species of M. pacificus SPO729T and M. harenosus HB161719T. The complete genome of strain H12T was 4 481 396 bp in size and its DNA G+C content was 56.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values among strain H12T and type species of genus Microbulbifer were below the cut-off levels of 95-96 and 70 %, respectively. The predominant cellular fatty acids of strain H12T were iso-C15 : 0 (22.5 %) and C18 : 1  ω7c (13.9 %). Ubiquinone-8 was detected as the major respiratory quinone. The polar lipids of strain H12T comprised one phosphatidylglycerol, one phosphatidylethanolamine, one unidentified aminoglycophospholipid, one unidentified glycophospholipid, three unidentified glycolipids, two unidentified aminolipids, and one unidentified lipid. Based on polyphasic evidence, strain H12T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer bruguierae sp. nov. is proposed. The type strain is H12T (=KCTC 92859T=MCCC 1K08451T). Comparative genomic analyses of strain H12T with strains of the genus Microbulbifer reveal its potential in degradation of pectin.

Marinimicrococcus flavescens gen. nov., sp. nov., a new member of the family Geminicoccaceae, isolated from a marine sediment of the South China Sea

A Gram-stain-negative, catalase-positive and oxidase-positive, nonmotile, aerobic, light yellow, spherical-shaped bacterial strain with no flagella, designated strain YIM 152171T, was isolated from sediment of the South China Sea. Colonies were smooth and convex, light yellow and circular, and 1.0-1.5×1.0-1.5 µm in cell diameter after 7 days of incubation at 28°C on YIM38 media supplemented with sea salt. Colonies could grow at 20-45°C (optimum 28-35°C) and pH 6.0-11.0 (optimum, pH 7.0-9.0), and they could proliferate in the salinity range of 0-6.0 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1  ω7c/C18 : 1 ω6c), C18 : 1 ω7c 11-methyl, C16 : 0, C16 : 1 ω11c, C16 : 1 ω5c, C17 : 1 ω6c and C18 : 1 ω5c. The respiratory quinone was ubiquinone 10, and the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified aminolipid. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain YIM 152171T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus. The 16S rRNA gene sequence similarities of YIM 152171T to those of Arboricoccus pini, Geminicoccus roseus and Constrictibacter antarcticus were 92.17, 89.25 and 88.91 %, respectively. The assembled draft genome of strain YIM 152171T had 136 contigs with an N50 value of 134704 nt, a total length of 3 001 346 bp and a G+C content of 70.27 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain YIM 152171T (=MCCC 1K08488T=KCTC 92884T) represents a type of novel species and genus for which we propose the name Marinimicrococcus gen. nov., sp. nov.

Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes

Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe-arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher acr3 (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher aoxA (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.

Metagenomics reveals the genetic diversity between sublineages of UCYN-A and their algal host plastids

UCYN-A (or Cand. Atelocyanobacterium thalassa) has been recognized as a globally distributed, early stage, nitrogen-fixing organelle (the "nitroplast") of cyanobacterial origin present in the haptophyte alga Braarudosphaera bigelowii. Although the nitroplast was recognized as UCYN-A2, not all sublineages of UCYN-A have been confirmed as nitroplasts, and full genomes are still lacking for several known sublineages. We investigated the differences between UCYN-A sublineages by sequencing and assembly of metagenomic sequences acquired from cultured biomass from NW Atlantic seawater, which yielded near-complete Metagenome Assembled Genomes (MAGs) corresponding to UCYN-A1, -A4, and the plastid of the UCYN-A4-associated B. bigelowii. Weekly time-series data paired with the recurrence of specific microbes in cultures used for metagenomics gave further insight into the microbial community associated with the algal/UCYN-A complex. The UCYN-A1 MAG was found to have 99% average nucleotide identity (ANI) to the Pacific-derived reference genome despite its Atlantic Ocean origin. Comparison of the UCYN-A4 MAG (the initial genome sequenced from this sublineage) to other genomes showed that UCYN-A4 is sufficiently genetically distinct from both UCYN-A1 and UCYN-A2 (ANI of ~83% and ~85%, respectively) to be considered its own sublineage, but more similar to UCYN-A2 than -A1, supporting its possible classification as a nitroplast. The B. bigelowii plastid sequence was compared with published plastid sequences (sharing 78% ANI with Chrysochromulina parva) adding to our understanding of genomic variation across Haptophyta organelles and emphasizing the need for further full genomic sequencing of B. bigelowii genotypes and their organelles.

Cover crop monocultures and mixtures enhance bacterial abundance and functionality in the maize root zone

Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Re-utilization of winter cover crop root channels by maize roots during summer allows the cash crop to extract resources from distal regions in the soil horizon. In this study, we investigated how cover cropping during winter followed by maize (Zea mays L.) during summer affects the spatiotemporal composition and function of the bacterial communities in the maize rhizosphere and surrounding soil samples using quantitative polymerase chain reaction (PCR), 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing, and metaproteomics. We found that the bacterial community differed significantly among cover crop species, soil depths, and maize growth stages. Bacterial abundance increased in reused root channels, and it continued to increase as cover crop diversity changed from monocultures to mixtures. Mixing Fabaceae with Brassicaceae or Poaceae enhanced the overall contributions of several steps of the bacterial carbon and nitrogen cycles, especially glycolysis and the pentose phosphate pathway. The deeper root channels of Fabaceae and Brassicaceae as compared to Poaceae corresponded to higher bacterial 16S rRNA gene copy numbers and improved community presence in the subsoil regimes, likely due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel reuse improved the expression of metabolic pathways of the carbon and nitrogen cycles and the bacterial communities, which is beneficial to the soil and to the growing crops.

The chromosome-level genome assembly of Fraxinus americana provides insights into the evolution of Oleaceae plants

White ash (Fraxinus americana linn.) originates from the southeastern United States. It is a tall and fast-growing tree species with strong salt-alkali resistance and cold tolerance, making it an important reforestation species and widely planted worldwide. Here, we completed the chromosome-level reference genome assembly of F. americana based on Illumina, PacBio, and Hi-C reads, with a genome size of 878.98 Mb, an N50 of 3.27 Mb, and a heterozygosity rate of 0.3 %. Based on de novo prediction, transcriptome prediction, and homology-based protein prediction, we obtained 39,538 genes. Approximately 843.21 Mb of the assembly genome was composed of 37,928 annotated protein-coding genes, with a gene function annotation rate of 95.93 %. 99.94 % of the overlap clusters (877.44 Mb) were anchored to 23 chromosomes. Synteny analysis of F. americana and other Oleaceae plants showed that F. americana underwent frequent chromosome rearrangements. The amplification of the Ale transposons effectively promoted the genome size of F. americana. Compared with other Oleaceae plants, the Glutathione S-transferase (GST) gene family in the F. americana genome has undergone significant expansion, which may help F. americana cope with adverse natural environments. Furthermore, we found that key enzyme-coding gene families related to lignin biosynthesis were expanded and highly expressed in F. americana leaves. These key genes drive lignin synthesis and benefit F. americana in fast-growing, as well as resisting biotic and abiotic stress. Overall, the F. americana genome assembly provides insights into the evolution of Oleaceae plants and provides abundant resources for breeding and germplasm conservation of white ash.

Roseomonas populi sp. nov., an acetate-degrading bacteria isolated from the stem of Populus tomentosa

Strain CN29T, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29T were Gram-stain negative, aerobic, nonspore-forming, and nonmotile coccoid. Growth occurred at 20-37 °C, pH 4.0-9.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CN29T was closely related to members of the genus Roseomonas and closest to Roseomonas pecuniae N75T (96.6%). This classification was further supported by phylogenetic analysis using additional core genes. The average nucleotide identity and digital DNA‒DNA hybridization values between strain CN29T and Roseomonas populi CN29T were 82.7% and 27.8%, respectively. The genome size of strain CN29T was 5.87 Mb, with a G + C content of 70.9%. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), C19:0 cyclo ω8c and C16:0. The major respiratory quinone was Q-10. The polar lipids were phosphatidylcholine, aminolipid, phosphatidylglycerol, and diphosphatidylglycerol. Strain CN29T can utilize acetate as a carbon source for growth and metabolism. Additionally, it contains acid phosphatase (2-naphthyl phosphate), which catalyzes the hydrolysis of phosphoric monoesters. The CN29T strain contains several genes, including maeB, gdhB, and cysJ, involved in carbon, nitrogen, and sulfur cycling. These findings suggest that the strain may actively participate in ecosystem cycling, leading to soil improvement and promoting the growth of poplar trees. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain CN29T is concluded to represent a novel species of the genus Roseomonas, for which the name Roseomonas populi sp. nov. is proposed. The type strain is CN29T (= JCM 35579T = GDMCC 1.3267T).

Genomic and proteomic analysis of Salmonella Enteritidis isolated from a patient with foodborne diarrhea

Salmonella is a major cause of foodborne diseases and clinical infections worldwide. This study aimed to investigate the drug resistance, genomic characteristics, and protein expression of foodborne Salmonella in Shanxi Province. We isolated a strain of Salmonella Enteritidis from patient feces and designated it 31A. The drug resistance of 31A against 14 antibiotics was determined using an antimicrobial susceptibility test. Whole-genome sequencing and quantitative proteomic analysis were performed on the 31A strain. Functional annotation of drug resistance genes/proteins and virulence genes/proteins was conducted using various databases, such as VFDB, ARDB, CAZY, COG, KOG, CARD, GO, and KEGG. The focus of this study was understanding the mechanisms related to food poisoning, and the genetic evolution of 31A was analyzed through comparative genomics. The 31A strain belonged to ST11 Salmonella Enteritidis and showed resistance to β-lactam and quinolone antibiotics. The genome of 31A had 70 drug resistance genes, 321 virulence genes, 12 SPIs, and 3 plasmid replicons. Functional annotation of these drug resistance and virulence genes revealed that drug resistance genes were mainly involved in defense mechanisms to confer resistance to antibiotics, while virulence genes were mainly associated with cellular motility. There were extensive interactions among the virulence genes, which included SPI-1, SPI-2, flagella, fimbriae, capsules and so on. The 31A strain had a close relationship with ASM2413794v1 and ASM130523v1, which were also ST11 Salmonella Enteritidis strains from Asia and originated from clinical patients, animals, and food. These results suggested minimal genomic differences among strains from different sources and the potential for interhost transmission. Differential analysis of the virulence and drug resistance-related proteins revealed their involvement in pathways related to human diseases, indicating that these proteins mediated bacterial invasion and infection. The integration of genomic and proteomic information led to the discovery that Salmonella can survive in a strong acid environment through various acid resistance mechanisms after entering the intestine with food and then invade intestinal epithelial cells to exert its effects. In this study, we comprehensively analyzed the drug resistance and virulence characteristics of Salmonella Enteritidis 31A using a combination of genomic and proteomic approaches, focusing on the pathogenic mechanism of Salmonella Enteritidis in food poisoning. We found significant fluctuations in various virulence factors during the survival, invasion, and infection of Salmonella Enteritidis, which collectively contributed to its pathogenicity. These results provide important information for the source tracing, prevention, and treatment of clinical infections caused by Salmonella Enteritidis.

Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice

Introduction

In recent years, a large number of studies have shown that Bacillus velezensis has the potential as an animal feed additive, and its potential probiotic properties have been gradually explored.

Methods

In this study, Illumina NovaSeq PE150 and Oxford Nanopore ONT sequencing platforms were used to sequence the genome of Bacillus velezensis TS5, a fiber-degrading strain isolated from Tibetan sheep. To further investigate the potential of B. velezensis TS5 as a probiotic strain, in vivo experiments were conducted using 40 five-week-old male specific pathogen-free C57BL/6J mice. The mice were randomly divided into four groups: high fiber diet control group (H group), high fiber diet probiotics group (HT group), low fiber diet control group (L group), and low fiber diet probiotics group (LT group). The H and HT groups were fed high-fiber diet (30%), while the L and LT groups were fed low-fiber diet (5%). The total bacteria amount in the vegetative forms of B. velezensis TS5 per mouse in the HT and LT groups was 1 × 109 CFU per day, mice in the H and L groups were given the same volume of sterile physiological saline daily by gavage, and the experiment period lasted for 8 weeks.

Results

The complete genome sequencing results of B. velezensis TS5 showed that it contained 3,929,788 nucleotides with a GC content of 46.50%. The strain encoded 3,873 genes that partially related to stress resistance, adhesion, and antioxidants, as well as the production of secondary metabolites, digestive enzymes, and other beneficial nutrients. The genes of this bacterium were mainly involved in carbohydrate metabolism, amino acid metabolism, vitamin and cofactor metabolism, biological process, and molecular function, as revealed by KEGG and GO databases. The results of mouse tests showed that B. velezensis TS5 could improve intestinal digestive enzyme activity, liver antioxidant capacity, small intestine morphology, and cecum microbiota structure in mice.

Conclusion

These findings confirmed the probiotic effects of B. velezensis TS5 isolated from Tibetan sheep feces and provided the theoretical basis for the clinical application and development of new feed additives.

Differential priority effects impact taxonomy and functionality of host-associated microbiomes

Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and have adapted to their habitat on a tropical coral island in China, but the lack of genome information regarding its genetic background is unclear. In this study, the genome was assembled using both short/long whole genome sequencing reads and Hi-C reads. The assembled genome was 475.3 Mb, with 468.7 Mb (99.22%) of the sequences assembled into 16 chromosomes. Repeat sequences accounted for 54.41% of the assembled genome. A total of 26,615 genes were predicted, and 25,730 genes were functionally annotated using different annotation databases. Based on its genome and the other 17 species, phylogenetic analysis using 336 single-copy genes obtained from ortholog analysis showed that C. subcordata was a sister to Coffea eugenioides, and the divergence time was estimated to be 77 MYA between the two species. Gene family evolution analysis indicated that the significantly expanded gene families were functionally related to chemical defenses against diseases. These results can provide a reference to a deeper understanding of the genetic background of C. subcordata and can be helpful in exploring its adaptation mechanism on tropical coral islands in the future.

A genome catalog of the early-life human skin microbiome

BACKGROUND

Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents.

RESULTS

Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants.

CONCLUSIONS

Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.

MGI short-read genome assemblies of Pythium insidiosum (reclassified as Pythium periculosum) strains Pi057C3 and Pi050C3

OBJECTIVES

Pythium insidiosum causes a difficult-to-treat infectious condition called pythiosis, with high morbidity and mortality. So far, genome data of at least 10 strains of P. insidiosum, primarily classified in the phylogenetic clades I and II, have been sequenced using various next-generation sequencing platforms. The MGI short-read platform was employed to obtain genome data of 2 clade-III strains of P. insidiosum (recently reclassified as Pythium periculosum) from patients in Thailand and the United States. This work is a part of our attempt to generate a comprehensive genome database from diverse pathogen strains.

DATA DESCRIPTION

A 150-bp paired-end library was prepared from a gDNA sample of P. insidiosum (P. periculosum) strains Pi057C3 and Pi050C3 (also known as ATCC90586) to generate draft genome sequences using an MGISEQ-2000RS sequencer. As a result, for the strain Pi057C3, we obtained a 42.5-Mb assembled genome (164x coverage) comprising 14,134 contigs, L50 of 241, N50 of 45,748, 57.6% CG content, and 12,147 ORFs. For the strain Pi050C3, we received a 43.3-Mb draft genome (230x coverage) containing 14,511 contigs, L50 of 245, N50 of 45,208, 57.7% CG content, and 12,249 ORFs. The genome sequences have been deposited in the NCBI/DDBJ databases under the accession numbers JAKCXM000000000.1 (strain Pi057C3) and JAKCXL000000000.1 (strain Pi050C3).

A novel marine bacterium Exiguobacterium marinum a-1 isolated from in situ plastisphere for degradation of additive-free polypropylene

As the ecological niche most closely associated with polymers, microorganisms in the 'plastisphere' have great potential for plastics degradation. Microorganisms isolated from the 'plastisphere' could colonize and degrade commercial plastics containing different additives, but the observed weight loss and surface changes were most likely caused by releasing the additives rather than actual degradation of the plastics itself. Unlike commercial plastics that contain additives, whether marine microorganisms in the 'plastisphere' have adapted to additive-free plastics as a surface to colonize and potentially degrade is not yet known. Herein, a novel marine bacterium, Exiguobacterium marinum a-1, was successfully isolated from mature 'plastisphere' that had been deployed in situ for up to 20 months. Strain a-1 could use additive-free polypropylene (PP) films as its primary energy and carbon source. After strain a-1 was incubated with additive-free PP films for 80 days, the weight of films decreased by 9.2%. The ability of strain a-1 to rapidly form biofilms and effectively colonize the surface of additive-free PP films was confirmed by Scanning Electron Microscopy (SEM), as reflected by the increase in roughness and visible craters on the surface of additive-free PP films. Additionally, the functional groups of -CO, -C-H, and -OH were identified on the treated additive-free PP films according to Fourier Transform Infrared (FTIR). Genomic data from strain a-1 revealed a suite of key genes involved in biosurfactant synthesis, flagellar assembly, and cellular chemotaxis, contributing to its rapid biofilm formation on hydrophobic polymer surfaces. In particular, key enzymes that may be responsible for the degradation of additive-free PP films, such as glutathione peroxidase, cytochrome p450 and esterase were also recognized. This study highlights the potential of microorganisms present in the 'plastisphere' to metabolize plastic polymers and points to the intrinsic importance of the new strain a-1 in the mitigation of plastic pollution.

Whole genome sequencing and annotation of Scleroderma yunnanense, the only edible Scleroderma species

Scleroderma yunnanense, an ectomycorrhizal fungus, is a popular edible mushroom within the Yunnan Province of Southwest China that holds great ecological and economic implications. However, despite its significance, there remains limited information about this species. Therefore, we sequenced S. yunnanense genome to identify the functional genes of S. yunnanense involved in secondary metabolite and carbohydrate production pathways. First, we present the 40.43 Mb high-quality reference genome for S. yunnanense, distributed across 35 contigs; moreover, the N50 contig size was found to reach 3.31 Mb and contained 8877 functional genes. Finally, genome annotation was conducted to compare the functional genes of S. yunnanense with protein sequences from different publicly available databases. Taken together, we identified 12 biosynthetic gene clusters across 10 contigs; among these were 13 key mevalonate (MVA) pathway enzymes, a key tyrosinase enzyme in the 3,4-dihydroxyphenylalanine (DOPA) pathway that is responsible for producing DOPA melanins, and 16 enzymes involved in uridine diphosphate glucose biosynthesis. Overall, this study presents the first genome assembly and annotation of S. yunnanense; ultimately, this information will be important in the elucidation of the biological activities and artificial domestication of this fungus.

Genomic and phenotypic-based safety assessment and probiotic properties of Streptococcus thermophilus FUA329, a urolithin A-producing bacterium of human milk origin

Streptococcus thermophilus FUA329, a urolithin A-producing bacterium, is isolated from human breast milk. The complete genome sequence of FUA329 did not contain any plasmids and at least 20 proteins were related to extreme environment resistance. Phenotypic assay results demonstrated that FUA329 was susceptible to 12 kinds of antibiotics and did not exhibit any hemolytic or nitrate reductase activity. Three free radical scavenging assays revealed that FUA329 have high antioxidant capability. FUA329 exhibited a cell surface hydrophobicity of 52.58 ± 1.17% and an auto-aggregation rate of 18.69 ± 2.48%. Moreover, FUA329 demonstrated a survival rate of over 60% in strong acid and bile salt environments, indicating that FUA329 may be stable colonization in the gastrointestinal tract. Additionally, we firstly found 3 potential proteins and 11 potential genes of transforming ellagic acid to urolithins in FUA329 genome. The above results indicate that FUA329 has credible safety and probiotic properties, as well as the potential to be developed as a new generation of urolithin A-producing probiotics.

ListiWiki: A database for the foodborne pathogen Listeria monocytogenes

Listeria monocytogenes is a Gram positive foodborne pathogen that regularly causes outbreaks of systemic infectious diseases. The bacterium maintains a facultative intracellular lifestyle; it thrives under a variety of environmental conditions and is able to infect human host cells. L. monocytogenes is genetically tractable and therefore has become an attractive model system to study the mechanisms employed by facultative intracellular bacteria to invade eukaryotic cells and to replicate in their cytoplasm. Besides its importance for basic research, L. monocytogenes also serves as a paradigmatic pathogen in genomic epidemiology, where the relative stability of its genome facilitates successful outbreak detection and elucidation of transmission chains in genomic pathogen surveillance systems. In both terms, it is necessary to keep the annotation of the L. monocytogenes genome up to date. Therefore, we have created the database ListiWiki (http://listiwiki.uni-goettingen.de/) which stores comprehensive information on the widely used L. monocytogenes reference strain EDG-e. ListiWiki is designed to collect information on genes, proteins and RNAs and their relevant functional characteristics, but also further information such as mutant phenotypes, available biological material, and publications. In its present form, ListiWiki combines the most recent annotation of the EDG-e genome with published data on gene essentiality, gene expression and subcellular protein localization. ListiWiki also predicts protein-protein interactions networks based on protein homology to Bacillus subtilis proteins, for which detailed interaction maps have been compiled in the sibling database SubtiWiki. Furthermore, crystallographic information of proteins is made accessible through integration of Protein Structure Database codes and AlphaFold structure predictions. ListiWiki is an easy-to-use web interface that has been developed with a focus on an intuitive access to all information. Use of ListiWiki is free of charge and its content can be edited by all members of the scientific community after registration. In our labs, ListiWiki has already become an important and easy to use tool to quickly access genome annotation details that we can keep updated with advancing knowledge. It also might be useful to promote the comprehensive understanding of the physiology and virulence of an important human pathogen.

Lactobacillus plantarum E2 regulates intestinal microbiota and alleviates Pseudomonas plecoglossicida induced inflammation and apoptosis in zebrafish (Danio rerio)

Pseudomonas plecoglossicida infection is a highly contagious epidemic in aquaculture, causing significant mortality among teleost. Our previous research has demonstrated that Lactobacillus plantarum E2 is beneficial for large yellow croaker in resisting infections caused by P. plecoglossicida. However, the relevant mechanisms remain largely unclear. In the present study, we used zebrafish (Danio rerio) to further explore the function of L. plantarum E2 and its mechanisms for resisting P. plecoglossicida infection. E2 supplementation diet significantly improved the growth rates and α-amylase and trypsin activities of the liver in zebrafish. After challenge with P. plecoglossicida strain PQLYC4, the survival rates of zebrafish were improved, and immune-related genes expression (IL-1β, TNF-α, IL-8, Ig-Z, TLR-22 and IL-12α) were down-regulated. Histological analysis showed that E2 group had a longer intestinal villus and thicker intestinal walls after 30 days of feeding and healthier intestinal structure after challenge with P. plecoglossicida strain PQLYC4. Furthermore, co-incubation of zebrafish embryo fibroblast (ZF-4 cells) with L. plantarum E2 reduced apoptosis of ZF-4 cells after exposed to P. plecoglossicida. Intestinal microbiota analysis showed that E2 strain significantly increased the relative abundance of Lactobacillus and Pseudomonas, and PCoA analysis revealed a noticeable divergence in the intestinal microbial communities after E2 supplement. Together, our results suggested that E2 strain may promote zebrafish survival against P. plecoglossicida infection by regulating the intestinal microbiota and alleviating inflammatory response and apoptosis, thus exhibiting the potential as a probiotic.

Supplementing branched-chain volatile fatty acids in dual-flow cultures varying in dietary forage and corn oil concentrations. III: Protein metabolism and incorporation into bacterial protein

Some cellulolytic bacteria cannot transport branched-chain AA (BCAA) and do not express complete synthesis pathways, thus depending on cross-feeding for branched-chain volatile fatty acid (BCVFA) precursors for membrane lipids or for reductive carboxylation to BCAA. Our objective was to assess BCVFA uptake for BCAA synthesis in continuous cultures administered high forage (HF) and low forage (LF) diets without or with corn oil (CO). We hypothesized that BCVFA would be used for BCAA synthesis more in the HF than in LF diets. To help overcome bacterial inhibition by polyunsaturated fatty acids in CO, BCVFA usage for bacterial BCAA synthesis was hypothesized to decrease when CO was added to HF diets. The study was an incomplete block design with 8 dual-flow fermenters used in 4 periods with 8 treatments (n = 4) arranged as a 2 × 2 × 2 factorial. The factors were: HF or LF (67 or 33% forage, 33:67 alfalfa:orchardgrass pellets), without or with supplemental CO (3% of dry matter), and without or with 2.15 mmol/d (5 mg/d 13C) each of isovalerate, isobutyrate, and 2-methylbutyrate for one combined BCVFA treatment. The flow of bacterial BCAA increased by 10.7% by supplementing BCVFA and 9.14% with LF versus HF; similarly, dosing BCVFA versus without BCVFA increased BCAA by 1.98% in total bacterial AA, whereas LF increased BCAA by 1.92% versus HF. Additionally, BCVFA supplementation increased bacterial AA flow by 16.6% when supplemented in HF - CO and 12.4% in LF + CO diets, but not in the HF + CO (-1.5%) or LF - CO (+6.7%) diets (Diet × CO × BCVFA interaction). The recovery of 13C in bacterial AA flow was 31% lower with LF than with HF. Of the total 13C recovered in bacteria, 13.8, 17.3, and 30.2% were recovered in Val, Ile, and Leu, respectively; negligible 13C was recovered in other AA. When fermenters were dosed with BCVFA, nonbacterial and total effluent flows of AA, particularly of alanine and proline, suggest decreased peptidolysis. Increased ruminal outflow of bacterial AA, especially BCAA, but also nonbacterial AA could potentially support postabsorptive responses from BCVFA supplementation to dairy cattle.

Phycicoccus sonneraticus sp. nov., a Novel Endophytic Actinobacterium Isolated from the Bark of Sonneratia apetala

A novel endophytic actinobacterial strain, designated MQZ13P-5T, was isolated from a piece of bark of Sonneratia apetala, collected from Guangxi Zhuang Autonomous Region, China. This strain was Gram-stain positive, aerobic, non-spore-forming, non-motile and rod-shaped. Comparative 16S rRNA gene sequence analysis showed that strain MQZ13P-5T was related to the genus Phycicoccus with exhibiting the highest similarity (98.0%) to Phycicoccus endophyticus IP6SC6T. The phylogenetic trees based on 16S rRNA gene sequences and core genes indicated that strain MQZ13P-5T belonged to the genus Phycicoccus and could not be assigned to any described species. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MQZ13P-5T and type strains of Phycicoccus species were less than 84% and 27%, respectively, below the thresholds for species delineation. This strain showed chemotaxonomic and phenotypic properties consistent with its classification in the genus Phycicoccus. Based on the taxonomic data, strain MQZ13P-5T should represent a novel species of the genus Phycicoccus, for which the name Phycicoccus sonneraticus sp. nov. is proposed, with the type strain MQZ13P-5T (= CGMCC 1.18744T = JCM 34337T).

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

BACKGROUND

Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes.

RESULTS

We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth.

CONCLUSION

Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.

Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in Pseudomonas sp. Strain 273

Pseudomonas sp. strain 273 grows with medium-chain terminally fluorinated alkanes under oxic conditions, releases fluoride, and synthesizes long-chain fluorofatty acids. To shed light on the genes involved in fluoroalkane metabolism, genome, and transcriptome sequencing of strain 273 grown with 1,10-difluorodecane (DFD), decane, and acetate were performed. Strain 273 harbors three genes encoding putative alkane monooxygenases (AlkB), key enzymes for initiating alkane degradation. Transcripts of alkB-2 were significantly more abundant in both decane- and DFD-grown cells compared to acetate-grown cells, suggesting AlkB-2 catalyzes the attack on terminal CH3 and CH2F groups. Coordinately expressed with alkB-2 was an adjacent gene encoding a fused ferredoxin-ferredoxin reductase (Fd-Fdr). Phylogenetic analysis distinguished AlkB that couples with fused Fd-Fdr reductases from AlkB with alternate architectures. A gene cluster containing an (S)-2-haloacid dehalogenase (had) gene was up-regulated in cells grown with DFD, suggesting a possible role in the removal of the ω-fluorine. Genes involved in long-chain fatty acid biosynthesis were not differentially expressed during growth with acetate, decane, or DFD, suggesting the bacterium's biosynthetic machinery does not discriminate against monofluoro-fatty acid intermediates. The analysis sheds first light on genes and catalysts involved in the microbial metabolism of fluoroalkanes.

Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach

The gastric human pathogen Helicobacter pylori has developed mechanisms to combat stress factors, including reactive oxygen species (ROS). Here, we present a comprehensive study on the redox switch protein HP1021 regulon combining transcriptomic, proteomic and DNA-protein interactions analyses. Our results indicate that HP1021 modulates H. pylori's response to oxidative stress. HP1021 controls the transcription of 497 genes, including 407 genes related to response to oxidative stress. 79 proteins are differently expressed in the HP1021 deletion mutant. HP1021 controls typical ROS response pathways (katA, rocF) and less canonical ones, particularly DNA uptake and central carbohydrate metabolism. HP1021 is a molecular regulator of competence in H. pylori, as HP1021-dependent repression of the comB DNA uptake genes is relieved under oxidative conditions, increasing natural competence. Furthermore, HP1021 controls glucose consumption by directly regulating the gluP transporter and has an important impact on maintaining the energetic balance in the cell.

The Resistance and Virulence Characteristics of Salmonella Enteritidis Strain Isolated from Patients with Food Poisoning Based on the Whole-Genome Sequencing and Quantitative Proteomic Analysis

Objective

This paper explores the drug resistance, genome and proteome expression characteristics of Salmonella from a food poisoning event.

Methods

A multidrug-resistant Salmonella Enteritidis strain, labeled as 27A, was isolated and identified from a food poisoning patient. Antimicrobial susceptibility testing determined the resistance of 27A strain to 14 antibiotics. Then, WGS analysis and comparative genomics analysis were performed on 27A, and the functional annotation of resistance genes, virulence genes were performed based on VFDB, ARDB, COG, CARD, GO, KEGG, and CAZY databases. Meanwhile, based on iTRAQ technology, quantitative proteomic analysis was conducted on 27A to analyze the functions and interactions of differentially expressed proteins related to bacterial resistance and pathogenicity.

Results

Strain 27A belonged to ST11 S. Enteritidis and was resistant to levofloxacin, ciprofloxacin, ampicillin, piperacillin, and ampicillin/sulbactam. There were 33 drug resistance genes, 384 virulence genes and 2 plasmid replicon, IncFIB(S) and IncFII(S), annotated by WGS. Proteomic analysis revealed significant changes in virulence and drug proteins, which were mainly involved in bacterial pathogenicity and metabolic processes. PPI prediction showed the relationship between virulence proteins and T3SS proteins, and PagN cooperated with proteins related to T3SS to jointly mediate the invasion of 27A strain on the human body. Phylogenetic analysis indicated that S. Enteritidis has potential transmission in humans, food, and animals.

Conclusion

This study comprehensively analyzed the drug resistance and virulence phenotypes of S. Enteritidis 27A using genomic and proteomic approaches. These helps reveal the drug resistance and virulence mechanisms of S. Enteritidis, and provides important information for the source tracing and the prevention of related diseases, which lays a foundation for research on food safety, public health monitoring, and the drug resistance and pathogenicity of S. Enteritidis.

Alsobacter ponti sp. nov., a novel denitrification and sulfate reduction bacterium isolated from Pearl River sediment

A Gram-staining negative, aerobic, motile, and short rods strain, designated SYSU M60028T, was isolated from a Pearl River sediment sample in Guangzhou, Guangdong, China. The isolate could be able to grow at pH 6.0-8.0 (optimum, pH 7.0), 25-37 °C (optimum, 28 °C) and in the presence of 0-2% (w/v) NaCl (optimum, 0% NaCl). The cellular polar lipids of this strain were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. The respiratory quinone of SYSU M60028T was found to be Q-10. The major fatty acids (> 5% of total) were summed feature 8, C16:0, and C18:1 ω7c 11-methy1. The genomic DNA G + C content was 69.9%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60028T belonged to the genus Alsobacter and had the highest sequences similarities to Alsobacter metallidurans SK200a-9T (96.87%) and Alsobacter soli SH9T (96.87%). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M0028T should be considered to represent a novel species of the genus Alsobacter, for which the name Alsobacter ponti sp. nov. is proposed. The type strain is SYSU M60028T (= CGMCC 1.19341T = KCTC 92046T).

Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent

Tepidibacter sp. SWIR-1, a putative new species isolated from deep-sea hydrothermal vent field on the Southwest Indian Ridge (SWIR), is an anaerobic, mesophilic and endospore-forming bacterium belonging to the family Peptostreptococcaceae. In this study, we present the complete genome sequence of strain SWIR-1, consists of a single circular chromosome comprising 4,122,966 nucleotides with 29.25% G + C content and a circular plasmid comprising 38,843 nucleotides with 29.46% G + C content. In total, 3861 protein coding genes, 104 tRNA genes and 46 rRNA genes were obtained. SWIR-1 genome contains numerous genes related to sporulation and germination. Compared with the other three Tepidibacter species, SWIR-1 contained more spore germination receptor proteins. In addition, SWIR-1 contained more genes involved in chemotaxis and two-component systems than other Tepidibacter species. These results indicated that SWIR-1 has developed versatile adaptability to the Southwest Indian Ridge hydrothermal vent environment. The genome of strain SWIR-1 will be helpful for further understanding adaptive strategies used by bacteria dwelling in the deep-sea hydrothermal vent environments of different oceans.

The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella

Propionate is a microbial metabolite formed in the gastrointestinal tract, and it affects host physiology as a source of energy and signaling molecule. Despite the importance of propionate, the biochemical pathways responsible for its formation are not clear in all microbes. For the succinate pathway used during fermentation, a key enzyme appears to be missing-one that oxidizes ferredoxin and reduces NAD. Here we show that Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)] is this key enzyme in two abundant bacteria of the rumen (Prevotella brevis and Prevotella ruminicola). We found these bacteria form propionate, succinate, and acetate with the classic succinate pathway. Without ferredoxin:NAD+ oxidoreductase, redox cofactors would be unbalanced; it would produce almost equal excess amounts of reduced ferredoxin and oxidized NAD. By combining growth experiments, genomics, proteomics, and enzyme assays, we point to the possibility that these bacteria solve this problem by oxidizing ferredoxin and reducing NAD with Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)]. Genomic and phenotypic data suggest many bacteria may use Rnf similarly. This work shows the ferredoxin:NAD+ oxidoreductase activity of Rnf is important to propionate formation in Prevotella species and other bacteria from the environment, and it provides fundamental knowledge for manipulating fermentative propionate production.

Genomic evidence of genetic diversity and functional evolution in Flavobacterium columnare

Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish. Columnaris disease can cause heavy economic losses in aquaculture. In this study, whole-genome sequencing was used to characterize this pathogen. F. columnare isolate AH-01 had a circular chromosome and plasmid that encoded a total of 3,022 genes. Isolate GX-01 only had a circular chromosome and encoded 2,965 genes. Genomic islands, prophage regions, and CRISPR/Cas systems were identified in both genomes. Both genomes presented evidence of gene variation and horizontal transfer, both of which are the essential components of genetic diversity, genome plasticity, and functional evolution. Single-gene phylogeny and comparative genome analyses were performed to investigate the variation and evolution of this pathogen. Genetic analysis of 16S rRNA and housekeeping gene sequences significantly clustered 55 F. columnare isolates into four clades. The intragroup identity of the 16S rRNA gene exceeded 99%, while the intergroup identity was below the species delineation threshold. We discovered significant translocation, inversion, and rearrangement events that influenced local synteny within each group. Notably, the observed alignments varied considerably among all the studied groups. The core genomes of all strains with available sequences comprised 747 genes, corresponding to approximately 25% of the genome. Core genome multilocus sequence typing, genome-wide orthology and phylogenetic analyses, and average nucleotide identity suggested that the currently existing F. columnare was an assemblage of several distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. The present investigation provided genomic evidence of gene variation and horizontal transfer, which were the basis of genetic diversity, genome plasticity, and functional evolution. The findings supported a proposed new taxonomic perspective on F. columnare.

Prevalence, drug resistance, molecular typing and comparative genomics analysis of MRSA strains from a tertiary A hospital in Shanxi Province, China

Staphylococcus aureus (S. aureus) is an important zoonotic pathogen that causes a high incidence rate and mortality worldwide. This study investigated the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains in a tertiary A hospital in Shanxi Province, China, in order to determine the major epidemic clones as well as their antibiotic resistance and virulence characteristics. A total of 212 S. aureus strains were collected in this hospital, and were subjected to antimicrobial susceptibility testing, detection of virulence genes, resistance genes, and efflux pump genes. Among them, 38 MRSA strains were further subjected to detection of biofilm genes, assessment of biofilm formation ability, MLST, spa typing, SCCmec typing, and phylogenetic analysis. The majority of S. aureus strains came from the neonatology department, with secretions and purulent fluid being the main source of samples. The strains showed high resistance to penicillin (98.11%), erythromycin (64.62%) and clindamycin (59.91%), while being sensitive to vancomycin and linezolid. The detection rates of efflux pump genes and resistance genes were high, and there was a significant correlation between resistance gene types and phenotypes, with mecA showing a close correlation with oxacillin. The detection rates of virulence genes and the toxin gene profiles of MSSA and MRSA strains showed significant differences. And the detection rate of biofilm genes in MRSA strains was relatively high, with 13.16% of MRSA strains showing strong biofilm formation ability. The most common epidemic clone of MRSA was ST59-SCCmecIV-t437, followed by ST59-SCCmecV-t437. The former had a higher detection rate of resistance genes and a stronger biofilm formation ability, while the latter had a higher positive rate for pvl gene and stronger pathogenicity, making it more likely to cause systemic infections. Phylogenetic analysis showed that all MRSA strains in this study clustered into three major branches, with distinct differences in antibiotic resistance and virulence characteristics among the branches. ST59-MRSA strains from different species showed consistency and inter-species transmission, but there were differences among ST59-MRSA strains from different geographical locations. In general, most MSSA and MRSA strains exhibited multidrug resistance and carried multiple resistance genes, virulence genes, and biofilm formation genes, warranting further research to elucidate the mechanisms of drug resistance and pathogenesis.

Halanaerobium polyolivorans sp. nov.-A Novel Halophilic Alkalitolerant Bacterium Capable of Polyol Degradation: Physiological Properties and Genomic Insights

A search for the microorganisms responsible for the anaerobic degradation of osmoprotectants in soda lakes resulted in the isolation of a novel halophilic and alkalitolerant strain, designated Z-7514T. The cells were Gram-stain-negative and non-endospore-forming rods. Optimal growth occurs at 1.6-2.1 M Na+, pH 8.0-8.5, and 31-35 °C. The strain utilized mainly sugars, low molecular polyols, and ethanolamine as well. The G+C content of the genomic DNA of strain Z-7514T was 33.3 mol%. Phylogenetic and phylogenomic analyses revealed that strain Z-7514T belongs to the genus Halanaerobium. On the basis of phenotypic properties and the dDDH and ANI values with close validly published species, it was proposed to evolve strain Z-7514T within the genus Halanaerobium into novel species, for which the name Halanaerobium polyolivorans sp. nov. was proposed. The type strain was Z-7514T (=KCTC 25405T = VKM B-3577T). For species of the genus Halanaerobium, the utilization of ethylene glycol, propylene glycol, and ethanolamine were shown for the first time. The anaerobic degradation of glycols and ethanolamine by strain Z-7514T may represent a novel metabiotic pathway within the alkaliphilic microbial community. Based on a detailed genomic analysis, the main pathways of catabolism of most of the used substrates have been identified.

Unique Raoultella species isolated from petroleum contaminated soil degrades polystyrene and polyethylene

Polyolefin plastics, such as polyethylene (PE) and polystyrene (PS), are the most widely used synthetic plastics in our daily life. However, the chemical structure of polyolefin plastics is composed of carbon-carbon (C-C) bonds, which is extremely stable and makes polyolefin plastics recalcitrant to degradation. The growing accumulation of plastic waste has caused serious environmental pollution and has become a global environmental concern. In this study, we isolated a unique Raoultella sp. DY2415 strain from petroleum-contaminated soil that can degrade PE and PS film. After 60 d of incubation with strain DY2415, the weight of the UV-irradiated PE (UVPE) film and PS film decreased by 8% and 2%, respectively. Apparent microbial colonization and holes on the surface of the films were observed by scanning electron microscopy (SEM). Furthermore, the Fourier transform infrared spectrometer (FTIR) results showed that new oxygen-containing functional groups such as -OH and -CO were introduced into the polyolefin molecular structure. Potential enzymes that may be involved in the biodegradation of polyolefin plastics were analyzed. These results demonstrate that Raoultella sp. DY2415 has the ability to degrade polyolefin plastics and provide a basis for further investigating the biodegradation mechanism.

Genomic Analysis of Leptolyngbya boryana CZ1 Reveals Efficient Carbon Fixation Modules

Cyanobacteria, one of the most widespread photoautotrophic microorganisms on Earth, have evolved an inorganic CO2-concentrating mechanism (CCM) to adapt to a variety of habitats, especially in CO2-limited environments. Leptolyngbya boryana, a filamentous cyanobacterium, is widespread in a variety of environments and is well adapted to low-inorganic-carbon environments. However, little is currently known about the CCM of L. boryana, in particular its efficient carbon fixation module. In this study, we isolated and purified the cyanobacterium CZ1 from the Xin'anjiang River basin and identified it as L. boryana by 16S rRNA sequencing. Genome analysis revealed that L. boryana CZ1 contains β-carboxysome shell proteins and form 1B of Rubisco, which is classify it as belonging to the β-cyanobacteria. Further analysis revealed that L. boryana CZ1 employs a fine CCM involving two CO2 uptake systems NDH-13 and NDH-14, three HCO3- transporters (SbtA, BicA, and BCT1), and two carboxysomal carbonic anhydrases. Notably, we found that NDH-13 and NDH-14 are located close to each other in the L. boryana CZ1 genome and are back-to-back with the ccm operon, which is a novel gene arrangement. In addition, L. boryana CZ1 encodes two high-affinity Na+/HCO3- symporters (SbtA1 and SbtA2), three low-affinity Na+-dependent HCO3- transporters (BicA1, BicA2, and BicA3), and a BCT1; it is rare for a single strain to encode all three bicarbonate transporters in such large numbers. Interestingly, L. boryana CZ1 also uniquely encodes two active carbonic anhydrases, CcaA1 and CcaA2, which are also rare. Taken together, all these results indicated that L. boryana CZ1 is more efficient at CO2 fixation. Moreover, compared with the reported CCM gene arrangement of cyanobacteria, the CCM-related gene distribution pattern of L. boryana CZ1 was completely different, indicating a novel gene organization structure. These results can enrich our understanding of the CCM-related gene arrangement of cyanobacteria, and provide data support for the subsequent improvement and increase in biomass through cyanobacterial photosynthesis.

Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics

Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.

Taxonomic Identification of the Arctic Strain Nocardioides Arcticus Sp. Nov. and Global Transcriptomic Analysis in Response to Hydrogen Peroxide Stress

Microorganisms living in polar regions rely on specialized mechanisms to adapt to extreme environments. The study of their stress adaptation mechanisms is a hot topic in international microbiology research. In this study, a bacterial strain (Arc9.136) isolated from Arctic marine sediments was selected to implement polyphasic taxonomic identification based on factors such as genetic characteristics, physiological and biochemical properties, and chemical composition. The results showed that strain Arc9.136 is classified to the genus Nocardioides, for which the name Nocardioides arcticus sp. nov. is proposed. The ozone hole over the Arctic leads to increased ultraviolet (UV-B) radiation, and low temperatures lead to increased dissolved content in seawater. These extreme environmental conditions result in oxidative stress, inducing a strong response in microorganisms. Based on the functional classification of significantly differentially expressed genes under 1 mM H2O2 stress, we suspect that Arc9.136 may respond to oxidative stress through the following strategies: (1) efficient utilization of various carbon sources to improve carbohydrate transport and metabolism; (2) altering ion transport and metabolism by decreasing the uptake of divalent iron (to avoid the Fenton reaction) and increasing the utilization of trivalent iron (to maintain intracellular iron homeostasis); (3) increasing the level of cell replication, DNA repair, and defense functions, repairing DNA damage caused by H2O2; (4) and changing the composition of lipids in the cell membrane and reducing the sensitivity of lipid peroxidation. This study provides insights into the stress resistance mechanisms of microorganisms in extreme environments and highlights the potential for developing low-temperature active microbial resources.

One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade

Mantamonads were long considered to represent an "orphan" lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the "CRuMs" supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.

Pangenome analysis of Corynebacterium striatum: insights into a neglected multidrug-resistant pathogen

BACKGROUND

Over the past two decades, Corynebacterium striatum has been increasingly isolated from clinical cultures with most isolates showing increased antimicrobial resistance (AMR) to last resort agents. Advances in the field of pan genomics would facilitate the understanding of the clinical significance of such bacterial species previously thought to be among commensals paving the way for identifying new drug targets and control strategies.

METHODS

We constructed a pan-genome using 310 genome sequences of C. striatum. Pan-genome analysis was performed using three tools including Roary, PIRATE, and PEPPAN. AMR genes and virulence factors have been studied in relation to core genome phylogeny. Genomic Islands (GIs), Integrons, and Prophage regions have been explored in detail.

RESULTS

The pan-genome ranges between a total of 5253-5857 genes with 2070 - 1899 core gene clusters. Some antimicrobial resistance genes have been identified in the core genome portion, but most of them were located in the dispensable genome. In addition, some well-known virulence factors described in pathogenic Corynebacterium species were located in the dispensable genome. A total of 115 phage species have been identified with only 44 intact prophage regions.

CONCLUSION

This study presents a detailed comparative pangenome report of C. striatum. The species show a very slowly growing pangenome with relatively high number of genes in the core genome contributing to lower genomic variation. Prophage elements carrying AMR and virulence elements appear to be infrequent in the species. GIs appear to offer a prominent role in mobilizing antibiotic resistance genes in the species and integrons occur at a frequency of 50% in the species. Control strategies should be directed against virulence and resistance determinants carried on the core genome and those frequently occurring in the accessory genome.

Genomic Sequence Resource of Talaromyces albobiverticillius, the Causative Pathogen of Pomegranate Pulp Rot Disease

Talaromyces albobiverticillius, a prominent pathogen responsible for pomegranate pulp rot disease, inflicts significant damage on Punica granatum L. Besides its pathogenicity, this fungus possesses the potential to produce substantial amounts of red pigments, making it promising for industrial applications. This study presents the genome annotation of T. albobiverticillius field strain Tp-2, isolated from pomegranates. The genome assembly, generated through a combination of Oxford Nanopore and Illumina sequencing reads, yielded a high-quality assembly with 14 contigs, featuring an N50 length of 4,594,200 bp. The complete genome of strain Tp-2 spans 38,354,882 bp, with a GC content of 45.78%. Importantly, the assembly exhibits remarkable integrity, with 98.3% of complete Benchmarking Universal Single-Copy Orthologs validating genome completeness. Genome prediction analysis reveals the presence of 10,380 protein-coding genes. To our knowledge, this study is the first report on the genome sequence of T. albobiverticillius, offering valuable insights into its genetic variation and molecular mechanisms of pigment production.

Protaetiibacter mangrovi sp. nov., isolated from mangrove soil

A novel Gram-stain-positive, aerobic, non-flagellated and rod-shaped actinobacterium, designated 10F1B-8-1T, was isolated from mangrove soil sampled at Futian Mangrove Nature Reserve, China. The isolate was able to grow at 10-40 °C (optimum 30-32 °C), at pH 6-8 (optimum 7) and in the presence of 0-6% (w/v) NaCl (optimum 0%). Strain 10F1B-8-1T shared the highest 16S rRNA gene sequence similarity to Protaetiibacter larvae NBRC 113051T (98.3%), followed by Protaetiibacter intestinalis NBRC 113050T (98.2%). Phylogenetic trees based on 16S rRNA gene sequences and the core proteomes exhibited that strain 10F1B-8-1T formed a new phyletic line in the clade of genus Protaetiibacter, indicating that this strain belonged to the genus Protaetiibacter. Strain 10F1B-8-1T showed low average nucleotide identity (<84%) and digital DNA-DNA hybridization values (<27%) with closely related taxa, suggesting that strain 10F1B-8-1T was a hitherto undescribed species of the genus Protaetiibacter. Strain 10F1B-8-1T contained D-2,4-diaminobutyric acid as the diagnostic diamino acid, and the peptidoglycan type was characterized as type B2β. The major fatty acids were iso-C16:0, anteiso-C15:0 and anteiso-C17:0. The major menaquinones were MK-13 and MK-14. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and five unidentified lipids. Notably, the ethyl acetate extracts of strain 10F1B-8-1T showed effective antibacterial activity against Bacillus subtilis CPCC 100029 and Escherichia coli △tolC. According to the polyphasic data, strain 10F1B-8-1T should be classified as a novel species of the genus Protaetiibacter, for which the name Protaetiibacter mangrovi sp. nov. is proposed, with the type strain 10F1B-8-1T (=JCM 33142T = CPCC 205428T).

Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor

To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.

Kaistella polysaccharea sp. nov., isolated from Antarctic intertidal sediment produces a novel extracellular polymeric substance

An exopolysaccharide-producing bacterial strain GW4-15T, belonging to the genus Kaistella, was isolated from intertidal sediment from King George Island, Antarctic. The strain was Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow-pigmented. The strain was able to grow in the presence of 0-2 % (w/v) NaCl (optimum, 0 %), at 4-30 °C (optimum, 20-28 °C) and at pH 5.0-10.0 (optimum, pH 8.0). A phylogenetic tree based on 16S rRNA gene sequences showed that strain GW4-15T formed a lineage within the genus Kaistella with the closest phylogenetic neighbours Kaistella carnis NCTC 13525T (98.3 %), Kaistella gelatinilytica G5-32T (97.7 %), Kaistella antarctica LMG 24720T (97.4 %) and Kaistella yonginensis HMD1043T (96.9 %). Digital DNA-DNA hybridization values of strain GW4-15T with K. carnis NCTC 13525T, K. antarctica LMG 24720T, K. gelatinilytica G5-32T and K. yonginensis HMD1043T were 22.8, 22.0, 21.7 and 21.6 %, respectively. The average nucleotide identity values between strain GW4-15T and K. carnis NCTC 13525T , K. antarctica LMG 24720T, K. gelatinilytica G5-32T and K. yonginensis HMD1043T were 79.3, 78.6, 77.5 and 77.2 %, respectively. The G+C content of the genome was 36.2 mol%. The major phospholipids were phosphatidylethanolamine and aminophospholipid. The predominant menaquinone was MK-6. The major fatty acids were anteiso-C15 : 0 (28.7 %), iso-C16 : 0 3-OH (15.7 %), iso-C16 : 0 H (10.0 %), iso-C16 : 0 (5.4 %), summed feature 9 (comprising iso-C17 : 1  ω9c and/or 10-methyl C16 : 0; 5.2 %) and iso-C15 : 0 (5.1 %). The monosaccharide composition of the new type of extracellular polymeric of GW4-15T was Glc, GalN, GlcN, Rha, Man and Gal with a molar ratio of 3.14 : 3.83 : 8.38 : 5.16 : 1 : 2.82. Based on phenotypic, phylogenetic and genotypic data, a novel species, Kaistella polysaccharea sp. nov., is proposed with the type strain GW4-15T (=CGMCC 1.19368T=KCTC 92753T).

Metabolomic rearrangement controls the intrinsic microbial response to temperature changes

Temperature is one of the key determinants of microbial behavior and survival, whose impact is typically studied under heat- or cold-shock conditions that elicit specific regulation to combat lethal stress. At intermediate temperatures, cellular growth rate varies according to the Arrhenius law of thermodynamics without stress responses, a behavior whose origins have not yet been elucidated. Using single-cell microscopy during temperature perturbations, we show that bacteria exhibit a highly conserved, gradual response to temperature upshifts with a time scale of ~1.5 doublings at the higher temperature, regardless of initial/final temperature or nutrient source. We find that this behavior is coupled to a temperature memory, which we rule out as being neither transcriptional, translational, nor membrane dependent. Instead, we demonstrate that an autocatalytic enzyme network incorporating temperature-sensitive Michaelis-Menten kinetics recapitulates all temperature-shift dynamics through metabolome rearrangement, which encodes a temperature memory and successfully predicts alterations in the upshift response observed under simple-sugar, low-nutrient conditions, and in fungi. This model also provides a mechanistic framework for both Arrhenius-dependent growth and the classical Monod Equation through temperature-dependent metabolite flux.

Navigating the Landscape: A Comprehensive Review of Current Virus Databases

Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.

Terabase-Scale Coassembly of a Tropical Soil Microbiome

Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.

Screening and genome-wide analysis of lignocellulose-degrading bacteria from humic soil

Crop straw contains huge amounts of exploitable energy, and efficient biomass degradation measures have attracted worldwide attention. Mining strains with high yields of cellulose-degrading enzymes is of great significance for developing clean energy and industrial production of related enzymes. In this study, we reported a high-quality genome sequence of Bacillus velezensis SSF6 strain using high-throughput sequencing technology (Illumina PE150 and PacBio) and assessed its lignocellulose degradation potential. The results demonstrated that the genome of B. velezensis SSF6 was 3.89 Mb and contained 4,015 genes, of which 2,972, 3,831 and 158 genes were annotated in the COGs (Clusters of Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes) and CAZyme (Carbohydrate-Active enZymes) databases, respectively, and contained a large number of genes related to carbohydrate metabolism. Furthermore, B. velezensis SSF6 has a high cellulose degradation capacity, with a filter paper assay (FPA) and an exoglucanase activity of 64.48 ± 0.28 and 78.59 ± 0.42 U/mL, respectively. Comparative genomic analysis depicted that B. velezensis SSF6 was richer in carbohydrate hydrolase gene. In conclusion, the cellulose-degrading ability of B. velezensis SSF6 was revealed by genome sequencing and the determination of cellulase activity, which laid a foundation for further cellulose degradation and bioconversion.

Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome

BACKGROUND

Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.

RESULTS

Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.

CONCLUSION

Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia

To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.

Complete Genome Sequence of Pantoea ananatis Strain LCFJ-001 Isolated from Bacterial Wilt Mulberry

A Pantoea ananatis strain, named LCFJ-001 (GDMCC: 1.6101), was isolated for the first time from bacterial wilt-diseased roots of mulberry (Morus atropurpurea) in the western part of the Guangxi Zhuang Autonomous Region, China. Moreover, through Koch's postulates, it was proven that LCFJ-001 can cause mulberry wilt, which is one of the pathogens of mulberry bacterial wilt. Here, we report a complete, annotated genome sequence of P. ananatis LCFJ-001. The entire genome sequence of P. ananatis strain LCFJ-001 was a 4,499,350 bp circular chromosome with 53.50% GC content. In total, 3,521 genes were annotated, of which 3,418 were assigned protein-coding genes. In addition, 22 ribosomal RNAs and 81 transfer RNAs were identified. The presented resource will help explore the pathogenetic mechanisms of mulberry wilt disease caused by the genus Pantoea.

A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii)

Due to potentially hostile behaviors and elusive habitats, moray eels (Muraenidae) as one group of apex predators in coral reefs all across the globe have not been well investigated. Here, we constructed a chromosome-level genome assembly for the representative Reeve's moray eel (Gymnothorax reevesii). This haplotype genome assembly is 2.17 Gb in length, and 97.87% of the sequences are anchored into 21 chromosomes. It contains 56.34% repetitive sequences and 23,812 protein-coding genes, of which 96.77% are functionally annotated. This sequenced marine species in Anguilliformes makes a good complement to the genetic resource of eel genomes. It not only provides a genetic resource for in-depth studies of the Reeve's moray eel, but also enables deep-going genomic comparisons among various eels.