ABSTRACT
In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
Subject(s)
Archaea , Eukaryota , Phylogeny , Archaea/classification , Archaea/cytology , Archaea/genetics , Eukaryota/classification , Eukaryota/cytology , Eukaryota/genetics , Eukaryotic Cells/classification , Eukaryotic Cells/cytology , Prokaryotic Cells/classification , Prokaryotic Cells/cytology , Datasets as Topic , Gene Duplication , Evolution, MolecularABSTRACT
Piwi-interacting RNAs (piRNAs) engage Piwi proteins to suppress transposons and nonself nucleic acids and maintain genome integrity and are essential for fertility in a variety of organisms. In Caenorhabditis elegans, most piRNA precursors are transcribed from two genomic clusters that contain thousands of individual piRNA transcription units. While a few genes have been shown to be required for piRNA biogenesis, the mechanism of piRNA transcription remains elusive. Here we used functional proteomics approaches to identify an upstream sequence transcription complex (USTC) that is essential for piRNA biogenesis. The USTC contains piRNA silencing-defective 1 (PRDE-1), SNPC-4, twenty-one-U fouled-up 4 (TOFU-4), and TOFU-5. The USTC forms unique piRNA foci in germline nuclei and coats the piRNA cluster genomic loci. USTC factors associate with the Ruby motif just upstream of type I piRNA genes. USTC factors are also mutually dependent for binding to the piRNA clusters and forming the piRNA foci. Interestingly, USTC components bind differentially to piRNAs in the clusters and other noncoding RNA genes. These results reveal the USTC as a striking example of the repurposing of a general transcription factor complex to aid in genome defense against transposons.
Subject(s)
Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Gene Expression Regulation/genetics , RNA, Small Interfering/genetics , Amino Acid Motifs , Animals , Caenorhabditis elegans Proteins/genetics , Genome, Helminth/genetics , Protein Binding , Proteomics , RNA, Small Interfering/biosynthesisABSTRACT
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
Subject(s)
Bacteria/virology , Bacteriophages/classification , Bacteriophages/genetics , Earth, Planet , Ecosystem , Genome, Viral/genetics , Phylogeny , Amino Acyl-tRNA Synthetases/genetics , Animals , Bacteria/genetics , Bacteriophages/isolation & purification , Bacteriophages/metabolism , Biodiversity , CRISPR-Cas Systems/genetics , Evolution, Molecular , Gene Expression Regulation, Bacterial , Gene Expression Regulation, Viral , Host Specificity , Humans , Lakes/virology , Molecular Sequence Annotation , Oceans and Seas , Prophages/genetics , Protein Biosynthesis , RNA, Transfer/genetics , Ribosomal Proteins/genetics , Seawater/virology , Soil Microbiology , Transcription, GeneticABSTRACT
Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.
Subject(s)
Cyanobacteria , Photosynthesis , Photosynthesis/genetics , Cyanobacteria/genetics , Cyanobacteria/metabolism , Biological Evolution , Phylogeny , Oxygen/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Evolution, MolecularABSTRACT
Complete sample digestion is a prerequisite for acquiring high-quality analytical results for geological samples. Closed-vessel acid digestion (bomb) has typically been used for the total digestion of refractory geological samples. However, the long digestion time (4-5 days) and insoluble fluoride complexes still pose challenges for digesting refractory geological samples using this approach. In this study, an efficient and simplified digestion technique combining ultrafine powders from planetary ball milling with bomb digestion was developed for trace element analysis of refractory geological samples: peridotite and granitoid. The method shows two significant improvements compared with previous approaches. (1) By performing dry planetary ultrafine milling, the initial 200 mesh peridotite (<74 µm) could be reduced to 800 mesh (<20 µm) in 6 min at a ball-to-powder mass ratio of approximately 15 using 3 mm tungsten carbide milling balls. (2) Complete peridotite and granitoid dissolution were achieved in approximately 2 h, 60 times faster than what is achievable using previous methods (2 h vs 120 h). Moreover, ultrafine powders effectively suppressed insoluble fluoride formation during bomb digestion. A suite of peridotite and granitoid reference materials were measured to evaluate the stability of this method. This efficient, simple, and reliable sample digestion method could benefit geological, food, environmental, and other fields requiring solid sample decomposition via wet acid, fusion, combustion, or dry ashing.
ABSTRACT
Multimode fiber lasers have become a new platform for investigating nonlinear phenomena since the report on spatiotemporal mode-locking. In this work, the multimode soliton pulsation with a tunable period is achieved in a spatiotemporal mode-locked fiber laser. It demonstrates that the pulsation period drops while increasing the pump power. Moreover, it is found that different transverse modes have the same pulsation period, asynchronous pulsation evolution and different dynamical characteristics through the spatial sampling technique and the dispersive Fourier transform technique. To further verify the experimental results, we numerically investigate the influences of the gain and the loss on the pulsation properties. It is found that within a certain parameter range, the pulsation period drops and rises linearly with the increase of the gain and the loss, respectively. The obtained results contribute to understanding the formation and regulating of soliton pulsations in fiber lasers.
ABSTRACT
Cymodocea serrulata mediated titanium dioxide nanoparticles (TiO2 NPs) were successfully synthesized. The XRD pattern and FTIR spectra demonstrated the crystalline structure of TiO2 NPs and the presence of phenols, flavonoids and alkaloids in the extract. Further SEM revealed that TiO2 NPs has uniform structure and spherical in shape with their size ranged from 58 to 117 nm. Antibacterial activity of TiO2 NPs against methicillin-resistant Staphylococcus aureus (MRSA) and Vibrio cholerae (V. cholerae), provided the zone of inhibition of 33.9 ± 1.7 and 36.3 ± 1.9 mm, respectively at 100 µg/mL concentration. MIC of TiO2 NPs against MRSA and V. cholerae showed 84% and 87% inhibition at 180 µg/mL and 160 µg/mL respectively. Subsequently, the sub-MIC of V. cholerae demonstrated minimal or no impact on bacterial growth at concentration of 42.5 µg/mL concentration. In addition, TiO2 NPs exhibited their ability to inhibit the biofilm forming V. cholerae which caused distinct morphological and intercellular damages analysed using CLSM and TEM. The antioxidant properties of TiO2 NPs were demonstrated through TAA and DPPH assays and exposed its scavenging activity with IC50 value of 36.42 and 68.85 µg/mL which denotes its valuable antioxidant properties with potential health benefits. Importantly, the brine shrimp based lethality experiment yielded a low cytotoxic effect with 13% mortality at 100 µg/mL. In conclusion, the multifaceted attributes of C. serrulata mediated TiO2 NPs encompassed the antibacterial, antioxidant and anti-biofilm inhibition effects with low cytotoxicity in nature were highlighted in this study and proved the bioderived TiO2 NPs could be used as a promising agent for biomedical applications.
Subject(s)
Metal Nanoparticles , Methicillin-Resistant Staphylococcus aureus , Nanoparticles , Titanium , Antioxidants/pharmacology , Antioxidants/chemistry , Plant Extracts/pharmacology , Plant Extracts/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Nanoparticles/chemistry , Biofilms , Metal Nanoparticles/chemistryABSTRACT
Spatiotemporal mode-locked (STML) fiber lasers have become a new platform for investigating nonlinear phenomena. In this work, spatiotemporal dual-periodic soliton pulsation (SDSP) is firstly observed in an STML fiber laser. It is found that in the SDSP, the long-period pulsations (LPPs) of different transverse modes are synchronous, while the short-period pulsations (SPPs) exhibit asynchronous modulations. The numerical simulation confirms the experimental results and further reveals that the proportion of transverse mode components can manipulate the periods of the LPP and SPP but does not affect the synchronous and asynchronous pulsations of different transverse modes. The obtained results bring the study of spatiotemporal dissipative soliton pulsation into the multi-period modulation stage, which helps to understand the complex spatiotemporal dynamics in STML fiber lasers and discover new dynamics in high-dimensional nonlinear systems.
ABSTRACT
Phytopathogenic microorganisms have caused blight diseases that present significant challenges to global agriculture. These diseases result in substantial crop losses and have a significant economic impact. Due to the limitations of conventional chemical treatments in effectively and sustainably managing these diseases, there is an increasing interest in exploring alternative and environmentally friendly approaches for disease control. Using endophytic fungi as biocontrol agents has become a promising strategy in recent years. Endophytic fungi live inside plant tissues, forming mutually beneficial relationships, and have been discovered to produce a wide range of bioactive metabolites. These metabolites demonstrate significant potential for fighting blight diseases and provide a plentiful source of new biopesticides. In this review, we delve into the potential of endophytic fungi as a means of biocontrol against blight diseases. We specifically highlight their significance as a source of biologically active compounds. The review explores different mechanisms used by endophytic fungi to suppress phytopathogens. These mechanisms include competing for nutrients, producing antifungal compounds, and triggering plant defense responses. Furthermore, this review discusses the challenges of using endophytic fungi as biocontrol agents in commercial applications. It emphasizes the importance of conducting thorough research to enhance their effectiveness and stability in real-world environments. Therefore, bioactive metabolites from endophytic fungi have considerable potential for sustainable and eco-friendly blight disease control. Additional research on endophytes and their metabolites will promote biotechnology solutions.
Subject(s)
Antifungal Agents , Fungi , Agriculture , Biological Control Agents , Disease ManagementABSTRACT
Two novel bacterial strains, designated as SYSU D00823T and SYSU D00873T, were isolated from sandy soil of the Gurbantunggut Desert in Xinjiang, north-west China. SYSU D00823T and SYSU D00873T shared 99.0â% 16S rRNA gene sequence identity, and were both most closely related to Pedobacter xinjiangensis 12157T with 96.1â% and 96.0â% similarities, respectively. Phylogenetic and phylogenomic analyses revealed that the two isolates and P. xinjiangensis 12157T formed a separate distinct cluster in a stable subclade with the nearby species Pedobacter mongoliensis 1-32T, as well as the genera Pararcticibacter and Arcticibacter. Furthermore, P. mongoliensis 1-32T formed a separate deep-branching lineage and did not form a cluster with members of the genus Pedobacter. The average nucleotide identity and digital DNA-DNA hybridization values between SYSU D00823T and SYSU D00873T and related species were well below the thresholds for species delineation (<81.0â% and <24.0â%, respectively). The genomes of SYSU D00823T and SYSU D00873T were 6.19 and 6.43 Mbp in size with 40.4â% and 40.5â% DNA G+C contents, respectively. The predominant fatty acids (>10â%) of SYSU D00823T and SYSU D00873T were iso-C15â:â0, iso-C17â:â0 3-OH and summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c). Menaquinone-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine, glycosphingolipid, aminoglycolipid/glycolipid, aminophospholipid and three or four unidentified polar lipids. These data indicated that strains SYSU D00823T and SYSU D00873T should be assigned to two novel species of a new genus within the family Sphingobacteriaceae, for which the names Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov. are proposed. The type strains are SYSU D00823T (=CGMCC 1.18630T=MCCC 1K04973T=KCTC 82278T) and SYSU D00873T (=CGMCC 1.18629T=MCCC 1K04974T=KCTC 82281T), respectively. Accordingly, the reclassification of P. xinjiangensis as Desertivirga xinjiangensis comb. nov., and P. mongoliensis as Paradesertivirga mongoliensis gen. nov., comb. nov. are also proposed.
Subject(s)
Pedobacter , Phylogeny , Soil Microbiology , Base Composition , China , Desert Climate , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Pedobacter/genetics , Pedobacter/classification , Pedobacter/isolation & purification , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivativesABSTRACT
Two Gram-stain-positive, aerobic, oxidase- and catalase-negative, non-motile, and short rod-shaped actinomycetes, named SYSU T00b441T and SYSU T00b490, were isolated from tidal flat sediment located in Guangdong province, PR China. The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU T00b441T and SYSU T00b490 were 99.3, 99.5 and 97.1â%, respectively. Strains SYSU T00b441T and SYSU T00b490 exhibited the highest 16S rRNA gene sequence similarities to Actinotalea ferrariae CF 5-4T (97.1â%/98.2â%), with ANI values of 74.01/73.88â% and dDDH values of 20.5/20.4â%. In the phylogenomic tree, the two isolates were affiliated with the genus Actinotalea. The genomes of strains SYSU T00b441T and SYSU T00b490 were 3.31 and 3.34 Mb, and both had DNA G+C contents of 72.8âmol%, coding 3077 and 3085 CDSs, three and three rRNA genes, and 53 and 51 tRNAs, respectively. Growth occurred at 15-40â°C (optimum, 28-30â°C), pH 4.0-10.0 (optimum, 7.0) and in the presence of 0-7â% (w/v) NaCl (optimum, 3â%). The major fatty acids (>10ââ%) of strains SYSU T00b441T and SYSU T00b490 were anteiso-C15â:â0 and C16â:â0. The major respiratory quinone was identified as MK-10(H4). The polar lipids of strains SYSU T00b441T and SYSU T00b490 were diphosphatidyl glycerol, phosphatidylglycerol, phosphoglycolipid, phosphatidyl ethanolamine, two phosphatidylinositol mannosides, two glycolipids and two phospholipids. Based on these data, the two strains (SYSU T00b441T and SYSU T00b490) represent a novel species of the genus Actinotalea, for which the name Actinotalea lenta sp. nov is proposed. The type strain is SYSU T00b441T (=GDMCC 1.3827T=KCTC 49943T).
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Geologic Sediments , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , Geologic Sediments/microbiology , DNA, Bacterial/genetics , China , Actinobacteria/isolation & purification , Actinobacteria/genetics , Actinobacteria/classification , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , Phospholipids/chemistryABSTRACT
A Gram-stain-negative, non-motile, and slightly halophilic alphaproteobacterium, designated strain EGI FJ00035T, was isolated from enrichment sediment samples of a saline lake in Xinjiang Uygur Autonomous Region, PR China. The taxonomic position of the isolate was determined using the polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain EGI FJ00035T formed a distinct clade with 'Chelativorans alearense' UJN715 and 'Chelativorans xinjiangense' lm93 with sequence similarities of 98.44 and 98.22â%, respectively, while sharing less than 96.7â% with other valid type strains. The novel isolate could be distinguished from other species of the genus Chelativorans by its distinct phenotypic, physiological, and genotypic characteristics. Optimal growth of strain EGI FJ00035T occurred on marine agar 2216 at pH 7.0 and 30â°C. The major respiratory quinone was Q-10, while the major fatty acids (>5â%) were C19â:â0 cyclo ω8c, summed feature 8 (C17â:â1 ω6c and/or C17â:â1 ω7c), C16â:â0, C18â:â0, and iso-C17â:â0. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipids, unidentified glycolipids, and an unidentified lipid. Based on its genome sequence, the G+C content of strain EGI FJ00035T was 63.2âmol%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values of strain EGI FJ00035T against related members of the genus Chelativorans were below the thresholds for delineation of a novel species. According our polyphasic taxonomic data, strain EGI FJ00035T represents a new species of the genus Chelativorans, for which the name Chelativorans salis sp. nov. is proposed. The type strain of the proposed novel isolate is EGI FJ00035T (=KCTC 92251T=CGMCC 1.19480T).
Subject(s)
Fatty Acids , Phyllobacteriaceae , Fatty Acids/chemistry , Phospholipids/chemistry , Ubiquinone/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Lakes/analysis , Base Composition , Bacterial Typing Techniques , DNA, Bacterial/genetics , Sequence Analysis, DNA , China , Phyllobacteriaceae/geneticsABSTRACT
Two Gram-stain-negative, aerobic, milk-white coloured, non-motile, short rod-shaped bacteria, designated as strains SYSU D60010T and SYSU D60012T, were isolated from sand samples collected from the Taklimakan Desert of Xinjiang Province in China. Both strains were positive for oxidase, catalase and nitrate reduction, but negative for amylase, H2S production, hydrolysis of gelatin and cellulase. Strains SYSU D60010T and SYSU D60012T grew well at 28â°C, at pH 7 and had the same NaCl tolerance range of 0-1â% (w/v). The major fatty acids (>5â%) of strains SYSU D60010T and SYSU D60012T were summed feature 8 (C18â:â1 ω7c and/or C18â:â1 ω6c), iso-C19â:â0 cyclo ω8c, C16â:â0 and iso-C18â:â1 2-OH. Q-10 was the only respiratory ubiquinone. Strains SYSU D60010T and SYSU D60012T showed high 16S rRNA gene sequence similarities to Aestuariivirga litoralis SYSU M10001T (94.2 and 94.1â%), Rhodoligotrophos jinshengii BUT-3T (92.0 and 91.9â%) and Rhodoligotrophos appendicifer 120-1T (91.8 and 91.7â%), and the genomes were 7.4 and 5.8 Mbp in size with DNA G+C contents of 62.8 and 63.0âmol%, respectively. Phylogenetic, phenotypic and chemotaxonomic characteristics indicated that these two strains represent a novel genus and two novel species within the family Aestuariivirgaceae. We propose the name Taklimakanibacter deserti gen. nov., sp. nov. for strain SYSU D60010T, representing the type strain of this species (=KCTC 52783T =NBRC 113344T) and Taklimakanibacter lacteus gen. nov., sp. nov. for strain SYSU D60012T, representing the type strain of this species (=KCTC 52785T=NBRC 113128T).
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Desert Climate , Fatty Acids , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Soil Microbiology , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , DNA, Bacterial/genetics , China , Ubiquinone/analogs & derivatives , Sand/microbiologyABSTRACT
Two strains, designated as SYSU M80004T and SYSU M80005T, were isolated from water sampled in the Pearl River Estuary, Guangzhou, Guangdong, PR China. The strains were Gram-stain-negative and aerobic. Strain SYSU M80004T could grow at pH 6.0-8.0 (optimum, pH 7.0), 22-30 °C (optimum, 28 °C) and in the presence of 0-1â% NaCl (w/v; optimum 0â%). Strain SYSU M80005T could grow at pH 6.0-8.0 (optimum, pH 7.0), 4-37 °C (optimum, 28 °C) and in the presence of 0-1â% NaCl (w/v; optimum 0%). Both strains contained MK-6 as the predominant menaquinone. C16â:â0 and iso-C15â:â0 were identified as the major fatty acids (>10â%) of strain SYSU M80004T while strain SYSU M80005T contained iso-C15â:â0 and iso-C17â:â0 3-OH as major fatty acids. Phosphatidylethanolamine was present as the major polar lipid in both strains. The average nucleotide identity and digital DNA-DNA hybridization values between these two strains and their closest relatives were 73.5-79.3â% and 19.6-23.2â%, respectively. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated they belonged to the genus Flavobacterium. Therefore, on the basis of phenotypic, physiological, chemotaxonomic and genomic evidence, two novel species, Flavobacterium adhaerens sp. nov. (type strain=SYSU M80004T=CDMCC 1.4522T=KCTC 102268T) and Flavobacterium maritimum sp. nov. (type strain=SYSU M80005T=CGMCC 1.4523T= KCTC 102269T) are proposed.
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Estuaries , Fatty Acids , Flavobacterium , Nucleic Acid Hybridization , Phosphatidylethanolamines , Phylogeny , RNA, Ribosomal, 16S , Rivers , Sequence Analysis, DNA , Vitamin K 2 , Flavobacterium/genetics , Flavobacterium/isolation & purification , Flavobacterium/classification , China , RNA, Ribosomal, 16S/genetics , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , Fatty Acids/chemistry , DNA, Bacterial/genetics , Rivers/microbiology , Water MicrobiologyABSTRACT
Two Gram-stain-negative strains, designed SYSU M86414T and SYSU M84420, were isolated from marine sediment samples of the South China Sea (Sansha City, Hainan Province, PR China). These strains were aerobic and could grow at pH 6.0-8.0 (optimum, pH 7.0), 4-37â°C (optimum, 28â°C), and in the presence of 0-10â% NaCl (w/v; optimum 3â%). The predominant respiratory menaquinone of strains SYSU M86414T and SYSU M84420 was MK-6. The primary cellular polar lipid was phosphatidylethanolamine. The major cellular fatty acids (>10â%) in both strains were iso-C15â:â0, iso-C15â:â1 G, and iso-C17â:â0 3-OH. The DNA G+C content of strains SYSU M86414T and SYSU M84420 were both 42.10âmol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that these novel strains belonged to the genus Flagellimonas and strain SYSU M86414T showed the highest 16S rRNA gene sequence similarity to Flagellimonas marinaquae JCM 11811T (98.83â%), followed by Flagellimonas aurea BC31-1-A7T (98.62â%), while strain SYSU M84420 had highest 16S rRNA gene sequence similarity to F. marinaquae JCM 11811T (98.76â%) and F. aurea BC31-1-A7T (98.55â%). Based on the results of polyphasic analyses, strains SYSU M86414T and SYSU M84420 should be considered to represent a novel species of the genus Flagellimonas, for which the name Flagellimonas halotolerans sp. nov. is proposed. The type strain of the proposed novel isolate is SYSU M86414T (=GDMCC 1.3806T=KCTC 102040T).
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Geologic Sediments , Phylogeny , RNA, Ribosomal, 16S , Seawater , Sequence Analysis, DNA , Vitamin K 2 , China , RNA, Ribosomal, 16S/genetics , Geologic Sediments/microbiology , Fatty Acids/analysis , Seawater/microbiology , DNA, Bacterial/genetics , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , Phosphatidylethanolamines , Molecular Sequence DataABSTRACT
A Gram-stain-negative, non-endospore-forming, motile, short rod-shaped strain, designated SYSU G07232T, was isolated from a hot spring microbial mat, sampled from Rehai National Park, Tengchong, Yunnan Province, south-western China. Strain SYSU G07232T grew at 25-50â°C (optimum, 37â°C), at pH 5.5-9.0 (optimum, pH 6.0) and tolerated NaCl concentrations up to 1.0â% (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SYSU G07232T showed closest genetic affinity with Chelatococcus daeguensis K106T. The genomic features and taxonomic status of this strain were determined through whole-genome sequencing and a polyphasic approach. The predominant quinone of this strain was Q-10. Major cellular fatty acids comprised C19â:â0 cyclo ω8c and summed feature 8. The whole-genome length of strain SYSU G07232T was 4.02 Mbp, and the DNA G+C content was 69.26âmol%. The average nucleotide identity (ANIm ≤84.85â% and ANIb ≤76.08ââ%) and digital DNA-DNA hybridization (≤ 21.9â%) values between strain SYSU G07232T and the reference species were lower than the threshold values recommended for distinguishing novel prokaryotic species. Thus, based on the provided phenotypic, phylogenetic, and genetic data, it is proposed that strain SYSU G07232T (=KCTC 8141T=GDMCC 1.4178T) be designated as representing a novel species within the genus Chelatococcus, named Chelatococcus albus sp. nov.
Subject(s)
Beijerinckiaceae , Hot Springs , Phylogeny , RNA, Ribosomal, 16S/genetics , Base Composition , China , Fatty Acids/chemistry , Sequence Analysis, DNA , DNA, Bacterial/genetics , Bacterial Typing Techniques , BacteriaABSTRACT
The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.
Subject(s)
Ecosystem , Rivers , Rivers/microbiology , Plankton/genetics , Estuaries , RNA, Ribosomal, 16S/genetics , Bacteria/genetics , WaterABSTRACT
Paclitaxel (PTX) serves as a primary chemotherapy agent against diverse solid tumors including breast cancer, lung cancer, head and neck cancer and ovarian cancer, having severe adverse effects including PTX-induced peripheral neuropathy (PIPN) and hypersensitivity reactions (HSR). A recommended anti-allergic agent diphenhydramine (DIP) has been used to alleviate PTX-induced HSR. Desloratadine (DLT) is a third generation of histamine H1 receptor antagonist, but also acted as a selective antagonist of 5HTR2A. In this study we investigated whether DLT ameliorated PIPN-like symptoms in mice and the underlying mechanisms. PIPN was induced in male mice by injection of PTX (4 mg/kg, i.p.) every other day for 4 times. The mice exhibited 50% reduction in mechanical threshold, paw thermal response latency and paw cold response latency compared with control mice. PIPN mice were treated with DLT (10, 20 mg/kg, i.p.) 30 min before each PTX administration in the phase of establishing PIPN mice model and then administered daily for 4 weeks after the model was established. We showed that DLT administration dose-dependently elevated the mechanical, thermal and cold pain thresholds in PIPN mice, whereas administration of DIP (10 mg/kg, i.p.) had no ameliorative effects on PIPN-like symptoms. We found that the expression of 5HTR2A was selectively elevated in the activated spinal astrocytes of PIPN mice. Spinal cord-specific 5HTR2A knockdown by intrathecal injection of AAV9-5Htr2a-shRNA significantly alleviated the mechanical hyperalgesia, thermal and cold hypersensitivity in PIPN mice, while administration of DLT (20 mg/kg) did not further ameliorate PIPN-like symptoms. We demonstrated that DLT administration alleviated dorsal root ganglion neuronal damage and suppressed sciatic nerve destruction, spinal neuron apoptosis and neuroinflammation in the spinal cord of PIPN mice. Furthermore, we revealed that DLT administration suppressed astrocytic neuroinflammation via the 5HTR2A/c-Fos/NLRP3 pathway and blocked astrocyte-neuron crosstalk by targeting 5HTR2A. We conclude that spinal 5HTR2A inhibition holds promise as a therapeutic approach for PIPN and we emphasize the potential of DLT as a dual-functional agent in ameliorating PTX-induced both PIPN and HSR in chemotherapy. In summary, we determined that spinal 5HTR2A was selectively activated in PIPN mice and DLT could ameliorate the PTX-induced both PIPN- and HSR-like pathologies in mice. DLT alleviated the damages of DRG neurons and sciatic nerves, while restrained spinal neuronal apoptosis and CGRP release in PIPN mice. The underlying mechanisms were intensively investigated by assay against the PIPN mice with 5HTR2A-specific knockdown in the spinal cord by injection of adeno-associated virus 9 (AAV9)-5Htr2a-shRNA. DLT inhibited astrocytic NLRP3 inflammasome activation-mediated spinal neuronal damage through 5HTR2A/c-FOS pathway. Our findings have supported that spinal 5HTR2A inhibition shows promise as a therapeutic strategy for PIPN and highlighted the potential advantage of DLT as a dual-functional agent in preventing against PTX-induced both PIPN and HSR effects in anticancer chemotherapy.
ABSTRACT
The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602 T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602 T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).
Subject(s)
Brevibacterium , Fatty Acids , Metals, Heavy , Phylogeny , RNA, Ribosomal, 16S , Brevibacterium/genetics , Brevibacterium/classification , Brevibacterium/isolation & purification , Brevibacterium/metabolism , Brevibacterium/physiology , RNA, Ribosomal, 16S/genetics , Metals, Heavy/metabolism , Pakistan , Fatty Acids/analysis , DNA, Bacterial/genetics , Bacterial Typing Techniques , Base Composition , Sequence Analysis, DNA , Phospholipids/analysis , Tanning , GenomicsABSTRACT
Two novel Gram-stain-negative, aerobic, and non-motile strains, designated FZY0004T and YYF002T, were isolated from an agar-degrading co-culture, which was obtained from seawater of the intertidal zone of Yancheng City, the Yellow Sea of China. Strain FZY0004T optimally grew at 28 °C, pH 7.0, and 2-6% NaCl, while strain YYF002T optimally grew at 28 °C, pH 7.5, and 2-4% NaCl. Strain FZY0004T possessed Q-9 as the major respiratory quinone, and its major fatty acids (> 10%) were summed feature 8 (C18:1 ω7c), C16:0, and summed feature 3 (C16:1 ω7c/C16:1 ω6c). The polar lipids identified in strain FZY0004T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and several unidentified phospholipids (PL) and lipids (L). On the other hand, strain YYF002T had MK-6 as the predominant respiratory quinone and its major fatty acids consisted of iso-C15:0, iso-C15:1 G, and iso-C15:0 3-OH. The polar lipids identified in strain YYF002T were aminolipid (AL), PE, and several unidentified lipids. Strain FZY0004T shared 99.5% 16S rRNA gene sequence similarity and 90.1% average nucleotide identity (ANI) with T. povalilytica Zumi 95T, and strain YYF002T shared 99.2% 16S rRNA gene sequence similarity and 88.2% ANI with W. poriferorum JCM 12885T. The genomic DNA G + C contents of strains FZY0004T and YYF002T were 54.5% and 33.5%, respectively. The phylogenetic, phenotypic, and physiological characteristics permitted the distinction of the two strains from their neighbors, and we thus propose the names Thalassospira aquimaris sp. nov. (type strain FZY0004T = JCM 35895T = MCCC 1K08380T) and Winogradskyella marincola sp. nov. (type strain YYF002T = JCM 35950T = MCCC 1K08382T).