scholarly journals Screening And Genome Sequencing of a di-n-butyl Phthalate Degrading Bacterium J2 Isolated From Peanut Field Soil

2021 ◽  
Author(s):  
Mingqing Wang ◽  
Lina Yu ◽  
Jie Sun ◽  
Jie Bi ◽  
Yu Song ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
Reading Frame ◽  
Plastic Films ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Protein Encoding ◽  
Butyl Phthalate

Abstract Di-n-butyl phthalate (DBP) is commonly used plasticizers in agricultural plastic films, and is a priority pollutant due to its toxicity to human health. A newly isolated strain J2, which used DBP as its sole carbon source, was screened from peanut filed soil by continuous enrichment cultivation. Based on morphological, physiological characteristics and 16S rRNA gene sequence analysis (GenBank accession No. OK598965), it was identified as Priestia sp. J2. The research results revealed the optimal conditions for DBP degradation as 35 oC and pH 8.0. The strain could effectively degrade 97.6% DBP within 5 days. Substrate tests showed that strain J2 could utilize shorter side-chained PAEs, but could not utilize long-chained PAEs. The whole genome comprises a complete chromosome of 5,067,299 bp and four plasmids of 147,924 bp, 75,940 bp, 11,604 bp, 11,333 bp (GenBank accession No. CP086208-CP086212). This genome harbors 5,585 predicted protein-encoding genes, 130 tRNA genes, and 42 rRNA genes. Gene annotation analyses showed a DBP-degrading gene contained an open reading frame of 930 bp, and the enzyme was named Est-J2-1. The amino acid sequence of the Est-J2-1 exhibited no significant homology with those of reported DBP-degrading enzymes, suggesting the enzyme is a novel enzyme. The gene of Est-J2-1 was found to be located on the chromosome. This study provided strain resource for DBP removal from farmland and other environments.

scholarly journals Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Hikaru Suenaga ◽  
Mamoru Oshiki ◽  
Shuichi Kawano ◽  
Toshikazu Fukushima
Keyword(s):  
Activated Sludge ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Coke Oven ◽  
Rrna Genes ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Degrading Bacterium

ABSTRACT A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

Frateuria flava sp. nov., isolated from soil

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Shahina Akter ◽  
Sun-Young Lee ◽  
Md. Amdadul Huq
Keyword(s):  
Type Species ◽  
Draft Genome ◽  
Nutrient Agar ◽  
Rrna Genes ◽  
Physiological Data ◽  
Trna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8–3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13T was found to be able to grow at 20–40 °C, at pH 5.0–10.0 and with 0–1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515T (98.2% similarity), Dyella thiooxydans ATSB10T (98.2 %), Frateuria defendens HyOGT (97.9 %), Rhodanobacter glycinis MO64T (97.8 %) and Frateuria aurantia DSM 6220T (97.8 %). The novel strain MAH-13T has a draft genome size of 3 682 848 bp (40 contigs), annotated with 3172 protein-coding genes, 49 tRNA genes and three rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAH-13T and five closely related type strains were in the range of 73.7–85.5 % and 20.7–30.1%, respectively. The genomic DNA G+C content was determined to be 68.0 mol%. The predominant isoprenoid quinone was ubiquinone 8. The major fatty acids were identified as iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16:0 10-methyl). On the basis of dDDH and ANI values, genotypic analysis, and chemotaxonomic and physiological data, strain MAH-13T represents a novel species within the genus Frateuria , for which the name Frateuria flava sp. nov. is proposed, with MAH-13T (=KACC 19743T=CGMCC 1.13655T) as the type strain.

Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2577-2582 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Joonhong Park ◽  
Soon-Ae Yoo
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

scholarly journals Complete genome sequence of Chryseobacterium sp. ZHDP1 with protease activity

2021 ◽  
Author(s):  
Huanshuai Zhao ◽  
Jianxin Wang ◽  
Jiamao Huang ◽  
Yuncheng Ma ◽  
Yunfei Chen ◽  
...  
Keyword(s):  
Complete Genome ◽  
Protease Activity ◽  
Fermentation Broth ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Maximum Similarity ◽  
Insight Into

Abstract This study reported a complete genome of Chryseobacterium sp. ZHDP1 isolated from the soils of a seafood market. The ZHDP1 genome with a size of 4,917,748 bp and a GC content of 35.95% possessed 4,478 coding genes, 5 rRNA genes, 26 sRNA genes, and 89 tRNA genes. The 16S rRNA gene sequence of ZHDP1 had a maximum similarity of 99.07% with that of C. gambrini 5-1St1a. The maximum values of average nucleotide identity and DNA-DNA hybridization of ZHDP1 genome were 91.39 and 47.8, respectively, which were lower than the thresholds for a new genome. Different protease genes were annotated in the genome of ZHDP1, and the protease activity was also detected in the fermentation broth of ZHDP1. Furthermore, the activity of protease in the fermentation broth was optimized through temperature, pH, and metal irons, and the results showed that 60°C and pH 7.0 were the optimum conditions and Fe3+ could positively increase the protease activity of ZHDP1. This study provides the first insight into the novel genomic information of Chryseobacterium sp. ZHDP1 and its protein-degrading ability, thereby broadening our knowledge of the industrial potentials in genus Chryseobacterium strains.

scholarly journals An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009939
Author(s):  
Xiao-Pan Hu ◽  
Martin J. Lercher
Keyword(s):  
Gene Dosage ◽  
Optimal Growth ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
Expression Ratio ◽  
Bacterial Proteins ◽  
Chromosomal Arrangement ◽  
Growth Laws ◽  
Partial Implementation

The distribution of cellular resources across bacterial proteins has been quantified through phenomenological growth laws. Here, we describe a complementary bacterial growth law for RNA composition, emerging from optimal cellular resource allocation into ribosomes and ternary complexes. The predicted decline of the tRNA/rRNA ratio with growth rate agrees quantitatively with experimental data. Its regulation appears to be implemented in part through chromosomal localization, as rRNA genes are typically closer to the origin of replication than tRNA genes and thus have increasingly higher gene dosage at faster growth. At the highest growth rates in E. coli, the tRNA/rRNA gene dosage ratio based on chromosomal positions is almost identical to the observed and theoretically optimal tRNA/rRNA expression ratio, indicating that the chromosomal arrangement has evolved to favor maximal transcription of both types of genes at this condition.

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

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Yanzhu Zhang ◽  
Shufen He ◽  
Liufei Shi ◽  
Yang Liu ◽  
Deqiang Mao ◽  
...  
Keyword(s):  
Amino Acid Identity ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Genomic Core

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

scholarly journals Comparative Sequence Analysis of Mycobacterium leprae and the New Leprosy-Causing Mycobacterium lepromatosis

2009 ◽  
Vol 191 (19) ◽  
pp. 6067-6074 ◽  
Author(s):  
Xiang Y. Han ◽  
Kurt C. Sizer ◽  
Erika J. Thompson ◽  
Juma Kabanja ◽  
Jun Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Mycobacterium Leprae ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Neutral Evolution ◽  
Rrna Gene ◽  
Protein Encoding ◽  
Mycobacterium Lepromatosis ◽  
Encoding Genes

ABSTRACT Mycobacterium lepromatosis is a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence from Mycobacterium leprae, a well-known cause of leprosy, that justifies the status of M. lepromatosis as a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences with M. leprae sequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dS values) and nonsynonymous substitutions (dN values) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placed M. lepromatosis and M. leprae in a tight cluster with long terminal branches, implying that the divergence occurred long ago. The dS and dN values were also much higher than those for other closest pairs of mycobacteria. The dS values were 14 to 28% of the dS values for M. leprae and Mycobacterium tuberculosis, a more divergent pair of species. These results thus indicate that M. lepromatosis and M. leprae diverged ∼10 million years ago. The M. lepromatosis pseudogenes analyzed that were also pseudogenes in M. leprae showed nearly neutral evolution, and their relative ages were similar to those of M. leprae pseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate that M. lepromatosis and M. leprae diverged from a common ancestor after the massive gene inactivation event described previously for M. leprae.

scholarly journals Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1138-1143 ◽  
Author(s):  
Li Wang ◽  
Liang Chen ◽  
Qi Ling ◽  
Chen-chen Li ◽  
Yong Tao ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Methyl Red ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Low Levels

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, L-1T, which was capable of degrading methyl red was isolated from a dye-manufacturing factory in China. Phenotypic, chemotaxonomic and phylogenetic analyses established affiliation of the isolate to the genus Dyadobacter . Cells occurred in pairs in young cultures but became chains of coccoid cells in old cultures, and produced a flexirubin-like yellow pigment. Strain L-1T could not hydrolyse cellulose, and had a DNA G+C content of 51.3 mol%. The major cellular fatty acids were iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). C16 : 0, iso-C15 : 0 3-OH and C16 : 0 3-OH were the other major fatty acid components. Comparative 16S rRNA gene sequence analysis showed that strainL-1T was most closely related to Dyadobacter fermentans DSM 18053T (99.2 %), Dyadobacter soli JCM 16232T (98.9 %) and Dyadobacter beijingensis CGMCC 1.6375T (98.7 %). However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to JCM 16232T (41.2±1.8 %), DSM 18053T (38.6±2.6 %) and CGMCC 1.6375T (35.0±2.1 %). Strain L-1T could also be differentiated from its closest phylogenetic relatives based on differences in several phenotypic characteristics. These data suggest that strain L-1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter jiangsuensis sp. is proposed. The type strain is L-1T (DSM 29057T = CGMCC 1.12969T).

scholarly journals Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Kristína Záhonová ◽  
Gordon Lax ◽  
Savar D. Sinha ◽  
Guy Leonard ◽  
Thomas A. Richards ◽  
...  
Keyword(s):  
Single Cell ◽  
Small Subunit ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Rrna Gene ◽  
Heterotrophic Flagellates ◽  
Small Subunit Rrna ◽  
Single Chromosome ◽  
Linear Chromosomes

Abstract Background The supergroup Euglenozoa unites heterotrophic flagellates from three major clades, kinetoplastids, diplonemids, and euglenids, each of which exhibits extremely divergent mitochondrial characteristics. Mitochondrial genomes (mtDNAs) of euglenids comprise multiple linear chromosomes carrying single genes, whereas mitochondrial chromosomes are circular non-catenated in diplonemids, but circular and catenated in kinetoplastids. In diplonemids and kinetoplastids, mitochondrial mRNAs require extensive and diverse editing and/or trans-splicing to produce mature transcripts. All known euglenozoan mtDNAs exhibit extremely short mitochondrial small (rns) and large (rnl) subunit rRNA genes, and absence of tRNA genes. How these features evolved from an ancestral bacteria-like circular mitochondrial genome remains unanswered. Results We sequenced and assembled 20 euglenozoan single-cell amplified genomes (SAGs). In our phylogenetic and phylogenomic analyses, three SAGs were placed within kinetoplastids, 14 within diplonemids, one (EU2) within euglenids, and two SAGs with nearly identical small subunit rRNA gene (18S) sequences (EU17/18) branched as either a basal lineage of euglenids, or as a sister to all euglenozoans. Near-complete mitochondrial genomes were identified in EU2 and EU17/18. Surprisingly, both EU2 and EU17/18 mitochondrial contigs contained multiple genes and one tRNA gene. Furthermore, EU17/18 mtDNA possessed several features unique among euglenozoans including full-length rns and rnl genes, six mitoribosomal genes, and nad11, all likely on a single chromosome. Conclusions Our data strongly suggest that EU17/18 is an early-branching euglenozoan with numerous ancestral mitochondrial features. Collectively these data contribute to untangling the early evolution of euglenozoan mitochondria.

scholarly journals Halorussus amylolyticus sp. nov., isolated from an inland salt lake

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3734-3738 ◽  
Author(s):  
Pan-Pan Yuan ◽  
Wei-Tao Ye ◽  
Jia-Xiang Pan ◽  
Dong Han ◽  
Wen-Jiao Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Salt Lake ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Shanxi Province ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Nacl Concentration ◽  
Optimum Ph

A halophilic archaeal strain, YC93T, was isolated from Yuncheng salt lake in Shanxi Province, China. Cells were pleomorphic rods, stained Gram-negative and formed light-red-pigmented colonies on agar plates. Strain YC93T was able to grow at 25–50 °C (optimum 37 °C), with 1.4–4.8 M NaCl (optimum 2.0 M), with 0–1.0 M MgCl2 (optimum 0.05 M) and at pH 6.0–9.5 (optimum pH 7.0). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). 16S rRNA gene sequence analysis revealed that strain YC93T had two dissimilar 16S rRNA genes both of which were phylogenetically related to those of the two recognized members of the genus Halorussus (93.0–95.3 % similarity). The rpoB′ gene of strain YC93T was phylogenetically related to the corresponding gene of Halorussus rarus TBN4T (91.3 % similarity) and Halorussus ruber YC25T (90.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and five glycolipids chromatographically identical to those of Halorussus rarus CGMCC 1.10122T. The DNA G+C content of strain YC93T was 64.6 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YC93T represents a novel species of the genus Halorussus, for which the name Halorussus amylolyticus sp. nov. is proposed. The type strain is YC93T ( = CGMCC 1.12126T = JCM 18367T).

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