scholarly journals Characterization and Genomic Analysis of an Efficient Dibutyl Phthalate-Degrading Bacterium Microbacterium sp. USTB-Y

2021 ◽  
Author(s):  
ZhenZhen Zhao ◽  
Chao Liu ◽  
Qianqian Xu ◽  
Shahbaz Ahmad ◽  
Haiyang Zhang ◽  
...  
Keyword(s):  
Dibutyl Phthalate ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Culture Conditions ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis ◽  
Degrading Bacterium ◽  
Holistic Understanding ◽  
Genes Encoding ◽  
Genetic Mechanisms

Abstract A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rDNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely removed by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq, and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. This information will be valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs-biodegrading Microbacterium sp. strains.

scholarly journals Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil

2018 ◽  
Author(s):  
Amalia Soenens ◽  
Juan Imperial
Keyword(s):  
Agricultural Soil ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Symbiotic Genes ◽  
16S Rdna Sequence ◽  
Pcr Screening ◽  
Selective Enrichment ◽  
16S Rdna Sequence Analysis ◽  
Fast Growing Rhizobia ◽  
Large Contigs

Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication / maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil.

scholarly journals Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil

2018 ◽  
Author(s):  
Amalia Soenens ◽  
Juan Imperial
Keyword(s):  
Agricultural Soil ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Symbiotic Genes ◽  
16S Rdna Sequence ◽  
Pcr Screening ◽  
Selective Enrichment ◽  
16S Rdna Sequence Analysis ◽  
Fast Growing Rhizobia ◽  
Large Contigs

Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication / maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil.

scholarly journals Novel, non-symbiotic isolates ofNeorhizobiumfrom a dryland agricultural soil

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4776 ◽  
Author(s):  
Amalia Soenens ◽  
Juan Imperial
Keyword(s):  
Agricultural Soil ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Symbiotic Genes ◽  
16S Rdna Sequence ◽  
Pcr Screening ◽  
Selective Enrichment ◽  
16S Rdna Sequence Analysis ◽  
Fast Growing Rhizobia ◽  
Large Contigs

Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genusNeorhizobium, as concluded from partialrpoBand near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group withinNeorhizobium, closer toN. galegaethan to the remainingNeorhizobiumspecies, but clearly differentiated from the former, and constituting at least one new genomospecies withinNeorhizobium.All the isolates lackednodandnifsymbiotic genes but contained arepABCreplication/maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. TheserepABCsequences were related, but not identical, torepABCsequences found in symbiotic plasmids fromN. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members ofNeorhizobiumfrom soil.

scholarly journals Gulosibacter molinativorax gen. nov., sp. nov., a molinate-degrading bacterium, and classification of ‘Brevibacterium helvolum’ DSM 20419 as Pseudoclavibacter helvolus gen. nov., sp. nov.

2004 ◽  
Vol 54 (3) ◽  
pp. 783-789 ◽  
Author(s):  
Célia M. Manaia ◽  
Balbina Nogales ◽  
Norbert Weiss ◽  
Olga C. Nunes
Keyword(s):  
Cell Wall ◽  
16S Rdna ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
Strictly Aerobic ◽  
16S Rdna Sequence ◽  
Cell Wall Peptidoglycan ◽  
16S Rdna Sequence Analysis ◽  
Degrading Bacterium ◽  
Phylogenetic Level

A Gram-positive, molinate-degrading bacterium, strain ON4T (=DSM 13485T=LMG 21909T), was isolated from a mixed bacterial culture able to mineralize the herbicide molinate. The strain was strictly aerobic, oxidase- and catalase-positive and non-acid-fast, with a growth temperature of 10–41 °C. It contained the major menaquinone MK-9 and a cell-wall peptidoglycan based on d-ornithine. 16S rDNA sequence analysis revealed that the strain formed a distinct line of descent in the family Microbacteriaceae, showing the highest 16S rDNA similarity (∼95 %) to members of the genus Curtobacterium and ‘Brevibacterium helvolum’ DSM 20419 (=ATCC 13715). The latter was reported to have the cell-wall peptidoglycan type B2γ and the major menaquinone MK-9, which are typical of Clavibacter, but it is clearly separated from this genus at the phylogenetic level. Based on low values of 16S rDNA sequence similarity to previously described genera and their distinctive phenotypic characteristics, it is proposed that strains ON4T and ‘B. helvolum’ DSM 20419 be classified as two novel genera and species, with the respective names Gulosibacter molinativorax gen. nov., sp. nov. and Pseudoclavibater helvolus gen. nov., sp. nov.

scholarly journals Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y

2021 ◽  
Vol 37 (12) ◽  
Author(s):  
Zhenzhen Zhao ◽  
Chao Liu ◽  
Qianqian Xu ◽  
Shahbaz Ahmad ◽  
Haiyang Zhang ◽  
...  
Keyword(s):  
Dibutyl Phthalate ◽  
Genomic Analysis ◽  
Degrading Bacterium

scholarly journals Identification of Genetic Bases ofVibrio fluvialisSpecies-Specific Biochemical Pathways and Potential Virulence Factors by Comparative Genomic Analysis

2014 ◽  
Vol 80 (6) ◽  
pp. 2029-2037 ◽  
Author(s):  
Xin Lu ◽  
Weili Liang ◽  
Yunduan Wang ◽  
Jialiang Xu ◽  
Jun Zhu ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Type Vi Secretion System ◽  
Biochemical Tests ◽  
Regulatory Pathways ◽  
Vibrio Fluvialis ◽  
Genes Encoding ◽  
Genetic Mechanisms

ABSTRACTVibrio fluvialisis an important food-borne pathogen that causes diarrheal illness and sometimes extraintestinal infections in humans. In this study, we sequenced the genome of a clinicalV. fluvialisstrain and determined its phylogenetic relationships with otherVibriospecies by comparative genomic analysis. We found that the closest relationship was betweenV. fluvialisandV. furnissii, followed by those withV. choleraeandV. mimicus. Moreover, based on genome comparisons and gene complementation experiments, we revealed genetic mechanisms of the biochemical tests that differentiateV. fluvialisfrom closely related species. Importantly, we identified a variety of genes encoding potential virulence factors, including multiple hemolysins, transcriptional regulators, and environmental survival and adaptation apparatuses, and the type VI secretion system, which is indicative of complex regulatory pathways modulating pathogenesis in this organism. The availability ofV. fluvialisgenome sequences may promote our understanding of pathogenic mechanisms for this emerging pathogen.

Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate

Microbiology ◽  
2005 ◽  
Vol 151 (2) ◽  
pp. 491-500 ◽  
Author(s):  
Jörg Overhage ◽  
Sonja Sielker ◽  
Stefan Homburg ◽  
Katja Parschat ◽  
Susanne Fetzner
Keyword(s):  
Southern Hybridization ◽  
Sole Source ◽  
Soil Samples ◽  
Linear Plasmid ◽  
Linear Plasmids ◽  
16S Rdna Sequence ◽  
Sequence Identity ◽  
16S Rdna Sequence Analysis ◽  
Genes Encoding ◽  
Arthrobacter Nicotinovorans

Arthrobacter nitroguajacolicus Rü61a, which utilizes quinaldine as sole source of carbon and energy, was shown to contain a conjugative linear plasmid of approximately 110 kb, named pAL1. It exhibits similarities with other linear plasmids from Actinomycetales in that it has proteins covalently attached to its 5′ ends. Southern hybridization with probes for the genes encoding quinaldine 4-oxidase and N-acetylanthranilate amidase indicated that pAL1 contains the gene cluster encoding the degradation of quinaldine to anthranilate. A mutant of strain Rü61a that had lost pAL1 indeed could not convert quinaldine, but was still able to grow on anthranilate. Conjugative transfer of pAL1 to the plasmid-less mutant of strain Rü61a and to Arthrobacter nicotinovorans DSM 420 (pAO1) occurred at frequencies of 5·4×10−4 and 2·0×10−4 per recipient, respectively, and conferred the ability to utilize quinaldine. Five other quinaldine-degrading Gram-positive strains were isolated from soil samples; 16S rDNA sequence analysis suggested the closest relationship to different Arthrobacter species. Except for strain K2-29, all isolates contained a pAL1-like linear plasmid carrying genes encoding quinaldine conversion. A 478 bp fragment that on pAL1 represents an intergenic region showed 100 % sequence identity in all isolates harbouring a pAL1-like plasmid, suggesting horizontal dissemination of the linear plasmid among the genus Arthrobacter.

scholarly journals Characterization and Genomic Analysis of a Highly Efficient Dibutyl Phthalate-Degrading Bacterium Gordonia sp. Strain QH-12

2016 ◽  
Vol 17 (7) ◽  
pp. 1012 ◽  
Author(s):  
Decai Jin ◽  
Xiao Kong ◽  
Huijun Liu ◽  
Xinxin Wang ◽  
Ye Deng ◽  
...  
Keyword(s):  
Dibutyl Phthalate ◽  
Genomic Analysis ◽  
Highly Efficient ◽  
Degrading Bacterium

scholarly journals Comparative Genomic Analysis of the Biotechnological Potential of the Novel Species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T

Diversity ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 204
Author(s):  
Dominik Rutz ◽  
David Frasson ◽  
Martin Sievers ◽  
Jochen Blom ◽  
Fabio Rezzonico ◽  
...  
Keyword(s):  
New Species ◽  
Plant Pathogens ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Yield Potential ◽  
Comparative Genomic ◽  
Genomic Features ◽  
Two New Species ◽  
Genes Encoding ◽  
Potential Applications

In recent years, the use of whole-cell biocatalysts and biocatalytic enzymes in biotechnological applications originating from the genus Pseudomonas has greatly increased. In 2014, two new species within the Pseudomonas putida group were isolated from Swiss forest soil. In this study, the high quality draft genome sequences of Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T were used in a comparative genomics approach to identify genomic features that either differed between these two new species or to selected members of the P. putida group. The genomes of P. wadenswilerensis CCOS 864T and P. reidholzensis CCOS 865T were found to share genomic features for the degradation of aromatic compounds or the synthesis of secondary metabolites. In particular, genes encoding for biocatalytic relevant enzymes belonging to the class of oxidoreductases, proteases and isomerases were found, that could yield potential applications in biotechnology. Ecologically relevant features revealed that both species are probably playing an important role in the degradation of soil organic material, the accumulation of phosphate and biocontrol against plant pathogens.

scholarly journals Draft Genome Sequence of Marine-Derived Aeromonas caviae CHZ306, a Potential Chitinase Producer Strain

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Flávio Augusto Cardozo ◽  
Cristina Kraemer Zimpel ◽  
Ana Marcia Sa Guimaraes ◽  
Adalberto Pessoa ◽  
Irma Nelly Gutierrez Rivera
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Draft Genome Sequence ◽  
Producer Strain ◽  
Degrading Enzymes ◽  
Aeromonas Caviae ◽  
Genes Encoding

We report here a draft genome sequence of Aeromonas caviae CHZ306, a marine-derived bacterium with the ability to hydrolyze chitin and express high levels of chitinases. The assembly resulted in 65 scaffolds with approximately 4.78 Mb. Genomic analysis revealed different genes encoding chitin-degrading enzymes that can be used for chitin derivative production.

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