scholarly journals Genomic Analysis of Bacillus megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Bin Wang ◽  
Dan Zhang ◽  
Shaohua Chu ◽  
Yuee Zhi ◽  
Xiaorui Liu ◽  
...  
Keyword(s):  
Bacillus Megaterium ◽  
Growth Promotion ◽  
Gc Content ◽  
Genomic Analysis ◽  
Circular Chromosome ◽  
Secondary Salinization ◽  
Great Ability ◽  
Indigenous Plasmids ◽  
Genetic Level ◽  
Phosphate Solubilizing

Bacillus megaterium NCT-2 is a nitrate-uptake bacterial, which shows high bioremediation capacity in secondary salinization soil, including nitrate-reducing capacity, phosphate solubilization, and salinity adaptation. To gain insights into the bioremediation capacity at the genetic level, the complete genome sequence was obtained by using a multiplatform strategy involving HiSeq and PacBio sequencing. The NCT-2 genome consists of a circular chromosome of 5.19 Mbp and ten indigenous plasmids, totaling 5.88 Mbp with an average GC content of 37.87%. The chromosome encodes 5,606 genes, 142 tRNAs, and 53 rRNAs. Genes involved in the features of the bioremediation in secondary salinization soil and plant growth promotion were identified in the genome, such as nitrogen metabolism, phosphate uptake, the synthesis of organic acids and phosphatase for phosphate-solubilizing ability, and Trp-dependent IAA synthetic system. Furthermore, strain NCT-2 has great ability of adaption to environments due to the genes involved in cation transporters, osmotic stress, and oxidative stress. This study sheds light on understanding the molecular basis of using B. megaterium NCT-2 in bioremediation of the secondary salinization soils.

scholarly journals Genome resource of Ancylobacter pratisalsi E130 T: A novel plant growth-promoting bacterium isolated from the rhizosphere

2021 ◽  
Author(s):  
Wenhan Nie ◽  
Xin Zheng ◽  
Sai Wang ◽  
Iftikhar Ahmad ◽  
Bo Zhu
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Complete Genome ◽  
Growth Promotion ◽  
Gc Content ◽  
Genomic Analysis ◽  
Rrna Genes ◽  
Alkaline Soil ◽  
Entire Genome ◽  
Salt Meadow

Ancylobacter pratisalsi sp. nov. strain E130T is a Gram negative, non-motile, aerobic and rod-shaped bacterium, which was recently isolated from the rhizosphere of Plantago winteri Wirtg from a natural salt meadow. This strain was described as novel species in Ancylobacter genus, however information about its complete genome has yet not been reported. In this study, its genome was completely sequenced by PacBio SMRT cell platform, analyzed, and compared with other selected complete genome sequences of Ancylobacter and elucidated its potential plant growth promotion abilities. The genomic analysis revealed that the genome of strain E130T consists of one circular DNA chromosome of 4,618,530 bp with a GC content of 66% and one plasmid of 159,741 bp with a GC content of 64.13%. The entire genome contains 4,322 predicted coding genes, 49 tRNAs and 6 rRNA genes. Genome analysis identified a siderophore natural product biosynthesis cluster, which produces fuscachelin. Knockout of several key genes in this cluster, significantly reduces the plant growth-promotion ability of the strain E130T. Besides plant growth-promotion, the strain E130T can grow well on 5 % NaCl (w/v), conferring this strain as potential bio-resource for successful production of economic crops in alkaline soil.

scholarly journals The complete genome sequence of Hafnia alvei A23BA; a potential antibiotic-producing rhizobacterium

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Opeyemi K. Awolope ◽  
Noelle H. O’Driscoll ◽  
Alberto Di Salvo ◽  
Andrew J. Lamb
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Growth Promotion ◽  
Gc Content ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Circular Chromosome ◽  
Hafnia Alvei

Abstract Objectives The urgent need for novel antibiotics cannot be overemphasized. Hafnia alvei A23BA was isolated from plant rhizosphere as part of an effort to recover novel antibiotic-producing bacterial strains from soil samples. The genome of the isolate was sequenced to facilitate mining for potential antibiotic-encoding biosynthetic gene clusters and to gain insights into how these gene clusters could be activated. Data description Here, we report the complete genome sequence of H. alvei A23BA obtained from the hybrid assembly of Illumina HiSeq and GridION reads. The genome, consisting of a circular chromosome and a circular plasmid, is 4.77 Mb in size with a GC content of 48.77%. The assembly is 99.5% complete with genomic features including 4,217 CDSs, 125 RNAs, and 30 pseudogenes. Thiopeptide, beta-lactone, siderophore, and homoserine lactone biosynthetic gene clusters were also identified. Other gene clusters of interest include those associated with bioremediation, biocontrol, and plant growth promotion- all of which are reported for H. alvei for the first time. This dataset serves to expedite the exploration of the biosynthetic and metabolic potentials of the species. Furthermore, being the first published genome sequence of a soil isolate, this dataset enriches the comparative genomics study of H. alvei strains.

scholarly journals Genome Sequence of a Food Spoilage Lactic Acid Bacterium, Leuconostoc gasicomitatum LMG 18811T, in Association with Specific Spoilage Reactions

2011 ◽  
Vol 77 (13) ◽  
pp. 4344-4351 ◽  
Author(s):  
Per Johansson ◽  
Lars Paulin ◽  
Elina Säde ◽  
Noora Salovuori ◽  
Edward R. Alatalo ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacterium ◽  
Gc Content ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Food Spoilage ◽  
Circular Chromosome ◽  
Knock Out ◽  
Content Type ◽  
Sequencing Project

ABSTRACTLeuconostoc gasicomitatumis a psychrotrophic lactic acid bacterium causing spoilage of cold-stored, modified-atmosphere-packaged (MAP), nutrient-rich foods. Its role has been verified by challenge tests in gas and slime formation, development of pungent acidic and buttery off odors, and greening of beef. MAP meats have especially been prone toL. gasicomitatumspoilage. In addition, spoilage of vacuum-packaged vegetable sausages and marinated herring has been reported. The genomic sequencing project ofL. gasicomitatumLMG 18811Twas prompted by a need to understand the growth and spoilage potentials ofL. gasicomitatum, to study its phylogeny, and to be able to knock out and overexpress the genes. Comparative genomic analysis was done withinL. gasicomitatumLMG 18811Tand the three fully assembledLeuconostocgenomes (those ofLeuconostoc mesenteroides,Leuconostoc citreum, andLeuconostoc kimchii) available. The genome ofL. gasicomitatumLMG 18811Tis plasmid-free and contains a 1,954,080-bp circular chromosome with an average GC content of 36.7%. It includes genes for the phosphoketolase pathway and alternative pathways for pyruvate utilization. As interesting features associated with the growth and spoilage potential, LMG 18811Tpossesses utilization strategies for ribose, external nucleotides, nucleosides, and nucleobases and it has a functional electron transport chain requiring only externally supplied heme for respiration. In respect of the documented specific spoilage reactions, the pathways/genes associated with a buttery off odor, meat greening, and slime formation were recognized. Unexpectedly, genes associated with platelet binding and collagen adhesion were detected, but their functionality and role in food spoilage and processing environment contamination need further study.

scholarly journals The complete genome sequence of a bile-isolated Stenotrophomonas maltophilia ZT1

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Min Zhang ◽  
Lixiang Li ◽  
Hongwei Pan ◽  
Tao Zhou
Keyword(s):  
Genome Sequence ◽  
Stenotrophomonas Maltophilia ◽  
Gc Content ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Functional Verification ◽  
Comparative Genomic ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Human Bile

Abstract Background Stenotrophomonas maltophilia is one of the most frequently isolated opportunistic pathogens that can cause infections in humans. Many researches concerned the mechanism of antibiotic resistance displayed by S. maltophilia, however, the mechanism of its pathogenesis and its adaptation to special niches, such as bile, remain unclear. Results In this study, the S. maltophilia strain ZT1 was isolated from human bile. Its genome was sequenced and a circular chromosome of 4,391,471 bp was obtained with a GC content of 66.51%. There were 3962 protein-coding sequences, 7 rRNAs and 74 tRNAs in the chromosome. Compared with Virulence Factor Database, we identified more than 500 candidate virulence genes including genes encoding fimbrial assembly protein, enterobactin synthesis pathway proteins, efflux pumps, and the DNA and/or proteins secretion system in the genome of strain ZT1. Additionally, there were at least 22 genes related to bile adaption, including emrAB, acrRAB, galU, rfbC, tolC and mdtABC. Conclusions This is the first study to reveal the whole genome sequence of the ZT1 strain of S. maltophilia isolated from human bile. We identified hundreds virulence factors and 22 bile adaptation-related genes in the genome of the S. maltophilia strain ZT1. Further comparative genomic analysis and functional verification would aid in understanding the pathogenesis and bile adaptation of S. maltophilia.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

scholarly journals Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
Jean N. Hakizimana ◽  
Jean B. Ntirandekura ◽  
Clara Yona ◽  
Lionel Nyabongo ◽  
Gladson Kamwendo ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
Gc Content ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Eastern Africa ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

Role of bacterial pyrroloquinoline quinone in phosphate solubilizing ability and in plant growth promotion on strain Serratia sp. S119

Symbiosis ◽  
2016 ◽  
Vol 72 (1) ◽  
pp. 31-43 ◽  
Author(s):  
Liliana Mercedes Ludueña ◽  
María Soledad Anzuay ◽  
Jorge Guillermo Angelini ◽  
Germán Barros ◽  
María Flavia Luna ◽  
...  
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Pyrroloquinoline Quinone ◽  
Phosphate Solubilizing

scholarly journals Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals

2020 ◽  
Vol 8 (2) ◽  
pp. 153 ◽  
Author(s):  
Francesca Luziatelli ◽  
Anna Grazia Ficca ◽  
Mariateresa Cardarelli ◽  
Francesca Melini ◽  
Andrea Cavalieri ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Plant Growth ◽  
Plant Growth Promotion ◽  
Plant Pathogens ◽  
Growth Promotion ◽  
Pantoea Agglomerans ◽  
Toxic Heavy Metals ◽  
Circular Chromosome ◽  
Plant Growth Promoting ◽  
Genetic Mechanisms

Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.

scholarly journals Isolation and identification of phosphate solubilizing bacteria and evaluate its effect on of Mung bean (Vigna radita [L.] R.Wilczek) growth

2019 ◽  
Vol 60 (5) ◽  
pp. 985-995
Author(s):  
Yusur Ramzi ◽  
Hutaf A. A. Alsalim
Keyword(s):  
Plant Growth ◽  
Bacillus Cereus ◽  
Mung Bean ◽  
Phosphate Solubilization ◽  
Growth Promotion ◽  
Hydrolytic Enzymes ◽  
Phosphate Solubilizing Bacteria ◽  
Biochemical Tests ◽  
Isolation And Identification ◽  
Phosphate Solubilizing

Sixteen soil samples were collected from wheat, barley and yellow corn rhizosphere in Abu-Ghraib, Aqraqof, Latifieh,Tarmiah, Jadriya and  of Agriculture in Baghdad university/ Baghdad city. The results found nine phosphate solubilizing bacteria (PSB) isolates (Y1, Y2, Y3, Y4, Y5, Y6, Y7, Y8, Y9), formed clear zones on National Botanical Research Institute's (NBRIP) agar. The solubility index (SI) of PSB isolates ranged from 2.00 to 3.66. Y4 have the highest SI (3.66) followed by Y3 and Y6 (3.33). Phosphate solubilization abilities varying from (20.10-39.00 μg.ml-1), Y4 was the highest (39.00 μg.ml-1) followed by Y3 (37.00μg.ml-1). The results of hydrolytic enzymes production showed that almost all nine isolates are able to produce protease and pectinase, while Y1 and Y2 showed negative results in cellulase production. Maximum ability for hydrogen cyanide (HCN) and indole acetic acid (IAA) production were showed byY3 and Y4 isolates. The isolate Y4 was found to be the most efficient isolate, so it was selected identified as Bacillus cereus using biochemical tests confirmed by VITEC 2 compact system. The results of High performance liquid chromatography (HPLC) revealed that Bacillus cereus produce oxalic acid (2.996), citric acid (9.117) and malic acid (3.734). Bacillus cereus (Y4) enhanced the growth of mung bean plants. A significant increase in branches number (12.33), plant length (83.0cm), fresh weight (27.25 g) and dry weight (1.427g) were obtained compared with control treatments. The main objective of this study is to isolate PSB and evaluate their roles in plant growth promotion. The results showed the high phosphate solubilization efficiency of PSB isolates and the identified isolates was found to be good enough for plant growth promoting.

Sign in / Sign up

Export Citation Format

Share Document