Structure and function of bacterial viruses and viral communities DOI Creative Commons
Ines Friedrich

Published: Jan. 1, 2023

Bacterial viruses, known as bacteriophages or phages, are the most abundant biological entities on planet and least studied in terms of abundance diversity. Searching sequence databases viral genomes, one becomes impression that sphere consists dsDNA bacteriophages. First objective studies was to verify whether this is true a methodical artefact our usual approach assessing world. Second, bacterial host strains were needed for investigation Third, besides classic overlay plaque assay isolation, dsDNA, ssDNA, dsRNA, ssRNA also isolated from phage plaques well. To accomplish endeavor, local system associated with various RNA DNA viruses required. Such hosts not available at beginning work making it necessary isolate suitable prokaryotic system. end, environmental samples successfully screened new hosts, resulting 37 candidate strains, eight which sequenced genomically analyzed (Brevundimonas pondensis, B. goettingensis, Serratia marcescens LVF3, Luteibacter flocculans, Stenotrophomonas indicatrix DAIF1, Kinneretia sp. DAIF2, Janthinobacterium lividum EIF1 EIF2). These evaluated their suitability systems (chapter 3.1 3.5, 3.8 3.9). A total four species discovered described. Using genomic analyses three these fully characterized Brevundimonas flocculans). pondensis LVF1 LVF3 proved be particularly promising candidates achieve main objectives thesis 3.7). They used classical 25 phages: 14 11 Serratia. TEM analysis revealed six myoviruses, 18 siphoviruses podovirus, while Brevundimonas-associated phages all siphoviruses. The complemented by Next Generation Sequencing (NGS)-based methods provided host-associated virome data. Furthermore, complementary NGS enabled identification vB_SmaP-Kaonashi vB_SmaM-Otaku. latter virus infects both systems. In addition, ssDNA results two contigs could detected. belong family Microviridae Inoviridae. Further, goettingensis contained contig Caulobacter-associated phiCb5 Leviviridae. bacteriophage isolates 3.8) 3.9) found. Here, using isolation approach, each produces medically relevant antivacterial substance violacein. We able identify, induction violacein phage-dependent organism. Both (Luteibacter vB_lflM-Pluto vB_JliS-Donnerlittchen) first respective conclusion, demeonstrates prominent. still practical but biased, has been demonstrated. Its limitations can overcome NGS-based access diversity efficiently possible.

Language: Английский

The Effect of Heavy Metals on Bacterial Community Structure and Functional Profile in Surface Soils of Baiji Oil Refinery and Baghdad City, Iraq DOI
Ahmed Ismael Naqee Al-bayatı,

Hülya Saide Özkoç,

Luay Burhan Mustafa

et al.

Geomicrobiology Journal, Journal Year: 2023, Volume and Issue: 41(1), P. 48 - 60

Published: Oct. 18, 2023

AbstractThe increasing accumulation of heavy metals (HMs) due to various human activities is a significant concern. This study has employed 16S rRNA amplicon sequencing and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) spectrometry investigate HMS concentrations identify bacterial strains exhibiting resistance HMS, used the PICRUSt tool assess metabolic pathways communities. Our primary focus was HMs in soils Baghdad (BG) Baiji Oil Refinery (BOR) area while examining diversity these regions. The results revealed that average levels Cadmium (Cd) Lead (Pb) BOR were higher than BG global average. In BOR, most prevalent genera Flavobacterium, Shewanella, Pseudomonas. Using tool, we identified Cd Pb substantially impacted marks first report Iraq employ gene analyze communities Iraqi soil how affect them. However, this can serve as reference for future research development innovative strategies sustainable management ecosystems.Keywords: oil refineryenvironmental assessmentheavy metal contaminationmetabolic pathwaysmetagenomics Disclosure statementNo potential conflict interest reported by author(s).

Language: Английский

Citations

1
Structure and function of bacterial viruses and viral communities DOI Creative Commons
Ines Friedrich

Published: Jan. 1, 2023

Bacterial viruses, known as bacteriophages or phages, are the most abundant biological entities on planet and least studied in terms of abundance diversity. Searching sequence databases viral genomes, one becomes impression that sphere consists dsDNA bacteriophages. First objective studies was to verify whether this is true a methodical artefact our usual approach assessing world. Second, bacterial host strains were needed for investigation Third, besides classic overlay plaque assay isolation, dsDNA, ssDNA, dsRNA, ssRNA also isolated from phage plaques well. To accomplish endeavor, local system associated with various RNA DNA viruses required. Such hosts not available at beginning work making it necessary isolate suitable prokaryotic system. end, environmental samples successfully screened new hosts, resulting 37 candidate strains, eight which sequenced genomically analyzed (Brevundimonas pondensis, B. goettingensis, Serratia marcescens LVF3, Luteibacter flocculans, Stenotrophomonas indicatrix DAIF1, Kinneretia sp. DAIF2, Janthinobacterium lividum EIF1 EIF2). These evaluated their suitability systems (chapter 3.1 3.5, 3.8 3.9). A total four species discovered described. Using genomic analyses three these fully characterized Brevundimonas flocculans). pondensis LVF1 LVF3 proved be particularly promising candidates achieve main objectives thesis 3.7). They used classical 25 phages: 14 11 Serratia. TEM analysis revealed six myoviruses, 18 siphoviruses podovirus, while Brevundimonas-associated phages all siphoviruses. The complemented by Next Generation Sequencing (NGS)-based methods provided host-associated virome data. Furthermore, complementary NGS enabled identification vB_SmaP-Kaonashi vB_SmaM-Otaku. latter virus infects both systems. In addition, ssDNA results two contigs could detected. belong family Microviridae Inoviridae. Further, goettingensis contained contig Caulobacter-associated phiCb5 Leviviridae. bacteriophage isolates 3.8) 3.9) found. Here, using isolation approach, each produces medically relevant antivacterial substance violacein. We able identify, induction violacein phage-dependent organism. Both (Luteibacter vB_lflM-Pluto vB_JliS-Donnerlittchen) first respective conclusion, demeonstrates prominent. still practical but biased, has been demonstrated. Its limitations can overcome NGS-based access diversity efficiently possible.

Language: Английский

Citations

0