Pandoraea oxalativorans DSM 23570(T) is an oxalate-degrading bacterium that was originally isolated from soil litter near to oxalate-producing plant of the genus Oxalis. Here, we report the first complete genome of P. oxalativorans DSM 23570(T) which would allow its potential biotechnological applications to be unravelled. Copyright © 2016. Published by Elsevier B.V.
Quorum sensing is a well-studied cell-to-cell communication method that involves a cell-density dependent regulation of genes expression mediated by signalling molecules. In this study, a bacterium isolated from a plant material compost pile was found to possess quorum sensing activity based on bioassay screening. Isolate YL12 was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and molecular typing using rpoD gene which identified the isolate as Aeromonas caviae. High resolution tandem mass spectrometry was subsequently employed to identify the N-acyl homoserine lactone profile of Aeromonas caviae YL12 and confirmed that this isolate produced two short chain N-acyl homoserine lactones, namely C4-HSL and C6, and the production was observed to be cell density-dependent. Using the thin layer chromatography (TLC) bioassay, both AHLs were found to activate C. violaceum CV026, whereas only C6-HSL was revealed to induce bioluminescence expression of E. coli [pSB401]. The data presented in this study will be the leading steps in understanding the role of quorum sensing in Aeromonas caviae strain YL12.
Pelosinus species can reduce metals such as Fe(III), U(VI), and Cr(VI) and have been isolated from diverse geographical regions. Five draft genome sequences have been published. We report the complete genome sequence for Pelosinus sp. strain UFO1 using only PacBio DNA sequence data and without manual finishing. Copyright © 2014 Brown et al.
Pseudomonas pseudoalcaligenes CECT5344, a Gram-negative bacterium isolated from the Guadalquir River (Córdoba, Spain), is able to utilize different cyano-derivatives. Here, the complete genome sequence of P. pseudoalcaligenes CECT5344 harboring a 4,686,340bp circular chromosome encoding 4513 genes and featuring a GC-content of 62.34% is reported. Necessarily, remaining gaps in the genome had to be closed by assembly of few long reads obtained from PacBio single molecule real-time sequencing. Here, the first complete genome sequence for the species P. pseudoalcaligenes is presented. Copyright © 2014 Elsevier B.V. All rights reserved.
Mycobacterium sp. strain djl-10, an efficient degrader of carbendazim, was isolated from a carbendazim manufacturing wastewater treatment system. Here, we report the complete genome sequence of djl-10, which consists of a chromosome and three plasmids. Copyright © 2017 Zhang et al.
Microbiologically induced calcium carbonate precipitation shows the potential for use in bioremediation and construction consolidation, but the efficiency of this process must be improved. Lysinibacillus sphaericus LMG 22257 is a gram-positive ureolytic strain that has recently been applied for consolidating construction by mediating calcium carbonate precipitation. The complete genome sequence of L. sphaericus LMG 22257 is 3,436,578 base pairs with a GC content of 38.99%. The urea degradation pathway and genes related to extracellular polymeric substance biosynthesis were also identified. The strain can tolerate high alkalinity (pH up to 10) and high urea concentration (up to 3M). These findings provide insights into the microbiologically induced carbonate precipitation and extend the application of the metabolic potential of L. sphaericus LMG 22257 for bioremediation. Copyright © 2017 Elsevier B.V. All rights reserved.
Shrimp is extensively cultured worldwide. Shrimp farming is suffering from a variety of diseases. Probiotics are considered to be one of the effective methods to prevent and cure shrimp diseases. Exiguobacterium arabatum W-01, a gram-positive and orange-pigmented bacterium, was isolated from the intestine of a healthy Penaeus vannamei specimen. Whole-genome sequencing revealed a genome of 2,914,854 bp, with 48.02% GC content. In total, 3,083 open reading frames (ORFs) were identified, with an average length of 843.98 bp and a mean GC content of 48.11%, accounting for 89.27% of the genome. Among these ORFs, 2,884 (93.5%) genes were classified into Clusters of Orthologous Groups (COG) families comprising 21 functional categories, and 1,650 ORFs were classified into 83 functional Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 27 rRNA operons and 68 tRNAs were identified, with all 20 amino acids represented. In addition, 91 genomic islands, 68 potential prophages, and 33 tandem repeats, but no clustered regularly interspaced short palindromic repeats (CRISPRs), were found. No resistance genes and only one virulence gene were identified. Among the 150 secreted proteins of E. arabatum W-01, a variety of transport system substrate-binding proteins, enzymes, and biosynthetic proteins, which play important roles in the uptake and metabolism of nutrients, were found. Two adherence-related protein genes and 31 flagellum-related protein genes were also identified. Taken together, these results indicate potential probiotic functions for E. arabatum W-01.© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
The toxic lineage (TL) of Lysinibacillus sphaericus has been extensively studied because of its potential biotechnological applications in biocontrol of mosquitoes and bioremediation of toxic metals. We previously proposed that L. sphaericus TL should be considered as a novel species based on a comparative genomic analysis. In the current work, we constructed the first manually curated metabolic reconstruction for this species on the basis of the available genomes. We elucidated the central metabolism of the proposed species and, beyond confirming the reported experimental evidence with genomic a support, we found insights to propose novel applications and traits to be considered in further studies. The strains belonging to this lineage exhibit a broad repertory of genes encoding insecticidal factors, some of them remain uncharacterized. These strains exhibit other unexploited biotechnological important traits, such as lactonases (quorum quenching), toxic metal resistance, and potential for aromatic compound degradation. In summary, this study provides a guideline for further research aimed to implement this organism in biocontrol and bioremediation. Similarly, we highlighted the unanswered questions to be responded in order to gain a deeper understanding of the L. sphaericus TL biology.
Denitrification is a crucial process for the global nitrogen cycle through the reduction of nitrates by heterotrophic bacteria. Denitrifying microorganisms play an important role in eliminating fixed nitrogen pollutants from the ecosystem, concomitant with N2O emission. Although many microbial denitrifiers have been identified, little is known about the denitrifying ability of the genus Geobacillus. Here, we report the first complete genome sequences of Geobacillus subterraneus KCTC 3922(T), isolated from Liaohe oil field in China, and G. thermodenitrificans KCTC 3902(T). The strain KCTC 3922(T) contains a complete set of genes involved in denitrification, cofactor biogenesis, and transport systems, which is consistent with a denitrifying activity. On the other hand, G. thermodenitrificans KCTC 3902(T) exhibited no denitrifying activity probably due to the lack of molybdnumtransferase (moeA) and nitrite transporter (nirC) genes. Therefore, comparative genome analysis of Geobacillus strains highlights the potential impact on treatment of nitrate-contaminated environments. Copyright © 2017 Elsevier B.V. All rights reserved.
Quinclorac is a widely used herbicide in rice filed. Unfortunately, quinclorac residues are phytotoxic to many crops/vegetables. The degradation of quinclorac in nature is very slow. On the other hand, degradation of quinclorac using bacteria can be an effective and efficient method to reduce its contamination. In this study, we isolated a quinclorac bioremediation bacterium strain F4 from quinclorac contaminated soils. Based on morphological characteristics and 16S rRNA gene sequence analysis, we identified strain F4 as Mycobacterium sp. We investigated the effects of temperature, pH, inoculation size and initial quinclorac concentration on growth and degrading efficiency of F4 and determined the optimal quinclorac degrading condition of F4. Under optimal degrading conditions, F4 degraded 97.38% of quinclorac from an initial concentration of 50 mg/L in seven days. Our indoor pot experiment demonstrated that the degradation products were non-phytotoxic to tobacco. After analyzing the quinclorac degradation products of F4, we proposed that F4 could employ two pathways to degrade quinclorac: one is through methylation, the other is through dechlorination. Furthermore, we reconstructed the whole genome of F4 through single molecular sequencing and de novo assembly. We identified 77 methyltransferases and eight dehalogenases in the F4 genome to support our hypothesized degradation path.
We report here the complete genome sequence of Mycobacterium dioxanotrophicus PH-06, which is capable of using 1,4-dioxane as a sole source of carbon and energy. The reported sequence will enable the elucidation of this novel metabolic pathway and the development of molecular biomarkers to assess bioremediation potential at contaminated sites. Copyright © 2017 He et al.
Pannonibacter phragmitetus is a bioremediation reagent for the detoxification of heavy metals and polycyclic aromatic compounds (PAHs) while it rarely infects healthy populations. However, infection by the opportunistic pathogen P. phragmitetus complicates diagnosis and treatments, and poses a serious threat to immunocompromised patients owing to its multidrug resistance. Unfortunately, genome features, antimicrobial resistance, and virulence potentials in P. phragmitetus have not been reported before. A predominant colony (31801) was isolated from a liver abscess patient, indicating that it accounted for the infection. To investigate its infection mechanism(s) in depth, we sequenced this bacterial genome and tested its antimicrobial resistance. Average nucleotide identity (ANI) analysis assigned the bacterium to the species P. phragmitetus (ANI, >95%). Comparative genomics analyses among Pannonibacter spp. representing the different living niches were used to describe the Pannonibacter pan-genomes and to examine virulence factors, prophages, CRISPR arrays, and genomic islands. Pannonibacter phragmitetus 31801 consisted of one chromosome and one plasmid, while the plasmid was absent in other Pannonibacter isolates. Pannonibacter phragmitetus 31801 may have a great infection potential because a lot of genes encoding toxins, flagellum formation, iron uptake, and virulence factor secretion systems in its genome. Moreover, the genome has 24 genomic islands and 2 prophages. A combination of antimicrobial susceptibility tests and the detailed antibiotic resistance gene analysis provide useful information about the drug resistance mechanisms and therefore can be used to guide the treatment strategy for the bacterial infection.© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
Bioremediation in hypersaline environments is particularly challenging since the microbes that tolerate such harsh environments and degrade pollutants are quite scarce. Haloarchaea, however, due to their inherent ability to grow at high salt concentrations, hold great promise for remediating the contaminated hypersaline sites. This study aimed to isolate and characterize novel haloarchaeal strains with potentials in hydrocarbon degradation. A haloarchaeal strain IM1011 was isolated from Changlu Tanggu saltern near Da Gang Oilfield in Tianjin (China) by enrichment culture in hypersaline medium containing hexadecane. It could degrade 57 ± 5.2% hexadecane (5 g/L) in the presence of 3.6 M NaCl at 37 °C within 24 days. To get further insights into the mechanisms of petroleum hydrocarbon degradation in haloarchaea, complete genome (3,778,989 bp) of IM1011 was sequenced. Phylogenetic analysis of 16S rRNA gene, RNA polymerase beta-subunit (rpoB’) gene and of the complete genome suggested IM1011 to be a new species in Halorientalis genus, and the name Halorientalis hydrocarbonoclasticus sp. nov., is proposed. Notably, with insights from the IM1011 genome sequence, the involvement of diverse alkane hydroxylase enzymes and an intact ß-oxidation pathway in hexadecane biodegradation was predicted. This is the first hexadecane-degrading strain from Halorientalis genus, of which the genome sequence information would be helpful for further dissecting the hydrocarbon degradation by haloarchaea and for their application in bioremediation of oil-polluted hypersaline environments.
Photosynthetic euglenids are major components of aquatic ecosystems and relatives of trypanosomes. Euglena gracilis has considerable biotechnological potential and great adaptability, but exploitation remains hampered by the absence of a comprehensive gene catalogue. We address this by genome, RNA and protein sequencing: the E. gracilis genome is >2Gb, with 36,526 predicted proteins. Large lineage-specific paralog families are present, with evidence for flexibility in environmental monitoring, divergent mechanisms for metabolic control, and novel solutions for adaptation to extreme environments. Contributions from photosynthetic eukaryotes to the nuclear genome, consistent with the shopping bag model are found, together with transitions between kinetoplastid and canonical systems. Control of protein expression is almost exclusively post-transcriptional. These data are a major advance in understanding the nuclear genomes of euglenids and provide a platform for investigating the contributions of E. gracilis and its relatives to the biosphere.
Klebsiella pneumoniae J1 is a Gram-negative strain, which belongs to a protein-based microbial flocculant-producing bacterium. However, little genetic information is known about this species. Here we carried out a whole-genome sequence analysis of this strain and report the complete genome sequence of this organism and its genetic basis for carbohydrate metabolism, capsule biosynthesis and transport system. Copyright © 2016. Published by Elsevier B.V.
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