- Juni Berlin, Germany Full list of author information is available at the end of the article. - Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.. - Sterile biogenic oxides formed by the strains did not show any influence on CYN removal, highlight- ing the importance of the active manganese oxidation.. - MOB form water-insoluble biogenic manganese oxides, which are one of the strongest natural oxidants [17, 19]. - For CYN transformation, a similar mechanism was assumed based on the requirement of active Mn 2+ oxidation for efficient CYN removal and the formation of the same transformation products among all tested MOB, includ- ing strain OF001 and A210 [3]. - Therefore, in this study, we analysed the draft ge- nomes of the MOB strains OF001 and A210, both of which are able to transform CYN during oxidation of MnCO 3 . - GTDB-tk analysis classified strain OF001 as a member of the. - The genus status of the strain OF001 in the Pseudo- monas_ K group was supported by the genetic related- ness determined by whole-genome analysis and 16S rRNA phylogeny (Additional file 1: Fig. - TETRA values of strain OF001 and the organisms of the Pseudomonas_K group were higher than 0.99, but ANI values were below the species limit. - Together, the data suggest strain OF001 is a po- tential new species of the Pseudomonas_K group.. - GTDB-tk analysis classified strain A210 as a member of the Rubrivivax genus. - Organ- isms with high similarity to the 16S rRNA gene se- quence of strain A210 were mainly bacteria of the genera incertae sedis from the Comamonadaceae family (Aquabacterium, Ideonella, Leptothrix, Roseateles, Rubri- vivax, Sphaerotilus). - with organisms of the genus Rubrivivax (Additional file 1: Fig. - Thus suggesting, strain A210 is a po- tential new species of the genus Rubrivivax.. - The pan-genome of the Pseudomonas_K group genomes comprised 20,296 genes belonging to 6805 Microscope gene Families (MICFAM) [44, 45]. - Pan- and core-genome size evolutions were estimated with the four available genomes of the Pseudomonas_K group and the genome of strain OF001. - The curve of the pan-genome of strain OF001 and Pseudomonas_K group did not reach the plateau, suggesting that the pan- genome of Pseudomonas_K group is open and the se- quences of other genomes from this group might in- crease the gene pool of novel genes (Additional file 1:. - The plateau of the core-genome is reached. - 1 Heatmap representing the degree of similarity of the MOB genomes. - TETRA: correlation indexes of the tetra-nucleotide frequencies. - According to the InterPro-based analysis, all three MO-mco’s contain non-cytoplasmic domain regions of membrane-bound proteins that cover more than 94% of the whole protein sequence. - Functional domains of the proteins and the ontology classification are shown in Additional file 1: Table S2.. - Expression of the MO-mco’s in P.. - Our results suggest that the regulation of the MO- mco’s of strain OF001 follows a similar regulation to the one observed in P. - non-cytoplasmic domains which cover more than 84% of the whole protein sequence, and possess either a trans- membrane domain or a transmembrane helix, except for RA210_ u420004. - In spite of the low homology between MO-mco’s from different organisms, we attempted to gain further evi- dence for the Mn 2+ oxidation activity of the suggested multicopper oxidases by using a phylogenetic approach.. - For this purpose, a phylogenetic tree was constructed with sequences of MO-mco and non-MO-mco retrieved form the NCBI database excluding the newly identified putative MO-mco homologues (Additional file 1: Table S3), to discard the possibility that the new sequences were the main factor driving the topology of the tree (Additional file 1: Fig. - Subsequently, the putative MO-mco homologues of the strains OF001 and A210 were added. - 3 Genetic organization of the MO-mco in L. - Note that in a the operon in strain SS-1 is represented based on the total length of the operon because the genome has not been sequenced. - In spite of the evidences found based on the genomic analysis, further experiments are required to determine which enzymes are involved in the oxida- tion of Mn 2+ in Pseudomonas sp. - A210 pos- sess all genes necessary for commonly found central carbohydrate metabolism in aerobic organism including glycolysis (Embden-Meyerhof-Parnas), gluconeogenesis, tricarboxylic acid cycle (Krebs cycle), and the non- oxidative branch of the pentose phosphate pathway, to support basic growth. - In both MOB, genes involved in the oxidative branch of the pentose phosphate pathway were incomplete which is in accordance with its absence in many aerobic and thermophilic organisms [56].. - The presence of genes coding for enzymes of the Calvin cycle in strain A210 is in accordance with their detection in the three described species of the Rubrivivax genus R. - OF001 possesses genes predicted to participate in ammonium uptake, including specific transporters like amtB and genes involved in the regula- tion of the process such as glnA, glnL, and glnK [62–67].. - The detection of the nifDKH genes is in ac- cordance with their detection in the genomes of the two taxonomically closest organisms to OF001, P. - A210 encodes genes predicted to participate in ammo- nium uptake in five predicted operons, including specific transporters like amtB and genes involved in the regula- tion of the process such as glnA, glnL, and glnK [62–67]. - The presence of the glnK and glnB genes in Rubrivivax sp. - Noteworthy, in the three de- scribed species of the Rubrivivax genus [41–43], genes coding for enzymes related to dissimilatory nitrate re- duction were not detected.The enzymes related with the dissimilatory and assimilatory nitrate reduction are orga- nized in two predicted operons.. - However, A210 lacks the adenylyl sulfate kinase cysC, responsible of the transformation of adenosine 5′-phosphosulfate (APS) to 3′-phosphoadenosine-5′-phosphosulfate (PAPS), which is an essential step in the assimilatory sul- fate reduction [86]. - Twenty-one out of the thirty- one genes detected in the genome of strain OF001, cor- respond to siderophores transport (Additional file 1:. - Twenty-two out of the thirty-six genes detected in A210 genome, corres- pond to siderophores transport (Additional file 1: Table S4).. - Genes encoding flagellar proteins in strain OF001 belong to the flg, and fli family, which are part of the core set of flagellar genes [92]. - This is in agree- ment with the description of the closest relatives of strain OF001, P. - Because strain OF001 is able to degrade the cyano- toxin CYN we were also interested in the potential of the strains to degrade other cyanobacterial toxins. - Although biodegradation of CYN is considered one of the main natural attenuation processes [96], no specific genes in- volved in their transformation are known yet [3].. - A summary of the distribution and genetic features of these prophages is shown in Additional file 1: Fig. - Multiple prophages have already been observed in other members of the genus Pseudo- monas [101–104].. - The seven cas genes are downstream of the repeat/spacer re- gion. - the complete CRISPR-Cas loci are downstream of the re- peat/spacer region. - The repeats and spacers of the CRIS PR region with a level of confidence 4 were compared with the CRISPRCas database [106] and, for the majority of them, no matching were found (Additional file 1:. - Implications of the metabolic potential of strains OF001 and A210. - In this study, we aimed at a better understanding of the metabolic capacities of the two CYN removing MOB which could potentially contribute to the biotechno- logical use of MOB for the removal of pollutants from water. - In agreement with the genomes of other MOB with so far uncharacterized degradation ability [35, 36], the content of the genomes of strain OF001 and strain A210 suggests a potential metabolic versatility and thus, a broader application potential.. - Together, this data suggests that studies investigating degradation potential of MOB should consider the phylogenetic and metabolic diversity of MOB to identify the most suitable organisms that ful- fil the requirements of the removal system.. - MOB strains with the abil- ity to denitrify and degrade CYN may be therefore tightly interconnected with the production and removal of the cyanotoxin. - The analysis of the general metabolism of two MOB strains able to re- move organic pollutants such as CYN and DCF might help to implement MOB in biotechnological applications and contributes to a better understanding of the natural niches of CYN-removing MOB in natural habitats.. - A210 were obtained from the culture collection of the Laboratory of Environmental Microbiology from the TU Berlin, Germany [2]. - Quality and quantity of the extracted DNA was determined using QubitTM fluorometric quantita- tion and NanoDrop 2000 (both Thermo Fisher Scientific, Bremen, Germany).. - In the present work, metabolic potential will refer to the possi- bility of the strains to follow a specific metabolic path- way based only on their genome information, without being so far experimentally corroborated.. - First classification of the genomes was determined ac- cording to the Genome Taxonomy Database (GTDB) using the GTDB-tool kit (GTDB-tk) v.1.1.0 integrated in the MicroScope web-based service . - GTDB-tk provides a taxonomic classification of bacterial and archaeal genomes based on the combination of the GTDB reference tree, the relative evolutionary diver- gence and the ANI value against reference genomes [123]. - For the ANI and TETRA analysis, the genome of strain A210 was compared to the genomes of the three species of the genus Rubrivivax: R. - Determination of the core- and pan-genome analysis was performed with the Pan/Core-genome tool from the MicroScope web-based service [119]. - InterPro web server classifies proteins into families, and predicts functional domains and important sites of the proteins, integrating protein signatures from 13 different databases. - PhAnToMe (Phage Annota- tion Tools and Methods), pVOGs [150], and SwissProt [151] databases were used for the identification of the homologs of the input genomes and its predicted gene and peptide sequences. - OF001 and the members of the Pseudomonas_K group, and b) among Rubrivivax sp. - A210 and the mem- bers of the Rubrivivax genus. - Sequences of the studied strains in the present study are not included. - a) Circular genome map of strain OF001, b) genetic features of the complete prophages in strain OF001, and b) circular genome map of strain A210. - In the genome maps location of prophages are highlighted in colors depending on the completeness of the prophages (Table S9).. - Characteristics of the cas genes detected within Pseudo- monas sp. - EBMR discussed the conceptualization and methodology of the project, extracted the DNA and performed all the bioinformatic analysis except those related with the phages and the assembly of the genomes, and wrote the original draft including all tables and figures. - MC supervised and discussed the conceptualization and methodology of the project, and participated in the revision and edition of the manuscript. - JBC performed the analysis related with the phages, and participated in the revision of the manuscript.. - IB coordinated the sequencing submission, and participated in the revision of the manuscript. - MASH performed the assembly of the genomes, and participated in the revision of the manuscript. - RW provided resources for the research, and participated in the revision of the manuscript. - edition of the manuscript. - Identification and molecular analysis of the Leptothrix discophora SS-1 mofA gene, a gene putatively encoding a manganese-oxidizing protein with copper domains. - Stimulation of Mn 2+ oxidation in Leptothrix discophora SS-1 by Cu 2+ and sequence analysis of the region flanking the gene encoding putative multicopper oxidase MofA. - The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. - Multi-step assembly pathway of the cbb 3 -type cytochrome c oxidase complex. - The Bradyrhizobium japonicum fixGHIS genes are required for the formation of the high-affinity cbb 3 -type cytochrome oxidase. - Biogenesis of the bacterial cbb 3 cytochrome c oxidase:. - Characterization of the GlnK protein of Escherichia coli. - Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation. - Altered regulation of the glnA gene in glutamine synthetase mutants of Bacillus subtilis. - Biology of the Nitrogen Cycle. - GlnB/GlnK PII proteins and regulation of the Sinorhizobium meliloti Rm1021 nitrogen stress response and symbiotic function. - Structure and function of a model member of the SulP transporter family. - Sulfate transport in Penicillium chrysogenum: cloning and characterization of the sutA and sutB genes. - Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cycIXHDNYZ gene cluster involved in assimilatory sulphate reduction. - phosphosulfate instead of 3 ′ -phosphoadenosine- 5 ′ -phosphosulfate in cysteine biosynthesis by Rhizobium meliloti and other members of the family Rhizobiaceae. - Stepwise formation of the bacterial flagellar system. - nov., isolated from an electroactive biofilm, and emended description of the genus Pseudomonas Migula 1894. - Complete genome sequence of the plant commensal Pseudomonas fluorescens pf-5. - TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. - Importance of the ornibactin and pyochelin siderophore transport systems in Burkholderia cenocepacia lung infections. - PHASTER: a better, faster version of the PHAST phage search tool
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