Marinomonas mediterranea synthesizes an R-type bacteriocin

Prophages integrated into bacterial genomes can become cryptic or defective prophages, which may evolve to provide various traits to bacterial cells. Previous research on Marinomonas mediterranea MMB-1 demonstrated the production of defective particles. In this study, an analysis of the genomes of three different strains (MMB-1, MMB-2, and MMB-3) revealed the presence of a region named MEDPRO1, spanning approximately 52 kb, coding for a defective prophage in strains MMB-1 and MMB-2. This prophage seems to have been lost in strain MMB-3, possibly due to the presence of spacers recognizing this region in an I-F CRISPR array in this strain. However, all three strains produce remarkably similar defective particles. Using strain MMB-1 as a model, mass spectrometry analyses indicated that the structural proteins of the defective particles are encoded by a second defective prophage situated within the MEDPRO2 region, spanning approximately 13 kb. This finding was further validated through the deletion of this second defective prophage. Genomic region analyses and the detection of antimicrobial activity of the defective prophage against other Marinomonas species suggest that it is an R-type bacteriocin. Marinomonas mediterranea synthesizes antimicrobial proteins with lysine oxidase activity, and the synthesis of an R-type bacteriocin constitutes an additional mechanism in microbial competition for the colonization of habitats such as the surface of marine plants.IMPORTANCEThe interactions between bacterial strains inhabiting the same environment determine the final composition of the microbiome. In this study, it is shown that some extracellular defective phage particles previously observed in Marinomonas mediterranea are in fact R-type bacteriocins showing antimicrobial activity against other Marinomonas strains. The operon coding for the R-type bacteriocin has been identified.

Biodetoxification mercury by using a marine bacterium Marinomonas sp. RS3 and its merA gene expression under mercury stress

Mercury (Hg) pollution in water has been a problem for the ecosystem and human health, thus eco-friendly remediation methods are gaining traction around the world. In this study, a bacterial strain designated as RS3 isolated from the Red Sea (Saudi Arabia) has shown tolerance to more than 250 mg/L of Hg²⁺ on minimum inhibitory studies. The isolate RS3 was identified as Marinomonas sp., (Accession No: OK271312) using 16s rRNA sequencing. Tracing the growth curve for the RS3 showed that maximum growth attained at 72 h and only 10% reduction than the control medium for 50 mg/L HgCl₂ supplemented seawater medium, which continued to reduce as 21% to 60 with the increment of HgCl₂ from 100 to 350 mg/L. The Hg²⁺ removal potential of RS3 is observed to be 78% at 50 mg/L HgCl₂/72 h, which is significantly altered with the addition of carbon source such as glucose (84.5%) > fructose (79.8%) > control (78%) > citrate (73.4%) > acetate (60.2%) > maltose (54.7%). Box-Behnken design (BBD) well proposed a model with R² value of 0.8922, which predict a utmost Hg²⁺ removal of 89.5% by RS2 at favorable conditions (pH-7; NaC 1% and glucose 5%) at 72 h. Mercuric reductase enzyme encoded merA gene expression was found to be high in RS3 isolates cultivated in 100 mg/L of HgCl₂ in comparison with other variables. Thus the seawater isolate Marinomonas sp. RS3 expressed a significant tolerance and removal potential towards the Hg²⁺, which would make it is a noteworthy applicant for effective mercury remediation practices.

A histidine kinase and a response regulator provide phage resistance to Marinomonas mediterranea via CRISPR-Cas regulation

CRISPR-Cas systems are used by many prokaryotes to defend against invading genetic elements. In many cases, more than one CRISPR-Cas system co-exist in the same cell. Marinomonas mediterranea MMB-1 possesses two CRISPR-Cas systems, of type I-F and III-B respectively, which collaborate in phage resistance raising questions on how their expression is regulated. This study shows that the expression of both systems is controlled by the histidine kinase PpoS and a response regulator, PpoR, identified and cloned in this study. These proteins show similarity to the global regulators BarA/UvrY. In addition, homologues to the sRNAs CsrB and CsrC and the gene coding for the post-transcriptional repressor CsrA have been also identified indicating the conservation of the elements of the BarA/UvrY regulatory cascade in M. mediterranea. RNA-Seq analyses have revealed that all these genetics elements are regulated by PpoS/R supporting their participation in the regulatory cascade. The regulation by PpoS and PpoR of the CRISPR-Cas systems plays a role in phage defense since mutants in these proteins show an increase in phage sensitivity.

Isolation and characterization marine bacteria capable of degrading lignin-derived compounds

Lignin, a characteristic component of terrestrial plants. Rivers transport large amounts of vascular plant organic matter into the oceans where lignin can degrade over time; however, microorganisms involved in this degradation have not been identified. In this study, several bacterial strains were isolated from marine samples using the lignin-derived compound vanillic acid (4-hydroxy-3-methoxybenzoic acid) as the sole carbon and energy source. The optimum growth temperature for all isolates ranged from 30 to 35°C. All isolates grew well in a wide NaCl concentration range of 0 to over 50 g/L, with an optimum concentration of 22.8 g/L, which is the same as natural seawater. Phylogenetic analysis indicates that these strains are the members of Halomonas, Arthrobacter, Pseudoalteromonas, Marinomonas, and Thalassospira. These isolates are also able to use other lignin-derived compounds, such as 4-hydroxybenzoic acid, ferulic acid, syringic acid, and benzoic acid. Vanillic acid was detected in all culture media when isolates were grown on ferulic acid as the sole carbon source; however, no 4-hydroxy-3-methoxystyrene was detected, indicating that ferulic acid metabolism by these strains occurs via the elimination of two side chain carbons. Furthermore, the isolates exhibit 3,4-dioxygenase or 4,5-dioxygenase activity for protocatechuic acid ring-cleavage, which is consistent with the genetic sequences of related genera. This study was conducted to isolate and characterize marine bacteria of degrading lignin-derived compounds, thereby revealing the degradation of aromatic compounds in the marine environment and opening up new avenues for the development and utilization of marine biological resources.

A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition

Prokaryotic CRISPR-Cas systems provide adaptive immunity by integrating portions of foreign nucleic acids (spacers) into genomic CRISPR arrays. Cas6 proteins then process CRISPR array transcripts into spacer-derived RNAs (CRISPR RNAs; crRNAs) that target Cas nucleases to matching invaders. We find that a Marinomonas mediterranea fusion protein combines three enzymatic domains (Cas6, reverse transcriptase [RT], and Cas1), which function in both crRNA biogenesis and spacer acquisition from RNA and DNA. We report a crystal structure of this divergent Cas6, identify amino acids required for Cas6 activity, show that the Cas6 domain is required for RT activity and RNA spacer acquisition, and demonstrate that CRISPR-repeat binding to Cas6 regulates RT activity. Co-evolution of putative interacting surfaces suggests a specific structural interaction between the Cas6 and RT domains, and phylogenetic analysis reveals repeated, stable association of free-standing Cas6s with CRISPR RTs in multiple microbial lineages, indicating that a functional interaction between these proteins preceded evolution of the fusion.

Exploring the Effects of Subfreezing Temperature and Salt Concentration on Ice Growth Inhibition of Antarctic Gram-Negative Bacterium Marinomonas Primoryensis Using Coarse-Grained Simulation

The aim of this work is to study the freezing process of water molecules surrounding Antarctic Gram-negative bacterium Marinomonas primoryensis antifreeze protein (MpAFP) and the MpAFP interactions to the surface of ice crystals under various marine environments (at different NaCl concentrations of 0.3, 0.6, and 0.8 mol/l). Our result indicates that activating temperature region of MpAFPs reduced as NaCl concentration increased. Specifically, MpAFP was activated and functioned at 0.6 mol/l with temperatures equal or larger 278 K, and at 0.8 mol/l with temperatures equal or larger 270 K. Additionally, MpAFP was inhibited by ice crystal network from 268 to 274 K and solid-liquid hybrid from 276 to 282 K at 0.3 mol/l concentration. Our results shed lights on structural dynamics of MpAFP among different marine environments.

An in silico, in vitro and in vivo investigation of indole-3-carboxaldehyde identified from the seawater bacterium Marinomonas sp. as an anti-biofilm agent against Vibrio cholerae O1

Biofilm formation is a major contributing factor in the pathogenesis of Vibrio cholerae O1 (VCO1) and therefore preventing biofilm formation could be an effective alternative strategy for controlling cholera. The present study was designed to explore seawater bacteria as a source of anti-biofilm agents against VCO1. Indole-3-carboxaldehyde (I3C) was identified as an active principle component in Marinomonas sp., which efficiently inhibited biofilm formation by VCO1 without any selection pressure. Furthermore, I3C applications also resulted in considerable collapsing of preformed pellicles. Real-time PCR studies revealed the down-regulation of virulence gene expression by modulation of the quorum-sensing pathway and enhancement of protease production, which was further confirmed by phenotypic assays. Furthermore, I3C increased the survival rate of Caenorhabditis elegans when infected with VCO1 by significantly reducing in vivo biofilm formation, which was corroborated by a survivability assay. Thus, this study revealed, for the first time, the potential of I3C as an anti-biofilm agent against VCO1.

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches.

Involvement of a novel copper chaperone in tyrosinase activity and melanin synthesis in Marinomonas mediterranea

Tyrosinase activity and melanin synthesis in the marine bacterium Marinomonas mediterranea in media with very low copper concentrations are dependent on the presence of a protein (PpoB2) that functions as a chaperone to deliver copper to tyrosinase (PpoB1). Under these conditions, mutants in ppoB2 (such as strain T105) produce PpoB1 as an apoenzyme that can be reconstituted to the active holoenzyme by the addition of cupric ions to cell extracts. To study PpoB2 functionality, a system was developed for genetic complementation in M. mediterranea. Using this approach, melanin synthesis was restored in strain T105 when a wild-type copy of ppoB2 was introduced. PpoB2 is a novel protein since it is believed to be the first to be described that contains several motifs similar to metal binding motifs present separately in other types of copper-related protein. At least three motifs, a His-rich N-terminal region, and the short CxxxC and MxxxMM sequences, are essential for the functionality of PpoB2, since site-directed mutagenesis of these motifs resulted in a non-functional protein. In addition, it was demonstrated that PpoB2 is a membrane copper transporter putatively participating in the delivery of this ion specifically to the tyrosinase of M. mediterranea and not to a second copper oxidase showing laccase activity that this micro-organism also expresses. PpoB2 has similarities with the COG5486 group encoding putative transmembrane metal binding proteins, and is believed to be the first protein in this group to be experimentally characterized. It may constitute the first example of a novel type of protein involved in copper trafficking in bacteria.

Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria

Dimethyl sulfide (DMS) is a key compound in global sulfur and carbon cycles. DMS oxidation products cause cloud nucleation and may affect weather and climate. DMS is generated largely by bacterial catabolism of dimethylsulfoniopropionate (DMSP), a secondary metabolite made by marine algae. We demonstrate that the bacterial gene dddD is required for this process and that its transcription is induced by the DMSP substrate. Cloned dddD from the marine bacterium Marinomonas and from two bacterial strains that associate with higher plants, the N(2)-fixing symbiont Rhizobium NGR234 and the root-colonizing Burkholderia cepacia AMMD, conferred to Escherichia coli the ability to make DMS from DMSP. The inferred enzymatic mechanism for DMS liberation involves an initial step in which DMSP is modified by addition of acyl coenzyme A, rather than the immediate release of DMS by a DMSP lyase, the previously suggested mechanism.

Arsenic resistance and removal by marine and non-marine bacteria

Arsenic resistance and removal was evaluated in nine bacterial strains of marine and non-marine origins. Of the strains tested, Marinomonas communis exhibited the second-highest arsenic resistance with median effective concentration (EC(50)) value of 510 mg As l(-1), and was capable of removing arsenic from culture medium amended with arsenate. Arsenic accumulation in cells amounted to 2290 microg As g(-1) (dry weight) when incubated on medium containing 5 mg As l(-1) of arsenate. More than half of the arsenic removed was related to metabolic activity: 45% of the arsenic was incorporated into the cytosol fraction and 10% was found in the lipid-bound fraction of the membrane, with the remaining arsenic considered to be adsorbed onto the cell surface. Potential arsenic resistance and removal were also examined in six marine and non-marine environmental water samples. Of the total bacterial colony counts, 28-100% of bacteria showed arsenic resistance. Some of the bacterial consortia, especially those from seawater enriched with arsenate, exhibited higher accumulated levels of arsenic than M. communis under the same condition. These results showed that arsenic resistant and/or accumulating bacteria are widespread in the aquatic environment, and that arsenic-accumulating bacteria such as M. communis are potential candidates for bioremediation of arsenic contaminated water.

Precipitation of minerals by 22 species of moderately halophilic bacteria in artificial marine salts media: Influence of salt concentration

Precipitation of minerals was shown by 22 species of moderately halophilic bacteria in both solid and liquid artificial marine salts media at different concentration and different Mg2+-to-Ca2+ ratio. Precipitation of minerals was observed for all the bacteria used. When salt concentration increased, the quantity and the size of bioliths decreased, the time required for precipitation being increased. The precipitated minerals were calcite, magnesian calcite, aragonite, dolomite, monohydrocalcite, hydromagnesite and struvite in variable proportions, depending on the bacterial species, the salinity and the physical state of the medium; the Mg content of the magnesian calcite also varied according to the same parameters. The precipitated minerals do not correspond exactly to those which could be precipitated inorganically according to the saturation indices. Scanning electron microscopy showed that the formation of the bioliths is initiated by grouping of calcified cells and that the dominant final morphologies were spherulitic with fibrous radiated interiors. It was demonstrated that moderately halophilic bacteria play an active role in the precipitation of carbonates and we hypothesize about this process of biomineralization.