Mn(II) oxidation in Pseudomonas putida GB-1 is influenced by flagella synthesis and surface substrate

Isolation, characterization, and genetic manipulation of cold-tolerant, manganese-oxidizing Pseudomonas sp. strains

Manganese-oxidizing bacteria (MnOB) produce Mn oxide minerals that can be used by humans for bioremediation, but the purpose for the bacterium is less clear. This study describes the isolation and characterization of cold-tolerant MnOB strains isolated from a compost pile in Morris, Minnesota, USA: Pseudomonas sp. MS-1 and DSV-1. The strains were preliminarily identified as members of species Pseudomonas psychrophila by 16S rRNA analysis and a multi-locus phylogenetic study using a database of 88 genomes from the Pseudomonas genus. However, the average nucleotide identity between these strains and the P. psychrophila sp. CF149 type strain was less than 93%. Thus, the two strains are members of a novel species that diverged from P. psychrophila. DSV-1 and MS-1 are cold tolerant; both grow at 4°C but faster at 24°C. Unlike the mesophilic MnOB P. putida GB-1, both strains are capable of robustly oxidizing Mn at low temperatures. Both DSV-1 and MS-1 genomes contain homologs of several Mn oxidation genes found in P. putida GB-1 (mnxG, mcoA, mnxS1, mnxS2, and mnxR). Random mutagenesis by transposon insertion was successfully performed in both strains and identified genes involved in Mn oxidation that were similar to those found in P. putida GB-1. Our results show that MnOB can be isolated from compost, supporting a role for Mn oxidation in plant waste degradation. The novel isolates Pseudomonas spp. DSV-1 and MS-1 both can oxidize Mn at low temperature and likely employ similar mechanisms and regulation as P. putida GB-1.IMPORTANCEBiogenic Mn oxides have high sorptive capacity and are strong oxidants. These two characteristics make these oxides and the microbes that make them attractive tools for the bioremediation of wastewater and contaminated environments. Identifying MnOB that can be used for bioremediation is an active area of research. As cold-tolerant MnOB, Pseudomonas sp. DSV-1 and MS-1 have the potential to expand the environmental conditions in which biogenic Mn oxide bioremediation can be performed. The similarity of these organisms to the well-characterized MnOB P. putida GB-1 and the ability to manipulate their genomes raise the possibility of modifying them to improve their bioremediation ability.

Advances in Research on Bacterial Oxidation of Mn(II): A Visualized Bibliometric Analysis Based on CiteSpace

Manganese (Mn) pollution poses a serious threat to the health of animals, plants, and humans. The microbial-mediated Mn(II) removal method has received widespread attention because of its rapid growth, high efficiency, and economy. Mn(II)-oxidizing bacteria can oxidize toxic soluble Mn(II) into non-toxic Mn(III/IV) oxides, which can further participate in the transformation of other heavy metals and organic pollutants, playing a crucial role in environmental remediation. This study aims to conduct a bibliometric analysis of research papers on bacterial Mn(II) oxidation using CiteSpace, and to explore the research hotspots and developmental trends within this field between 2008 and 2023. A series of visualized knowledge map analyses were conducted with 469 screened SCI research papers regarding annual publication quantity, author groups and their countries and regions, journal categories, publishing institutions, and keywords. China, the USA, and Japan published the most significant number of research papers on the research of bacterial Mn(II) oxidation. Research hotspots of bacterial Mn(II) oxidation mainly focused on the species and distributions of Mn(II)-oxidizing bacteria, the influencing factors of Mn(II) oxidation, the mechanisms of Mn(II) oxidation, and their applications in environment. This bibliometric analysis provides a comprehensive visualized knowledge map to quickly understand the current advancements, research hotspots, and academic frontiers in bacterial Mn(II) oxidation.

Sublethal nickel toxicity shuts off manganese oxidation and pellicle biofilm formation in Pseudomonas putida GB-1

In sediments, the bioavailability and toxicity of Ni are strongly influenced by its sorption to manganese (Mn) oxides, which largely originate from the redox metabolism of microbes. However, microbes are concurrently susceptible to the toxic effects of Ni, which establishes complex interactions between toxicity and redox processes. This study measured the effect of Ni on growth, pellicle biofilm formation and oxidation of the Mn-oxidizing bacteria Pseudomonas putida GB-1. In liquid media, Ni exposure decreased the intrinsic growth rate but allowed growth to the stationary phase in all intermediate treatments. Manganese oxidation was 67% less than control for bacteria exposed to 5 μM Ni and completely ceased in all treatments above 50 μM. Pellicle biofilm development decreased exponentially with Ni concentration (maximum 92% reduction) and was replaced by planktonic growth in higher Ni treatments. In solid media assays, growth was unaffected by Ni exposure, but Mn oxidation completely ceased in treatments above 10 μM of Ni. Our results show that sublethal Ni concentrations substantially alter Mn oxidation rates and pellicle biofilm development in P. putida GB-1, which has implications for toxic metal bioavailability to the entire benthic community and the environmental consequences of metal contamination.

Simultaneous antibiotic removal and mitigation of resistance induction by manganese bio-oxidation process

Microbial degradation to remove residual antibiotics in wastewater is of growing interest. However, biological treatment of antibiotics may cause resistance dissemination by mutations and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). In this study, a Mn(Ⅱ)-oxidizing bacterium (MnOB), Pseudomonas aeruginosa MQ2, simultaneously degraded antibiotics, decreased HGT, and mitigated antibiotic resistance mutation. Intracellular Mn(II) levels increased during manganese oxidation, and biogenic manganese oxides (BioMnOx, including Mn(II), Mn(III) and Mn(IV)) tightly coated the cell surface. Mn(II) bio-oxidation mitigated antibiotic resistance acquisition from an E. coli ARG donor and mitigated antibiotic resistance inducement by decreasing conjugative transfer and mutation, respectively. BioMnOx also oxidized ciprofloxacin (1 mg/L) and tetracycline (5 mg/L), respectively removing 93% and 96% within 24 h. Transcriptomic analysis revealed that two new multicopper oxidase and one peroxidase genes are involved in Mn(II) oxidation. Downregulation of SOS response, multidrug resistance and type Ⅳ secretion system related genes explained that Mn(II) and BioMnOx decreased HGT and mitigated resistance mutation by alleviating oxidative stress, which makes recipient cells more vulnerable to ARG acquisition and mutation. A manganese bio-oxidation based reactor was constructed and completely removed tetracycline with environmental concentration within 4-hour hydraulic retention time. Overall, this study suggests that Mn (II) bio-oxidation process could be exploited to control antibiotic contamination and mitigate resistance propagation during water treatment.

Cyclic di-GMP Signaling Links Biofilm Formation and Mn(II) Oxidation in Pseudomonas resinovorans

Bioaugmentation of biological sand filters with Mn(II)-oxidizing bacteria (MOB) is used to increase the efficiency of Mn removal from groundwater. While the biofilm-forming ability of MOB is important to achieve optimal Mn filtration, the regulatory link between biofilm formation and Mn(II) oxidation remains unclear. Here, an environmental isolate of Pseudomonas resinovorans strain MOB-513 was used as a model to investigate the role of c-di-GMP, a second messenger crucially involved in the regulation of biofilm formation by Pseudomonas, in the oxidation of Mn(II). A novel role for c-di-GMP in the upregulation of Mn(II) oxidation through induction of the expression of manganese-oxidizing peroxidase enzymes was revealed. MOB-513 macrocolony biofilms showed a strikingly stratified pattern of biogenic Mn oxide (BMnOx) accumulation in a localized top layer. Remarkably, elevated cellular levels of c-di-GMP correlated not only with increased accumulation of BMnOx in the same top layer but also with the appearance of a second BMnOx stratum in the bottom region of macrocolony biofilms, and the expression of mop genes correlated with this pattern. Proteomic analysis under Mn(II) conditions revealed changes in the abundance of a PilZ domain protein. Subsequent analyses supported a model in which this protein sensed c-di-GMP and affected a regulatory cascade that ultimately inhibited mop gene expression, providing a molecular link between c-di-GMP signaling and Mn(II) oxidation. Finally, we observed that high c-di-GMP levels were correlated with higher lyophilization efficiencies and higher groundwater Mn(II) oxidation capacities of freeze-dried bacterial cells, named lyophiles, showing the biotechnological relevance of understanding the role of c-di-GMP in MOB-513. IMPORTANCE The presence of Mn(II) in groundwater, a common source of drinking water, is a cause of water quality impairment, interfering with its disinfection, causing operation problems, and affecting human health. Purification of groundwater containing Mn(II) plays an important role in environmental and social safety. The typical method for Mn(II) removal is based on bacterial oxidation of metals to form insoluble oxides that can be filtered out of the water. Evidence of reducing the start-up periods and enhancing Mn removal efficiencies through bioaugmentation with appropriate biofilm-forming and MOB has emerged. As preliminary data suggest a link between these two phenotypes in Pseudomonas strains, the need to investigate the underlying regulatory mechanisms is apparent. The significance of our research lies in determining the role of c-di-GMP for increased biofilm formation and Mn(II)-oxidizing capabilities in MOB, which will allow the generation of super-biofilm-elaborating and Mn-oxidizing strains, enabling their implementation in biotechnological applications.

Anti-bacterial Effects of MnO2 on the Enrichment of Manganese-oxidizing Bacteria in Downflow Hanging Sponge Reactors

We focused on the use of abiotic MnO2 to develop reactors for enriching manganese-oxidizing bacteria (MnOB), which may then be used to treat harmful heavy metal-containing wastewater and in the recovery of useful minor metals. Downflow hanging sponge (DHS) reactors were used under aerobic and open conditions to investigate the potential for MnOB enrichment. The results of an experiment that required a continuous supply of organic feed solution containing Mn(II) demonstrated that MnOB enrichment and Mn(II) removal were unsuccessful in the DHS reactor when plain sponge cubes were used. However, MnOB enrichment was successful within a very short operational period when sponge cubes initially containing abiotic MnO2 were installed. The results of a microbial community analysis and MnOB isolation revealed that MnOB belonging to Comamonadaceae or Pseudomonas played a major role in Mn(II) oxidation. Successful MnOB enrichment was attributed to several unidentified species of Chitinophagaceae and Gemmataceae, which were estimated to be intolerant of MnO2, being unable to grow on sponge cubes containing MnO2. The present results show that MnO2 exerted anti-bacterial effects and inhibited the growth of certain non-MnOB groups that were intolerant of MnO2, thereby enabling enriched MnOB to competitively consume more substrate than MnO2-intolerant bacteria.

Mechanistic insights into manganese oxidation of a soil-borne Mn(II)-oxidizing Escherichia coli strain by global proteomic and genetic analyses

An iTRAQ-based comparative and quantitative proteomics analysis of a soil-borne Mn(II)-oxidizing bacterium, Escherichia coli MB266, was conducted during the exponential and stationary growth phases. A total of 1850 proteins were identified in 4 samples, of which 373 and 456 proteins were significantly up- or down-regulated in at least one pairwise comparison, respectively. The iTRAQ data indicated that several enzymes involved in fatty acid metabolism (i.e., FabA, FabD and FabZ) and pyruvate metabolism (particularly pyruvate oxidase PoxB) were significantly up-regulated, while those related to the tricarboxylic acid cycle (such as FrdB, FumB and AcnA) and methylcitrate cycle (i.e., PrpC) were inactivated in the presence of 1 mM Mn(II); the amounts of some stress response and signal transduction system-related proteins (i.e., Spy) were remarkably increased, and the cold shock protein CspD was significantly up-regulated during the exponential growth phase. However, all verified heat shock proteins remained unchanged. The reactive oxygen species response and some redox enzymes might also be involved in Mn oxidation processes. The involvement of several cellular proteins in Mn(II) oxidation, including PoxB, Spy and MCO266, was further confirmed by gene disruption and expression complementation experiments. Based on these results, a signal transduction mechanism coupled to Mn oxidation was proposed.

Antimony oxidation and adsorption by in-situ formed biogenic Mn oxide and Fe-Mn oxides

Antimony (Sb), which can be toxic at relatively low concentrations, may co-exist with Mn(II) and/or Fe(II) in some groundwater and surface water bodies. Here we investigated the potential oxidation and adsorption pathways of Sb (III and V) species in the presence of Mn(II) and Mn-oxidizing bacteria, with or without Fe(II). Batch experiments were conducted to determine the oxidation and adsorption characteristics of Sb species in the presence of biogenic Mn oxides (BMOs), which were formed in-situ via the oxidation of Mn(II) by a Mn-oxidizing bacterium (Pseudomonas sp. QJX-1). Results indicated that Sb(III) ions could be oxidized to Sb(V) ions by BMO, but only Sb(V) originating from Sb(III) oxidation was adsorbed effectively by BMO. Introduced Fe(II) was chemically oxidized to FeOOH, the precipitates of which mixed with BMO to form a new compound, biogenic Fe-Mn oxides (BFMO). The BMO part of the BFMO mainly oxidized and the FeOOH of the BFMO mainly adsorbed the Sb species. In aquatic solutions containing both As(III) and Sb(III), the BFMO that formed in-situ preferentially oxidized Sb over As but adsorbed As more efficiently. Chemical analysis and reverse transcription real-time polymerase chain reaction revealed that the presence of Fe(II), As(III) and Sb(III) accelerated the oxidation of Mn(II) but inhibited the activity of Mn-oxidizing bacteria. These results provide significant insights into the biogeochemical pathways of Sb, Mn(II) in aquatic ecosystems, with or without Fe(II).

Identification of a Third Mn(II) Oxidase Enzyme in Pseudomonas putida GB-1

The oxidation of soluble Mn(II) to insoluble Mn(IV) is a widespread bacterial activity found in a diverse array of microbes. In the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1, two Mn(II) oxidase genes, named mnxG and mcoA, were previously identified; each encodes a multicopper oxidase (MCO)-type enzyme. Expression of these two genes is positively regulated by the response regulator MnxR. Preliminary investigation into putative additional regulatory pathways suggested that the flagellar regulators FleN and FleQ also regulate Mn(II) oxidase activity; however, it also revealed the presence of a third, previously uncharacterized Mn(II) oxidase activity in P. putida GB-1. A strain from which both of the Mn(II) oxidase genes and fleQ were deleted exhibited low levels of Mn(II) oxidase activity. The enzyme responsible was genetically and biochemically identified as an animal heme peroxidase (AHP) with domain and sequence similarity to the previously identified Mn(II) oxidase MopA. In the ΔfleQ strain, P. putida GB-1 MopA is overexpressed and secreted from the cell, where it actively oxidizes Mn. Thus, deletion of fleQ unmasked a third Mn(II) oxidase activity in this strain. These results provide an example of an Mn(II)-oxidizing bacterium utilizing both MCO and AHP enzymes.

IMPORTANCE

The identity of the Mn(II) oxidase enzyme in Pseudomonas putida GB-1 has been a long-standing question in the field of bacterial Mn(II) oxidation. In the current work, we demonstrate that P. putida GB-1 employs both the multicopper oxidase- and animal heme peroxidase-mediated pathways for the oxidation of Mn(II), rendering this model organism relevant to the study of both types of Mn(II) oxidase enzymes. The presence of three oxidase enzymes in P. putida GB-1 deepens the mystery of why microorganisms oxidize Mn(II) while providing the field with the tools necessary to address this question. The initial identification of MopA as a Mn(II) oxidase in this strain required the deletion of FleQ, a regulator involved in both flagellum synthesis and biofilm synthesis in Pseudomonas aeruginosa Therefore, these results are also an important step toward understanding the regulation of Mn(II) oxidation.

Biological Low-pH Mn(II) Oxidation in a Manganese Deposit Influenced by Metal-Rich Groundwater

The mechanisms, key organisms, and geochemical significance of biological low-pH Mn(II) oxidation are largely unexplored. Here, we investigated the structure of indigenous Mn(II)-oxidizing microbial communities in a secondary subsurface Mn oxide deposit influenced by acidic (pH 4.8) metal-rich groundwater in a former uranium mining area. Microbial diversity was highest in the Mn deposit compared to the adjacent soil layers and included the majority of known Mn(II)-oxidizing bacteria (MOB) and two genera of known Mn(II)-oxidizing fungi (MOF). Electron X-ray microanalysis showed that romanechite [(Ba,H2O)2(Mn(4+),Mn(3+))5O10] was conspicuously enriched in the deposit. Canonical correspondence analysis revealed that certain fungal, bacterial, and archaeal groups were firmly associated with the autochthonous Mn oxides. Eight MOB within the Proteobacteria, Actinobacteria, and Bacteroidetes and one MOF strain belonging to Ascomycota were isolated at pH 5.5 or 7.2 from the acidic Mn deposit. Soil-groundwater microcosms demonstrated 2.5-fold-faster Mn(II) depletion in the Mn deposit than adjacent soil layers. No depletion was observed in the abiotic controls, suggesting that biological contribution is the main driver for Mn(II) oxidation at low pH. The composition and species specificity of the native low-pH Mn(II) oxidizers were highly adapted to in situ conditions, and these organisms may play a central role in the fundamental biogeochemical processes (e.g., metal natural attenuation) occurring in the acidic, oligotrophic, and metalliferous subsoil ecosystems.

IMPORTANCE

This study provides multiple lines of evidence to show that microbes are the main drivers of Mn(II) oxidation even at acidic pH, offering new insights into Mn biogeochemical cycling. A distinct, highly adapted microbial community inhabits acidic, oligotrophic Mn deposits and mediates biological Mn oxidation. These data highlight the importance of biological processes for Mn biogeochemical cycling and show the potential for new bioremediation strategies aimed at enhancing biological Mn oxidation in low-pH environments for contaminant mitigation.

Manganese (Mn) oxidation increases intracellular Mn in Pseudomonas putida GB-1

Bacterial manganese (Mn) oxidation plays an important role in the global biogeochemical cycling of Mn and other compounds, and the diversity and prevalence of Mn oxidizers have been well established. Despite many hypotheses of why these bacteria may oxidize Mn, the physiological reasons remain elusive. Intracellular Mn levels were determined for Pseudomonas putida GB-1 grown in the presence or absence of Mn by inductively coupled plasma mass spectrometry (ICP-MS). Mn oxidizing wild type P. putida GB-1 had higher intracellular Mn than non Mn oxidizing mutants grown under the same conditions. P. putida GB-1 had a 5 fold increase in intracellular Mn compared to the non Mn oxidizing mutant P. putida GB-1-007 and a 59 fold increase in intracellular Mn compared to P. putida GB-1 ∆2665 ∆2447. The intracellular Mn is primarily associated with the less than 3 kDa fraction, suggesting it is not bound to protein. Protein oxidation levels in Mn oxidizing and non oxidizing cultures were relatively similar, yet Mn oxidation did increase survival of P. putida GB-1 when oxidatively stressed. This study is the first to link Mn oxidation to Mn homeostasis and oxidative stress protection.