High-level resistance to cobalt and nickel but probably no transenvelope efflux: Metal resistance in the Cuban Serratia marcescens strain C-1

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria

The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.

Metallophore Activity toward the Rare Earth Elements by Bacteria Isolated from Acid Mine Drainage Due to Coal Mining

The field of microbe-metal interactions has been gaining significant attention. While the direct impact of metal oxyanions on bacteria has been investigated, significantly less attention has been placed on the ability of certain microbes to 'collect' such metal ions via secreted proteins. Many bacteria possess low-weight molecules called siderophores, which collect Fe from the environment to be brought back to the cell. However, some appear to have additional roles, including binding other metals, termed 'metallophores'. Microbes can remove/sequester these from their surroundings, but the breadth of those that can be removed is still unknown. Using the Chromeazurol S assay, we identified eight isolates, most belonging to the genus Pseudomonas, possessing siderophore activity, mainly from sites impacted by coal mine drainage, also possessing a metallophore activity toward the rare earth elements that does not appear to be related to ionic radii or previously reported EC50 concentrations for E. coli. We found the strength of metallophore activity towards these elements was as follows: Pr > Sc > Eu > Tm > Tb > Er > Yb > Ce > Lu > Sm > Ho > La > Nd > Dy > Gd > Y. This is the first study to investigate such activity and indicates bacteria may provide a means of removal/recovery of these critical elements.

Impact of lead (Pb2+) on the growth and biological activity of Serratia marcescens selected for wastewater treatment and identification of its zntR gene-a metal efflux regulator

Microorganisms isolated from contaminated areas play an important role in bioremediation processes. They promote heavy metal removal from the environment by adsorbing ions onto the cell wall surface, accumulating them inside the cells, or reducing, complexing, or precipitating these substances in the environment. Microorganism-based bioremediation processes can be highly efficient, low-cost and have low environmental impact. Thus, the present study aimed to select Pb²⁺-resistant bacteria and evaluate the growth rate, biological activity, and the presence of genes associated with metal resistance. Serratia marcescens CCMA 1010, that was previously isolated from coffee processing wastewater, was selected since was able to growth in Pb²⁺ concentrations of up to 4.0 mM. The growth rate and generation time did not differ from those of the control (without Pb²⁺), although biological activity decreased in the first hour of exposure to these ions and stabilized after this period. The presence of the zntR, zntA and pbrA genes was analysed, and only zntR was detected. The zntR gene encodes a protein responsible for regulating the production of ZntA, a transmembrane protein that facilitates Pb²⁺ extrusion out of the cell. S. marcescens CCMA 1010 demonstrated a potential for use as bioindicator that has potential to be used in bioremediation processes due to its resistance to high concentrations of Pb²⁺, ability to grow until 24 h of exposure, and possession of a gene that indicates the existence of mechanisms associated with resistance to lead (Pb²⁺).

Diversity of microbiota found in coffee processing wastewater treatment plant

Cultivable microbiota presents in a coffee semi-dry processing wastewater treatment plant (WTP) was identified. Thirty-two operational taxonomic units (OTUs) were detected, these being 16 bacteria, 11 yeasts and 4 filamentous fungi. Bacteria dominated the microbial population (11.61 log CFU mL^- 1), and presented the highest total diversity index when observed in the WTP aerobic stage (Shannon = 1.94 and Simpson = 0.81). The most frequent bacterial species were Enterobacter asburiae, Sphingobacterium griseoflavum, Chryseobacterium bovis, Serratia marcescens, Corynebacterium flavescens, Acetobacter orientalis and Acetobacter indonesiensis; these showed the largest total bacteria populations in the WTP, with approximately 10 log CFU mL^- 1. Yeasts were present at 7 log CFU mL^- 1 of viable cells, with Hanseniaspora uvarum, Wickerhamomyces anomalus, Torulaspora delbrueckii, Saturnispora gosingensis, and Kazachstania gamospora being the prevalent species. Filamentous fungi were found at 6 log CFU mL^- 1, with Fusarium oxysporum the most populous species. The identified species have the potential to act as a biological treatment in the WTP, and the application of them for this purpose must be better studied.

Comparative mathematical modelling of a green approach for bioaccumulation of cobalt from wastewater

Cobalt is an essential element, but its wide use in industry generates important environmental and biological problems. The present study explores theoretical and empirical models of a green process for cobalt {Co²⁺} bioaccumulation from aqueous solutions. Two Gram-positive Bacillus subtilis species, strains CECT 4522 and LMM (the latter a former laboratory isolate from wastewater samples, which was phylogenetically characterized for the present work), were selected among others as the best Co²⁺ accumulation systems. Mathematical models representing kinetic and steady-state conditions for discrete and large amounts of bacterial biomass were expanded. In this way, it was possible to theoretically calculate the amount of Co²⁺ retained on the outer cell wall layer and incorporated inside the cell at any time. Theoretical and empirical hyperbolic-type models were suitable to fit the experimental bioaccumulation data for discrete amounts of bacteria biomass. In addition, kinetic relationships between the amount of Co²⁺ accumulated and the time before (or after) reaching steady state were established for large amounts of bacterial biomass. Other kinetic approaches were also satisfactorily tested. The two Gram-positive bacteria assayed are promising agents for developing heavy metal removal systems from industrial waste.

Ammonia-Oligotrophic and Diazotrophic Heavy Metal-Resistant Serratia liquefaciens Strains from Pioneer Plants and Mine Tailings

Mine tailings are man-made environments characterized by low levels of organic carbon and assimilable nitrogen, as well as moderate concentrations of heavy metals. For the introduction of nitrogen into these environments, a key role is played by ammonia-oligotrophic/diazotrophic heavy metal-resistant guilds. In mine tailings from Zacatecas, Mexico, Serratia liquefaciens was the dominant heterotrophic culturable species isolated in N-free media from bulk mine tailings as well as the rhizosphere, roots, and aerial parts of pioneer plants. S. liquefaciens strains proved to be a meta-population with high intraspecific genetic diversity and a potential to respond to these extreme conditions. The phenotypic and genotypic features of these strains reveal the potential adaptation of S. liquefaciens to oligotrophic and nitrogen-limited mine tailings with high concentrations of heavy metals. These features include ammonia-oligotrophic growth, nitrogen fixation, siderophore and indoleacetic acid production, phosphate solubilization, biofilm formation, moderate tolerance to heavy metals under conditions of diverse nitrogen availability, and the presence of zntA, amtB, and nifH genes. The acetylene reduction assay suggests low nitrogen-fixing activity. The nifH gene was harbored in a plasmid of ∼60 kb and probably was acquired by a horizontal gene transfer event from Klebsiella variicola.

Cloning of the cnr operon into a strain of Bacillaceae bacterium for the development of a suitable biosorbent

In this study, a potential microbial biosorbent was engineered to improve its capacity to remediate heavy metal contaminated water resources. A Bacillaceae bacterium isolated from a mining area was transformed with a plasmid carrying the (pECD312)-based cnr operon that encodes nickel and cobalt resistance. The bioadsorption ability of the transformed strain was evaluated for removal of nickel from metallurgical water relative to the wildtype strain. Results showed that transformation improved the adsorption capacity of the bacterium by 37 % at nickel concentrations equivalent to 150 mg/L. Furthermore it was possible to apply prediction modelling to study the bioadsorption behaviour of the transformed strain. As such, this work may be extended to the design of a nickel bioremediation plant utilising the newly developed Bacillaceae bacterium as a biosorbent.

The LysE Superfamily of Transport Proteins Involved in Cell Physiology and Pathogenesis

The LysE superfamily consists of transmembrane transport proteins that catalyze export of amino acids, lipids and heavy metal ions. Statistical means were used to show that it includes newly identified families including transporters specific for (1) tellurium, (2) iron/lead, (3) manganese, (4) calcium, (5) nickel/cobalt, (6) amino acids, and (7) peptidoglycolipids as well as (8) one family of transmembrane electron carriers. Internal repeats and conserved motifs were identified, and multiple alignments, phylogenetic trees and average hydropathy, amphipathicity and similarity plots provided evidence that all members of the superfamily derived from a single common 3-TMS precursor peptide via intragenic duplication. Their common origin implies that they share common structural, mechanistic and functional attributes. The transporters of this superfamily play important roles in ionic homeostasis, cell envelope assembly, and protection from excessive cytoplasmic heavy metal/metabolite concentrations. They thus influence the physiology and pathogenesis of numerous microbes, being potential targets of drug action.

Comparative study on Ni(2+)-affinity transport of nickel/cobalt permeases (NiCoTs) and the potential of recombinant Escherichia coli for Ni(2+) bioaccumulation

Comparative evaluation on Ni(2+)-uptake of two nickel-affinity transmembrane proteins (NiCoTs) respectively from Helocobacter pylori (NixA) and Staphylococcus aureus (NisA) was performed. Expression of NiCoTs alone did not promote Ni(2+) uptake of the recombinant strains and made the growth susceptible to Ni(2+). However, recombinant strains expressing both NiCoTs and Metallothionein (MT) showed enhanced tolerance to Ni(2+) and Ni(2+) uptake. The maximum Ni(2+)-uptake capacity of recombinant strain N1c expressing NixA+MT reached 83.33mgg(-1), higher than 45.45mgg(-1) of recombinant strain N1d expressing NisA+MT. N1c exhibited more effective Ni(2+) accumulation than N1d in the presence of Na(+), Co(2+) and Cd(2+). NiCoTs promoted intracellular Ni(2+) uptake of the recombinant strains. Phosphate groups dominated Ni(2+) binding of wild type Escherichia coli, but carboxyl groups contributed more for N1c and N1d. The result suggested that NixA has a higher specificity in Ni(2+) binding than NisA, and both NiCoTs and MT are important for Ni(2+) bioaccumulation.

Possible use of Serratia marcescens in toxic metal biosorption (removal)

BACKGROUND, AIM AND SCOPE

Metal pollution is a serious problem for environmental safety and programmes of monitoring and bioremediation are needed. Among the processes of bioremediation, the use of microbes to remove and degrade contaminants is considered a biotechnological approach to clean up polluted environments.

AIM

The aim of this study was to evaluate the ability of Serratia marcescens in Pb, Cd and Cr removal and the potential use of these bacteria in toxic metal bioremediation from polluted environments.

METHODS

A short-term study (120 min) was carried out to study the bacterial growth in the presence of sub-inhibitory concentrations of each metal analysed and the kinetics of metal biosorption in S. marcescens strain. In addition, metal influence on the biosynthesis of the red pigment 'prodigiosina' by S. marcescens was monitored.

RESULTS

The results obtained in this study show metals biosorption by S. marcescens (range: 0.0133-0.213 μg/g for Pb; 0.097-0.1853 μg/g for Cd; and 0.105-0.176 μg/g for Cr) and confirm the possible use of this bacterium to realize bioremediation processes, especially for Pb removal, and as a bioindicator of metal pollution.

MrdH, a novel metal resistance determinant of Pseudomonas putida KT2440, is flanked by metal-inducible mobile genetic elements

We report here the identification and characterization of mrdH, a novel chromosomal metal resistance determinant, located in the genomic island 55 of Pseudomonas putida KT2440. It encodes for MrdH, a predicted protein of approximately 40 kDa with a chimeric domain organization derived from the RcnA and RND (for resistance-nodulation-cell division) metal efflux proteins. The metal resistance function of mrdH was identified by the ability to confer nickel resistance upon its complementation into rcnA mutant (a nickel- and cobalt-sensitive mutant) of Escherichia coli. However, the disruption of mrdH in P. putida resulted in an increased sensitivity to cadmium and zinc apart from nickel. Expression studies using quantitative reverse transcription-PCR showed the induction of mrdH by cadmium, nickel, zinc, and cobalt. In association with mrdH, we also identified a conserved hypothetical gene mreA whose encoded protein showed significant homology to NreA and NreA-like proteins. Expression of the mreA gene in rcnA mutant of E. coli enhanced its cadmium and nickel resistance. Transcriptional studies showed that both mrdH and mreA underwent parallel changes in gene expression. The mobile genetic elements Tn4652 and IS1246, flanking mrdH and mreA were found to be induced by cadmium, nickel, and zinc, but not by cobalt. This study is the first report of a single-component metal efflux transporter, mrdH, showing chimeric domain organization, a broad substrate spectrum, and a location amid metal-inducible mobile genetic elements.

Changes in protein expression in Burkholderia vietnamiensis PR1 301 at pH 5 and 7 with and without nickel

Burkholderia vietnamiensis PR1(301) (PR1) exhibits pH-dependent nickel (Ni) tolerance, with lower Ni toxicity observed at pH 5 than at pH 7. The Ni tolerance mechanism in PR1 is currently unknown, and traditional mechanisms of Ni resistance do not appear to be present. Therefore, 2D gel electrophoresis was used to examine changes in protein expression in PR1 with and without Ni (3.4 mM) at pH 5 and 7. Proteins with both a statistically significant and at least a twofold difference in expression level between conditions (pH, Ni) were selected and identified using MALDI-TOF-MS or LC-MS. Results showed increased expression of proteins involved in cell shape and membrane composition at pH 5 compared with pH 7. Scanning electron microscopy indicated elongated cells at pH 5 and 6 compared with pH 7 in the absence of Ni. Fatty acid methyl ester analysis showed a statistically significant difference in the percentages of long- and short-chain fatty acids at pH 5 and 7. These findings suggest that changes in membrane structure and function may be involved in the ability of PR1 to grow at higher concentrations of Ni at pH 5 than at pH 7.

The RcnRA (YohLM) system of Escherichia coli: A connection between nickel, cobalt and iron homeostasis

The transporter RcnA has previously been implicated in Ni(II) and Co(II) detoxification in E. coli probably through efflux. Here we demonstrate that the divergently described rcnA and rcnR gene products constitute a link between nickel, cobalt and iron homeostasis. Deletion of the rcnA gene resulted in increased cellular nickel, cobalt and iron concentrations. Expression of rcnA was induced by Ni(II) or Co(II). Overproduction of rcnR inhibited induction of rcnA by metal cations but RcnR did not bind to the rcnA promoter in vitro. When rcnR or fur, the gene of the global repressor of iron homeostasis, was deleted, expression of rcnA was also induced by iron. The promoter region of rcnA was positive in a Fur titration (FURTA) in vivo assay indicative of Fur binding. Thus, rcnA is part of the Fur regulon of E. coli. The implications of a connection between the homoeostasis of closely related transition metals are discussed.