Resistance to cadmium, cobalt, zinc, and nickel in microbes

Bacterial community composition and function vary with farmland type and soil depth around a mining area

Heavy metal pollution can have adverse impacts on microorganisms, plants and even human health. To date, the impact of heavy metals on bacteria in farmland has yielded poor attention, and there is a paucity of knowledge on the impact of land type on bacteria in mining area with heavy metal pollution. Around a metal-contaminated mining area, two soil depths in three types of farmlands were selected to explore the composition and function of bacteria and their correlations with the types and contents of heavy metals. The compositions and functions of bacterial communities at the three different agricultural sites were disparate to a certain extent. Some metabolic functions of bacterial community in the paddy field were up-regulated compared with those at other site. These results observed around mining area were different from those previously reported in conventional farmlands. In addition, bacterial community composition in the top soils was relatively complex, while in the deep soils it became more unitary and extracellular functional genes got enriched. Meanwhile, heavy metal pollution may stimulate the enrichment of certain bacteria to protect plants from damage. This finding may aid in understanding the indirect effect of metal contamination on plants and thus putting forward feasible strategies for the remediation of metal-contaminated sites. MAIN FINDINGS OF THE WORK: This was the first study to comprehensively explore the influence of heavy metal pollution on the soil bacterial communities and metabolic potentials in different agricultural land types and soil depths around a mining area.

Biocompatible Co-organic Composite Thin Film Deposited by VHF Plasma-Enhanced Atomic Layer Deposition at a Low Temperature

Although metal-organic thin films are required for many biorelated applications, traditional deposition methods have proven challenging in preparing these composite materials. Here, a Co-organic composite thin film was prepared by plasma-enhanced atomic layer deposition (PEALD) with cobaltocene (Co(Cp)2) on polydimethylsiloxane (PDMS), using two very high frequency (VHF) NH3 plasmas (60 and 100 MHz), for use as a tissue culture scaffold. VHF PEALD was employed to reduce the temperature and control the thickness and composition. In the result of the VHF PEALD process, the Young's modulus of the Co-organic composite thin film ranged from 82.0 ± 28.6 to 166.0 ± 15.2 MPa, which is similar to the Young's modulus of soft tissues. In addition, the deposited Co ion on the Co-organic composite thin film was released into the cell culture media under a nontoxic level for the biological environment. The proliferation of both L929, the mouse fibroblast cell line, and C2C12, the mouse myoblast cell line, increased to 164.9 ± 23.4% during 7 days of incubation. Here, this novel bioactive Co-organic composite thin film on an elastic PDMS substrate enhanced the proliferation of L929 and C2C12 cell lines, thereby expanding the application range of VHF PEALD in biological fields.

The genes mgtE and spoVG are involved in zinc tolerance of Staphylococcus aureus

Metals are essential for all living organisms, but the type of metal and its concentration determines its action. Even low concentrations of metals may have toxic effects on organisms and therefore exhibit antimicrobial activities. In this study, we investigate the evolutionary adaptation processes of Staphylococcus aureus to metals and common genes for metal tolerance. Laboratory and clinical isolates were treated with manganese, cobalt, zinc, or nickel metal salts to generate growth-adapted mutants. After growth in medium supplemented with zinc, whole-genome sequencing identified, among others, two genes, mgtE (SAUSA300_0910), a putative magnesium transporter and spoVG (SAUSA300_0475), a global transcriptional regulator, as hot spots for stress-induced single-nucleotide polymorphisms (SNPs). SNPs in mgtE were also detected in mutants treated with high levels of cobalt or nickel salts. To investigate the effect of these genes on metal tolerance, deletion mutants and complementation strains in an S. aureus USA300 LAC* laboratory strain were generated. Both, the mgtE and spoVG deletion strains were more tolerant to cobalt, manganese, and zinc. The mgtE mutant was also more tolerant to nickel exposure. Inductively coupled plasma mass spectrometry analysis demonstrated that the mgtE deletion mutant accumulated less intracellular zinc than the wild type, explaining increased tolerance. From these results, we conclude that mgtE gene inactivation increases zinc tolerance presumably due to reduced uptake of zinc. For the SpoVG mutant, no direct effect on the intracellular zinc concentration was detected, indicating toward different pathways to increase tolerance. Importantly, inactivation of these genes offers a growth advantage in environments containing certain metals, pointing toward a common tolerance mechanism.

IMPORTANCE

Staphylococcus aureus is an opportunistic pathogen causing tremendous public health burden and high mortality in invasive infections. Treatment is becoming increasingly difficult due to antimicrobial resistances. The use of metals in animal husbandry and aquaculture to reduce bacterial growth and subsequent acquisition of metal resistances has been shown to co-select for antimicrobial resistance. Therefore, understanding adaptive mechanisms that help S. aureus to survive metal exposure is essential. Using a screening approach, we were able to identify two genes encoding the transporter MgtE and the transcriptional regulator SpoVG, which conferred increased tolerance to specific metals such as zinc when inactivated. Further testing showed that the deletion of mgtE leads to reduced intracellular zinc levels, suggesting a role in zinc uptake. The accumulation of mutations in these genes when exposed to other metals suggests that inactivation of these genes could be a common mechanism for intrinsic tolerance to certain metals.

Novel insights into the co-selection of metal-driven antibiotic resistance in bacteria: a study of arsenic and antibiotic co-exposure

The simultaneous development of antibiotic resistance in bacteria due to metal exposure poses a significant threat to the environment and human health. This study explored how exposure to both arsenic and antibiotics affects the ability of an arsenite oxidizer, Achromobacter xylosoxidans CAW4, to transform arsenite and its antibiotic resistance patterns. The bacterium was isolated from arsenic-contaminated groundwater in the Chandpur district of Bangladesh. We determined the minimum inhibitory concentration (MIC) of arsenite, cefotaxime, and tetracycline for A. xylosoxidans CAW4, demonstrating a multidrug resistance (MDR) trait. Following this determination, we aimed to mimic an environment where A. xylosoxidans CAW4 was exposed to both arsenite and antibiotics. We enabled the strain to grow in sub-MIC concentrations of 1 mM arsenite, 40 µg/mL cefotaxime, and 20 µg/mL tetracycline. The expression dynamics of the arsenite oxidase (aioA) gene in the presence or absence of antibiotics were analyzed. The findings indicated that simultaneous exposure to arsenite and antibiotics adversely affected the bacteria's capacity to metabolize arsenic. However, when arsenite was present in antibiotics-containing media, it promoted bacterial growth. The study observed a global downregulation of the aioA gene in arsenic-antibiotic conditions, indicating the possibility of increased susceptibility through co-resistance across the entire bacterial population of the environment. This study interprets that bacterial arsenic-metabolizing ability can rescue the bacteria from antibiotic stress, further disseminating environmental cross-resistance. Therefore, the co-selection of metal-driven antibiotic resistance in bacteria highlights the need for effective measures to address this emerging threat to human health and the environment.

Eco-friendly management of Meloidogyne incognita in cadmium-contaminated soil by using nematophagous fungus Purpureocillium lavendulum YMF1.683: Efficacy and mechanism

Root-knot nematodes (RKNs) are distributed globally, including in agricultural fields contaminated by heavy metals (HM), and can cause serious crop damages. Having a method that could control RKNs in HM-contaminated soil while limit HM accumulation in crops could provide significant benefits to both farmers and consumers. In this study, we showed that the nematophagous fungus Purpureocillium lavendulum YMF1.683 exhibited a high nematocidal activity against the RKN Meloidogyne incognita and a high tolerance to CdCl2. Comparing to the P. lavendulum YMF1.838 which showed low tolerance to Cd2+, strain YMF1.683 effectively suppressed M. incognita infection and significantly reduced the Cd2+ uptake in tomato root and fruit in soils contaminated by 100 mg/kg Cd2+. Transcriptome analyses and validation of gene expression by RT-PCR revealed that the mechanisms contributed to high Cd-resistance in YMF1.683 mainly included activating autophagy pathway, increasing exosome secretion of Cd2+, and activating antioxidation systems. The exosomal secretory inhibitor GW4869 reduced the tolerance of YMF1.683 to Cd2+, which firstly demonstrated that fungal exosome was involved in HM tolerance. The up-regulation of glutathione synthesis pathway, increasing enzyme activities of both catalase and superoxide dismutase also played important roles in Cd2+ tolerance of YMF1.683. In Cd2+-contaminated soil, YMF1.683 limited Cd2+-uptake in tomato by up-regulating the genes of ABCC family in favor of HM sequestration in plant, and down-regulating the genes of ZIP, HMA, NRAMP, YSL families associated with HM absorption, transport, and uptake in plant. Our results demonstrated that YMF1.683 could be a promising bio-agent in eco-friendly management of M. incognita in Cd2+ contaminated soils.

Adaptability of sulfur-disproportionating bacteria for mine water remediation under the pressures of heavy metal ions and high sulfate content

Biological sulfide production processes mediated by sulfate/sulfur reduction have gained attention for metal removal from industrial wastewater (e.g., mine water (MW) and metallurgical wastewater) via forming insoluble metal sulfides. However, these processes often necessitate the addition of external organic compounds as electron donors, which poses a constraint on the broad application of this technology. A recent proof of concept study reported that microbial sulfur disproportionation (SD) produced sulfide with no demand for organics, which could achieve more cost-benefit MW treatment against the above-mentioned processes. However, the resistance of SD bioprocess to different metals and high sulfate content in MW remains mysterious, which may substantially affect the practical applicability of such process. In this study, the sulfur-disproportionating bacteria (SDB)-dominated consortium was enriched from a previously established SD-driven bioreactor, in which Dissulfurimicrobium sp. with a relative abundance of 39.9 % was the predominated SDB. When exposed to the real pretreated acidic MW after the pretreatment process of pH amelioration, the sulfur-disproportionating activity remained active, and metals were effectively removed from the MW. Metal tolerance assays further demonstrated that the consortium had a good tolerance to different metal ions (i.e., Pb2+, Cu2+, Ni2+, Mn2+, Zn2+), especially for Mn2+ with a concentration of approximately 20 mg/L. It suggested the robustness of Dissulfurimicrobium sp. likely due to the presence of genes encoding for the enzymes associated with metal(loid) resistance/uptake. Additionally, although high sulfate content resulted in a slight inhibition on the sulfur-disproportionating activity, the consortium still achieved sulfide production rates of 27.3 mg S/g VSS-d on average under an environmentally relevant sulfate level (i.e., 1100 mg S/L), which is comparable to those reported in sulfate reduction. Taken together, these findings imply that SDB could ensure sustainable MW treatment in a more cost-effective and organic-free way.

Discriminating Susceptibility of Xanthine Oxidoreductase Family to Metals

The xanthine oxidoreductase (XOR) family are metal-containing enzymes that use the molybdenum cofactor (Moco), 2Fe-2S clusters, and flavin adenine dinucleotide (FAD) for their catalytic activity. This large molybdoenzyme family includes xanthine, aldehyde, and CO dehydrogenases. XORs are widely distributed from bacteria to humans due to their key roles in the catabolism of purines, aldehydes, drugs, and xenobiotics, as well as interconversions between CO and CO2. Assessing the effect of excess metals on the Rubrivivax gelatinosus bacterium, we found that exposure to copper (Cu) or cadmium (Cd) caused a dramatic decrease in the activity of a high-molecular-weight soluble complex exhibiting nitroblue tetrazolium reductase activity. Mass spectrometry and genetic analyses showed that the complex corresponds to a putative CO dehydrogenase (pCOD). Using mutants that accumulate either Cu+ or Cd2+ in the cytoplasm, we show that Cu+ or Cd2+ is a potent inhibitor of XORs (pCOD and the xanthine dehydrogenase [XDH]) in vivo. This is the first in vivo demonstration that Cu+ affects Moco-containing enzymes. The specific inhibitory effect of these compounds on the XOR activity is further supported in vitro by direct addition of competing metals to protein extracts. Moreover, emphasis is given on the inhibitory effect of Cu on bovine XOR, showing that the XOR family could be a common target of Cu. Given the conservation of XOR structure and function across the tree of life, we anticipate that our findings could be transferable to other XORs and organisms. IMPORTANCE The high toxicity of Cu, Cd, Pb, As, and other metals arises from their ability to cross membranes and target metalloenzymes in the cytoplasm. Identifying these targets provides insights into the toxicity mechanisms. The vulnerability of metalloenzymes arises from the accessibility of their cofactors to ions. Accordingly, many enzymes whose cofactors are solvent exposed are likely to be targets of competing metals. Here, we describe for the first time, with in vivo and in vitro experiments, a direct effect of excess Cu on the xanthine oxidoreductase family (XOR/XDH/pCOD). We show that toxic metal affects these Moco enzymes, and we suggest that access to the Moco center by Cu ions could explain the Cu inhibition of XORs in living organisms. Human XOR activity is associated with hyperuricemia, xanthinuria, gout arthritis, and other diseases. Our findings in vivo highlight XOR as a Cu target and thus support the potential use of Cu in metal-based therapeutics against these diseases.

Molecular Characterization of Indigenous Rhizobia from Kenyan Soils Nodulating with Common Beans

Kenya is the seventh most prominent producer of common beans globally and the second leading producer in East Africa. However, the annual national productivity is low due to insufficient quantities of vital nutrients and nitrogen in the soils. Rhizobia are symbiotic bacteria that fix nitrogen through their interaction with leguminous plants. Nevertheless, inoculating beans with commercial rhizobia inoculants results in sparse nodulation and low nitrogen supply to the host plants because these strains are poorly adapted to the local soils. Several studies describe native rhizobia with much better symbiotic capabilities than commercial strains, but only a few have conducted field studies. This study aimed to test the competence of new rhizobia strains that we isolated from Western Kenya soils and for which the symbiotic efficiency was successfully determined in greenhouse experiments. Furthermore, we present and analyze the whole-genome sequence for a promising candidate for agricultural application, which has high nitrogen fixation features and promotes common bean yields in field studies. Plants inoculated with the rhizobial isolate S3 or with a consortium of local isolates (COMB), including S3, produced a significantly higher number of seeds and seed dry weight when compared to uninoculated control plants at two study sites. The performance of plants inoculated with commercial isolate CIAT899 was not significantly different from uninoculated plants (p > 0.05), indicating tight competition from native rhizobia for nodule occupancy. Pangenome analysis and the overall genome-related indices showed that S3 is a member of R. phaseoli. However, synteny analysis revealed significant differences in the gene order, orientation, and copy numbers between S3 and the reference R. phaseoli. Isolate S3 is phylogenomically similar to R. phaseoli. However, it has undergone significant genome rearrangements (global mutagenesis) to adapt to harsh conditions in Kenyan soils. Its high nitrogen fixation ability shows optimal adaptation to Kenyan soils, and the strain can potentially replace nitrogenous fertilizer application. We recommend that extensive fieldwork in other parts of the country over a period of five years be performed on S3 to check on how the yield changes with varying whether conditions.

Sequestration of cobalt and nickel by biofilm forming bacteria isolated from spent nuclear fuel pool water

In the current study, six bacterial types, isolated from spent nuclear fuel (SNF) pool facility, were investigated for their ability to sequester heavy metals (cobalt and nickel). Biofilm formation by the six bacterial isolates, viz., Bacillus subtilis, Staphylococcus species, Staphylococcus arlettae, Staphylococcus epidermidis, Staphylococcus auricularis, and Chryseobacterium gleum, were assayed, and they were found to have significant biofilm forming property. Their biofilms were characterised using confocal scanning laser microscopy, and their potential to accumulate Co²⁺ and Ni²⁺ from bulk solutions was analysed with respect to time. A comparative assessment of bioaccumulation capacity was done using biofilms, planktonic cells, and live vs dead cells. The strains accumulated Co²⁺ and Ni²⁺ in the range of 4 × 10^-4 to 1 × 10^-5 g/mg of cell biomass. It is interesting to note that dead biomass also showed significant removal of the two metal ions, suggesting an alternative process for metal removal. This study suggests that hostile environments can be a repertoire of putative bacterial species with potential heavy metals and other contaminants remediation properties.

Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India

Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.

Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site

Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.

Gradient Magnetic Field Accelerates Division of E. coli Nissle 1917

Cell-cycle progression is regulated by numerous intricate endogenous mechanisms, among which intracellular forces and protein motors are central players. Although it seems unlikely that it is possible to speed up this molecular machinery by applying tiny external forces to the cell, we show that magnetic forcing of magnetosensitive bacteria reduces the duration of the mitotic phase. In such bacteria, the coupling of the cell cycle to the splitting of chains of biogenic magnetic nanoparticles (BMNs) provides a biological realization of such forcing. Using a static gradient magnetic field of a special spatial configuration, in probiotic bacteria E. coli Nissle 1917, we shortened the duration of the mitotic phase and thereby accelerated cell division. Thus, focused magnetic gradient forces exerted on the BMN chains allowed us to intervene in the processes of division and growth of bacteria. The proposed magnetic-based cell division regulation strategy can improve the efficiency of microbial cell factories and medical applications of magnetosensitive bacteria.

Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

Background

The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4.

Results

Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms.

Conclusion

The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08738-8.

Genomic analysis of Acinetobacter pittii CEP14 reveals its extensive biodegradation capabilities, including cometabolic degradation of cis-1,2-dichloroethene

Halogenated organic compounds are naturally occurring in subsurface environments; however, accumulation of the degradative intermediate cis-1,2-dichloroethene (cDCE) at soil and groundwater sites contaminated with xenobiotic chlorinated ethenes is a global environmental and public health issue. Identifying microorganisms capable of cDCE degradation in these environments is of interest because of their potential application to bioremediation techniques. In this study, we sequenced, assembled, and analyzed the complete genome of Acinetobacter pittii CEP14, a strain isolated from chloroethene-contaminated groundwater, that has demonstrated the ability for aerobic cometabolic degradation of cDCE in the presence of n-hexane, phenol, and toluene. The A. pittii CEP14 genome consists of a 3.93 Mbp-long chromosome (GenBank accession no. CP084921) with a GC content of 38.9% and three plasmids (GenBank accession no. CP084922, CP084923, and CP084924). Gene function was assigned to 83.4% of the 3,930 coding DNA sequences. Functional annotation of the genome revealed that the CEP14 strain possessed all genetic elements to mediate the degradation of a range of aliphatic and aromatic compounds, including n-hexane and phenol. In addition, it harbors gene clusters involved in cytosol detoxification and oxidative stress resistance, which could play a role in the mitigation of toxic chemical intermediates that can arise during the degradation of cDCE. Gene clusters for heavy metal and antibiotic resistance were also identified in the genome of CEP14. These results suggest that CEP14 may be a versatile degrader of xenobiotic compounds and well-adapted to polluted environments, where a combination of heavy metal and organic compound pollution is often found.

Zinc Essentiality, Toxicity, and Its Bacterial Bioremediation: A Comprehensive Insight

Zinc (Zn) is one of the most abundantly found heavy metals in the Earth's crust and is reported to be an essential trace metal required for the growth of living beings, with it being a cofactor of major proteins, and mediating the regulation of several immunomodulatory functions. However, its essentiality also runs parallel to its toxicity, which is induced through various anthropogenic sources, constant exposure to polluted sites, and other natural phenomena. The bioavailability of Zn is attributable to various vegetables, beef, and dairy products, which are a good source of Zn for safe consumption by humans. However, conditions of Zn toxicity can also occur through the overdosage of Zn supplements, which is increasing at an alarming rate attributing to lack of awareness. Though Zn toxicity in humans is a treatable and non-life-threatening condition, several symptoms cause distress to human activities and lifestyle, including fever, breathing difficulty, nausea, chest pain, and cough. In the environment, Zn is generally found in soil and water bodies, where it is introduced through the action of weathering, and release of industrial effluents, respectively. Excessive levels of Zn in these sources can alter soil and aquatic microbial diversity, and can thus affect the bioavailability and absorption of other metals as well. Several Gram-positive and -negative species, such as Bacillus sp., Staphylococcus sp., Streptococcus sp., and Escherichia coli, Pseudomonas sp., Klebsiella sp., and Enterobacter sp., respectively, have been reported to be promising agents of Zn bioremediation. This review intends to present an overview of Zn and its properties, uses, bioavailability, toxicity, as well as the major mechanisms involved in its bioremediation from polluted soil and wastewaters.

Assessment of Metal Accumulation by Arthrospira platensis and Its Adaptation to Iterative Action of Nickel Mono- and Polymetallic Synthetic Effluents

Cyanobacteria-mediated wastewater remediation is an economical, efficient, and eco-friendly technology. The present work deals with the bioaccumulation performance of Arthrospira platensis (Spirulina) grown for four cycles in a medium containing nickel mono- and polymetallic synthetic effluents. The metal uptake by spirulina biomass was evaluated using neutron activation analysis. The effects of effluents on biomass production, protein, and phycobiliprotein content were assessed. Metal accumulation in the biomass depended on the effluent composition and metal ion concentrations. Nickel accumulation in the biomass was directly proportional to its concentration in effluents, and maximum uptake (1310 mg/kg) was attained in the Ni/Cr/Fe system. In the same system, biomass accumulated 110 times more chromium and 4.7 times more iron than control. The highest accumulation of copper (2870 mg/kg) was achieved in the Ni/Cu/Zn/Mo system and zinc (1860 mg/kg)—in the Ni/Cu/Zn/Sr system. In biomass grown in the media loaded with nickel and also chromium, iron, copper, strontium, zinc, and molybdenum, a decrease in productivity (on average by 10%) during the first cycle of cultivation and moderate reduction of protein content (by 15–27%) was observed. The presence of metals in the cultivation media inhibited phycobiliprotein synthesis, especially of phycocyanin, and promoted the synthesis of allophycocyanin. The maximum reduction of phycocyanin content was 77%, and the increase of allophycocyanin content—by 45%. Arthrospira platensis may be deemed as bioremediation of nickel-polluted wastewaters of complex composition.

Soil ridge cultivation maintains grain As and Cd at low levels and inhibits As methylation by changing arsM-harboring bacterial communities in paddy soils

The simultaneous mitigation of toxic arsenic (As) and cadmium (Cd) in rice grain remains a global challenge. The over-accumulation of husk dimethylarsinic acid (DMAs) induces the rice straight-head disease, which threatens rice production worldwide. In this study, we investigated various soil ridge height treatments with Eh ranging from - 225-87 mV and pH ranging from 6.3 to 4.1. Soil ridge cultivation can maintain grain As and Cd at low levels for slightly co-contaminated paddy soils, especially when the ridge height is 11 cm (Eh of 43 mV and pH of 4.6), where grain inorganic As decreased-at maximum-by 48% and DMAs by 55%. Grain Cd (0.14 mg kg^-1) increased but was still below the limit (0.2 mg kg^-1) in China, and the cost of ridging is acceptable. There were definite correlations among porewater As, Cd, Fe, S, and Mn contents across various Eh and pH values. Soil ridge cultivation significantly (P < 0.05) diminished the copy number of As-reducing (harboring arsC and arrA), As-methylating (harboring arsM), and sulfate-reducing (harboring dsrA) bacteria. Moreover, soil ridge cultivation shifted the arsM-harboring microbiota. In response to ridge height increase, the abundance of the bacterial biomarker phylum Euryachaeota declined and the families Halorubrum and Planctomyces were gradually replaced by Sandaracinus in paddy soil.

Sustainable approaches for nickel removal from wastewater using bacterial biomass and nanocomposite adsorbents: A review

In this article, the nickel (Ni²⁺) ions removal from the wastewater is reviewed. Adsorption is widely used to remove Ni²⁺ ions from waters and wastewaters. The usage of biomass is becoming more common for Ni²⁺ ions removal, while the commercial activated carbon from different agriculture wastes is preferred as an adsorbent for Ni²⁺ ion removal. The present review aimed to organise the available information regarding sustainable approaches for Ni²⁺ ions removal from water and wastewaters. These include adsorption by nanoparticles, bacterial biomass, and activated carbon from agriculture wastes, since they are the most common used for the Ni²⁺ ions removal. The bacterial and agricultural waste adsorbents exhibited high efficiency with a renewable source of biomass for Ni²⁺ ion removal. The biosorption capacity of the Ni²⁺ ions by the bacterial biomass range from 5.7 to 556 mg/g, while ranging from 5.8 to 150 mg/g by the activated carbon from different organic materials. The biosorption capacity of the nanocomposite adsorbents might reach to 400 mg/g. It appeared that the elimination of nickel ions need a selective biomass adsorbent such as the tolerant bacterial cells biomass which acts as a store for Ni²⁺ ion accumulations as a results for the active and passive transportation of the Ni²⁺ ions through the bacterial cell membrane.

Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria

Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.

Bacterial strains found in the soils of a municipal solid waste dumping site facilitated phosphate solubilization along with cadmium remediation

Phosphate solubilizing bacteria (PSB) that can withstand high cadmium (Cd) stress is a desired combination for bioremediation. This study evaluated the Cd bioremediation potential of four PSB strains isolated from the contaminated soils of a municipal solid waste (MSW) discarding site (Guwahati, India). PSB strains were cultured in Pikovskaya (PVK) media, which led to higher acid phosphatase (ACP) activity and the release of organic acid. Optical density (OD) measurements were performed to determine the growth pattern of PSB; furthermore, Cd uptake by PSB was evaluated using infrared spectroscopy (IR) and X-Ray Diffraction (XRD) analyses. The 16S rRNA taxonomic analysis revealed that all the four promising PSB strains belonged to either Bacillus sp. or Enterobacter sp. One strain (SM_SS8) demonstrated higher tolerance towards Cd (up to 100 mg L^-1). Flow cytometry analysis revealed 70.92%, 46.93% and 20.4% viability of SM_SS8 in 10, 50 and 100 mg L^-1, respectively in PVK media containing Cd. This study has therefore substantiated the bioremediation of Cd from polluted soil by the PSB isolates. Thus, experimental results revealed a potential combo benefit, phosphate solubilization along with Cd remediation.

Transcriptional and Translational Responsiveness of the Neisseria gonorrhoeae Type IV Secretion System to Conditions of Host Infections

The type IV secretion system of Neisseria gonorrhoeae translocates single-stranded DNA into the extracellular space, facilitating horizontal gene transfer and initiating biofilm formation. Expression of this system has been observed to be low under laboratory conditions, and multiple levels of regulation have been identified. We used a translational fusion of lacZ to traD, the gene for the type IV secretion system coupling protein, to screen for increased type IV secretion system expression. We identified several physiologically relevant conditions, including surface adherence, decreased manganese or iron, and increased zinc or copper, which increase gonococcal type IV secretion system protein levels through transcriptional and/or translational mechanisms. These metal treatments are reminiscent of the conditions in the macrophage phagosome. The ferric uptake regulator, Fur, was found to repress traD transcript levels but to also have a second role, acting to allow TraD protein levels to increase only in the absence of iron. To better understand type IV secretion system regulation during infection, we examined transcriptomic data from active urethral infection samples from five men. The data demonstrated differential expression of 20 of 21 type IV secretion system genes during infection, indicating upregulation of genes necessary for DNA secretion during host infection.

Soil bacteria, genes, and metabolites stimulated during sulfur cycling and cadmium mobilization under sodium sulfate stress

Sodium sulfate stress is known to improve cadmium (Cd) mobilization in soil and microbial sulfur oxidation, Cd resistance, and the accumulation of stress tolerance-associated metabolites has been correlated with increased soil Cd availability and toxicity. In this study, aerobic soil microcosms with Cd-contamination were stimulated with sodium sulfate to investigate its effects on soil microbial community structure, functional genes, and associated metabolite profiles. Metagenomic analysis revealed that sulfur oxidizing and Cd-resistant bacteria carried gene clusters encoding sox, dsr, and sqr genes, and znt, czc, and cad genes, respectively. Exposure to sodium sulfate resulted in the reprogram of soil metabolites. In particular, intensification of sulfur metabolism triggered an up-regulation in the tricarboxylic acid (TCA) cycle, which promoted the secretion of carboxylic acids and their precursors by soil bacteria. The accumulation of organic acids induced in response to high sodium sulfate dosages potentially drove an observed increase in Cd mobility. Pseudomonas and Erythrobacter spp. exhibited a high capacity for adaptation to heavy metal- or sulfur-induced stress, evident by an increased abundance of genes and metabolites for sulfur cycling and Cd resistance. These results provide valuable insights towards understanding the microbial mechanisms of sulfur transformation and Cd dissolution under saline stress.

The Influencing Factors of Bacterial Resistance Related to Livestock Farm: Sources and Mechanisms

Bacterial resistance is a complex scientific issue. To manage this issue, we need to deeply understand the influencing factors and mechanisms. Based on the background of livestock husbandry, this paper reviews the factors that affect the acquisition of bacterial resistance. Meanwhile, the resistance mechanism is also discussed. “Survival of the fittest” is the result of genetic plasticity of bacterial pathogens, which brings about specific response, such as producing adaptive mutation, gaining genetic material or changing gene expression. To a large extent, bacterial populations acquire resistance genes directly caused by the selective pressure of antibiotics. However, mobile resistance genes may be co-selected by other existing substances (such as heavy metals and biocides) without direct selection pressure from antibiotics. This is because the same mobile genetic elements as antibiotic resistance genes can be co-located by the resistance determinants of some of these compounds. Furthermore, environmental factors are a source of resistance gene acquisition. Here, we describe some of the key measures that should be taken to mitigate the risk of antibiotic resistance. We call on the relevant governments or organizations around the world to formulate and improve the monitoring policies of antibiotic resistance, strengthen the supervision, strengthen the international cooperation and exchange, and curb the emergence and spread of drug-resistant strains.

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Current knowledge about the microbial communities that occur in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials used to remove dissolved heavy metals from two different SQIDs were analyzed to determine microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated with intl1 and with microbial genera. The filter media itself was enriched with Intl1 gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.

Elucidation of crude siderophore extracts from supernatants of Pseudomonas sp. ZnCd2003 cultivated in nutrient broth supplemented with Zn, Cd, and Zn plus Cd

This research aimed to study siderophores secreted from Pseudomonas sp. PDMZnCd2003, a Zn/Cd tolerant bacterium. The effects of Zn and/or Cd stress were examined in nutrient broth to achieve the actual environmental conditions. Acid and alkali supernatants and liquid-liquid extraction with ethyl acetate and butanol were carried out to obtain crude extracts containing different amounts of the metals. The bacterial growth, UV-visible spectra of the supernatants and siderophore production indicated that the production of siderophores tended to be linked to primary metabolites. Pyocyanin was produced in all treatments, while pyoverdine was induced by stress from the metals, especially Cd. FT-IR spectra showed C=O groups and sulfur functional groups that were involved in binding with the metals. LC-MS revealed that pyocyanin, 1-hydroxy phenazine, pyoverdine, and pyochelin were present in the crude extracts. S K-edge XANES spectra showed that the main sulfur species in the extracts were the reduced forms of sulfide, thiol, and disulfide, and their oxidation states were affected by coordination with Zn and/or Cd. In addition, Zn K-edge EXAFS spectra and Cd K-edge EXAFS spectra presented Zn-O and Cd-O as coordination in the first shell, in case the extracts contained less metal. Although the mix O/S ligands had chelation bonding with Zn and Cd in the other extracts. For the role of S groups in pyochelin binding with the metals, this was the first report. The results of these experiments could be extended to Pseudomonas that respond to metal contaminated environments.

Insights into the effects of Zn exposure on the fate of tylosin resistance genes and dynamics of microbial community during co-composting with tylosin fermentation dregs and swine manure

Though heavy metals are widely reported to induce antibiotic resistance propagation, how antibiotic resistance changes in response to heavy metal abundances remains unclearly. In this study, the tylosin fermentation dregs (TFDs) and swine manure co-composting process amended with two exposure levels of heavy metal Zn were performed. Results showed that the bioavailable Zn contents decreased 2.6-fold averagely, and the removal percentage of total tylosin resistance genes was around 23.5% after the co-composting completed. Furthermore, the tylosin resistance genes and some generic bacteria may exhibited a hormetic-like dose-response with the high-dosage inhibition and low dosage stimulation induced by bioavailable Zn contents during the co-composting process, which represented a beneficial aspect of adaptive responses to harmful environmental stimuli. This study provided a comprehensive understanding and predicted risk assessment for the Zn-contaminate solid wastes deposal and suggested that low levels of Zn or other heavy metals should receive more attention for their potential to the induction of resistance bacteria and propagation of antibiotic resistance genes.

Critical Review: Propensity of Premise Plumbing Pipe Materials to Enhance or Diminish Growth of Legionella and Other Opportunistic Pathogens

Growth of Legionella pneumophila and other opportunistic pathogens (OPs) in drinking water premise plumbing poses an increasing public health concern. Premise plumbing is constructed of a variety of materials, creating complex environments that vary chemically, microbiologically, spatially, and temporally in a manner likely to influence survival and growth of OPs. Here we systematically review the literature to critically examine the varied effects of common metallic (copper, iron) and plastic (PVC, cross-linked polyethylene (PEX)) pipe materials on factors influencing OP growth in drinking water, including nutrient availability, disinfectant levels, and the composition of the broader microbiome. Plastic pipes can leach organic carbon, but demonstrate a lower disinfectant demand and fewer water chemistry interactions. Iron pipes may provide OPs with nutrients directly or indirectly, exhibiting a high disinfectant demand and potential to form scales with high surface areas suitable for biofilm colonization. While copper pipes are known for their antimicrobial properties, evidence of their efficacy for OP control is inconsistent. Under some circumstances, copper's interactions with premise plumbing water chemistry and resident microbes can encourage growth of OPs. Plumbing design, configuration, and operation can be manipulated to control such interactions and health outcomes. Influences of pipe materials on OP physiology should also be considered, including the possibility of influencing virulence and antibiotic resistance. In conclusion, all known pipe materials have a potential to either stimulate or inhibit OP growth, depending on the circumstances. This review delineates some of these circumstances and informs future research and guidance towards effective deployment of pipe materials for control of OPs.

A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated Environment

The use of heavy metals in economic and social development can create an accumulation of toxic waste in the environment. High concentrations of heavy metals can damage human and animal health, lead to the development of antibiotic resistance, and possibly change in bovine microbiota. It is important to investigate the influence of heavy metals in food systems to determine potential harmful effects environmental heavy metal contamination on human health. Because of a mining dam rupture, 43 million cubic meters of iron ore waste flowed into the Doce river basin surrounding Mariana City, Brazil, in 2015. Following this environmental disaster, we investigated the consequences of long-term exposure to contaminated drinking water on the microbiome and resistome of dairy cattle. We identified bacterial antimicrobial resistance (AMR) genes in the feces, rumen fluid, and nasopharynx of 16 dairy cattle 4 years after the environmental disaster. Cattle had been continuously exposed to heavy metal contaminated water until sample collection (A) and compared them to analogous samples from 16 dairy cattle in an unaffected farm, 356 km away (B). The microbiome and resistome of farm A and farm B differed in many aspects. The distribution of genes present in the cattle's nasopharynx, rumen, and feces conferring AMR was highly heterogeneous, and most genes were present in only a few samples. The relative abundance and prevalence (presence/absence) of AMR genes were higher in farm A than in farm B. Samples from farm A had a higher prevalence (presence) of genes conferring resistance to multiple drugs, metals, biocides, and multi-compound resistance. Fecal samples had a higher relative abundance of AMR genes, followed by rumen fluid samples, and the nasopharynx had the lowest relative abundance of AMR genes detected. Metagenome functional annotation suggested that selective pressures of heavy metal exposure potentially skewed pathway diversity toward fewer, more specialized functions. This is the first study that evaluates the consequences of a Brazilian environmental accident with mining ore dam failure in the microbiome of dairy cows. Our findings suggest that the long-term persistence of heavy metals in the environment may result in differences in the microbiota and enrichment of antimicrobial-resistant bacteria. Our results also suggest that AMR genes are most readily detected in fecal samples compared to rumen and nasopharyngeal samples which had relatively lower bacterial read counts. Since heavy metal contamination has an effect on the animal microbiome, environmental management is warranted to protect the food system from hazardous consequences.

Plant Growth-Promoting Rhizobacteria Isolated from Degraded Habitat Enhance Drought Tolerance of Acacia (Acacia abyssinica Hochst. ex Benth.) Seedlings

Drought stress (DS) is the most impacting global phenomenon affecting the ecological balance of a particular habitat. The search for potential plant growth-promoting rhizobacteria (PGPR) capable of enhancing plant tolerance to drought stress is needed. Thus, this study was initiated to evaluate the effect of inoculating Acacia abyssinica seedlings with PGPR isolated from rhizosphere soil of Ethiopia to enhance DS tolerance. The strains were selected based on in vitro assays associated with tolerance to drought and other beneficial traits such as salinity, acidity, temperature, heavy metal tolerances, biofilm formation, and exopolysaccharide (EPS) production. The strains with the best DS tolerance ability were selected for the greenhouse trials with acacia plants. The results indicate that out of 73 strains, 10 (14%) were completely tolerant to 40% polyethylene glycol. Moreover, 37% of the strains were strong biofilm producers, while 66 (90.41%) were EPS producers with a better production in the medium containing sucrose at 28 ± 2°C and pH 7 ± 0.2. Strains PS-16 and RS-79 showed tolerance to 11% NaCl. All the strains were able to grow in wider ranges of pH (4–10) and temperature (15–45°C) and had high tolerance to heavy metals. The inoculated bacterial strains significantly (p ≤ 0.05) increased root and shoot length and dry biomass of acacia plants. One of the strains identified as P. fluorescens strain FB-49 was outstanding in enhancing DS tolerance compared to the single inoculants and comparable to consortia. Stress-tolerant PGPR could be used to enhance acacia DS tolerance after testing other phytobeneficial traits.

Evaluating the protection of bacteria from extreme Cd (II) stress by P-enriched biochar

Cadmium cations (Cd²⁺) are extremely toxic to organisms, which limits the remediation of Cd by microorganisms. This study investigated the feasibility of applying biochar to protect bacteria from extreme Cd²⁺ stress (1000 mg/L). An alkaline biochar (RB) and a slightly acidic biochar (SB) were selected. SB revealed a higher Cd²⁺ removal than RB (15.5% vs. 4.8%) due to its high surface area. Addition of Enterobacter sp. induced formation of Cd phosphate and carbonate on both SB and RB surface. However, Cd²⁺ removal by RB enhanced more evidently than SB (78.9% vs. 30.2%) due to the substantial microbial regulation and surficial alkalinity. Thermogravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS) and geochemical modeling (GWB) all confirmed that the formation of stable Cd phosphate on RB was superior to that in SB. These biomineralization, together with biochar pore structure, protect bacterial cells from Cd stress. Moreover, the alkalinity of biochar promoted the formation of carbonate, which strengthened the decline of Cd²⁺ toxicity. The protection by RB was also confirmed by the intense microbial respiration and biomass (PLFA). Furthermore, this protection induced a positive feedback between P-abundant biochar and Enterobacter sp.: biochar provides P source (the most common limiting nutrient) to support microbial growth; bacteria secrete more organic acids to drive P release. This study therefore elucidated the protection of bacteria by P-enriched biochar based on both physic-chemical and microbial insights.

An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25

BACKGROUND

Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd²⁺ resistance.

RESULTS

In this study, we isolated two different Cd²⁺ resistance Bacillus sp. strains, Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25, which could be grown in the presence of Cd²⁺ at concentration up to 0.3 mM and 0.8 mM, respectively. According to the genomic sequencing, transcriptome analysis under cadmium stress, and other related experiments, a gene cluster in plasmid p25 was found to be a major contributor to Cd²⁺ resistance in B. marisflavi 151-25. The cluster in p25 contained orf4802 and orf4803 which encodes an ATPase transporter and a transcriptional regulator protein, respectively. Although 151-6 has much lower Cd²⁺ resistance than 151-25, they contained similar gene cluster, but in different locations. A gene cluster on the chromosome containing orf4111, orf4112 and orf4113, which encodes an ATPase transporter, a cadmium efflux system accessory protein and a cadmium resistance protein, respectively, was found to play a major role on the Cd²⁺ resistance for B. vietamensis 151-6.

CONCLUSIONS

This work described cadmium resistance mechanisms in newly isolated Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. Based on homologies to the cad system (CadA-CadC) in Staphylococcus aureus and analysis of transcriptome under Cd²⁺ induction, we inferred that the mechanisms of cadmium resistance in B. marisflavi 151-25 was as same as the cad system in S. aureus. Although Bacillus vietamensis 151-6 also had the similar gene cluster to B. marisflavi 151-25 and S. aureus, its transcriptional regulatory mechanism of cadmium resistance was not same. This study explored the cadmium resistance mechanism for B. vietamensis 151-6 and B. marisflavi 151-25 and has expanded our understanding of the biological effects of cadmium.

Endophytic Bacillus megaterium BM18-2 mutated for cadmium accumulation and improving plant growth in Hybrid Pennisetum

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The endophytic Bacillus megaterium isolated from Hybrid Pennisetum is promising isolate for Cd bioremediation.

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The mutated strain BM18-2 showed higher capacity to resist Cd until 70 μM and improving plant growth.

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Six different genes of BM18-2 are involved in Cd resistance mechanism.

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Hybrid Pennisetum inoculated with BM18-2 showed higher amount of growth and toleranc to Cd toxicity than uninoculated plants.

Hybrid Pennisetum (Pennisetum americanum × P. purpureum Schumach L.) is a tall and rapidly growing perennial C₄ bunch grass. It has been considered as a promising plant for phytoremediation of heavy metal-contaminated soil due to its high biomass, high resistance to environmental stress, pests and diseases. Heavy metal bioavailability level is the most important parameter for measurement of the phytoremediation efficiency. Endophytic bacteria were used to further enhance phytoremediation of heavy metals through bioaccumulation or bioabsorption process. In the present study, the endophytic Bacillus megaterium strain ‘BM18’ isolated from hybrid Pennisetum was screened under 10-70 μM cadmium (Cd) stress for Cd-resistant mutant colonies. And one such mutant colony‘BM18-2’ was obtained from the screen. Comparably, ‘BM18-2’ was more Cd-tolerant and had higher Cd removal ability than the original strain‘BM18’. The amount of IAA and ammonia production, and phosphate solubilization were 1.09, 1.23 and 1.24 times in ‘BM18-2’ than those of ‘BM18’, respectively. Full genome sequencing of these two strains revealed 6 different genes: BM18GM000901, BM18GM005669 and BM18GM005870 encoding heavy metal efflux pumps, BM18GM003487 and BM18GM005818 encoding transcriptional regulators for metal stress biosensor and BM18GM001335 encoding a replication protein. Inoculation with ‘BM18-2’ or ‘BM18’ both significantly reduced the toxic effect of Cd on hybrid Pennisetum, while the effect of ‘BM18-2’ on plant growth promotion in the presence of Cd was significantly better that of ‘BM18’. Therefore, the mutated strain ‘BM18-2’ could be used as a potential agent for Cd bioremediation, improving growth and Cd absorption of hybrid Pennisetum in Cd contaminated soil.

Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae

Background

Enterobacter cloacae (EC) is a Gram-negative bacterium that has been utilized extensively in biotechnological and environmental science applications, possibly because of its high capability for adapting itself and surviving in hazardous conditions. A search for the EC from agricultural and industrial areas that possesses high capability to tolerate and/or accumulate cadmium ions has been conducted in this study. Plausible mechanisms of cellular adaptations in the presence of toxic cadmium have also been proposed.

Methods

Nine strains of EC were isolated and subsequently identified by biochemical characterization and MALDI-Biotyper. Minimum inhibitory concentrations (MICs) against cadmium, zinc and copper ions were determined by agar dilution method. Growth tolerance against cadmium ions was spectrophotometrically monitored at 600 nm. Cadmium accumulation at both cellular and protein levels was investigated using atomic absorption spectrophotometer. Proteomics analysis by 2D-DIGE in conjunction with protein identification by QTOF-LC-MS/MS was used to study differentially expressed proteins between the tolerant and intolerant strains as consequences of cadmium exposure. Expression of such proteins was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatics tools were applied to propose the functional roles of cadmium-binding protein and its association in cadmium tolerance mechanisms.

Results

The cadmium-tolerant strain (EC01) and intolerant strain (EC07) with the MICs of 1.6 and 0.4 mM, respectively, were isolated. The whole cell lysate of EC01 exhibited approximately two-fold higher in cadmium binding capability than those of the EC07 and ATCC 13047, possibly by the expression of Cd-binding proteins. Our proteomics analysis revealed the higher expression of DUF326-like domain (a high cysteine-rich protein) of up to 220 fold in the EC01 than that of the EC07. Confirmation of the transcription level of this gene by qRT-PCR revealed a 14-fold induction in the EC01. Regulation of the DUF326-like domain in EC01 was more pronounced to mediate rapid cadmium accumulation (in 6 h) and tolerance than the other resistance mechanisms found in the ATCC 13047 and the EC07 strains. The only one major responsive protein against toxic cadmium found in these three strains belonged to an antioxidative enzyme, namely catalase. The unique proteins found in the ATCC 13047 and EC07 were identified as two groups: (i) ATP synthase subunit alpha, putative hydrolase and superoxide dismutase and (ii) OmpX, protein YciF, OmpC porin, DNA protection during starvation protein, and TrpR binding protein WrbA, respectively.

Conclusion

All these findings gain insights not only into the molecular mechanisms of cadmium tolerance in EC but also open up a high feasibility to apply the newly discovered DUF326-like domain as cadmium biosorbents for environmental remediation in the future.

Symbiotic microbes of Saxifraga stellaris ssp. alpigena from the copper creek of Schwarzwand (Austrian Alps) enhance plant tolerance to copper

Saxifraga stellaris var. alpigena grows as one of the very few higher plants in the copper rich area of the "blue creek" in Austria. Two endophytes were isolated from it: Mortierella sp. (fungus), and Stenotrophomonas maltophilia (bacterium). Both microbes were practically inseparable due to resistance of the bacteria to the antibiotics tested. On PDA media, the fungus showed higher tolerance to copper than the bacterium, which disappeared from both the media and the surface of the fungus in the presence of 150 μM of Cu. However, at this Cu concentration, the bacteria were still detectable inside the mycelium and reappeared on the outside when transferred to media of lower Cu concentration. Microscopic studies of in vitro cultivated plants showed that the fungus was present in both, the roots and shoots of the plant. The effects of endophytes on plant performance were assessed in rhizoboxes filled with Cu-rich substratum; plants inoculated with both microbes showed better growth, survival and photosynthesis performance than the non-inoculated controls. The results of this study prove the beneficial influence of the isolated endophytes on the Cu tolerance of S. stellaris, and indicate the ecological potential of applying microbial consortia to plants under extreme environmental conditions.

Multimetal tolerance mechanisms in bacteria: The resistance strategies acquired by bacteria that can be exploited to 'clean-up' heavy metal contaminants from water

Heavy metal pollution is one of the major environmental concerns worldwide. Toxic heavy metals when untreated get accumulated in environment and can pose severe threats to living organisms. It is well known that metals play a major role either directly or indirectly in different metabolic processes of bacteria. This allows bacterial cells to grow even in the presence of some toxic heavy metals. Microbial biotechnology has thus emerged as an effective and eco friendly solution in recent years for bioremediation of heavy metals. Therefore, this review is focused on summarising bacterial adaptation mechanisms for various heavy metals. It also shares some applications of have metal tolerant bacteria in bioremediation. Bacteria have evolved a number of processes for heavy metal tolerance viz., transportation across cell membrane, accumulation on cell wall, intra as well as extracellular entrapment, formation of complexes and redox reactions which form the basis of different bioremediation strategies. The genetic determinants for most of these resistances are located on plasmids however some may be chromosomal as well. Bacterial cells can uptake heavy by both ATP dependent and ATP independent processes. Bacterial cell wall also plays a very important role in accumulating heavy metals by bacterial cells. Gram-positive bacteria accumulate much higher concentrations of heavy metals on their cell walls than that of metals gram -ve bacteria. The role of bacterial metallothioneins (MTs) in heavy metal has also been reported. Thus, heavy metal tolerant bacteria are important for bioremediation of heavy metal pollutants from areas containing high concentrations of particular heavy metals.

The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia

A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp) sequences tentatively assigned to CzcA family heavy metal efflux pump [YP_001899332] from Ralstonia picketii 12J with 99% similarity. In this study the bacterium MR-CH-I2 and its heavy-metal resistance determinant were more precisely identified. This bacterial isolate was on the base of phylogenetic analysis of almost the whole (1,500 bp) 16S rDNA (16S rRNA) sequence, MR-CH-I2 [MF102046], and sequence for gyrB gene and its product respectively, MR-CH-I2-gyrB [MF134666], assigned to R. picketii 12J [CP001068] with 99 and 100% similarities, respectively. In addition, the whole nccA-like heavy-metal resistance gene sequence (3,192 bp), marked as MR-CH-I2-nccA [KR476581], was obtained and on the base of phylogenetic analysis its assignment was confirmed to MULTISPECIES: cation efflux system protein CzcA [WP_004635342] from Burkholderiaceae with 98% similarity. Furthermore, although the bacterium carried one high molecular plasmid of about 50 kb in size, nccA-like gene was not located on this plasmid. Finally, the results from RT-PCR analysis showed that MR-CH-I2-nccA gene was significantly induced only by the addition of nickel.

Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station

Several evolutionarily distinct, near full-length draft metagenome-resolved genomes (MRG), were assembled from sequences recovered from the International Space Station (ISS) environments. The retrieval of MRGs facilitated the exploration of a large collection of archived strains (~ 500 isolates) and assisted in isolating seven related strains. The whole genome sequences (WGS) of seven ISS strains exhibited 100% identity to the 4.85 × 10⁶ bp of four MRGs. The "metagenome to phenome" approach led to the description of a novel bacterial genus from the ISS samples. The phylogenomics and traditional taxonomic approaches suggested that these seven ISS strains and four MRGs were not phylogenetically affiliated to any validly described genera of the family Erwiniaceae, but belong to a novel genus with the proposed name Kalamiella. Comparative genomic analyses of Kalamiella piersonii strains and MRGs showed genes associated with carbohydrate (348 genes), amino acid (384), RNA (59), and protein (214) metabolisms; membrane transport systems (108), pathways for biosynthesis of cofactors, vitamins, prosthetic groups, and pigments (179); as well as mechanisms for virulence, disease, and defense (50). Even though Kalamiella genome annotation and disc diffusion tests revealed multidrug resistance, the PathogenFinder algorithm predicted that K. piersonii strains are not human pathogens. This approach to isolating microbes allows for the characterization of functional pathways and their potential virulence properties that can directly affect human health. The isolation of novel strains from the ISS has broad applications in microbiology, not only because of concern for astronaut health but it might have a great potential for biotechnological relevance. The metagenome to phenome approach will help to improve our understanding of complex metabolic networks that control fundamental life processes under microgravity and in deep space.

Multifunctional Zn doped hollow mesoporous silica/polycaprolactone electrospun membranes with enhanced hair follicle regeneration and antibacterial activity for wound healing

Due to the complexity of the skin tissue structure, the regeneration of the entire skin, including skin appendages such as hair follicles, is a big challenge. In addition, skin trauma is often accompanied by bacterial infections that delay the wound healing. Therefore, developing wound dressings, which promote hair follicle regeneration and inhibit bacterial infection in the wound healing process, is of great clinical significance. In this study, Zn doped hollow mesoporous silica nanospheres (HMZS) were synthesized by a sol-gel method and a novel wound healing dressing was prepared by incorporation of drug ciprofloxacin hydrochloride (CiH)-loaded Zn containing mesoporous silica nanospheres (CiH-HMZS) into polycaprolactone (PCL) electrospun fibers. The CiH-HMZS/P nano-composite electrospun fibers exhibit the ability to promote angiogenesis and skin regeneration by releasing Si ions, and the activity to enhance hair follicle regeneration and inhibit bacterial growth by releasing zinc ions and achieve the synergistic antibacterial effect with both Zn ions and CiH in low concentrations. Thus, the CiH-HMZS/P nano-composite membrane is a promising multi-functional wound healing material for inhibiting bacterial growth in infected wounds and enhancing skin wound healing including hair follicle regeneration.

High-throughput transcriptomics: Insights into the pathways involved in (nano) nickel toxicity in a key invertebrate test species

Nickel nanoparticles (NiNPs) have an estimated production of ca. 20 tons per year in the US. Nickel has been risk-assessed for long in Europe, but not NiNPs, hence the concern for the environment. In the present study, we focused on investigating the mechanisms of toxicity of NiNPs and the comparison to NiNO₃. The high-throughput microarray for the soil ecotox model Enchytraeus crypticus (Oligochaeta) was used. To anchor gene to phenotype effect level, organisms were exposed to reproduction effect concentrations EC20 and EC50, for 3 and 7 days. Results showed commonly affected pathways between NiNPs and NiNO₃, including increase in proteolysis, apoptosis and inflammatory response, and interference with the nervous system. Mechanisms unique to NiNO₃ were also observed (e.g. glutathione synthesis). No specific mechanisms for NiNPs were found, which could indicate that longer exposure period (>7 days) is required to capture the peak response to NiNPs. A mechanisms scheme is assembled, showing both common and unique mechanisms to NiNO₃ and NiNPs, providing an important framework for further, more targeted, studies.

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

BACKGROUND

The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.

RESULTS

The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.

CONCLUSIONS

There was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.

Impact of heavy metals on inhibitory concentration of Escherichia coli-a case study of river Yamuna system, Delhi, India

The occurrence of resistant bacteria to specific heavy metals can be associated with increasing load of the metals in the environment. River Yamuna is polluted by various toxic heavy metals discharged by several industrial and agricultural sources. Therefore, the use of heavy metal-resistant bacteria as an indicator of metal pollution was tested in the present study. For the purpose of the study, the heavy metal resistance status of 42 Escherichia coli strains isolated from River Yamuna water from 7 sampling sites within a span of 2 years was determined using growth curves and plate dilution method in terms of minimum inhibitory concentration (MIC) values by comparing with MIC value of control strain. Seasonally, the lowest mean MIC value was observed for bacterial strains isolated in post-monsoon (December) 2013 and highest mean MIC value was observed for bacterial strains isolated in monsoon (August) 2015. Site-wise analysis of the maximum mean MIC values for all the isolated strains showed the highest mean Ni MIC value for the bacterial strains isolated from site S4 (ITO), highest mean Cu MIC, Cr MIC, and Fe MIC values for the bacterial strains isolated from site S2 (Najafgarh drain intermixing zone) and highest mean Cd MIC, Pb MIC, and Zn MIC values for the bacterial strains isolated from site S7 (Shahdara drain intermixing zone). Correlation analysis between mean MIC site-wise results with mean heavy metal site-wise concentrations showed significant positive correlation indicating that the higher the mean concentration of a given heavy metal at a given site, the higher the mean MIC value for the strains isolated from the same site indicating higher level of resistance. Overall, the present study has shown that the presence of heavy metals in River Yamuna caused due to indiscriminate discharge of various effluents from different kind of sources as well as due to insufficient treatment capacity of sewage treatment plants as well as common effluent treatment plants, has serious impacts on its bacterial microflora as it leads to the development of resistant strains.

Molecular Characterization of Plasmids Harbored by Actinomycetes Isolated From the Great Salt Plains of Oklahoma Using PFGE and Next Generation Whole Genome Sequencing

One of the unique features of actinomycetes, especially the genus Streptomyces, is the presence of linear plasmids. These range in size from 12 to 600 kb, and are often termed mega-plasmids. While many of the genes involved in secondary metabolite production reside in clusters on the chromosome, several studies have identified biosynthetic clusters on large linear plasmids that produce important secondary metabolites, including antibiotics. In this study, Pulse Field Gel Electrophoresis (PFGE) was used to screen 176 actinomycete isolates for the presence of plasmids; these bacterial strains were previously isolated from the Great Salt Plains of Oklahoma. Seventy-eight of the 176 actinomycete isolates (44%) contained plasmids. Several strains contained more than one plasmid, accounting for a total of 109 plasmids. Ten isolates showed extrachromosomal DNA larger than 200 kb, thus falling into the category of mega-plasmids. A subset of plasmids from 55 isolates was treated with S1 nuclease to determine topology; all plasmids examined appeared to be linear and ranged from ~55 to 400 kb. Eleven isolates were chosen for Whole Genome Next Generation Sequencing. From the 11 sequenced isolates, seven plasmids were partially assembled. While the majority of the genes identified on the plasmids coded for hypothetical proteins, others coded for general functions, stress response, and antibiotic and heavy metal resistance. Draft genome sequences of two mega-plasmid-bearing Streptomyces sp. strains, BF-3 and 4F, revealed the presence of genes involved in antibiotic production, antibiotic, and heavy metal resistance, osmoregulation, and stress response, which likely facilitate their survival in this extreme halophilic environment. To our knowledge, this is the first study to explore plasmids harbored by actinomycetes isolated from the Great Salt Plains of Oklahoma.

Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth

Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.

Metal complexation by histidine-rich peptides confers protective roles against cadmium stress in Escherichia coli as revealed by proteomics analysis

The underlying mechanism and cellular responses of bacteria against toxic cadmium ions is still not fully understood. Herein, Escherichia coli TG1 expressing hexahistidine-green fluorescent protein (His6GFP) and cells expressing polyhistidine-fused to the outer membrane protein A (His-OmpA) were applied as models to investigate roles of cytoplasmic metal complexation and metal chelation at the surface membrane, respectively, upon exposure to cadmium stress. Two-dimensional gel electrophoresis (2-DE) and two-dimensional difference in gel electrophoresis (2D-DIGE) in conjunction with mass spectrometry-based protein identification had successfully revealed the low level expression of antioxidative enzymes and stress-responsive proteins such as manganese-superoxide dismutase (MnSOD; +1.65 fold), alkyl hydroperoxide reductase subunit C (AhpC; +1.03 fold) and DNA starvation/stationary phase protection protein (Dps; −1.02 fold) in cells expressing His6GFP in the presence of 0.2 mM cadmium ions. By contrarily, cadmium exposure led to the up-regulation of MnSOD of up to +7.20 and +3.08 fold in TG1-carrying pUC19 control plasmid and TG1 expressing native GFP, respectively, for defensive purposes against Cd-induced oxidative cell damage. Our findings strongly support the idea that complex formation between cadmium ions and His6GFP could prevent reactive oxygen species (ROS) caused by interaction between Cd²⁺ and electron transport chain. This coincided with the evidence that cells expressing His6GFP could maintain their growth pattern in a similar fashion as that of the control cells even in the presence of harmful cadmium. Interestingly, overexpression of either OmpA or His-OmpA in E. coli cells has also been proven to confer protection against cadmium toxicity as comparable to that observed in cells expressing His6GFP. Blockage of metal uptake as a consequence of anchored polyhistidine residues on surface membrane limited certain amount of cadmium ions in which some portion could pass through and exert their toxic effects to cells as observed by the increased expression of MnSOD of up to +9.91 and +3.31 fold in case of TG1 expressing only OmpA and His-OmpA, respectively. Plausible mechanisms of cellular responses and protein mapping in the presence of cadmium ions were discussed. Taken together, we propose that the intracellular complexation of cadmium ions by metal-binding regions provides more efficiency to cope with cadmium stress than the blockage of metal uptake at the surface membrane. Such findings provide insights into the molecular mechanism and cellular adaptation against cadmium toxicity in bacteria.

Potential of 2, 2'-dipyridyl diselane as an adjunct to antibiotics to manage cadmium-induced antibiotic resistance in Salmonella enterica serovar Typhi Ty2 strain

One of the reasons for increased antibiotic resistance in Salmonella enterica serovar Typhi Ty2 is the influx of heavy metal ions in the sewage, from where the infection is transmitted. Therefore, curbing these selective agents could be one of the strategies to manage the emergence of multidrug resistance in the pathogen. As observed in our earlier study, the present study also confirmed the links between cadmium accumulation and antibiotic resistance in Salmonella. Therefore, the potential of a chemically-synthesised compound 2, 2'-dipyridyl diselane (DPDS) was explored to combat the metal-induced antibiotic resistance. Its metal chelating and antimicrobial properties were evidenced by fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FE-SEM), and microbroth dilution method. Owing to these properties of DPDS, further, this compound was evaluated for its potential to be used in combination with conventional antibiotics. The data revealed effective synergism at much lower concentrations of both the agents. Thus, it is indicated from the study that the combination of these two agents at their lower effective doses might reduce the chances of emergence of antibiotic resistance, which can be ascribed to the multi-pronged action of the agents.

Effect of Nickel and Cobalt on Methanogenic Enrichment Cultures and Role of Biogenic Sulfide in Metal Toxicity Attenuation

Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulfide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulfate or sulfide. The addition of sulfide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulfate, possibly due to competition of hydrogenotrophic methanogens by sulfate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulfide had a positive effect and more methane was produced in these incubations than in similar assays without sulfate addition. The outcome of competition between methanogens and sulfate-reducing bacteria is a determinant factor for the success of using biogenic sulfide as detoxification method.

Analysis of zntA gene in environmental Escherichia coli and additional implications on its role in zinc translocation

Escherichia coli strains from sewage sample were screened for the presence and expression of heavy metal-translocating zntA gene by PCR and RT-PCR analysis with type culture of K-12 as standard strain. The strain which showed high level of gene expression (SBVP1) was chosen to further study the growth and heavy metal translocation. This superior strain was grown in the presence of ZnSO₄, Pb (CH₃COO)₂ and mixture of ZnSO₄, Pb(CH₃COO)₂ metal salts and the growth was observed at different time points. The cell pellet fraction was found to have more of zinc than lead as determined by atomic absorption spectroscopy indicating the translocation of these metals from media to the cells. However, the intracellular translocation of zinc is affected by the presence of lead in the media. Expression of the zntA gene in bacteria grown in the presence of ZnSO₄ was also studied and the molecular analysis results correlate with spectroscopic observations.

Functional components of the bacterial CzcCBA efflux system reduce cadmium uptake and accumulation in transgenic tobacco plants

Cadmium (Cd) is a toxic trace element released into the environment by industrial and agricultural practices, threatening the health of plants and contaminating the food/feed chain. Biotechnology can be used to develop plant varieties with a higher capacity for Cd accumulation (for use in phytoremediation programs) or a lower capacity for Cd accumulation (to reduce Cd levels in food and feed). Here we generated transgenic tobacco plants expressing components of the Pseudomonas putida CzcCBA efflux system. Plants were transformed with combinations of the CzcC, CzcB and CzcA genes, and the impact on Cd mobilization was analysed. Plants expressing PpCzcC showed no differences in Cd accumulation, whereas those expressing PpCzcB or PpCzcA accumulated less Cd in the shoots, but more Cd in the roots. Plants expressing both PpCzcB and PpCzcA accumulated less Cd in the shoots and roots compared to controls, whereas plants expressing all three genes showed a significant reduction in Cd levels only in shoots. These results show that components of the CzcCBA system can be expressed in plants and may be useful for developing plants with a reduced capacity to accumulate Cd in the shoots, potentially reducing the toxicity of food/feed crops cultivated in Cd-contaminated soils.

Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics

Bovine respiratory disease (BRD) is a multifactorial disorder responsible for severe economic losses in dairy and feedlot herds. Advances in next-generation sequencing mean that microbial communities in clinical samples, including non-culturable bacteria, can be characterized. Our aim was to evaluate the microbiota of the upper respiratory tract of healthy calves and calves with BRD using whole-genome sequencing (shotgun metagenomics). We performed deep nasopharyngeal swabs on 16 Holstein heifer calves (10 healthy and 6 diagnosed with BRD during the study) at 14 and 28 d of life in 1 dairy herd near Ithaca, New York. Total DNA was extracted, and whole-genome sequencing was performed using the MiSeq Illumina platform (Illumina Inc., San Diego, CA). Samples included 5 predominant phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Tenericutes. At the genus level, we observed differences between groups for Pseudomonas spp. At the species level, Mannheimia haemolytica was the most abundant bacterium detected. We detected significant differences between groups of calves in the relative abundance of Pseudomonas fluorescens. Pasteurella multocida was among the 20 most abundant species, and Moraxella catarrhalis, commonly associated with pneumonia in humans, was detected in all groups. Analysis of resistance to antibiotics and compounds profiling revealed differences in cobalt-zinc-cadmium resistance. Further research to elucidate the role of Moraxella catarrhalis in BRD is warranted. Genes that were resistant to cobalt-zinc-cadmium, observed mostly in calves with BRD, might be associated with difficulties in antibiotic treatment.