Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress

The quorum sensing SinI/SinR-TraI/TraR systems promote Pb stabilization by Ensifer adhaerens S24 in the Pb-polluted aquatic environment

In this study, the Pb-resistant Ensifer adhaerens strain S24, which contains quorum sensing (QS) systems responsible for N-acyl homoserine lactone (AHL) production, was investigated for QS system-mediated Pb stabilization and the underlying mechanisms. Whole-genome sequence analysis revealed the QS SinI/R and TraI/R systems in strain S24. Subsequently, strains S24 and the S24∆sinI/R, S24∆traI/R, S24∆traI/R/sinR, and S24∆sinI/R-traI/R/sinR mutants were constructed and compared for QS SinI/SinR-TraI/TraR system-mediated Pb stabilization in the solution and the mechanisms involved. After 5 days of incubation, strain S24 significantly decreased the Pb concentration in the Pb-contaminated solution compared with the mutants. The S24∆sinI/R-traI/R/sinR mutant exhibited reduced Pb stabilization and AHL activity than the other mutants. The S24∆sinI/R-traI/R/sinR mutant had significantly greater Pb concentrations in the solution and lower cell surface-adsorbed and extracellular precipitated Pb (PbS) contents as well as lower expression of H2S-producing genes of metC and sseA than did strain S24. Furthermore, the S24∆sinI/R-traI/R/sinR mutant displayed reduced interactions between the hydroxyl, amino, carboxyl, and ether groups and Pb, compared with strain S24. These findings implied the vital role of the SinI/SinR-TraI/TraR systems in strain S24 for Pb stabilization through enhanced cell surface adsorption and extracellular precipitation in Pb-polluted aquatic environments.

The quorum sensing SinI/R system contributes to cadmium immobilization in Ensifer adhaerens NER9 in the cadmium-contaminated solution

In this study, the cadmium (Cd)-tolerant Ensifer adhaerens strain NER9 with quorum sensing (QS) systems (responsible for N-acyl homoserine lactone (AHL) production) was characterized for QS system-mediated Cd immobilization and the underlying mechanisms involved. Whole-genome sequence analysis revealed that strain NER9 contains the QS SinI/R and TraI/R systems. Strains NER9 and the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants were constructed and compared for QS SinI/R and TraI/R system-mediated Cd immobilization in the solution and the mechanisms involved. After 24 h of incubation, strain NER9 significantly decreased the Cd concentration in the Cd-contaminated solution compared with the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants. The NER9∆sinI/R mutant had a greater impact on Cd immobilization and a lower impact on the activities of AHLs than did the NER9∆traI/R mutant. The NER9∆sinI/R mutant had significantly greater Cd concentrations and lower cell wall- and exopolysaccharide (EPS)-adsorbed Cd contents than did strain NER9. Furthermore, the NER9∆sinI/R mutant presented a decrease in the number of functional groups interacting with Cd, compared with strain NER9. These results suggested that the SinI/R system in strain NER9 contributed to Cd immobilization by mediating cell wall- and EPS-adsorption in Cd-containing solution.

Cysteine and thiosulfate promoted cadmium immobilization in strain G303 by the formation of extracellular CdS

Bacteria have evolved a variety of strategies to defend themselves against cadmium toxicity, however, the specific mechanisms involved in the enhancement of bacterial cadmium resistance by sulfur sources are unclear. In this study, a novel cadmium (Cd)-tolerant bacterium, Stenotrophomonas geniculata G303, was isolated from activated sludge. The growth of strain G303 under diverse Cd concentrations was investigated, and the minimum inhibitory concentration of Cd was found to be 1 mM. Strain G303 effectively remove 94.7 % of Cd after 96 h of culture. Extracellular CdS was detected using multiple methods, with the CdS formed being aggregated in the biofilm. The addition of cysteine and thiosulfate to the medium significantly enhanced the Cd resistance and removal capacity of strain G303. Integrated genomic and proteomic analyses revealed that heavy metal transporters cooperate to resist Cd stress. Cysteine and thiosulfate improved Cd tolerance in strain G303 by upregulating nitrogen and energy metabolism. Proteins associated with nitrate reduction likely played a pivotal role in cysteine and thiosulfate metabolism. Notably, cysteine synthase and the SUF system played crucial roles in CdS formation. This study systematically explored the impact of cysteine and thiosulfate on the Cd resistance of strain G303, deepening our understanding of the microbial response mechanism to heavy metals.

Comparative genomics of fungal mutants provides a systemic view of extreme cadmium tolerance in eukaryotic microbes

Whether eukaryotic organisms can evolve for higher heavy metal resistance in laboratory conditions remains unknown. In this study, we challenged a macrofungi, Pleurotus ostreatus, in a designed microbial evolution and growth arena (MEGA)-plate with an extreme Cd gradient. Within months, the wild-type strain developed 10 mutants, exhibiting a maximum three-fold increase in Cd tolerance and slower growth rates. Genomic sequencing and re-sequencing of the wild-type and ten mutant strains generated about 51 GB data, allowing a comprehensive comparative genomics analysis. As a result, a total of 2512 common single nucleotide polymorphisms, 70 inserts and deletes, 39 copy number variations and 21 structural variations were found in the 10 mutants. The mutant genes were primarily involved in substrate transport. In combination with transcriptome analysis, we discovered that the ten mutants had a distinct Cd-resistant mechanism compared to the wild-type strain. Genes involved in oxidation-reduction, ion transmembrane transport, and metal compartment/efflux are primarily responsible for the extreme Cd tolerance in the P. ostreatus mutants. Our findings contribute to the understanding of eukaryotic Cd resistance at the genome level and establish a foundation for developing bioremediation tools utilizing highly tolerant macrofungi.

Competition of Cd(II) and Pb(II) on the bacterial cells: a new insight from bioaccumulation based on NanoSIMS imaging

Polymetallic exposure causes complex toxicity to microorganisms. In this study, we investigated the responses of Escherichia coli under co-existence of cadmium (Cd) and lead (Pb), primarily based on biochemical analysis and RNA sequencing. Cd completely inhibited bacterial growth at a concentration of 2.41 mmol/L, with its removal rate as low as <10%. In contrast, the Pb removal rate was >95% under equimolar sole Pb stress. In addition, the Raman analysis confirmed the loss of proteins for the bacterial cells. Under the co-existence of Cd and Pb, the Cd toxicity to E. coli was alleviated. Meanwhile, the biosorption of Pb cations was more intense during the competitive sorption with Cd. Transmission electron microscopy images showed that a few cells were elongated during incubation, i.e., the average cellular length increased from 1.535 ± 0.407 to 1.845 ± 0.620 µm. Moreover, NanoSIMS imaging showed that the intracellular distribution of Cd and Pb was coupled with sulfur. Genes regulating sulfate transporter were also upregulated to promote sulfate assimilation. Then, the subsequent production of biogenic sulfide and sulfur-containing amino acids was enhanced. Although this strategy based on S enrichment could resist the polymetallic stress, not all related genes were induced to upregulate under sole Cd stress. Therefore, the S metabolism might remodel the microbial resistance to variable occurrence of heavy metals. Furthermore, the competitive sorption (in contrast to sole Cd stress) could prevent microbial cells from strong Cd toxicity.IMPORTANCEMicrobial tolerance and resistance to heavy metals have been widely studied under stress of single metals. However, the polymetallic exposure seems to prevail in the environment. Though microbial resistance can alleviate the effects of exogenous stress, the taxonomic or functional response to polymetallic exposure is still not fully understood. We determined the strong cytotoxicity of cadmium (Cd) on growth, and cell elongation would be driven by Cd stress. The addition of appropriate lead (Pb) showed a stimulating effect on microbial bioactivity. Meanwhile, the biosorption of Pb was more intense during co-existence of Pb and Cd. Our work also revealed the spatial coupling of intracellular S and Cd/Pb. In particular, the S assimilation was promoted by Pb stress. This work elucidated the microbial responses to polymetallic exposure and may provide new insights into the antagonistic function during metal stresses.

Zinc and cadmium change the metabolic activities and vegetable cellulose degradation of Bacillus cellulasensis in vegetable soils

Bacillus cellulasensis Zn-B isolated from vegetable soil was highly adaptable to Zinc (Zn) and Cadmium (Cd). Cd, but not Zn, adversely affected the total protein spectrum and functional groups of Bacillus cellulasensis Zn-B. Up to 31 metabolic pathways and 216 metabolites of Bacillus cellulasensis Zn-B were significantly changed by Zn and Cd (Zn&Cd). Some metabolic pathways and metabolites related to functional groups of sulfhydryl (-SH) and amine (-NH-) metabolism were enhanced by Zn&Cd addition. The cellulase activity of Bacillus cellulasensis Zn-B was up to 8.58 U mL^-1, increased to 10.77 U mL^-1 in Bacillus cellulasensis Zn-B + 300 mg L^-1 Zn, and maintained at 6.13 U mL^-1 in Bacillus cellulasensis Zn-B + 50 mg L^-1 Cd. The vegetables' cellulose content was decreased by 25.05-52.37% and 40.28-70.70% under the action of Bacillus cellulasensis Zn-B and Bacillus cellulasensis Zn-B + 300 mg L^-1 Zn. Those results demonstrated that Zn could significantly enhance cellulase activity and biodegradability of Bacillus cellulasensis Zn-B to vegetable cellulose. Bacillus cellulasensis Zn-B can survive in vegetable soil accumulated with Zn&Cd. The tolerance concentration and adsorption capacity of Bacillus cellulasensis Zn-B to Zn were up to 300 mg L^-1 and 56.85%, indicating that Bacillus cellulasensis Zn-B acting as a thermostability biological agent had an essential advantage in accelerating the degradation of discarded vegetables by Zn and were beneficial to maintain organic matter content of vegetable soil.

Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus

BACKGROUND

The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies.

RESULTS

In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur.

CONCLUSIONS

This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles.

Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg

The waterborne Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. Pollution of heavy metals in aquatic environments is proposed to link high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution and heavy metal tolerance mechanism of V. parahaemolyticus in aquatic animals remain to be largely unveiled. Here, we overcome the limitation by characterizing an MDR V. parahaemolyticus N10-18 isolate with high cadmium (Cd) tolerance using genomic and transcriptomic techniques. The draft genome sequence (4,910,080 bp) of V. parahaemolyticus N10-18 recovered from Ostrea gigas Thunberg was determined, and 722 of 4653 predicted genes had unknown function. Comparative genomic analysis revealed mobile genetic elements (n = 11) and heavy metal and antibiotic-resistance genes (n = 38 and 7). The bacterium significantly changed cell membrane structure to resist the Cd2+ (50 μg/mL) stress (p < 0.05). Comparative transcriptomic analysis revealed seven significantly altered metabolic pathways elicited by the stress. The zinc/Cd/mercury/lead transportation and efflux and the zinc ATP-binding cassette (ABC) transportation were greatly enhanced; metal and iron ABC transportation and thiamine metabolism were also up-regulated; conversely, propanoate metabolism and ribose and maltose ABC transportation were inhibited (p < 0.05). The results of this study demonstrate multiple strategies for the Cd tolerance in V. parahaemolyticus.