Draft Genome Sequence of Shewanella decolorationis S12, a Dye-Degrading Bacterium Isolated from a Wastewater Treatment Plant

Metagenomic profiling of antibiotic resistance and virulence removal: Activated sludge vs. algal wastewater treatment system

Conventional activated sludge-based (CAS) wastewater treatment plants are known to be a source of antibiotic resistance genes (ARGs) and virulence genes (VGs). As an alternative, a single-step mixotrophic algal wastewater treatment (A-WWT) system is proposed here to effectively reduce ARGs and VGs in the final effluent while meeting all the discharge standards. In this study, we applied the metagenomic profiling approach to compare the A-WWT system against the CAS system in terms of removal efficacy of ARG and VGs. A total of 111 ARG and 93 VG subtypes belonging to 10 antibiotic resistant classes and 19 virulence classes were detected in this study. Although the CAS system reduced the relative abundance of most classes of ARGs (7 of 10) and VGs (11 of 19), 3 ARG classes and 7 VG classes had increased abundances. On the other hand, the A-WWT system reduced the relative abundance of all classes of ARGs and VGs, and effectively eliminated most subtypes of ARGs and VGs. In the CAS system, the bacterial genera carrying ARGs and VGs was expanded, and the diversity index was increased greatly, suggesting the occurrence of horizontal gene transfer (HGT). In contrast, the A-WWT system narrowed down the potential host range and decreased their diversity substantially. Results of this study highlight the potential risk of ARGs and VGs in CAS system and demonstrate the feasibility of the algal-based system in removing ARGs and VGs.

The first complete genome sequence of species Shewanella decolorationis, from a bioremediation competent strain Ni1-3

Shewanella decolorationis are Gram-negative γ-Proteobacteria with environmental bioremediation potential because they can perform anaerobic respiration using various types of pollutants as terminal electron acceptors. So far, three isolated and cultured strains of S. decolorationis have been reported. However, no complete S. decolorationis genome has been published yet, which limited exploring their metabolism and feasibility in application. Here, S. decolorationis Ni1-3 isolated from an electroplating wastewater treatment plant showed strong reduction capabilities on azo dyes and oxidized metals. In order to construct the complete genome, high-quality whole-genome sequencing of strain Ni1-3 were performed by using both Nanopore MinION and Illumina NovaSeq platforms, from which the first complete genome of S. decolorationis was obtained by hybrid assembly. The genome of strain Ni1-3 contains a megaplasmid and a circular chromosome which encodes more proteins than that of the strains LDS1 and S12 belonging to the same species. In addition, more Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are identified in strain Ni1-3 genome. Importantly, 32 cytochrome-c and AzoR azoreductase coding genes are identified in the genome, which make strain Ni1-3 competent to degrade the azo dyes and versatile to bioremediate some other environmental pollution. The complete genome sequence of strain Ni1-3 can expand our knowledge toward its metabolic capabilities and potential, meanwhile, provide a reference to reassemble genomes of other S. decolorationis strains.

Isolation, nucleotide sequencing and genomic comparison of a Novel SXT/R391 ICE mobile genetic element isolated from a municipal wastewater environment

Integrative Conjugative Elements (ICE’s) of the SXT/R391 family have largely been detected in clinical or environmental isolates of Gammaproteobacteria, particularly Vibrio and Proteus species. As wastewater treatment plants accumulate a large and diverse number of such species, we examined raw water samples taken from a municipal wastewater treatment plant initially using SXT/R391 family integrase gene-specific PCR probes to detect the presence of such elements in a directed approach. A positive amplification occurred over a full year period and a subsequent Restriction Fragment Length Polymorphism (RFLP) analysis revealed a very limited diversity in the treatment plant examined. Samples demonstrating positive amplification were cultured using Vibrio and Proteus selective media and PCR amplification tracking was utilized to monitor SXT/R391-ICE family containing strains. This screening procedure resulted in the isolation and identification of a Proteus mirabilis strain harbouring an ICE. Whole-genome sequencing of this ICE containing strain using Illumina sequencing technology revealed a novel 81 kb element that contained 75 open reading frames on annotation but contained no antibiotic or metal resistance determinants. Comparative genomics revealed the element contained a conserved ICE core with one of the insertions containing a novel bacteriophage defence mechanism. This directed isolation suggests that ICE elements are present in the environment without apparent selective pressure but may contain adaptive functions allowing survival in particular environments such as municipal wastewater which are reservoirs for large bacterial phage populations.

A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements

ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (E. coli) isolate K802 (which contains the ICEpMERPH) was carried out using Illumina sequencing technology. ICEpMERPH has a size of 110 Kb and 112 putative open reading frames (ORFs). The “hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences, and heavy metal resistance genes that encoded resistance to mercury, as previously reported, but also surprisingly to arsenate. A novel arsenate resistance system was identified in hotspot 4 of the element, unrelated to other SXT/R391 elements. This arsenate resistance system was potentially linked to two genes: orf69, encoding an organoarsenical efflux major facilitator superfamily (MFS) transporter-like protein related to ArsJ, and orf70, encoding nicotinamide adenine dinucleotide (NAD)-dependent glyceraldehyde-3-phosphate dehydrogenase. Phenotypic analysis using isogenic strains of Escherichia coli strain AB1157 with and without the ICEpMERPH revealed resistance to low levels of arsenate in the range of 1–5 mM. This novel, low-level resistance may have an important adaptive function in polluted environments, which often contain low levels of arsenate contamination. A bioinformatic analysis on the novel determinant and the phylogeny of ICEpMERPH was presented.

Adaptive Responses of Shewanella decolorationis to Toxic Organic Extracellular Electron Acceptor Azo Dyes in Anaerobic Respiration

Bacterial anaerobic respiration using an extracellular electron acceptor plays a predominant role in global biogeochemical cycles. However, the mechanisms of bacterial adaptation to the toxic organic pollutant as the extracellular electron acceptor during anaerobic respiration are not clear, which limits our ability to optimize the strategies for the bioremediation of a contaminated environment. Here, we report the physiological characteristics and the global gene expression of an ecologically successful bacterium, Shewanella decolorationis S12, when using a typical toxic organic pollutant, amaranth, as the extracellular electron acceptor. Our results revealed that filamentous shift (the cells stretched to fiber-like shapes as long as 18 μm) occurred under amaranth stress. Persistent stress led to a higher filamentous cell rate and decolorization ability in subcultural cells compared to parental strains. In addition, the expression of genes involved in cell division, the chemotaxis system, energy conservation, damage repair, and material transport in filamentous cells was significantly stimulated. The detailed roles of some genes with significantly elevated expressions in filamentous cells, such as the outer membrane porin genes ompA and ompW, the cytochrome c genes arpC and arpD, the global regulatory factor gene rpoS, and the methyl-accepting chemotaxis proteins genes SHD_2793 and SHD_0015, were identified by site-directed mutagenesis. Finally, a conceptual model was proposed to help deepen our insights into both the bacterial survival strategy when toxic organics were present and the mechanisms by which these toxic organics were biodegraded as the extracellular electron acceptors.IMPORTANCE Keeping toxic organic pollutants (TOPs) in tolerable levels is a huge challenge for bacteria in extremely unfavorable environments since TOPs could serve as energy substitutes but also as survival stresses when they are beyond some thresholds. This study focused on the underlying adaptive mechanisms of ecologically successful bacterium Shewanella decolorationis S12 when exposed to amaranth, a typical toxic organic pollutant, as the extracellular electron acceptor. Our results suggest that filamentous shift is a flexible and valid way to solve the dilemma between the energy resource and toxic stress. Filamentous cells regulate gene expression to enhance their degradation and detoxification capabilities, resulting in a strong viability. These novel adaptive responses to TOPs are believed to be an evolutionary achievement to succeed in harsh habitats and thus have great potential to be applied to environment engineering or synthetic biology if we could picture every unknown node in this pathway.

Characterization of the enhancement of zero valent iron on microbial azo reduction

BACKGROUND

The microbial method for the treatment of azo dye is promising, but the reduction of azo dye is the rate-limiting step. Zero valent iron (Fe(0)) can enhance microbial azo reduction, but the interactions between microbes and Fe(0) and the potential mechanisms of enhancement remain unclear. Here, Shewanella decolorationis S12, a typical azo-reducing bacterium, was used to characterize the enhancement of Fe(0) on microbial decolorization.

RESULTS

The results indicated that anaerobic iron corrosion was a key inorganic chemical process for the enhancement of Fe(0) on microbial azo reduction, in which OH(-), H2, and Fe(2+) were produced. Once Fe(0) was added to the microbial azo reduction system, the proper pH for microbial azo reduction was maintained by OH(-), and H2 served as the favored electron donor for azo respiration. Subsequently, the bacterial biomass yield and viability significantly increased. Following the corrosion of Fe(0), nanometer-scale Fe precipitates were adsorbed onto cell surfaces and even accumulated inside cells as observed by transmission electron microscope energy dispersive spectroscopy (TEM-EDS).

CONCLUSIONS

A conceptual model for Fe(0)-assisted azo dye reduction by strain S12 was established to explain the interactions between microbes and Fe(0) and the potential mechanisms of enhancement. This model indicates that the enhancement of microbial azo reduction in the presence of Fe(0) is mainly due to the stimulation of microbial growth and activity by supplementation with elemental iron and H2 as an additional electron donor. This study has expanded our knowledge of the enhancement of microbial azo reduction by Fe(0) and laid a foundation for the development of Fe(0)-microbial integrated azo dye wastewater treatment technology.

Physiological and electrochemical effects of different electron acceptors on bacterial anode respiration in bioelectrochemical systems

To understand the interactions between bacterial electrode respiration and the other ambient bacterial electron acceptor reductions, alternative electron acceptors (nitrate, Fe2O3, fumarate, azo dye MB17) were added singly or multiply into Shewanella decolorationis microbial fuel cells (MFCs). All the added electron acceptors were reduced simultaneously with current generation. Adding nitrate or MB17 resulted in more rapid cell growth, higher flavin concentration and higher biofilm metabolic viability, but lower columbic efficiency (CE) and normalized energy recovery (NER) while the CE and NER were enhanced by Fe2O3 or fumarate. The added electron acceptors also significantly influenced the cyclic voltammetry profile of anode biofilm probably via altering the cytochrome c expression. The highest power density was observed in MFCs added with MB17 due to the electron shuttle role of the naphthols from MB17 reduction. The results provided important information for MFCs applied in practical environments where contains various electron acceptors.