Glucose facilitates the acclimation of organohalide-respiring bacteria

Construction of a synthetic anaerobic dechlorination microbiome to degrade chlorinated ethenes by application of metabolic interactions principle

Bioaugmentation is a bioremediation approach to treat groundwater contaminated with chlorinated ethenes, but currently it faces challenges such as poor microbiome stability and effectiveness, due to blind species integration and metabolic inhibition. The objective of this study was to create a controllable and functionally stable microbial community for dichlorination application. For this, we utilized targeted screening to identify dechlorinating bacteria from contaminated groundwater, that in combination would form an anaerobic dechlorination microbial community with stabilizing metabolic interactions between the constituents. The results showed that two organohalide-respiring bacterial (OHRB) species were isolated, and these were identified as Enterobacter bugandensis X4 and Enterobacter sichuanensis C4. Upon co-cultivation with lactic acid as the carbon source, the strains demonstrated metabolic interactions and synergistic dehalogenation ability towards trichloroethene (TCE). It was further demonstrated that the functional microbiome constructed with the strains was stable over time and exhibited a robust TCE degradation rate of 80.85% at 13.13 mg/L TCE within 10 days. Additionally, the complete conversion of TCE was achieved through microbiome bioaugmentation, this augmented microbiome increased the degradation rate towards 52.55 mg/L TCE by approximately 30% within 6 days. Additionally, bioaugmentation stimulated the growth of indigenous OHRB, such as Dehalobacter and Desulfovibrio. It also promoted a positive succession of the microbial community. These findings offer valuable insights into the microbial remediation of chlorinated ethenes-contaminated groundwater and offers novel ideas for the construction of an artificial functional microbiome.

Biogenic amorphous FeOOH activated additional intracellular electron flow pathways for accelerating reductive dechlorination of tetrachloroethylene

Dissimilatory iron-reducing bacteria (DIRB) with extracellular electron transfer (EET) capabilities have shown significant potential for bioremediating halogenated hydrocarbon contaminated sites rich in iron and humic substances. However, the role and microbial molecular mechanisms of iron-humic acid (Fe-HA) complexes in the reductive dehalogenation process of DIRB remains inadequately elucidated. In this study, we developed a sustainable carbon cycling approach using Fe-HA complexes to modulate the electron flux from sawdust (SD), enabling almost complete reductive dechlorination by most DIRB (e.g., Shewanella oneidensis MR-1) that lack complex iron-sulfur molybdo enzymes. The SD-Fe-HA/MR-1 system achieved a 96.52% removal efficiency of tetrachloroethylene (PCE) at concentrations up to 250 μmol/L within 60 days. Material characterization revealed that DIRB facilitated the hydrolysis of macromolecular carbon sources by inducing the formation of amorphous ferrihydrite (FeOOH) in Fe-HA complexes. More importantly, the bioavailable FeOOH activated additional intracellular electron flow pathways, increasing the activity of potential dehalogenases. Transcriptome further highlight the innovative role of biogenic amorphous FeOOH in integrating intracellular redox metabolism with extracellular charge exchange to facilitate reductive dechlorination in DIRB. These findings provide novel insights into accelerating reductive dechlorination in-situ contaminated sites lacking obligate dehalogenating bacteria.

Fe(0)-Dissimilatory Nitrate Reduction to Ammonium for Autotrophic Recovery of Reactive Nitrogen

Bioreduction of nitrate to value-added ammonium is a potentially sustainable strategy to recycle nutrients from wastewater. Here, we have proven the feasibility of the reduction of autotrophic nitrate to ammonium with electrons extracted from Fe(0). Using a Geobacter-dominated anodic biofilm as an inoculum, we achieved nitrate-to-ammonium efficiency up to 90 ± 3% with a nitrate reduction rate of 35 ± 1.3 mg N/d/L. An electron acceptor instead of an inoculum greatly influenced the Fe(0)-dissimilatory nitrate reduction to ammonium (DNRA), where nitrite as the electron acceptor provided an effective selective pressure to enrich Geobacter from initial 5 to 56%. The DNRA repressing denitrification was demonstrated by the reverse tendencies of upregulated nrfA and downregulated nirS gene transcription. This finding provides a new route for autotrophic nitrate removal and recycling from water, which has a broader implication on biogeochemical nitrogen and iron cycling.

Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination

The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg^-1). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.