Metabolic mechanism of Cr(VI) pollution remediation by Alicycliphilus denitrificans Ylb10.

Cr(VI) is a well-known toxic pollutant and its remediation has attracted great attention. It is important to continuously discover and explore new high-efficiency Cr(VI) reducing bacteria to further improve the efficiency of Cr(VI) pollution remediation. In this paper, metabolic mechanism of Cr(VI) reduction in a new highly efficient Cr(VI) reducing bacterium, Alicycliphilus denitrificans Ylb10, was investigated. The results showed that Ylb10 could tolerate and completely reduce 450 mg/L Cr(VI). Cr(VI) can be reduced in the intracellular compartment, membrane and the extracellular compartment, with the plasma membrane being the main active site for Cr(VI) reduction. With the addition of NADH, the reduction efficiency of cell membrane components for Cr(VI) increased 2.3-fold. The omics data analysis showed that sulfite reductase CysJ, thiosulfate dehydrogenase TsdA, nitrite reductase NrfA, nitric oxide reductase NorB, and quinone oxidoreductase ChrR play important roles in the reduction of Cr(VI), in the intracellular, and the extracellular compartment, and the membrane of Ylb10, and therefore Cr(VI) was reduced by the combined action of several reductases at these three locations.

Corrigendum: A Markerless Method for Genome Engineering in Zymomonas mobilis ZM4.

[This corrects the article DOI: 10.3389/fmicb.2019.02216.].

Enrichment and characterization of an effective hexavalent chromium-reducing microbial community YEM001.

Chromium (Cr) is one of the most widely used heavy metals in industrial processes, resulting in water and soil pollution that seriously threaten environmental safety. In this paper, we have directionally enriched a Cr(VI)-reducing bacterial community YEM001 from no-Cr(VI) polluted pond sedimental sludge by selectively growing it in Cr(VI)-containing media. This community could effectively reduce Cr(VI) in laboratory rich media containing different concentrations of Cr(VI), such as 61% reduction at 435 mg/L Cr(VI), 85% reduction at 355 mg/L Cr(VI), and complete reduction at 269 mg/L Cr(VI) in 93.5 h. It was also able to completely reduce 100 mg/L and 300 mg/L Cr(VI) in landfill leachate and natural sludge in 48 h, respectively. Optimal pH for Cr(VI) reduction of the YEM001 is between 7 and 8 and the best efficiency for Cr(VI) reduction occurs at 30 °C. Metagenomic data demonstrated that the YEM001 community was composed of multiple bacteria, including well-known Cr(VI)-reducing bacteria and non-Cr(VI)-reducing bacteria. Delftia, Comamonas, Alicycliphilus, Acidovorax, Bacillus, and Clostridioides account for 83% of total community abundance. The stability of the composition of the YEM001 community and its Cr(VI)-reducing activity allows for its application in bioremediation of environmental Cr(VI) pollution.

A Markerless Method for Genome Engineering in Zymomonas mobilis ZM4.

Metabolic engineering of the biofuel-producing Zymomonas mobilis is necessary if we are to unlock the metabolic potential present in this non-model microbe. Manipulation of such organisms can be challenging because of the limited genetic tools for iterative genome modification. Here, we have developed an efficient method for generating markerless genomic deletions or additions in Z. mobilis. This is a two-step process that involves homologous recombination of an engineered suicide plasmid bearing Z. mobilis targeting sequences and a subsequent recombination event that leads to loss of the suicide plasmid and a genome modification. A key feature of this strategy is that GFP expressed from the suicide plasmid allows easy identification of cells that have lost the plasmid by using a fluorescence activated cell sorter. Using this method, we demonstrated deletion of the gene encoding lactate dehydrogenase (ldh) and the operon for cellulose synthase (bcsABC). In addition, by modifying the plasmid design, we demonstrated targeted insertion of the crtIBE operon encoding a neurosporene biosynthetic pathway into the Z. mobilis genome without addition of any antibiotic resistance genes. We propose this approach will provide an efficient and flexible platform for improved genetic engineering of Z. mobilis.

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032.

BACKGROUND: Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2-8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain. RESULTS: In this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1-2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion. CONCLUSIONS: The complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.

Effective degradation of aflatoxin B1 using a novel thermophilic microbial consortium TADC7.

We constructed a novel thermophilic microbial consortium, TADC7, with stable and efficient aflatoxin B1 (AFB1) degradation activity. The microbial consortium degraded more than 95% of the toxin within 72h when cultured with AFB1, and the optimum temperature was 55-60°C. TADC7 tolerated high doses of AFB1, with no inhibitory effects up to 5000µgL-1 AFB1; moreover, the degradation kinetics fit well with the Monod model. The proteins or enzymes in the TADC7 cell-free supernatant played a major role in AFB1 degradation. AFB1 degradation by the cell-free supernatant was stable up to 90°C, with an optimal pH of 8-10. We performed 16S rRNA sequencing to determine TADC7 community structure dynamics; the results indicated that Geobacillus and Tepidimicrobium played major roles in AFB1 degradation.