Critical Effect of H2O2 in the Agar Plate on the Growth of Laboratory and Environmental Strains

Environmental micro-molar H2O2 reduces the efficiency of glyphosate biodegradation in soil

Glyphosate is one of the most widely used pesticides globally. The environmental micro-molar hydrogen peroxide (H2O2)-driven Fenton reaction has been reported to degrade herbicides in natural water. However, the impact of micro-molar H2O2 (50 μM) on the degradation of glyphosate in soil and glyphosate-degrading bacteria remains unclear. In this study, degradation of glyphosate in the sterilized and unsterilized soil system and MSM medium under micro-molar H2O2 was investigated; bacterial diversity, enzyme activity and gene abundance in the soil following micro-molar H2O2 addition were also investigated. The results indicated that the addition of micro-molar H2O2 facilitated the degradation of glyphosate in a sterilized environment, resulting in a 76.30% decrease in glyphosate within 30 days. The degradation of glyphosate increased by 52.32% compared to the control treatment. However, in an unsterilized environment, the addition of micro-molar H2O2 leads to a reduction in the biodegradation efficiency of glyphosate. Bacteria, enzymes and specific genes were found to be affected to varying degrees. Firstly, micro-molar H2O2 affects the relative abundance of functional bacteria related to glyphosate degradation, such as Afipia, Microcoleus and Pseudomonas. Secondly, micro-molar H2O2 resulted in a decrease in soil phosphatase activity. Thirdly, the expression of resistance genes was affected, particularly the glyphosate resistance gene aroA. The findings presented a novel research perspective on the degradation of soil glyphosate by micro-molar H2O2.

Extraction Methods Determine the Quality of Soil Microbiota Acquisition

The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources.

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.

Genome Sequences of Comamonadaceae Bacteria OS-1 and OS-4, Two Highly H2O2-Sensitive Strains Isolated from Pond Water

The Comamonadaceae bacterial strains OS-1 and OS-4 were isolated from pond water and were found to be highly sensitive to hydrogen peroxide in the agar plates. Here, we report the nearly complete and complete genome sequences, respectively, of these two strains.

Chlorate Contamination in Commercial Growth Media as a Source of Phenotypic Heterogeneity within Bacterial Populations

Under anaerobic conditions, chlorate is reduced to chlorite, a cytotoxic compound that triggers oxidative stress within bacterial cultures. We previously found that BD Bacto Casamino Acids were contaminated with chlorate. In this study, we investigated whether chlorate contamination is detectable in other commercial culture media. We provide evidence that in addition to different batches of BD Bacto Casamino Acids, several commercial agar powders are contaminated with chlorate. A direct consequence of this contamination is that, during anaerobic growth, Escherichia coli cells activate the expression of msrP, a gene encoding periplasmic methionine sulfoxide reductase, which repairs oxidized protein-bound methionine. We further demonstrate that during aerobic growth, progressive oxygen depletion triggers msrP expression in a subpopulation of cells due to the presence of chlorate. Hence, we propose that chlorate contamination in commercial growth media is a source of phenotypic heterogeneity within bacterial populations. IMPORTANCE Agar is arguably the most utilized solidifying agent for microbiological media. In this study, we show that agar powders from different suppliers, as well as certain batches of BD Bacto Casamino Acids, contain significant levels of chlorate. We demonstrate that this contamination induces the expression of a methionine sulfoxide reductase, suggesting the presence of intracellular oxidative damage. Our results should alert the microbiology community to a pitfall in the cultivation of microorganisms under laboratory conditions.

Self-cloning of the Catalase Gene in Environmental Isolates Improves Their Colony-forming Abilities on Agar Media

Hydrogen peroxide (H₂O₂) inhibits microbial growth at a specific concentration. However, we previously isolated two environmental bacterial strains that exhibited sensitivity to a lower H₂O₂ concentration in agar plates. Putative catalase genes, which degrade H₂O₂, were detected in their genomes. We herein elucidated the characteristics of these putative genes and their products using a self-cloning technique. The products of the cloned genes were identified as functional catalases. The up-regulation of their expression increased the colony-forming ability of host cells under H₂O₂ pressure. The present results demonstrated high sensitivity to H₂O₂ even in microbes possessing functional catalase genes.