Microbiological Research

To feed all of the world's people, it is necessary to sustainably increase agricultural productivity. One way to do this is through the increased use of plant growth-promoting bacteria; recently, scientists have developed a more profound understanding of the mechanisms employed by these bacteria to facilitate plant growth. Here, it is argued that the ability of plant growth-promoting bacteria that produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase to lower plant ethylene levels, often a result of various stresses, is a key component in the efficacious functioning of these bacteria. The optimal functioning of these bacteria includes the synergistic interaction between ACC deaminase and both plant and bacterial auxin, indole-3-acetic acid (IAA). These bacteria not only directly promote plant growth, they also protect plants against flooding, drought, salt, flower wilting, metals, organic contaminants, and both bacterial and fungal pathogens. While a considerable amount of both basic and applied work remains to be done before ACC deaminase-producing plant growth-promoting bacteria become a mainstay of plant agriculture, the evidence indicates that with the expected shift from chemicals to soil bacteria, the world is on the verge of a major paradigm shift in plant agriculture.

Zobellella denitrificans MW1 is a halotolerant, facultatively anaerobic bacterium with high poly(3-hydroxybutyrate) (PHB) productivity that lacked a complete genome sequence. Here we report its first complete circular genome (4.10 Mb, 63.6% GC), obtained by hybrid Illumina–Nanopore assembly, with multi-scale cultivation data. The genome encodes a conserved phaCAB operon, multiple sucrose uptake and catabolic systems, and a canonical Pho regulon with polyphosphate metabolism genes ( ppk , ppx ). Ten CRISPR arrays, an intact prophage and no acquired multidrug resistance determinants were identified. Carbohydrate utilization was broad yet selective: sucrose, glucose and fructose supported the highest biomass, sucrose yielding up to 76% PHB of cell dry weight (CDW) in flasks; sucrose-rich beet molasses sustained PHB accumulation in flasks and 5 L bioreactors. In single, non-replicated fed-batch runs, a high-phosphate process reached 23 g L⁻¹ CDW with minimal PHB, whereas a low-phosphate process reached 53 g L⁻¹ CDW with 78% PHB. Because each regime was run once, these data are observations rather than a statistically supported comparison; they suggest that phosphate availability may be an important variable governing the growth-versus-storage balance, and that sucrose-rich industrial side-streams can be converted into PHB. The genomic co-occurrence of the Pho regulon, polyphosphate metabolism and phaCAB offers a hypothesis that remains to be tested by expression, enzyme-activity and targeted genetic experiments. Overall, MW1 is established as a genomically resolved platform for PHB production from low-cost, sucrose-rich feedstocks under saline conditions.

Mercury (Hg) is a widespread contaminant that poses significant risks to human health, mainly through dietary exposure to methylmercury (MeHg). Strategies to reduce Hg bioaccesibility in the gastrointestinal tract are therefore of increasing interest. In this study, a probiotic bacterium, Lacticaseibacillus paracasei, was engineered to express different combinations of mer genes involved in Hg detoxification. Recombinant strains were evaluated for resistance to inorganic Hg [Hg(II)] and MeHg, as well as for their ability to remove these species from culture media. Expression of mer genes enhanced Hg resistance of the L. paracasei cells, with the strain carrying the full merETPAB1 gene set showing the highest tolerance. In contrast, expression of merB1 without merA increased MeHg-induced growth inhibition, indicating the toxicity of intracellularly generated Hg(II). Strains co-expressing merA and merB1 efficiently removed MeHg from culture media, achieving up to 93% decrease, likely via its reduction to volatile elemental mercury [Hg(0)], whereas Hg(II) removal was limited. MeHg removal by an L. paracasei strain expressing merETPAB1 was also observed in the presence of human intestinal microbiota under anaerobic conditions. However, when applied to the bioaccessible fraction of simulated digests of Hg-contaminated fish (Makaira nigricans), Hg removal was lower (20-40%) compared with pure MeHg conditions. These results provide proof of concept that genetically engineered lactic acid bacteria expressing mer genes can reduce Hg contents in food within simulated gastrointestinal environments. This approach represents a promising strategy to mitigate dietary exposure to Hg, although further optimization and in vivo validation are required.

The aerobic electron transport chain (ETC) is a major determinant of metabolic flexibility and ecological success in Pseudomonas, yet the evolutionary dynamics shaping its regulatory architecture remain poorly understood. Here we combine phylogenomics, promoter analysis, and functional assays across 249 Pseudomonas species to reveal extensive diversification in ETC composition and in the regulatory control of a key aerobic terminal oxidase, the Cyo ubiquinol oxidase. Cyo was detected in 83.5% of strains, and the regulatory regions controlling its expression displayed remarkable divergence. Promoter sequences upstream of cyoA segregated into five major classes with low or no similarity between groups. Reporter assays demonstrated that this promoter diversification translates into distinct regulatory behaviours. When cultured in a rich medium, Pseudomonas putida KT2440 exhibited a sharp early-exponential induction of cyoA, whereas Pseudomonas fluorescens, Pseudomonas syringae, Pseudomonas rhizosphaerae, and Pseudomonas aeruginosa showed a much lower induction. In a defined growth medium, Cyo activation varied strongly depending on the carbon source. These species-specific patterns were independent of growth rate, highlighting that regulatory evolution, rather than metabolic demand alone, drives Cyo expression dynamics. Loss of Cyo in P. putida reduced growth rate up to 37% and triggered broad transcriptional reprogramming involving respiration, carbon assimilation, and stress responses. Notably, lack of Cyo led to a > 13-fold increase in the expression of the CIO ubiquinol oxidase. Together, these results show that both the composition and regulatory control have undergone extensive evolutionary diversification in Pseudomonas. This regulatory rewiring enables lineage-specific respiratory behaviours that likely contribute to ecological adaptation.