Carbon Source Influence on Extracellular pH Changes along Bacterial Cell-Growth

Antibiotic Indexing and Heavy Metal Reduction Potential of Four Multi-metal Tolerant Bacterial Strains in Real-Time Sanitary Landfill Leachate Matrix

Sanitary leachate from urban landfills is known to be contaminated with multi-metals and residual antibiotics. Current research edges on exploring the multi-metal and antibiotic sensitivity profile of four indigenous strains, "Brevibacillus spp. Leclercia spp. Pseudescherichia spp., and Brucella spp." isolated from the leachate of a sanitary landfill in a tropical region. Indigenous isolates were observed to be antibiotic-resistant and have high tolerance against eight of the ten tested metals except Cu & Co. It was observed that interaction with multi-metals in laboratory conditions significantly altered the cell morphology of bacterial strains, as depicted by Scanning Electron Microscope. Metal adsorption onto the microbial surface was deciphered through Electron Dispersive Spectrometer analysis and elemental mapping. Application of isolated strains into real-time leachate matrix exhibits a complete reduction of Ag and Zn and for other tested metals. Their response to these toxicants may facilitate their application in bioremediation-based treatment technologies for urban landfill leachate.

ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction

Adenosine-5'-triphosphate (ATP), the primary energy currency in cellular processes, drives metabolic activities and biosynthesis. Despite its importance, understanding intracellular ATP dynamics' impact on bioproduction and exploiting it for enhanced bioproduction remains largely unexplored. Here, we harness an ATP biosensor to dissect ATP dynamics across different growth phases and carbon sources in multiple microbial strains. We find transient ATP accumulations during the transition from exponential to stationary growth phases in various conditions, coinciding with fatty acid (FA) and polyhydroxyalkanoate (PHA) production in Escherichia coli and Pseudomonas putida, respectively. We identify carbon sources (acetate for E. coli, oleate for P. putida) that elevate steady-state ATP levels and boost FA and PHA production. Moreover, we employ ATP dynamics as a diagnostic tool to assess metabolic burden, revealing bottlenecks that limit limonene bioproduction. Our results not only elucidate the relationship between ATP dynamics and bioproduction but also showcase its value in enhancing bioproduction in various microbial species.

Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation

Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in E. coli populations experimentally evolved under repeated long-term starvation conditions, during which feast and famine result in drastic environmental pH fluctuations. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers a plastic alkaline-induced reduction of Rho function that, when found in tandem with a ΔydcI allele, leads to intracellular alkalinization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species originating from fluctuating alkaline environments. Our results suggest that Arg to His substitutions in global regulators of gene expression can serve to rapidly coordinate complex responses through pH sensing and shed light on how cellular populations across the tree of life use environmental cues to coordinate rapid responses to complex, fluctuating environments.

The Metabolomics Changes in Luria-Bertani Broth Medium under Different Sterilization Methods and Their Effects on Bacillus Growth

Luria-Bertani broth (LB) culture medium is a commonly used bacterial culture medium in the laboratory. The nutrient composition, concentration, and culture conditions of LB medium can influence the growth of microbial strains. The purpose of this article is to demonstrate the impact of LB liquid culture medium on microbial growth under different sterilization conditions. In this study, LB medium with four different treatments was used, as follows: A, LB medium without treatments; B, LB medium with filtration; C, LB medium with autoclaving; and D, LB medium with autoclaving and cultured for 12 h. Subsequently, the protein levels and antioxidant capacity of the medium with different treatments were measured, and the effects of the different LB medium treatments on the growth of microorganisms and metabolites were determined via 16s rRNA gene sequencing and metabolomics analysis, respectively. Firmicutes and Lactobacillus were the dominant microorganisms, which were enriched in fermentation and chemoheterotrophy. The protein levels and antioxidant capacity of the LB medium with different treatments were different, and with the increasing concentration of medium, the protein levels were gradually increased, while the antioxidant capacity was decreased firstly and then increased. The growth trend of Bacillus subtilis, Bacillus paralicheniformis, Micrococcus luteus, and Alternaria alternata in the medium with different treatments was similar. Additionally, 220 and 114 differential metabolites were found between B and C medium, and between C and D medium, which were significantly enriched in the "Hedgehog signaling pathway", "biosynthesis of plant secondary metabolites", "ABC transporters", "arginine and proline metabolism", and "linoleic acid metabolism". LB medium may be a good energy source for Lactobacillus growth with unsterilized medium, and LB medium filtered with a 0.22 μm filter membrane may be used for bacterial culture better than culture medium after high-pressure sterilization. LB medium still has the ability for antioxidation and to keep bacteria growth whether or not autoclaved, indicating that there are some substances that can resist a high temperature and pressure and still maintain their functions.

Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes

Following the completion of an adaptive evolution experiment, fitness evaluations are routinely conducted to assess the magnitude of adaptation. In doing so, proper consideration should be given when determining the appropriate methods as trade-offs may exist between accuracy and throughput. Here, we present three instances in which small changes in the framework or execution of fitness evaluations significantly impacted the outcomes. The first case illustrates that discrepancies in fitness conclusions can arise depending on the approach to evaluating fitness, the culture vessel used, and the sampling method. The second case reveals that variations in environmental conditions can occur associated with culture vessel material. Specifically, these subtle changes can greatly affect microbial physiology leading to changes in the culture pH and distorting fitness measurements. Finally, the last case reports that heterogeneity in CFU formation time can result in inaccurate fitness conclusions. Based on each case, considerations and recommendations are presented for future adaptive evolution experiments.

β-Alanine Metabolism Leads to Increased Extracellular pH during the Heterotrophic Ammonia Oxidation of Pseudomonas putida Y-9

The mechanisms underlying the increase in external pH caused by heterotrophic nitrification and aerobic denitrification microorganisms during ammonia oxidation were unclear. This work demonstrated that after culturing Pseudomonas putida Y-9 for 60 h in a medium with ammonium nitrogen as the sole nitrogen source at an initial pH of 7.20, the pH value increased to 9.21. GC-TOF-MS analysis was used to compare the significantly regulated metabolites and related metabolic pathways between different time points. The results showed that the consumption of H+ in the conversion of malonic acid to 3-hydroxypropionic acid in the β-alanine metabolic pathway was the main reason for the increase in pH. RT-qPCR confirmed that the functional gene ydfG dominated the consumption of H+. This study provides new research ideas for the change of external pH caused by bacterial metabolism and further expands the understanding of the interaction between bacteria and the environment.

Valorization of agro-industrial wastes into polyhydroxyalkanoates-rich single-cell proteins to enable a circular waste-to-feed economy

Recovering and converting carbon and nutrients from waste streams into healthy single-cell proteins (SCPs) can be an effective strategy to address costly waste management and support the increasing animal feed demand for the global food supply. Recently, SCPs rich in polyhydroxybutyrate (PHB) have been identified as an effective biocontrol healthy feed to replace conventional antibiotics-supplemented aquaculture feed. PHB, an intercellular polymer of short-chain-length (SCL) hydroxy-fatty acids, is a common type of polyhydroxyalkanoates (PHA) that can be microbially produced from various organics, including agro-industrial wastes. The complex chemical properties of agro-industrial wastes might produce SCPs containing PHA with SCL and/or medium chain-length (MCL) hydroxy-fatty acids. However, the effects of MCL-PHA-containing SCPs on aqua species' health and disease-fighting ability remains poorly understood. This study investigated the feasibility of producing various PHA-containing SCPs from renewable agro-industrial wastes/wastewaters, the effectiveness of SCL- and MCL-PHA as biocontrol agents, and the effects of these PHA-rich SCPs on the growth and disease resistance of an aquaculture animal model, brine shrimp Artemia. Zobellella denitrificans ZD1 and Pseudomonas oleovorans were able to grow on different pure substrates and agro-industrial wastes/wastewaters to produce various SCL- and/or MCL-PHA-rich SCPs. Low doses of MCL-fatty acids (i.e., PHA intermediates) efficiently suppressed the growth of aquaculture pathogens. Moreover, MCL-PHA-rich SCPs served as great food/energy sources for Artemia and improved Artemia's ability to fight pathogens. This study offers a win-win approach to address the challenges of wastes/wastewater management and feed supply faced by the aquaculture industry.

Harnessing the Potential of Bacillus altitudinis MT422188 for Copper Bioremediation

The contamination of heavy metals is a cause of environmental concern across the globe, as their increasing levels can pose a significant risk to our natural ecosystems and public health. The present study was aimed to evaluate the ability of a copper (Cu)-resistant bacterium, characterized as Bacillus altitudinis MT422188, to remove Cu from contaminated industrial wastewater. Optimum growth was observed at 37°C, pH 7, and 1 mm phosphate, respectively. Effective concentration 50 (EC50), minimum inhibitory concentration (MIC), and cross-heavy metal resistance pattern were observed at 5.56 mm, 20 mm, and Ni > Zn > Cr > Pb > Ag > Hg, respectively. Biosorption of Cu by live and dead bacterial cells in its presence and inhibitors 1 and 2 (DNP and DCCD) was suggestive of an ATP-independent efflux system. B. altitudinis MT422188 was also able to remove 73 mg/l and 82 mg/l of Cu at 4th and 8th day intervals from wastewater, respectively. The presence of Cu resulted in increased GR (0.004 ± 0.002 Ug−1FW), SOD (0.160 ± 0.005 Ug−1FW), and POX (0.061 ± 0.004 Ug−1FW) activity. Positive motility (swimming, swarming, twitching) and chemotactic behavior demonstrated Cu as a chemoattractant for the cells. Metallothionein (MT) expression in the presence of Cu was also observed by SDS-PAGE. Adsorption isotherm and pseudo-kinetic-order studies suggested Cu biosorption to follow Freundlich isotherm as well as second-order kinetic model, respectively. Thermodynamic parameters such as Gibbs free energy (∆G°), change in enthalpy (∆H° = 10.431 kJ/mol), and entropy (∆S° = 0.0006 kJ/mol/K) depicted the biosorption process to a feasible, endothermic reaction. Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), and Energy-Dispersive X-Ray Spectroscopy (EDX) analyses revealed the physiochemical and morphological changes in the bacterial cell after biosorption, indicating interaction of Cu ions with its functional groups. Therefore, these features suggest the potentially effective role of B. altitudinis MT422188 in Cu bioremediation.

Influence of the Carbon and Nitrogen Sources on Diabolican Production by the Marine Vibrio diabolicus Strain CNCM I-1629

Recent advances in glycobiotechnology show that bacterial exopolysaccharides (EPS) presenting glycosaminoglycan (GAG)-like properties can provide a valuable source of bio-active macromolecules for industrial applications. The HE800 EPS, named diabolican, is a marine-derived anionic high-molecular-weight polysaccharide produced by Vibrio diabolicus CNCM I-1629 which displays original structural features close to those of hyaluronic acid. We investigated the impact of carbon and nitrogen substrates on both Vibrio diabolicus growth and diabolican production. Both substrates were screened by a one-factor-at-a-time method, and experimental designs were used to study the effect of glucose, mannitol, and ammonium acetate various concentrations. Results showed that the medium composition affected not only the bacterium growth and EPS yield, but also the EPS molecular weight (MW). EPS yields of 563 and 330 mg L⁻¹ were obtained in the presence of 69.3 g L⁻¹ glucose and 24.6 g L⁻¹ mannitol, respectively, both for 116.6 mM ammonium acetate. MW was the highest, with 69.3 g L⁻¹ glucose and 101.9 mM ammonium acetate (2.3 × 10⁶ g mol⁻¹). In parallel, the bacterial maximum specific growth rate was higher when both carbon and nitrogen substrate concentrations were low. This work paves the way for the optimization of marine exopolysaccharide production of great interest in the fields of human health and cosmetics.

Insight into the biotechnology potential of Alicyclobacillus tolerans from whole genome sequence analysis and genome-scale metabolic network modeling

Extremophilic bacteria have numerous uncovered biotechnological potentials. Acidophilic bacteria are important iron oxidizers that are valuable in bioleaching and in studying extreme environments on earth and in space. Despite their obvious potential, little is known about the genetic traits that underpin their metabolic functions, which are equally poorly understood from a mechanistic perspective. Novel bioinformatics and computational biology pipelines can be used to analyze whole genomes to obtain insights into the phenotypic potential of organisms as well as develop a mathematical model representation of metabolism. Whole-genome sequence analysis and a genome-scale metabolic network model was curated for an iron-oxidizing bacterium initially isolated from an acid mine drainage in Turkey, previously identified as Alicyclobacillus tolerans. The genome contained a high proportion of genes for energy generation from carbohydrates, amino acids synthesis and conversion, nucleic acid metabolism and repair which contribute to robust adaption to their extreme environments. Several candidate genes for pyrite metabolism, iron uptake, regulation and storage, as well as genes for resistance to important heavy metals were annotated. A curated genome-scale metabolic network analysis accurately predicted facultative anaerobic growth, heterotrophic characteristics, and growth on a wide variety of carbon sources. This is the first in-depth in silico analysis of A. tolerans to the best of our knowledge which is expected to lay the groundwork for future research and drive innovations in environmental microbiology and biotechnological applications. The genomic data and mechanistic framework will have applications in biomining, synthetic geomicrobiology on earth, as well as for space exploration and settlement.

Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family level. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (one sugar-one organic acid). Furthermore, sugar-acid communities are generally more similar to the sugar than the acid community, which may be explained by family-level asymmetries in nutrient benefits. Overall, our results suggest that regularities in how nutrients interact may help predict community responses to dietary changes.

Assessment of heavy metal bioremediation potential of bacterial isolates from landfill soils

Indiscriminate disposal of wastes on landfills has led to increase in heavy metal contamination in landfill soils. However, the ability of the indigenous microorganisms to remediate the polluted environment can be of great influence in reclamation of such soils. The objectives of this study were to assess the bioremediation potential of the screened indigenous bacteria and evaluate the effects of carbon source and pH in the enhancement of the bioremediation process. Bacterial isolates from landfill sites were screened for their capability to utilize heavy metal (Cd and Pb). Nutrient Agar was supplemented with five different concentrations of each metal (25 to 600 mgL^-1). Viable counts of the isolates were taken four times at two days interval. Pseudomonas aeruginosa, Klebsiella edwardsii and Enterobacter cloacae were selected based on their tolerance to heavy metal for remediation process. Peptone broth was also supplemented using different concentrations of heavy metals. The remediation process was assessed by monitoring the growth of biomass using UV spectrophotometer at 600 nm and the residual heavy metal was evaluated after 8 days of incubation using AAS. Pseudomonas aeruginosa exhibited the highest bioremediation potential among the bacterial isolates with 58.80 and 33.67 remediation percentage in 50 mg Cd L^-1 and 300 mg Pb L^-1 . However, higher remediation percentage (79.87 and 92.41) was observed by Klebsiella edwardsii through addition of carbon source (5 g/L) and varying the pH (6) of the media in the heavy metal contaminated medium. The results of this study indicate that the effectiveness of the indigenous bacteria in remediation process can be enhanced through the addition of carbon source and increase pH for effective reclamation of contaminated soil.