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Sensors (Basel, Switzerland) Nov 2022Microbial mediator biosensors for surface water toxicity determination make it possible to carry out an early assessment of the environmental object’s quality without...
Microbial mediator biosensors for surface water toxicity determination make it possible to carry out an early assessment of the environmental object’s quality without time-consuming standard procedures based on standard test-organisms, and provide broad opportunities for receptor element modifying depending on the required operational parameters analyzer. Four microorganisms with broad substrate specificity and nine electron acceptors were used to form a receptor system for toxicity assessment. Ferrocene was the most effective mediator according to its high rate constant of interaction with the microorganisms (0.33 ± 0.01 dm3/(g × s) for yeast Saccharomyces cerevisiae). Biosensors were tested on samples containing four heavy metal ions (Cu2+, Zn2+, Pb2+, Cd2+), two phenols (phenol and p-nitrophenol), and three natural water samples. The «ferrocene- Escherichia coli» and «ferrocene-Paracoccus yeei, E. coli association» systems showed good operational stability with a relative standard deviation of 6.9 and 7.3% (14 measurements) and a reproducibility of 7 and 5.2% using copper (II) ions as a reference toxicant. Biosensor analysis with these systems was shown to highly correlate with the results of the standard method using Chlorella algae as a test object. Developed biosensors allow for a valuation of the polluted natural water’s impact on the ecosystem via an assessment of the influence on bacteria and yeast in the receptor system. The systems could be used in toxicological monitoring of natural waters.
Topics: Metallocenes; Water; Escherichia coli; Saccharomyces cerevisiae; Reproducibility of Results; Chlorella; Ecosystem; Biosensing Techniques; Metals, Heavy; Water Pollutants, Chemical
PubMed: 36366221
DOI: 10.3390/s22218522 -
Microorganisms Oct 2022Hydrogen sulfide (H2S) is a toxic and corrosive component that commonly occurs in biogas. In this study, H2S removal from swine-waste biogas using sulfur-oxidizing...
Hydrogen sulfide (H2S) is a toxic and corrosive component that commonly occurs in biogas. In this study, H2S removal from swine-waste biogas using sulfur-oxidizing Paracoccus versutus CM1 immobilized in porous glass (PG) and polyurethane foam (PUF) biofilters was investigated. Bacterial compositions in the biofilters were also determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The biofilters were first tested on a laboratory scale under three space velocities (SV): 20, 30, and 40 h−1. Within 24 h, at an SV of 20 h−1, PG and PUF biofilters immobilized with P. versutus CM1 removed 99.5% and 99.7% of H2S, respectively, corresponding to the elimination capacities (EC) of 83.5 and 86.2 gm−3 h−1. On a pilot scale, with the horizontal PG-P. versutus CM1 biofilter operated at an SV of 30 h−1, a removal efficiency of 99.7% and a maximum EC of 113.7 gm−3 h−1 were achieved. No reduction in methane content in the outlet biogas was observed under these conditions. The PCR-DGGE analysis revealed that Paracoccus, Acidithiobacillus, and Thiomonas were the predominant bacterial genera in the biofilters, which might play important roles in H2S removal. This PG−P. versutus CM1 biofiltration system is highly efficient for H2S removal from swine-waste biogas.
PubMed: 36363739
DOI: 10.3390/microorganisms10112148 -
Frontiers in Microbiology 2022Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria...
Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. , , , , , , , and were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to , , , , , and , whose degradation rates were higher in crude oil (70.3-78.0%) than that in diesel oil (62.7-66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, F7, F1, F8, J5, N3, and N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.
PubMed: 36338091
DOI: 10.3389/fmicb.2022.920067 -
Frontiers in Microbiology 2022Complex dynamic bacterial-fungal interactions play key roles during mushroom growth, ranging from mutualism to antagonism. These interactions convey a large influence on...
Complex dynamic bacterial-fungal interactions play key roles during mushroom growth, ranging from mutualism to antagonism. These interactions convey a large influence on mushroom's mycelial and fruiting body formation during mushroom cultivation. In this study, high-throughput amplicon sequencing was conducted to investigate the structure of bacterial communities in spent mushroom substrates obtained from cultivation of two different groups of with (A) high yield and (B) low yield of fruiting body production. It was found that species richness and diversity of microbiota in group (A) samples were significantly higher than in group (B) samples. Among the identified 765 bacterial OTUs, 5 bacterial species found to exhibit high differential abundance between group (A) and group (B) were , , , , and . The co-cultivation with selected bacterial strains showed that TBRC 12900 co-cultivated with TBRC-BCC 42794 promoted a high level of mycelial growth. Proteomics analysis was performed to elucidate the biological activities involved in the mutualistic association between TBRC 12900 and TBRC-BCC 42794. After co-cultivation of TBRC 12900 and TBRC-BCC 42794, 1,616 proteins were detected including 578 proteins of origin and 1,038 proteins of origin. Functional analysis and PPI network construction revealed that the high level of mycelial growth in the co-culture condition most likely resulted from concerted actions of (a) carbohydrate-active enzymes including hydrolases, glycosyltransferases, and carbohydrate esterases important for carbohydrate metabolism and cell wall generation/remodeling, (b) peptidases including cysteine-, metallo-, and serine-peptidases, (c) transporters including the ABC-type transporter superfamily, the FAT transporter family, and the VGP family, and (d) proteins with proposed roles in formation of metabolites that can act as growth-promoting molecules or those normally contain antimicrobial activity (e.g., indoles, terpenes, -lactones, lanthipeptides, iturins, and ectoines). The findings will provide novel insights into bacterial-fungal interactions during mycelial growth and fruiting body formation. Our results can be utilized for the selection of growth-promoting bacteria to improve the cultivation process of with a high production yield, thus conveying potentially high socio-economic impact to mushroom agriculture.
PubMed: 36299733
DOI: 10.3389/fmicb.2022.1006446 -
Membranes Oct 2022Biomembranes based on an organosilica sol-gel matrix were used to immobilize bacteria VKM B-3302 as part of a biochemical oxygen demand (BOD) biosensor....
Biomembranes based on an organosilica sol-gel matrix were used to immobilize bacteria VKM B-3302 as part of a biochemical oxygen demand (BOD) biosensor. Diethoxydimethylsilane (DEDMS) and tetraethoxysilane (TEOS) were used as precursors to create the matrix in a 1:1 volume ratio. The use of scanning electron microscopy (SEM) and the low-temperature nitrogen adsorption method (BET) showed that the sol-gel matrix forms a capsule around microorganisms that does not prevent the exchange of substrates and waste products of bacteria to the cells. The use of DEDMS as part of the matrix made it possible to increase the sensitivity coefficient of the biosensor for determining BOD by two orders of magnitude compared to a biosensor based on methyltriethoxysilane (MTES). Additionally, the long-term stability of the bioreceptor increased to 68 days. The use of such a matrix neutralized the effect of heavy metal ions on the microorganisms' catalytic activity in the biosensor. The developed biosensor was used to analyze water samples from water sources in the Tula region (Russia).
PubMed: 36295743
DOI: 10.3390/membranes12100983 -
Microbiology Spectrum Dec 2022High temperature growth/survival was revealed in a phylogenetic relative (SMMA_5) of the mesophilic isolated from the 78 to 85°C water of a Trans-Himalayan...
High temperature growth/survival was revealed in a phylogenetic relative (SMMA_5) of the mesophilic isolated from the 78 to 85°C water of a Trans-Himalayan sulfur-borax spring. After 12 h at 50°C, or 45 min at 70°C, in mineral salts thiosulfate (MST) medium, SMMA_5 retained ~2% colony forming units (CFUs), whereas comparator had 1.5% and 0% CFU left at 50°C and 70°C, respectively. After 12 h at 50°C, the thermally conditioned sibling SMMA_5_TC exhibited an ~1.5 time increase in CFU count; after 45 min at 70°C, SMMA_5_TC had 7% of the initial CFU count. 1,000-times diluted Reasoner's 2A medium, and MST supplemented with lithium, boron, or glycine-betaine, supported higher CFU-retention/CFU-growth than MST. Furthermore, with or without lithium/boron/glycine-betaine, a higher percentage of cells always remained metabolically active, compared with what percentage formed single colonies. SMMA_5, compared with other , contained 335 unique genes: of these, 186 encoded hypothetical proteins, and 83 belonged to orthology groups, which again corresponded mostly to DNA replication/recombination/repair, transcription, secondary metabolism, and inorganic ion transport/metabolism. The SMMA_5 genome was relatively enriched in cell wall/membrane/envelope biogenesis, and amino acid metabolism. SMMA_5 and SMMA_5_TC mutually possessed 43 nucleotide polymorphisms, of which 18 were in protein-coding genes with 13 nonsynonymous and seven radical amino acid replacements. Such biochemical and biophysical mechanisms could be involved in thermal stress mitigation which streamline the cells' energy and resources toward system-maintenance and macromolecule-stabilization, thereby relinquishing cell-division for cell-viability. Thermal conditioning apparently helped inherit those potential metabolic states which are crucial for cell-system maintenance, while environmental solutes augmented the indigenous stability-conferring mechanisms. For a holistic understanding of microbial life's high-temperature adaptation, it is imperative to explore the biology of the phylogenetic relatives of mesophilic bacteria which get stochastically introduced to geographically and geologically diverse hot spring systems by local geodynamic forces. Here, endurance of high heat up to the extent of growth under special (habitat-inspired) conditions was discovered in a hot-spring-dwelling phylogenetic relative of the mesophilic species. Thermal conditioning, extreme oligotrophy, metabolic deceleration, presence of certain habitat-specific inorganic/organic solutes, and potential genomic specializations were found to be the major enablers of this conditional (acquired) thermophilicity. Feasibility of such phenomena across the taxonomic spectrum can well be paradigm changing for the established scopes of microbial adaptation to the physicochemical extremes. Applications of conditional thermophilicity in microbial process biotechnology may be far reaching and multifaceted.
Topics: Betaine; Hot Springs; Phylogeny; Paracoccus; Boron; Lithium; Amino Acids; Glycine
PubMed: 36287077
DOI: 10.1128/spectrum.01606-22 -
Applied and Environmental Microbiology Nov 2022Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic...
Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic respiration. This implies a selective advantage of the stringent O repression of denitrification gene transcription, which is found in most denitrifying bacteria. In some bacteria, the metabolic burden of adaptation can be minimized further by phenotypic diversification, colloquially termed "bet-hedging," where all cells synthesize the NO reductase (NosZ) but only a minority synthesize nitrite reductase (NirS), as demonstrated for the model strain Paracoccus denitrificans. We hypothesized that the cells lacking NirS would be entrapped in anoxia but with the possibility of escape if supplied with O or NO. To test this, cells were exposed to gradual O depletion or sudden anoxia and subsequent spikes of O and NO. The synthesis of NirS in single cells was monitored by using an fusion replacing the native , and their growth was detected as dilution of green, fluorescent fluorescein isothiocyanate (FITC) stain. We demonstrate anoxic entrapment due to e-acceptor deprivation and show that O spiking leads to bet-hedging, while NO spiking promotes NirS synthesis and growth in all cells carrying NosZ. The cells rescued by the NO spike had much lower respiration rates than those rescued by the O spike, however, which could indicate that the well-known autocatalytic synthesis of NirS via NO production requires O. Our results bring into relief a fitness advantage of pairing restrictive expression with universal NosZ synthesis in energy-limited systems. Denitrifying bacteria have evolved elaborate regulatory networks securing their respiratory metabolism in environments with fluctuating oxygen concentrations. Here, we provide new insight regarding their bet-hedging in response to hypoxia, which minimizes their NO emissions because all cells express NosZ, reducing NO to N, while a minority express NirS + Nor, reducing NO to NO. We hypothesized that the cells without Nir were entrapped in anoxia, without energy to synthesize Nir, and that they could be rescued by short spikes of O or NO. We confirm such entrapment and the rescue of all cells by an NO spike but only a fraction by an O spike. The results shed light on the role of O repression in bet-hedging and generated a novel hypothesis regarding the autocatalytic expression via NO production. Insight into the regulation of denitrification, including bet-hedging, holds a clue to understanding, and ultimately curbing, the escalating emissions of NO, which contribute to anthropogenic climate forcing.
Topics: Bacteria; Denitrification; Hypoxia; Nitrite Reductases; Nitrous Oxide; Oxidoreductases; Paracoccus denitrificans
PubMed: 36250705
DOI: 10.1128/aem.01053-22 -
International Journal of Molecular... Oct 2022Yeasts provide attractive host/vector systems for heterologous gene expression. The currently used yeast-based expression platforms include mesophilic and thermotolerant...
Yeasts provide attractive host/vector systems for heterologous gene expression. The currently used yeast-based expression platforms include mesophilic and thermotolerant species. A eukaryotic expression system working at low temperatures could be particularly useful for the production of thermolabile proteins and proteins that tend to form insoluble aggregates. For this purpose, an expression system based on an Antarctic psychrotolerant yeast Debaryomyces macquariensis strain D50 that is capable of growing at temperatures ranging from 0 to 30 °C has been developed. The optimal physical culture conditions for D. macquariensis D50 in a fermenter are as follows: temperature 20 °C, pH 5.5, aeration rate of 1.5 vvm, and a stirring speed of 300 rpm. Four integrative plasmid vectors equipped with an expression cassette containing the constitutive GAP promoter and CYC1 transcriptional terminator from D. macquariensis D50 were constructed and used to clone and express a gene-encoding cold-active β-d-galactosidase of Paracoccus sp. 32d. The yield was 1150 U/L of recombinant yeast culture. Recombinant D. macquariensis D50 strains were mitotically stable under both selective and non-selective conditions. The D. macquariensis D50 host/vector system has been successfully utilized for the synthesis of heterologous thermolabile protein, and it can be an alternative to other microbial expression systems.
Topics: Fermentation; Galactosidases; Paracoccus; Saccharomycetales; beta-Galactosidase
PubMed: 36232994
DOI: 10.3390/ijms231911691 -
Biochemical and Biophysical Research... Nov 2022To explore the association between phenotype and the gut microbiome following damage to the GRID2 gene.
OBJECTIVE
To explore the association between phenotype and the gut microbiome following damage to the GRID2 gene.
METHODS
Ten wild-type (WT) mice and 11 GRID2 knockout heterozygous mice (GRID2(±)) of a similar age and weight were randomly selected. Fresh feces were collected from both groups of mice under specified pathogen-free (SPF) conditions. The bacterial genomes were extracted from the feces, the 16S rRNA genes were sequenced, and the data were analyzed to determine clustering, diversity, abundance, LEfSe, and functional differences. Differential expression and enrichment analyses of the RNA-seq and protein levels of the GRID2 gene were also performed using data in the GENE database and the new version of the Human Protein Atlas portal (www.proteinatlas.org).
RESULTS
The diversity analysis showed differences in species composition between the two groups at different levels. At phylum level, compared with the WT group, the distribution was more bacteriophages but showed a lower content of Tenericutes in the GRID2(±) group. At the order level, compared with the WT group, a higher content of Actinomycetales and Bacteriophages were found in the GRID2(±) group. The species difference analysis showed that 17 species, including E. faecalis and Paracoccus spp., showed differences in content between the two groups. LEfSe analysis showed that the abundance of Clostridiaceae, Allobaculum, and other groups decreased in the GRID2(±) group compared with the WT group, while Mycoplasma, Sphingomonas, and Alphaproteobacteria increased in abundance. Functional analysis revealed eight differential functions between the WT and GRID2(±) group (P < 0.05). The most significantly disrupted were neuroactive ligand-receptor interactions (P < 9.99e-4). In addition, the differential expression and enrichment analyses performed at RNA-seq and protein levels revealed that the GRID2 gene showed organ-specific expression and was mainly enriched in the brain tissue.
CONCLUSIONS
Compared with the WT group, the defective GRID2 gene affected the species richness and composition of gut microbes in the GRID2(±) mice, which in turn affected the function of gut microbes, leading to the disruption of neuroactive ligand-receptor interactions. Our findings indicate that the host gene, GRID2, can influence the abundance of a subset of gut microbes but the exact mechanisms still need further investigation.
Topics: Animals; Humans; Mice; Bacteria; Bacteriophages; Feces; Gastrointestinal Microbiome; Ligands; RNA, Ribosomal, 16S; Receptors, Glutamate; Host Microbial Interactions
PubMed: 36162328
DOI: 10.1016/j.bbrc.2022.09.006 -
Integrated pathway engineering and transcriptome analysis for improved astaxanthin biosynthesis in .Synthetic and Systems Biotechnology Dec 2022Astaxanthin is a high value carotenoid with a broad range of commercial applications due to its superior antioxidant properties. In this study, β-carotene-producing...
Astaxanthin is a high value carotenoid with a broad range of commercial applications due to its superior antioxidant properties. In this study, β-carotene-producing XK17 constructed in the lab was employed for astaxanthin biosynthesis. The catalytic effects of β-carotene ketolase CrtW and β-carotene hydroxylase CrtZ from various species were investigated. The PspCrtW from sp. and HpCrtZ from were confirmed to be the best combination in converting β-carotene. Several key bottlenecks in biomass and astaxanthin biosynthesis were effectively eliminated by optimizing the expression of the above enzymes and restoring uracil/leucine biosynthesis. In addition, the effects of astaxanthin biosynthesis on cell metabolism were investigated by integrated analysis of pathway modification and transcriptome information. After further optimization, strain DN30 was able to synthesize up to 730.3 mg/L astaxanthin in laboratory 5-L fermenter. This study provides a good metabolic strategy and a sustainable development platform for high-value carotenoid production.
PubMed: 36092272
DOI: 10.1016/j.synbio.2022.08.001