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Current Microbiology Jul 2024Pantoea agglomerans inhabit diverse ecological niches, ranging from epiphytes and endophytes in plants, body of animals, and occasionally in the human system. This... (Comparative Study)
Comparative Study
Pantoea agglomerans inhabit diverse ecological niches, ranging from epiphytes and endophytes in plants, body of animals, and occasionally in the human system. This multifaceted bacterium contributes substantially to plant growth promotion, stress resilience, and biocontrol but can also act as a pathogen to its host. The genetic determinants underlying these diverse functions remain largely unfathomed and to uncover this phenomenon, nineteen strains of Pantoea agglomerans were selected and analyzed. Genome-to-Genome Distance Calculator (GGDC) which uses the Genome Blast Distance Phylogeny (GBDP) technique to calculate digital DDH values. Phylogenetic analysis via Genome-to-Genome distance, Average Nucleotide Identity, and Amino Acid Identity calculation revealed that all strains belonged to the genus Pantoea. However, strain 33.1 had a lower value than the threshold for the same species delineation. Bacterial Pan Genome Analysis (BPGA) Pipeline and MinPath analysis revealed genetic traits associated with environmental resilience, such as oxidative stress, UV radiation, temperature extremes, and metabolism of distinct host-specific carbohydrates. Protein-protein interactome analysis illustrated osmotic stress proteins closely linked with core proteins, while heavy metal tolerance, nitrogen metabolism, and Type III and VI secretion systems proteins generally associated with pathogenicity formed a separate network, indicating strain-specific characteristics. These findings shed new light on the intricate genetic architecture of Pantoea agglomerans, revealing its adaptability to inhabit diverse niches and thrive in varied environments.
Topics: Pantoea; Genome, Bacterial; Phylogeny; Genomics; Adaptation, Physiological; Humans; Animals; Plants; Bacterial Proteins
PubMed: 38955887
DOI: 10.1007/s00284-024-03763-0 -
World Journal of Microbiology &... Jul 2024The aim of the present study is to develop a pH-sensing biopolymer film based on the immobilization of red cabbage extract (RCE) within bacterial cellulose (BC) to...
The aim of the present study is to develop a pH-sensing biopolymer film based on the immobilization of red cabbage extract (RCE) within bacterial cellulose (BC) to detect contamination and gamma radiation exposure in cucumbers. The results obtained show a sensitivity to pH changes for RCE in its aqueous form and that incorporated within BC films (RCE-BC), both showed color change correlated to bacterial growth (R = 0.91), this was supported with increase in pH values from 2 to 12 (R = 0.98). RCE and RCE-BC exposure to gamma radiation (0, 2.5, 5, 10, 15, 20, 25 kGy) resulted in gradual decrease in color that was more evident in RCE aqueous samples. To sense bacterial contamination of cucumbers, the total count was followed at 0, 5, 10 and 15 days in cold storage conditions and was found to reach 9.13 and 5.47 log cfu/mL for non-irradiated and 2 kGy irradiated samples, respectively. The main isolates detected throughout this storage period were identified as Pseudomonas fluorescens, Erwinia sp. Pantoea agglomerans using matrix assisted laser desorption ionization-time of flight-ms (MALDI-TOF-MS). Bacterial growth in stored irradiated cucumbers was detected by color change within 5 and 10 days of storage, after which there was no evident change. This is very useful since contamination within the early days of storage cannot be sensed with the naked eye. This study is the first to highlight utilizing RCE and RCE-BC as eco-friendly pH-sensing indicator films for intelligent food packaging to detect both food contamination and gamma preservation for refrigerator stored cucumbers.
Topics: Brassica; Cellulose; Gamma Rays; Cucumis sativus; Hydrogen-Ion Concentration; Plant Extracts; Food Microbiology; Bacteria; Food Packaging; Food Contamination; Food Storage; Food Irradiation; Colony Count, Microbial
PubMed: 38954148
DOI: 10.1007/s11274-024-04047-2 -
Food Research International (Ottawa,... Aug 2024Infants have digestive environments that are more favorable for microbial proliferation and subsequent endogenous nitrite production than those of adults, but direct...
Infants have digestive environments that are more favorable for microbial proliferation and subsequent endogenous nitrite production than those of adults, but direct evidence of this has been lacking. In this study, we propose a novel epidemiology of infant methemoglobinemia by demonstrating the risk posed by nitrite-producers in the gastrointestinal tract. Nitrite-producers from vegetables (n = 323) were exposed to stress factors of the gastrointestinal environment (gastric pH, intestinal bile salts, anaerobic atmosphere) reflecting 4 different postnatal age periods (Neonate, ≤1 month; Infant A, 1-3 months; Infant B, 3-6 months; Infant C, 6-12 months). "High-risk" strains with a nitrate-to-nitrite conversion rate of ≥1.3 %, the minimum rate corresponding to nitrite overproduction, under the Neonate stress condition were analyzed for intestinal adhesion. Among all the phyla, Pseudomonadota achieved the highest survival (P < 0.05; survival rate of 51.3-71.8 %). Possible cross-protection against bile resistance due to acid shock was observed for all the phyla. All the high-risk strains exhibited moderate autoaggregation (14.0-36.4 %), whereas only a few exhibited satisfactory surface hydrophobicity (>40 %). The Pantoea agglomerans strain strongly adhered to Caco-2 cells (7.4 ± 1.1 %). This study showed the ability of the Pantoea, Enterobacter, and Klebsiella strains to survive under gastrointestinal stress for ≤12 months, to excessively produce nitrite under neonatal stress conditions, and to settle in the human intestine. To our knowledge, this is the first study to reveal the role of the natural flora of vegetables in the epidemiology of infant methemoglobinemia through a multilateral approach.
Topics: Humans; Vegetables; Infant; Methemoglobinemia; Nitrites; Infant, Newborn; Bacterial Adhesion; Bile Acids and Salts; Gastrointestinal Tract; Hydrogen-Ion Concentration; Gastrointestinal Microbiome
PubMed: 38945602
DOI: 10.1016/j.foodres.2024.114582 -
Frontiers in Bioscience (Elite Edition) May 2024Fall armyworm () is a highly destructive maize pest that significantly threatens agricultural productivity. Existing control methods, such as chemical insecticides and...
BACKGROUND
Fall armyworm () is a highly destructive maize pest that significantly threatens agricultural productivity. Existing control methods, such as chemical insecticides and entomopathogens, lack effectiveness, necessitating alternative approaches.
METHODS
Gut-associated bacteria were isolated from the gut samples of fall armyworm and screened based on their chitinase and protease-producing ability before characterization through 16S rRNA gene sequence analysis. The efficient chitinase-producing FGE4 and FGE18 were chosen to test the biocontrol efficacy. As their respective cell suspensions and extracted crude chitinase enzyme, these two isolates were applied topically on the larvae, supplemented with their feed, and analyzed for their quantitative food use efficiency and survivability.
RESULTS
Twenty-one high chitinase and protease-producing bacterial isolates were chosen. Five genera were identified by 16S rRNA gene sequencing: , , , , and . In the biocontrol efficacy test, the consumption index and relative growth rate were lowered in larvae treated with FGE18 by topical application and feed supplementation. Similarly, topical treatment of FGE4 to larvae decreased consumption index, relative growth rate, conversion efficiency of ingested food, and digested food values.
CONCLUSION
The presence of gut bacteria with high chitinase activity negatively affects insect health. Utilizing gut-derived bacterial isolates with specific insecticidal traits offers a promising avenue to control fall armyworms. This research suggests a potential strategy for future pest management.
Topics: Animals; Spodoptera; Chitinases; RNA, Ribosomal, 16S; Bacteria; Bacillus licheniformis; Enterobacter cloacae; Larva; Pest Control, Biological; Gastrointestinal Tract
PubMed: 38939914
DOI: 10.31083/j.fbe1602015 -
Microorganisms May 2024Halo-alkali soil threatens agriculture, reducing growth and crop yield worldwide. In this study, physicochemical and molecular techniques were employed to explore the...
Halo-alkali soil threatens agriculture, reducing growth and crop yield worldwide. In this study, physicochemical and molecular techniques were employed to explore the potential of halo-alkali-tolerant endophytic bacteria strains sp. pp01, sp. pp02, sp. pp04, and sp. pp06 to enhance the growth of hybrid under varying saline conditions. The strains exhibited tolerance to high salt concentrations, alkaline pH, and high temperatures. Under controlled conditions, all four strains showed significant growth-promoting effects on hybrid inoculated individually or in combination. However, the effects were significantly reduced in coastal saline soil. The best growth-promoting effect was achieved under greenhouse conditions, increasing shoot fresh and dry weights of hybrid by up to 457.7% and 374.7%, respectively, using irrigating trials. Metagenomic sequencing analysis revealed that the diversity and composition of rhizosphere microbiota underwent significant changes after inoculation with endophytic bacteria. Specifically, pp02 and co-inoculation significantly increased the and population. Firmicutes, Mycobacteria, and Proteobacteria phyla were enriched in PP02 samples. These may explain the best growth-promoting effects of pp02 and co-inoculation on hybrid under greenhouse conditions. Our findings reveal the performance of endophytic bacterial inoculants in enhancing beneficial microbiota, salt stress tolerance, and hybrid growth.
PubMed: 38930444
DOI: 10.3390/microorganisms12061062 -
Foods (Basel, Switzerland) Jun 2024Research into microbial interactions during coffee processing is essential for developing new methods that adapt to climate change and improve flavor, thus enhancing the...
Research into microbial interactions during coffee processing is essential for developing new methods that adapt to climate change and improve flavor, thus enhancing the resilience and quality of global coffee production. This study aimed to investigate how microbial communities interact and contribute to flavor development in coffee processing within humid subtropical climates. Employing Illumina sequencing for microbial dynamics analysis, and high-performance liquid chromatography (HPLC) integrated with gas chromatography-mass spectrometry (GC-MS) for metabolite assessment, the study revealed intricate microbial diversity and associated metabolic activities. Throughout the fermentation process, dominant microbial species included , , , and from the prokaryotic group, and , , , , , and from the eukaryotic group. The key metabolites identified were ethanol, and lactic, acetic, and citric acids. Notably, the bacterial community plays a crucial role in flavor development by utilizing metabolic versatility to produce esters and alcohols, while plant-derived metabolites such as caffeine and linalool remain stable throughout the fermentation process. The undirected network analysis revealed 321 interactions among microbial species and key substances during the fermentation process, with , , and showing strong connections with sugar and various volatile compounds, such as hexanal, benzaldehyde, 3-methylbenzaldehyde, 2-butenal, and 4-heptenal. These interactions, including inhibitory effects by and , suggest microbial adaptability to subtropical conditions, potentially influencing fermentation and coffee quality. The sensory analysis showed that the final beverage obtained a score of 80.83 ± 0.39, being classified as a specialty coffee by the Specialty Coffee Association (SCA) metrics. Nonetheless, further enhancements in acidity, body, and aftertaste could lead to a more balanced flavor profile. The findings of this research hold substantial implications for the coffee industry in humid subtropical regions, offering potential strategies to enhance flavor quality and consistency through controlled fermentation practices. Furthermore, this study contributes to the broader understanding of how microbial ecology interplays with environmental factors to influence food and beverage fermentation, a topic of growing interest in the context of climate change and sustainable agriculture.
PubMed: 38928813
DOI: 10.3390/foods13121871 -
Journal of the Science of Food and... Jun 2024Saccharomyces cerevisiae CECA was a potential indigenous Chinese wine yeast that can produce aroma and flavor in Cabernet Sauvignon wines. High-throughput sequencing...
Influence of an indigenous yeast, CECA, from the Ningxia wine region of China, on the fungal and bacterial dynamics and function during Cabernet Sauvignon wine fermentation.
BACKGROUND
Saccharomyces cerevisiae CECA was a potential indigenous Chinese wine yeast that can produce aroma and flavor in Cabernet Sauvignon wines. High-throughput sequencing combined with metabolite analysis was applied to analyze the effects of CECA inoculation on the native microbial community interaction and metabolism during Cabernet Sauvignon wine fermentation.
RESULTS
Fermentations were performed with three different inoculant strategies: spontaneous fermentation without inoculation, inoculation with CECA after grape must sterilization, and direct inoculation of CECA. Results showed that the diversity of bacteria (P = 0.033) is more sensitive to CECA inoculation than fungi (P = 0.563). In addition, CECA inoculation altered the species composition of core microorganisms (relative abundance >1%) and the keystone species (accounting for the top 1% of the most important interactions), as well as of the biomarkers (linear discriminant analysis > 3.0, P < 0.05). Furthermore, the inoculation could change the cluster of metabolites, and these differential metabolite sets were correlated with four fungal taxa of Issatchenkia, Issatchenkia orientalis, Saccharomycetales, Saccharomycetes and two bacterial taxa of Pantoea, Tatumella ptyseos, were significantly correlated. Inoculated fermentation also altered the correlation between dominant microorganisms and aroma compounds, giving Cabernet Sauvignon wines more herbal, floral, fruity, and cheesy aromas.
CONCLUSION
Saccharomyces cerevisiae CECA and dimethyl dicarbonate (DMDC) inhibition treatments significantly altered the microbial community structure of Cabernet Sauvignon wines, which in turn affected the microbial-metabolite correlation. These findings will help winemakers to control the microbial dynamics and functions during wine fermentation, and be more widely used in regional typical wine fermentations. © 2024 Society of Chemical Industry.
PubMed: 38922891
DOI: 10.1002/jsfa.13696 -
Journal of Fungi (Basel, Switzerland) Jun 2024The sustainable production of natural compounds is increasingly important in today's industrial landscape. This study investigates the metabolic engineering of for the...
The sustainable production of natural compounds is increasingly important in today's industrial landscape. This study investigates the metabolic engineering of for the efficient biosynthesis of valuable carotenoids: canthaxanthin, zeaxanthin, and astaxanthin. Utilizing a tailored parental yeast strain, Sp_Bc, we optimized the carotenoid pathway by screening and identifying CrtW and CrtZ enzymatic variants. The CrtW variant from sp. achieved a canthaxanthin titer of 425.1 ± 69.1 µg/L, while the CrtZ variant from achieved a zeaxanthin titer of 70.5 ± 10.8 µg/L. Additionally, we optimized carotenoid production by exploring enzyme fusion strategies for all three studied carotenoids and organelle compartmentalization specifically for enhancing astaxanthin synthesis. We further improved carotenoid production by integrating the optimal gene constructs into the yeast genome and deleting the gene, enabling the use of sucrose as a carbon source. The engineered strain Sp_Bc-Can001 was evaluated in a 5 L bioreactor fermentation, achieving a notable canthaxanthin titer of 60.36 ± 1.51 mg/L using sucrose. This research conclusively establishes as a viable platform for efficient carotenoid biosynthesis and, for the first time in this yeast system, illustrates sucrose's viability as a carbon source for canthaxanthin production. These findings pave the way for sustainable, cost-effective carotenoid production at an industrial scale.
PubMed: 38921419
DOI: 10.3390/jof10060433 -
Scientific Reports Jun 2024Aloe barbadensis is a drought-tolerant perennial medicinal plant with both nutritional and cosmetic uses. Drought is one of the main abiotic stresses limiting plant...
Evaluation of the benefits of plant growth-promoting rhizobacteria and mycorrhizal fungi on biochemical and morphophysiological traits of Aloe barbadensis Mill under water deficit stress.
Aloe barbadensis is a drought-tolerant perennial medicinal plant with both nutritional and cosmetic uses. Drought is one of the main abiotic stresses limiting plant growth and development. However, the use of drought-resistant plants combined with beneficial soil micro-organisms could improve the effectiveness of biological methods to mitigate drought damage. This research aims to evaluate the effects of Funneliformis mosseae (MF), plant growth-promoting rhizobacteria (PGPR) (including Pseudomonas putida and Pantoea agglomerans), and their co-inoculation on the macronutrient status, antioxidant enzyme activities, and other morphophysiological traits of A. barbadensis under four irrigation regimes [25%, 50%, 75% and 100% of water requirement (WR)]. Three harvests were conducted, revealing that inoculation enhanced the survival rate and shoot fresh weight (SFW) compared to the control plants. However, at 25% WR, the SFW was reduced by 43% more than the control. across all harvests, while the PGPR + MF treatment showed increases of more than 19%, 11%, and 17% compared to the control, MF, and PGPR treatments, respectively. The results also showed that A. barbadensis exhibited innate drought tolerance up to a 50% WR level by enhancing physiological defenses, such as antioxidant enzyme activity. Inoculation increased the macronutrient status of the plant at all levels of irrigation regimes especially under severe drought conditions. The highest levels of nitrogen (N) (16.24 mg g DW) and phosphorus (P) (11.29 mg g DW) were observed in the PGPR + MF treatment at 100% WR. The maximum relative water content under MF inoculation and 75% WR (98.24%) (98.24%) was reached. PGPR + MF treatment alleviated drought-induced osmotic stress, as indicated by reduced antioxidant enzyme activities and electrolyte leakage. However, P. putida and P. agglomerans strains alone or in combination with F. mosseae increased plant yield, macronutrient uptake and antioxidant enzyme activity. This study underscores the potential of these PGPR and MF strains as invaluable biological tools for the cultivation of A. barbadensis in regions with severe drought stress.
Topics: Aloe; Mycorrhizae; Droughts; Pseudomonas putida; Antioxidants; Plant Roots; Water; Stress, Physiological; Soil Microbiology; Pantoea; Dehydration; Fungi
PubMed: 38914637
DOI: 10.1038/s41598-024-64878-9 -
Chemosphere Jun 2024Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition...
Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.
PubMed: 38908447
DOI: 10.1016/j.chemosphere.2024.142680