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Environment International Aug 2023The polyethylene (PE) film mulching as a water conservation technology has been widely used in dryland agriculture, yet the long-term mulching has led to increasing...
The polyethylene (PE) film mulching as a water conservation technology has been widely used in dryland agriculture, yet the long-term mulching has led to increasing accumulation of secondary pollutants in soils. The decomposition of PE film-sourced pollutants is directly associated with the enrichment of specific bacterial communities. We therefore hypothesized that plant biomass may act as an organic media to mediate the pollutant decomposition via reshaping bacterial communities. To validate this hypothesis, plant biomass (dried maize straw and living clover) was embedded at the underlying surface of PE film, to track the changes in the composition and function of bacterial communities in maize field across two years. The results indicated that both dry crop straw and alive clover massively promoted the α-diversity and abundance of dominant bacteria at plastisphere, relative to bulk soil. Bacterial communities tended to be clustered at plastisphere, forming the bacteria islands to enrich pollutant-degrading bacteria, such as Sphingobacterium, Arthrobacter and Paracoccus. As such, plastisphere bacteria islands substantially enhanced the degradation potential of chloroalkene and benzoate (p < 0.05). Simultaneously, bacterial network became stabilized and congregated at plastisphere, and markedly improved the abundance of plastisphere module hubs and connectors bacteria via stochastic process. Particularly, bacterial community composition and plastic film-sourced pollutants metabolism were evidently affected by soil pH, carbon and nitrogen sources that were mainly derived from the embedded biomass. To sum up, plant biomass embedding as a nature-based strategy (NbS) can positively mediate the decomposition of plastic-sourced pollutants through plastisphere bacteria island effects.
Topics: Soil; Biomass; Polyethylene; Environmental Pollutants; Water; Agriculture; Plastics; Bacteria; Soil Microbiology
PubMed: 37499460
DOI: 10.1016/j.envint.2023.108114 -
Journal of Global Infectious Diseases 2023
PubMed: 37469470
DOI: 10.4103/jgid.jgid_236_22 -
Microbiological Research Oct 2023Soil amino acids (AAs) are the most active components of soil N, which can be mineralized or absorbed by bacteria as N and C sources. We hypothesized that exogenous AAs...
Soil amino acids (AAs) are the most active components of soil N, which can be mineralized or absorbed by bacteria as N and C sources. We hypothesized that exogenous AAs could regulate the bacterial community and affect soil N cycling, and the effect sizes could vary depending on individual AAs. Here, we applied feather (keratin)-based compost rich in AAs to Poncirus trifoliata (L.) to evaluate the regulation of bacterial community by AAs; furthermore, we applied six individual AAs to test their effects. The compost significantly increased soil hydrolysable AA content, ammonia monooxygenase gene abundance, and plant growth and changed bacterial community structure. Redundancy analysis revealed that the effects of AAs on the bacterial community composition were greater than those of soil chemical properties, and phenylalanine (Phe) was the most effective among thirteen individual AAs. When applied individually, Phe caused the greatest increase in N cycling-related enzyme activity and plant growth and most significantly altered the bacterial community structure among the six exogenous AAs. Notably, Phe significantly increased the relative abundances of Burkholderia-Caballeronia-Paraburkholderia, Azospirillum, Cupriavidus, and Achromobacter, whose abundances were significantly positively correlated with plant biomass, and significantly reduced the relative abundances of Arachidicoccus, Pseudopedobacter, Sphingobacterium, and Paenibacillus, whose abundances were significantly negatively correlated with plant biomass. We demonstrate that soil AAs strongly shape the bacterial community. Particularly, Phe enhances N cycling and plant growth by increasing the potentially beneficial bacterial taxa and inhibiting the potentially harmful bacterial taxa, which needs further validation.
Topics: Soil; Phenylalanine; Bacteria; Nitrogen Cycle; Nitrogen; Soil Microbiology
PubMed: 37441843
DOI: 10.1016/j.micres.2023.127447 -
Applied Microbiology and Biotechnology Sep 2023Pharmaceuticals are of concern to our planet and health as they can accumulate in the environment. The impact of these biologically active compounds on ecosystems is...
Pharmaceuticals are of concern to our planet and health as they can accumulate in the environment. The impact of these biologically active compounds on ecosystems is hard to predict, and information on their biodegradation is necessary to establish sound risk assessment. Microbial communities are promising candidates for the biodegradation of pharmaceuticals such as ibuprofen, but little is known yet about their degradation capacity of multiple micropollutants at higher concentrations (100 mg/L). In this work, microbial communities were cultivated in lab-scale membrane bioreactors (MBRs) exposed to increasing concentrations of a mixture of six micropollutants (ibuprofen, diclofenac, enalapril, caffeine, atenolol, paracetamol). Key players of biodegradation were identified using a combinatorial approach of 16S rRNA sequencing and analytics. Microbial community structure changed with increasing pharmaceutical intake (from 1 to 100 mg/L) and reached a steady-state during incubation for 7 weeks on 100 mg/L. HPLC analysis revealed a fluctuating but significant degradation (30-100%) of five pollutants (caffeine, paracetamol, ibuprofen, atenolol, enalapril) by an established and stable microbial community mainly composed of Achromobacter, Cupriavidus, Pseudomonas and Leucobacter. By using the microbial community from MBR1 as inoculum for further batch culture experiments on single micropollutants (400 mg/L substrate, respectively), different active microbial consortia were obtained for each single micropollutant. Microbial genera potentially responsible for degradation of the respective micropollutant were identified, i.e. Pseudomonas sp. and Sphingobacterium sp. for ibuprofen, caffeine and paracetamol, Sphingomonas sp. for atenolol and Klebsiella sp. for enalapril. Our study demonstrates the feasibility of cultivating stable microbial communities capable of degrading simultaneously a mixture of highly concentrated pharmaceuticals in lab-scale MBRs and the identification of microbial genera potentially responsible for the degradation of specific pollutants. KEY POINTS: • Multiple pharmaceuticals were removed by stable microbial communities. • Microbial key players of five main pharmaceuticals were identified.
Topics: Ibuprofen; RNA, Ribosomal, 16S; Atenolol; Acetaminophen; Caffeine; Microbiota; Bioreactors; Biodegradation, Environmental; Environmental Pollutants; Water Pollutants, Chemical; Pharmaceutical Preparations
PubMed: 37436483
DOI: 10.1007/s00253-023-12677-z -
BMC Microbiology Jul 2023It has been demonstrated in the literature that a dysbiotic microbiome could have a negative impact on the host immune system and promote disease onset or...
BACKGROUND
It has been demonstrated in the literature that a dysbiotic microbiome could have a negative impact on the host immune system and promote disease onset or exacerbation. Co-occurrence networks have been widely adopted to identify biomarkers and keystone taxa in the pathogenesis of microbiome-related diseases. Despite the promising results that network-driven approaches have led to in various human diseases, there is a dearth of research pertaining to key taxa that contribute to the pathogenesis of lung cancer. Therefore, our primary goal in this study is to explore co-existing relationships among members of the lung microbial community and any potential gained or lost interactions in lung cancer.
RESULTS
Using integrative and network-based approaches, we integrated four studies assessing the microbiome of lung biopsies of cancer patients. Differential abundance analyses showed that several bacterial taxa are different between tumor and tumor-adjacent normal tissues (FDR adjusted p-value < 0.05). Four, fifteen, and twelve significantly different associations were found at phylum, family, and genus levels. Diversity analyses suggested reduced alpha diversity in the tumor microbiome. However, beta diversity analysis did not show any discernible pattern between groups. In addition, four distinct modules of bacterial families were detected by the DBSCAN clustering method. Finally, in the co-occurrence network context, Actinobacteria, Firmicutes, Bacteroidetes, and Chloroflexi at the phylum level and Bifidobacterium, Massilia, Sphingobacterium, and Ochrobactrum at the genus level showed the highest degree of rewiring.
CONCLUSIONS
Despite the absence of statistically significant differences in the relative abundance of certain taxa between groups, it is imperative not to overlook them for further exploration. This is because they may hold pivotal central roles in the broader network of bacterial taxa (e.g., Bifidobacterium and Massilia). These findings emphasize the importance of a network analysis approach for studying the lung microbiome since it could facilitate identifying key microbial taxa in lung cancer pathogenesis. Relying exclusively on differentially abundant taxa may not be enough to fully grasp the complex interplay between lung cancer and the microbiome. Therefore, a network-based approach can offer deeper insights and a more comprehensive understanding of the underlying mechanisms.
Topics: Humans; Carcinoma, Non-Small-Cell Lung; Lung Neoplasms; Actinobacteria; Bifidobacterium; Microbiota; Lung
PubMed: 37434142
DOI: 10.1186/s12866-023-02931-9 -
Applied Microbiology and Biotechnology Aug 2023The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic...
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr trait is spread across different bacterial taxonomic classes. • The core-code for the Myr trait was detected in a novel ICE, only found in Pseudomonas spp.
Topics: Rhizosphere; Acyclic Monoterpenes; Bacteria; Pseudomonas
PubMed: 37405434
DOI: 10.1007/s00253-023-12650-w -
Frontiers in Microbiology 2023sp. PT13 is a wild strain with multiple predatory properties that prey on multiple model microorganisms preserved in the laboratory. However, the lysis spectrum of PT13...
INTRODUCTION
sp. PT13 is a wild strain with multiple predatory properties that prey on multiple model microorganisms preserved in the laboratory. However, the lysis spectrum of PT13 on typical soil bacteria and its driving effect on soil microecosystems are still unclear.
METHODS
In this study, the lawn predation method was used to determine the predation diameter of 62 typical soil bacteria by myxobacteria PT13 and analyze their lysis spectra.
RESULTS AND DISCUSSION
The results showed that PT13 had a predation diameter greater than 15 mm against typical soil microorganisms such as , , , , and and had an outstanding lysis effect but a significant preference ( < 0.05). Absolute high-throughput sequencing results showed that PT13 predation drove the microcosmic system composed of 16 bacterial genera, with a significant decrease in the Shannon index by 11.8% (CK = 2.04, = 1.80) and a significant increase in the Simpson index by 45.0% (CK = 0.20, = 0.29). The results of principal coordinate analysis (PCoA) showed that myxobacterial addition significantly disturbed the microcosmic microbial community structure (ANOSIM, < 0.05). LEfSe analysis showed that the relative and absolute abundances (copy numbers) of , , , and decreased significantly very likely due to myxobacterial predation ( < 0.05). However, the predatory effect of PT13 also increased the relative or absolute abundances of some species, such as , , and . It can be concluded that PT13 has a broad-spectrum lysis spectrum but poor cleavage ability for , and the interaction between complex microorganisms limits the predation effect of PT13 on some prey bacteria. This in turn allows some prey to coexist with myxobacteria. This paper will lay a theoretical foundation for the regulation of soil microecology dominated by myxobacteria.
PubMed: 37378286
DOI: 10.3389/fmicb.2023.1211756 -
Saudi Medical Journal Jun 2023To develop a candidate vaccine aginst the .
OBJECTIVES
To develop a candidate vaccine aginst the .
METHODS
Since there is currently no vaccine against this pathogen, we employed in-silico methods to extensively explore the outer membrane toxin-producing proteins found specifically in to forecast a multi-epitope chimeric vaccine design. This computational study was conducted in Saudi Arabia in 2022 (study design: computational; ethical approval not applicable).
RESULTS
TThe vaccine peptide comprises multiple linear and conformational B-cell epitopes, which have the potential to elicit humoral immunity. Projected B-cell- derived T-cell epitopes for outer membrane proteins are present in the produced protein. The docking and molecular dynamic simulation results indicating that the chimeric vaccine had adequate binding stability with TLR-4. Following the immunological simulation, significant levels of immune cell expression were observed as immunoglobulin (Ig) M and IgG, IgM, IgM1, and IgM2, and independently IgG1 and IgG2.
CONCLUSION
The developed vaccine candidate is suitable for further testing and can assist experimental vaccinologists in developing an effective vaccine against .
Topics: Humans; Vaccinology; Sphingobacterium; Epitopes, B-Lymphocyte; Saudi Arabia
PubMed: 37343981
DOI: 10.15537/smj.2023.44.6.20220733 -
Food Science & Nutrition Jun 2023The salt-reducing pickling method has been applied to the industrial production of . In order to reveal the succession of the microbial community structure and flavor...
The salt-reducing pickling method has been applied to the industrial production of . In order to reveal the succession of the microbial community structure and flavor components during the pickling process, this study used PacBio Sequel to sequence the full length of 16S rRNA (bacteria, 1400 bp) and ITS (fungi, 1200 bp) genes, and detected flavor components simultaneously, including organic acids, volatile flavor components (VFC), monosaccharides, and amino acids. Eleven phyla and 148 genera were identified in the bacterial community, and 2 phyla and 60 genera in the fungal community. During the four stages of pickling, the dominant bacterial genera were , , , and , while the dominant fungal genera were , , , and , respectively. There were 32 main flavor components (5 organic acids, 19 VFCs, 3 monosaccharides, and 5 amino acids). Correlation heat mapping and bidirectional orthogonal partial least squares (O2PLS) analysis showed that the flora having close relation to flavor components included 14 genera of bacteria (, , , , , , , , , , , , , and ) and 3 genera of fungi (, , and ). This study provides detailed data regarding the microbial community and flavor components during the salt-reducing pickling process of , which can be used as a reference for the development and improvement of salt-reducing pickling methods.
PubMed: 37324844
DOI: 10.1002/fsn3.3297 -
Journal of Hazardous Materials Sep 2023Nicotine and nornicotine are all toxic alkaloids involved in the formation of carcinogenic tobacco-specific nitrosamines. Microbes play an important role in removing...
Characterization of a novel nornicotine-degrading strain Mycolicibacterium sp. SMGY-1XX from a nornicotine-degrading consortium and preliminary elucidation of its biodegradation pathway by multi-omics analysis.
Nicotine and nornicotine are all toxic alkaloids involved in the formation of carcinogenic tobacco-specific nitrosamines. Microbes play an important role in removing these toxic alkaloids and their derivatives from tobacco-polluted environments. By now, microbial degradation of nicotine has been well studied. However, limited information is available on the microbial catabolism of nornicotine. In the present study, a nornicotine-degrading consortium was enriched from a river sediment sample and characterized by metagenomic sequencing using a combination of Illumina and Nanopore technologies. The metagenomic sequencing analysis demonstrated that Achromobacter, Azospirillum, Mycolicibacterium, Terrimonas, and Mycobacterium were the dominant genera in the nornicotine-degrading consortium. A total of 7 morphologically distinct bacterial strains were isolated from the nornicotine-degrading consortium. These 7 bacterial strains were characterized by whole genome sequencing and examined for their ability to degrade nornicotine. Based on a combination of 16 S rRNA gene similarity comparisons, 16 S rRNA gene-based phylogenetic analysis, and ANI analysis, the accurate taxonomies of these 7 isolated strains were identified. These 7 strains were identified as Mycolicibacterium sp. strain SMGY-1XX, Shinella yambaruensis strain SMGY-2XX, Sphingobacterium soli strain SMGY-3XX, Runella sp. strain SMGY-4XX, Chitinophagaceae sp. strain SMGY-5XX, Terrimonas sp. strain SMGY-6XX, Achromobacter sp. strain SMGY-8XX. Among these 7 strains, Mycolicibacterium sp. strain SMGY-1XX, which has not been reported previously to have the ability to degrade nornicotine or nicotine, was found to be capable of degrading nornicotine, nicotine as well as myosmine. The degradation intermediates of nornicotine and myosmine by Mycolicibacterium sp. strain SMGY-1XX were determined and the nornicotine degradation pathway in strain SMGY-1XX was proposed. Three novel intermediates, myosmine, pseudooxy-nornicotine, and γ-aminobutyrate, were identified during the nornicotine degradation process. Further, the most likely candidate genes responsible for nornicotine degradation in Mycolicibacterium sp. strain SMGY-1XX were identified by integrating genomic analysis, transcriptomic analysis, and proteomic analysis. The findings in this study will help to expand our understanding on the microbial catabolism of nornicotine and nicotine and provide new insights into the nornicotine degradation mechanism by consortia and pure culture, laying a foundation for the application of strain SMGY-1XX for the removal, biotransformation, or detoxification of nornicotine.
Topics: Nicotine; Phylogeny; Multiomics; Proteomics; Biodegradation, Environmental; Alkaloids; Nicotiana
PubMed: 37290356
DOI: 10.1016/j.jhazmat.2023.131777