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Microorganisms Sep 2023Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH,...
Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH, with very high degradation efficiency was isolated from soil exposed to long-term PHE contamination. The results of GC analysis showed that the consortium HJ-SH degraded 98% of 100 mg/L PHE in 3 days and 93% of 1000 mg/L PHE in 5 days, an efficiency higher than that of any other natural consortia, and even most of the engineered strains and consortia reported so far. Seven dominating strains were isolated from the microbial consortium HJ-SH, named SH-1 to SH-7, which were identified according to morphological observation and 16S rDNA sequencing as sp., sp., sp., sp., sp., sp., and sp., respectively. Among all the seven single strains, SH-4 showed the strongest PHE degradation ability, and had the biggest degradation contribution. However, it is very interesting that the microbial consortium can hold its high degradation ability only with the co-existence of all these seven single strains. Moreover, HJ-SH exhibited a very high tolerance for PHE, up to 4.5 g/L, and it can degrade some other typical organic pollutants such as biphenyl, anthracene, and n-hexadecane with the degradation ratios of 93%, 92% and 70%, respectively, under 100 mg/L initial concentration in 5 days. Then, we constructed an artificial consortium HJ-7 consisting of the seven single strains, SH-1 to SH-7. After comparing the degradation ratios, cell growth, and relative degradation rates, it was concluded that the artificial consortium HJ-7 with easier reproducibility, better application stability, and larger room for modification can largely replace the natural consortium HJ-SH. In conclusion, this research provided novel tools and new insights for the bioremediation of PHE and other typical organic pollutants using microbial consortia.
PubMed: 37894041
DOI: 10.3390/microorganisms11102383 -
Scientific Reports Apr 2024Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled....
Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled. Resistance to chemical pesticides have been reported in some T. absoluta populations. Insect microbiome plays an important role in the behavior, physiology, and survivability of their host. In a bid to explore and develop an alternative control method, the associated microbiome of this insect was studied. In this study, we unraveled the bacterial biota of T. absoluta larvae and adults by sequencing and analyzing the 16S rRNA V3-V4 gene regions using Illumina NovaSeq PE250. Out of 2,092,015 amplicon sequence variants (ASVs) recovered from 30 samples (15 larvae and 15 adults), 1,268,810 and 823,205 ASVs were obtained from the larvae and adults, respectively. A total of 433 bacterial genera were shared between the adults and larval samples while 264 and 139 genera were unique to the larvae and adults, respectively. Amplicon metagenomic analyses of the sequences showed the dominance of the phylum Proteobacteria in the adult samples while Firmicutes and Proteobacteria dominated in the larval samples. Linear discriminant analysis effect size (LEfSe) comparison revealed the genera Pseudomonas, Delftia and Ralstonia to be differentially enriched in the adult samples while Enterococcus, Enterobacter, Lactococcus, Klebsiella and Wiessella were differentially abundant in the larvae. The diversity indices showed that the bacterial communities were not different between the insect samples collected from different geographical regions. However, the bacterial communities significantly differed based on the sample type between larvae and adults. A co-occurrence network of significantly correlated taxa revealed a strong interaction between the microbial communities. The functional analysis of the microbiome using FAPROTAX showed that denitrification, arsenite oxidation, methylotrophy and methanotrophy as the active functional groups of the adult and larvae microbiomes. Our results have revealed the core taxonomic, functional, and interacting microbiota of T. absoluta and these indicate that the larvae and adults harbor a similar but transitory set of bacteria. The results provide a novel insight and a basis for exploring microbiome-based biocontrol strategy for this invasive insect pest as well as the ecological significance of some of the identified microbiota is discussed.
Topics: Animals; Moths; RNA, Ribosomal, 16S; Insecta; Larva; Microbiota; Solanum lycopersicum; Bacteria
PubMed: 38594362
DOI: 10.1038/s41598-024-58753-w -
Current Microbiology Dec 2021Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root...
Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.
Topics: Bacteria; Biodegradation, Environmental; Ecosystem; Metabolomics; Metals, Heavy; Microbiota; Rhizosphere; Wetlands
PubMed: 34962589
DOI: 10.1007/s00284-021-02748-7 -
Ecotoxicology and Environmental Safety Jan 2023Carbamazepine (CBZ) in the aquatic environment is recognized as a potential threat to aquatic organisms and public health. However, the response of organism intestinal...
Carbamazepine (CBZ) in the aquatic environment is recognized as a potential threat to aquatic organisms and public health. However, the response of organism intestinal health, resistome, microbiota, and their relationship after CBZ exposure has been rarely reported. This study aimed to explore the impacts of CBZ on gut microbiota, antibiotic resistance genes (ARGs) and the expression of intestinal health related genes as well as their interaction using the zebrafish model. 16 S ribosomal RNA sequencing indicated CBZ altered the composition of gut microbiota. Using high-throughput quantitative polymerase chain reaction (HT-qPCR), we found the number and abundance of ARGs were impacted by CBZ levels and exposure duration. We also observed the upregulated expression of the pro-inflammatory gene IL6 and downregulated expression of toll-like receptor gene TLR2 and intestinal barrier gene TJP2a at different exposure times. Correlation analyses revealed that Geobacillus, Rhodococcus, Ralstonia, Delftia, Luteolibacter and Escherichia-Shigella might be the main bacterial genera carrying ARGs. Meanwhile, Cetobacterium and Aeromonas could be the dominant bacteria affecting intestinal health related genes. Our results could contribute to understanding the health risks of CBZ to the intestinal microecology of aquatic animals.
Topics: Animals; Gastrointestinal Microbiome; Anti-Bacterial Agents; Zebrafish; Genes, Bacterial; Drug Resistance, Microbial; Bacteria; Carbamazepine
PubMed: 38321688
DOI: 10.1016/j.ecoenv.2022.114473 -
New Microbes and New Infections Sep 2020Multiple studies have established the contamination of hospital sinks and transmission to hospital personnel. Few studies have assessed the contamination and...
Multiple studies have established the contamination of hospital sinks and transmission to hospital personnel. Few studies have assessed the contamination and transmission of microorganisms from the faucets of operating bay scrub sinks to operating room (OR) personnel, a potential route of infection for patients. This study aimed to investigate if there was pathogenic contamination of scrub sinks and possible transmission of those pathogens to the hands of OR personnel after preoperative hand disinfection. Swabs were taken from the hands of 50 OR personnel and from the faucets of 24 scrubs sinks at two different hospital sites, and were cultured. Hands were swabbed after completing a surgical hand scrub. Results were reported in colony-forming units per millilitre. There was significant scrub sink contamination with primarily Gram-negative organisms, such as and . There was no overlap in bacterial species between the cultures from hands and scrub sinks. Cultures from the sinks and the hands of the OR personnel from one site had significantly higher bacterial growth compared with the other site (p < 0.0001 and p < 0.0118, respectively). The data showed significant contamination on the faucets of operating bay scrub sinks. However, there was no observed transmission of pathogens from the scrub sinks to OR personnel, shown by the lack of overlap in bacterial species. Routine hygienic maintenance of scrub sinks is recommended.
PubMed: 32995014
DOI: 10.1016/j.nmni.2020.100754 -
Plants (Basel, Switzerland) Mar 2023Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and...
Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and various stakeholders have shown an interest in understanding and utilizing ecological interactions between trees and their associated microorganisms. Endophyte microbes can influence the health of trees either by directly interacting with the damaging agents or modulating host responses to infection. In the framework of this work, ten morphotypes of endophytic bacteria from the tissues of unripe acorns of L. were isolated. Based on the results of the sequenced 16S rRNA genes, four species of endophytic bacteria were identified: , , , and . Determining the activity of pectolytic enzymes showed that the isolates and could not cause maceration of plant tissues. Screening for these isolates revealed their fungistatic effect against phytopathogenic micromycetes, namely , , and . Inoculation of , , and their complex in oak leaves, in contrast to phytopathogenic bacteria, contributed to the complete restoration of the epidermis at the sites of damage. The phytopathogenic bacteria and caused a 2.0 and 2.2 times increase in polyphenol concentration in the plants, respectively, while the ratio of antioxidant activity to total phenolic content decreased. Inoculation of and isolates into oak leaf tissue were accompanied by a decrease in the total pool of phenolic compounds. The ratio of antioxidant activity to total phenolic content increased. This indicates a qualitative improvement in the overall balance of the oak leaf antioxidant system induced by potential PGPB. Thus, endophytic bacteria of the genus isolated from the internal tissues of unripe oak acorns have the ability of growth biocontrol and spread of phytopathogens, indicating their promise for use as biopesticides.
PubMed: 36987039
DOI: 10.3390/plants12061352 -
NPJ Biofilms and Microbiomes Feb 2020The microbiota colonizing the root endophytic compartment and surrounding rhizosphere soils contribute to plant growth and health. However, the key members of plant soil...
The microbiota colonizing the root endophytic compartment and surrounding rhizosphere soils contribute to plant growth and health. However, the key members of plant soil and endophytic microbial communities involved in inhibiting or assisting pathogen invasion remain elusive. By utilizing 16S high-throughput sequencing and a molecular ecological network (MEN) approach, we systematically studied the interactions within bacterial communities in plant endophytic compartments (stem and root) and the surrounding soil (bulk and rhizosphere) during bacterial wilt invasion. The endophytic communities were found to be strongly influenced by pathogen invasion according to analysis of microbial diversity and community structure and composition. Endophytic communities of the infected plants were primarily derived from soil communities, as assessed by the SourceTracker program, but with rare migration from soil communities to endophytic communities observed in healthy plants. Soil and endophytic microbiomes from infected plants showed modular topology and greater complexity in network analysis, and a higher number of interactions than those in healthy plants. Furthermore, interactions among microbial members revealed that pathogenic Ralstonia members were positively correlated with several bacterial genera, including Delftia, Stenotrophomonas, Bacillus, Clostridium XlVa, Fontibacillus, Acidovorax, Herminiimonas, and three unclassified bacterial genera, in infected plant roots. Our findings indicated that the pathogen invasion in the rhizosphere and endophytic compartments may be highly associated with bacteria that are normally not detrimental, and sometimes even beneficial, to plants.
Topics: Bacteria; DNA, Bacterial; DNA, Ribosomal; High-Throughput Nucleotide Sequencing; Phylogeny; Plant Diseases; Plant Roots; RNA, Ribosomal, 16S; Rhizosphere; Sequence Analysis, DNA; Soil Microbiology; Nicotiana
PubMed: 32060424
DOI: 10.1038/s41522-020-0117-2 -
Microbiology Spectrum Apr 2022Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans....
Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective. D. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.
Topics: Anti-Infective Agents; Delftia; Genetic Variation; Genome, Bacterial; Humans; Phosphate Transport Proteins; Phylogeny; Virulence; Virulence Factors
PubMed: 35230132
DOI: 10.1128/spectrum.02072-21 -
PloS One 2020The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the...
The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95-105 versus 36-44). In these treatments the share of subdominant Actinobacteria (0.4-0.8%), Firmicutes (0.5-0.9%) and Bacteroidetes (0.2-0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.
Topics: Actinobacteria; Bacteroidetes; Biodegradation, Environmental; Cadmium; Chromium; DNA, Bacterial; Ferns; Firmicutes; High-Throughput Nucleotide Sequencing; Lead; Microbiota; RNA, Ribosomal, 16S; Soil Microbiology; Soil Pollutants
PubMed: 32374760
DOI: 10.1371/journal.pone.0232699 -
Life (Basel, Switzerland) Oct 2022Agarwood () is one of the most important resin-containing plants used to produce agar around the world and it is a precious herbal medicine usually combined with other...
Agarwood () is one of the most important resin-containing plants used to produce agar around the world and it is a precious herbal medicine usually combined with other herbs. In this study, we used the Illumina sequencing technique to explore the agarwood bacterial community structure from four different incense formations of agarwood, including healthy agarwood, drilling agarwood, liquid fermentation agarwood, and insect attack agarwood. Our results showed that 20 samples of three different incense-formation methods of agarwood and healthy agarwood acquired 1,792,706 high-quality sequences. In-depth investigation showed that when the diversity of agarwood bacterial species was higher, the agarwood incense quality was higher as well. Among healthy agarwood, drilling agarwood, fermentation agarwood, and insect attack agarwood, the bacterial community structure had significant changes. Natural agarwood, such as insect attack agarwood, kept more bacterial community structure, and the incense quality was better. Furthermore, we observed that in the healthy agarwood, and were the predominant bacteria. , , and were the dominant bacteria in the drilling agarwood. Additionally, and were some of the main bacteria in the fermentation liquid agarwood and the insect attack agarwood, while and were the dominant bacteria. This research provides a basis for further research into the underlying mechanisms of incense production, as well as the bacterial community applications of agarwood production.
PubMed: 36362852
DOI: 10.3390/life12111697