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Frontiers in Plant Science 2022Azoxystrobin, a quinone outside inhibitor fungicide, reduced tobacco target spot caused by by 62%, but also affected the composition and diversity of other microbes on...
Azoxystrobin, a quinone outside inhibitor fungicide, reduced tobacco target spot caused by by 62%, but also affected the composition and diversity of other microbes on the surface and interior of treated tobacco leaves. High-throughput sequencing showed that the dominant bacteria prior to azoxystrobin treatment were on healthy leaves and on diseased leaves, and the dominant fungi were (teleomorph of ) and on healthy leaves and on diseased leaves. Both bacterial and fungal diversity significantly increased 1 to 18 days post treatment (dpt) with azoxystrobin for healthy and diseased leaves. For bacteria on healthy leaves, the relative abundance of , and declined, while and increased. On diseased leaves, the relative abundance of and declined, while and increased. For fungi on healthy leaves, the relative abundance of declined, while , , , and increased. On diseased leaves, the relative abundance of declined, while , , , , , and , increased. Compared to healthy leaves, azoxystrobin treatment of diseased leaves resulted in greater reductions in , and , a greater increase in , and similar changes in , and . Azoxystrobin had a semi-selective effect altering the microbial diversity of the tobacco leaf microbiome, which could be due to factors, such as differences among bacterial and fungal species in sensitivity to quinone outside inhibitors, ability to use nutrients and niches as certain microbes are affected, and metabolic responses to azoxystrobin.
PubMed: 36816485
DOI: 10.3389/fpls.2022.1101039 -
AIMS Microbiology 2018complex (MAC) organisms are waterborne, opportunistic pathogens whose source is natural waters and soils and proliferates and persists in premise plumbing, for example... (Review)
Review
complex (MAC) organisms are waterborne, opportunistic pathogens whose source is natural waters and soils and proliferates and persists in premise plumbing, for example household and hospital plumbing. complex and other environmental mycobacteria grow slowly, not because their metabolism is slow, but because they synthesize long chain (C-C) fatty acids that make up its hydrophobic and impermeable outer membrane. There are costs and benefits to the presence of that lipid-rich outer membrane. One benefit is that cell-surface hydrophobicity drives complex cells to adhere to surfaces to reduce their interaction with charged ions in suspension; they are likely "biofilm pioneers", adhering to a wide variety of surface materials. The result is that the slow-growing complex cells (1 gen/day at 37 °C) will not be washed out of any flowing system, whether a stream or plumbing in the built environment. Although the slow permeation of nutrients in complex organisms limits growth, they are also resistant to disinfectants, thus increasing their survival in water distribution systems, premise plumbing, and medical equipment. There are three components to the antimicrobial resistance of complex in biofilms: (1) innate resistance due to the hydrophobic, impermeable outer membrane, (2) residence in a matrix of extracellular polysaccharide, lipid, DNA, and protein that prevents access of antimicrobials to cells, and (3) an adaptive and transient increased resistance of biofilm-grown cells grown in biofilms. As expected in biofilms will display neutral, antagonistic, or beneficial interactions with other biofilm inhabitants. spp., the common pink-pigmented, waterborne bacteria compete with for surface binding, suggested an approach to reducing biofilm formation and hence persistence in premise plumbing.
PubMed: 31294225
DOI: 10.3934/microbiol.2018.3.428 -
MBio Feb 2022is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like...
is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. In two temperate forests, we investigated how phylogenetic diversity within is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we uncovered a considerable diversity of in the phyllosphere. We cultured different subsets of lineages depending upon the temperature of isolation and growth (20°C or 30°C), suggesting long-term adaptation to temperature. To a lesser extent than temperature adaptation, diversity was also structured across large (>100 km; between forests) and small (<1.2 km; within forests) geographical scales, among host tree species, and was dynamic over seasons. By measuring the growth of 79 isolates during different temperature treatments, we observed contrasting growth performances, with strong lineage- and season-dependent variations in growth strategies. Finally, we documented a progressive replacement of lineages with a high-yield growth strategy typical of cooperative, structured communities in favor of those characterized by rapid growth, resulting in convergence and homogenization of community structure at the end of the growing season. Together, our results show how is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This work paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus. is a bacterial group tied to plants. Despite the ubiquity of methylobacteria and the importance to their hosts, little is known about the processes driving community dynamics. By combining traditional culture-dependent and -independent (metabarcoding) approaches, we monitored diversity in two temperate forests over a growing season. On the surface of tree leaves, we discovered remarkably diverse and dynamic communities over short temporal (from June to October) and spatial (within 1.2 km) scales. Because we cultured different subsets of diversity depending on the temperature of incubation, we suspected that these dynamics partly reflected climatic adaptation. By culturing strains under laboratory conditions mimicking seasonal variations, we found that diversity and environmental variations were indeed good predictors of growth performances. Our findings suggest that community dynamics at the surface of tree leaves results from the succession of strains with contrasting growth strategies in response to environmental variations.
Topics: Methylobacterium; Phylogeny; Forests; Plants; Host Specificity; Plant Leaves
PubMed: 35073752
DOI: 10.1128/mbio.03175-21 -
PeerJ 2022Dental unit waterlines (DUWLs) provide water for handpieces, air/water syringes, and mouth-rinse water outlets. DUWL contamination can negatively affect the operating...
BACKGROUND
Dental unit waterlines (DUWLs) provide water for handpieces, air/water syringes, and mouth-rinse water outlets. DUWL contamination can negatively affect the operating environment and public health. Therefore, it is important to elucidate the bacterial concentrations and microbial composition in the DUWLs from different dental specialties.
METHODS
We collected 350 5-mL dental water samples (from high-speed handpieces, air/water syringes, and mouth-rinse water outlets) from 60 dental chair units (DCUs) at a dental hospital to determine the bacterial concentrations by culture methods. Meanwhile, to investigate the diversity and community structure of microbe in the DUWLs, 17 high-quality DNA from 60 250-mL air/water syringe water samples, which were collected from the same 60 DCUs, were analyzed using 16S rDNA high-throughput sequencing.
RESULTS
The median bacterial concentration was 166 (31.5, 672.5) CFU/mL and the range was 0-3,816,000 CFU/mL. Only 42.6% of the water samples had bacterial concentrations below 100 CFU/mL. The Kruskal-Wallis -test revealed that the water samples from three dental specialties had significantly different bacterial concentrations ( = 27.441, < 0.01). High-throughput sequencing results showed significant differences in bacterial community structure between periodontics and the other two dental specialties. In the samples from three dental specialties, 508 OTUs were detected, with 160, 182 and 176 OTUs unique to the periodontics, endodontics and prosthodontics specialties, respectively. Linear discriminant analysis (LDA) effect size (LEfSe) suggested that Hydrocarboniphaga, Zoogloea, Aquabacterium, and Hydrogenophaga were enriched in the periodontics specialty; Acinetobacter, Geothrix, and Desulfovibrio were enriched in the prosthodontics specialty; and Alistipes, Clostridium XIVa, and Serratia were enriched in the endodontics specialty. Seven potentially human-pathogenic genera (Pseudomonas, Acinetobacter, Sphingomonas, Ochrobactrum, Rhizobium, Brevundimonas, and Methylobacterium) with relative abundance exceeding 1% were also detected in the DUWLs.
CONCLUSIONS
The bacterial concentrations and microbial composition were influenced by different dental specialties, so a validated disinfection protocol should be used to control DUWL contamination in different dental specialties.
Topics: Humans; Equipment Contamination; Bacteria; Disinfection; Microbiota; Biofilms
PubMed: 35036099
DOI: 10.7717/peerj.12723 -
Microbiome Apr 2022Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere...
BACKGROUND
Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, the collective community-level change and effect of the phyllosphere microbiome in response to pathogen invasion remains largely elusive.
RESULTS
Here, we integrated 16S metabarcoding, shotgun metagenomics and culture-dependent methods to systematically investigate the changes in phyllosphere microbiome between infected and uninfected citrus leaves by Diaporthe citri, a fungal pathogen causing melanose disease worldwide. Multiple microbiome features suggested a shift in phyllosphere microbiome upon D. citri infection, highlighted by the marked reduction of community evenness, the emergence of large numbers of new microbes, and the intense microbial network. We also identified the microbiome features from functional perspectives in infected leaves, such as enriched microbial functions for iron competition and potential antifungal traits, and enriched microbes with beneficial genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated with the microbiome shift could positively affect plant performance under D. citri challenge, with reductions in disease index ranging from 65.7 to 88.4%. Among them, Pantoea asv90 and Methylobacterium asv41 identified as "recruited new microbes" in the infected leaves, exhibited antagonistic activities to D. citri both in vitro and in vivo, including inhibition of spore germination and/or mycelium growth. Sphingomonas spp. presented beneficial genomic characteristics and were found to be the main contributor for the functional enrichment of iron complex outer membrane receptor protein in the infected leaves. Moreover, Sphingomonas asv20 showed a stronger suppression ability against D. citri in iron-deficient conditions than iron-sufficient conditions, suggesting a role of iron competition during their antagonistic action.
CONCLUSIONS
Overall, our study revealed how phyllosphere microbiomes differed between infected and uninfected citrus leaves by melanose pathogen, and identified potential mechanisms for how the observed microbiome shift might have helped plants cope with pathogen pressure. Our findings provide novel insights into understanding the roles of phyllosphere microbiome responses during pathogen challenge. Video abstract.
Topics: Bacteria; Melanosis; Microbiota; Plant Leaves; Rhizosphere
PubMed: 35366955
DOI: 10.1186/s40168-022-01234-x -
Microbiology Spectrum Feb 2023Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic...
Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic bacterial communities of boxwood shoots and determine how they may respond to commonly used fungicides. In early summer and early fall, shoot samples were collected immediately before and 1, 7, and 14 days after three fungicides containing chlorothalonil and/or propiconazole were applied to the canopy. Total genomic DNA from shoot surface washings and surface-sterilized shoot tissues was used as the template for 16S rRNA metabarcoding, and the amplicons were sequenced on a Nanopore MinION sequencer to characterize the epiphytic and endophytic communities. The bacterial communities were phylogenetically more diverse on the boxwood shoot surface than in the internal tissue, although the two communities shared 12.7% of the total 1,649 identified genera. The most abundant epiphytes were and , while and were the dominant endophytes. Fungicide treatments had strong impacts on epiphytic bacterial community structure and composition. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) and analysis of variance (ANOVA)-like differential expression (ALDEx2) together identified 312 and 1,362 epiphytes changed in abundance due to fungicide treatments in early summer and early fall, respectively, and over 50% of these epiphytes were negatively impacted by fungicide. The two chlorothalonil-based contact fungicides demonstrated more marked effects than the propiconazole-based systemic fungicide. These results are foundational for exploring and utilizing the full potential of the microbiome and fungicide applications and developing a systems approach to boxwood health and production. Agrochemicals are important tools for safeguarding plants from invasive pathogens, insects, mites, and weeds. How they may affect the plant microbiome, a critical component of crop health and production, was poorly understood. Here, we used boxwood, an iconic low-maintenance landscape plant, to characterize shoot epiphytic and endophytic bacterial communities and their responses to contact and systemic fungicides. This study expanded our understanding of the above-ground microbiome in ornamental plants and is foundational for utilizing the full benefits of the microbiome in concert with different fungicide chemistries to improve boxwood health. This study also sets an example for a more thorough evaluation of these and other agrochemicals for their effects on boxwood microbiomes during production and offers an expanded systems approach that could be used with other crops for enhanced integrated pest management.
PubMed: 36853063
DOI: 10.1128/spectrum.04163-22 -
Microbiome Jun 2023Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the...
BACKGROUND
Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics.
RESULTS
In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination (Kalamiella piersonii) and one novel bacterial species (Methylobacterium ajmalii). In addition, four bins exhibited fungal genomes; this is the first-time fungal genomes were assembled from ISS metagenomes. Phylogenetic analyses of five bacterial species showed ISS-specific evolution. The genes pertaining to cell membranes, such as transmembrane transport, cell wall organization, and regulation of cell shape, were enriched. Variations in the antimicrobial-resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. Among these 20 MAGs characterized, AMR genes were more prevalent in the Enterobacter bugandensis MAG, which has been predominantly isolated from clinical samples. MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure.
CONCLUSIONS
Comparative analyses of MAGs and whole-genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. The Pantoea/Kalamiella strains have the maximum single-nucleotide polymorphisms found within the ISS strains examined. This may suggest that Pantoea/Kalamiella strains are much more subjective to microgravity changes. The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low-dose irradiation compared to the evolution of microbes here on Earth. Video Abstract.
Topics: Metagenome; Phylogeny; Bacteria; Space Flight; Gammaproteobacteria; Anti-Infective Agents; Metagenomics
PubMed: 37264385
DOI: 10.1186/s40168-023-01545-7 -
Microbiology Spectrum Aug 2022Greenhouses are highly productive environments in which conditions are regulated to optimize plant growth. The enclosed character of greenhouses usually results in...
Greenhouses are highly productive environments in which conditions are regulated to optimize plant growth. The enclosed character of greenhouses usually results in reduced microbial diversity, while it is known that a diverse microbiome is important for plant health. Therefore, we explored the phyllosphere microbiome of tomatoes and strawberries grown in greenhouses. We observed that the microbiome of both crops was low in diversity and abundance and varied considerably over time and space. Interestingly, the core taxa of tomatoes were Snodgrasella and Gilliamella, genera typically associated with bumblebees. The same amplicon sequence variants (ASVs) were found on reared bumblebees, indicating that the bumblebees, present in the sampled greenhouses to pollinate flowers, had introduced and dispersed these bacteria in the greenhouses. Overall, we found that 80% of plants contained bumblebee-associated taxa, and on these plants, bumblebee-associated reads accounted for up to a quarter of the reads on tomatoes and a tenth of the reads on strawberries. Furthermore, predatory mites had been introduced for the control of spider mites. Their microbiome was composed of a diverse set of bacteria, which varied between batches ordered at different times. Still, identical ASVs were found on mites and crops, and these belonged to the genera Sphingomonas, Staphylococcus, Methylobacterium, and Pseudomonas. These new insights should now be further explored and utilized to diversify ecosystems that are characterized by low diversity and abundancy of microbes. Greenhouses, though highly effective agricultural environments, are characterized by reduced sources of bacterial diversity and means of dispersal compared to more natural settings. As it is known that plant health and productivity are affected by associated bacteria, improving our knowledge on the bacterial communities on greenhouse crops is key to further innovate in horticulture. Our findings show that tomato and strawberry crops cultivated in greenhouses harbor poor and variable bacterial communities. Furthermore, commonly implemented biological solutions (i.e., those based on living organisms such as bumblebees and predatory mites) are important sources and means of dispersal of bacteria in greenhouses. This study shows that there is great potential in using these biological solutions to enrich the greenhouse microbiome by introducing and dispersing microbes which have beneficial effects on crop production and protection, provided that the dispersed microbes have a beneficial function.
Topics: Agriculture; Animals; Bacteria; Bees; Crops, Agricultural; Microbiota; Predatory Behavior
PubMed: 35862945
DOI: 10.1128/spectrum.01755-22 -
Frontiers in Pediatrics 2023To investigate the dynamic changes in the intestinal microbiota in preterm infants with necrotizing enterocolitis (NEC) before and after treatment a prospective...
PURPOSE
To investigate the dynamic changes in the intestinal microbiota in preterm infants with necrotizing enterocolitis (NEC) before and after treatment a prospective case-control study.
METHODS
Preterm infants with NEC and preterm infants with similar age and weight (control group) were enrolled in this study. They were divided into NEC_Onset (diagnosis time), NEC_Refeed (refeed time), NEC_FullEn (full enteral nutrition time), Control_Onset, and Control_FullEn groups according to the time of the fecal material collected. Except for basic clinical information, fecal specimens of the infants were obtained as well at indicated times for 16S rRNA gene sequencing. All infants were followed up after discharge from the NICU, and the growth data of the corrected age of 12 months were acquired from the electronic outpatient system and telephonic interviews.
RESULTS
A total of 13 infants with NEC and 15 control infants were enrolled. A gut microbiota analysis showed that the Shannon and Simpson indices were lower in the NEC_FullEn group than in the Control_FullEn group (< .05). Methylobacterium, Clostridium_butyricum, and Acidobacteria were more abundant in infants with NEC during diagnosis. Methylobacterium and Acidobacteria were remained plentiful in the NEC group until the end of treatment. These bacteria species were significantly positively correlated with CRP and negatively correlated with platelet count. The rate of delayed growth was higher in the NEC group than in the control group (25% vs. 7.1%) at 12 months of corrected age, but there was no significant difference. In addition, the pathways of synthesis and degradation of ketone bodies were more active in the NEC subgroups, including both the NEC_Onset group and the NEC_FullEn group. The pathway of sphingolipid metabolism was more active in the Control_FullEn group.
CONCLUSION
Even after reaching the full enteral nutrition period, alpha diversity in infants with NEC who underwent surgery was lower than that in the control group infants. It may take more time to reestablish the normal gut flora of NEC infants after surgery. The pathways of the synthesis and degradation of ketone bodies and sphingolipid metabolism might be related to the pathogenesis of NEC and physical development after the occurrence of NEC.
PubMed: 36793334
DOI: 10.3389/fped.2023.993759 -
Frontiers in Bioengineering and... 2022Growing concerns over the use of limited fossil fuels and their negative impacts on the ecological niches have facilitated the exploration of alternative routes. The use... (Review)
Review
Growing concerns over the use of limited fossil fuels and their negative impacts on the ecological niches have facilitated the exploration of alternative routes. The use of conventional plastic material also negatively impacts the environment. One such green alternative is polyhydroxyalkanoates, which are biodegradable, biocompatible, and environmentally friendly. Recently, researchers have focused on the utilization of waste gases particularly those belonging to C1 sources derived directly from industries and anthropogenic activities, such as carbon dioxide, methane, and methanol as the substrate for polyhydroxyalkanoates production. Consequently, several microorganisms have been exploited to utilize waste gases for their growth and biopolymer accumulation. Methylotrophs such as produced highest amount of PHA up to 88% using CH as the sole carbon source and 52-56% with CHOH. On the other hand , produced 71-81% of PHA by utilizing CO and CO as a substrate. The present review shows the potential of waste gas valorization as a promising solution for the sustainable production of polyhydroxyalkanoates. Key bottlenecks towards the usage of gaseous substrates obstructing their realization on a large scale and the possible technological solutions were also highlighted. Several strategies for PHA production using C1 gases through fermentation and metabolic engineering approaches are discussed. Microbes such as autotrophs, acetogens, and methanotrophs can produce PHA from CO, CO, and CH. Therefore, this article presents a vision of C1 gas into bioplastics are prospective strategies with promising potential application, and aspects related to the sustainability of the system.
PubMed: 36686222
DOI: 10.3389/fbioe.2022.907500