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MBio Jan 2024Bacteria known as pink-pigmented facultative methylotrophs colonize many diverse environments on earth, play an important role in the carbon cycle, and in some cases...
Bacteria known as pink-pigmented facultative methylotrophs colonize many diverse environments on earth, play an important role in the carbon cycle, and in some cases promote plant growth. However, little is known about how these organisms interact with each other and their environment. In this work, we identify one of the chemical signals commonly used by these bacteria and discover that this signal controls swarming motility in the pink-pigmented facultative methylotroph DSM5686. This work provides new molecular details about interactions between these important bacteria and will help scientists predict these interactions and the group behaviors they regulate from genomic sequencing information.
Topics: Quorum Sensing; Acyl-Butyrolactones; Methylobacterium
PubMed: 38085021
DOI: 10.1128/mbio.01999-23 -
BioRxiv : the Preprint Server For... Nov 2023The influence of lanthanide biochemistry during methylotrophy demands a reassessment of how the composition and metabolic potential of methylotrophic phyllosphere...
The influence of lanthanide biochemistry during methylotrophy demands a reassessment of how the composition and metabolic potential of methylotrophic phyllosphere communities are affected by the presence of these metals. To investigate this, methylotrophs were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors. Of the 344 pink-pigmented facultative methylotroph isolates, none were obligately lanthanide-dependent. Phylogenetic analyses revealed that all strains were nearly identical to each other and to model strains from the clade of , with providing higher resolution than 16s RNA for strain-specific identification. Despite the low species diversity, the metabolic capabilities of the community diverged greatly. Strains encoding identical PQQ-dependent alcohol dehydrogenases displayed significantly different growth from each other on alcohols in the presence and absence of lanthanides. Several strains also lacked well-characterized lanthanide-associated genes thought to be important for phyllosphere colonization. Additionally, 3% of our isolates were capable of growth on sugars and 23% were capable of growth on aromatic acids, substantially expanding the range of multicarbon substrates utilized by members of the clade in the phyllosphere. Whole genome sequences of eleven novel strains are reported. Our findings suggest that the expansion of metabolic capabilities, as well as differential usage of lanthanides and their influence on metabolism among closely related strains, point to evolution of niche partitioning strategies to promote colonization of the phyllosphere.
PubMed: 38077020
DOI: 10.1101/2023.06.28.546956 -
Environmental Pollution (Barking, Essex... Feb 2024While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome,...
While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaea, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were non-culturable using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the phyla Proteobacteria and Planctomycetes. Notably, the genus Methylobacterium was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp. Archaeal DNA (Euryarchaeota, Crenarchaeota) was found in trace amounts in some DW samples. Viruses such as rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2 were negative in all DW samples using colloidal gold and real-time reverse transcription polymerase chain reaction (RT‒PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (Ortervirales) and Herpesvirales was found in some DW samples. The metabolic pathways of the entire microbial community involve cell‒cell communication and signal secretion, contributing to cooperation between different microbial populations in the water. This study provides insight into the microbial community and metabolic process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.
Topics: Humans; Drinking Water; Pandemics; Bacteria; Archaea; Microbiota; RNA, Ribosomal, 16S
PubMed: 38048871
DOI: 10.1016/j.envpol.2023.123066 -
Microorganisms Nov 2023is the causal agent of several plant diseases affecting fruit and nut crops. strain SR1.6/6 was isolated from and shown to promote plant growth by producing...
is the causal agent of several plant diseases affecting fruit and nut crops. strain SR1.6/6 was isolated from and shown to promote plant growth by producing phytohormones, providing nutrients, inhibiting , and preventing Citrus Variegated Chlorosis. However, the molecular mechanisms involved in the interaction among these microbes are still unclear. The present work aimed to analyze physiological and molecular aspects of SR1.6/6 and 9a5c in co-culture. The transcriptome and secretome analyses indicated that down-regulates cell division and transport genes and up-regulates stress via induction of chaperones and pathogenicity-related genes including, the lipase-esterase LesA, a protease, as well as an oligopeptidase in response to competition. On the other hand, also down-regulated transport genes, except for iron uptake, which was up-regulated. Secretome analysis identified four proteins in exclusively produced in co-culture with , among these, three are related to phosphorous uptake. These results suggest that inhibits growth mainly due to nutrient competition for iron and phosphorous, thus promoting starvation, besides producing enzymes that degrade cell wall, mainly hydrolases. The understanding of these interactions provides a direction for control and management of the phytopathogen , and consequently, helps to improve citrus growth and productivity.
PubMed: 38004766
DOI: 10.3390/microorganisms11112755 -
Life (Basel, Switzerland) Nov 2023Suppressing the growth of species without the use of toxic chemicals has been a challenging task owing to their robustness against previous antimicrobial techniques. In...
Suppressing the growth of species without the use of toxic chemicals has been a challenging task owing to their robustness against previous antimicrobial techniques. In this work, we prepared porous materials with various numbers and types of oxygen functional groups and investigated their ability to suppress the growth of . It turned out that the number and type of oxygen functional groups in the porous materials greatly affected the growth of the bacterium. Three porous materials (resorcinol-formaldehyde gel (RF), hydrothermally treated RF (RFH), and Wakkanai siliceous shale (WS)) were tested, and RF exhibited the best performance in suppressing the growth of the bacterium. This performance is possibly due to abundant phenolic groups in the porous material.
PubMed: 38004325
DOI: 10.3390/life13112185 -
FEMS Microbiology Letters Jan 2023Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell...
Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.
Topics: Methylobacterium; Ecosystem; RNA, Ribosomal, 16S; Methanol; New Zealand; Plants; Plant Leaves
PubMed: 37985695
DOI: 10.1093/femsle/fnad124 -
Frontiers in Microbiology 2023Motile bacteria take a competitive advantage in colonization of plant surfaces to establish beneficial associations that eventually support plant health. Plant exudates...
Motile bacteria take a competitive advantage in colonization of plant surfaces to establish beneficial associations that eventually support plant health. Plant exudates serve not only as primary growth substrates for bacteria but also as bacterial chemotaxis attractants. A number of plant-derived compounds and corresponding chemotaxis sensors have been documented, however, the sensors for methanol, one of the major volatile compounds released by plants, have not been identified. species are ubiquitous plant surface-symbiotic, methylotrophic bacteria. A plant-growth promoting bacterium, strain 22A exhibits chemotaxis toward methanol (methylotaxis). Its genome encodes 52 methyl-accepting chemotaxis proteins (MCPs), among which we identified three MCPs (methylotaxis proteins, MtpA, MtpB, and MtpC) responsible for methylotaxis. The triple gene mutant of the MCPs exhibited no methylotaxis, slower gathering to plant tissues, and less efficient colonization on plants than the wild type, suggesting that the methylotaxis mediates initiation of plant- symbiosis and engages in proliferation on plants. To examine how these MCPs are operating methylotaxis, we generated multiple gene knockouts of the MCPs, and Ca-dependent MxaFI and lanthanide (Ln)-dependent XoxF methanol dehydrogenases (MDHs), whose expression is regulated by the presence of Ln. MtpA was found to be a cytosolic sensor that conducts formaldehyde taxis (formtaxis), as well as methylotaxis when MDHs generate formaldehyde. MtpB contained a dCache domain and exhibited differential cellular localization in response to La. MtpB expression was induced by La, and its activity required XoxF1. MtpC exhibited typical cell pole localization, required MxaFI activity, and was regulated under MxbDM that is also required for MxaF expression. Strain 22A methylotaxis is realized by three independent MCPs, two of which monitor methanol oxidation by Ln-regulated MDHs, and one of which monitors the common methanol oxidation product, formaldehyde. We propose that methanol metabolism-linked chemotaxis is the key factor for the efficient colonization of on plants.
PubMed: 37901831
DOI: 10.3389/fmicb.2023.1258452 -
Animals : An Open Access Journal From... Oct 2023Marine crustaceans are severely threatened by environmental factors such as ocean acidification, but, despite the latter's negative impact on growth, molting, and...
Marine crustaceans are severely threatened by environmental factors such as ocean acidification, but, despite the latter's negative impact on growth, molting, and immunity, its effects on intestinal microflora remain poorly understood. This work studied the gut morphology and intestinal microflora of , grown in seawater of different pH levels: 8.1 (control group), 7.4 (AC74 group), and 7.0 (AC70 group). Ocean acidification was found to cause intestinal damage, while significantly altering the microflora's composition. However, the α-diversity did not differ significantly between the groups. At the phylum level, the relative abundance of Proteobacteria decreased in the acidification groups, while at the genus level, the relative abundance of decreased. was a prominent discriminative biomarker in the AC74 group, with Actinobacteriota, Micrococcales, Beijerinckiaceae, , and Flavobacteriales being the main ones in the AC70 group. The function prediction results also indicated an enrichment of pathways related to metabolism for the acidification groups. At the same time, those related to xenobiotics' biodegradation and metabolism were inhibited in AC74 but enhanced in AC70. This is the first study examining the impact of ocean acidification on the intestinal microflora of crustaceans. The results are expected to provide a better understanding of the interactions between shrimp and their microflora in response to environmental stressors.
PubMed: 37894023
DOI: 10.3390/ani13203299 -
Journal of Microorganism Control 2023Bedside dialysis monitoring equipment for hemodialysis are located in the bioburden section upstream of the endotoxin-retentive filter for dialysis fluid sterilization....
Bedside dialysis monitoring equipment for hemodialysis are located in the bioburden section upstream of the endotoxin-retentive filter for dialysis fluid sterilization. We observed 26 equipment at our institution for bacterial contamination at least once every 4 weeks for 5 years with another ultrafiltration membrane upstream to prevent bacterial contamination. Bacterial contamination levels were highest and most diverse at the time of the first flush. During subsequent initial cleanng, the contamination level decreased, and bacterial species converged almost exclusively to one genus, namely Methylobacterium spp. During clinical use, the equipment were cleaned and disinfected daily after dialysis, and daily operations and maintenance were performed using aseptic techniques. Although the frequency of bacterial detection decreased annually, the same bacterial genotypes observed at the first flush were isolated even after long time periods and were thought to persist in the equipment possibly by forming biofilm. Pseudomonas aeruginosa was newly detected after the replacement of parts during breakdown maintenance, indicating the need to sterilize replacement parts. Thus, the bioburden should be assessed regularly as part of the management of in-house-produced dialysis fluid.
Topics: Renal Dialysis; Bacteria; Dialysis Solutions; Ultrafiltration; Endotoxins
PubMed: 37866898
DOI: 10.4265/jmc.28.3_69 -
Frontiers in Bioengineering and... 2023It is challenging to capture carbon dioxide (CO), a major greenhouse gas in the atmosphere, due to its high chemical stability. One potential practical solution to...
It is challenging to capture carbon dioxide (CO), a major greenhouse gas in the atmosphere, due to its high chemical stability. One potential practical solution to eliminate CO is to convert CO into formate using hydrogen (H) (CO hydrogenation), which can be accomplished with inexpensive hydrogen from sustainable sources. While industrial flue gas could provide an adequate source of hydrogen, a suitable catalyst is needed that can tolerate other gas components, such as carbon monoxide (CO) and oxygen (O), potential inhibitors. Our proposed CO hydrogenation system uses the hydrogenase derived from H16 (ReSH) and formate dehydrogenase derived from AM1 (MeFDH1). Both enzymes are tolerant to CO and O, which are typical inhibitors of metalloenzymes found in flue gas. We have successfully demonstrated that combining ReSH- and MeFDH1-immobilized resins can convert H and CO in real flue gas to formate via a nicotinamide adenine dinucleotide-dependent cascade reaction. We anticipated that this enzyme system would enable the utilization of diverse H and CO sources, including waste gases, biomass, and gasified plastics.
PubMed: 37854886
DOI: 10.3389/fbioe.2023.1265272