-
Molecules (Basel, Switzerland) May 2020Nitrile hydratases (NHase) catalyze the hydration of nitriles to the corresponding amides. We report on the heterologous expression of various nitrile hydratases. Some...
Nitrile hydratases (NHase) catalyze the hydration of nitriles to the corresponding amides. We report on the heterologous expression of various nitrile hydratases. Some of these enzymes have been investigated by others and us before, but sixteen target proteins represent novel sequences. Of 21 target sequences, 4 iron and 16 cobalt containing proteins were functionally expressed from BL21 (DE3) Gold. Cell free extracts were used for activity profiling and basic characterization of the NHases using the typical NHase substrate methacrylonitrile. Co-type NHases are more tolerant to high pH than Fe-type NHases. A screening for activity on three structurally diverse nitriles was carried out. Two novel Co-dependent NHases from and and a new Fe-type NHase from were very well expressed and hydrated methacrylonitrile, pyrazine-carbonitrile, and 3-amino-3-(-toluoyl)propanenitrile. The Co-dependent NHases from and , as well as two Fe-dependent NHases from , were-in addition-able to produce the amide from cinnamonitrile. Summarizing, seven so far uncharacterized NHases are described to be promising biocatalysts.
Topics: Burkholderiaceae; Catalysis; Cobalt; Escherichia coli; Hydro-Lyases; Iron; Metalloproteins; Methylobacteriaceae; Pseudomonas
PubMed: 32481666
DOI: 10.3390/molecules25112521 -
Genome Biology and Evolution Aug 2022Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well...
Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer (HGT). We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content, and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.
Topics: Ecosystem; Methylobacterium; Phylogeny; Plant Leaves; Plants; RNA, Ribosomal, 16S
PubMed: 35906926
DOI: 10.1093/gbe/evac123 -
Microorganisms Jan 2022Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These...
Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were , , , and , of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed (26.7%) (23.6%) and (10%), while the gene revealed (70.3%) and (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; (39%) and (24.4%) (all legumes), (7.9%), (4.6%) and (3%) (, , ) (4.2%; ), (4%; , ), (3.1%; ), and (2.7%; ) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of species was common in all rhizosphere soils considered. had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.
PubMed: 35208671
DOI: 10.3390/microorganisms10020216 -
BMC Microbiology Feb 2022Symbiotic Methylobacterium strains comprise a significant part of plant microbiomes. Their presence enhances plant productivity and stress resistance, prompting...
BACKGROUND
Symbiotic Methylobacterium strains comprise a significant part of plant microbiomes. Their presence enhances plant productivity and stress resistance, prompting classification of these strains as plant growth-promoting bacteria (PGPB). Methylobacteria can synthesize unusually high levels of plant hormones, called cytokinins (CKs), including the most active form, trans-Zeatin (tZ).
RESULTS
This study provides a comprehensive inventory of 46 representatives of Methylobacterium genus with respect to phytohormone production in vitro, including 16 CK forms, abscisic acid (ABA) and indole-3-acetic acid (IAA). High performance-liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analyses revealed varying abilities of Methylobacterium strains to secrete phytohormones that ranged from 5.09 to 191.47 pmol mL for total CKs, and 0.46 to 82.16 pmol mL for tZ. Results indicate that reduced methanol availability, the sole carbon source for bacteria in the medium, stimulates CK secretion by Methylobacterium. Additionally, select strains were able to transform L-tryptophan into IAA while no ABA production was detected.
CONCLUSIONS
To better understand features of CKs in plants, this study uncovers CK profiles of Methylobacterium that are instrumental in microbe selection for effective biofertilizer formulations.
Topics: Chromatography, High Pressure Liquid; Cytokinins; Methylobacterium; Tandem Mass Spectrometry
PubMed: 35135483
DOI: 10.1186/s12866-022-02454-9 -
JCI Insight May 2018The underlying pathology of atopic dermatitis (AD) includes impaired skin barrier function, susceptibility to Staphylococcus aureus skin infection, immune dysregulation,...
The underlying pathology of atopic dermatitis (AD) includes impaired skin barrier function, susceptibility to Staphylococcus aureus skin infection, immune dysregulation, and cutaneous dysbiosis. Our recent investigation into the potential role of Gram-negative skin bacteria in AD revealed that isolates of one particular commensal, Roseomonas mucosa, collected from healthy volunteers (HVs) improved outcomes in mouse and cell culture models of AD. In contrast, isolates of R. mucosa from patients with AD worsened outcomes in these models. These preclinical results suggested that interventions targeting the microbiome could provide therapeutic benefit for patients with AD. As a first test of this hypothesis in humans, 10 adult and 5 pediatric patients were enrolled in an open-label phase I/II safety and activity trial (the Beginning Assessment of Cutaneous Treatment Efficacy for Roseomonas in Atopic Dermatitis trial; BACTERiAD I/II). Treatment with R. mucosa was associated with significant decreases in measures of disease severity, topical steroid requirement, and S. aureus burden. There were no adverse events or treatment complications. We additionally evaluated differentiating bacterial metabolites and topical exposures that may contribute to the skin dysbiosis associated with AD and/or influence future microbiome-based treatments. These early results support continued evaluation of R. mucosa therapy with a placebo-controlled trial.
Topics: Adolescent; Adult; Animals; Biological Therapy; Child; Dermatitis, Atopic; Dysbiosis; Female; Humans; Male; Methylobacteriaceae; Mice; Microbiota; Severity of Illness Index; Skin; Staphylococcus aureus; Steroids; Young Adult
PubMed: 29720571
DOI: 10.1172/jci.insight.120608 -
Heliyon Aug 2021f.sp. (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or...
f.sp. (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or fungicides strongly affect the soil microbiomes ecosystem. Suppressive soil is a promising method for controlling soil-borne pathogens in which soil microbiomes may affect the suppressiveness. The comparative analysis of microbial diversity was conducted from suppressive and conducive soils by analyzing whole shotgun metagenomic DNA data. Two suppressive soil samples and two conducive soil samples were collected from a banana plantation in Sukabumi, West Java, Indonesia. Each soil sample was prepared by mixing the soil samples collected from three points sampling sites with 20 cm depth. Analysis of microbial abundance, diversity, co-occurrence network using Metagenome Analyzer 6 (MEGAN6) and functional analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed. Data showed the abundance of s, and were higher in the suppressive than conducive soils. Interestingly, those bacteria groups are known functionally as members of Plant Growth Promoting Rhizobacteria (PGPR). The co-occurrence analysis showed , and were present in the suppressive soils, while and more were found in the conducive soils. Furthermore, the relative abundance of , , , and was performed. The analysis showed that the relative abundance of and was higher in the suppressive than conducive soils. Therefore, it assumed and play a role in suppressing Foc based on co-occurrence and abundance analysis. Functional analysis of and showed that the zinc/manganese transport system was higher in the suppressive than conducive soils. In contrast, the phosphate transport system was not found in conducive soils. Both functions are may be responsible for the synthesis of a siderophore and phosphate solubilization. In conclusion, this study provides information that PGPR may be contributing to Foc growth suppressing by releasing secondary metabolites.
PubMed: 34401567
DOI: 10.1016/j.heliyon.2021.e07636 -
PloS One 2020The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology...
The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology and evolution is not well understood. Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most abundant and widespread plant-associated bacteria. In addition, many of these species impact plant fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East (NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and we expected that the divergent selection on hosts may have also generated divergence in associated Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent with our expectation, across spatial scales this phenotypic variation was largely explained by host landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed that at least some rice landraces gain an early growth advantage from their specific phyllosphere-colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and understand diversity in one of the most important food crops of the world.
Topics: Carbon; Crops, Agricultural; Ecosystem; Genetic Variation; Host-Pathogen Interactions; India; Methylobacterium; Oryza; Phenotype; Phylogeny; Plant Leaves
PubMed: 32092057
DOI: 10.1371/journal.pone.0228550 -
BMC Microbiology May 2012Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application...
BACKGROUND
Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application of selected bacterial species in crop improvement and protection. Medicago sativa L. is a legume crop of high economic importance as forage in temperate areas and one of the most popular model plants for investigations on the symbiosis with nitrogen fixing rhizobia (mainly belonging to the alphaproteobacterial species Sinorhizobium meliloti). However, despite its importance, no studies have been carried out looking at the total bacterial community associated with the plant. In this work we explored for the first time the total bacterial community associated with M. sativa plants grown in mesocosms conditions, looking at a wide taxonomic spectrum, from the class to the single species (S. meliloti) level.
RESULTS
Results, obtained by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis, quantitative PCR and sequencing of 16 S rRNA gene libraries, showed a high taxonomic diversity as well as a dominance by members of the class Alphaproteobacteria in plant tissues. Within Alphaproteobacteria the families Sphingomonadaceae and Methylobacteriaceae were abundant inside plant tissues, while soil Alphaproteobacteria were represented by the families of Hyphomicrobiaceae, Methylocystaceae, Bradyirhizobiaceae and Caulobacteraceae. At the single species level, we were able to detect the presence of S. meliloti populations in aerial tissues, nodules and soil. An analysis of population diversity on nodules and soil showed a relatively low sharing of haplotypes (30-40%) between the two environments and between replicate mesocosms, suggesting drift as main force shaping S. meliloti population at least in this system.
CONCLUSIONS
In this work we shed some light on the bacterial communities associated with M. sativa plants, showing that Alphaproteobacteria may constitute an important part of biodiversity in this system, which includes also the well known symbiont S. meliloti. Interestingly, this last species was also found in plant aerial part, by applying cultivation-independent protocols, and a genetic diversity analysis suggested that population structure could be strongly influenced by random drift.
Topics: Bacteria; Biota; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Medicago sativa; Molecular Sequence Data; Phylogeny; Polymorphism, Restriction Fragment Length; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 22607312
DOI: 10.1186/1471-2180-12-78 -
Pendimethalin biodegradation by soil strains of Burkholderia sp. and Methylobacterium radiotolerans.Anais Da Academia Brasileira de Ciencias 2021Pendimethalin herbicide is widely used and persists in the environment as a contaminant causing negative impacts, including for human health. Microorganisms have the...
Pendimethalin herbicide is widely used and persists in the environment as a contaminant causing negative impacts, including for human health. Microorganisms have the capacity to remove many contaminants from the environment. Thus, the aim of this work was to evaluate the efficiency of soil bacterial species prospected by molecular modelling of cytochrome P450 in to degrade pendimethalin. Strains of Burkholderia sp. and Methylobacterium radiotolerans were cultivated in a mineral saline medium enriched with 281 mg/L pendimethalin (MSPEN) and another containing glucose 1.0 g/L as extra carbon source (MSPENGLI). Both strains were able to degrade pendimethalin under the two conditions experienced. Burkholderia sp. F7G4PR33-4 was more efficient in degrading 65% of the herbicide in MSPEN medium, with 49.3% in MSPENGLI; while Methylobacterium radiotolerans A6A1PR46-4 degraded 55.4% in MSPEN and 29.8% in MSPENGLI mediums. These findings contribute to the expansion of knowledge on the competence of isolates of these two bacterial genera in degrading herbicidal xenobiotics and biotechnological potential for pendimethalin degradation and bioremediation.
Topics: Aniline Compounds; Biodegradation, Environmental; Burkholderia; Humans; Methylobacterium; Soil; Soil Microbiology
PubMed: 34909833
DOI: 10.1590/0001-3765202120210924 -
ACS Chemical Biology Aug 2021Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific...
Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific precursor; however, this approach is limited by the availability of isotopically enriched precursors. We used an inverse stable isotopic labeling approach to identify natural products by growing bacteria on a C-carbon source and then identifying C-precursor incorporation by mass spectrometry. We applied this approach to methylotrophs, ecologically important bacteria predicted to have significant yet underexplored biosynthetic potential. We demonstrate that this method identifies acyl homoserine lactone quorum sensing signals produced by diverse methylotrophs grown on three different one-carbon compounds. We then apply this approach to simultaneously detect five previously unidentified signals produced by a methylotroph and link these compounds to their synthases. We envision that this method can be used to identify other natural product classes synthesized by methylotrophs and other organisms that grow on relatively inexpensive C-carbon sources.
Topics: Acyl-Butyrolactones; Carbon; Carbon Isotopes; Isotope Labeling; Methylobacteriaceae; Methylococcaceae; Proof of Concept Study; Quorum Sensing
PubMed: 34328722
DOI: 10.1021/acschembio.1c00329