-
Frontiers in Microbiology 2023Denitrification is vital to nitrogen removal and NO release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying...
Denitrification is vital to nitrogen removal and NO release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of NO emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential NO emission rate, enzymatic activity for NO production and reduction, gene abundance, and community composition during denitrification were investigated using the N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential NO emission rates were 0.51 ± 0.20 μmol⋅N⋅kg⋅h, which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for NO production was 2.77-8.94 times than that for NO reduction, indicating an imbalance between NO production and reduction. The gene abundance ratio of to Z from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the B gene without Z genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to NO emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g NO⋅m⋅yr in surface paddy soils.
PubMed: 37396352
DOI: 10.3389/fmicb.2023.1218207 -
Microorganisms Sep 2022Predatory bacteria, which prey on other bacteria, have significant functions in microbial ecosystems and have attracted increasing attention for their biotechnological...
Predatory bacteria, which prey on other bacteria, have significant functions in microbial ecosystems and have attracted increasing attention for their biotechnological use. However, knowledge of the characteristics of wild-type environmental predatory bacteria remains limited. This study isolated two predatory bacteria, HI3 and sp. MH1, from a freshwater pond and characterized their predation capabilities. Determination of the prey range using 53 potential prey strains, including 52 environmental strains, revealed that HI3 and sp. MH1 could prey on a wide spectrum of Gram-negative bacteria and a broader range of bacteria, irrespective of phylogeny, in accordance with the common characteristics of and like organisms and myxobacteria, respectively. Liquid culture assays also found that although predation by HI3 rapidly and largely occurred, the prey bacteria regrew, possibly through plastic phenotypic resistance to predation. In contrast, predation by sp. MH1 occurred at relatively low efficiency but was longer lasting. The two strains exhibited slightly distinct temperature preferences but commonly preferred slightly alkaline pH. The novel findings of this study provide evidence for the coexistence of predatory bacteria with diverse predation capabilities in the natural aquatic environment.
PubMed: 36144418
DOI: 10.3390/microorganisms10091816 -
Malaria Journal Feb 2021Insecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito...
BACKGROUND
Insecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito microbiota and insecticide resistance, the microbiota of Anopheles gambiae sensu stricto (s.s.) from Tulukuyi village, Bungoma, Kenya, with differing permethrin resistance profiles were comparatively characterized.
METHODS
Using the CDC bottle bioassay, 133 2-3 day-old, virgin, non-blood fed female F progeny of field-caught An. gambiae s.s. were exposed to five times (107.5 µg/ml) the discriminating dose of permethrin. Post bioassay, 50 resistant and 50 susceptible mosquitoes were subsequently screened for kdr East and West mutations, and individually processed for microbial analysis using high throughput sequencing targeting the universal bacterial and archaeal 16S rRNA gene.
RESULTS
47 % of the samples tested (n = 133) were resistant, and of the 100 selected for further processing, 99 % were positive for kdr East and 1 % for kdr West. Overall, 84 bacterial taxa were detected across all mosquito samples, with 36 of these shared between resistant and susceptible mosquitoes. A total of 20 bacterial taxa were unique to the resistant mosquitoes and 28 were unique to the susceptible mosquitoes. There were significant differences in bacterial composition between resistant and susceptible individuals (PERMANOVA, pseudo-F = 2.33, P = 0.001), with presence of Sphingobacterium, Lysinibacillus and Streptococcus (all known pyrethroid-degrading taxa), and the radiotolerant Rubrobacter, being significantly associated with resistant mosquitoes. On the other hand, the presence of Myxococcus, was significantly associated with susceptible mosquitoes.
CONCLUSIONS
This is the first report of distinct microbiota in An. gambiae s.s. associated with intense pyrethroid resistance. The findings highlight differentially abundant bacterial taxa between resistant and susceptible mosquitoes, and further suggest a microbe-mediated mechanism of insecticide resistance in mosquitoes. These results also indicate fixation of the kdr East mutation in this mosquito population, precluding further analysis of its associations with the mosquito microbiota, but presenting the hypothesis that any microbe-mediated mechanism of insecticide resistance would be likely of a metabolic nature. Overall, this study lays initial groundwork for understanding microbe-mediated mechanisms of insecticide resistance in African mosquito vectors of malaria, and potentially identifying novel microbial markers of insecticide resistance that could supplement existing vector surveillance tools.
Topics: Animals; Anopheles; Female; Insecticide Resistance; Insecticides; Kenya; Microbiota; Mosquito Control; Mosquito Vectors; Permethrin
PubMed: 33557825
DOI: 10.1186/s12936-021-03606-4 -
PLoS Computational Biology Jan 2021The mechanisms and design principles of regulatory systems establishing stable polarized protein patterns within cells are well studied. However, cells can also...
The mechanisms and design principles of regulatory systems establishing stable polarized protein patterns within cells are well studied. However, cells can also dynamically control their cell polarity. Here, we ask how an upstream signaling system can switch the orientation of a polarized pattern. We use a mathematical model of a core polarity system based on three proteins as the basis to study different mechanisms of signal-induced polarity switching. The analysis of this model reveals four general classes of switching mechanisms with qualitatively distinct behaviors: the transient oscillator switch, the reset switch, the prime-release switch, and the push switch. Each of these regulatory mechanisms effectively implements the function of a spatial toggle switch, however with different characteristics in their nonlinear and stochastic dynamics. We identify these characteristics and also discuss experimental signatures of each type of switching mechanism.
Topics: Bacterial Proteins; Cell Polarity; Computational Biology; Gene Regulatory Networks; Intercellular Signaling Peptides and Proteins; Membrane Proteins; Models, Biological; Myxococcus xanthus; Signal Transduction; Stochastic Processes
PubMed: 33465073
DOI: 10.1371/journal.pcbi.1008587 -
Microbiology Resource Announcements Mar 2023Myxococcus xanthus is a social Gram-negative soil bacterium and the best studied member of the order in the class Deltaproteobacteria, which was recently reclassified...
Myxococcus xanthus is a social Gram-negative soil bacterium and the best studied member of the order in the class Deltaproteobacteria, which was recently reclassified as the phylum . Here, we report complete genomes, obtained using Illumina and PacBio sequencing, of M. xanthus strains DK1050 and DK101 (GenBank accession numbers CP104804 and CP104803, respectively).
PubMed: 36749079
DOI: 10.1128/mra.01020-22 -
International Journal of Molecular... Oct 2023The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new...
The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new signals and molecules produced by one species that affects other species' behavior. In this work, we have studied the effects of the interaction of nine species (, , , , , , , , and ) with the predator bacteria , five of which (, , , , and ) induce mound formation of on complex media (Casitone Yeast extract (CYE) and Casitone tris (CTT); media on which does not form these aggregates under normal culture conditions. An in-depth study on - interactions (the strain producing the strongest effect) has allowed the identification of two siderophores produced by , demethylenenocardamine and nocardamine, responsible for this grouping effect over . Experiments using pure commercial nocardamine and different concentrations of FeSO show that iron depletion is responsible for the behavior of . Additionally, it was found that molecules, smaller than 3 kDa, produced by can induce the production of DK-xanthenes by .
Topics: Myxococcus; Myxococcus xanthus; Streptomyces; Microbial Interactions; Iron
PubMed: 37958645
DOI: 10.3390/ijms242115659 -
Genome Biology and Evolution Dec 2020Members of the predatory Myxococcales (myxobacteria) possess large genomes, undergo multicellular development, and produce diverse secondary metabolites, which are being... (Comparative Study)
Comparative Study
Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and...
Members of the predatory Myxococcales (myxobacteria) possess large genomes, undergo multicellular development, and produce diverse secondary metabolites, which are being actively prospected for novel drug discovery. To direct such efforts, it is important to understand the relationships between myxobacterial ecology, evolution, taxonomy, and genomic variation. This study investigated the genomes and pan-genomes of organisms within the Myxococcaceae, including the genera Myxococcus and Corallococcus, the most abundant myxobacteria isolated from soils. Previously, ten species of Corallococcus were known, whereas six species of Myxococcus phylogenetically surrounded a third genus (Pyxidicoccus) composed of a single species. Here, we describe draft genome sequences of five novel species within the Myxococcaceae (Myxococcus eversor, Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis, Myxococcus vastator, Pyxidicoccus caerfyrddinensis, and Pyxidicoccus trucidator) and for the Pyxidicoccus type species strain, Pyxidicoccus fallax DSM 14698T. Genomic and physiological comparisons demonstrated clear differences between the five novel species and every other Myxococcus or Pyxidicoccus spp. type strain. Subsequent analyses of type strain genomes showed that both the Corallococcus pan-genome and the combined Myxococcus and Pyxidicoccus (Myxococcus/Pyxidicoccus) pan-genome are large and open, but with clear differences. Genomes of Corallococcus spp. are generally smaller than those of Myxococcus/Pyxidicoccus spp. but have core genomes three times larger. Myxococcus/Pyxidicoccus spp. genomes are more variable in size, with larger and more unique sets of accessory genes than those of Corallococcus species. In both genera, biosynthetic gene clusters are relatively enriched in the shell pan-genomes, implying they grant a greater evolutionary benefit than other shell genes, presumably by conferring selective advantages during predation.
Topics: Genome, Bacterial; Genomics; Myxococcales; Phylogeny; RNA, Ribosomal, 16S
PubMed: 33022031
DOI: 10.1093/gbe/evaa212 -
Science Advances Feb 2023The predatory deltaproteobacterium Myxococcus xanthus uses a helically-trafficked motor at bacterial focal-adhesion (bFA) sites to power gliding motility. Using total...
The predatory deltaproteobacterium Myxococcus xanthus uses a helically-trafficked motor at bacterial focal-adhesion (bFA) sites to power gliding motility. Using total internal reflection fluorescence and force microscopies, we identify the von Willebrand A domain-containing outer-membrane (OM) lipoprotein CglB as an essential substratum-coupling adhesin of the gliding transducer (Glt) machinery at bFAs. Biochemical and genetic analyses reveal that CglB localizes to the cell surface independently of the Glt apparatus; once there, it is recruited by the OM module of the gliding machinery, a heteroligomeric complex containing the integral OM β barrels GltA, GltB, and GltH, as well as the OM protein GltC and OM lipoprotein GltK. This Glt OM platform mediates the cell-surface accessibility and retention of CglB by the Glt apparatus. Together, these data suggest that the gliding complex promotes regulated surface exposure of CglB at bFAs, thus explaining the manner by which contractile forces exerted by inner-membrane motors are transduced across the cell envelope to the substratum.
Topics: Myxococcales; Focal Adhesions; Adhesins, Bacterial; Bacterial Adhesion; Lipoproteins; Bacterial Proteins
PubMed: 36812310
DOI: 10.1126/sciadv.abq0619 -
Applied and Environmental Microbiology Nov 2018Myxobacteria utilize the catechol natural products myxochelin A and B in order to maintain their iron homeostasis. Recently, the production of these siderophores, along...
Myxobacteria utilize the catechol natural products myxochelin A and B in order to maintain their iron homeostasis. Recently, the production of these siderophores, along with a new myxochelin derivative named pseudochelin A, was reported for the marine bacterium S2040. The latter derivative features a characteristic imidazoline moiety, which was proposed to originate from an intramolecular condensation reaction of the β-aminoethyl amide group in myxochelin B. To identify the enzyme catalyzing this conversion, we compared the myxochelin regulons of two myxobacterial strains that produce solely myxochelin A and B with those of S2040. This approach revealed a gene exclusive to the myxochelin regulon in S2040, coding for an enzyme of the amidohydrolase superfamily. To prove that this enzyme is indeed responsible for the postulated conversion, the reaction was reconstituted using a hexahistidine-tagged recombinant protein made in , with myxochelin B as the substrate. To test the production of pseudochelin A under conditions, the amidohydrolase gene was cloned into the myxobacterial plasmid pZJY156 and placed under the control of a copper-inducible promoter. The resulting vector was introduced into the myxobacterium DSM 16526, a native producer of myxochelin A and B. Following induction with copper, the myxobacterial expression strain was found to synthesize small quantities of pseudochelin A. Replacement of the copper-inducible promoter with the constitutive promoter led to increased production levels in , which facilitated the isolation and subsequent structural verification of the heterologously produced compound. In this study, an enzyme for imidazoline formation in pseudochelin biosynthesis was identified. Evidence for the involvement of this enzyme in the postulated reaction was obtained after reconstitution. Furthermore, the function of this enzyme was demonstrated by transferring the corresponding gene into the bacterium , which thereby became a producer of pseudochelin A. In addition to clarifying the molecular basis of imidazoline formation in siderophore biosynthesis, we describe the heterologous expression of a gene in a myxobacterium without chromosomal integration. Due to its metabolic proficiency, represents an interesting alternative to established host systems for the reconstitution and manipulation of biosynthetic pathways. Since the plasmid used in this study is easily adaptable for the expression of other enzymes as well, we expand the conventional expression strategy for myxobacteria, which is based on the integration of biosynthetic genes into the host genome.
Topics: Amidohydrolases; Bacterial Proteins; Biosynthetic Pathways; Catechols; Gene Expression Regulation, Bacterial; Genetic Engineering; Lysine; Myxococcus xanthus; Plasmids; Promoter Regions, Genetic; Regulon
PubMed: 30217842
DOI: 10.1128/AEM.01789-18 -
ACS Chemical Biology Apr 2023In this study, an unprecedented myxobacterial siderophore termed sorangibactin was discovered by heterologous expression of a coelibactin-like nonribosomal peptide...
In this study, an unprecedented myxobacterial siderophore termed sorangibactin was discovered by heterologous expression of a coelibactin-like nonribosomal peptide synthetase (NRPS) gene cluster from the strain MSr11367 in the host DK1622. De novo structure elucidation uncovered a linear polycyclic structure consisting of an N-terminal phenol group, an oxazole, tandem -methyl-thiazolidines, and an unusual C-terminal γ-thiolactone moiety. Except for the unprecedented oxazoline dehydrogenation to form an oxazole, which we show to be catalyzed by a cytochrome P450-dependent enzyme, other tailoring steps were found necessary for efficient downstream processing. The unusual thioesterase (TE) domain is proposed to select homocysteine or methionine for offloading involving an intramolecular γ-thiolactone formation. Its active site comprises a rare cysteine, which was found essential for product formation by point mutation to alanine or serine, which both abolished its activity. This unusual release mechanism and the resulting rare thiolactone structure can serve as a starting point for detailed biochemical investigations.
Topics: Myxococcales; Myxococcus xanthus; Phenols; Oxazoles
PubMed: 37014749
DOI: 10.1021/acschembio.3c00063