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Microbiology Resource Announcements Apr 2024() was recently described as a new species isolated from copper globemallow (). Here, we report the complete genome of CoE-159-22, which was obtained from...
() was recently described as a new species isolated from copper globemallow (). Here, we report the complete genome of CoE-159-22, which was obtained from traditionally produced Montenegrin cheese.
PubMed: 38451213
DOI: 10.1128/mra.00035-24 -
Microorganisms Jan 2024Cellulolytic microorganisms play a crucial role in agricultural waste disposal. Strain QXD-8 was isolated from soil in northern China. Similarity analyses of the 16S...
Cellulolytic microorganisms play a crucial role in agricultural waste disposal. Strain QXD-8 was isolated from soil in northern China. Similarity analyses of the 16S rRNA gene, as well as the 120 conserved genes in the whole-genome sequence, indicate that it represents a novel species within the genus . The sp. QXD-8 was able to grow on the CAM plate with sodium carboxymethyl cellulose as a carbon source at 15 °C, forming a transparent hydrolysis circle after Congo red staining, even though the optimal temperature for the growth and cellulose degradation of strain QXD-8 was 28 °C. In the liquid medium, it effectively degraded cellulose and produced reducing sugars. Functional annotation revealed the presence of encoding genes for the GH5, GH6, and GH10 enzyme families with endoglucanase activity, as well as the GH1, GH3, GH39, and GH116 enzyme families with -glucosidase activity. Additionally, two proteins in the GH6 family, one in the GH10, and two of nine proteins in the GH3 were predicted to contain a signal peptide and transmembrane region, suggesting their potential for extracellularly degrade cellulose. Based on the physiological features of the type strain QXD-8, we propose the name for this novel species. This study expands the diversity of psychrotolerant cellulolytic bacteria and provides a potential microbial resource for straw returning in high-latitude areas at low temperatures.
PubMed: 38399707
DOI: 10.3390/microorganisms12020303 -
Microbiology Resource Announcements Mar 2024Whole-genome sequence of ET2 strain, isolated from the roots of leafless orchid, constitutes a single circular chromosome of 3,604,840 bp (69.44% G + C content)....
Whole-genome sequence of ET2 strain, isolated from the roots of leafless orchid, constitutes a single circular chromosome of 3,604,840 bp (69.44% G + C content). BLAST+-based average nucleotide identity (ANIb) and digital DNA-DNA hybridization values indicate that ET2 may be a novel species. Genes putatively involved in plant-microbial interactions were predicted.
PubMed: 38385669
DOI: 10.1128/mra.00899-23 -
Applied Microbiology and Biotechnology Feb 2024The extracellular heteropolysaccharide xanthan, synthesized by bacteria of the genus Xanthomonas, is widely used as a thickening and stabilizing agent across the food,... (Review)
Review
The extracellular heteropolysaccharide xanthan, synthesized by bacteria of the genus Xanthomonas, is widely used as a thickening and stabilizing agent across the food, cosmetic, and pharmaceutical sectors. Expanding the scope of its application, current efforts target the use of xanthan to develop innovative functional materials and products, such as edible films, eco-friendly oil surfactants, and biocompatible composites for tissue engineering. Xanthan-derived oligosaccharides are useful as nutritional supplements and plant defense elicitors. Development and processing of such new functional materials and products often necessitate tuning of xanthan properties through targeted structural modification. This task can be effectively carried out with the help of xanthan-specific enzymes. However, the complex molecular structure and intricate conformational behavior of xanthan create problems with its enzymatic hydrolysis or modification. This review summarizes and analyzes data concerning xanthan-degrading enzymes originating from microorganisms and microbial consortia, with a particular focus on the dependence of enzymatic activity on the structure and conformation of xanthan. Through a comparative study of xanthan-degrading pathways found within various bacterial classes, different microbial enzyme systems for xanthan utilization have been identified. The characterization of these new enzymes opens new perspectives for modifying xanthan structure and developing innovative xanthan-based applications. KEY POINTS: • The structure and conformation of xanthan affect enzymatic degradation. • Microorganisms use diverse multienzyme systems for xanthan degradation. • Xanthan-specific enzymes can be used to develop xanthan variants for novel applications.
Topics: Dietary Supplements; Hydrolysis; Microbial Consortia; Mutagenesis, Site-Directed; Polysaccharides, Bacterial
PubMed: 38381223
DOI: 10.1007/s00253-024-13016-6 -
The ISME Journal Jan 2024The widespread occurrence of sulfonamides raises significant concerns about the evolution and spread of antibiotic resistance genes. Biodegradation represents not only a...
The widespread occurrence of sulfonamides raises significant concerns about the evolution and spread of antibiotic resistance genes. Biodegradation represents not only a resistance mechanism but also a clean-up strategy. Meanwhile, dynamic and diverse environments could influence the cellular function of individual sulfonamide-degrading strains. Here, we present Paenarthrobacter from different origins that demonstrated diverse growth patterns and sulfonamide-degrading abilities. Generally, the degradation performance was largely associated with the number of sadA gene copies and also relied on its genotype. Based on the survey of sad genes in the public database, an independent mobilization of transposon-borne genes between chromosome and plasmid was observed. Insertions of multiple sadA genes could greatly enhance sulfonamide-degrading performance. Moreover, the sad gene cluster and sadA transposable element showed phylogenetic conservation currently, being identified only in two genera of Paenarthrobacter (Micrococcaceae) and Microbacterium (Microbacteriaceae). Meanwhile, Paenarthrobacter exhibited a high capacity for genome editing to adapt to the specific environmental niche, opening up new opportunities for bioremediation applications.
Topics: Sulfonamides; Biodegradation, Environmental; Phylogeny; Sulfanilamide; Micrococcaceae
PubMed: 38366247
DOI: 10.1093/ismejo/wrad040 -
The ISME Journal Jan 2024Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions...
Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.
Topics: In Situ Hybridization, Fluorescence; RNA, Ribosomal, 16S; Biofilms; Microbial Interactions; Symbiosis
PubMed: 38365935
DOI: 10.1093/ismejo/wrae012 -
Scientific Reports Feb 2024Mining has led to severe environmental pollution in countries with exhaustive mining production and inadequate industrial waste regulation. Microorganisms in...
Mining has led to severe environmental pollution in countries with exhaustive mining production and inadequate industrial waste regulation. Microorganisms in contaminated sites, like mine tailings, have adapted to high concentrations of heavy metals, developing the capacity of reducing or removing them from these environments. Therefore, it is essential to thoroughly characterize bacteria present in these sites to find different ways of bioremediation. In this regard, in this study, an enrichment and isolation procedure were performed to isolate bacteria with lower nutritional requirements and high tolerance to Cu(II) and Fe(II) from two Sonoran River basin mining tails. Two Staphylococcus species and a Microbacterium ginsengisoli strain were isolated and identified from the San Felipe de Jesús mining tail. Also, three strains were isolated from the Nacozari de García mining tail: Burkholderia cenocepacia, Sphingomonas sp. and Staphylococcus warneri. Significant microbiological differences were found between the two sites. All these species exhibited tolerance up to 300 mg/L for Cu (II)-Fe (II) solutions, indicating their capacity to grow in these conditions. Moreover, a consortium of isolated bacteria was immobilized in two different biocomposites and the biocomposite with larger pore size achieved greater bacterial immobilization showcasing the potential of these bacteria in biotechnological applications.
Topics: Metals, Heavy; Industrial Waste; Mining; Biodegradation, Environmental; Bacteria; Soil Pollutants
PubMed: 38351239
DOI: 10.1038/s41598-024-54090-0 -
Microbiology Resource Announcements Mar 2024In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in...
In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in Funes, Argentina. Its 41,522 bp circularly permuted genome contains 63 putative protein-coding genes. Based on gene content similarity, Garey24 was assigned to subcluster EA1.
PubMed: 38315107
DOI: 10.1128/mra.01215-23 -
Frontiers in Microbiology 2023This research aims to elucidate the physiological mechanisms behind the accidental acquisition of high-concentration cesium ions (Cs) tolerance of and apply this...
This research aims to elucidate the physiological mechanisms behind the accidental acquisition of high-concentration cesium ions (Cs) tolerance of and apply this understanding to develop bioremediation technologies. Bacterial Cs resistance has attracted attention, but its physiological mechanism remains largely unknown and poorly understood. In a prior study, we identified the Cs/H antiporter TS_CshA in sp. TS-1, resistant to high Cs concentrations, exhibits a low Cs affinity with a value of 370 mM at pH 8.5. To enhance bioremediation efficacy, we conducted random mutagenesis of using Error-Prone PCR, aiming for higher-affinity mutants. The mutations were inserted downstream of the P promoter in the pBAD24 vector, creating a mutant library. This was then transformed into -competent cells. As a result, we obtained a Cs-resistant strain, ZX-1, capable of thriving in 400 mM CsCl-a concentration too high for ordinary . Unlike the parent strain Mach1, which struggled in 300 mM CsCl, ZX-1 showed robust growth even in 700 mM CsCl. After 700 mM CsCl treatment, the 70S ribosome of Mach1 collapsed, whereas ZX-1 and its derivative ΔZX-1/pBR322ΔAp remained stable. This means that the ribosomes of ZX-1 are more stable to high Cs. The inverted membrane vesicles from strain ZX-1 showed an apparent value of 28.7 mM (pH 8.5) for Cs/H antiport activity, indicating an approximately 12.9-fold increase in Cs affinity. Remarkably, the entire plasmid isolated from ZX-1, including the region, was mutation-free. Subsequent whole-genome analysis of ZX-1 identified multiple SNPs on the chromosome that differed from those in the parent strain. No mutations in transporter-related genes were identified in ZX-1. However, three mutations emerged as significant: genes encoding the ribosomal bS6 modification enzyme RimK, the phage lysis regulatory protein LysB, and the flagellar base component protein FlgG. These mutations are hypothesized to affect post-translational modifications, influencing the value of TS_CshA and accessory protein expression. This study unveils a novel Cs resistance mechanism in ZX-1, enhancing our understanding of Cs resistance and paving the way for developing technology to recover radioactive Cs from water using TS_CshA-expressing inverted membrane vesicles.
PubMed: 38304862
DOI: 10.3389/fmicb.2023.1340033 -
Microbiology Resource Announcements Mar 2024Cluster EA4 Guetzie and SirVictor are lytic siphoviral bacteriophages that were isolated from soil in Waverly, Iowa, using NRRL B-24224 as the host. The Guetzie and...
Cluster EA4 Guetzie and SirVictor are lytic siphoviral bacteriophages that were isolated from soil in Waverly, Iowa, using NRRL B-24224 as the host. The Guetzie and SirVictor genomes are both 39,758 bp each, and both contain 58 predicted protein-coding genes with one tRNA gene each.
PubMed: 38294214
DOI: 10.1128/mra.01074-23