-
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 -
Microbial Ecology Jan 2024Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions...
Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3-1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.
Topics: Ecosystem; Lakes; Metagenome; Bacteria; Potamogetonaceae; Nitrogen
PubMed: 38286834
DOI: 10.1007/s00248-024-02346-7 -
Frontiers in Plant Science 2023In flowering plants, after being released from pollen grains, the male gametes use the style channel to migrate towards the ovary where they fertilize awaiting eggs....
In flowering plants, after being released from pollen grains, the male gametes use the style channel to migrate towards the ovary where they fertilize awaiting eggs. Environmental pathogens exploit the style passage, resulting in diseased progeny seed. The belief is that pollen also transmits pathogens into the style. By contrast, we hypothesized that pollen carries beneficial microbes that suppress environmental pathogens on the style passage. No prior studies have reported pollen-associated bacterial functions in any plant species. Here, bacteria were cultured from maize (corn) pollen encompassing wild ancestors and farmer-selected landraces from across the Americas, grown in a common field in Canada for one season. In total, 298 bacterial isolates were cultured, spanning 45 genera, 103 species, and 88 OTUs, dominated by , and . Full-length 16S DNA-based taxonomic profiling showed that 78% of bacterial taxa from the major wild ancestor of maize (Parviglumis teosinte) were present in at least one cultivated landrace. The species names of the bacterial isolates were used to search the pathogen literature systematically; this preliminary evidence predicted that the vast majority of the pollen-associated bacteria analyzed are not maize pathogens. The pollen-associated bacteria were tested against a style-invading pathogen shown to cause Gibberella ear rot (GER): 14 isolates inhibited this pathogen. Genome mining showed that all the anti- bacterial species encode , associated with biosynthesis of the natural fungicide, phenazine. To mimic the male gamete migration route, three pollen-associated bacterial strains were sprayed onto styles (silks), followed by inoculation; these bacteria reduced GER symptoms and mycotoxin accumulation in progeny seed. Confocal microscopy was used to search for direct evidence that pollen-associated bacteria can defend living silks against (); bacterial strain AS541 (), isolated from pollen of ancestral Parviglumis, was observed to colonize the susceptible style/silk entry points of (silk epidermis, trichomes, wounds). Furthermore, on style/silk tissue, AS541 colonized/aggregated on hyphae, and was associated with hyphal breaks. These results suggest that pollen has the potential to carry bacteria that can defend the style/silk passage against an environmental pathogen - a novel observation.
PubMed: 38269134
DOI: 10.3389/fpls.2023.1286199 -
Foods (Basel, Switzerland) Nov 2023The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages...
The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages on the composition and function of donkey milk microbiota. The milk samples were collected at 1, 30, 60, 90, 120, 150, and 180 days post-delivery. The result showed that the microbial composition and functions in donkey milk were significantly affected by different lactation stages. The dominant bacterial phyla in donkey milk are (60%) and (22%). (39%), (4%), and (2%) were the predominant bacterial genera detected in all milk samples. In the mature milk, the abundance of lactic acid bacteria (7%) was higher. (5%) and (3%) were more plentiful in milk samples from middle and later lactation stages (90-180 d). Furthermore, the pathogens and and thermoduric bacteria , , and were also detected. Donkey milk is rich in beneficial bacteria and also poses a potential health risk. The above findings have improved our understanding of the composition and function changes of donkey milk microbiota, which is beneficial for the rational utilization of donkey milk.
PubMed: 38231735
DOI: 10.3390/foods12234272 -
Microbiology Resource Announcements Feb 2024We report the discovery and genome sequence of CandC, a lytic bacteriophage with siphovirus morphology. CandC was isolated from a soil sample from Plattsburgh, NY, USA...
We report the discovery and genome sequence of CandC, a lytic bacteriophage with siphovirus morphology. CandC was isolated from a soil sample from Plattsburgh, NY, USA (Fall 2021). It has a genome size of 62,344 bp with 106 predicted protein-encoding genes, 30 of which are assigned putative functions.
PubMed: 38231186
DOI: 10.1128/mra.01117-23