Frontiers in Microbiology最新文献

Desert environments harbor unique microbial communities. This study focuses on Cellulosimicrobium funkei isolate RVMD1, isolated from rock varnish in the Ma'an Desert. Initial identification was achieved using 16S rRNA gene sequencing, followed by whole-genome sequencing (WGS) for comprehensive characterization. The genome comprises 4,264,015 base pairs (857 contigs) with a high G + C content of 74.59%. A total of 4,449 proteins were predicted. Comparative analysis utilizing OrthoANI, ANI, AAI, and dDDH metrics suggests that RVMD1 belongs to the C. cellulans group, with the highest similarity to C. funkei (97.71% ANI). Phylogenomic analysis of 43 Cellulosimicrobium genomes revealed significant heterogeneity within the genus. Our results challenge current systematics, with C. cellulans potentially representing up to 9 distinct genomospecies. Isolate RVMD1 shows genetic adaptations to its desert environment, including genes for denitrification, oxygen and sulfur cycling, and diverse hydrogen metabolism. Pangenomic analysis uncovered a considerable number of unique genes within RVMD1, highlighting its genetic distinctiveness. Gene family expansions suggest evolution in response to stressors like UV radiation and nutrient limitation. This study represents the first whole-genome analysis of a bacterium isolated from Jordanian rock varnish, emphasizing the value of WGS in understanding microbial diversity and adaptation in extreme environments.

Wetland systems are known methane (CH₄) sources. However, flooded rice fields are periodically drained. The paddy soils can absorb atmospheric CH₄ during the dry seasons due to high-affinity methane-oxidizing bacteria (methanotroph). Atmospheric CH₄ uptake can be induced during the low-affinity oxidation of high-concentration CH₄ in paddy soils. Multiple interacting factors control atmospheric CH₄ uptake in soil ecosystems. Broader biogeographical data are required to refine our understanding of the biotic and abiotic factors related to atmospheric CH₄ uptake in paddy soils. Thus, here, we aimed to assess the high-affinity CH₄ oxidation activity and explored the community composition of active atmospheric methanotrophs in nine geographically distinct Chinese paddy soils. Our findings demonstrated that high-affinity oxidation of 1.86 parts per million by volume (ppmv) CH₄ was quickly induced after 10,000 ppmv high-concentration CH₄ consumption by conventional methanotrophs. The ratios of 16S rRNA to rRNA genes (rDNA) for type II methanotrophs were higher than those for type I methanotrophs in all acid-neutral soils (excluding the alkaline soil) with high-affinity CH₄ oxidation activity. Both the 16S rRNA:rDNA ratios of type II methanotrophs and the abundance of ¹³C-labeled type II methanotrophs positively correlated with high-affinity CH₄ oxidation activity. Soil abiotic factors can regulate methanotrophic community composition and atmospheric CH₄ uptake in paddy soils. High-affinity methane oxidation activity, as well as the abundance of type II methanotroph, negatively correlated with soil pH, while they positively correlated with soil nutrient availability (soil organic carbon, total nitrogen, and ammonium-nitrogen). Our results indicate the importance of type II methanotrophs and abiotic factors in atmospheric CH₄ uptake in paddy soils. Our findings offer a broader biogeographical perspective on atmospheric CH₄ uptake in paddy soils. This provides evidence that periodically drained paddy fields can serve as the dry-season CH₄ sink. This study is anticipated to help in determining and devising greenhouse gas mitigation strategies through effective farm management in paddy fields.

The phyllosphere of plants hosts diverse fungal microbial communities. Despite the significant impact of plant fungal diseases on productivity and community ecology, the relationship between phyllosphere fungal communities and plant health in natural environments remains poorly understood. This study utilized high-throughput sequencing and field investigations to explore the composition, dynamics, and incidence of fungal diseases across 29 plant species from four functional groups (forbs, grasses, legumes, and sedges) in alpine meadow plant communities of the Qinghai-Tibetan Plateau. We identified Ascomycetes and Basidiomycetes as the predominant phyllosphere fungi. Significant differences were observed in the Shannon diversity index, β-diversity, indicator fungi, and hub fungi among the functional groups. With the exception of the sedge group, the incidence of fungal diseases in other groups was positively correlated with the proportion of pathogens in the phyllosphere fungal community. Predictive analyses revealed that Ascochyta was strongly associated with high disease incidence in grasses, Cercospora in forbs, and Podosphaera in legumes, while Calophoma was associated with low disease incidence in sedges. These findings enhance our understanding of how plant phyllosphere fungal communities assemble in natural environments and improve our ability to predict and manage foliar fungal diseases in alpine meadows.

Background: Acute hematogenous osteomyelitis is the most common form of osteomyelitis in children. In recent years, the incidence of osteomyelitis has been steadily increasing. For pediatric patients, clearly describing their symptoms can be quite challenging, which often necessitates the use of complex diagnostic methods, such as radiology. For those who have been diagnosed, the ability to culture the pathogenic bacteria significantly affects their treatment plan.

Method: A total of 634 patients under the age of 18 were included, and the correlation between laboratory indicators and osteomyelitis, as well as several diagnoses often confused with osteomyelitis, was analyzed. Based on this, a Transformer-based deep learning model was developed to identify osteomyelitis patients. Subsequently, the correlation between laboratory indicators and the length of hospital stay for osteomyelitis patients was examined. Finally, the correlation between the successful cultivation of pathogenic bacteria and laboratory indicators in osteomyelitis patients was analyzed, and a deep learning model was established for prediction.

Result: The laboratory indicators of patients are correlated with the presence of acute hematogenous osteomyelitis, and the deep learning model developed based on this correlation can effectively identify patients with acute hematogenous osteomyelitis. The laboratory indicators of patients with acute hematogenous osteomyelitis can partially reflect their length of hospital stay. Although most laboratory indicators lack a direct correlation with the ability to culture pathogenic bacteria in patients with acute hematogenous osteomyelitis, our model can still predict whether the bacteria can be successfully cultured.

Conclusion: Laboratory indicators, as easily accessible medical information, can identify osteomyelitis in pediatric patients. They can also predict whether pathogenic bacteria can be successfully cultured, regardless of whether the patient has received antibiotics beforehand. This not only simplifies the diagnostic process for pediatricians but also provides a basis for deciding whether to use empirical antibiotic therapy or discontinue treatment for blood cultures.

Introduction: Wheat dwarf virus (WDV), the species Mastrevirus hordei of the genus Mastrevirus in the family Geminiviridae, is a cereal virus commonly detected in several European, African and Asian countries that causes economic losses.

Methods: In the spring of 2019, a severe outbreak of wheat dwarfing and yellowing was observed in many winter wheat crops across Serbia. A total of 161 samples were tested for the presence of WDV and other common wheat viruses using double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). To obtain the complete genome of 23 selected isolates, several overlapping segments of the WDV genome were amplified and sequenced. A phylogenetic tree was constructed using the whole genome sequences of the WDV isolates identified in this study and 40 selected sequences from GenBank.

Results and discussion: The results of DAS-ELISA indicated the presence of WDV in all samples collected from 21 sites in all nine districts surveyed. Further molecular characterization based on complete genome sequencing of 23 selected isolates showed that the Serbian WDV isolates had low nucleotide diversity and were closely related to wheat-infecting isolates from Europe, suggesting the presence of wheat-adapted forms of WDV in Serbia. The constructed phylogenetic tree revealed that Serbian isolates grouped in clade E within the wheat-adapted forms. This study provided the first insight into the genetic structure of WDV in Serbia based on its whole genome sequence. Further studies on the vector biology and population dynamics are needed to better understand the factors influencing the emergence and spread of WDV under local agroecological conditions.

Cyanobacterial harmful algal blooms (CHABs) are promoted by excessive nutrient loading and, while fertilizers and sewage are the most prevalent external nutrient sources in most watersheds, the differential effects of these nutrient sources on CHABs are unknown. Here, we tracked CHABs and performed experiments in five distinct lakes across the Northern US including Lake Erie. Fertilizers with ammonium and orthophosphate, membrane (0.2 μm)-filtered sewage (dominated by reduced forms of nitrogen) sand-and membrane-filtered sewage (dominated by nitrate), and an inorganic nutrient solution of ammonium and orthophosphate were used as experimental nutrient sources for CHABs at N-equivalent, environmentally realistic concentrations. Phytoplankton communities were evaluated fluorometrically, microscopically, and via high throughput sequencing of the 16S rRNA gene, and levels of microcystin and the δ¹⁵N content of particulate organic nitrogen (δPO¹⁵N) were quantified. Fertilizer and both sources of wastewater increased the abundance of cyanobacteria in all experiments across all five lakes (p < 0.05 for all) whereas effects on eukaryotic phytoplankton were limited. Sand-filtered sewage contained less P, organic matter, and ammonium but more nitrate and had a 25% less potent stimulatory effect on cyanobacteria than membrane-filtered sewage, suggesting nitrification may play a role in reducing CHABs. Fertilizer increased microcystin levels and decreased the δPO¹⁵N whereas wastewater increased δPO¹⁵N (p < 0.05 for all). Microcystis was the genus most consistently promoted by nutrient sources (p < 0.05 in all experiments), followed by Cyanobium (p < 0.05 in 50% of experiments), with increases in Microcystis biomass consistently elicited by membrane-filtered wastewater. Collectively, results demonstrate that differing types of sewage discharge and fertilizers can promote CHAB intensity and toxicity, while concurrently altering CHAB diversity and δPO¹⁵N. While membrane-filtered sewage consistently favored Microcystis, the discharge of sewage through sands muted bloom intensity suggesting sand-beds may represent a tool to remove key nutrients and partially mitigate CHABs.

Bacillus pseudomycoides, Paenibacillus polymyxa, and B. velezensis are potent bacterial endophytes, which typically exhibit host-specific interactions. However, comparative studies of these endophytes in vitro and in planta in non-host crops are lacking. Therefore, in this study, we evaluated the potential of endophytes B. pseudomycoides strain HP3d, P. polymyxa strain PGSS1, B. velezensis strain A6, and P42, isolated from various crop ecosystems in promoting plant growth and inducing systemic resistance against early blight disease in tomato. In vitro, endophytes exhibited 44.44-55.56% and 37.50-87.50% inhibition of Alternaria solani in dual culture and volatilome bioassay, respectively. In the glasshouse, individual and combined applications via seed treatment (ST), seedling dip (SD), and foliar spray (FS) significantly enhanced shoot growth (23.63-57.61%), root growth (43.27-118.23%), number of leaves (77.52-93.58%), number of shoots (33.42-45.28%) and root dry matter (42.17-43.86%), reducing early blight (PDI) by 70.95-76.12% compared to uninoculated control. Enzymatic activities, including such as polyphenol oxidase (30-40 fold), peroxidase (65.00-75.00 fold), superoxide dismutase (34.20-37.20 fold) and phenylalanine ammonia-lyase (44.44-45.56 fold) were elevated post-inoculation in endophytes treated tomato plants challenged with A. solani compared to control treated only with A. solani and declined after the fifth day. The total chlorophyll content declined from the 0th to the 10th day, but endophyte treated plants exhibited lesser reductions (2.03-2.09) than uninoculated control. Field trials confirmed the glasshouse findings, showing reduced early blight and improved growth parameters in tomato where the ST + SD + FS combination emerged as the most effective treatment for all endophytes showing 1.06-1.88 fold increase in fruit yield per plant and 28.92-32.52% decrease in PDI compared to untreated control. Thus, the study highlights the broad-spectrum potential of these strains in promoting plant growth and controlling early blight in tomato, demonstrating non-host specificity. These endophytes offer eco-friendly alternatives to chemical pesticides, supporting sustainable agriculture. Their success in field trials suggests the potential for commercialization and large-scale use across diverse crops and pave the way for further interdisciplinary research to optimize their application in integrated pest management strategies.

Introduction: Uropathogenic bacteria employ multiple strategies to colonize the urinary tract, including biofilm formation, invasion of urothelial cells, and the production of adhesins, toxins, and siderophores. Among the most prevalent pathogens causing urinary tract infections (UTIs) are Uropathogenic Escherichia coli and Proteus mirabilis. A notable feature of Gram-negative bacteria is their ability to produce outer membrane vesicles (OMVs), which play critical roles in bacterial survival, virulence, and host-pathogen interactions, including UTIs.

Methods: In this study, OMVs were isolated and characterized from two clinical strains, E. coli U144 and P. mirabilis 2,921, cultured in both Luria-Bertani broth and artificial urine.

Result and discussion: The OMVs ranged in size from 85 to 260 nm, with the largest vesicles observed in artificial urine. Proteomic analysis allowed the identification of 282 proteins in OMVs from E. coli and 353 proteins from P. mirabilis when cultured LB medium, while 215 were identified from E. coli and 103 from P. mirabilis when cultured in artificial urine. The majority of these proteins originated from the bacterial envelope, while others were linked to motility and adhesion. Notably, the protein composition of OMVs varied depending on the growth medium, and proteins associated with zinc and iron uptake being more prominent in artificial urine, suggesting their importance in the urinary environment. Crucially, this is the first report to characterize P. mirabilis OMVs under different culture conditions, offering novel insights into the role of OMVs in UTI pathogenesis. These findings provide a deeper understanding of the molecular mechanisms by which OMVs contribute to bacterial virulence, establishing the foundation for potential therapeutic interventions targeting OMV-mediated processes in UTIs.

The objectives of this study were to evaluate the potential of using thermophilic aerobic digestion (TAD) to hydrolyze aquaculture sludge, and to investigate the hydrolysis efficiency and changes in microbial community structure during TAD at 0, 15, and 30 practical salinity units (psu). As digestion progressed, soluble organic matter concentrations in all reactors increased to their maximum values at 6 h. The hydrolysis efficiency at 6 h decreased as salinity increased: 2.42% at 0 psu, 1.78% at 15 psu, and 1.04% at 30 psu. The microbial community compositions at the genus level prominently differed in the relative abundances of dominant bacteria between 0 psu and 30 psu. The relative abundance of genera Iodidimonas and Tepidiphilus increased significantly as salinity increased. Increase in the salinity at which thermophilic aerobic digestion of aquaculture sludge was conducted altered the microbial community structure, which in turn decreased the efficiency of organic matter hydrolysis.

Klebsiella aerogenes is an opportunistic nosocomial bacterial pathogen that commonly causes urinary tract infections. Over the past decades, K. aerogenes strains have acquired resistance to common antibiotics that has led to the rise of multidrug-resistant and even pandrug-resistant strains. Infections produced by these strains are nearly impossible to treat, which makes K. aerogenes a global priority to develop new antibiotics and there is an urgent need to identify targets to treat infections against this pathogen. However, very little is known about the metabolism and metabolic adaptations of this bacterium in infection sites. In this work, we investigated the respiratory metabolism of K. aerogenes in conditions that resemble human urine, allowing us to identify novel targets for antibiotic development. Here we describe that, unlike other gram-negative pathogens, K. aerogenes utilizes the type-2 NADH dehydrogenase (NDH-2) as the main entry point for electrons in the respiratory chain in all growth conditions evaluated. Additionally, in urine-like media, the aerobic metabolism as a whole is upregulated, with significant increases in succinate and lactate dehydrogenase activity. Moreover, our data show that the bd-I type oxidoreductases are the main terminal oxidases of this microorganism. Our findings support an initial identification of NDH-2 and bd-I oxidase as attractive targets for the development of new drugs against K. aerogenes as they are not found in human hosts.