Bacterial Gene Research Articles

Cutibacterium acnes-derived extracellular vesicles promote tumor growth in renal cell carcinoma.

Bacterial flora are present in various parts of the human body, including the intestine, and are thought to be involved in the etiology of various diseases such as multiple sclerosis, intestinal diseases, cancer, and uterine diseases. In recent years, the presence of bacterial 16S rRNA genes has been revealed in blood, which was previously thought to be a sterile environment, and characteristic blood microbiomes have been detected in various diseases. However, the mechanism and the origin of the bacterial information are unknown. In this study, we performed 16S rRNA metagenomic analysis of bacterial DNA in serum extracellular vesicles from five healthy donors and seven patients with renal cell carcinoma and detected Cutibacterium acnes DNA as a characteristic bacterial DNA in the serum extracellular vesicles of patients with renal cell carcinoma. In addition, C. acnes DNA was significantly reduced in postoperative serum extracellular vesicles from patients with renal cell carcinoma compared with that in preoperative serum extracellular vesicles from these patients and was also detected in tumor tissue and extracellular vesicles from tumor tissue-associated microbiota, suggesting an association between C. acnes extracellular vesicles and renal cell carcinoma. C. acnes extracellular vesicles were taken up by renal carcinoma cells to enhance their proliferative potential. C. acnes extracellular vesicles also exhibited tumor-promoting activity in a mouse model of renal cancer allografts with enhanced angiogenesis. These results suggest that extracellular vesicles released by C. acnes localized in renal cell carcinoma tissues act in a tumor-promoting manner.

Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange.

Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.

Analysis of Microbial Diversity in Rhizosphere Soil of Panax notoginseng under Different Water and Microbial Fertilizer Conditions

Panax notoginseng is a highly regarded medicinal plant that has obstacles associated with continuous cropping. Understanding soil microorganisms is crucial, as they play a major role in this regard. However, soil microorganisms are affected by multiple factors; therefore, we need to conduct more in-depth research. This study investigated the combined effects of irrigation and microbial fertilizer treatments (J1F1, J1F2, J2F1, J2F2, J3F1, J3F2, and CK) on the diversity of bacterial and fungal microbial communities in the rhizosphere of Panax notoginseng. The bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) sequences were sequenced using Illumina HiSeq. The results showed that, without microbial fertilizer (CK), the microbial community abundance and diversity were significantly lower than in the other treatments; moreover, among the microbial fertilizer treatments, the microbial abundance in F1 was higher than that in F2. Under the same microbial fertilizer application, the incidence rate of Panax notoginseng root rot was J2 > J1 > J3, and the yield of Panax notoginseng was J3 > J2 > J1. Under the same irrigation conditions, the incidence rate of Panax notoginseng root rot was F1 > F2, and the yield of Panax notoginseng was F2 > F1. This study provides important guidance for Panax notoginseng plant microbiota and sustainable agriculture.

Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution

Bacteria in the oral microbiome are poorly identified owing to the lack of established culture methods for them. Thus, this study aimed to use culture-free analysis techniques, including bacterial single-cell genome sequencing, to identify bacterial species and investigate gene distribution in saliva. Saliva samples from the same individual were classified as inactivated or viable and then analyzed using 16S rRNA sequencing, metagenomic shotgun sequencing, and bacterial single-cell sequencing. The results of 16S rRNA sequencing revealed similar microbiota structures in both samples, with Streptococcus being the predominant genus. Metagenomic shotgun sequencing showed that approximately 80 % of the DNA in the samples was of non-bacterial origin, whereas single-cell sequencing showed an average contamination rate of 10.4 % per genome. Single-cell sequencing also yielded genome sequences for 43 out of 48 wells for the inactivated samples and 45 out of 48 wells for the viable samples. With respect to resistance genes, four out of 88 isolates carried cfxA, which encodes a β-lactamase, and four isolates carried erythromycin resistance genes. Tetracycline resistance genes were found in nine bacteria. Metagenomic shotgun sequencing provided complete sequences of cfxA, ermF, and ermX, whereas other resistance genes, such as tetQ and tetM, were detected as fragments. In addition, virulence factors from Streptococcus pneumoniae were the most common, with 13 genes detected. Our average nucleotide identity analysis also suggested five single-cell-isolated bacteria as potential novel species. These data would contribute to expanding the oral microbiome data resource.

Analysis of the characteristics of intestinal microbiota after oral tolerance in infants with food protein-induced proctocolitis.

To understand the characteristics of the intestinal microbiota after oral tolerance in infants with food protein-induced proctocolitis (FPIAP) treated with amino acid formula and their differences from healthy children, aiming to provide a scientific basis for guiding the application of probiotics during treatment. FPIAP infants were prospectively enrolled, fecal specimens were obtained, and DNA was extracted for PCR amplification of the bacterial 16S rRNA gene V4 region. Library construction and sequencing were performed, and bioinformatic analysis was performed after obtaining valid data. There were 36 patients in the FPIAP group: 20 males and 16 females, age 21.944 ± 13.277 months. Diarrhea with blood in the stool were the main symptom, with an average course of 14.83 ± 9.33 days. Thirty infants (83.33%) had mucus stool, 11.11% (4/36) of them experiencing vomiting, and 55.56% (20/36) of the infants displaying poor intake and weight gain, 28 (77.78%) patients with moderate eczema, 2 (5.6%) patients with chronic respiratory symptoms. The treatment time with amino acid formula was 5.51 ± 2.88 months. A control group comprising of 25 healthy infants who were full-term, natural delivery, bottle fed, and matched in terms of age (24.840 ± 12.680 months) and gender (15 males and 10 females) was selected. Anaerobic bacteria were less abundant in FPIAP infants than healthy infants (P = 4.811 × 10-5), but potentially pathogenic bacteria were more abundant (P = 0.000). The abundance of Actinobacteria was low in FPIAP infants, the abundance of Proteobacteria was high, and the abundance of Firmicutes was reduced. Bifidobacterium could be used as a bacterial genus to differentiate healthy and FPIAP infants. Both α-and β-diversity indicators of intestinal microbiota were lower in FPIAP infants. In FPIAP infants, glucose and energy metabolism and amino acid anabolism were decreased, and inflammation-related lipopolysaccharide synthesis pathways were increased. Compared with healthy infants, FPIAP infants with oral tolerance after amino acid formula treatment had differences in the structure and diversity of intestinal microbiota, among which Bifidobacterium was significantly reduced. This trial was registered on https://register.clinicaltrials.gov/.

New Insights into the Biological Functions of Essential TsaB/YeaZ Protein in Staphylococcus aureus.

TsaB/YeaZ represents a promising target for novel antibacterial agents due to its indispensable role in bacterial survival, high conservation within bacterial species, and absence of eukaryotic homologs. Previous studies have elucidated the role of the essential staphylococcal protein, TsaB/YeaZ, in binding DNA to mediate the transcription of the ilv-leu operon, responsible for encoding key enzymes involved in the biosynthesis of branched-chain amino acids-namely isoleucine, leucine, and valine (ILV). However, the regulation of ILV biosynthesis does not account for the essentiality of TsaB/YeaZ for bacterial growth. In this study, we investigated the impact of TsaB/YeaZ depletion on bacterial morphology and gene expression profiles using electron microscopy and deep transcriptomic analysis, respectively. Our results revealed significant alterations in bacterial size and surface smoothness upon TsaB/YeaZ depletion. Furthermore, we pinpointed specific genes and enriched biological pathways significantly affected by TsaB/YeaZ during the early and middle exponential phases and early stationary phases of growth. Crucially, our research uncovered a regulatory role for TsaB/YeaZ in bacterial autolysis. These discoveries offer fresh insights into the multifaceted biological functions of TsaB/YeaZ within S. aureus.

Probing the interaction of Paenibacillus larvae bacteriophage as a biological agent to control the american foulbrood disease in honeybee

American foulbrood (AFB) is a harmful honeybee diseaseprimarily caused by Paenibacillus larvae. The study aims to isolate and identify the AFB causative agent P. larvae and their specific phages to use as a new biological method for AFB disease control. Eight apiaries were inspected for AFB infections. Symptoms of diseased brood comb, were odd brood cells with soft brown decayed brood amongst healthy brood, were identified in the field and demonstrated the prevalence of AFB in every apiary. Three P. larvae isolates were identified using traditional techniques usinga 452-bp PCR amplicon specific to the bacterial 16SrRNA gene andwas compared between Paenibacillus isolates. Additionally, specific phages of P. larvae strains were applied to examine their efficiency in reducing the infection rate under the apiary condition. The infection rate was reduced to approximately 94.6 to 100 % through the application of a phage mixture, as opposed to 20 to 85.7 % when each phage was administered individually or 78.6 to 88.9 % when antibiotic treatment was implemented. Histological studies on phage-treated bee larvae revealed some cells regaining normal shape, with prominent nuclei and microvilli. The gastrointestinal tract showed normal longitudinal and circular muscles, unlike bee larvae treated with bacterial strains with abnormal and destroyed tissues, as shown by the basement membrane surrounding the mid-gut epithelium. Phage techniques exhibited promise in resolving the issue of AFB in honeybees due to their ease of application, comparatively lower cost, and practicality for beekeepers in terms of laboratory preparation.

The potential of enhanced phytoremediation to clean up multi-contaminated soil – insights from metatranscriptomics

This study aimed to (i) investigate the potential for enhanced phytoremediation to remove contaminants from soil historically co-contaminated with petroleum hydrocarbons (PHs) and heavy metals (HMs) and (ii) analyze the expression of crucial bacterial genes and whole metatranscriptomics profiles for better understanding of soil processes during applied treatment. Phytoremediation was performed using Zea mays and supported by the Pseudomonas qingdaonensis ZCR6 strain and a natural biofertilizer: meat and bone meal (MBM). In previous investigations, mechanisms supporting plant growth and PH degradation were described in the ZCR6 strain. Here, ZCR6 survived in the soil throughout the experiment, but the efficacy of PH removal from all soils fertilized with MBM reached 32 % regardless of the bacterial inoculation. All experimental groups contained 2 % (w/w) MBM. The toxic effect of this amendment on plants was detected 30 days after germination, irrespective of ZCR6 inoculation. Among the 17 genes tested using the qPCR method, only expression of the acdS gene, encoding 1-aminocyclopropane-1-carboxylic acid deaminase, and the CYP153 gene, encoding cytochrome P450-type alkane hydroxylase, was detected in soils. Metatranscriptomic analysis of soils indicated increased expression of methane particulated ammonia monooxygenase subunit A (pmoA-amoA) by Nitrosomonadales bacteria in all soils enriched with MBM compared to the non-fertilized control. We suggest that the addition of 2 % (w/w) MBM caused the toxic effect on plants via the rapid release of ammonia, and this led to high pmoA-amoA expression. In parallel, due to its wide substrate specificity, enhanced bacterial hydrocarbon removal in MBM-treated soils was observed. The metatranscriptomic results indicate that MBM application should be considered to improve bioremediation of soils polluted with PHs rather than phytoremediation. However, lower concentrations of MBM could be considered for phytoremediation enhancement. From a broader perspective, these results indicated the superior capability of metatranscriptomics to investigate the microbial mechanisms driving various bioremediation techniques.

MicroRNAs from edible plants reach the human gastrointestinal tract and may act as potential regulators of gene expression.

MicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules that regulate gene expression at the post-transcriptional level. A cross-kingdom regulatory function has been unveiled for plant miRNAs (xenomiRs), which could shape inter-species interactions of plants with other organisms (bacteria and humans) and thus, be key functional molecules of plant-based food in mammals. However, discrepancies regarding the stability and bioavailability of dietary plant miRNAs on the host cast in doubt whether these molecules could have a significant impact on human physiology. The aim of the present study was to identify miRNAs in edible plants and determine their bioavailability on humans after an acute intake of plant-based products. It was found that plant food, including fruits, vegetables and greens, nuts, legumes, and cereals, contains a wide range of miRNAs. XenomiRs miR156e, miR159 and miR162 were detected in great abundance in edible plants and were present among many plant foods, and thus, they were selected as candidates to analyse their bioavailability in humans. These plant miRNAs resisted cooking processes (heat-treatments) and their relative presence increased in faeces after and acute intake of plant-based foods, although they were not detected in serum. Bioinformatic analysis revealed that these miRNAs could potentially target human and bacterial genes involved in processes such as cell signalling and metabolism. In conclusion, edible plants contain miRNAs, such as miR156e, miR159 and miR162, that could resist degradation during cooking and digestion and reach the distal segments of the gastrointestinal tract. Nevertheless, strategies should be developed to improve their absorption to potentially reach host tissues and organs and modulate human physiology.

KASP genotyping reveals disease resistance and yield enhancement in swarna introgression lines

Deployment of marker-assisted selection (MAS) in the molecular breeding programmes has transformed the crop breeding over the last decade, bringing speed and precision to the breeding programmes. The experiment was conducted during rainy (kharif) seasons of 2019, 2020, and 2021 at ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana for validation of the Kompetitive Allele Specific PCR (KASP) SNP markers for routine marker- assisted selection through genotyping and phenotyping of a set of breeding lines segregating for grain number, yield and resistance to bacterial blight and blast diseases. Initially, 150 introgression lines of Swarna possessing bacterial leaf blight (Xa21), blast (Pi54) and yield enhancing gene (Gn1a) at ICF4 generation were genotyped using trait specific KASP markers, and a set of 22 plants was identified to be homozygous for all the three genes, 68 plants were found positive for two genes possessing either Xa21 + Gn1a and Pi54 + Gn1a, rest were having different single gene. Simultaneously, plants which were triple gene positives were also subjected for stringent phenotypic screening for the targeted stresses, viz. bacterial blight and blast disease resistance and further evaluated for grain number and other key agronomic traits. All the three-gene positive plants exhibited high level of resistance to bacterial blight and blast diseases in comparison with positive checks and displayed higher grain number and yield than the recurrent parent, Swarna. The efficiency of SNP marker system provided by Intertek is accurate, cost effective and accurate with phenotype.

KASP genotyping reveals disease resistance and yield enhancement in swarna introgression lines

Deployment of marker-assisted selection (MAS) in the molecular breeding programmes has transformed the crop breeding over the last decade, bringing speed and precision to the breeding programmes. The experiment was conducted during rainy (kharif) seasons of 2019, 2020, and 2021 at ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana for validation of the Kompetitive Allele Specific PCR (KASP) SNP markers for routine marker- assisted selection through genotyping and phenotyping of a set of breeding lines segregating for grain number, yield and resistance to bacterial blight and blast diseases. Initially, 150 introgression lines of Swarna possessing bacterial leaf blight (Xa21), blast (Pi54) and yield enhancing gene (Gn1a) at ICF4 generation were genotyped using trait specific KASP markers, and a set of 22 plants was identified to be homozygous for all the three genes, 68 plants were found positive for two genes possessing either Xa21 + Gn1a and Pi54 + Gn1a, rest were having different single gene. Simultaneously, plants which were triple gene positives were also subjected for stringent phenotypic screening for the targeted stresses, viz. bacterial blight and blast disease resistance and further evaluated for grain number and other key agronomic traits. All the three-gene positive plants exhibited high level of resistance to bacterial blight and blast diseases in comparison with positive checks and displayed higher grain number and yield than the recurrent parent, Swarna. The efficiency of SNP marker system provided by Intertek is accurate, cost effective and accurate with phenotype.

Rumen Development of Tianhua Mutton Sheep Was Better than That of Gansu Alpine Fine Wool Sheep under Grazing Conditions.

The purpose of this experiment was to investigate the differences in rumen tissue morphology, volatile fatty acid content, and rumen microflora between Tianhua mutton sheep and Gansu alpine fine wool sheep under the same grazing conditions. Twelve 30-day-old lambs were randomly selected from two different flocks in Duolong Village and grazed together for a period of 150 days. The rumen tissue was fixed with 4% paraformaldehyde and brought back to the laboratory for H&E staining, the volatile fatty acid content of the rumen contents was detected by gas chromatography, and the rumen flora structure was sequenced by full-length sequencing of the bacterial 16S rRNA gene using the PacBio sequencing platform. The acetic acid and total acid contents of the rumen contents of Tianhua mutton sheep were significantly higher than those of Gansu alpine fine wool sheep (p < 0.05). The rumen papillae height of Tianhua mutton sheep was significantly higher than that of Gansu alpine fine wool sheep (p < 0.05). The diversity and richness of the rumen flora of Tianhua mutton sheep were higher than those of Gansu alpine fine wool sheep, and Beta analysis showed that the microflora structure of the two fine wool sheep was significantly different. At the phylum level, Firmicutes and Bacteroidetes dominated the rumen flora of Tianhua mutton sheep and Gansu alpine fine wool sheep. At the genus level, the dominant strains were Christensenellaceae_R_7_group and Rikenellaceae_RC9_gut_group. LEfSe analysis showed that Prevotella was a highly abundant differential species in Tianhua mutton sheep and lachnospiraccac was a highly abundant differential species in Gansu alpine fine wool sheep. Finally, both the KEGG and COG databases showed that the enrichment of biometabolic pathways, such as replication and repair and translation, were significantly higher in Tianhua mutton sheep than in Gansu alpine fine wool sheep (p < 0.05). In general, there were some similarities between Tianhua mutton sheep and Gansu alpine fine wool sheep in the rumen tissue morphology, rumen fermentation ability, and rumen flora structure. However, Tianhua mutton sheep had a better performance in the rumen acetic acid content, rumen papillae height, and beneficial bacteria content. These differences may be one of the reasons why Tianhua mutton sheep are more suitable for growing in alpine pastoral areas than Gansu alpine fine wool sheep.

Anthropogenic and biological activities elevate microplastics pollution in headwater ecosystem of Yangtze tributaries in Hindu Kush-Himalayan region

Microplastic (MP) pollution is widely spread in oceans, freshwater, and terrestrial environments but MPs in mountainous headwater ecosystem are rarely reported. This study focuses on the headwater of Yangtze tributaries of the Hindu Kush-Himalayan (HKH) region. Five streams at elevations of 900 to 3300 m were selected to investigate the distribution of MPs in water and sediments across altitudes. MPs were found in all water and sediment samples from top stream zone nearly in absence of anthropogenic activity, low anthropogenic zone, and high anthropogenic zone, increased from 12–54, 81–185 to 334–847 items/L, and 2–35, 26–84 to 124–428 items/kg, respectively. This elevation-dependent MP distribution indicated that as elevation decreased, anthropogenic activities intensified and increased MPs input and their abundance, size, and diversity. Notably, hydraulic projects, such as damming, were identified as potential barriers to the migration of MPs downstream. Microbiome analyses revealed the presence of bacterial genes associated with plastic biodegradation in all sediment samples. The study indicates that Shangri-la mountainous streams have been polluted with MPs for years with potential risk of generation of nano-sized particles via natural fragmentation and biodegradation, and thus raises concern on MPs pollution in headwaters streams in mountainous regions.

Correlation of lesion severity with bacterial changes in Treponeme-Associated Hoof Disease from free-roaming wild elk (Cervus canadensis)

BackgroundTreponeme-Associated Hoof Disease (TAHD) is a polybacterial, multifactorial disease affecting free-ranging wild elk (Cervus canadensis) in the Pacific Northwest. Previous studies have indicated a bacterial etiology similar to digital dermatitis in livestock, including isolation of Treponema species from lesions. The lesions appear to progress rapidly from ulcerative areas in the interdigital space or along the coronary band to severe, ulcerative, necrotic, proliferative lesions under-running the hoof wall, perforating the sole, and contributing to hoof elongation, deformity, and overgrowth. Eventually the lesions undermine the laminal structure leading to sloughing of the hoof horn capsule. The objective of this study was to characterize the bacterial communities associated with hoof lesions, which were categorized into 5 stages or disease grade severities, with 0 being unaffected tissue and 4 being sloughed hoof capsule. We also wanted to determine if the etiology of TAHD through morphological changes was dominated by Treponema, as observed in hoof diseases in livestock.ResultsThe bacterial 16S rRNA gene was sequenced from 66 hoof skin biopsy samples representing 5 lesion grades from samples collected by Washington Department of Fish and Wildlife as part of a voluntary hunter program. Analysis of the relative abundance of bacterial sequences showed that lesions were dominated by members of the bacterial phyla Proteobacteria, Firmicutes, Spirochaetes, Bacteroidetes and Actinobacteria. In lesion samples, members of the genus Treponema, Porphyromonas, and Mycoplasma increased with lesion severity. Association analysis indicated frequent identification of Treponema with Porphyromonas, Bacteroides and other anaerobic Gram-positive cocci.ConclusionsThe bacterial 16S rRNA gene sequencing confirmed the presence of Treponema species at all stages of TAHD lesions, treponeme specie-specific PCR and histopathology, indicating that the morphological changes are a continual progression of disease severity with similar bacterial communities. Association and abundance of these other pathogenic genera within lesions may mean synergistic role with Treponema in hoof disease pathogenesis. Characterizing bacteria involved in lesion development, and their persistence during disease progression, provides evidence for science-based management decisions in TAHD infected elk populations.

Diet and the gut microbiome in patients with Parkinson’s disease

It has been suggested that gut microbiota influence Parkinson’s disease (PD) via the gut–brain axis. Here, we examine associations between diet and gut microbiome composition and its predicted functional pathways in patients with PD. We assessed gut microbiota in fecal samples from 85 PD patients in central California using 16S rRNA gene sequencing. Diet quality was assessed by calculating the Healthy Eating Index 2015 (HEI-2015) based on the Diet History Questionnaire II. We examined associations of diet quality, fiber, and added sugar intake with microbial diversity, composition, taxon abundance, and predicted metagenomic profiles, adjusting for age, sex, race/ethnicity, and sequencing platform. Higher HEI scores and fiber intake were associated with an increase in putative anti-inflammatory butyrate-producing bacteria, such as the genera Butyricicoccus and Coprococcus 1. Conversely, higher added sugar intake was associated with an increase in putative pro-inflammatory bacteria, such as the genera Klebsiella. Predictive metagenomics suggested that bacterial genes involved in the biosynthesis of lipopolysaccharide decreased with higher HEI scores, whereas a simultaneous decrease in genes involved in taurine degradation indicates less neuroinflammation. We found that a healthy diet, fiber, and added sugar intake affect the gut microbiome composition and its predicted metagenomic function in PD patients. This suggests that a healthy diet may support gut microbiome that has a positive influence on PD risk and progression.

The OsICS1 is directly regulated by OsWRKY6 and increases resistance against Xanthomonas oryzae pv. oryzae.

OsICS1 but not OsICS1-L mediates the rice response to Xoo inoculation, with its overexpression increasing resistance against this pathogen. OsICS1 but not OsICS-L is directly upregulated by OsWRKY6. Rice (Oryza sativa) is a staple crop for about half of the global population and is particularly important in the diets of people living in Asia, Latin America, and Africa. This crop is continually threatened by bacterial leaf blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which drastically reduces yields; therefore, it is needed to elucidate the plant's resistance mechanisms against Xoo. Isochorismate synthase (ICS1) generates salicylic acid (SA) and increases resistance against bacterial disease. The OsICS1 is differently annotated in rice genome databases and has not yet been functionally characterized in the context of Xoo infection. Here, we report that the expression of the OsICS1 is directly regulated by OsWRKY6 and increases plant resistance against Xoo. Inoculation with Xoo increased the expression of OsICS1 but not that of the long variant of OsICS1 (OsICS1-L). OsWRKY6 directly activated the OsICS1 promoter but not the OsICS1-L promoter. OsICS1 overexpression in rice increased resistance against Xoo through the induction of SA-dependent bacterial defense genes. These data show that OsICS1 promotes resistance against Xoo infection.

Screening for disease resistance and profiling the expression of defense-related genes contributing to resistance against bacterial blight (Xanthomonas oryzae pv. oryzae) in rice genotypes

Bacterial Bight profoundly affects global rice-growing regions. Breeding resistant cultivars is a reliable, effective, and eco-friendly way to control bacterial blight. The study was conducted during 2021–2022 to evaluate the resistance of rice genotypes to bacterial blight under glasshouse conditions. A total of 137 rice genotypes were screened for their resistance against two Xanthomonas oryzae pv. oryzae strains (TXO01 and TXO08) using the leaf clipping method. The results revealed diverse disease reactions among the genotypes, with some exhibiting high levels of resistance characterized by hypersensitive reactions and shorter lesion lengths. To further investigate the genetic basis of resistance, we screened moderately resistant and resistant genotypes for major bacterial blight resistance genes, including Xa21, xa5, and xa13, using gene-specific markers. Five genotypes viz., ADT55, CB MAS 13056, CB MAS 13060, CB MAS 13066, and ACM 18234 confirmed the presence of all R genes in a homozygous state, indicating a potentially robust resistance background. In addition, we examined the expression patterns of five defense-related genes involved in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways using quantitative real-time PCR (qRT-PCR). The resistant genotypes exhibited significantly elevated expression levels of OsNPR1, OsWRKY45, OsPAL1, OsPR1a, and OsPR10a, ranging from 2 to 20-fold changes compared with the susceptible genotype. In conclusion, our findings suggest that the resistant genotypes not only harbor multiple bacterial blight resistance genes but also manifest up regulated defense responses against Xanthomonas oryzae pv. oryzae, possibly substantiating their elevated level of disease resistance.

Environmental health of water bodies from a Brazilian Amazon Metropolis based on a conventional and metagenomic approach.

The present study aimed to use a conventional and metagenomic approach to investigate the microbiological diversity of water bodies in a network of drainage channels and rivers located in the central area of the city of Belém, northern Brazil, which is considered one of the largest cities in the Brazilian Amazon. In eight of the analyzed points, both bacterial and viral microbiological indicators of environmental contamination-physical-chemical and metals-were assessed. The bacterial resistance genes, drug resistance mechanisms, and viral viability in the environment were also assessed. A total of 473 families of bacteria and 83 families of viruses were identified. Based on the analysis of metals, the levels of three metals (Cd, Fe, and Mn) were found to be above the recommended acceptable level by local legislation. The levels of the following three physicochemical parameters were also higher than recommended: biochemical oxygen demand, dissolved oxygen, and turbidity. Sixty-three bacterial resistance genes that conferred resistance to 13 different classes of antimicrobials were identified. Further, five mechanisms of antimicrobial resistance were identified and viral viability in the environment was confirmed. Intense human actions combined with a lack of public policies and poor environmental education of the population cause environmental degradation, especially in water bodies. Thus, urgent interventions are warranted to restore the quality of this precious and scarce asset worldwide.

Strategic implementation of upflow microbubble airlift photocatalytic process to control heavy metal resistant-MDR bacteria and the associated genes in wastewater

The emergence of multidrug resistance (MDR) and heavy metal resistance (HMR) in bacterial pathogens and genes through mobile genetic elements (MGEs) from wastewater effluents needs to be eradicated using green technology. HMR is critical to controlling antimicrobial resistance but has been neglected in most photocatalytic disinfection (PCD) studies. Advanced photocatalysis in antimicrobial studies requires a strategic approach to enhance the disinfection efficiency. This study applied an optimized upflow airlift photocatalytic reactor (UAPR) with microbubble air and blue light to remove the antimicrobial resistance (HMR–MDR bacteria (HMR–MDRB), HMR genes (HMRGs), antibiotic resistant genes (ARGs) and MGEs) and inhibit pathogenicity in a mixed culture of high-strength HMR–MDRB isolated from wastewater. Stable dissolved oxygen (DO) supplementation and blue light significantly affected the HMRGs and MGE reduction, resulting in enhanced disinfection activity (30 %) and reaction time (60 min) required for the complete inactivation of HMR-MDRB mixed culture. The process effectively reduced the blaNDM-1 (3.37 log), pbrT (2.18 log), intl1 (2.16 log), and tn916/1545 (4.07 log), with a PCD rate constant (kg) of 0.0515 min−1, 0.0359 min−1, 0.0292 min−1, and 0.0662 min−1, respectively. Process mechanism studies showed that the stable supplementation of DO was a critical factor in controlling the type of reactive oxygen species (ROS), resulting in type II ROS, 1O2, as the critical free radical contributing to the reduction of ARGs and integron, whereas h+ was the ROS for pbrT and transposon.

Lung Tissue Multilayer Network Analysis Uncovers the Molecular Heterogeneity of Chronic Obstructive Pulmonary Disease.

Rationale: Chronic obstructive pulmonary disease (COPD) is a heterogeneous condition. Objectives: We hypothesized that the unbiased integration of different COPD lung omics using a novel multilayer approach might unravel mechanisms associated with clinical characteristics. Methods: We profiled mRNA, microRNA and methylome in lung tissue samples from 135 former smokers with COPD. For each omic (layer), we built a patient network on the basis of molecular similarity. The three networks were used to build a multilayer network, and optimization of multiplex modularity was used to identify patient communities across the three distinct layers. Uncovered communities were related to clinical features. Measurements and Main Results: We identified five patient communities in the multilayer network that were molecularly distinct and related to clinical characteristics, such as FEV1 and blood eosinophils. Two communities (C#3 and C#4) had both similarly low FEV1 values and emphysema but were molecularly different: C#3, but not C#4, presented B- and T-cell signatures and a downregulation of secretory (SCGB1A1/SCGB3A1) and ciliated cells. A machine learning model was set up to discriminate C#3 and C#4 in our cohort and to validate them in an independent cohort. Finally, using spatial transcriptomics, we characterized the small airway differences between C#3 and C#4, identifying an upregulation of T-/B-cell homing chemokines and bacterial response genes in C#3. Conclusions: A novel multilayer network analysis is able to identify clinically relevant COPD patient communities. Patients with similarly low FEV1 and emphysema can have molecularly distinct small airways and immune response patterns, indicating that different endotypes can lead to similar clinical presentation.