-
Plant Physiology and Biochemistry : PPB May 2024Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more...
Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, "amino acid and peptides", "monosaccharides", and "TCA" classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction.
Topics: Solanum lycopersicum; Micrococcaceae; Soil Microbiology; Gene Expression Regulation, Plant
PubMed: 38615442
DOI: 10.1016/j.plaphy.2024.108609 -
Marine Drugs Feb 2024Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control...
Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control the degree of sulfation, are being more extensively researched. In this work, a novel sulfatase (SulA1) encoded by the gene was characterized. The -gene is located upstream of a chondroitin lyase encoding gene in the genome of the marine Arthrobacter strain (MAT3885). The sulfatase was produced in . Based on the primary sequence, the enzyme is classified under sulfatase family 1 and the two catalytic residues typical of the sulfatase 1 family-Cys57 (post-translationally modified to formyl glycine for function) and His190-were conserved. The enzyme showed increased activity, but not improved stability, in the presence of Ca, and conserved residues for Ca binding were identified (Asp17, Asp18, Asp277, and Asn278) in a structural model of the enzyme. The temperature and pH activity profiles (screened using -nitrocatechol sulfate) were narrow, with an activity optimum at 40-50 °C and a pH optimum at pH 5.5. The was significantly higher (67 °C) than the activity optimum. Desulfation activity was not detected on polymeric substrates, but was found on GalNAc4S, which is a sulfated monomer in the repeated disaccharide unit (GlcA-GalNAc4S) of, e.g., chondroitin sulfate A. The position of the sulA1 gene upstream of a chondroitin lyase gene and combined with the activity on GalNAc4S suggests that there is an involvement of the enzyme in the chondroitin-degrading cascade reaction, which specifically removes sulfate from monomeric GalNAc4S from chondroitin sulfate degradation products.
Topics: Sulfates; Acetylgalactosamine; Arthrobacter; Sulfatases; Escherichia coli; Galactosamine; Chondroitin Lyases; Cloning, Molecular
PubMed: 38535445
DOI: 10.3390/md22030104 -
Developmental and Comparative Immunology Jul 2024Renibacterium salmoninarum causes Bacterial Kidney Disease (BKD) in several fish species. Atlantic lumpfish, a cleaner fish, is susceptible to R. salmoninarum. To...
Renibacterium salmoninarum causes Bacterial Kidney Disease (BKD) in several fish species. Atlantic lumpfish, a cleaner fish, is susceptible to R. salmoninarum. To profile the transcriptome response of lumpfish to R. salmoninarum at early and chronic infection stages, fish were intraperitoneally injected with either a high dose of R. salmoninarum (1 × 10 cells dose) or PBS (control). Head kidney tissue samples were collected at 28- and 98-days post-infection (dpi) for RNA sequencing. Transcriptomic profiling identified 1971 and 139 differentially expressed genes (DEGs) in infected compared with control samples at 28 and 98 dpi, respectively. At 28 dpi, R. salmoninarum-induced genes (n = 434) mainly involved in innate and adaptive immune response-related pathways, whereas R. salmoninarum-suppressed genes (n = 1537) were largely connected to amino acid metabolism and cellular processes. Cell-mediated immunity-related genes showed dysregulation at 98 dpi. Several immune-signalling pathways were dysregulated in response to R. salmoninarum, including apoptosis, alternative complement, JAK-STAT signalling, and MHC-I dependent pathways. In summary, R. salmoninarum causes immune suppression at early infection, whereas lumpfish induce a cell-mediated immune response at chronic infection. This study provides a complete depiction of diverse immune mechanisms dysregulated by R. salmoninarum in lumpfish and opens new avenues to develop immune prophylactic tools to prevent BKD.
Topics: Animals; Head Kidney; Fish Diseases; Renibacterium; Gene Expression Profiling; Transcriptome; Immunity, Innate; Fish Proteins; Adaptive Immunity; Fishes; Chronic Disease; Perciformes; Gram-Negative Bacterial Infections; Kidney Diseases; Micrococcaceae
PubMed: 38499166
DOI: 10.1016/j.dci.2024.105165 -
Environmental Microbiome Mar 2024Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial...
BACKGROUND
Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2.
RESULTS
Our results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere.
CONCLUSIONS
The study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.
PubMed: 38461269
DOI: 10.1186/s40793-024-00558-5 -
Microbiome Feb 2024Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous...
BACKGROUND
Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope probing (DNA-SIP) and metagenomic analysis were conducted to decipher the bioaugmentation mechanisms in stabilization pond sediment microcosms inoculated with sulfamethoxazole (SMX)-degrading bacteria (Pseudomonas sp. M2 or Paenarthrobacter sp. R1).
RESULTS
The bioaugmentation with both strains M2 and R1, especially strain R1, significantly improved the biodegradation rate of SMX, and its biodegradation capacity was sustainable within a certain cycle (subjected to three repeated SMX additions). The removal strategy using exogenous degrading bacteria also significantly abated the accumulation and transmission risk of antibiotic resistance genes (ARGs). Strain M2 inoculation significantly lowered bacterial diversity and altered the sediment bacterial community, while strain R1 inoculation had a slight effect on the bacterial community and was closely associated with indigenous microorganisms. Paenarthrobacter was identified as the primary SMX-assimilating bacteria in both bioaugmentation systems based on DNA-SIP analysis. Combining genomic information with pure culture evidence, strain R1 enhanced SMX removal by directly participating in SMX degradation, while strain M2 did it by both participating in SMX degradation and stimulating SMX-degrading activity of indigenous microorganisms (Paenarthrobacter) in the community.
CONCLUSIONS
Our findings demonstrate that bioaugmentation using SMX-degrading bacteria was a feasible strategy for SMX clean-up in terms of the degradation efficiency of SMX, the risk of ARG transmission, as well as the impact on the bacterial community, and the advantage of bioaugmentation with Paenarthrobacter sp. R1 was also highlighted. Video Abstract.
Topics: Sulfamethoxazole; Water Pollutants, Chemical; Wastewater; Anti-Bacterial Agents; Bacteria; Micrococcaceae; Biodegradation, Environmental; DNA
PubMed: 38424602
DOI: 10.1186/s40168-023-01741-5 -
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 -
Dermatology (Basel, Switzerland) 2024Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection...
INTRODUCTION
Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection of skin lesions is common, and Staphylococcus aureus commonly colonizes these lesions. The aim of the study was to characterize the bacterial microbiome of cutaneous Darier lesions compared to normal-looking skin and disease severity.
METHODS
All patients with a history of Darier followed up at Emek Medical Center were invited to participate in the study. Patients that did not use antibiotics in the past month and signed informed consent had four skin sites sampled with swabs: scalp, chest, axilla, and palm. All samples were analyzed for bacterial microbiome using 16S rDNA sequencing.
RESULTS
Two hundred and eighty microbiome samples obtained from lesional and non-lesional skin of the scalp, chest, axilla, and palm of 42 Darier patients were included in the analysis. The most abundant bacterial genera across all skin sites were Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, and Anaerococcus. Scalp and chest lesions featured a distinct microbiome configuration that was mainly driven by an overabundance of Staphylococci species. Patients with more severe disease exhibited microbiome alterations in the chest, axilla, and palm compared with patients with only mild disease, driven by Peptoniphilus and Moryella genera in scalp and palmar lesions, respectively.
CONCLUSION
Staphylococci were significantly associated with Darier lesions and drove Darier-associated dysbiosis. Severity of the disease was associated with two other bacterial genera. Whether these associations also hold a causative role and may serve as a therapeutic target remains to be determined and requires further investigation.
Topics: Humans; Darier Disease; Male; Female; Dysbiosis; Adult; Middle Aged; Microbiota; Axilla; Skin; Corynebacterium; Young Adult; Propionibacterium; Micrococcus; Severity of Illness Index; Hand; Thorax; Scalp; Aged; Adolescent
PubMed: 38330926
DOI: 10.1159/000537714 -
Applied and Environmental Microbiology Feb 2024Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two...
Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, VR04 sp. and GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets' growth, became a predominant taxon, and considering untreated plantlets as references, sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.IMPORTANCEA better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.
Topics: Agricultural Inoculants; Phylogeny; Plant Roots; Bacteria; Enterobacteriaceae; Endophytes
PubMed: 38289136
DOI: 10.1128/aem.02078-23 -
Rhode Island Medical Journal (2013) Feb 2024Peritonitis, a serious complication of peritoneal dialysis (PD), can be caused by opportunistic pathogens like Micrococcus species on rare occasions. We present a case...
Peritonitis, a serious complication of peritoneal dialysis (PD), can be caused by opportunistic pathogens like Micrococcus species on rare occasions. We present a case of Micrococcus sp peritonitis in a 55-year-old female with end-stage kidney disease on continuous cycling peritoneal dialysis for one year who presented with cloudy effluent. Initial treatment against Micrococcus sp with vancomycin, gentamicin, and prophylactic oral nystatin was successful. However, one month later, the patient presented with abdominal pain and dialysate culture again grew Micrococcus sp. Treatment with vancomycin was unsuccessful in resolving culture positivity. The patient was transitioned to hemodialysis for non-medical reasons and then was later restarted on PD without further peritonitis episodes. Micrococcus sp peritonitis in PD poses treatment challenges due to limited guidelines. Intraperitoneal vancomycin is commonly used to target Micrococcus isolates although there is a high incidence of treatment failure. This case report highlights the need for continued reporting to enhance identification, prevention, and patient outcomes in Micrococcus sp peritonitis during PD.
Topics: Female; Humans; Middle Aged; Vancomycin; Micrococcus; Peritoneal Dialysis; Peritonitis; Kidney Failure, Chronic; Anti-Bacterial Agents
PubMed: 38285745
DOI: No ID Found -
Applied Microbiology and Biotechnology Jan 2024As the problem of antimicrobial resistance is constantly increasing, there is a renewed interest in antimicrobial products derived from natural sources, particularly...
As the problem of antimicrobial resistance is constantly increasing, there is a renewed interest in antimicrobial products derived from natural sources, particularly obtained from innovative and eco-friendly materials. Insect lipids, due to their fatty acid composition, can be classified as natural antimicrobial compounds. In order to assess the antibacterial efficacy of Hermetia illucens lipids, we extracted this component from the larval stage, fed on different substrates and we characterized it. Moreover, we analyzed the fatty acid composition of the feeding substrate, to determine if and how it could affect the antimicrobial activity of the lipid component. The antimicrobial activity was evaluated against Gram-positive Micrococcus flavus and Gram-negative bacteria Escherichia coli. Analyzing the fatty acid profiles of larval lipids that showed activity against the two bacterial strains, we detected significant differences for C4:0, C10:0, C16:1, C18:3 n3 (ALA), and C20:1. The strongest antimicrobial activity was verified against Micrococcus flavus by lipids extracted from larvae reared on strawberry, tangerine, and fresh manure substrates, with growth inhibition zones ranged from 1.38 to 1.51 mm, while only the rearing on manure showed the effect against Escherichia coli. Notably, the fatty acid profile of H. illucens seems to not be really influenced by the substrate fatty acid profile, except for C18:0 and C18:2 CIS n6 (LA). This implies that other factors, such as the rearing conditions, larval development stages, and other nutrients such as carbohydrates, affect the amount of fatty acids in insects. KEY POINTS: • Feeding substrates influence larval lipids and fatty acids (FA) • Generally, there is no direct correlation between substrate FAs and the same larvae FAs • Specific FAs influence more the antimicrobial effect of BSF lipids.
Topics: Animals; Manure; Larva; Escherichia coli; Fatty Acids; Micrococcus luteus; Diptera; Micrococcus
PubMed: 38261012
DOI: 10.1007/s00253-024-13005-9