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Scientific Reports Mar 2020Returning crop residues is a possible practice for balancing soil carbon (C) loss. The turnover rate of organic C from crop residues to soil C is dependent on soil...
Returning crop residues is a possible practice for balancing soil carbon (C) loss. The turnover rate of organic C from crop residues to soil C is dependent on soil microbial community dynamics. However, the relationship between any temporal changes in the soil microbial community after crop straw inputs and the dynamics of straw-C distribution in the soil organic carbon (SOC) pool remains unclear. The present study investigated the allocation of straw-C into soil dissolved organic carbon (DOC), microbial biomass carbon (MBC), particulate organic carbon (POC) and mineral-associated organic carbon (MaOC) using stable isotope probing, as well as the temporal changes in the soil bacterial and fungal communities using high-throughput sequencing. After the first 180 days of straw decomposition, approximately 3.93% and 19.82% of straw-C was transformed into soil MaOC and POC, respectively, while 0.02% and 2.25% of straw-C was transformed into soil DOC and MBC, respectively. The temporal change of the soil microbial community was positively correlated with the dynamics of straw-C distribution to SOC (R > 0.5, P < 0.05). The copiotrophic bacteria (e.g., Streptomyces, Massilia and Sphingobacterium), cellulolytic bacteria and fungi (e.g., Dyella and Fusarium, Talaromyces), acidophilic bacteria (e.g., Edaphobacter and unclassified Acidobacteriaceae), denitrifying and N-fixing microbes (e.g., Burkholderia-Paraburkholderia, Paraphaeosphaeria and Bradyrhizobium), and fungi unclassified Sordariomycetes were significantly correlated with straw-C distribution to specific SOC fractions (P < 0.05), which explained more than 90% of the variation of straw-C allocation into soils. Copiotrophic, certain cellulolytic and denitrifying microbes had positively correlated with DOC- and MaOC-derived from straw, and other cellulolytic fungi (e.g., Talaromyces) and specific bacteria (e.g. Bradyrhizobium) were positively correlated with POC-derived from straw. Our results highlight that the temporal change of soil microbial community structure well reflects the conversion and distribution process of straw-C to SOC fractions.
Topics: Bacteria; Carbon; Carbon Sequestration; DNA, Bacterial; DNA, Fungal; Fungi; High-Throughput Nucleotide Sequencing; Isotope Labeling; Microbiota; Phylogeny; Sequence Analysis, DNA; Soil; Soil Microbiology
PubMed: 32218459
DOI: 10.1038/s41598-020-62198-2 -
Plants (Basel, Switzerland) Mar 2021Microalgae are considered a potential source of valuable compounds for multiple purposes and are potential agents for bioremediation of aquatic environments contaminated...
Microalgae are considered a potential source of valuable compounds for multiple purposes and are potential agents for bioremediation of aquatic environments contaminated with different pollutants. This work evaluates the use of agricultural waste, unsterilized and anaerobically digested, to produce biomass from a strain of . Furthermore, the presence of bacteria in these wastes was investigated based on the bacterial 16S rRNA gene sequencing. The results showed a specific growth rate ranging between 0.82 and 1.45 day, while the final biomass yield in different digestate-containing treatments (bacterial-contaminated cultures) ranged between 0.33 and 0.50 g L day. Besides, substantial amounts of ammonium, phosphate, and sulfate were consumed by during the experimental period. The predominant bacteria that grew in the presence of in the effluent-containing treatments belonged to the genera , , , , , , and . Therefore, this microalga can tolerate and grow in the presence of other microorganisms. Finally, these results show that anaerobically digested agricultural waste materials are a good substitute for growth media for green microalgae; however, phosphate and sulfate levels must also be controlled in the media to maintain adequate growth of microalgae.
PubMed: 33802500
DOI: 10.3390/plants10030478 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Dec 2022Polyphosphate kinase plays an important role in the catalytic synthesis of ATP . In order to find a polyphosphate kinase that can efficiently synthesize ATP using...
Polyphosphate kinase plays an important role in the catalytic synthesis of ATP . In order to find a polyphosphate kinase that can efficiently synthesize ATP using short-chain polyphosphate (polyP) as substrate, the polyphosphate kinase 2 (PPK2) from was cloned and expressed in BL21(DE3). As an enzyme for ATP regeneration, PPK2 was used in combination with l-amino acid ligase (YwfE) to produce l-alanyl-l-glutamine (Ala-Gln). The length of of . is 810 bp, encoding 270 amino acids. The SDS-PAGE showed that PPK2 was expressed correctly and its molecular weight was 29.7 kDa as expected. The reaction conditions of PPK2 were optimized. PPK2 could maintain good activity in the range of 22-42 ℃ and pH 7-10. The highest enzyme activity was observed at 37 ℃, pH 7, 30 mmol/L magnesium ion (Mg), 5 mmol/L ADP and 10 mmol/L sodium hexametaphosphate, and the yield of ATP reached 60% of the theoretical value in 0.5 hours at this condition. When used in combination with YwfE to produce Ala-Gln, the PPK2 showed a good applicability as an ATP regeneration system, and the effect was similar to that of direct addition of ATP. The PPK2 from . shows good performance in a wide range of temperature and pH, synthesizes ATP with cheap and readily available short chain polyP as substrate. The PPK2 thus provides a new enzyme source for ATP dependent catalytic reaction system.
Topics: Sphingobacterium; Phosphotransferases (Phosphate Group Acceptor); Amino Acids; Adenosine Triphosphate; Regeneration; Polyphosphates
PubMed: 36593201
DOI: 10.13345/j.cjb.220320 -
PloS One 2022This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different...
This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different degradation periods was analyzed using MiSeq high-throughput sequencing. The results showed that 14 days after inoculation, the filter paper enzyme and endoglucanase activities increased to 2.55 U·mL-1 and 2.34 U·mL-1. The xylanase, laccase, and lignin peroxidase activities rose to 9.86 U·mL-1, 132.16 U·L-1, and 85.43 U·L-1 after 28 d, which was consistent with changes in the straw degradation rate. The degradation rates of straw, lignin, cellulose, and hemicellulose were 31.43%, 13.67%, 25.04%, and 21.69%, respectively, after 28 d of fermentation at 15°C. Proteobacteria, Firmicutes, and Bacteroidetes were the main bacterial species in samples at different degradation stages. The dominant genera included Pseudomonas, Delftia, and Paenibacillus during the initial stage (1 d, 7 d) and the mid-term stage (14 d). The key functional microbes during the late stage (21 d, 28 d) were Rhizobium, Chryseobacterium, Sphingobacterium, Brevundimonas, and Devosia. Changes in the bacterial consortium structure and straw degradation characteristics during different degradation periods were clarified to provide a theoretical basis for the rational utilization of microbial decomposer M44.
Topics: Bacteria; Cellulose; Fermentation; Lignin; Microbial Consortia; Temperature
PubMed: 35802565
DOI: 10.1371/journal.pone.0270162 -
PloS One 2017Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral...
Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations-Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (P<0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, P = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, Cardiobacterium and Riemerella were higher in VWD-E dogs, and Sphingobacterium was higher in the P-NDD group. In the oral samples Enterococcus and Capnocytophaga were higher in the P-NDD group. Gemella and Aggregatibacter were higher in S-PE, and Pigmentiphaga, Chryseobacterium, Parabacteroides amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines.
Topics: Animals; Biodiversity; Cohort Studies; Discriminant Analysis; Dogs; Drug and Narcotic Control; Explosive Agents; Female; Linear Models; Male; Microbiota; Military Personnel; Mouth; Nose; Pets; Police; RNA, Bacterial; RNA, Ribosomal, 16S; Smell; Time Factors
PubMed: 28934260
DOI: 10.1371/journal.pone.0184899 -
Malaria Journal Feb 2021Insecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito...
BACKGROUND
Insecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito microbiota and insecticide resistance, the microbiota of Anopheles gambiae sensu stricto (s.s.) from Tulukuyi village, Bungoma, Kenya, with differing permethrin resistance profiles were comparatively characterized.
METHODS
Using the CDC bottle bioassay, 133 2-3 day-old, virgin, non-blood fed female F progeny of field-caught An. gambiae s.s. were exposed to five times (107.5 µg/ml) the discriminating dose of permethrin. Post bioassay, 50 resistant and 50 susceptible mosquitoes were subsequently screened for kdr East and West mutations, and individually processed for microbial analysis using high throughput sequencing targeting the universal bacterial and archaeal 16S rRNA gene.
RESULTS
47 % of the samples tested (n = 133) were resistant, and of the 100 selected for further processing, 99 % were positive for kdr East and 1 % for kdr West. Overall, 84 bacterial taxa were detected across all mosquito samples, with 36 of these shared between resistant and susceptible mosquitoes. A total of 20 bacterial taxa were unique to the resistant mosquitoes and 28 were unique to the susceptible mosquitoes. There were significant differences in bacterial composition between resistant and susceptible individuals (PERMANOVA, pseudo-F = 2.33, P = 0.001), with presence of Sphingobacterium, Lysinibacillus and Streptococcus (all known pyrethroid-degrading taxa), and the radiotolerant Rubrobacter, being significantly associated with resistant mosquitoes. On the other hand, the presence of Myxococcus, was significantly associated with susceptible mosquitoes.
CONCLUSIONS
This is the first report of distinct microbiota in An. gambiae s.s. associated with intense pyrethroid resistance. The findings highlight differentially abundant bacterial taxa between resistant and susceptible mosquitoes, and further suggest a microbe-mediated mechanism of insecticide resistance in mosquitoes. These results also indicate fixation of the kdr East mutation in this mosquito population, precluding further analysis of its associations with the mosquito microbiota, but presenting the hypothesis that any microbe-mediated mechanism of insecticide resistance would be likely of a metabolic nature. Overall, this study lays initial groundwork for understanding microbe-mediated mechanisms of insecticide resistance in African mosquito vectors of malaria, and potentially identifying novel microbial markers of insecticide resistance that could supplement existing vector surveillance tools.
Topics: Animals; Anopheles; Female; Insecticide Resistance; Insecticides; Kenya; Microbiota; Mosquito Control; Mosquito Vectors; Permethrin
PubMed: 33557825
DOI: 10.1186/s12936-021-03606-4 -
Journal of Translational Medicine Feb 2023Gut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still...
BACKGROUND
Gut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still inconclusive.
METHOD
A paired-sample study was designed by retrieving original multicenter 16 s-rRNA data of IBS patients and healthy controls from the GMrepo database. The propensity score matching (PSM) algorithm was applied to reduce confounding bias. The differential analysis of microbiota composition was performed at different taxonomic levels. The co-occurrence network was established. Subgroup analysis was performed to identify specific microbial compositions in different IBS subtypes.
RESULTS
A total of 1522 amplicon samples were initially enrolled. After PSM, 708 individuals (354 IBS and 354 healthy controls) were eligible for further analysis. A total of 1,160 genera were identified. We identified significantly changed taxa in IBS groups (IBS-enriched: the families Enterobacteriaceae, Moraxellaceae and Sphingobacteriaceae; the genera Streptococcus, Bacillus, Enterocloster, Sphingobacterium, Holdemania and Acinetobacter. IBS-depleted: the phyla Firmicutes, Euryarchaeota, Cyanobacteria, Acidobacteria and Lentisphaerae; the families Bifidobacteriaceae, Ruminococcaceae, Methanobacteriaceae and the other 25 families; the genera Faecalibacterium, Bifidobacterium and other 68 genera). The co-occurrence network identified three hub genera and six hub species (including Faecalibacterium prausnitzii) that may be involved in IBS pathophysiology. Strong positive interactions were identified among the Bifidobacterium longum, Bifidobacterium breve and Bifidobacterium adolescentis in the Bifidobacterium community.
CONCLUSION
This study provides quantitative analysis and visualization of the interaction between the gut microbiota and IBS. The identification of key species should be further validated to evaluate their causal relationships with the pathogenesis of IBS.
Topics: Humans; Irritable Bowel Syndrome; Gastrointestinal Microbiome; Bacteria; RNA, Ribosomal, 16S; Feces
PubMed: 36774467
DOI: 10.1186/s12967-023-03953-7 -
Frontiers in Microbiology 2023The antibacterial properties of nanoparticles are of particular interest because of their potential to serve as an alternative therapy to combat antimicrobial...
The antibacterial properties of nanoparticles are of particular interest because of their potential to serve as an alternative therapy to combat antimicrobial resistance. Metal nanoparticles such as silver and copper nanoparticles have been investigated for their antibacterial properties. Silver and copper nanoparticles were synthesized with the surface stabilizing agents cetyltrimethylammonium bromide (CTAB, to confer a positive surface charge) and polyvinyl pyrrolidone (PVP, to confer a neutral surface charge). Minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and viable plate count assays were used to determine effective doses of silver and copper nanoparticles treatment against , and . Results show that CTAB stabilized silver and copper nanoparticles were more effective antibacterial agents than PVP stabilized metal nanoparticles, with MIC values in a range of 0.003 μM to 0.25 μM for CTAB stabilized metal nanoparticles and 0.25 μM to 2 μM for PVP stabilized metal nanoparticles. The recorded MIC and MBC values of the surface stabilized metal nanoparticles show that they can serve as effective antibacterial agents at low doses.
PubMed: 36846763
DOI: 10.3389/fmicb.2023.1119550 -
Frontiers in Cellular and Infection... 2018Mounting evidence indicates that microbiome plays an important role in the development and progression of cancer. The dogma that urine in healthy individuals must be...
Mounting evidence indicates that microbiome plays an important role in the development and progression of cancer. The dogma that urine in healthy individuals must be sterile has been overturned. Dysbiosis of the urinary microbiome has been revealed responsible for various urological disorders, including prostate cancer. The link between chronic inflammation, microbiome and solid tumors has been established for various neoplastic diseases. However, a detailed and comprehensive analysis of urinary microenvironment of bladder cancer has not been yet reported. We performed this study to characterize the potential urinary microbial community possibly associated with bladder cancer. Mid-stream urine was collected from 31 male patients with bladder cancer and 18 non-neoplastic controls. DNA was extracted from urine pellet samples and processed for high throughput 16S rRNA amplicon sequencing of the V4 region using Illumina MiSeq. Sequencing reads were filtered using QIIME and clustered using UPARSE. We observed increased bacterial richness (Observed Species, Chao 1 and Ace indexes; cancer vs. control; 120.0 vs. 56.0; 134.5 vs. 68.3; and 139.6 vs. 72.9, respectively), enrichment of some bacterial genera (e.g., ) and decrease of some bacterial genera (e.g., , and ) in cancer group when compared to non-cancer group. Significant difference in beta diversity was found between cancer and non-cancer group, among different risk level, but not among different tumor grade. Enrichment of , and was observed in cancer patients with high risk of recurrence and progression, which means these genera maybe potential biomarkers for risk stratification. The PICRUSt showed that various functional pathways were enriched in cancer group, including infection, glycerolipid metabolism and retinol metabolism. To our knowledge, we performed the most comprehensive study to date to characterize the urinary microbiome associated with bladder cancer. A better understanding of the role of microbiome in the development and progression of bladder cancer could pave a new way for exploring new therapeutic options and biomarkers.
Topics: Aged; Biomarkers, Tumor; Carcinoma; China; DNA, Bacterial; Disease Progression; Humans; Male; Microbiota; Middle Aged; RNA, Ribosomal, 16S; Statistics, Nonparametric; Urinary Bladder; Urinary Bladder Neoplasms; Urothelium
PubMed: 29904624
DOI: 10.3389/fcimb.2018.00167 -
Applied Microbiology and Biotechnology Aug 2023The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic...
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr trait is spread across different bacterial taxonomic classes. • The core-code for the Myr trait was detected in a novel ICE, only found in Pseudomonas spp.
Topics: Rhizosphere; Acyclic Monoterpenes; Bacteria; Pseudomonas
PubMed: 37405434
DOI: 10.1007/s00253-023-12650-w