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Microbiology Resource Announcements Mar 2024Here, we present the genomes of two soil actinobacteria: sp. strain AZCC_0090 and sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern...
Here, we present the genomes of two soil actinobacteria: sp. strain AZCC_0090 and sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.
PubMed: 38376218
DOI: 10.1128/mra.01089-23 -
BMC Microbiology Feb 2024In this study, we investigated the effects of alpine meadow in different phenological periods on ruminal fermentation, serum biochemical indices, and gastrointestinal...
Effects of the alpine meadow in different phenological periods on rumen fermentation and gastrointestinal tract bacteria community in grazing yak on the Qinghai-Tibetan Plateau.
BACKGROUND
In this study, we investigated the effects of alpine meadow in different phenological periods on ruminal fermentation, serum biochemical indices, and gastrointestinal tract microbes in grazing yak on the Qinghai-Tibetan Plateau. A total of eighteen female freely grazing yaks with an average age of 3 years old and a body weight of 130 ± 19 kg were selected. According to the plant phenological periods, yaks were randomly allocated to one of three treatments: (1) regreen periods group (RP, n = 6); (2) grassy periods group (GP, n = 6); and (3) hay periods group (HP, n = 6). At the end of the experiment, the blood, rumen fluids, and rectal contents were collected to perform further analysis.
RESULTS
The concentrations of total volatile fatty acid (TVFA), acetate, glucose (GLU), triglyceride (TG), cholesterol (CHO), high density lipoprotein (HDL), and low density lipoprotein (LDL) were higher in the GP group than in the HP group (P < 0.05). However, compared with the RP and GP groups, the HP group had higher concentrations of isobutyrate, isovalerate, valerate, and creatinine (CREA) (P < 0.05). The abundance of Prevotella in the rumen, and the abundances of Rikenellaceae_RC9_gut_group, Eubacterium_coprostanoligenes_group, and Prevotellaceae_UCG-004 in the gut were higher in the GP group compared with the HP group (P < 0.05). The HP had higher abundance of Eubacterium_coprostanoligenes_group in the rumen as well as the abundances of Romboutsia and Arthrobacter in the gut compared with the RP and GP groups (P < 0.05).
CONCLUSIONS
Based on the results of rumen fermentation, serum biochemical, differential biomarkers, and function prediction, the carbohydrate digestion of grazing yak would be higher with the alpine meadow regreen and grassy due to the gastrointestinal tract microbes. However, the risk of microbe disorders and host inflammation in grazing yak were higher with the alpine meadow wither.
Topics: Animals; Cattle; Bacteria; Bacteroidetes; Fermentation; Gastrointestinal Tract; Grassland; Rumen; Tibet
PubMed: 38373936
DOI: 10.1186/s12866-024-03182-y -
Heliyon Feb 2024Taking rural dispersed sewage for research objects, the treatment effect and microbial community structure characteristics of a bio filter (BF) reactor was studied. At...
Taking rural dispersed sewage for research objects, the treatment effect and microbial community structure characteristics of a bio filter (BF) reactor was studied. At fixed time and location, the removal efficiencies of common pollutants were investigated. By using high-throughput sequencing method, the heterogeneities of microbial community structure in fillers and plant roots were analyzed. The results showed that the average annual removal rates of COD, NH-N, TN, and TP by the BF were 83.10 %, 65.67 %, 60.25 %, and 80.32 % respectively, and the effluent could reach the first grade of the water pollutant discharge standard of rural sewage treatment facility (DB51/2626-2019). During the sewage treatment process, Scindapsus could effectively establish complex and stable microbial communities, and could better degrade pollutants, especially nitrogen removal. The dominant microbial communities were more than 11 phyla and 19 classes. At the genus level, the dominant bacteria included , etc.
PubMed: 38317885
DOI: 10.1016/j.heliyon.2024.e25301 -
Applied Microbiology and Biotechnology Feb 2024Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and...
Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.
Topics: Petroleum; Oil and Gas Fields; Hordeum; Soil Pollutants; Hydrocarbons, Aromatic; Bacillus subtilis; Carbon; Soil; Biodegradation, Environmental; Soil Microbiology; Hydrocarbons
PubMed: 38305872
DOI: 10.1007/s00253-024-13010-y -
Microorganisms Dec 2023Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and...
Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to study the physiology and growth in oil at temperatures below 0 °C of four strains of bacteria of the genera , , , and -previously isolated from diesel-contaminated soils of the Franz Josef Land archipelago-as well as genomic analysis of the sp. AR_OL41 strain. The studied strains grew on hydrocarbons at temperatures from -1.5 °C to 35 °C in the presence of 0-8% NaCl (/). Growth at a negative temperature was accompanied by visual changes in the size of cells as well as a narrowing of the spectrum of utilized -alkanes. The studied strains were psychrotolerant, degraded natural biopolymers (xylan, chitin) and -alkanes of petroleum, and converted phosphates into a soluble form. The ability to degrade -alkanes is rare in members of the genus . To understand how the sp. AR_OL41 strain has adapted to a cold, diesel-contaminated environment, its genome was sequenced and analyzed. The Illumina HiSeq 2500 platform was used for AR_OL41 genome strain sequencing. The genome analysis of the AR_OL41 strain showed the presence of genes encoding enzymes of -alkane oxidation, pyruvate metabolism, desaturation of membrane lipids, and the formation of exopolysaccharides, confirming the adaptation of the strain to hydrocarbon pollution and low habitat temperature. Average nucleotide identity and digital DNA-DNA hybridization values for genomes of the AR_OL41 strain with that of the phylogenetically relative DSM 22537 strain were 81.9% and 20.9%, respectively, which allows the AR_OL41 strain to be assigned to a new species of the genus . Phenomenological observations and genomic analysis indicate the possible participation of the studied strains in the self-purification of Arctic soils from hydrocarbons and their potential for biotechnological application in bioremediation of low-temperature environments.
PubMed: 38257905
DOI: 10.3390/microorganisms12010079 -
Frontiers in Microbiology 2023wilt is the most devastating soil-borne disease affecting in the progress of urban landscape construction in China.
INTRODUCTION
wilt is the most devastating soil-borne disease affecting in the progress of urban landscape construction in China.
METHODS
To assess the variability of the rhizosphere-associated soil microbiome in response to wilt occurrence, we investigated the microbial diversity, taxonomic composition, biomarker species, and co-occurrence network of the rhizosphere-associated soil in wiltaffected using Illumina sequencing.
RESULTS
The alpha diversity indices of the rhizosphere bacteria in wilt-affected plants showed no significant variability compared with those in healthy plants, except for a moderate increase in the Shannon and Invsimpson indices, while the fungal alpha diversity indices were significantly decreased. The abundance of certain dominant or crucial microbial taxa, such as , , , and , displayed significant variations among different soil samples. The bacterial and fungal community structures exhibited distinct variability, as evidenced by the Bray-Curtis dissimilarity matrices. Co-occurrence networks unveiled intricate interactions within the microbial community of wilt-affected , with greater edge numbers and higher network density. The phenomenon was more evident in the fungal community, showing increased positive interaction, which may be associated with the aggravation of wilt with the aid of . The proportions of bacteria involved in membrane transport and second metabolite biosynthesis functions were significantly enriched in the diseased rhizosphere soil samples.
DISCUSSION
These findings suggested that healthy harbored an obviously higher abundance of beneficial microbial consortia, such as while wilt-affected plants may recruit antagonistic members such as in response to infection. This study provides a theoretical basis for understanding the soil micro-ecological mechanism of wilt occurrence, which may be helpful in the prevention and control of the disease in from the microbiome perspective.
PubMed: 38249458
DOI: 10.3389/fmicb.2023.1279096 -
Advanced Science (Weinheim,... Apr 2024Low-carbon alkaline thermal hydrolysis of sewage sludge for the production of high-quality plant-growth-promoting nutrients and biostimulants is a growing concern for...
Double Advantages of Nutrients and Biostimulants Derived from Sewage Sludge by Alkaline Thermal Hydrolysis Process for Agricultural Use: Quality Promotion of Soil and Crop.
Low-carbon alkaline thermal hydrolysis of sewage sludge for the production of high-quality plant-growth-promoting nutrients and biostimulants is a growing concern for sludge resource utilization in agriculture. Thus, this study aims to investigate functional characteristics and soil biochemical effects of sewage sludge-derived nutrients and biostimulants (SS-NB). The content of heavy metals in SS-NB decreased by 47.39-100%, and an increase in soil protease, invertase, and soil nutrient utilization rates are observed in SS-NB groups. SS-NB substituted for chemical fertilizer increased the diversity and evenness of microbial community and reduced the abundance of the soil-borne bacterial genus Arthrobacter. The dominant community of SS-NB100 group is mainly enriched in Microvirga, Ensifer, Novosphingobium, Bosea and Ellin6055, which are principally beneficial symbiotic bacteria of plants and participated in C and N cycles. Moreover, SS-NB reduced the accumulation of Ktedonobacteria and Nitrosospira, which are involved in the production of CO and NO, and also enhanced the coordination of soil microorganisms with enzyme activities and nutrient utilization rate. In conclusion, the results suggest that SS-NB exerts a positive effect on reducing greenhouse gas emissions and preventing soil-borne diseases, and can further enhance collaboration with soil enzyme activity and soil nutrient utilization by stimulating soil microorganisms.
Topics: Soil; Sewage; Hydrolysis; Agriculture; Nutrients
PubMed: 38240362
DOI: 10.1002/advs.202307793 -
Foods (Basel, Switzerland) Nov 2023The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages...
The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages on the composition and function of donkey milk microbiota. The milk samples were collected at 1, 30, 60, 90, 120, 150, and 180 days post-delivery. The result showed that the microbial composition and functions in donkey milk were significantly affected by different lactation stages. The dominant bacterial phyla in donkey milk are (60%) and (22%). (39%), (4%), and (2%) were the predominant bacterial genera detected in all milk samples. In the mature milk, the abundance of lactic acid bacteria (7%) was higher. (5%) and (3%) were more plentiful in milk samples from middle and later lactation stages (90-180 d). Furthermore, the pathogens and and thermoduric bacteria , , and were also detected. Donkey milk is rich in beneficial bacteria and also poses a potential health risk. The above findings have improved our understanding of the composition and function changes of donkey milk microbiota, which is beneficial for the rational utilization of donkey milk.
PubMed: 38231735
DOI: 10.3390/foods12234272 -
Microbiology Spectrum Feb 2024Reductive soil disinfestation (RSD) is an effective method to inhibit soilborne pathogens. However, it remains unclear how RSD combined with different types of organic...
Reductive soil disinfestation (RSD) is an effective method to inhibit soilborne pathogens. However, it remains unclear how RSD combined with different types of organic materials affects the soil ecosystems of perennial plants. Pot experiments were conducted to investigate the effects of RSD incorporated with perilla (PF), alfalfa (MS), ethanol, and acetic acid on soil properties, enzyme activities, microbial communities and functions, and seedling growth. Results showed that RSD-related treatments improved soil properties and enzyme activities, changed microbial community composition and structure, enhanced microbial interactions and functions, and facilitated seedling growth. Compared with CK, RSD-related treatments increased soil pH, available nitrogen, and available potassium contents, sucrase and catalase activities, and decreased soil electric conductivity values. Meanwhile, RSD-related treatment also significantly reduced the relative abundance of while increasing the relative abundance of , , and . The reduction was more evident in PF and MS treatment, suggesting the potential for RSD combined with solid agricultural wastes to suppress pathogens. Furthermore, the microbial network of RSD-related treatment was more complex and interconnected, and the functions related to carbon, nitrogen, sulfur, and hydrogen cycling were significantly increased, while the functions of bacterial and fungal plant pathogens were decreased. Importantly, RSD-related treatments also significantly promoted seed germination and seedling growth. In summary, RSD combined with solid agricultural wastes is better than liquid easily degradable compounds by regulating the composition and function of microbial communities to improve soil quality and promote plant growth.IMPORTANCEReductive soil disinfestation (RSD) is an effective agricultural practice. We found that RSD combined with solid agricultural wastes is better than that of liquid easily degradable compounds, may improve soil quality and microbial community structure, inhibit the proliferation of pathogenic bacteria, and contribute to the growth of replanted crops. Thus, RSD combined with solid agricultural wastes is more effective than liquid easily degradable compounds.
Topics: Soil; Microbiota; Agriculture; Bacteria; Nitrogen; Soil Microbiology
PubMed: 38230941
DOI: 10.1128/spectrum.00802-23 -
Frontiers in Microbiology 2023As tick-borne diseases rise to become the second most prevalent arthropod-transmitted disease globally, the increasing investigations focus on ticks correspondingly....
INTRODUCTION
As tick-borne diseases rise to become the second most prevalent arthropod-transmitted disease globally, the increasing investigations focus on ticks correspondingly. Factors contributed to this increase include anthropogenic influences, changes in vertebrate faunal composition, social-recreational shifts, and climatic variation. Employing the 16S gene sequence method in next-generation sequencing (NGS) allows comprehensive pathogen identification in samples, facilitating the development of refined approaches to tick research omnidirectionally.
METHODS
In our survey, we compared the microbial richness and biological diversity of ticks in Wuwei City, Gansu province, differentiating between questing ticks found in grass and parasitic ticks collected from sheep based on 16S NGS method.
RESULTS
The results show , , and were detected in all 50 samples, suggesting that the co-infection may be linked to specific symbiotic bacteria in ticks. Our findings reveal significant differences in the composition and diversity of microorganisms, with the and genera existing more prevalent in parasitic ticks than in questing ticks ( < 0.05). Additionally, the network analysis demonstrates that the interactions among bacterial genera can be either promotive or inhibitive in ticks exhibiting different lifestyles with the correlation index || > 0.6. For instance, restrains the development of 10 other bacteria in parasitic ticks, whereas and enhance colonization across all tick species.
DISCUSSION
By leveraging NGS techniques, our study reveals a high degree of species and phylogenetic diversity within the tick microbiome. It further highlights the potential to investigate the interplay between bacterial genera in both parasitic and questing ticks residing in identical habitat environments.
PubMed: 38192286
DOI: 10.3389/fmicb.2023.1264939