scholarly journals Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco

2022 ◽  
Vol 9 ◽  
Author(s):  
Min-Chong Shen ◽  
Yu-Zhen Zhang ◽  
Guo-Dong Bo ◽  
Bin Yang ◽  
Peng Wang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Agricultural Soil ◽  
Rhizosphere Soil ◽  
Alpha Diversity ◽  
Low Fertility ◽  
Control Group ◽  
Beneficial Bacteria ◽  
Chemical Fertilizers ◽  
Agricultural Resources ◽  
Microbial Responses

The overuse of chemical fertilizers has resulted in the degradation of the physicochemical properties and negative changes in the microbial profiles of agricultural soil. These changes have disequilibrated the balance in agricultural ecology, which has resulted in overloaded land with low fertility and planting obstacles. To protect the agricultural soil from the effects of unsustainable fertilization strategies, experiments of the reduction of nitrogen fertilization at 10, 20, and 30% were implemented. In this study, the bacterial responses to the reduction of nitrogen fertilizer were investigated. The bacterial communities of the fertilizer-reducing treatments (D10F, D20F, and D30F) were different from those of the control group (CK). The alpha diversity was significantly increased in D20F compared to that of the CK. The analysis of beta diversity revealed variation of the bacterial communities between fertilizer-reducing treatments and CK, when the clusters of D10F, D20F, and D30F were separated. Chemical fertilizers played dominant roles in changing the bacterial community of D20F. Meanwhile, pH, soil organic matter, and six enzymes (soil sucrase, catalase, polyphenol oxidase, urease, acid phosphatase, and nitrite reductase) were responsible for the variation of the bacterial communities in fertilizer-reducing treatments. Moreover, four of the top 20 genera (unidentified JG30-KF-AS9, JG30-KF-CM45, Streptomyces, and Elsterales) were considered as key bacteria, which contributed to the variation of bacterial communities between fertilizer-reducing treatments and CK. These findings provide a theoretical basis for a fertilizer-reducing strategy in sustainable agriculture, and potentially contribute to the utilization of agricultural resources through screening plant beneficial bacteria from native low-fertility soil.

scholarly journals Identification of a Phosphorus-Solubilizing Tsukamurella Tyrosinosolvens Strain and its Effect on the Bacterial Diversity of the Rhizosphere Soil of Peanuts Growth-Promoting

2021 ◽  
Author(s):  
Lizhen Han ◽  
Hong Zhang
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Ph Value ◽  
Alpha Diversity ◽  
Significant Negative Correlation ◽  
Potassium Nitrate ◽  
P Solubilization ◽  
Significant Difference ◽  
Growth Promoting ◽  
Phosphate Solubilizing

Abstract Phosphate Solubilizing Microorganisms widely exist in plant rhizosphere soil, but report about the P solubilization and multiple growth-promoting properties of rare actinomycetes are scarce. In this paper, a phosphate solubilizing Tsukamurella tyrosinosolvens P9 strain was isolated from the rhizosphere soil of tea plants. Phosphorus-dissolving abilities of this strain were different under different carbon and nitrogen sources, the soluble phosphorus content was 442.41 mg/L with glucose and potassium nitrate as nutrient sources. The secretion of various organic acids, such as lactic acid, maleic acid, oxalic acid, etc, was the main mechanism for P solubilization and pH value in culture was very significant negative correlation with soluble P content. In addition, this strain had multiple growth-promoting characteristics with 37.26 μg/mL of IAA and 72.01% of siderophore relative content. Under pot experiments, P9 strain improved obviously the growth of peanut seedlings. The bacterial communities of peanut rhizoshpere soil were assessed after inoculated with P9 strain. It showed that there was no significant difference in alpha-diversity indices between the inoculation and control groups, but the P9 treatment group changed the composition of bacterial communities, which increased the relative abundance of beneficial and functional microbes, which relative abundances of Chitinophagaceae and Beijerinckiaceae at the family level, and of Flavihumibacter , Ramlibacter and Microvirga at the genus level, were all siginificant increased. Specially, Tsukamurella tyrosinosolvens were only detected in the rhizosphere of the inoculated group. This study not only founded growth-promoting properties of T . tyrosinosolvens P9 strain and its possible phosphate solublizing mechanism, but also expected to afford an excellent strain resource in biological fertilizers.

scholarly journals Study on the Diversity of Fungal and Bacterial Communities in Continuous Cropping Fields of Chinese Chives (Allium tuberosum)

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Yizhu Gu ◽  
Yuxin Wang ◽  
Pingzhi Wang ◽  
Chaonan Wang ◽  
Jinhai Ma ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Nutrient Content ◽  
Scientific Management ◽  
Continuous Cropping ◽  
Potassium Fertilizer ◽  
Beneficial Bacteria ◽  
Bacterial Phyla ◽  
Chinese Chives

In this study, high-throughput sequencing technology was used to analyse the diversity and composition of fungal and bacterial communities in continuous cropping soil of Chinese chives. The soil nutrient was also measured to explore the rationality of current fertilization management. These results can provide a basis for the prevention and control of the continuous cropping obstacles of Chinese chives and further scientific management. Soil samples from fields continuously cropped with Chinese chives for one year, three years, and five years were collected and analysed. The results showed that the nutrient content of TP, AP, AK and TK increased significantly with increasing continuous cropping years. Short-term continuous cropping soil nutrients have not deteriorated. Alpha-diversity analysis showed that significant differences were not found in the diversity of the fungal and bacterial community among different years. Ascomycota, Basidiomycota and Mortierellomycota were the three most dominant fungal phyla. Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria were the dominant bacterial phyla. Continuous cropping makes Fusarium increase, and the beneficial bacteria Pseudomonas decreased significantly. According to the correlation heat map analysis of environmental factors, excessive phosphorus may lead to the increase of Fusarium, potassium may promote the proliferation of beneficial bacteria in the continuous cropping process, and it is necessary to regulate the application of phosphate and potassium fertilizer.

scholarly journals The Effects of Microbial Inoculants on Bacterial Communities of the Rhizosphere Soil of Maize

Agriculture ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 389
Author(s):  
Minchong Shen ◽  
Jiangang Li ◽  
Yuanhua Dong ◽  
Zhengkun Zhang ◽  
Yu Zhao ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Agricultural Practices ◽  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Diversity Indices ◽  
Microbial Inoculants ◽  
Application Rates ◽  
And Function ◽  
Commercial Inoculants

The bacterial community of rhizosphere soil maintains soil properties, regulates the microbiome, improves productivity, and sustains agriculture. However, the structure and function of bacterial communities have been interrupted or destroyed by unreasonable agricultural practices, especially the excessive use of chemical fertilizers. Microbial inoculants, regarded as harmless, effective, and environmentally friendly amendments, are receiving more attention. Herein, the effects of three microbial inoculants, inoculant M and two commercial inoculants (A and S), on bacterial communities of maize rhizosphere soil under three nitrogen application rates were compared. Bacterial communities treated with the inoculants were different from those of the non-inoculant control. The OTU (operational taxonomic unit) numbers and alpha diversity indices were decreased by three inoculants, except for the application of inoculant M in CF group. Beta diversity showed the different structures of bacterial communities changed by three inoculants compared with control. Furthermore, key phylotypes analyses exhibited the differences of biomarkers between different treatments visually. Overall, inoculant M had shared and unique abilities of regulating bacterial communities compared with the other two inoculants by increasing potentially beneficial bacteria and decreasing the negative. This work provides a theoretical basis for the application of microbial inoculants in sustainable agriculture.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

scholarly journals The change of gut microbiota in MDD patients under SSRIs treatment

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yang Shen ◽  
Xiao Yang ◽  
Gaofei Li ◽  
Jiayu Gao ◽  
Ying Liang
Keyword(s):  
Gut Microbiota ◽  
Maximum Dose ◽  
Antidepressant Treatment ◽  
Intestinal Flora ◽  
Alpha Diversity ◽  
The Other ◽  
Control Group ◽  
Depressed Patients ◽  
Metabolic Functions

AbstractThe alterations in the gut microbiota have been reported to be correlated with the development of depression. The purpose of this study was to investigate the changes of intestinal microbiota in depressed patients after antidepressant treatment. We recruited 30 MDD patients (MDD group) and 30 healthy controls (control group). The MDD group received individualized treatment with escitalopram at a maximum dose of 20 mg/day. After depressive symptoms improved to a HAMD scale score > 50%, a fecal sample was collected again and used as the follow-up group. The differences of gut microbiota between patients and controls, the characteristics of gut microbiota under treatment and the potential differences in metabolic functions were thus investigated. The Firmicutes/Bacteroidetes ratio was significantly different within three groups, and the ratio of follow-up group was significantly lower than those of the other two groups. Alpha diversity was significantly higher in MDD group than those of the other groups, and the alpha diversity was not significantly different between control and follow-up groups. The beta diversity of some patients resembled participants in the control group. The metabolic function of gut microbiota after treatment was still different from that of the control group. This study suggests that the intestinal flora of depressed patients has a tendency to return to normal under escitalopram treatment.

scholarly journals Gut Digestive Function and Microbiome after Correction of Experimental Dysbiosis in Rats by Indigenous Bifidobacteria

2021 ◽  
Vol 9 (3) ◽  
pp. 522
Author(s):  
Lyudmila V. Gromova ◽  
Elena I. Ermolenko ◽  
Anastasiya L. Sepp ◽  
Yulia V. Dmitrieva ◽  
Anna S. Alekseeva ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Digestive Enzymes ◽  
Specific Activity ◽  
Control Group ◽  
Enteropathogenic Escherichia Coli ◽  
Beneficial Bacteria ◽  
Opportunistic Bacteria ◽  
Dyspeptic Symptoms ◽  
Specific Activities ◽  
Impaired Motor Function

In recent years, great interest has arisen in the use of autoprobiotics (indigenous bacteria isolated from the organism and introduced into the same organism after growing). This study aimed to evaluate the effects of indigenous bifidobacteria on intestinal microbiota and digestive enzymes in a rat model of antibiotic-associated dysbiosis. Our results showed that indigenous bifidobacteria (the Bf group) accelerate the disappearance of dyspeptic symptoms in rats and prevent an increase in chyme mass in the upper intestine compared to the group without autoprobiotics (the C1 group), but significantly increase the mass of chyme in the colon compared to the C1 group and the control group (healthy animals). In the Bf group in the gut microbiota, the content of opportunistic bacteria (Proteus spp., enteropathogenic Escherichia coli) decreased, and the content of some beneficial bacteria (Bifidobacterium spp., Dorea spp., Blautia spp., the genus Ruminococcus, Prevotella, Oscillospira) changed compared to the control group. Unlike the C1 group, in the Bf group there was no decrease in the specific activities of maltase and alkaline phosphatase in the mucosa of the upper intestine, but the specific activity of maltase was decreased in the colon chyme compared to the control and C1 groups. In the Bf group, the specific activity of aminopeptidase N was reduced in the duodenum mucosa and the colon chyme compared to the control group. We concluded that indigenous bifidobacteria can protect the microbiota and intestinal digestive enzymes in the intestine from disorders caused by dysbiosis; however, there may be impaired motor function of the colon.

Impacts of cover crops and nitrogen fertilization on agricultural soil fungal and bacterial communities

2021 ◽  
Author(s):  
Sarah C. Castle ◽  
Deborah A. Samac ◽  
Jessica L. Gutknecht ◽  
Michael J. Sadowsky ◽  
Carl J. Rosen ◽  
...  
Keyword(s):  
Cover Crops ◽  
Nitrogen Fertilization ◽  
Bacterial Communities ◽  
Agricultural Soil

scholarly journals Fecal Viral Community Responses to High-Fat Diet in Mice

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Anjelique Schulfer ◽  
Tasha M. Santiago-Rodriguez ◽  
Melissa Ly ◽  
Joshua M. Borin ◽  
Jessica Chopyk ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Fat Diet ◽  
Alpha Diversity ◽  
Diet Shift ◽  
Significant Shift ◽  
Diet Change ◽  
Gi Tract ◽  
High Fat ◽  
Viral Community ◽  
Viral Communities

ABSTRACT Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes. Examining fecal contents of mice as the mice were transitioned from normal chow to HFD, we found significant changes in the relative abundances and the diversity in the gut of bacteria and their viruses. Alpha diversity of the bacterial community was significantly diminished in response to the diet change but did not change significantly in the viral community. However, the diet shift significantly impacted the beta diversity in both the bacterial and viral communities. There was a significant shift away from the relatively abundant Siphoviridae accompanied by increases in bacteriophages from the Microviridae family. The proportion of identified bacteriophage structural genes significantly decreased after the transition to HFD, with a conserved loss of integrase genes in all four experimental groups. In total, this study provides evidence for substantial changes in the intestinal virome disproportionate to bacterial changes, and with alterations in putative viral lifestyles related to chromosomal integration as a result of shift to HFD. IMPORTANCE Prior studies have shown that high-fat diet (HFD) can have profound effects on the gastrointestinal (GI) tract microbiome and also demonstrate that bacteria in the GI tract can affect metabolism and lean/obese phenotypes. We investigated whether the composition of viral communities that also inhabit the GI tract are affected by shifts from normal to HFD. We found significant and reproducible shifts in the content of GI tract viromes after the transition to HFD. The differences observed in virome community membership and their associated gene content suggest that these altered viral communities are populated by viruses that are more virulent toward their host bacteria. Because HFD also are associated with significant shifts in GI tract bacterial communities, we believe that the shifts in the viral community may serve to drive the changes that occur in associated bacterial communities.

scholarly journals Alteration of Bacterial Communities in Anterior Nares and Skin Sites of Patients Undergoing Arthroplasty Surgery: Analysis by 16S rRNA and Staphylococcal-Specific tuf Gene Sequencing

2020 ◽  
Vol 8 (12) ◽  
pp. 1977
Author(s):  
Søren Iversen ◽  
Thor Bech Johannesen ◽  
Anna Cäcilia Ingham ◽  
Sofie Marie Edslev ◽  
Staffan Tevell ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Gene Sequencing ◽  
Alpha Diversity ◽  
Clinical Samples ◽  
Staphylococcal Species ◽  
Tuf Gene ◽  
Staphylococcus Hominis ◽  
The Impact ◽  
Arthroplasty Surgery

The aim was to study alterations of bacterial communities in patients undergoing hip or knee arthroplasty to assess the impact of chlorhexidine gluconate soap decolonisation and systemic antibiotic prophylaxis. A Swedish multicentre, prospective collection of samples obtained from elective arthroplasty patients (n = 83) by swabbing anterior nares, skin sites in the groin and the site of planned surgery, before and after arthroplasty surgery, was analysed by 16S rRNA (V3-V4) gene sequencing and a complementary targeted tuf gene sequencing approach to comprehensively characterise alterations in staphylococcal communities. Significant reductions in alpha diversity was detected for both bacterial (p = 0.04) and staphylococcal (p = 0.03) groin communities after arthroplasty surgery with significant reductions in relative Corynebacterium (p = 0.001) abundance and Staphylococcus hominis (p = 0.01) relative staphylococcal abundance. In nares, significant reductions occurred for Staphylococcus hominis (p = 0.02), Staphylococcus haemolyticus (p = 0.02), and Staphylococcus pasteuri (p = 0.003) relative to other staphylococci. Staphylococcus aureus colonised 35% of anterior nares before and 26% after arthroplasty surgery. Staphylococcus epidermidis was the most abundant staphylococcal species at all sampling sites. No bacterial genus or staphylococcal species increased significantly after arthroplasty surgery. Application of a targeted tuf gene sequencing approach provided auxiliary staphylococcal community profiles and allowed species-level characterisation directly from low biomass clinical samples.

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