Microbial Diversity Analysis Using 16S rRNA Gene Amplicon Sequencing of Rhizosphere Soils from Double-Cropping Rice and Rice-Shrimp Farming Systems in Soc Trang, Vietnam
Ontology highlight
ABSTRACT:
SUBMITTER: Do T
PROVIDER: S-EPMC8567788 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In the history of rice-shrimp farming (RSF) in the Mekong Delta, in saline acid sulfate soils (ASS), RSF has proved its sustainability as there is no long-term accumulation of acidity and salinity that adversely affect RSF production. However, the soil processes involved in this phenomenon are not well understood. This study aimed to determine the significant changes in soil and water chemical indicators associated with soil processes during different stages of RSF. Sampling was conducted in six stages to determine the pH and electrical conductivity (EC) of canal and field water, and the pHe, ECe, and sodium-soluble saturated extract (Na-sol) of surface soil (surS) and subsurface soil (subS) in the low-salinity area (LSA) and high salinity area (HSA) of Bac Lieu province. Putative exchange (exch.) Na+ hydrolysis occurs at the beginning of the rainy season when excess salts are leached. This drastically increases the pH of the field water by 0.6 pH units, from 8.2 to 8.8 in stages 1 to 2, respectively. Putative sulfurization has been shown to occur in subS in both LSAs and HSAs, with a significant decrease of 0.5 pH units from stages 4 to 5, leading to a decrease in the Na-sol of subS through exch. Na+ transformation. Simultaneously, with active soil preparation and liming for RSF, chemical processes such as exch. Na+ hydrolysis, sulfurization, and Na+ transformation are the main factors promoting exch. Na+ desorption, which help to reduce the long-term build-up of salinity and acidity that adversely affect RSF production. Although gypsum is considered an effective material in improving saline soils, in Vietnam, gypsum is the liming material of CaSO4; however, it is not commonly used in agriculture because of its high cost. By using CaCO3 or dolomite as a liming material in saline ASS, the dissolution of lime by sulfuric acid can provide a good opportunity for soil improvement and rice growth in RSF.
| S-EPMC9929475 | biostudies-literature
Project description:Based on a total of 6,295,650 sequences from the V3 and V4 regions (16S ribosomal RNA), the composition of the microorganism communities in the water of three Litopenaeus vannamei (Decapoda, Whiteleg shrimp; Soc Trang, Vietnam) ponds were identified. Pseudomonas (10-20.29%), Methylophilus (13.26-24.28%), and Flavobacterium (2.6-19.29%) were the most abundant genera. The total ammonia (TAN) concentration (p = 0.025) and temperature (p = 0.015) were significantly correlated with the relative abundance of Pseudomonas in two bacterial communities (ST1, ST4), whereas the predictive functions of microorganism communities based on 16S rRNA gene data was estimated using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST), which showed that nitrogen metabolism was significantly negatively correlated (p = 0.049) with TAN concentration. The abundance of Pseudomonas and nitrogen metabolism increased with a decrease in TAN concentration. The correlation between TAN concentration and the abundance of Pseudomonas was followed by the isolation, and heterotrophic nitrifying performance analysis was used to confirm our findings. Six Pseudomonas strains capable of heterotrophic nitrification were isolated from the three water samples and showed a complete reduction of 100 mg/L NH4Cl during a 96-h cultivation. These results indicate the potential of applying Pseudomonas in shrimp ponds for water treatment.
| S-EPMC6616971 | biostudies-literature
Project description:Data on the 16S rRNA gene amplicon sequences from Pteris vittata rhizosphere soils are reported. The following phyla were recorded in arsenic-rich soils: Actinobacteria (59%), Proteobacteria (26%), Chloroflexi (17%), and Acidobacteria (9%). Actinobacteria (45%), Proteobacteria (22%), Chloroflexi (10%), and Acidobacteria (11%) were in natural-mineral soils.
| S-EPMC10019286 | biostudies-literature
Project description:Background: Generally, the yield of ratoon rice is at most 50% of the main crop. However, a cropping method "SALIBU" achieved more yield than the main crop and enables the perennial cropping. Although the SALIBU method is implementing 10 additional management practices to conventional method in Indonesia, the effect of each management practice is unclear. Methodology: We evaluated the effect size using an L 16 orthogonal array design pot experiment in triple-cropping rice in Vietnam. The robustness was checked by duplicating the experiment under standard and poor conditions. Results and Discussion: Positive large effects were shown in the poor conditions only. Cutting twice most affected the number of ratoon tillers. Importantly, the effect was positive under poor conditions but negative under standard conditions. Late irrigation had a robust negative effect. No treatment is effective in the triple-cropping of standard conditions. The SALIBU includes practices with unstable, negative, or minimal effects. The unstable effects show the interaction with the condition. The practices that have negative effects should exclude. Using practice on small effect size should depend on a cost-benefit analysis. Conclusions: No additional practice is effective for changing the triple-cropping to perennial ratoon cropping except harvesting near the ground. However, further work will be conducted to clarify the interaction between cutting twice and the cultivation condition.
| S-EPMC7542297 | biostudies-literature
Project description:Sponge microbiomes Vietnam (Nha Trang) Raw sequence reads
| PRJNA453898 | ENA
Project description:Vietnam is endemic for dengue. We conducted a series of retrospective and prospective studies to characterize the epidemiology of dengue and population mobility patterns in Nha Trang city, Vietnam, with a view to rational design of trials of community-level interventions. A 10-year time series of dengue case notifications showed pronounced interannual variability, as well as spatial heterogeneity in ward-level dengue incidence (median annual coefficient of variation k = 0.47). Of 451 children aged 1-10 years enrolled in a cross-sectional serosurvey, almost one-third had evidence of a past dengue virus (DENV) infection, with older children more likely to have a multitypic response indicative of past exposure to ≥ 1 serotype. All four DENV serotypes were detected in hospitalized patients during 8 months of sampling in 2015. Mobility data collected from 1,000 children and young adults via prospective travel diaries showed that, although all ages spent approximately half of their daytime hours (5:00 am-9:00 pm) at home, younger age groups (≤ 14 years) spent a significantly greater proportion of their time within 500 m of home than older respondents. Together these findings inform the rational design of future trials of dengue preventive interventions in this setting by identifying 1) children < 7 years as an optimal target group for a flavivirus-naive serological cohort, 2) children and young adults as the predominant patient population for a study with a clinical end point of symptomatic dengue, and 3) substantial spatial and temporal variations in DENV transmission, with a consequent requirement for a trial to be large enough and of long enough duration to overcome this heterogeneity.
| S-EPMC5929208 | biostudies-literature
Project description:We used wheat as rotational crop to assess the influence of continuous cropping on microbiome in Pinellia ternata rhizosphere and the remediation of rotational cropping to the impacted microbiota. Illumina high-throughput sequencing technology was utilized for this method to explore the rhizosphere microbial structure and diversity based on continuous and rotational cropping.
2016-12-10 | GSE91083 | GEO
Project description:Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production.
| S-EPMC3896389 | biostudies-literature
Project description:Arecanut (Areca catechu L.) is an important plantation crop cultivated predominantly in the Indian states of Karnataka, Kerala, Assam, West Bengal, and Maharashtra in an area of 5.19 lakh ha, with Karnataka State alone accounting for about 68.41% of the area and 79.97% of production. Arecanut production has recently been hampered due to environmental and disease pressures, especially the escalating incidence of Yellow Leaf Disease (YLD). The involvement of phytoplasma as the etiological agent of YLD has been reported. Symptoms include yellowing at the tip of leaflets of two or three fronds of the outer most whorl which gradually spreads to the inner whorl of leaves. As the disease progresses, the entire crown becomes yellow leaving only the spear leaf green. In severe cases, the affected leaves often show necrosis from their tips. In advanced stages, the leaves are reduced in size and become stiff and pointed and the crown ultimately falls off. Degeneration of cortex is commonly observed in the diseased roots. The kernel of affected nuts shows discolouration and later turns blackish. The reduction in yield over a period of three years, immediately after the incidence of the disease, has been estimated to be around 50%. Harnessing the arecanut-microbiome interactions to address the biotic and abiotic stresses of the host plant offers immense opportunity to increase arecanut production sustainably. Here, we report a comprehensive analysis of the structural composition of the arecanut rhizosphere bacterial diversity utilizing next-generation sequencing (NGS) technology. We have used amplicon sequencing (V3-V4 regions of the 16S rRNA gene) of bulk soil and rhizosphere samples collected from YLD endemic regions of Aranthodu, Sullia Taluk, Dakshina Kannada District, Karnataka State, India, to assess the microbial diversity. The results revealed that while there is a great diversity of bacterial communities, relatively few bacterial phyla predominate with higher relative abundance. The phyla viz., Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria, Planctomycetes, Patescibacteria, Chloroflexi, Actinobacteria, Fusobacteria, and Verrucomicrobia were found to be dominant in the rhizosphere of the arecanut.
| S-EPMC8551408 | biostudies-literature
Project description:Long-term continuous cropping influences the nutrient of soil and microbiome of the rhizosphere, resulting in the yield decrease of crops. Tibetan barley is a dominant cereal crop cultivated at high altitudes in Tibet. Its growth and yield are negatively affected by continuous cropping; however, the response of the rhizosphere microbial community to continuous cropping remains poorly understood. To address this question, we investigated the bacterial community structure and conducted predictive functional profiling on rhizosphere soil from Tibetan barley monocropped for 2-6 years. The results revealed that long-term continuous cropping markedly decreased total nitrogen and available nitrogen in rhizosphere soil. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community was altered by continuous cropping; operational taxonomic units (OTUs), Shannon index, and Faith Phylogenetic Diversity decreased with increasing monocropping duration. Relative abundances of family Pseudomonadaceae, Cytophagaceae, and Nocardioidaceae were significantly increased, while those of Chitinophagaceae and Sphingomonadaceae were significantly decreased (all p < 0.05). Besides, continuous cropping significantly increased the abundance of bacteria associated with chemoheterotrophy, aromatic compound degradation, and nitrate reduction (p < 0.05). Generalized boosted regression model analysis indicated that total nitrogen was the most important contributor to the bacterial community diversity, indicating their roles in shaping the rhizosphere bacterial community during continuous cropping. Overall, continuous cropping had a significant impact on the structure of bacterial communities in rhizosphere soil of Tibetan barley, and these results will improve our understanding of soil bacterial community regulation and soil health maintenance in Tibetan barley farm systems.
| S-EPMC7734106 | biostudies-literature