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
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ABSTRACT:
SUBMITTER: Do T
PROVIDER: S-EPMC8567788 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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.
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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.
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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:BackgroundThe microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants.ResultsThe results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different.ConclusionHere, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.
| S-EPMC9840269 | 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:This study makes an ecological economic comparison between three different rice farming strategies in the Mekong Delta. Interviews were made with 30 farmers with two crops of rice and low dikes (2RLd), 30 farmers with three crops of rice and high dikes (3RHd) and 18 farmers with two crops of rice and one crop of fish (2RF). 2RF farmers had the highest annual net income and benefit cost ratio, because of low production costs and high yields of rice and fish. 2RLd farmers had the lowest annual net income. 3RHd had the highest annual rice yield, but also used the highest amount of rice seeds and agrochemicals, generating the lowest benefit cost ratio. Most farmers (70%) preferred two crops because of a higher production efficiency. High dikes and frequent use of pesticides and fertilizers were seen to decrease the water and rice quality, connectivity and biodiversity in farms with three crops. It is concluded that rice farming with two crops, and especially if integrated with fish and applying IPM, provides a sustainable alternative to rice farming with three crops and high dikes, because it makes use of the high connectivity within the rice-field ecosystem for an efficient production of healthy food through increased recycling of nutrients and natural pest control mechanisms.
| S-EPMC10406997 | biostudies-literature
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.
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