Agronomy

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14 pages, 1130 KiB

Open AccessFeature PaperArticle

Temporal Assessment of Biofumigation Using Mustard and Oilseed Rape Tissues on Verticillium dahliae, Soil Microbiome and Yield of Eggplant

by Lingbo Meng, Yuhang Zhang, Shaopeng Yu, Abiola O. Ogundeji, Shu Zhang and Shumin Li

Agronomy 2022, 12(12), 2963; https://doi.org/10.3390/agronomy12122963 - 25 Nov 2022

Cited by 1 | Viewed by 1675

Abstract

Verticillium dahliae is a soil-borne pathogen that is difficult to eliminate, causes a severe reduction in the yield and quality of eggplant, and could be controlled through environmentally friendly biofumigation. However, the mechanisms of its effects on the dynamic changes of soil microbes [...] Read more.

Verticillium dahliae is a soil-borne pathogen that is difficult to eliminate, causes a severe reduction in the yield and quality of eggplant, and could be controlled through environmentally friendly biofumigation. However, the mechanisms of its effects on the dynamic changes of soil microbes is not clear. In this study, we examined the efficacy of two Brassica vegetables, mustard (Brassica napiformis, BFN) and oilseed rape (Brassica napus, BFC), as biofumigants to control Verticillium dahliae and observed their effects on the soil microbial community compared with chemical fumigants (CF) and a control (CN) in a greenhouse where eggplant was continuously cultivated for 12 years. Illumina MiSeq sequencing was used to analyse the soil microbiome. Real-time PCR was used to assay in order to estimate the soil abundance of Verticillium dahlia, and the glucosinolate concentration in biofumigants was determined using HPLC. Results showed that the BFN treatment had a significant biocidal effect on V. dahliae in the soil, decreasing its abundance by 64.74% compared to the control (CN). No significant difference was observed between BFC and CN treatments. Yield in the BFN treatment improved due to a lower disease incidence rate and disease index. Biofumigation had significant effects on the community structure and abundance of bacteria and fungi. The bacterial diversity of the BFN treatment was significantly lower than those of the other treatments, and beneficial bacterial community relative abundance, such as Flavobacteria, Pseudomonas and Bacillus, increased after the soil was biofumigated for 15 days. However, the temporal difference in bacterial and fungi structure among the different treatments was reduced with the development of the eggplant growth stage. The Mortierella, Altemaria and Chaetomium genera were significantly abundant across all treatments. Soil enzyme activities were also improved. In summary, biofumigation using mustard was efficient in controlling eggplant Verticillium wilt due to changes in the soil bacterial composition at the early eggplant growth stage; the initial conditions in the soil bacterial community are a key determinant of what is going to happen after Brassica biofumigation, which could be considered a practical addition to integrated pest management for the reduction of soil-borne pathogens. Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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17 pages, 4657 KiB

Open AccessArticle

Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt

by Mohamed Hassan Korkar, Mahmoud Magdy, Samah Mohamed Rizk, Yosur Gamal Fiteha, Aiman Hanafy Atta and Mohamed Abdel-Salam Rashed

Agronomy 2022, 12(10), 2543; https://doi.org/10.3390/agronomy12102543 - 18 Oct 2022

Cited by 7 | Viewed by 2631

Abstract

Plants especially in their natural habitat are considered part of a rich ecosystem that includes many various microorganisms in the soil. The current study aimed to identify the bacterial profile of agriculture-related soil samples using the metabarcoding technique to compare and explore relevant [...] Read more.

Plants especially in their natural habitat are considered part of a rich ecosystem that includes many various microorganisms in the soil. The current study aimed to identify the bacterial profile of agriculture-related soil samples using the metabarcoding technique to compare and explore relevant rhizosphere bacteria associated with plant cultivations in newly reclaimed land and habitual cultivated ones. The total environmental DNA was extracted from rhizosphere and noncultivated samples derived from three land types in Egypt. The bacterial 16S rDNA was amplified and sequenced by NGS technology to profile each sample. The microbial profile was characterized by statistical and literature-based methods. Among all samples, the most identified phyla were Actinobacteriota (28%), followed by Proteobacteriota (26%), Firmicutes (14%), Acidobacteriota and Chloroflexi (7%), Gemmatimonadota (5%), Bacteriodota and Crenarchaeota (3%), and Myxococcota (2%), in addition to 37 other phyla with <1% counts. A total of 74 OTUs were unique to the plant rhizosphere area and classified as Bacteriodota (5.1%:0.3%), Firmicutes (2.4%:0.1%), and Proteobacteria (3.5%:2%) phyla in agricultural and reclaimed lands, respectively. Moreover, the rhizosphere profile included a large portion of uncultured and unidentified bacterial species, which opened a window to further analysis. Our analysis provides a key knowledge about the rhizosphere microbiome and highlights its possible use to create microbial-based biofertilizers targeting plant performance in contrast to traditional fertilizers and their side effect on the agriculture sector. Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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14 pages, 2108 KiB

Open AccessArticle

Effects of Ionized Water Addition on Soil Nitrification Activity and Nitrifier Community Structure

by Zhi Qu, Mingjiang Li, Quanjiu Wang, Yan Sun, Yichen Wang and Jian Li

Agronomy 2022, 12(6), 1399; https://doi.org/10.3390/agronomy12061399 - 10 Jun 2022

Cited by 2 | Viewed by 2077

Abstract

Water ionization is an efficient physical water treatment technology, and crop water and nutrient use efficiencies can be improved using ionized water for irrigation. In order to explore the effect of ionized water on soil nitrification and nitrifying microorganisms, we conducted a laboratory [...] Read more.

Water ionization is an efficient physical water treatment technology, and crop water and nutrient use efficiencies can be improved using ionized water for irrigation. In order to explore the effect of ionized water on soil nitrification and nitrifying microorganisms, we conducted a laboratory soil incubation experiment with the addition of ionized water and ordinary water under different soil water contents (equal to 30%, 60%, 100% and 175% of the field capacity, θ_FC). During the soil incubation, we analyzed soil inorganic nitrogen transformation, ammonia oxidation gene abundances and nitrifying microbial community structure. The results showed that, no matter adding ordinary water or ionized water, the soil nitrification rate and the abundance of ammonia oxidizing bacteria in the 100%θ_FC treatment were significantly higher than those in other water conditions, while the abundance of ammonia oxidizing archaea was not affected by the soil water content. With the same soil water content, the nitrification rate of ionized water treatment was stronger than that of the ordinary water treatment. Although the absolute abundance of ammonia-oxidizing microorganisms in ionized water treatment was significantly lower than that of ordinary water (p < 0.05), the relative abundance of some dominant nitrifying microbial genera in the ionized water treatment was significantly higher (p < 0.05). The dominant genera may play a key role in the nitrification process. The results show that ionized water irrigation can significantly promote the nitrification of silt loam soil, especially under 100%θ_FC conditions, and may regulate soil nitrification by affecting some dominant nitrifying microorganisms. This study provides a theoretical basis for understanding the biological regulation mechanism of ionized water irrigation on soil nutrient transformation and for application of ionized water to field irrigation. Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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14 pages, 2001 KiB

Open AccessArticle

Temporal Response of Bacterial Community Associated Fe(III) Reduction to Initial pH Shift of Paddy Soils

by Rong Jia, Fangmei Fan, Lina Li and Dong Qu

Agronomy 2022, 12(6), 1304; https://doi.org/10.3390/agronomy12061304 - 29 May 2022

Cited by 1 | Viewed by 1763

Abstract

The temporal response of bacterial community, especially that of bacteria with Fe(III) reducing ability, in flooded paddy soils to initial pH changes, is not well-documented. This work demonstrated variations in concentration of Fe species, bacterial activity and community succession in paddy soils with [...] Read more.

The temporal response of bacterial community, especially that of bacteria with Fe(III) reducing ability, in flooded paddy soils to initial pH changes, is not well-documented. This work demonstrated variations in concentration of Fe species, bacterial activity and community succession in paddy soils with initial pH shift to acidic or alkaline level. The causal links of pH shift-induced bacterial community succession with Fe(III) reduction was also assessed. Results showed that soil initial pH shifts greatly influenced bacterial community and Fe(III) reduction. A soil pH shift from acidic to alkaline level enhanced bacterial abundance and dehydrogenase activity (DHA), which accordingly caused an increase in Fe(III) reducing ratio by 22.26% on day One of flooding. The stimulated putative Fe(III) reducing species, Bacillus and Solibacillus, caused stimulation of Fe(III) reduction with pH increase. However, there was continuous inhibition of Fe(III) reduction with a pH shift from alkaline to acidic, with Fe(III) reducing ratios decreased by 11.98–40.04%. The inhibited DHA and Fe(III) reducing bacteria were amenable for the suspension of Fe(III) reduction. This study suggests that bacterial activity and Fe(III) concentration, in responses to initial soil pH shift, are primarily responsible for pH shift-induced Fe(III) reduction in paddy soils. Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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25 pages, 7484 KiB

Open AccessArticle

Spatiotemporal Characteristics of Dryness/Wetness in the Wine Regions of China from 1981 to 2015

by Xiaojuan Yang, Ning Yao, Wei Hu, Xingjie Ji, Qingzu Luan, Yuan Liu, Wei Bai, Di Chen and Buchun Liu

Agronomy 2022, 12(4), 843; https://doi.org/10.3390/agronomy12040843 - 29 Mar 2022

Cited by 2 | Viewed by 2103

Abstract

China has a marked continental monsoon climate characterized by dry and wet hazards that have destructive impacts on grape yields and quality. The purpose of this study was to analyze the spatiotemporal characteristics of dryness/wetness in the wine regions of China and explore [...] Read more.

China has a marked continental monsoon climate characterized by dry and wet hazards that have destructive impacts on grape yields and quality. The purpose of this study was to analyze the spatiotemporal characteristics of dryness/wetness in the wine regions of China and explore the links between these variations and large-scale climatic factors. The crop-specific standardized precipitation evapotranspiration index (SPEI) was used to characterize the dryness/wetness using meteorological data collected at 168 meteorological stations located in or near the wine regions from 1981–2015. Results showed that most wine regions of China experienced a wetting trend. The drought and wet event characteristics were region- and site-specific. The main wine regions of China (e.g., Xinjiang, Helan Mountain and Hexi Corridor) were characterized by relatively high drought severity; the extreme drought frequencies of the three regions were higher as well (11.5%, 3.3%, and 3.6%, respectively). Xinjiang was also characterized by a high wetness severity and an extremely high wetness frequency of 16%, but the wetness severity decreased over time. A 4–6-year periodical oscillation was commonly detected over the wine regions. The dryness/wetness characteristics were highly associated with the Southern Oscillation Index, Niño 3.4 and the Indian Ocean Dipole, with highest correlation coefficients of −0.40, 0.36 and 0.43 at lag times of 11, 8, and 11 months, respectively. The serious dry and wet events that occurred in 2001 and 1998, respectively, were speculated to be associated with anomalous atmospheric circulation patterns. These results can be used to inform grapevine stakeholders at various levels (e.g., farmer and industry) for developing strategies to mitigate and adapt dryness/wetness events in the wine regions of China. It is expected that the approach proposed in this study can also be applicable to wine regions of other countries. Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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15 pages, 3414 KiB

Open AccessArticle

Differing Roles of Bacterial and Fungal Communities in Cotton Fields by Growth Stage

by Dongwei Li, Yuhui Yang, Yulong Zhao, Guangli Tian, Mingsi Li, Husen Qiu and Xinguo Zhou

Agronomy 2022, 12(3), 657; https://doi.org/10.3390/agronomy12030657 - 9 Mar 2022

Cited by 3 | Viewed by 2116

Abstract

The global demand for cotton makes sustainable cotton production an important issue that can be improved by a better understanding of the influence of soil microbes on cotton growth. We collected cotton field soils at the seedling and flowering/boll-setting (FBS) stages in order [...] Read more.

The global demand for cotton makes sustainable cotton production an important issue that can be improved by a better understanding of the influence of soil microbes on cotton growth. We collected cotton field soils at the seedling and flowering/boll-setting (FBS) stages in order to obtain soil properties and cotton growth indices. Bacterial and fungal community compositions were assessed by high-throughput sequencing of 16S rRNA and internal transcribed spacer genes, respectively, after which the differences in microbial functions and their influencing factors at different growth stages were analyzed. Both the diversity and composition of soil bacterial and fungal communities were found to be significantly different between the seedling and FBS stages. Microbes in the seedling stage had significantly higher richness and biomass than those in the FBS stage. Compared with the seedling stage, the stability of the soil bacterial communities was decreased. The cotton growth indices at both the seedling and FBS stages were associated with compositional shifts in the bacterial community and but not the fungal community. The abundance of specific soil microbial taxa (e.g., Pseudarthrobacter, Thiobacillus, Cephalotrichum, Chaetomium, and Fusarium) were correlated with cotton growth indices at the seedling stage, being mainly regulated by soil salinity and nitrate content. Our results highlight the importance of soil microbial communities in mediating cotton growth and will be useful in providing better strategies for the improvement of cotton agriculture. Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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16 pages, 16784 KiB

Open AccessArticle

Impacts of Litter Composition on the Structure and Functional Pathways of Soil Microbial Community during Phyllostachys Edulis Expansion

by Huiyun Dong, Shuai Shao, Chenfei Liang, Qiufang Xu, Junhui Chen and Hua Qin

Agronomy 2022, 12(1), 220; https://doi.org/10.3390/agronomy12010220 - 17 Jan 2022

Cited by 4 | Viewed by 2693

Abstract

Forest ecosystem succession plays an important role in soil microbiota variation, and soil microbes will re-establish ecosystem function after disturbance events. A distinctive disturbance of the expansion of bamboo forest into the surrounding broadleaved ecosystem is the change in litter type input. We [...] Read more.

Forest ecosystem succession plays an important role in soil microbiota variation, and soil microbes will re-establish ecosystem function after disturbance events. A distinctive disturbance of the expansion of bamboo forest into the surrounding broadleaved ecosystem is the change in litter type input. We conducted a 6-month microcosm experiment to examine the effects of proportional changes in leaf litter composition due to moso bamboo (Phyllostachys edulis) invasion into a broadleaved forest on soil microbial community. A series of mixed litters were prepared with bamboo litter occupying at 0%, 33%, 50%, 67% and 100% in proportion (with a decrease in litter carbon (C)/nitrogen (N) from 36.23 to 31.35), and they were then amended into a broadleaved forest soil at a rate of 1%, respectively. Soil bacterial and fungal communities at different incubation stages were determined by high-throughput sequencing. With the increasing proportion of bamboo litter, the broadleaved forest soil exhibited strong changes in microbiome assembly, including reducing bacteria alpha-diversity, the relative abundance of Acidobacteria and Basidiomycota, while increasing the relative abundance of Actinbacteria, Proteobacteria and Ascomycota. Moreover, the increased proportion of bamboo litter (0% PP→100% PP) increased the relative abundance of membrane transport and carbohydrate metabolism of soil bacteria but decreased the relative abundance of saprotrophic soil fungi. Redundancy analysis showed that bacteria rather than fungal communities changed greatly during incubation (p < 0.05). Additionally, the activities of soil pH, NO₃⁻-N, NH₄⁺-N, dissolved nitrogen and C- and N- acquiring enzymes were the main factors affecting bacterial and fungal community structure (p < 0.05). The soil physicochemical properties were significantly correlated with the composition of microbial phyla among different litter amendment treatments. These results indicated that different proportions of bamboo litter dramatically alter the soil bacterial rather than the fungal community, most likely by changing edaphic patterns. This study has important implications for understanding the litter–soil–microbe synergy during the bamboo forest expansion and provides a basis for assessing the ecological risk of bamboo forest expansion. Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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22 pages, 7087 KiB

Open AccessArticle

Understanding the Responses of Soil Bacterial Communities to Long-Term Fertilization Regimes Using DNA and RNA Sequencing

by Juan Li, Yanchen Wen and Xiangdong Yang

Agronomy 2021, 11(12), 2425; https://doi.org/10.3390/agronomy11122425 - 28 Nov 2021

Cited by 4 | Viewed by 2159

Abstract

Studies of soil DNA-based and RNA-based bacterial communities under contrasting long-term fertilization regimes can provide valuable insights into how agricultural management affects soil microbial structure and functional diversity. In this study, soil bacterial communities subjected to six fertility treatments in an alkaline soil [...] Read more.

Studies of soil DNA-based and RNA-based bacterial communities under contrasting long-term fertilization regimes can provide valuable insights into how agricultural management affects soil microbial structure and functional diversity. In this study, soil bacterial communities subjected to six fertility treatments in an alkaline soil over 27 years were investigated by 454 pyrosequencing based on 16S rDNA and 16S rRNA. Long-term fertilization showed significant influences on the diversity of the soil DNA-based bacteria, as well as on their RNA-based members. The top five phyla (Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, and Planctomycetes) were found in both the DNA- and RNA-based samples. However, the relative abundances of these phyla at both DNA and RNA levels were showed significantly different. Analysis results showed that the diversity of the 16S rRNA samples was consistently lower than that of the rDNA samples, however, 16S rRNA samples had higher relative abundance. PICRUSt analysis indicated that glycan biosynthesis and metabolism were detected mainly in the DNA samples, while metabolism and degradation of xenobiotics and the metabolism of amino acids, terpenoids and polyketides were relatively higher in the RNA samples. Bacilli were significantly more abundant in all the OM-fertilized soils. Redundancy analysis indicated that the relative abundances of both DNA- and RNA-based bacterial groups were correlated with soil total organic carbon content, nitrogen content, Olsen-P, and soil pH. Moreover, the RNA-based Bacilli were positively correlated with available phosphorus (Olsen-P). Full article

(This article belongs to the Special Issue Soil Microbiome and Agriculture Management)

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