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Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility.

The effect of plant invasion on soil microbial communities in various ecosystems has increasingly become the focus of research over the last decade. Moso bamboo (Phyllostachys edulis) invasion of native forests in Tianmushan National Nature Reserve located in southeastern China has resulted in greatly decreased biodiversity of plants and birds. We combined three different microbial community techniques (Biolog, cellular fatty acids, and 16S-PCR–DGGE) to examine whether changes in the overstory of plant taxa, or any associated environmental changes, modified soil microbial communities. Three types of forests were examined: mono-bamboo forest, mixed forest of bamboo and broadleaf, and native broadleaf forest. The fatty acid and DGGE results showed that bamboo invasion of the native forest influenced soil community structure and increased microbial biomass and taxonomic diversity despite decreased plant diversity. The Biolog results indicated no change in microbial functional diversity as a result of bamboo invasion. Evidence from bacterial PCR–DGGE suggested that bamboo stimulated the growth of otherwise undetected soil bacterial species. Overall, the results indicate that bamboo invasion may significantly affect associated soil microbial communities.

The effects of different contents of biochar and vermicompost on the microbial and enzymatic activities of greenhouse soil were determined to provide a theoretical basis for improving the quality of greenhouse soil. The experiment was conducted in a greenhouse using potted tomatoes. Five treatments consisted of different amount ratios of organic amendments: 1% biochar (BC1), 3% biochar (BC3), 5% biochar (BC5), 3% vermicompost (VC3), and 5% vermicompost (VC5), with no addition of organic amendments as the control (CK). Compared with CK, the pH, organic matter content, and DOC concentration increased in treatment groups. The organic matter content of BC3 and BC5 significantly increased by 54.6% and 72.8%, respectively, and DOC concentration of BC3 significantly increased by 43.9%. Biochar and vermicompost significantly increased the diversity of bacterial and fungal communities in soil, as well as the abundance of Actinomycetes, Acidobacteria, Ascomycetes, and Aspergillus, and reduced the abundance of Aspergillus. The activities of urease and alkaline phosphatase were significantly increased, and the activity of nitrate reductase was inhibited in all treatment groups compared with CK. In addition, a highly significant positive correlation was observed among pH, Acidobacteria phylum abundance, and alkaline phosphatase activity in all treatments. DOC concentration was positively correlated with pH, organic matter content, Acidobacteria phylum abundance and alkaline phosphatase activity. Biochar and vermicompost were effective in improving the physicochemical properties of greenhouse soil, enhancing microbial diversity, and affecting enzymatic activities. Therefore, BC3 (3% biochar) had the most significant effect on community diversity and alkaline phosphatase and nitrate reductase activities. VC5 (5% vermicompost) had the best promotion effect on urease activity. This study highlights that biochar and vermicompost as organic amendments are recommended to improve the quality of greenhouse soils.

Biochar, a late-model environmental functional material, has been widely applied in environmental remediation, agricultural production, and energy utilization due to its excellent characteristics such as porosity and high specific surface area. In recent years, many studies on the effects of biochar on agricultural soil and crop quality have been performed. The application of biochar can influence soil microbial status directly or indirectly by changing the physicochemical properties of soil. Apart from increasing soil pH, biochar can also increase soil organic matter and nutrient elements, which ultimately affect crop yield and quality. This review summarizes and overviews the recent research advances on the influence of biochar application on soil microbial community diversity, microbial ecological functions, soil enzymes and their functional genes, and on crop quality and yield from the perspective of soil microorganisms. This review provides guidance and references for further research into biochar applications.

Diesel is frequently encountered in coastal ecosystems due to land run-off from road surfaces. The current study investigates how partially weathered diesel at environmentally relevant concentrations, as may be seen during a run-off event, affect coastal microbial communities. A mesocosm experiment using seawater from the Bedford Basin, Nova Scotia, was followed for 72 h after the addition of partially weathered diesel. Sequencing data suggests partially weathered diesel acts quickly to alter the prokaryotic community, as both opportunistic (Vibrio and Lentibacter) and oil-degrading (Colwellia, Sulfitobacter, and Pseudoalteromonas) bacteria proliferated after 24 h in comparison to the control. In addition, total prokaryotes seemed to recover in abundance after 24 h, where eukaryotes only ceased to decrease slightly at 72 h, likely because of an inability to adapt to the oil-laden conditions, unlike the prokaryotes. Considering there were no highly volatile components (benzene, toluene, ethylbenzene, and xylene) present in the diesel when the communities were exposed, the results indicate that even a relatively small concentration of diesel run-off can cause a drastic change to the microbial community under low energy conditions. Higher energy conditions due to wave action may mitigate the response of the microbial communities by dilution and additional weathering of the diesel.

High-throughput sequencing of the 16 S rRNA gene of bacteria and the 18 S rRNA gene of fungi was employed to characterize the compositional diversity of the rhizosphere microbial community in cucumbers ( Cucumis sativus L.), bitter gourds ( Momordica charantia L.), and eggplants ( Solanum melongena L.) with or without asparagus straw return. Asparagus straw return caused significant changes in the bacterial and fungal community composition and abundance of the three vegetables. The dominant bacterial phyla in all the treatments were primarily Actinobacteria , Firmicutes , Gemmatimonadetes , Bacteroidetes , Chloroflexi , Acidobacteria , and Proteobacteria. The dominant fungal phyla were Ciliophora , Ascomycota , and Basidiomycota. The relative abundance of the bacterial phylum Actinobacteria was greater in HG1, KG1, and QZ1 and decreased by approximately 20% with asparagus straw return, whereas that of Firmicutes was greater in the two treatments to which asparagus straw was added to all three vegetable soils, which were nearly 20–30 times greater than those in HG1, KG1, and QZ1. Asparagus straw return was a crucial factor in the formation of clusters according to the dominant OTUs. Asparagus straw return increased the bacterial diversity in the rhizosphere of eggplants. Special beneficial functional microbes, such as some Paenibacillus and Cephaliophora_tropica for cucumbers and Lysinibacillus and Ramlibacter for eggplants, are affected by certain vegetables. Moreover, the vigour of eggplants treated with asparagus straw return was greater than that of the other vegetables. The fresh weights increased at straw rates of 15 g/kg and 25 g/kg in eggplants (QZ2 and QZ3), with the greatest percentage reaching approximately 200%. Thus, eggplants might be considered a better option for planting after asparagus straw application in the field. Straw return was the main factor affecting rhizosphere microorganisms but it also affected plant species in the soil microbial community, which could allow us to understand the use of straw return.

Purpose Microorganisms are important in tobacco aging. These are used to improve the quality of tobacco leaves after threshing and redrying. However, the response of microbial community to the storage environment and time during the tobacco aging process has been less explored. This study aimed to characterize the dynamic changes in microbial community composition and diversity in tobacco leaf samples. Methods In this study, 16S and ITS rRNA gene amplicon sequencing techniques were used to characterize the composition, diversity, and co-occurrence of the microbial community in tobacco leaves stored in two different cities during the 24-month aging. Furthermore, the activities of several enzymes were measured spectrophotometrically, and the correlation between the microbiota and enzyme activity was analyzed by network analysis. Results Shannon diversity and Chao richness of bacterial communities gradually increased during the first 18 months, whereas those of the fungal community decreased. The relative abundance of Proteobacteria decreased, whereas that of Actinobacteria and Bacteroidetes increased. The proportion of Ascomycota gradually increased during the first 18 months and then rapidly decreased, whereas the proportion of Basidiomycota exhibited a completely opposite pattern. The change in the composition of bacterial community and dominant genera in leaves was not significant between Guiyang city and Maotai city storerooms, but that in the fungal community was significant. The network analysis revealed that fungal networks were more complex and compact than bacterial networks, and a strong negative correlation existed between bacteria and fungi. Moreover, the bacterial microbiome showed a strong positive association with amylase activity, while the fungal microbiome positively correlated with cellulase activity. Conclusions This study demonstrated a significant spatiotemporal heterogeneity in the composition of the microbial community during tobacco aging and highlighted the possible influence of the interactions and enzyme activity on microbial diversity and composition. The findings provided a scientific basis for using microorganisms to regulate and control tobacco aging.

Heavy metal contamination is among the most prominent environmental problems in China, posing serious threats to both ecosystem and human health. Among the diverse heavy metal contaminants, cadmium is the most serious. The whitefly Bemisia tabaci is a cosmopolitan pest capable of causing severe damage to a broad range of agricultural crops, especially vegetables. At present, little is known about the effects of cadmium stress on B. tabaci, including on its bacterial and fungal communities. In the current study, we investigated the effects of cadmium on bacterial and fungal communities in whiteflies. Meta-barcode sequencing of the 16S rRNA gene revealed that the whitefly bacterial community contained 264 operational taxonomic units (OTUs) belonging to 201 known genera and 245 known species. The top five most frequent bacterial genera were Rickettsia, Rhodococcus, Candidatus Portiera, Candidatus Hamiltonella, and Achromobacter. Meta-barcode sequencing of the fungal ITS locus revealed that the whitefly fungal community contained 357 OTUs belonging to 187 known genera and 248 known species. The top five most frequent fungal genera were Wallemia, unclassified_f_Dipodascaceae, Apiotrichum, Penicillium, and unclassified_o_Saccharomycetales. Cadmium exposure reduced the fungal OTU richness but increased the bacterial Shannon and Simpson diversity indices in whiteflies. In addition, upon exposure to cadmium, the microbial community composition in whiteflies changed significantly, with increased prevalence of the bacterial genera Rhodococcus and Exiguobacterium and fungal genus Wallemia. Our results indicate that the whitefly microbiota likely contributed to their adaptation and resistance to cadmium and suggested that whiteflies may contain microbes that could help remediate cadmium contamination in natural environments and agricultural fields.

Due to its high efficacy as a wide-spectrum disinfectant and its potential for the degradation of pollutants and pesticides, ozone has broad application prospects in agricultural production. In this study, micro/nano bubble technology was applied to achieve a saturation state of bubble nutrient solution, including micro-nano oxygen (O 2 group) and micro-nano ozone (O 3 group) bubble nutrient solutions. The effects of these solutions on lettuce physiological indices as well as changes in the microbial community within the rhizosphere substrate were studied. The application of micro/nano (O 2 and O 3 ) bubble nutrient solutions to substrate-cultured lettuce plants increased the amount of dissolved oxygen in the nutrient solution, increased the lettuce yield, and elevated the net photosynthetic rate, conductance of H 2 O and intercellular carbon dioxide concentration of lettuce plants. Diversity analysis of the rhizosphere microbial community revealed that both the abundance and diversity of bacterial and fungal communities in the substrate increased after plant cultivation and decreased following treatment with micro/nanobubble nutrient solutions. RDA results showed that the microbial community in the S group was positively associated with EC, that in the CK and O 2 groups exhibited a positive correlation with SC, and that in the O 3 group displayed a positive correlation with CAT and POD. Overall, the implementation of micro/nanobubble generation technology in soilless substrates can effectively increase the lettuce growth and yield, and O 3 had a more pronounced effect on lettuce yield and quality and the microbial community structure in the substrate than O 2 . Our study would provide a reference and theoretical basis for developing sustainable and green technology for promoting lettuce production and can be a promising alternative to conventional methods for improving crop yields.

The microbial community diversity and succession of Chinese Sichuan sausages during the spontaneous fermentation were demonstrated using high-throughput sequencing technology. The bacterial diversity was abundant and the succession of bacterial community along the direction of Lactobacillus spp. increased and Weissella spp. decreased. While fungal diversity was single and trace fungal population was detected. The core functional microbiota were lactic acid bacteria, including Lactobacillus spp., Weissella spp. and Pediococcus spp. In initial fermentation, Weissella spp. was the dominant bacteria and its relative abundance was 49.84%, but then its relative abundance decreased to 11.96% during fermentation before recovering to 26.74% at the end of fermentation. Meanwhile, Lactobacillus spp. rose from 24.70 to 55.74% and became the dominant genus. Moreover, Pediococcus spp. increased from 0.06 to 18.05% on day 20 but then decreased to 1.89% on day 30. These results revealed that the primary microorganisms contributing to spontaneous fermentation of Chinese Sichuan sausages were bacteria, while eukaryotic microorganisms such as yeast scarcely contributed to fermentation.