Research progress in biological control of tomato bacterial wilt.

Bacterial wilt caused by the infection of Ralstonia solanacearum, is one of the most harmful diseases to tomatoes, one of the most important greenhouse vegetables in China. R. solanacearum can survive and remain active in the deep soil for a long time, and the chemical control of tomato bacterial wilt is consequently limited. In this study, we introduced the characteristics of tomato bacterial wilt disease and the types of R. solanacearum, and systematically reviewed the research progresses of biological control methods from the aspects of botanical insecticides, agricultural antibiotics, biocontrol bacteria. We emphatically introduced the principle and current status of these methods, discussed the limitations and the improvement strategies, and prospected a new environmental protection and efficient biological control system based on micro-ecological regulation would be the development direction of biological control of tomato bacterial wilt.

Nitrous oxide emissions from tea plantations: A review.

Tea plantations are an important N2O source. Fertilizer-induced N2O emission factors of tea plantations are much higher than other upland agricultural ecosystems. According to the basic information on characteristics and knowledge of N2O emissions from tea plantations around the world, we comprehensively reviewed N2O emission characteristics, production process, influencing factors, and reduction measures from tea plantations. The global means of ambient N2O emission and N2O emission stimulated by nitrogen fertilizer application from tea plantations were (2.68±2.92) kg N·hm-2 and (11.29±9.45) kg N·hm-2, respectively. The fertilizer-induced N2O emission factor in tea plantations (2.2%±2.1%) was much higher than the IPCC-estimated N2O emission factor for agricultural land (1%). N2O emission from tea plantation soil (a typical acid soil) were mainly produced during nitrification and denitrification, with denitrification being dominant. N2O emission from tea plantations were significantly related to the amount of fertilizer application. Other factors, such as fertilizer type, could also affect soil N2O emissions in tea plantations. The main reduction methods of N2O emission from tea plantations included optimizing the amount and type of fertilizer, amending biochar, and rationally using nitrification inhibitors. In future, we should strengthen in-situ observations of soil N2O emission from tea plantations at both temporal and spatial scales, combine lab incubation and field studies to elucidate the mechanisms underling tea plantation soil N2O emissions, and use a data-model fusion approach to reduce uncertainties in the estimation of global N2O emission. These would provide theoretical support and practical guidance for reasonable N2O emission reduction in tea plantations.

[Research progress on primers and molecular ecology of comammox Nitrospira]. / å®Œå ¨æ°¨æ°§åŒ–èŒçš„åˆ†å­ç”Ÿæ€å­¦ç ”ç©¶è¿›å±•.

Nitrification is a key process in nitrogen cycling, which has received considerable attention in the research field of soil biochemistry. In 2015, the discovery of complete ammonia oxidizers (Comammox) challenged conventional two-step nitrification perspective, which represented a paradigm shift in the understanding of soil nitrogen cycling. Comammox are a group of microorganisms capable of conducting both steps of nitrification. In this review, we summarized current understan-ding of the molecular ecology of comammox, including specific molecular biomarkers for comammox, phylogenetic and genomic surveys of comammox and particularly the distribution, diversity and ecological significance of comammox in soil. Further studies should focus on: 1) designing specific molecular biomarkers to examine the distribution and diversity of comammox; 2) optimizing cultivation techniques to isolate/enrich comammox cultures and expending our insights into physiological traits of comammox; 3) characterizing their distribution and in situ activities to elucidate the contribution of comammox processes to soil nitrification and their ecological features, which may assist in unco-vering the mechanisms of nitrogen cycling and promote the environmental protection of soil ecosystem.

[Effects of changes in water status on soil microbes and their response mechanism: A review]. / æ°´åˆ†æ¡ä»¶å˜åŒ–å¯¹åœŸå£¤å¾®ç”Ÿç‰©çš„å½±å“åŠå ¶å“åº”æœºåˆ¶ç ”ç©¶è¿›å±•.

Soil microbes play essential roles in maintaining terrestrial ecosystem services. Soil moisture is a primary determinant of soil microbial activities and ecosystem functions, which may fluctuate dramatically with the altered precipitation patterns and extreme drought caused by the ongoing global climate change. Due to the distinct soil microbial tolerance and life-strategy approaches to drought stress and different water status, fluctuation of soil moisture has a direct impact on microbial activities and community structure, thereby profoundly affecting microbial-mediated processes and ecosystem functions. Thus, it is of great significance to understand the dynamics and mechanisms that underlie the microbial responses to soil water status. In this review, we summarized recent progress in the study of responses of soil microbial activities (e.g. soil respiration and enzyme activities) and community structure to soil water status. We summarized underlying microbial physiological and ecological mechanisms, particularly 1) the cellular physiological accommodation such as osmolyte accumulation, exopolysaccharide production and transition into dormant states, and 2) the ecological strategies such as stress-resistant gene transfer and functional redundancy. Therefore, this investigation on the underlying relationship between soil microbial assembly and ecosystem functions under different water status could further demonstrate the microbially-mediated soil biogeochemical processes and provide a theoretical basis for future research and modelling of terrestrial ecosystem responses to climate change.

Application of substrate utilization patterns and terminal restriction fragment length polymorphism analysis to characterize the oral bacterial community of healthy subjects and patients with periodontitis.

Understanding the association between the bacterial community and oral health status is essential for the diagnosis and therapy of periodontal diseases. The aim of the present study was to apply three methods [conventional culture, substrate utilization using the MicroResp™ system and terminal restriction fragment length polymorphism (T-RFLP)] to investigate the oral bacterial community in saliva from 20 healthy subjects and 20 patients with periodontitis. The three methods all revealed that there was a systematic change in the microbial ecological characteristics associated with oral health status. Compared with the control group, the oral bacterial flora in the patients with chronic periodontitis had a greater culturable population and altered preferred carbon source and TRFLP patterns. TRFLP analysis was found to give more information and exhibit a higher sensitivity than the substrate utilization and conventional culture methods. In conclusion, TRFLP analysis is a potentially rapid method to assess the composition of the oral microbial community and for the diagnosis of chronic periodontitis.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.

Potential contribution of anammox to nitrogen loss from paddy soils in Southern China.

The anaerobic oxidation of ammonium (anammox) process has been observed in diverse terrestrial ecosystems, while the contribution of anammox to N2 production in paddy soils is not well documented. In this study, the anammox activity and the abundance and diversity of anammox bacteria were investigated to assess the anammox potential of 12 typical paddy soils collected in southern China. Anammox bacteria related to "Candidatus Brocadia" and "Candidatus Kuenenia" and two novel unidentified clusters were detected, with "Candidatus Brocadia" comprising 50% of the anammox population. The prevalence of the anammox was confirmed by the quantitative PCR results based on hydrazine synthase (hzsB) genes, which showed that the abundance ranged from 1.16 × 10(4) to 9.65 × 10(4) copies per gram of dry weight. The anammox rates measured by the isotope-pairing technique ranged from 0.27 to 5.25 nmol N per gram of soil per hour in these paddy soils, which contributed 0.6 to 15% to soil N2 production. It is estimated that a total loss of 2.50 × 10(6) Mg N per year is linked to anammox in the paddy fields in southern China, which implied that ca. 10% of the applied ammonia fertilizers is lost via the anammox process. Anammox activity was significantly correlated with the abundance of hzsB genes, soil nitrate concentration, and C/N ratio. Additionally, ammonia concentration and pH were found to be significantly correlated with the anammox bacterial structure.

Biochar impacts soil microbial community composition and nitrogen cycling in an acidic soil planted with rape.

Biochar has been suggested to improve acidic soils and to mitigate greenhouse gas emissions. However, little has been done on the role of biochar in ameliorating acidified soils induced by overuse of nitrogen fertilizers. In this study, we designed a pot trial with an acidic soil (pH 4.48) in a greenhouse to study the interconnections between microbial community, soil chemical property changes, and N2O emissions after biochar application. The results showed that biochar increased plant growth, soil pH, total carbon, total nitrogen, C/N ratio, and soil cation exchange capacity. The results of high-throughput sequencing showed that biochar application increased α-diversity significantly and changed the relative abundances of some microbes that are related with carbon and nitrogen cycling at the family level. Biochar amendment stimulated both nitrification and denitrification processes, while reducing N2O emissions overall. Results of redundancy analysis indicated biochar could shift the soil microbial community by changing soil chemical properties, which modulate N-cycling processes and soil N2O emissions. The significantly increased nosZ transcription suggests that biochar decreased soil N2O emissions by enhancing its further reduction to N2.

Methane production and methanogenic archaeal communities in two types of paddy soil amended with different amounts of rice straw.

Soil type and returning straw to the field are the important factors that regulate CH4 formation in paddy soil, and the variations of biogeochemical parameters and methanogens communities play important roles in the formation of CH4 . In the present study, two paddy soil types [silt loam soil (JX) and silty clay loam soil (GD)] with different amounts of rice straw additions were incubated under anaerobic conditions to investigate the relationship between CH4 production, biogeochemical variations, and methanogenic archaeal communities. Straw incorporation significantly stimulated CH4 production in two soil types. CH4 production in JX soil was higher than the GD soil with equal straw addition. Significant differences between biogeochemical parameters and methanogenic archaeal communities were observed between two soil types. Straw addition increased archaeal 16S rRNA genes and mcrA genes copy numbers, especially in JX soil. Multiple regression analysis indicated that variations in H2 , sulfate, Fe (II) concentrations, archaeal 16S rRNA genes and mcrA genes copy numbers, methanogens diversity index, and the relative abundance of Methanosarcinaceae and Methanobacteriaceae together influenced CH4 production in two soil types. These results indicated that methane production was influenced by the comprehensive effects of biotic and abiotic factors in paddy soils.

Effect of long-term wastewater irrigation on potential denitrification and denitrifying communities in soils at the watershed scale.

Wastewater irrigation mitigates the problem of water shortage but leads to the potential accumulation of pollutants and causes corresponding changes in denitrifying communities and denitrification, hence the potential ecological risk of long-term wastewater irrigation should not be overlooked. We investigated the relative contributions of different environmental factors to the abundance and diversity of denitrifying communities harboring nirK, nirS, and nosZ genes and the relative importance of these biotic and abiotic variables in potential denitrification activity (PDA) in soils with wastewater irrigation for around 25 years at a large watershed scale. Results showed that soil physicochemical properties, pollutants, including heavy metals and PAHs, and vegetation are the major factor groups influencing the abundance and structure of the three denitrifying communities and PDA. NirK-, nirS-, or nosZ-harboring denitrifiers responded in different manners to environmental changes, and were mainly influenced by substrate concentration, carbon source, or pollutants, respectively. The structure of the three denitrifying communities was more relevant to the environmental changes than their abundance. Conversely, the abundance, rather than diversity, was correlated with PDA. Pollutants and vegetation could affect PDA by both direct and indirect paths through soil physicochemical properties including pH, carbon and nitrogen sources, or through the abundance of denitrifying functional genes. The abundance of denitrifying functional genes is a valuable index that integrates potential activity and various environmental factors, and is therefore a good predictor of denitrification in the presence of environmental changes.

Phospholipid fatty acid patterns of microbial communities in paddy soil under different fertilizer treatments.

The microbial communities under irrigated rice cropping with different fertilizer treatments, including control (CK), PK, NK, NP, NPK fertilization, were investigated using phospholipid fatty acid (PLFA) profile method. The results of this study revealed that the fertilizer practice had an impact on the community structure of specific microbial groups. The principal components analysis (PCA) showed that proportion of the actinomycete PLFAs (10Me 18:0 and 10Me 16:0) were the lowest in the PK treatment and the highest in the NPK treatment, which means that soil nitrogen status affected the diversity of actinomycetes, whereas nitrogen cycling was related to the actinomycets. Under CK treatment, the ratio of Gram-positive to Gram-negative bacteria was lower compared with that in fertilizer addition treatments, indicating that fertilizer application stimulated Gram-positive bacterial population in paddy soil. The fatty acid 18:2omega6,9, which is considered to be predominantly of fungal origin, was at low level in all the treatments. The ratio of cyl9:0 to 18: 1omega7, which has been proposed as an indicator of stress conditions, decreased in PK treatment. Changes of soil microbial community under different fertilizer treatments of paddy soil were detected in this study; however, the causes that lead to changes in the microbial community still needs further study.

[Genetic diversity of microbial communities in tea orchard soil].

In this paper, the total microbial DNA was extracted from the soils in 8-, 50- and 90 years old tea orchards, adjacent wasteland, and 90 years old forestland in Meijiawu tea area of Hangzhou. The 16S rDNA V3 fragment was amplified by PCR, and the polymorphism of this fragment was analyzed by DGGE. The results indicated that both the tea orchard age and the land use type had significant effects on soil microbial genetic diversity. There was a significant difference (P < 0.05) in the microbial genetic diversity index among wasteland, tea orchards and forestland, which was decreased in the order of wasteland > tea orchard > forestland. For the tea orchards of different ages, the soil microbial genetic diversity index, microbial biomass C, and basal respiration were significantly higher in 50 years old than in 8 and 90 years old tea orchards.

Effect of copper on phospholipid fatty acid composition of microbial communities in two red soils.

The phospholipid fatty acid (PLFA) composition was analyzed in two red soils experimentally contaminated with copper at different concentrations. The total amounts of phospholipid fatty acids (PLFAs) in both red soils were significantly correlated with soil microbial biomass C and N, which decreased consistently with increasing levels of copper. The relative quantities of the PLFAs 17:0 (10 Me), i16:0, i15:0 and 16:1w5c, decreased with increasing heavy metal concentration, while those of cy17:0, which is an indicator of gram-negative bacteria, increased. The Shannon index calculated from the PLFA data indicated that Cu addition in the red soils decreased the population diversity of soil microbial communities. Multivariate analysis of PLFA data demonstrated that high levels of Cu application had a significant impact on microbial community structure and there is a threshold metal concentration for PLFA composition. Comparatively higher toxic effect on microbial biomass and community structure were found in the red sandy soil than those in the red clayey soil. The differential effect of Cu addition on microbial communities in the two soils may be due to differences in soil texture and cation exchange capacity.