Changes of soil microbiological properties caused by land use changing from rice-wheat rotation to vegetable cultivation

Streptomyces solincola sp. nov., isolated from soil in Malaysia

A urease-producing Gram-stain-positive actinobacterium, designated strain T5^T, was isolated from a soil sample collected at a highway hillslope in Selangor, Malaysia. The strain was found to produce pale yellowish-pink aerial mycelia with smooth long chain spores and extensively branched light yellowish-pink substrate mycelia on oatmeal agar. Strain T5^T grew at 15-37 °C, pH 6-11, and tolerated up to 9 % (w/v) NaCl, with optimal growth occurring at 28 °C, pH 6-9 and without NaCl. The whole-cell sugar hydrolysate of strain T5^T contained galactose, glucose and ribose. The ll-diaminopimelic acid isomer was detected in the cell wall. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were found to be the predominant polar lipids. The main fatty acids were anteiso-C_17 : 0, iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_14 : 0. Comparative analysis of the 16S rRNA gene sequences indicated that strain T5^T belonged to Streptomyces of the family Streptomycetaceae with the highest 16S rRNA gene sequence similarity to Streptomyces lichenis LCR6-01^T (99.0 %). The overall genome relatedness indices revealed that the closest related species was S. lichenis LCR6-01^T with 89.4 % average nucleotide identity and 33.7 % digital DNA-DNA hybridization. Phylogeny analyses showed that strain T5^T was closely related to Streptomyces fradiae, Streptomyces lavendofoliae, Streptomyces lichenis, Streptomyces roseolilacinus and Streptomyces somaliensis. Based on these polyphasic data, strain T5^T represents a novel species, for which the name Streptomyces solincola sp. nov. is proposed. The type strain is T5^T (=TBRC 5137^T= DSM 42166^T).

Dissecting the combined effects of cultivar, fertilization, and irrigation on rhizosphere bacterial communities and nitrogen productivity in rice

Rice cultivars, fertilizer types, and irrigation modes can affect soil bacterial communities and thus influence nitrogen utilization by soil microorganisms and plants. However, the combined effects of these three factors on soil bacterial communities and nitrogen productivity in rice plants remain unknown. Here, we examined the response of rhizosphere bacteria and nitrogen productivity to different combinations of cultivar (japonica or indica), fertilization (organic plus chemical or chemical), and irrigation (controlled or shallow-frequent). The results demonstrated the interactive effects of cultivars with fertilizers and irrigation on rhizosphere bacterial communities, nitrogen accumulation, and grain yield. These significant interactive effects were related to differences in the response to soil environment (soil inorganic nitrogen concentration and moisture condition) between diverse rhizosphere bacteria recruited by indica and japonica. We found that rhizosphere bacterial communities recruited by indica were more active in soil fertilized with organic plus chemical nitrogen, while those recruited by japonica were suitable for living in soil fertilized with chemical nitrogen. Rhizosphere bacteria diversity positively correlated with soluble inorganic nitrogen in soil, suggesting that more diverse bacterial communities and greater contents of NH₄⁺-N might favor nitrogen accumulation in rice plants under shallow-frequent irrigation. The combinations of cultivars, fertilizer types, and irrigation greatly affected rhizosphere bacterial communities, thus triggering a significant difference in soil inorganic nitrogen content, which could play an essential role in affecting nitrogen productivity.

Sloping Farmlands Conversion to Mixed Forest Improves Soil Carbon Pool on the Loess Plateau

Vegetation restoration is considered a potentially useful strategy for controlling soil erosion and improving soil organic carbon (SOC) in arid and semiarid ecosystems. However, there is still debate regarding which vegetation restoration type is the best choice. In this study, four vegetation restoration types (i.e., grasslands, shrubs, forests and mixed forests) converted from sloping farmlands were selected to explore the SOC variation among the four types and to investigate which soil factors had the greatest effect on SOC. The results showed while the magnitude of effect differed between vegetation restoration type, all studied systems significantly increased SOC and labile organic carbon contents (p < 0.01), soil nutrients such as total nitrogen (TN) (p < 0.01), available nitrogen (AN) (p < 0.01), total phosphorus (TP) (p < 0.05) and available phosphorus (AP) (p < 0.05), soil enzyme activities such as phosphatase (p < 0.01), soil microbial biomass carbon (MBC) (p < 0.05), and basal respiration (BR) (p < 0.05), but had significant negative correlationswith polyphenol oxidase (p < 0.05). However, the effects of vegetation restoration of farmland converted to natural grasslands, shrubs, forests and mixed forests varied. Among the types studied, the mixed forests had the largest overall positive effects on SOC overall, followed by the natural grasslands. Soil nutrients such as N and P and soil microbial activities were the main factors that affected SOC after vegetation restoration. Mixed forests such as Robinia pseudoacacia and Caragana korshinskii are the best choice for farmland conversion on the central of the Loess Plateau.

Agricultural land-use change and rotation system exert considerable influences on the soil antibiotic resistome in Lake Tai Basin

In this study, we use high-throughput quantitative polymerase chain reaction approaches to comprehensively assess the effects of agricultural land-use change on the antibiotic resistome of agricultural runoffs after rainfalls in Lake Tai Basin. For the first time in this region, our findings show that orchard runoffs harbored more diverse and abundant antibiotic resistance genes (ARGs) than traditional cropland runoffs. Network analysis demonstrated that orchard runoffs possessed a strong ability for ARG dissemination via horizontal gene transfer. These results suggest that residents might be exposed to a higher public health threat than before. Moreover, the present study confirmed that the rice-wheat rotation system plays a key role in regulating the soil antibiotic resistome profile. Using 16S rRNA high-throughput sequencing technology, this study clarified the relationships between the antibiotic resistome and soil microbiome composition. Finally, we discuss the key environmental factors driving changes in the soil antibiotic resistome. In summary, this study gives insight into the dissemination of environmental ARGs to the people living in the Lake Tai Basin.

Factors influencing cultivated ginseng (Panax ginseng C. A. Meyer) bioactive compounds

We aimed to investigate the effects of genome, age, and soil factors on cultivated Panax ginseng C. A. Meyer (CPG) compounds under identical climate and agronomic practices. Eight populations of CPG from different years and rhizosphere soils were collected from garden and cropland in the city of Ji'an, China. Inter-simple sequence repeat (ISSR) primers were used to detect genetic diversity and identity, and soil microbial community diversity. Soil enzyme activities and nutrients were also measured. The contents of total ginsenosides (TG), Rg1, Re, Rf, Rd, and ginsenoside extractions of CPG were analyzed by spectrophotometry and HPLC. The relative importance of each factor was analyzed by mathematical methods such as correlation analysis, stepwise line regression, and path analysis. Regression equations of similarity values of HPLC fingerprint (SVHF), richness index of HPLC fingerprint (RIHF) and the TG, Rg1, Re, Rf, and Rd contents with their respective significant correlation factors were obtained. For SVHF, the relative importance is age>microbial community diversity>genetic diversity. For RIHF, the relative importance is age>genetic diversity>microbial community diversity. For TG, Rg1, and Rf contents, the relative importance is age>microbial community diversity. Ginseng age and genetic identity influenced Rd content, and age was more important. Total phosphorus was the only directly negative effect on Re. According to regression equations and path analysis, increasing age and decreasing Shannon (H') could improve the TG, Rg1, and Rf contents, with little effect on SVHF. Adding age, genetic diversity, and decreasing Shannon (H') increased RIHF. Adding age and genetic identity could also improve Rd content. Appropriate decreases in total phosphorus might increase Re content. These findings are significant for CPG scientific cultivation methods, through which CPG bioactive ingredients could be finely controlled via regulation of genotypes and cultural conditions.

Impact of continuous Panax notoginseng plantation on soil microbial and biochemical properties

Panax notoginseng is a highly regarded medicinal plant that has been cultivated for more than 400 years in Southwest China. The obstacles associated with the continuous cropping of P. notoginseng are the greatest issues for the development this plant. In the present study, the micro-ecologies of soils differing in the duration of P. notoginseng planting were compared, the results of which could provide important information to aid in solving the problems associated with the continuous cropping of P. notoginseng. Soils in which P. notoginseng had grown for 1, 3 or 5 years, as well as unplanted or fallow soil, which had a P. notoginseng planting interval of 1, 3, 6 or 9 years, were collected in Yunnan Province, China. The numbers and physiological groups of microorganisms, soil enzyme activities and nutrients present in the soil were analyzed to identify the effects of continuous cropping and determine the influence of crop rotation on the soil. After P. notoginseng was planted, the ecological structure of the soil and the balance of soil nutrients changed. These changes in the soil ecosystem prevented the soil from adapting to the continuous cropping of P. notoginseng, which eventually limited the growth of P. notoginseng and increased the incidence of diseases. After rotation of P. notoginseng, some soil indicators were restored, and some indicators with irregular changes may have been caused by crop rotation and field fertilization management practices. Thus, the selection of suitable crop rotations will facilitate the use of continuous cropping for P. notoginseng.

Effects of soil improvement technology on soil quality in solar greenhouse

Currently, cucumber cultivation is mainly through monoculture, as continuous culture leads to the decrease of crop yield and soil quality. In order to improve soil quality to achieve continuous monocultures, soil physicochemical properties, microbial biomass, content of phenolic compounds, and the size of bacterial, fungal, ammonia-oxidizing bacteria (AOB), and Fusarium oxysporum were first evaluated in cucumber monoculture solar greenhouse. Soil improvement technology, including catch wheat (CW), calcium cyanamide disinfection (LN), and straw reactor technology (SR) during summer fallow period, was compared with conventional fallow (CK). Results showed that CW, LN, and SR all significantly increased soil pH, and LN and SR increased soil electrical conductivity (EC); however, CW decreased soil EC. Meanwhile, LN increased soil available N content significantly and SR increased available P content significantly. CW had negative effect on the accumulation of soil available nutrients, conversely, CW and SR had positive effect on the accumulation of microbial biomass carbon (MBC). All the treatments increased the total phenol content in the soil compared with CK. While CW increased the size of bacteria, AOB in the soil inhibited fungal and wilt pathogen size. LN also increased the size of soil bacteria and reduced the size of fungi. The comprehensive evaluation of all treatments showed that CW could control soil nutrient loss and improve the continuous cropping soil, making the soil transform from fungi to bacteria type. All the treatments accelerate the accumulation of phenolic compound, while whether or not developing autotoxicity requires further investigation.

Effect of land use pattern change from paddy soil to vegetable soil on the adsorption-desorption of cadmium by soil aggregates

The influence of land use change from paddy soil to vegetable soil on the adsorption-desorption behavior of Cd in soil aggregates and the variation in soil properties were investigated. The vegetable soil was characterized by lower pH, organic matter content, cation exchange capacity (CEC), free iron oxides, manganese oxides, and catalase activity and higher urease activity compared with the paddy soil. In the isothermal adsorption and desorption experiments, the adsorption characteristics of Cd of the two soils could be well described by Langmuir and Freundlich equations. The adsorption capacity of vegetable soil decreased 22.72 %, and the desorption rate increased 35 % with respect to paddy soil. Therefore, conversion from paddy to vegetable field can reduce the adsorption ability to Cd of the soil to a certain extent. Both the two soils reached the maximum adsorption capacity and the minimum desorption rate in the <0.002-mm faction. The adsorption capacity of Cd in paddy and vegetable soils exhibited great reliance on the content of CEC. Desorption rate was negatively correlated with the four indicators: organic matter, CEC, free iron oxides, and manganese oxides, and specific adsorption was primarily controlled by soil organic matter and manganese oxides.

Shifts in indigenous microbial communities during the anaerobic degradation of pentachlorophenol in upland and paddy soils from southern China

Pentachlorophenol (PCP) is a common persistent pesticide in soil that has generated a significant environmental problem worldwide. Therefore, anaerobic degradation of PCP by the soil indigenous microbial community has gained increasing attention. However, little information is available concerning the functional microorganisms and the potential shifts in the microbial community associated with PCP degradation. In this study, we conducted a set of experiments to determine which components of the indigenous microbial community were capable of degrading PCP in soils of two land use types (upland and paddy soils) in southern China. Our results showed that the PCP degradation rate was significantly higher in paddy soils than that in upland soils. 16S ribosomal RNA (rRNA) high-throughput sequencing revealed significant differences in microbial taxonomic composition between the soil with PCP and blank (soil without PCP) with Acinetobacter, Clostridium, Coprococcus, Oxobacter, and Sedimentibacter dominating the PCP-affected communities. Acinetobacter was also apparently enriched in the paddy soils with PCP (up to 52.2 %) indicated this genus is likely to play an important role in PCP degradation. Additionally, the Fe(III)-reducing bacteria Clostridium may also be involved in PCP degradation. Our data further revealed hitherto unknown metabolisms of potential PCP degradation by microorganisms including Coprococcus, Oxobacter, and Ruminiclostridium. Overall, these findings indicated that land use types may affect the PCP anaerobic degradation rate via the activities of indigenous bacterial populations and extend our knowledge of the bacterial populations responsible for PCP degradation.

Comparative effects of 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) on ammonia-oxidizing bacteria and archaea in a vegetable soil

Nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) have been used extensively to improve nitrogen fertilizer utilization in farmland. However, their comparative effects on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in agricultural soils are still unclear. Here, we compared the impacts of these two inhibitors on soil nitrification, AOA and AOB abundance as well as their community structure in a vegetable soil by using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP). Our results showed that urea application significantly increased the net nitrification rates, but were significantly inhibited by both NIs, and the inhibitory effect of DMPP was significantly greater than that of DCD. AOB growth was more greatly inhibited by DMPP than by DCD, and the net nitrification rate was significantly related to AOB abundance, but not to AOA abundance. Application of urea and NIs to soil did not change the diversity of the AOA community, with the T-RFs remaining in proportions that were similar to control soils, while the community structure of AOB exhibited obvious shifts within all different treatments compared to the control. Phylogenetic analysis showed that all AOA sequences fell within group 1.1a and group 1.1b, and the AOB community consisted of Nitrosospira cluster 3, cluster 0, and unidentified species. These results suggest that DMPP exhibited a stronger inhibitory effect on nitrification than DCD by inhibiting AOB rather than AOA.

The production of phytolith-occluded carbon in China's forests: implications to biogeochemical carbon sequestration

The persistent terrestrial carbon sink regulates long-term climate change, but its size, location, and mechanisms remain uncertain. One of the most promising terrestrial biogeochemical carbon sequestration mechanisms is the occlusion of carbon within phytoliths, the silicified features that deposit within plant tissues. Using phytolith content-biogenic silica content transfer function obtained from our investigation, in combination with published silica content and aboveground net primary productivity (ANPP) data of leaf litter and herb layer in China's forests, we estimated the production of phytolith-occluded carbon (PhytOC) in China's forests. The present annual phytolith carbon sink in China's forests is 1.7 ± 0.4 Tg CO2  yr(-1) , 30% of which is contributed by bamboo because the production flux of PhytOC through tree leaf litter for bamboo is 3-80 times higher than that of other forest types. As a result of national and international bamboo afforestation and reforestation, the potential of phytolith carbon sink for China's forests and world's bamboo can reach 6.8 ± 1.5 and 27.0 ± 6.1 Tg CO2  yr(-1) , respectively. Forest management practices such as bamboo afforestation and reforestation may significantly enhance the long-term terrestrial carbon sink and contribute to mitigation of global climate warming.

Growth and enzymatic responses of phytopathogenic fungi to glucose in culture media and soil

The effect of inoculation of Aspergillus flavus , Fusarium verticillioides , and Penicillium sp. in Dystrophic Red Latosol (DRL) and Eutroferric Red Latosol (ERL) soils with or without glucose on the total carbohydrate content and the dehydrogenase and amylase activities was studied. The fungal growth and spore production in culture medium with and without glucose were also evaluated. A completely randomized design with factorial arrangement was used. The addition of glucose in the culture medium increased the growth rate of A. flavus and Penicillium sp. but not of F. verticillioides . The number of spores increased 1.2 for F. verticillioides and 8.2 times for A. flavus in the medium with glucose, but was reduced 3.5 times for Penicillium sp. The total carbohydrates contents reduced significantly according to first and second degree equations. The consumption of total carbohydrates by A. flavus and Penicillium sp. was higher than the control or soil inoculated with F. verticillioides . The addition of glucose to soils benefited the use of carbohydrates, probably due to the stimulation of fungal growth. Dehydrogenase activity increased between 1.5 to 1.8 times ( p <0.05) in soils with glucose and inoculated with the fungi (except F. verticillioides ), in relation to soil without glucose. Amylase activity increased 1.3 to 1.5 times due to the addition of glucose in the soil. Increased amylase activity was observed in the DRL soil with glucose and inoculated with A. flavus and Penicillium sp. when compared to control.

Bacterial diversity and distribution in the southeast edge of the Tengger Desert and their correlation with soil enzyme activities

The nature of microbial communities and their relation to enzyme activities in desert soils is a neglected area of investigation. To address this, the bacterial diversity and distribution and soil physico-chemical factors were investigated in the soil crust, the soil beneath the crust and rhizosphere soil at the southeast edge of the Tengger Desert, using the denaturing gradient gel electrophoresis of 16S rRNA genes amplified by the polymerase chain reaction. Phylogenetic analysis of the sequenced DGGE bands revealed a great diversity of bacteria. The Proteobacteria, consisting of the alpha, beta, and gamma subdivisions, were clearly the dominant group at all depths and in rhizosphere soil. Analysis of the enzyme activities indicated that the rhizosphere soil of Caragana korshinskii exhibited the highest protease and polyphenol oxidase activities, and in the soil crust there were increased activities of catalase, urease, dehydrogenase and sucrase. The bacterial community abundance closely correlated with soil enzyme activities in different soils. The presence of Cyanobacteria correlated with significant increases in protease, catalase and sucrase in the soil crust, and increased urease in the rhizosphere soil of Artemisia ordosica. The occurrence of Acidobacteria was associated with significant increases in urease, dehydrogenase, and sucrase in the rhizosphere soil of C. korshinski. The presence of gamma-Proteobacteria correlated with a significant increase in polyphenol oxidase in the rhizosphere soil of A. ordosica. The study indicated a close relationship between the soil bacterial community and soil enzymes, suggesting the necessity of further investigations into bacterial function in this desert ecosystem.

Rice to vegetables: short- versus long-term impact of land-use change on the indigenous soil microbial community

Land-use change is known to have a significant effect on the indigenous soil microbial community, but it is unknown if there are any general trends regarding how this effect varies over time. Here, we describe a comparative analysis of microbial communities from three adjacent agricultural fields: one-century-old paddy field (OP) and two vegetable fields (new vegetable field (NV) and old vegetable field (OV)) that were established on traditional paddy fields 10 and 100 years ago, respectively. Soil chemical and physical analysis showed that both vegetable fields were more nutrient rich than the paddy field in terms of organic C, total N, total P, and available K. The vegetable fields possessed relatively higher abundance of culturable bacteria, fungi, and specific groups of bacteria (Actinomyces, nitrifying bacteria, and cellulose-decomposing bacteria) but lower levels of microbial biomass C and N. Notably, the decrease of biomass was further confirmed by analysis of seven additional soils in chronosequence sampled from the same area. Next we examined the metabolic diversity of the microbial community using the EcoPlate(TM) system from Biolog Inc. (Hayward, CA, USA). The utilization patterns of 31 unique C substrates (i.e., community-level physiological profile) showed that microorganisms in vegetable soil and paddy soil prefer to use different C substrates (polymeric compounds for NV and OV soils, phenolic acids for OP soil). Principal component analysis and the average well color development data showed that the NV is metabolically more distinct from the OV and OP. The effect was likely attributable to the elevated soil pH in NV soil. Furthermore, we assessed the diversity of soil bacterial populations using the cultivation-independent technology of amplified ribosomal DNA restriction analysis (ARDRA). Results showed that levels of bacterial diversity in OP and NV soils were similar (Shannon's diversity index H = 4.83 and 4.79, respectively), whereas bacteria in OV soil have the lowest score of diversity (H = 3.48). The low level of bacterial diversity in OV soil was supported by sequencing of ten randomly selected 16S rDNA clones from each of the three rDNA libraries. Phylogenetic analysis showed that all the ten OV clones belonged to Proteobacteria with eight in the gamma-subdivision and two in the alpha-subdivision. In contrast, the ten clones from NV and OP soils were classified into four and eight bacterial classes or unclassified groups, respectively. Taken together, our data suggest that land-use change from rice to vegetables resulted in a decrease of bacterial diversity and soil biomass despite an increase in the abundance of culturable microorganisms and, moreover, the decrease of bacterial diversity occurred during long-term rather than short-term vegetable cultivation.