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Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules. [ABSTRACT FROM AUTHOR]

Summary: In the processes controlling ecosystem fertility, fungi are increasingly acknowledged as key drivers. However, our understanding of the rules behind fungal community assembly regarding the effect of soil fertility level remains limited.Using soil samples from typical tea plantations spanning c. 2167 km north‐east to south‐west across China, we investigated the assemblage complexity and assembly processes of 140 fungal communities along a soil fertility gradient.The community dissimilarities of total fungi and fungal functional guilds increased with increasing soil fertility index dissimilarity. The symbiotrophs were more sensitive to variations in soil fertility compared with pathotrophs and saprotrophs. Fungal networks were larger and showed higher connectivity as well as greater potential for inter‐module connection in more fertile soils. Environmental factors had a slightly greater influence on fungal community composition than spatial factors. Species abundance fitted the Zipf–Mandelbrot distribution (niche‐based mechanisms), which provided evidence for deterministic‐based processes.Overall, the soil fungal communities in tea plantations responded in a deterministic manner to soil fertility, with high fertility correlated with complex fungal community assemblages. This study provides new insights that might contribute to predictions of fungal community complexity. [ABSTRACT FROM AUTHOR]

Interactions among soil bacteria occur widely and play important roles in the maintenance of soil functions. Long-term fertilization management practices have distinct effects on soil fertility and the soil microbial activity and community, which are closely associated with soil microbial interactions. Red soil is typically low-productivity soil in South China. Chemical nitrogen fertilization caused serious soil acidification and low-productivity (defined as the acidified soil group, Ac), whereas the application of lime to the acidified soil increased the soil pH (defined as the quicklime improvement soil group, Qlime). Long-term manure or fallow treatment maintained the soil pH and increased the soil fertility (defined as the high-productivity potential soil group, HPP). A molecular ecological network analysis method was used to analyze 454 pyrosequencing data of bacterial communities from the HPP, Ac and Qlime soils. Several major differences were observed among the three constructed networks. First, the HPP network contained the largest ratio of positive to negative correlations, whereas the Ac network contained the smallest. Second, the HPP and Ac networks shared only 8.67% of their operational taxonomic units (OTUs), whereas Ac and Qlime shared 27.04%. Third, the HPP network contained the most “module hubs” (A set of OTUs that have strong interactions or common functions are grouped as a “module” in network analysis. These OTUs are called “nodes”. And the nodes with high connectivity to many other nodes within the same module are “module hubs”.), whereas Ac contained the fewest. These results demonstrated that the bacterial community of HPP was a better organized or a better operated community than Ac and that quicklime application helped to order the bacterial community. By comparing the topological roles of nodes in different networks, we proposed that there should be more module hubs in the networks of higher-productivity soils and hypothesized that these OTUs could be indicators of high-productivity. [ABSTRACT FROM AUTHOR]

A nationwide survey of animal manure-based composts was carried out in China. Two hundred and twelve samples were collected and analyzed for the concentrations of 9 heavy metals or metalloids and arsenic (As) speciation. The concentrations of heavy metals vary widely (Zn 11.8–3692, Cu 3.6–916, Cr 0.7–6603, Ni 0.7–73, Pb 0.05–189, As 0.4–72, Co 0.1–94, Cd 0.01–8.7 and Hg 0.01–1.9 mg kg −1 dry weight). Compared with the maximum permissible values of the Chinese standard for organic fertilizers, 13.7% and 2.4% of the composts exceeded the limits for As (15 mg kg −1 ) and Cd (3 mg kg −1 ), respectively. Some samples contained very high concentrations of Zn and Cu, although no limits have been set for these two metals in China. Further analysis showed that As was present mainly as arsenate (As Ⅴ ), with dimethylarsenate (DMA) and monomethylarsenate (MMA) as the minor species in composts. There were significant correlations between the concentrations of Zn, Cu and As, suggesting co-contamination of these elements in some composts. Monte Carlo simulations based on the distributions of metal concentrations and application rate showed that repeated applications of compost likely increase the concentrations of Zn, Cu, Cd and Hg in soil significantly compared with the soil background levels. This study highlights a need to minimize the concentrations of Zn, Cu, Cd, Hg and As in animal manures to ensure their safe recycling to agricultural soils. [ABSTRACT FROM AUTHOR]

Intensive cultivation in greenhouses of China has degraded the soil through acidification, salinization, and has caused an increase in soil-borne pathogens accumulation that negatively impacts vegetable production. In this study, six treatments, i.e. CK, degraded soil collected from greenhouse was irrigated to maximum field capacity and covered with plastic film; Al-RSD-F, flooding soil incorporated with alfalfa; Al-RSD, soil was incorporated with alfalfa, irrigated to maximum field capacity and covered with plastic film; Al-RSD + T37, inoculating Trichoderma harzianium T37 into soil at the end of the Al-RSD; Et-RSD, soil was incorporated with ethanol, irrigated to maximum field capacity and covered with plastic film; AW, soil was incorporated with ammonia and covered with plastic film, were conducted to investigate their effects on the physicochemical properties of degraded soil and disinfestations of Rhizoctonia solani , to control the damping-off disease in the two consecutive plantings of cucumber seedlings after the treatments. Treatments with Al-RSD-F, Al-RSD, Al-RSD + T37 and Et-RSD increased the pH and reduced the electrical conductivity of the soils, reduced population of R. solani and damping off of cucumber seedlings. These treatments with exception of Et-RSD, increased the populations of bacteria and fungi and showed higher diversity of bacteria after the second season of cucumber seedlings. Treatment AW was toxic and did not allow the survival of the cucumber seedlings. The treatments Al-RSD + T37 and Et-RSD showed the higher control of damping off, probably because the antagonist was favored by the previous treatment and could efficiently colonize the cucumber seedlings roots, and the Et-RSD was favored by the highest accumulation of toxic acetic acid in the soil. Alfalfa-amended soil disinfestations with or without Trichoderma , as well as an ethanol soil disinfestation could be used to recover degraded greenhouse soils. [ABSTRACT FROM AUTHOR]

A 3-year field experiment was conducted to investigate the effects of different organic fertilization strategies for rice–wheat annual rotation systems on net global warming potential (net GWP) and greenhouse gas intensity (GHGI) by incorporating methane, nitrous oxide emissions, the changes in soil organic carbon (SOC) derived from the net ecosystem carbon budget (NECB), and the CO 2 equivalent emissions from manure and chemical nitrogen (N) fertilizer manufacturing. Six fertilization strategies were studied, including control (CK), N fertilizer (CF), pig manure compost + N fertilizer (MC), straw + N fertilizer (SC), straw + pig manure compost + N fertilizer (SM), and straw + straw-decomposing inoculant + N fertilizer (SI). The results indicated that the application of organic amendments did not change the seasonal pattern of GHG emissions but significantly affected their seasonal quantities. Averaged over the 3 cycles, the annual SOC sequestration rates contributed significantly to the net GWPs and were estimated to be 1.01 t C ha −1  yr −1 for the control and 1.13–1.27 t C ha −1  yr −1 for the fertilized plots. Compared to CF, the MC strategy significantly increased SOC while had similar size of net GWP and GHGI, thus deserving recommendation regarding sustainable soil productivity and GHGs mitigations. However, the other proposed organic strategies of SC, SM, and SI significantly increased net GWP and GHGI as well as SOC thus requiring further researches for GHGs mitigations. Therefore, we recommend that the application of manure substituting half chemical fertilizer be an effective strategy while straw returning in any currently studied strategies should be re-examined in the rice–wheat annual rotation system. [ABSTRACT FROM AUTHOR]

Aims and background: Soil fertility quality index is a useful indicator that helps to improve sustainable land use management and achieve economical yield in agriculture production. The objectives of this study were to evaluate the changes of soil fertility quality between the 1980s and 2000s in different cropping systems and its significance to crop productivity and sustainability. Methods: We collected all published data on crop yields and soil parameters from 58 long-term experiments in three typical double-cropping systems in China, including maize-wheat (M-W), rice-rice (R-R) and rice-wheat (R-W) cropping systems, and selected seven fertilizer treatments in each experiment, including inorganic fertilizer [nitrogen and phosphorus fertilizer (NP), nitrogen and potassium fertilizer (NK), phosphorus and potassium fertilizer (PK) and balanced mineral fertilizer (NPK)], combined NPK with farmyard manure (NPKM) or crop straw (NPKS), and no fertilizer application (served as control). For comparison, an integrated fertility quality index (IFQI) was used to estimate the variations in soil fertility in different cropping systems. Moreover, the mean production variability index (PVI, %) in each cropping system was calculated to evaluate the stability of crop production. Results: Over cropping systems, the averaged relative yields of PK, NK and NP ranged from 38.0 to 97.4 %, while the mean yields can be increased by 2.4-5.1 % in NPKM, compared to NPK. The mean yields were similar between NPK and NPKS for maize and wheat crops, but the yield was increased by 4.3-10.0 % in NPKS. Among the different treatments, the highest variability of cereal productivity was obtained in NK, PK or Control, while the lowest value was mostly recorded in NPKM or NPKS in these three cropping systems. Relative to the control, the IFQIs in fertilization treatments were increased by 9.4-150.0 %, 6.2-41.5 % and 1.3-17.5 % in M-W, R-W and R-R systems, respectively (except for PK treatment in R-R system). However, changes of IFQI in topsoil differed among fertilizer treatments, and greater increases existed in the treatments receiving organic residues (NPKM and NPKS). Conclusions: The increase in crop yield is exponentially correlated with the increased IFQI over treatments in three cropping systems. Over the treatments and systems, production variability among years is shown to be negatively, linearly related to IFQI ( P < 0.001). Therefore, the high grain yield and low production variability can be simultaneously achieved by increasing soil fertility in all three cropping systems. [ABSTRACT FROM AUTHOR]

[Display omitted] • Clinically important ARGs bla-NDM and mcr-1 were detected in composts from a national survey. • Raw material rather than composting process type had a significant effect on the ARG abundance. • Composts with feces origins had higher loads of ARGs and MGEs than those without. • MGEs exerted a greater influence on ARG composition than bacterial community. Compost-based organic fertilizers made from animal manures may contain high levels of antibiotic resistance genes (ARGs). However, the factors affecting the abundance and profile of ARGs in organic fertilizers remain unclear. We conducted a national-wide survey in China to investigate the effect of material type and composting process on ARG abundance in commercial organic fertilizers and quantified the contributions of bacterial composition and mobile genetic elements (MGEs) to the structuring of ARGs, using quantitative PCR and Illumina sequencing of 16S rRNA gene amplicons. The tetracycline, sulfonamide, aminoglycoside and macrolide resistance genes were present at high levels in all organic fertilizers. Seven ARGs that confer resistance to clinically important antibiotics, including three β-lactam resistance genes, three quinolone resistance genes and the colistin resistance gene mcr-1 , were detected in 8 – 50% the compost samples, whereas the vancomycin resistance gene vanC was not detected. Raw material type had a significant (p < 0.001) effect on the ARG abundance, with composts made from animal feces except some cattle feces generally having higher loads of ARGs than those from non-animal raw materials. Composting process type showed no significant (p > 0.05) effect on ARG abundance in the organic fertilizers. MGEs exerted a greater influence on ARG composition than bacterial community, suggesting a strong mobility of ARGs in the organic fertilizers. Our study highlights the need to manage the risk of ARG dissemination from agricultural wastes. [ABSTRACT FROM AUTHOR]

Abstract: Fertilization plays a pivotal role on soil biological process and affects the soil bacterial community, which act as hosts for viruses. The effect of fertilization on soil viral community has not been well explored. In this study, a Haplic Acrisol soil, which is the soil type for 13 provinces in Southern China, was analyzed after 22 years different fertilization regimes for their viral composition. The soil responded to organic fertilizations with an increased amount of soil organic matter (SOM) and pH (increased from 5.7 to 6.6), while with the decreased SOM and pH for chemical fertilization, especially for single nitrogen fertilization. The combined effects of SOM and pH caused by long-term different fertilization regimes on soil viral communities were investigated by direct calculation of virus-like particles (VLPs) through epifluorescence microscopy. The highest VLP abundance (13.1 × 107 per gram dry soil) was detected in soil applied with chemical and organic fertilizers. The viral and bacterial abundances of organic soil were 4 and 5 times higher than those of inorganic soil respectively. Transmission electron microscopy observation revealed a higher frequency of Myoviridae viruses in soil with organic amendments than without organic amendments, and vice versa for Podoviridae viruses. These results demonstrate that organic fertilizer could increase viral abundance and morphological diversity through suppressing soil acidification and improving soil organic matter. [Copyright &y& Elsevier]

The composting industry has been growing rapidly in China because of a boom in the animal industry. Therefore, a rapid and accurate assessment of the quality of commercial organic fertilizers is of the utmost importance. In this study, a novel technique that combines near infrared (NIR) spectroscopy with partial least squares (PLS) analysis is developed for rapidly and accurately assessing commercial organic fertilizers quality. A total of 104 commercial organic fertilizers were collected from full-scale compost factories in Jiangsu Province, east China. In general, the NIR-PLS technique showed accurate predictions of the total organic matter, water soluble organic nitrogen, pH, and germination index; less accurate results of the moisture, total nitrogen, and electrical conductivity; and the least accurate results for water soluble organic carbon. Our results suggested the combined NIR-PLS technique could be applied as a valuable tool to rapidly and accurately assess the quality of commercial organic fertilizers. [ABSTRACT FROM AUTHOR]

Nitrogen fertilizer-induced direct nitrous oxide (N2O) emissions depend on water regimes in paddy fields, such as seasonal continuous flooding (F), flooding–midseason drainage–reflooding (F-D-F), and flooding–midseason drainage–reflooding–moist intermittent irrigation but without water logging (F-D-F-M). In order to estimate the changes in direct N2O emission from paddy fields during the rice-growing season in Mainland of China between the 1950s and the 1990s, the country-specific emission factors of N2O-N under different water regimes combined with rice production data were adopted in the present study. Census statistics on rice production showed that water management and nitrogen input regimes have changed in rice paddies since the 1950s. During the 1950s–1970s, about 20–25% of the rice paddy was continuously waterlogged, and 75–80% under the water regime of F-D-F. Since the 1980s, about 12–16%, 77%, and 7–12% of paddy fields were under the water regimes of F, F-D-F, and F-D-F-M, respectively. Total nitrogen input during the rice-growing season has increased from 87.5 kg N ha−1 in the 1950s to 224.6 kg N ha−1 in the 1990s. The emission factors of N2O-N were estimated to be 0.02%, 0.42%, and 0.73% for rice paddies under the F, F-D-F, and F-D-F-M water regimes, respectively. Seasonal N2O emissions have increased from 9.6 Gg N2O-N each year in the 1950s to 32.3 Gg N2O-N in the 1990s, which is accompanied by the increase in rice yield over the period 1950s–1990s. The uncertainties in N2O estimate were estimated to be 59.8% in the 1950s and 37.5% in the 1990s. In the 1990s, N2O emissions during the rice-growing season accounted for 8–11% of the reported annual total of N2O emissions from croplands in China, suggesting that paddy rice development could have contributed to mitigating agricultural N2O emissions in the past decades. However, seasonal N2O emissions would be increased, given that saving-water irrigation and nitrogen inputs are increasingly adopted in rice paddies in China. [ABSTRACT FROM AUTHOR]

• A novel psychrophilic fungus Aureobasidium was screened and used in low temperature composting. • This psychrophilic fungus accelerated temperature rises at early stage of composting. • This psychrophilic fungus increased the compost maturity and improved compost quality. This study aimed to isolate psychrotrophic cellulose-degrading fungi and to investigate their application potential for composting in cold climate regions in China. One out of five psychrotrophic cellulose-degrading fungal isolates was identified as a novel fungal species, Aureobasidium paleasum sp. nov., with a strong straw degradation potential. Enzyme activity assays and FITR spectroscopy revealed high cellulolytic activities of this psychrotrophic fungus at lower temperatures, with high thermal adaptability from 5 °C to 50 °C (optimum at 10 °C). A. paleasum efficiently decomposed rice straws and cellulose at 10 °C compared to the common cellulose-degrading fungus Penicillium oxalicum. In comparison to P. oxalicum , A. paleasum shortened the thermophilic stage, enhanced compost maturity and improved compost quality. Our work suggests that the psychrotrophic fungus A. paleasum is efficient for rice straw degradation and composting at low temperatures, highlighting its application potential for composting in colder regions. [ABSTRACT FROM AUTHOR]

Utilization of arbuscular mycorrhizal (AM) resources to improve, or even maintain agroecosystem sustainability requires a thorough understanding of the biotic and abiotic factors that impact AM fungal communities. AM symbiosis is important in mango and litchi trees, two economically important fruit crops in China, but there is little information on the AM fungi associated with these trees or their responses to organic fertilizer. Using Illumina high-throughput sequencing we analyzed AM colonization, spore density, and community composition and diversity in the rhizospheric soil from 16 mango orchards and 16 litchi orchards located in southern China. Ours was a regional scale study and in general, we found that the majority of AM fungi OTUs belonged to the families Glomeraceae, followed by Gigasporaceae, Paraglomeraceae, Acaulosporaceae and Diversisporaceae. Glomus and Paraglomus were the genera that differed most in abundance between the rhizospheric soil of mango and litchi. AMF community composition was impacted by latitude and longitude and soil characteristics such as, NO 3 −-N, NH 4 +-N, available-P, and soil organic carbon (SOC). The sampling sites were in areas of medium to low altitude, and there was no significant correlation between altitude and AM fungal richness. We found that higher soil nutrient content, particularly available-P, was negatively correlated with AM colonization. Our results also showed that some of the AM genera responded differently to environmental variables. Structural equation modeling (SEM) demonstrated that SOC not only had a direct positive effect on AMF richness, but also an indirect negative effect, due to increased soil fertility. Our findings have enabled a deeper insight into the impacts of organic fertilizer on AM fungal communities, which will be valuable when considering AM symbiosis in orchard management. • The abundance of Glomus and Paraglomus differed greatly between the rhizospheric soil of mango and litchi. • Geographical distances and soil properties jointly shaped the AM fungal communities. • Some AM genera responded differently to environmental variables. • SOC resulting from increased manure input had a direct positive effect on AMF richness. • Excessive use of manure is detrimental to AMF occurrence. [ABSTRACT FROM AUTHOR]

Closing yield (YG) and nitrogen use efficiency (NUE) gaps amongst smallholder farmers are critical to ensuring food security and environmental sustainability. Here we report a comprehensive analysis of a data set derived from farm-surveys and previously published studies in a typical high N input area of China. Using scenario analysis, farmers from both sources were divided into four rice production levels to assess the YG and NUE of smallholder farmers. Farm surveys showed that rice yield and partial factor productivity of applied N (PFPN) averaged 8273 kg ha−1 and 23.1 kg kg−1 at regional-scale, with a potential increase of 21–43% and 33–52%, respectively. A wide variation in yield and PFPN across different types of farmer was observed. Optimized N management significantly narrowed YGs by 3.7% and PFPN gap by 63.5% on average based on the published literature. Multiple factors, including excessive N rates, small rice planting area (0.33 ha), the aging (51 years old) and low education level (6 years of education) of the major labor force, can partly explain causes of yield and NUE gaps. These findings provide farm-based evidence that centralized management, good agronomy plus advances in knowledge and technologies are essential for future agricultural development. [ABSTRACT FROM AUTHOR]

Soils play a vital role in the global carbon (C) cycle, yet little is known about the calcium (Ca)-mediated stabilization of soil organic carbon (SOC) in calcareous soils. With wet sieving, density fractionation and an incubation experiment from field soils, we investigated the effects of long-term fertilization on the Ca-mediated stabilization of aggregate-associated organic C and on the SOC stock at a soil depth of 0–20 cm in a reclaimed Cambisol on the Loess Plateau of China. Compared to the initial soil, after ten years the SOC stock increased by 50%, 76%, 94% and 110% in soils amended with no fertilizer (control), 100% chemical fertilizer, 50% chemical fertilizer plus 50% chicken manure compost and 100% chicken manure compost, respectively. The specific C mineralization rate (SCMR, rate per unit SOC) decreased as silt and clay > macroaggregate > microaggregate, indicating that SOC in microaggregates was more stable than in macroaggregates and the silt and clay fraction. The exchangeable Ca in the bulk soil (P < 0.001) and soil aggregates (P < 0.001) were positively correlated with the SOC, whereas the Ca carbonate (CaCO 3) was negatively correlated with the SCMR (P < 0.001). The application of compost not only increased the exogenous C inputs but also promoted the transformation of CaCO 3 to exchangeable Ca compared with the sole chemical fertilization. Furthermore, organic fertilization significantly increased the organic C in the heavy fraction (> 2.0 g cm−3) compared with the sole chemical fertilization, which was positively correlated with the mass proportion of macroaggregates (P < 0.001). These results indicate that organic fertilization can enhance the availability of Ca for C binding possibly by forming organo-Ca complexes, which in turn improve soil aggregation, and thus contribute to a long-term SOC sequestration in reclaimed soils of the Loess Plateau of China. • Exchangeable Ca was positively correlated with soil organic carbon (C). • CaCO 3 was negatively correlated with the specific C mineralization rate. • Organic C in microaggregates was relatively stable. • The formation of organo-Ca complexes improved soil aggregation. • Organic fertilization promoted soil aggregation and enhanced C sequestration. [ABSTRACT FROM AUTHOR]