Ecological rice-cropping systems mitigate global warming - A meta-analysis.

Ecological rice-cropping systems (ERSs) are prosperous rice ecosystems that have a profound influence on global greenhouse (GHG) effects. However, the high variation in research results requires an accurate evaluation of the ERS effects. In this study, three typical ERS modes, rice-crayfish, rice-duck, and rice-fish were selected, and a meta-analysis was conducted using the data of 34 studies to comprehensively evaluate the effects of ERSs on GHG emissions, the global warming potential (GWP), and GHG intensity (GHGI). The results showed that the ERSs reduced CH4 emissions significantly (-12.5%), but increased N2O emissions by 11.3% as compared with traditional rice-cropping systems (TRSs). Further, ERSs have slightly lower GWP, rice yield, and GHGI values (6.5%, 5.5%, and 5.6%, respectively) than TRSs. The rice-crayfish and rice-duck modes significantly alleviated the GWP by 18.0% and 11.1%, respectively, whereas the rice-fish mode enhanced the GWP by 20.8%. Moreover, the rice-duck mode significantly reduced the GHGI by 17.2%, while the ricecrayfish and rice-fish modes increased the GHGI by 9.7% and 8.8%, respectively. Further, the ERSs significantly changed the dissolved oxygen concentration in the flood water as well as the Eh, dissolved organic carbon, and ammonium nitrogen in the soil, wherein the effect sizes of the ERSs on the GHG emissions were significantly correlated with their respective increase. Considering the net ecosystem economic budget and CO2 emissions equivalent/output, ERSs were found to be effective "green technologies". Further, we found that the rice-duck ERS was a good ecological ricecropping system for global warming mitigation. Our study provided new ideas for sustainable agriculture.

Microbiomes inhabiting rice roots and rhizosphere.

Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.

Anaerobic ammonium oxidation in agricultural soils-synthesis and prospective.

Denitrification is considered as the dominant nitrogen (N) removing pathway, however, anaerobic oxidation of ammonium (anammox) also plays a significant part in N loss in agricultural ecosystems. Large N inputs into agricultural soils may stimulate the growth of anammox bacteria, resulting in high activity and diversity of anammox bacteria and subsequent more N loss. In some specific niches, like oxic-anoxic interface, three processes, nitrification, anammox and denitrification couple with each other, and significant anammox reaction could be observed. Soil parameters like pH, dissolved oxygen, salinity, oxidation-reduction potential (ORP), and substrate concentrations impact the anammox process. Here we summarize the current knowledge on anammox activity and contribution to N loss, abundance and diversity of anammox bacteria, factors affecting anammox, and the relationship between anammox and other N loss pathways in agricultural soils. We propose that more investigations are required for (1) the role of anammox to N loss with different agricultural management strategies; (2) microscale research on the coupling of nitrification-anammox-denitrification, that might be a very complex process but ideal model for further studies responsible for N cycling in terrestrial ecosystems; and (3) new methods to estimate differential contributions of anammox, codenitrification and denitrification in total N loss in agricultural ecosystems. New research will provide much needed information to quantify the contribution of anammox in N loss from soils at landscape, ecosystem and global scales.

Changes in Metal Availability and Improvements in Microbial Properties After Phytoextraction of a Cd, Zn and Pb Contaminated Soil.

Assessing the effects of phytoextraction on soil properties is important for successful implementation of this method. This study was conducted to evaluate the effects of phytoextraction by Sedum alfredii Hance on the availability of metals and improvement of the microbial community (biomass and structure) of a Cd, Zn and Pb contaminated soil. Phytoextraction significantly decreased the acid extractable, Mn/Fe oxide and organic matter bound fractions of Cd and Zn as well as the acid extractable Pb in the rhizosphere soil. Soil microbial biomass, total, bacterial, actinomycete, fungal, AM fungal, and protozoa phospholipid fatty acids (PLFAs) were significantly enhanced. The ratio of fungal to bacterial and gram-positive to gram-negative bacterial PLFAs were significantly changed. Redundancy analysis showed that microbial biomass and specific groups of PLFAs were negatively correlated with available metals while positively correlated with dissolved organic carbon/organic acids. In conclusion, phytoextraction by S. alfredii reduced available metal concentrations and improved soil microbial properties.

[Responses of fungal community structure and functional group to fertilization in yellow clayey soil.] / 黄泥田土壤真菌群落结构和功能类群组成对施肥的响应.

We investigated the responses and underlying mechanisms of community composition, and function group of fungi in yellow clayey paddy soil to different long-term fertilization, which may provide scientific basis for rational fertilization and sustainable development in agriculture ecosystems. There were four treatments, including control (CK), inorganic fertilizer (NPK), inorganic fertilizer combined with manure (NPKM), and inorganic fertilizer combined with straw (NPKS). Illumina high-throughput sequencing and FUNGuild were performed to investigate the fungal community structure and functional group, respectively. Ascomycota, Basidiomycota, and Zygomycota were identified as the three dominant ones. The proportion of Ascomycota in NPKM and NPKS were significantly lower (49% and 47%, respectively) compared with CK (71%) and NPK (74%) treatments, with the main reduced orders of Hypocreales, Pleosporales and Eurotiales. While there was higher relative abundance of Basidiomycota in NPKM and NPKS (18% and 28%) compared to CK (14%) and NPK (10%), the orders with enhancement were Tremellales, Trechisporales, and Agaricales. The ratio of Basidiomycota was decreased with sole inorganic fertilizer. Moreover, the relative abundance of Zygomycota was increased after 33 years of fertilization, which was dominated by Mortierellales and Basidiobolales at order level. Diversity indices including Shannon, Simpson, Chao1 and ACE were all significantly declined in NPK compared with CK, NPKM and NPKS treatments, whereas Chao1 index and ACE index in NPKM and NPKS were higher than that in CK and NPK. Saprotroph was the main fungal functional group across all the four treatments (48%-57%). Higher proportion of symbiotroph fungi was identified in soils with NPKS and NPKM (17%) in comparison to CK and NPK. The main guilds with the increasing proportion were arbuscular mycorrhizal fungi and ectomycorrhizal fungi. However, significantly higher proportion of animal pathogen fungi were detected in NPK (10%) than other treatments. Redundancy analysis (RDA) showed that moisture, salinity and porosity in soil were more strongly related with fungal community composition and fungal functional composition than soil organic matter and total nitrogen. Our results suggest that sole application of inorganic fertilizer results in great changes in fungal community compositions and the hazard of over production of pathogen fungi, whereas combined organic-inorganic fertilization would be beneficial to maintain the healthy environment through increasing fungal diversity and the ratio of symbiotrophic fungi in yellow clayey paddy soil.

Nitrogen loss by anaerobic oxidation of ammonium in rice rhizosphere.

Anaerobic oxidation of ammonium (anammox) is recognized as an important process for nitrogen (N) cycling, yet its role in agricultural ecosystems, which are intensively fertilized, remains unclear. In this study, we investigated the presence, activity, functional gene abundance and role of anammox bacteria in rhizosphere and non-rhizosphere paddy soils using catalyzed reporter deposition-fluorescence in situ hybridization, isotope-tracing technique, quantitative PCR assay and 16S rRNA gene clone libraries. Results showed that rhizosphere anammox contributed to 31-41% N2 production with activities of 0.33-0.64 nmol N2 g(-1) soil h(-1), whereas the non-rhizosphere anammox bacteria contributed to only 2-3% N2 production with lower activities of 0.08-0.26 nmol N2 g(-1) soil h(-1). Higher anammox bacterial cells were observed (0.75-1.4 × 10(7) copies g(-1) soil) in the rhizosphere, which were twofold higher compared with the non-rhizosphere soil (3.7-5.9 × 10(6) copies g(-1) soil). Phylogenetic analysis of the anammox bacterial 16S rRNA genes indicated that two genera of 'Candidatus Kuenenia' and 'Candidatus Brocadia' and the family of Planctomycetaceae were identified. We suggest the rhizosphere provides a favorable niche for anammox bacteria, which are important to N cycling, but were previously largely overlooked.

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.

[Dynamics of the mineralization and transformation of rice photosynthesized carbon in paddy soils--a batch incubation experiment].

Photosynthesized carbon is an important part in C cycling of "atmosphere-plant-soil" and is the source of soil organic carbon (SOC), but its mineralization and transformation dynamics in paddy soils remains still unclear. Therefore, a batch incubation experiment was conducted to investigate the mineralization and transformation of rice photosynthesized carbon in paddy soils after rice harvest. The results showed that the mineralization rate of native SOC ranged from 4.44 to 17.8 microg x (g x d)(-1), while that of photosynthesized carbon (new carbon) was 0.15- 1.51 micro x (gx d)(-1) during the course of 100-day-incubation span. Rice photosynthesized carbon input significantly influenced the soil active carbon (DOC, MBC) transformation. During the incubation period (100 d), the amount of 14C-DOC transformation ranged from 1.89 to 5.32 mg x 8 kg(-1), and that of native DOC varied from 61.13 to 90.65 mg x kg(-2), with the transformation rates ranged from 0.18 to 0.34 mg x (kg x d)(-1) and from 4.10 to 5.48 mg. (kg x d)(-1), respectively. However, the 14C-MBC and native original MBC were 10.92-44.11 mg x kg(-1) and 463.31-1153.46 mg x kg(-1), respectively, and their transformation rates were 0.80-2.87, 41.60-74.46 mg x (kg-d)(-1), respectively. It suggested that the turnover of MBC was greater than that of DOC. Furthermore, "new carbon" was easier to be mineralized and decomposed than native SOC. The mineralized portion in "new carbon" was 13.5%-20.2%, whereas that in native SOC was only 2.2%-3.7%. Therefore, we concluded that the incorporation of rice photosynthesized carbon was vital to maintain the soil carbon sink for paddy soils.

Does urbanization shape bacterial community composition in urban park soils? A case study in 16 representative Chinese cities based on the pyrosequencing method.

Although the geographical distribution patterns of microbes have been studied for years, few studies have focused on urban soils. Urbanization may have detrimental effects on the soil ecosystem through pollution discharge and changes in urban climate. It is unclear whether urbanization-related factors have any effect on soil bacterial communities. Therefore we investigated geographical patterns of soil microbial communities in parks in 16 representative Chinese cities. The microbial communities in these 95 soil samples were revealed by 454-pyrosequencing. There were 574,442 effective sequences among the total of 980,019 16S rRNA gene sequences generated, showing the diversity of the microbial communities. Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Chloroflexi and Bacteroidetes were found to be the six dominant phyla in all samples. Canonical correspondence analysis showed that pH, followed by annual average precipitation, annual average temperature, annual average relative humidity and city sunshine hours, Mn and Mg were the factors most highly correlated with the bacterial community variance. Urbanization did have an effect on bacterial community composition of urban park soils but it contributed less to the total variance compared with geographical locations and soil properties, which explained 6.19% and 16.78% of the variance, respectively.

[Distribution characteristics of rice photosynthesized carbon in soil aggregates of different size and density].

Rice growth affects the distribution of organic matter in soils and soil fractions, and is thus an important factor to control the storage of soil organic matter. The aims of our study were to quantify the photosynthesized C in soil fraction pools of different size and density during the rice growth, and also to offer data evidence not only in the mechanisms of SOC accumulation, but also in C sequestration potential in paddy soils. Therefore, the microcosm experiment was carried out to quantify the input and distribution of photo-assimilated carbon (C) in soils size and density aggregates pools by using continuous 14C labeling technique. Destructive samplings of rice (Oryza sativa) were conducted after labeling for 80 days. The allocation of 14C-labeled photosynthates in soil C pools was examined in rice-planted soil over the 14C labeling span using the size (250-2 000 microm, 20-250 microm, < 20 microm) and density (light and heavy) fractionation procedure. The amount of 14C in the soil organic C (SOC14) in the 250-2 000 microm particle size was dependent on the soils, ranged from 118.23 mg x kg(-1) to 309.94 mg x kg(-1), accounting for 0.52%-1.55% of its SOC, respectively, which was much larger than those of aggregates with the other two sizes (20-250 microm, < 20 microm). Moreover, the amounts of SOC14 in light fractions of 250-2 000 microm and 20-250 microm particle size aggregate were significantly greater than those in their heavy fractions (P < 0.05). The data suggested that rice photosynthesize C mainly entered into the light fraction of 250-2 000 microm particle size aggregate by rhizodeposition, which enhanced the contents of SOC. There was a significant positive correlation between the light and heavy fraction and 250-2000 microm particle size aggregate, 20-250 microm and < 20 microm particle size aggregate of SOC14, although significant negative correlation between light fractions in < 20 microm, 20-250 microm aggregates was observed.

[Quantifying rice (Oryza sativa L.) photo-assimilated carbon input into soil organic carbon pools following continuous 14C labeling].

The microcosm experiment was carried out to quantify the input and distribution of photo-assimilated C into soil C pools by using a 14C continuous labeling technique. Destructive samplings of rice (Oryza sativa) were conducted after labeling for 80 days. The allocation of 14C-labeled photosynthates in plants and soil C pools such as dissolved organic C (DOC) and microbial biomass C (MBC) in rice-planted soil were examined over the 14C labeling span. The amounts of rice shoot and root biomass C was ranged from 1.86 to 5.60 g x pot(-1), 0.46 to 0.78 g x pot(-1) in different tested paddy soils after labeling for 80 days, respectively. The amount of 14C in the soil organic C (14C-SOC) was also dependent on the soils, ranged from 114.3 to 348.2 mg x kg(-1), accounting for 5.09% to 6.62% of the rice biomass 14C, respectively. The amounts of 14C in the dissolved organic C (14C-DOC) and in the microbial biomass C(14C-MBC), as proportions of 14C-SOC, were 2.21%-3.54% and 9.72% -17.2%, respectively. The 14C-DOC, 14C-MBC, and 14C-SOC as proportions of total DOC, MBC, and SOC, respectively, were 6.72% -14.64%, 1.70% -7.67%, and 0.73% -1.99%, respectively. Moreover, the distribution and transformation of root-derived C had a greater influence on the dynamics of DOC and MBC than on the dynamics of SOC. Further studies are required to ascertain the functional significance of soil microorganisms (such as C-sequestering bacteria and photosynthetic bacteria) in the paddy system.