Jinbo Zhang

Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea

The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, 15N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and forest soil (pH 5.4) and was inhibited by acetylene. Nitrification activity was significantly stimulated by urea fertilization and coupled well with abundance changes in archaeal amoA genes in acidic soils. Pyrosequencing of 16S rRNA genes at whole microbial community level demonstrates the active growth of AOA in urea-amended soils. Molecular fingerprinting further shows that changes in denaturing gradient gel electrophoresis fingerprint patterns of archaeal amoA genes are paralleled by nitrification activity changes. However, bacterial amoA and 16S rRNA genes of AOB were not detected. The results strongly suggest that archaeal ammonia oxidation is supported by hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate nitrification in two acidic soils tested.

Mechanisms for the retention of inorganic N in acidic forest soils of southern China

The mechanisms underlying the retention of inorganic N in acidic forest soils in southern China are not well understood. Here, we simultaneously quantified the gross N transformation rates of various subtropical acidic forest soils located in southern China (southern soil) and those of temperate forest soils located in northern China (northern soil). We found that acidic southern soils had significantly higher gross rates of N mineralization and significantly higher turnover rates but a much greater capacity for retaining inorganic N than northern soils. The rates of autotrophic nitrification and NH3 volatilization in acidic southern soils were significantly lower due to low soil pH. Meanwhile, the relatively higher rates of NO3− immobilization into organic N in southern soils can counteract the effects of leaching, runoff, and denitrification. Taken together, these processes are responsible for the N enrichment of the humid subtropical forest soils in southern China.

N2O production pathways in the subtropical acid forest soils in China.

To date, N(2)O production pathways are poorly understood in the humid subtropical and tropical forest soils. A (15)N-tracing experiment was carried out under controlled laboratory conditions to investigate the processes responsible for N(2)O production in four subtropical acid forest soils (pH<4.5) in China. The results showed that denitrification was the main source of N(2)O emission in the subtropical acid forest soils, being responsible for 56.1%, 53.5%, 54.4%, and 55.2% of N(2)O production, in the GC, GS, GB, and TC soils, respectively, under aerobic conditions (40%-52%WFPS). The heterotrophic nitrification (recalcitrant organic N oxidation) accounted for 27.3%-41.8% of N(2)O production, while the contribution of autotrophic nitrification was little in the studied subtropical acid forest soils. The ratios of N(2)O-N emission from total nitrification (heterotrophic+autotrophic nitrification) were higher than those in most previous references. The soil with the lowest pH and highest organic-C content (GB) had the highest ratio (1.63%), suggesting that soil pH-organic matter interactions may exist and affect N(2)O product ratios from nitrification. The ratio of N(2)O-N emission from heterotrophic nitrification varied from 0.02% to 25.4% due to soil pH and organic matter. Results are valuable in the accurate modeling of N2O production in the subtropical acid forest soils and global budget.

Heterotrophic nitrification is the predominant NO 3 − production mechanism in coniferous but not broad-leaf acid forest soil in subtropical China

A study was carried out to investigate the potential gross nitrogen (N) transformations in natural secondary coniferous and evergreen broad-leaf forest soils in subtropical China. The simultaneously occurring gross N transformations in soil were quantified by a 15N tracing study. The results showed that N dynamics were dominated by NH4+ turnover in both soils. The total mineralization (from labile and recalcitrant organic N) in the broad-leaf forest was more than twice the rate in the coniferous forest soil. The total rate of mineral N production (NH4+ + NO3−) from the large recalcitrant organic N pool was similar in the two forest soils. However, appreciable NO3− production was only observed in the coniferous forest soil due to heterotrophic nitrification (i.e. direct oxidation of organic N to NO3−), whereas nitrification in broad-leaf forest was little (or negligible). Thus, a distinct shift occurred from predominantly NH4+ production in the broad-leaf forest soil to a balanced production of NH4+ and NO3− in the coniferous forest soil. This may be a mechanism to ensure an adequate supply of available mineral N in the coniferous forest soil and most likely reflects differences in microbial community patterns (possibly saprophytic, fungal, activities in coniferous soils). We show for the first time that the high nitrification rate in these soils may be of heterotrophic rather than autotrophic nature. Furthermore, high NO3− production was only apparent in the coniferous but not in broad-leaf forest soil. This highlights the association of vegetation type with the size and the activity of the SOM pools that ultimately determines whether only NH4+ or also a high NO3− turnover is present.

Illumina MiSeq investigations on the changes of microbial community in the Fusarium oxysporum f.sp. cubense infected soil during and after reductive soil disinfestation

Although reductive soil disinfestation (RSD) is increasingly used for the control of soil-borne diseases, its impact on the soil microbial community during and after RSD remains poorly understood. MiSeq pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the changes of microbial community in the Fusarium oxysporum f. sp. cubense (FOC) infected soil during RSD and at the simulative banana cultivation after RSD. The results showed that RSD significantly increased soil microbial populations and a different microbial community with the pathogenic soil was established after RSD. Specifically, the number of Firmicutes mainly containing Ruminococcus and Coprococcus followed by a small part of Clostridium which were the dominant bacterial genera significantly increased during RSD. In contrast, Symbiobacterium and Flavisolibacter were the dominant genera in the flooding soil. When the soils were recovered under aerobic condition, the relative abundances of the bacteria belonging to the phylum Bacteroidetes, Acidobacteria, Planctomycetes increased as alternatives to the reducing Firmicutes. For fungi, the population of F. oxysporum significantly decreased during RSD accompanied with the pH decline, which resulted in the significant decrease of relative abundance in the phylum Ascomycota. Alternatively, the relative abundances of some other fungal species increased, such as Chaetomium spp. and Penicillium spp. belonging to Ascomycota and the family Clavulinaceae belonging to Basidiomycota. Then, the relative abundance of Ascomycota re-increased after RSD with Podospora and Zopfiella as dominant genera, whereas the relative abundance of Fusarium further decreased. Overall, the microbial populations and community re-established by RSD made the soil more disease-suppressive and beneficial to the soil nutrient cycling and plant growth compared with the previous pathogenic soil.

Effects of soil moisture, temperature, and nitrogen fertilization on soil respiration and nitrous oxide emission during maize growth period in northeast China

Abstract To evaluate the response of soil respiration and nitrous oxide (N2O) emission to soil moisture, temperature and nitrogen fertilization, and to estimate the contribution of soil and rhizosphere to total soil carbon dioxide (CO2) and N2O emissions, a field experiment was conducted in the Sanjiang Mire Wetland Experimental Station, Chinese Academy of Sciences, in the northeast of China. The experiment included four treatments: bare soil fertilized with 150 kg N ha−1 yr−1 (CK), and maize-cropped soils amended with 0 (N0), 150 (N150), and 250 (N250) kg N ha−1 yr−1. The cumulative soil CO2 emission in the CK, N0, N150, and N250 treatments was estimated to be 698, 863, 962, and 854 g CO 2 C m−2, respectively. The seasonal soil CO2 fluxes were significantly affected by soil temperature, with a Q 10 value between 1.99 and 2.47. Analysis of the stepwise regression indicated that the CO2 flux can be quantitatively described by a linear combination of soil moisture content and soil temperature 5 cm below ground. Approximately 70, 58, 60, and 44% of the variability in CO2 flux can be explained by these two parameters, in CK, N0, N150, and N250, respectively. Nitrogen fertilization with 150 kg N ha−1 yr−1 increased CO2 fluxes by 14.5% compared with soils fertilized with 0 kg N ha−1 yr−1. However, in the soil fertilized with 250 kg N ha−1 yr−1, high N fertilization suppressed soil respiration. There was an exponential relationship between soil temperature 5 cm below ground and N2O flux, with a Q 10 value of 1.30–2.91. Mean cumulative soil N2O emissions during the maize-growing season in the CK, N0, N150, and N250 treatments were estimated to be 86, 44, 200, and 484 mg N2O-N m−2, respectively. In contrast to the maize planting, soil fertilized with 150 kg N ha−1 yr−1 and with 250 kg N ha−1 yr−1 increased N2O fluxes by 354 and 1000%, compared with soils fertilized with 0 kg N ha−1 yr−1, respectively. Soil respiration and N2O fluxes measurement using the root-exclusion technique indicated that the rhizosphere of the maize could be the dominant habitat of soil respiration and N2O formation.

Toxic organic acids produced in biological soil disinfestation mainly caused the suppression of Fusarium oxysporum f. sp. cubense

Biological soil disinfestation (BSD) is an effective and environmentally friendly way to suppress soil-borne pathogens. Although it is increasingly used in USA, the Netherlands and Japan, its precise mechanism has not been well quantified so far. Quantitative real-time PCR, denaturing gradient gel electrophoresis and high performance liquid chromatography were used for investigating the role of organic acids in the mechanisms of BSD. The results showed that BSD significantly reduced the population of Fusarium oxysporum in soil. Simultaneously, in BSD treatments, the soil pH significantly decreased and some organic acid producers, such as Clostridia sp., were observed. Four kinds of toxic organic acids to F. oxysporum were detected in soil solutions of BSD treatments. Acetic acid and butyric acid were the primary organic acids, followed by small amounts of isovaleric acid and propionic acid. The verification test directly demonstrated that the toxic organic acids with the maximal doses detected in BSD significantly suppressed F. oxysporum, Rhizoctonia solani and Ralstonia solanacearum.

Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation.

Reductive soil disinfestation (RSD) has been proven to be an effective and environmentally friendly way to control many soilborne pathogens and diseases. In this study, the RSDs using ethanol (Et-RSD) and alfalfa (Al-RSD) as organic carbons were performed in a Rhizoctonia solani-infected soil, and the dissimilarities of microbial communities during the RSDs and after planting two seasons of cucumber seedlings in the RSDs-treated soil were respectively investigated by MiSeq pyrosequencing. The results showed that, as for bacteria, Coprococcus, Flavisolibacter, Rhodanobacter, Symbiobacterium, and UC-Ruminococcaceae became the dominant bacterial genera at the end of Al-RSD. In contrast, Et-RSD soil involved more bacteria belonging to Firmicutes, such as Sedimentibacter, UC-Gracilibacteraceae, and Desulfosporosinus. For fungi, Chaetomium significantly increased at the end of RSDs, while Rhizoctonia and Aspergillus significantly decreased. After planting two seasons of cucumber seedlings, those bacteria belonging to Firmicutes significantly decreased, but Lysobacter and Rhodanobacter belonging to the phylum Proteobacteria as well as UC-Sordariales and Humicola belonging to Ascomycota alternatively increased in Al- and Et-RSD-treated soils. Besides, some nitrification, denitrification, and nitrogen fixation genes were apparently increased in the RSD-treated soils, but the effect was more profound in Al-RSD than Et-RSD. Overall, Et-RSD could induced more antagonists belonging to Firmicutes under anaerobic condition, whereas Al-RSD could continuously stimulate some functional microorganisms (Lysobacter and Rhodanobacter) and further improve nitrogen transformation activities in the soil at the coming cropping season.

Soil pH was the main controlling factor of the denitrification rates and N2/N2O emission ratios in forest and grassland soils along the Northeast China Transect (NECT)

The Northeast China Transect (NECT) is a mid-latitude terrestrial transect in the International Geosphere-Biosphere Programme. Its major environmental gradient is precipitation, which gradually decreases from the eastern mountainous region to the western pastoral area. In this investigation, a series of forest and grassland soils were sampled along the NECT, and the denitrification rate and nitrogen/nitrous oxide (N2/N2O) ratio were studied under laboratory conditions by the acetylene inhibition method. Forest soils were all acidic, with soil pH values ranging from 4.3 to 5.9 and soil organic carbon ranging from 32.0 to 54.7 g kg−1. Soil pH for grassland soils was approximately neutral, ranging from 6.1 to 7.8, while soil organic carbon ranged from 14.8 to 32.2 g kg−1. The highest denitrification rates (average 1.1 ± 0.2 mg N kg−1 h−1) were in grassland soils in the western part of the NECT, while the lowest were in forest soils (average 0.25 ± 0.1 mg N kg h−1) in the eastern part of the NECT. The denitrification rate increased linearly from east to west along the NECT (p < 0.01). Nitrous oxide was the main component of gas products of denitrification in forest soils, while N2 was the dominant denitrification product in grassland soils. The ratio of N2/N2O increased linearly from east to west along the NECT (p < 0.01). Soil pH was the best predictor of the denitrification rate and of the N2/N2O ratio in grassland and forest soils along the NECT.

The characteristics of soil N transformations regulate the composition of hydrologic N export from terrestrial ecosystem

It is important to clarify the quantity and composition of hydrologic N export from terrestrial ecosystem and its primary controlling factors, because it affected N availability, productivity, and C storage in natural ecosystems. The most previous investigations were focused on the effects of N deposition and human disturbance on the composition of hydrologic N export. However, few studies were aware of whether there were significant differences in the concentrations and composition of hydrologic N export from natural ecosystems in different climate zones and what is the primary controlling factor. In the present study, three natural forest ecosystems and one natural grassland ecosystem that were located in different climate zones and with different soil pH range were selected. The concentrations of total dissolved N, dissolved organic nitrogen (DON), NH4+, NO3- in soil solution and stream water, soil properties, and soil gross N transformation rates were measured to answer above questions. Our results showed that NO3- concentrations and the composition pattern of hydrologic N export from natural ecosystems varied greatly in the different climate zones. The NO3- concentrations in stream water varied largely, ranging from 0.1mgNL(-1) to 1.6mgNL(-1), while DON concentration in stream water, ranging from 0.1 to 0.9mgNL(-1), did not differ significantly, and the concentrations of NH4+ were uniformly low (average 0.1mgNL(-1)) in all studied sites. There was a trade-off relationship between the proportions of NO3- and DON to total dissolved N in stream water. In subtropical strongly acidic forests soil site, DON was the dominance in total dissolved N in stream water, while NO3--N became dominance in temperate acidic forests soil site, subtropical alkaline forests soil region, and the alpine meadow sites on the Tibetan Plateau. The proportions of NO3- to total dissolved N in both soil solution and stream water significantly increased with the increasing of the gross autotrophic nitrification rates (p<0.01). Our results indicated that the characteristics of soil N transformations were the most primary factor regulating the composition of hydrologic N losses from ecosystems. The nitrification was the central soil N transformation processes regulating N composition in soil solution and hydrologic N losses. These results provided important information on understanding easily the composition of hydrologic N export from terrestrial ecosystem.