Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing

Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.     

Spectral Exploration of Calcium Accumulation in Organic Matter in Gray Desert Soil from Northwest China

Little attention has been paid to the accumulation of soil organic matter (SOM) in the fringes of the mid-latitude desert. In this paper, soil samples from a long-term field experiment conducted from 1990 to 2013 at a research station in Urumqi, China by different fertilizer treatments, were used to determine soil properties and soil dissolved organic matter (DOM) by chemical analysis, fluorescence excitation emission matrix (EEM) spectroscopy, and high resolution-transmission electron microscopy (HR-TEM). The binding features of DOM under the addition of Ca²⁺ were analyzed using a two-dimensional (2D) Fourier transform infrared (FTIR) spectrometer further to explore the response of the DOM to increasing concentrations of Ca²⁺. Long-term application of chemical fertilizers and goat manure increased soil organic carbon (SOC) by 1.34- and 1.86-fold, respectively, relative to the non-fertilized control (8.95g.kg^-1). Compared with the control, application of chemical fertilizers and manure significantly increased the concentrations of Ca, Mg, Si, humic and fulvic acid-like substances in DOM but decreased the amounts of trivalent metals (Al and Fe) and protein-like substances. Although crystalline Al/Fe nanoparticles and amorphous or short-range-order Si/Al nanoparticles existed in all DOM samples, crystalline Ca/Si nanoparticles were predominant in the samples treated with goat manure. Although organic matter and Si-O-containing nanoparticles were involved in the binding of Ca²⁺ to DOM, application of chemical fertilizers weakened Ca²⁺ association with components of the amide II group (1510 cm^-1) and Si-O linkage (1080 cm^-1), whereas application of goat manure enhanced the affinity of Ca²⁺ for Si-O linkage. Our results suggested that the enrichment of Ca in gray desert soil possibly helps accumulate SOM by forming crystalline Ca/Si nanoparticles in addition to Ca²⁺ and organic matter complexes.     

蚓粪中的植物激素及其对绿豆插条不定根发生的促进作用

利用高效液相色谱证实了环毛蚓（Pheretima sp.)蚓粪中至少存在两种植物激素（IAA和GA3）,蚓粪中IAA和GA3的含量分别可达13.9mg/kg和49.9mg/kg。为原土的13.6和8.2倍,采用包括蚓粪提取液,原土提取液,Haogland营养液,蒸馏水,IAA,GA3等在内的11种供试液进行绿豆插条不定根发生的生物试验,结果表明,在相同条件下,蚓粪提取液处理的绿豆插条比其它处理提早3天出现不定根,统计证明,与原土提取液,Haogland营养液,蒸馏水等处理相比,蚓粪提取液处理可显提高绿豆插条不定根的数量,长度和生物量,蚓粪提取液对不定根发生数量的诱导效应与85-170μmol/L的IAA溶液相当,但从不定根根长和根生长量来看,蚓粪提取液的效果优于IAA。     

根瘤菌在小麦与紫云英混作中的作用

采用盆钵实验,在小麦与紫云英混作系统中,通过对紫云英接种根瘤菌,研究了小麦与紫云英生长过程中植株生长、植株生物量、植株与土壤氮素变化情况及根瘤菌的酶活性．结果表明,在有根瘤菌接种的混作体系中,植株的生长得到促进,植株及土壤全氮均有增加,酶活性比单作也有所提高．     

变性梯度凝胶电泳法研究我国不同土壤氨氧化细菌群落组成及活性

实验选用了我国3种不同土壤研究土壤硝化活性、硝化细菌数量,并使用变性梯度凝胶电泳(DGGE)的方法研究了不同土壤中氨氧化细菌(AOB)区系变化。通过28d的土壤培养实验研究发现,潮土具有最强的硝化势,几乎100%的铵态氮转化为硝态氮;而红壤中的硝化势最弱,只有4.9%的铵态氮转化为硝态氮。对这3种土壤硝化细菌进行计数发现,3种土壤氨氧化菌数量差异显著,而3种土壤亚硝酸氧化菌(NOB)处于一个数量级。采用氨氧化菌功能基因amoA(氨单加氧酶ammoniamonooxygenase)特异PCR结合DGGE的方法对土壤氨氧化菌区系进行分析。红壤有4个氨氧化菌种属,与潮土和黄泥土没有共同的氨氧化菌种属。4个种属中两个是与潮土和黄泥土亲源性比较远的,特有的氨氧化菌种属,这两个种属与已知的Nitrosospira属的cluster3bz97838和Nitrosospira属的cluster3aAF353263亲源性比较近。潮土有5个氨氧化菌种属,潮土与黄泥土有两个共同的氨氧化菌种属,这两个种属中的一个是潮土和黄泥土特有的,与其他氨氧化菌种属亲源性比较远的氨氧化菌种属,这个种属与已知的Nitrosospira属的cluster3bZ97849亲源性比较近。黄泥土有4个氨氧化菌种属,除了与潮土共有的一个种属是两种土壤特有的氨氧化菌种属外,黄泥土还有一个与其他氨氧化菌种属亲源性比较远的,黄泥土特有的种属,与Nitrosospira属的cluster3aAF353263亲源性很近。3种土壤中分离到的硝化细菌表现出不同的硝化能力。实验结果表明,以amoA基因为目标的PCR-DGGE是比以16SrDNA为目标的PCR-DGGE更有效的研究氨氧化菌种群的方法;3种土壤的氨氧化菌种群差异显著,尤其是红壤的氨氧化菌种群与另外两种土壤差异明显,这种差异可能与红壤的低pH条件对氨氧化菌种群的长期选择有关;3种土壤中的硝化活性与土壤中的硝化细菌数量没有显著相关,可能由于3种土壤差异显著的土壤环境对硝化活性的影响造成。因此在对不同土壤硝化细菌进行研究时不仅需要对硝化细菌数量进行研究,还需要研究不同土壤中硝化细菌的种属及不同土壤环境条件对硝化细菌硝化活性的影响。     

Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition

The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hypothesized that inhibiting such pathogen helpers may help reduce pathogen densities. We examined tripartite interactions between a model pathogen, Ralstonia solanacearum, two model helper strains and a collection of 46 bacterial isolates recovered from the tomato rhizosphere. This system allowed us to examine the importance of direct (effects of rhizobacteria on pathogen growth) and indirect (effects of rhizobacteria on helper growth) pathways affecting pathogen growth. We found that the interaction between rhizosphere isolates and the helper strains was the major determinant of pathogen suppression both in vitro and in vivo. We therefore propose that controlling microbiome composition to prevent the growth of pathogen helpers may become part of sustainable strategies for pathogen control.Subject terms: Microbial ecology, Microbial ecology, Microbial ecology     

An Ex Vivo Model for Anti-Angiogenic Drug Testing on Intact Microvascular Networks

New models of angiogenesis that mimic the complexity of real microvascular networks are needed. Recently, our laboratory demonstrated that cultured rat mesentery tissues contain viable microvascular networks and could be used to probe pericyte-endothelial cell interactions. The objective of this study was to demonstrate the efficacy of the rat mesentery culture model for anti-angiogenic drug testing by time-lapse quantification of network growth. Mesenteric windows were harvested from adult rats, secured in place with an insert, and cultured for 3 days according to 3 experimental groups: 1) 10% serum (angiogenesis control), 2) 10% serum + sunitinib (SU11248), and 3) 10% serum + bevacizumab. Labeling with FITC conjugated BSI-lectin on Day 0 and 3 identified endothelial cells along blood and lymphatic microvascular networks. Comparison between day 0 (before) and 3 (after) in networks stimulated by 10% serum demonstrated a dramatic increase in vascular density and capillary sprouting. Growing networks contained proliferating endothelial cells and NG2+ vascular pericytes. Media supplementation with sunitinib (SU11248) or bevacizumab both inhibited the network angiogenic responses. The comparison of the same networks before and after treatment enabled the identification of tissue specific responses. Our results establish, for the first time, the ability to evaluate an anti-angiogenic drug based on time-lapse imaging on an intact microvascular network in an ex vivo scenario.     

Optimization, purification, characterization and antioxidant activity of an extracellular polysaccharide produced by Paenibacillus polymyxa SQR-21

The optimization, purification and characterization of an extracellular polysaccharide (EPS) from a bacterium Paenibacillus polymyxa SQR-21 (SQR-21) were investigated. The results showed that SQR-21 produced one kind of EPS having molecular weight of 8.96 × 10⁵ Da. The EPS was comprised of mannose, galactose and glucose in a ratio of 1.23:1.14:1. The ratio of monosaccharides and glucuronic acid was 7.5:1. The preferable culture conditions for EPS production were pH 6.5, temperature 30 °C for 96 h with yeast extract and galactose as best N and C sources, respectively. The maximum EPS production (3.44 g L⁻¹) was achieved with galactose 48.5 g L⁻¹, Fe³⁺ 242 μM and Ca²⁺ 441 μM. In addition, the EPS showed good superoxide scavenging, flocculating and metal chelating activities while moderate inhibition of lipid peroxidation and reducing activities were determined. These results showed the great potential of EPS produced by SQR-21 to be used in industry in place of synthetic compounds.