Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe

Serious nitrogen (N) deposition in terrestrial ecosystems causes soil acidification and changes the structure and function of the microbial community. However, it is unclear how these changes are dependent on N deposition rates, other factors induced by N (e.g., pH), and their interactions. In this study, we investigated the responses of soil prokaryotic community structure and stability after a 13-year N addition in the semi-arid Leymus chinensis steppe in Inner Mongolia, China. Our results demonstrated that the prokaryotic community structure changed at the low N addition rate of 1.75 g N m⁻² yr⁻¹; however, dramatic changes in microbial abundance, respiratory quotient, and prokaryotic diversity occurred at N addition rates of more than 5.25 g N m⁻² yr⁻¹ when the soil pH dropped below 6.0. The two patterns indicated the difference in driving forces for different microbial properties. The N-driven and pH-driven processes are likely the most important mechanisms determining the responses of bacterial community to N. Some copiotrophic/oligotrophic bacteria, e.g., Proteobacteria and Acidobacteria, changed their relative abundances with the N addition continuously even at a low rate, indicating that they were more sensitive to N directly. Some bacterial groups significantly changed their relative abundance at a high N addition rate when pH dropped below 6.0, e.g., Verrucomicrobia and Armatimonadetes, indicating that they were more sensitive to pH below 6.0. N addition altered the prokaryotic community structure through enrichment of copiotrophic bacteria (species adjustment) at low N addition rates and through enrichment of nitrophilous taxa and significant loss of diversity at high N rates. The results also demonstrated that a high N addition diminished the stability of the prokaryotic community structure and activity through reduction in species diversity and bacterial interaction. Overall, this study supported the hypothesis that the responses of prokaryota to N were dependent on deposition rates, and N-driven and pH-driven processes were the important mechanisms to control the shift of the prokaryotic community.     

Oscillating dynamics of bacterial populations and their predators in response to fresh organic matter added to soil: The simulation model ‘BACWAVE-WEB’

Recently, regular oscillations in bacterial populations and growth rates of bacterial feeding nematodes (BFN) were shown to occur after addition of fresh organic matter to soil. This paper presents a model developed to investigate potential mechanisms of those oscillations, and whether they were initiated by bacteria-substrate interactions or by predatory regulation of bacteria. The model was also used to investigate mineral nitrogen release during short-term organic matter decomposition. Experimental data originated from several microcosm experiments with a sandy soil amended with clover-grass mixture. Numbers of bacteria and BFN, and nitrate and ammonium content in soil were measured daily during about a month, whereas protozoa were counted occasionally. A substrate-based food web model was constructed with 3 plant residue and 5 soil organic matter compartments, 3 trophic groups of bacteria (copiotrophic, oligotrophic and hydrolytic), and two predatory groups (BFN and protozoa). Both carbon and nitrogen flows between these compartments were modelled. Fluctuations in microbial populations in soil after plant residue incorporation could be reproduced with and without participation of predators. The first two peaks in bacterial numbers were mainly related to bacteria-substrate interactions, while predators (particularly protozoa) influenced bacterial dynamics during later stages of bacterial community development. Oligotrophic bacteria had a stabilizing effect on fluctuations of other trophic groups, and were the main source of nutrients for predators. A peak in soil ammonium occurred within 1 week after residue incorporation. Nitrate increased sigmoidally after a short lag phase. The final nitrate concentration was primarily determined by bacterial dynamics, and to a lesser extent by protozoa and nematodes. This model indicates the importance of substrate-consumer relations for regulation of populations at different trophic levels and nutrient release from fresh organic matter added to soil.     

黑钙土中真菌的时空分布及其在贫营养条件下菌落特征研究

[目的]对黑钙土中真菌的时空分布及其在贫营养条件下菌落特征进行研究。[方法]采用稀释平板法对真菌进行分离,用单孢子分离法进行纯化,用不同稀释浓度的察贝克培养基进行培养计数。[结果]从供试黑钙土中分离出9种真菌菌属,并且确定了4种优势菌属,同时发现黑钙土中真菌数量分布呈现出明显的季节性,并且随采样深度增加其数量呈现减少的趋势,在贫营养条件下真菌种类和数量均明显减少。[结论]该研究可为黑钙土中微生物的相关研究提供理论依据。     

陕北黄土寡营养环境微生物次生代谢产物的初步研究

[目的]探索适合陕北黄土寡营养环境微生物的分离和培养方法。[方法]采用寡营养培养基分离筛选法与单菌丝顶端挑取法,对陕北黄土土样中的极端寡营养环境微生物进行分离纯化,通过硅胶薄层层析法,对筛选出的菌株的次生代谢产物进行分析。[结果]从黄土中分离出18株极端寡营养环境微生物,从石样风化土中分离出2株极端寡营养环境微生物。其中由pH值为4的培养基中分离出8株菌株,pH值为10的培养基中分离出12株菌株。JDA-03、JDA-04、JDA-05、JDA-06、JDA-07、JDB-11、JDB-13菌株的次生代谢产物丰富,JDB-9、JDB-10菌株的次生代谢产物中含有萜类物质。[结论]该研究为开发利用陕北黄土中特有的微生物资源奠定了基础。     

Linear versus Monod representation of ammonia oxidation rates in oligotrophic recirculating aquaculture systems

Monod kinetics are widely used to model nitrifying biofilters. However, these kinetics are incapable of representing the collapse of volumetric TAN conversion rate (VTR) under high organic loadings. Failure to recognize the underlying heterotrophic interference can lead to calibration issues as a single Monod function is applied across contrasting levels of carbon loading. This, plus an historic bias towards the analysis of peak carrying capacities leave modelers poorly prepared to serve the needs of a mariculture industry demanding oligotrophic designs for broodstock maturation and larval/fingerling production. Consequently, data was generated by a Monte Carlo technique under the assumption of heterotrophic inhibition to nitrification. The data was used to compare the accuracy of calibration of the Monod relationship using the traditional Lineweaver–Burke and Eadie–Hofstee calibration methods against direct linear regression for low substrate (mesotrophic/oligotrophic) regimes. The results indicate that a simple linear relationship with a zero intercept, calibrated on data ranging from 0.1 to 0.5 g-TAN m⁻³, is most suitable for the representation of the mesotrophic/oligotrophic performance of nitrifying biofilters based on a comparison of SSE for both the Monte Carlo and field data analyzed herein. Additionally, the coefficient of variation was found to be between 7 and 8% for the parameter τ, which is the slope of the linear relationship between total ammonia nitrogen (TAN) and VTR while the CV for the Monod parameters ranged between 22 and 143% for VTR_max and between 29 and 137% for the apparent half-saturation constant showing the improved stability of the linear model to that of the Monod model.     

A quantitative evaluation and phylogenetic characterization of oligotrophic denitrifying bacteria harbored in subsurface upland soil using improved culturability

This is the first investigation to show that oligotrophic denitrifying bacteria are dominant denitrifiers in subsurface upland soil. We examined the vertical distribution of denitrifying bacterial populations in upland soil using two kinds of enumeration media. The number of denitrifying bacteria, enumerated in subsurface soil layers by a 100-fold diluted nutrient broth (DNB) medium with NO₃ ⁻, was two to three orders of magnitude greater than those enumerated by a conventional nutrient broth medium with NO₃ ⁻, suggesting the dominance of oligotrophic denitrifying bacteria. Seventy-four percent of the total denitrifying bacterial isolates were DNB organisms of the oligotrophic type, which did not show appreciable growth on a conventional nutrient broth medium. The isolates were heterogeneous and were categorized as alpha (35 strains) and beta (19 strains) subdivisions of proteobacteria and high G+C gram-positive bacteria (7 strains) by 16S rRNA gene sequence analysis. The 35-alpha subdivision of proteobacterial isolates was of oligotrophic type and widely distributed from the surface to subsurface soil layers. Phylogenetic analysis indicated that some isolates belonged to groups with few or no cultivated representatives, and that one isolate may be a member of a new genus. This isolation procedure, using diluted media, is valuable in detecting diverse and novel denitrifying bacteria in the subsurface soil.     

Grouping of soil bacteria by analysis of colony formation on agar plates

Summary The colony formation of soil bacteria was studied in relation to incubation time. The process was simulated by a colony-forming curve (CFC) which was a superposition of several component curves (cCFC) given theoretically by the first-order reaction (FOR) model. This model had been previously proposed to define the colony formation of cells of a single culture. Soil bacteria were divided into several groups by these cCFC, as different types of bacteria produced their own colonies. Bacteria belonging to a single group grew at a similar rate on the plating medium and each group was characterized by a different growth rate. Most copiotrophic bacteria were fast growers and most oligotrophic bacteria slow growers.     

偏最小二乘回归法在海洋初级生产力影响因子分析中的应用

叶绿素a浓度是浮游植物生物量的重要指标,能反映出海洋初级生产力的状况。从海洋监测数据中,分析影响叶绿素a浓度的理化环境因子,尝试找出海洋初级生产力的主导因子。将数据标准化,运用变量投影重要性分析和T2椭圆图等辅助分析技术进行成分提取,进行偏最小二乘回归分析。实验结果表明,在贫营养化的川岛外水域,对叶绿素a影响能力最大的因子为磷酸盐和无机氮,其次为酸碱度、盐度和水温,溶解氧影响能力最小。但在富营养化的沙堤口水域,影响能力最大的因子为化学需氧量和溶解氧,水温也成为影响海洋初级生产力的重要因子,而无机氮却成为非重要因子。从以上结果可见,运用偏最小二乘回归法对叶绿素a影响因子进行探讨,既能在监测数据较少的条件下建立数学模型,又能解决多元回归分析时各理化环境因子之间存在多重相关性的问题,具有较高的相关分析精度。