Changes in microbial nutrient status during secondary succession and its modification by earthworms

Summary Microbial biomass, nutrient (N and P) status, and carbon and nutrient limitation of the microflora were investigated in soils from five different sites (field, 5-, 12-, and about 50-year-old fallow, beechwood), which represent different stages of a secondary succession from a wheat field to the climax ecosystem of a beechwood on limestone. In addition, the effect of faeces production by the substrate feeding earthworm species Octolasion lacteum (Örley) on the nutrient status of the soil microflora of these sites was studied. Humus had accumulated in the soil of the third fallow site, with an enhanced biomass of microflora. However, in the beechwood soil, which had the highest humus content, microbial biomass was lower than in the soil of the third fallow site and similar to that of the field and the two younger fallow sites. In general, soil microbial biomass was little affected by the passage of soil through the gut of O. lacteum. The soil microflora of the field, the 5-, 12-, and about 50-year-old fallow was limited by carbon, whereas in the beechwood soil phosphorus limited microbial growth. NItrogen availability to the soil microflora was low in the two younger fallow sites and high in the field and the third fallow. In the beechwood soil nitrogen supply did not affect microbial carbon utilization. Application of phosphorus stimulated glucose mineralization in the soil of the field, the third fallow, and the beechwood, but not in the two younger fallow sites. Therefor, the nutrient status of the soil microflora seems to have changed during secondary succession: presumably, during the first phase the availability of nitrogen decreased, whereas during the second phase microbial phosphorus supply became more important, which resulted in phosphorus limitation of the soil microflora in the climax ecosystem. The passage of soil through the gut of O. lacteum caused an alteration in the microbial nutrient status. Generally, microbial growth in earthworm casts was limited by carbon. The relative effect of the gut passage of the soils on microbial carbon utilization seems to increase during succession. Therefore, the effect of decomposer invertebrates on microbial nutrient supply seems to increase during secondary succession. In general, nitrogen did not limit microbial carbon utilization in earthworm casts. Phosphorus requirements of the soil microflora were lowered by the gut passage of the soil of the third fallow site and the beechwood, which indicates an increased phosphorus supply in earthworm casts. Howerver, this additional supply was not sufficient to enable optimal carbon utilization by the soil microflora. The results indicate that the effect of decomposer invertebrates on the soil microflora depends on the nutrient status of the ecosystem.     

Insecticidal and nematicidal properties of microbial metabolites

Summary Metabolites from 942 microbial isolates were screened for insecticidal and nematicidal properties. The isolates included 302 streptomycetes, 502 novel actinomycetes including representatives of 18 genera, 28 unidentified aerobic actinomycetes, 70 fungi and 40 bacteria other than actinomycetes. When diluted 10-fold, the metabolites from 55 isolates caused nearly 100% mortality in mosquito larvae (Aedes aegypti) within 24 h. These isolates included 27 isolates ofStreptomyces, four ofActinoplanes, three isolates each ofActinomadura andStreptoverticillium, two isolates each ofMicromonospora, Bacillus andPaecilomyces, and one isolate each ofMicropolyspora, Nocardiopsis, Streptosporangium, Oerskovia, Thermomonospora, Chainia, Pseudomonas, Fusarium, Monilia andSyncephalestrum. Two fungal isolates could not be identified to the generie level. Extracts from the culture broth of 18 isolates caused 100% mortality in mosquito larvae within 15 min to 24 h at a concentration of 1000 ppm. The LC₅₀ of partially purified products from two isolates was 1–2.5 ppm and that of the semipurified preparations from four other isolates was 50 ppm. Valinomycin was identified as an active component in the culture broth from one isolate. The culture broth from 15 isolates of aerobic actinomycetes and 4 of fungi were toxic toPanagrellus redivivus (Nematoda); these included 12 isolates with selective nematicidal properties.Michigan Agriculture Experiment Station, Journal Article No. 12321.     

宏基因组学与动物病原微生物检测

宏基因组学（ metagenome）是直接从土壤、海水、人及动物胃肠道、口腔、呼吸道、皮肤等环境中获取样品DNA,利用载体将其克隆到替代宿主细胞中构建宏基因文库,以高通量检测为主要技术来研究特定环境中全部微生物的基因组及筛选活性物质和基因的新兴学科。利用宏基因组学技术不仅能够有效地检测特定环境的微生物群落结构,扩展了微生物资源的利用空间,发展了新兴的高通量检测技术,丰富了生物信息学内容。基于宏基因组学研究方法在环境微生物研究中的优势,对近年来相关领域、方法及其在人及动物病原微生物研究中的应用进行综述,以期将此方法用于实验动物病原微生物的调查分析及动物疫情、生物安全的监测。     

海洋微生物学：新机遇，新挑战

海洋占地球表面积的71%,海洋微生物对海洋及人类的生活有重大影响。由于特殊的生存环境,海洋微生物能产生陆栖微生物所不能产生的结构新颖、作用特殊的生物活性物质,有潜力应用于医疗、食品、环境保护等各个领域。海洋微生物研究充满了新的机遇,同时也面临着新的挑战。《微生物学通报》本期推出了"海洋微生物学主题刊",旨在展现我国海洋微生物学研究的最新进展和成果,促进我国海洋微生物学的交流和发展。     

Electroactive mixed culture derived biofilms in microbial bioelectrochemical systems: the role of pH on biofilm formation, performance and composition

The pH-value played a crucial role for the development and current production of anodic microbial electroactive biofilms. It was demonstrated that only a narrow pH-window, ranging from pH 6 to 9, was suitable for growth and operation of biofilms derived from pH-neutral wastewater. Any stronger deviation from pH neutral conditions led to a substantial decrease in the biofilm performance. Thus, average current densities of 151, 821 and 730 μA cm(-2) were measured for anode biofilms grown and operated at pH 6, 7 and 9 respectively. The microbial diversity of the anode chamber community during the biofilm selection process was studied using the low cost method flow-cytometry. Thereby, it was demonstrated that the pH value as well as the microbial inocula had an impact on the resulting anode community structure. As shown by cyclic voltammetry the electron transfer thermodynamics of the biofilms was strongly depending on the solution's pH-value.     

Long-term cathode performance and the microbial communities that develop in microbial fuel cells fed different fermentation endproducts

To better understand how cathode performance and substrates affected communities that evolved in these reactors over long periods of time, microbial fuel cells were operated for more than 1 year with individual endproducts of lignocellulose fermentation (acetic acid, formic acid, lactic acid, succinic acid, or ethanol). Large variations in reactor performance were primarily due to the specific substrates, with power densities ranging from 835 ± 21 to 62 ± 1 mW/m³. Cathodes performance degraded over time, as shown by an increase in power of up to 26% when the cathode biofilm was removed, and 118% using new cathodes. Communities that developed on the anodes included exoelectrogenic families, such as Rhodobacteraceae, Geobacteraceae, and Peptococcaceae, with the Deltaproteobacteria dominating most reactors. Pelobacter propionicus was the predominant member in reactors fed acetic acid, and it was abundant in several other MFCs. These results provide valuable insights into the effects of long-term MFC operation on reactor performance.     

DGGE/TGGE技术及其在微生物分子生态学中的应用

变性梯度凝胶电泳(DGGE)和温度梯度凝胶电泳(TGGE)是近些年微生物分子生态学研究中的热点技术之一。由于DGGE／TGGE技术具有可靠性强、重现性高、方便快捷等优点,被广泛地应用于微生物群落多样性和动态性分析。文章对DGGE／TGGE技术原理与关键环节、局限性和应用前景进行了综述。     

Simultaneous organics removal and bio-electrochemical denitrification in microbial fuel cells

Simultaneous organics removal and bio-electrochemical denitrification using a microbial fuel cell (MFC) reactor were investigated in this study. The electrons produced as a result of the microbial oxidation of glucose in the anodic chamber were transferred to the anode, which then flowed to the cathode in the cathodic chamber through a wire, where microorganisms used the transferred electrons to reduce the nitrate. The highest power output obtained on the MFCs was 1.7 mW/m(2) at a current density of 15 mA/m(2). The maximum volumetric nitrate removal rate was 0.084 mg NO(3)(-)-N cm(-2) (electrode surface area) day(-1). The coulombic efficiency was about 7%, which demonstrated that a substantial fraction of substrate was lost without current generation.     

Application of biocathode in microbial fuel cells: cell performance and microbial community

Instead of the utilization of artificial redox mediators or other catalysts, a biocathode has been applied in a two-chamber microbial fuel cell in this study, and the cell performance and microbial community were analyzed. After a 2-month startup, the microorganisms of each compartment in microbial fuel cell were well developed, and the output of microbial fuel cell increased and became stable gradually, in terms of electricity generation. At 20 ml/min flow rate of the cathodic influent, the maximum power density reached 19.53 W/m3, while the corresponding current and cell voltage were 15.36 mA and 223 mV at an external resistor of 14.9 Omega, respectively. With the development of microorganisms in both compartments, the internal resistance decreased from initial 40.2 to 14.0 Omega, too. Microbial community analysis demonstrated that five major groups of the clones were categorized among those 26 clone types derived from the cathode microorganisms. Betaproteobacteria was the most abundant division with 50.0% (37 of 74) of the sequenced clones in the cathode compartment, followed by 21.6% (16 of 74) Bacteroidetes, 9.5% (7 of 74) Alphaproteobacteria, 8.1% (6 of 74) Chlorobi, 4.1% (3 of 74) Deltaproteobacteria, 4.1% (3 of 74) Actinobacteria, and 2.6% (2 of 74) Gammaproteobacteria.     

The need to study the holobiome for gainful uses of endophytes

It is established that endophytes (bacteria and fungi) affect positively several traits of their host plants including growth, nutrient acquisition, and tolerance to abiotic and biotic stressors. Owing to this, endophytes are envisaged as a route to improve sustainable agricultural production. However, such effects of endophytes on crops although evident under lab conditions, are devoid of consistency under field conditions. The main reason for this could be the lack of our understanding of the functioning of the endophytes as a consortium within the plant (holobiome). It is essential to study the complex web of interactions which operate in the inner tissues of plants harboring endophytes. I highlight here, alluding to the work on foliar fungal endophytes, the importance of studying endophytes as a consortium rather than merely as one species in isolation to better appreciate their role in the plant holobiome. Such an approach should aid in harnessing the technological potential of endophytes.     

Investigation of the microbial community structure and activity as indicators of compost stability and composting process evolution

In a bid to identify suitable microbial indicators of compost stability, the process evolution during windrow composting of poultry manure (PM), green waste (GW) and biowaste was studied. Treatments were monitored with regard to abiotic factors, respiration activity (determined using the SOUR test) and functional microflora. The composting process went through typical changes in temperature, moisture content and microbial properties, despite the inherent feedstock differences. Nitrobacter and pathogen indicators varied as a monotonous function of processing time. Some microbial groups have shown a potential to serve as fingerprints of the different process stages, but still they should be examined in context with respirometric tests and abiotic parameters. Respiration activity reflected well the process stage, verifying the value of respirometric tests to access compost stability. SOUR values below 1 mg O₂/g VS/h were achieved for the PM and the GW compost.     

微生物“暗物质”研究曙光

微生物是地球上生命的主体之一,拥有极为丰富多彩的代谢途径,在很大程度上塑造了使人类宜居的地球。由于绝大部分环境中的微生物无法被分离和培养,微生物被喻为生命物质中的"暗物质"。近年来,迅猛发展的基因组学技术有力地推动了微生物"暗物质"的研究,使我国微生物生态学科发展从"诞生期"和"启蒙期"跨越式发展到"暴发期",乐观预测未来可能进入一个具有鲜明特色的"领航期"。     

Impact of moisture dynamic and sun light on anthracene removal from soil

In a previous study, remediation of anthracene from soil was faster in the top 0–2 cm layer than in the lower soil layers. It was not clear whether this faster decrease was due to biotic or abiotic processes. Anthracene-contaminated soil columns were covered with black or transparent perforated polyethylene so that aeration occurred but that fluctuations in water content were minimal and light could reach (LIGHT treatment) or not reach the soil surface (DARK treatment), or left uncovered so that soil water content fluctuate and light reached the soil surface (OPEN treatment). The amount of anthracene, microbial biomass C, and microbial activity as reflected by the amount of CO₂ produced within 3 days were determined in the 0–2 cm, 2–8 cm, and 8–15 cm layer after 0, 3, 7, 14, and 28 days. In the 0–2 cm layer of the OPEN treatment, 17% anthracene remained, 48% in the LIGHT treatment and 61% in the DARK treatment after 28 days. In the 2–8 cm and 8–15 cm layer, treatment had no significant effect on the dissipation of anthracene from soil after 14 and 28 days. It was found that light and fluctuations in water content stimulated the removal of anthracene from the top 0–2 cm soil layer, but not from the lower soil layers. It can be speculated that covering contaminated soil or pilling it up will inhibit the dissipation of the contaminant.     

克拉玛依石油污染土壤微生物群落结构及其代谢特征

为了分析克拉玛依油区内土壤中正构烷烃含量间的差异,微生物群落生理多样性、微生物代谢活性在不同石油污染梯度土壤中的变化规律。本研究采用GC、平板稀释法、Biolog微平板技术探讨了土壤微生物群落特征在3种不同污染程度下的变化情况。研究表明,石油污染土壤烷烃含量与微生物代谢活性呈显著负相关(r=-0.783, p<0.05)。随着石油污染程度增加微生物数量呈下降趋势,不同石油污染土壤中细菌数量占决定优势,细菌>真菌>放线菌。不同石油污染土壤微生物群落对6大碳源的利用体现出差异。主成分分析(PCA)表明,清洁土壤与石油污染土壤对底物利用有明显差异。石油污染严重土样碳源利用率为"酯类>酸类>胺类>氨基酸类>单糖/糖苷/聚合糖类>醇类"。本研究成果为后期修复污染土壤时调整投入的碳源底物等提供科学帮助。     

微生物生态学驱动社会与经济“绿色高效发展”

面对物种数量繁多、生态分布广泛、生态功能强大的微生物资源,微生物生态学的任务一方面在于不断发现和认识这类生命"暗物质"及其存在机制,另一方面要充分挖掘和利用这些微生物资源。微生物生态学的应用从最早的混合发酵发展到极端微生物资源利用、微生物生态制剂开发逐渐拓展到合成微生物生态等多个领域。2019年10月在湖南省长沙市举行的"中国生态学学会微生物生态专业委员会学术年会"设立了3个与微生物生态学应用相关的分会场,本期《微生物学通报》也开辟了"人工生态系统微生物"栏目,凸显了我国微生物生态学在资源、能源和环境等应用领域的成果,让我们看到了其成为社会与经济"绿色高效发展"重要驱动力的希望。     

Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest

To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbondioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO₂ production and soil NH₄⁺ concentration, while microbial community characteristics correlated with N₂O production, nitrification potential, gross N-mineralization, and soil NO₃^– concentration, independent of environmentalcontrollers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes,particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2 years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology.     

Linking soil process and microbial ecology in freshwater wetland ecosystems

Soil microorganisms mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. These processes are of particular interest in freshwater wetland ecosystems where nutrient cycling is highly responsive to fluctuating hydrology and nutrients and soil gas releases may be sensitive to climate warming. In this review we briefly summarize research from process and taxonomic approaches to the study of wetland biogeochemistry and microbial ecology, and highlight areas where further research is needed to increase our mechanistic understanding of wetland system functioning. Research in wetland biogeochemistry has most often been focused on processes (e.g., methanogenesis), and less often on microbial communities or on populations of specific microorganisms of interest. Research on process has focused on controls over, and rates of, denitrification, methanogenesis, and methanotrophy. There has been some work on sulfate and iron transformations and wetland enzyme activities. Work to date indicates an important process level role for hydrology and soil nutrient status. The impact of plant species composition on processes is potentially critical, but is as yet poorly understood. Research on microbial communities in wetland soils has primarily focused on bacteria responsible for methanogenesis, denitrification, and sulfate reduction. There has been less work on taxonomic groups such as those responsible for nitrogen fixation, or aerobic processes such as nitrification. Work on general community composition and on wetland mycorrhizal fungi is particularly sparse. The general goal of microbial research has been to understand how microbial groups respond to the environment. There has been relatively little work done on the interactions among environmental controls over process rates, environmental constraints on microbial activities and community composition, and changes in processes at the ecosystem level. Finding ways to link process-based and biochemical or gene-based assays is becoming increasingly important as we seek a mechanistic understanding of the response of wetland ecosystems to current and future anthropogenic perturbations. We discuss the potential of new approaches, and highlight areas for further research.     

不同煤阶生物成因煤层气微生物群落的功能及多样性研究进展

生物成因煤层气是煤层气形成的主要途径之一,在各种煤阶的煤层气田中均发现有生物成因煤层气。高通量测序技术、宏基因组学等高新技术的应用逐步揭示了生物成因煤层气微生物群落的组成及多样性,为揭示煤层气资源的微生物生成机理提供了理论依据。本文综述了近年来国内外针对不同煤阶条件下微生物群落结构及多样性方面的研究进展,总结了煤层气生物成因过程中主要微生物的功能及产气途径,并探讨了生物成因煤层气领域的研究前景。