微生物发酵琥珀酸的研究进展

琥珀酸是一种重要的C_4平台化合物,生物基琥珀酸可作为合成大宗化学品的起始原料,在食品、医药、表面活性剂、洗涤剂、绿色溶剂、生物可降解塑料和动植物生长刺激物剂领域有广泛的应用前景。从可再生原料出发,发酵过程固定CO_2,使得微生物发酵生产琥珀酸具有良好的环境优势,成为近年研究的热点。围绕微生物发酵法生产琥珀酸迫切需要解决的主要问题,综述了国内外对琥珀酸生产菌的选育、其代谢机理与产酸条件、发酵过程工艺、产品提取等方面的研究现状。     

一株生物絮凝剂产生菌的筛选及絮凝活性研究

从活性污泥中筛选到一株产絮凝剂的菌株WJ-100。该菌株产絮凝剂的适宜pH塑6．5。适宜温度为25℃～40℃,摇床速度为80～240r／min;Na^＋、K^＋、Ca^2＋、Fe^3＋均有较好的促絮凝作用,Ca^2＋尤为显著;WJ-100以多种糖类为良好碳源,絮凝率达99.2％、99．8％甚至100％;该菌株在高岭土悬液pH2．0～10．0范围均有较好的絮凝效果。WJ-100在较大的pH、温度、碳源、摇床速度、搅拌速度等范围内均具有很高的絮凝活性,显示出重要的研究和应用价值。     

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

Freshwater is a critical resource for human survival but severely threatened by anthropogenic activities and climate change. These changes strongly impact the abundance and diversity of the microbial communities which are key players in the functioning of these aquatic ecosystems. Although widely documented since the emergence of high-throughput sequencing approaches, the information on these natural microbial communities is scattered among thousands of publications and it is therefore difficult to investigate the temporal dynamics and the spatial distribution of microbial taxa within or across ecosystems. To fill this gap and in the FAIR principles context we built a manually curated and standardized microbial freshwater –omics database (FreshOmics). Based on recognized ontologies (ENVO, MIMICS, GO, ISO), FreshOmics describes 29 different types of freshwater ecosystems and uses standardized attributes to depict biological samples, sequencing protocols and article attributes for more than 2487 geographical locations across 71 countries around the world. The database contains 24,808 sequence identifiers (i.e., Run_Id / Exp_ID, mainly from SRA/DDBJ SRA/ENA, GSA and MG-RAST repositories) covering all sequence-based -omics approaches used to investigate bacteria, archaea, microbial eukaryotes, and viruses. Therefore, FreshOmics allows accurate and comprehensive analyses of microbial communities to answer questions related to their roles in freshwater ecosystems functioning and resilience, especially through meta-analysis studies. This collection also highlights different sort of errors in published works (e.g., wrong coordinates, sample type, material, spelling).     

Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil

Successful application of microbial biofertilizers, such as phosphorus (P) solubilizing fungi to agroecosystems, is constrained from the lack of knowledge about their ecology; for example in terms of how they respond to an external input of carbon (C) to get established in the soil. In two soil incubation experiments we examined the performance of the P solubilizing fungus Penicillium aculeatum in non-sterile and semi-sterile (γ-irradiated) soil with different C and P sources. Results from the first experiment with C sources showed that starch and cellulose generally improved P solubilization by P. aculeatum measured as water extractable P (P_wep), though only significantly in non-sterile soil. This coincided with an increased population density of P. aculeatum measured with a hygromycin B resistant strain of this fungus. Soil respiration used to measure soil microbial activity was overall much higher in treatments with C compounds than without C in both non-sterile and semi-sterile soil. However, soil respiration was highest with cellulose in semi-sterile soil, especially in combination with P. aculeatum. Hence, for the second experiment with P sources (tricalcium phosphate (TCP) and sewage sludge ash) cellulose was used as a C source for P. aculeatum growth in all treatments. Main results showed that P. aculeatum in combination with cellulose soil amendment increased soil P_wep independent of soil sterilization and P source treatments. Soil resin P (P_res) and microbial P (P_mic), which represents stocks of potentially plant available P, were also affected from P. aculeatum inoculation. Increased soil P_res from TCP and sewage sludge ash was observed with P. aculeatum independent of soil type. On the other hand soil P_mic was higher after P. aculeatum inoculation only in semi-sterile soil. Population density of P. aculeatum measured with qPCR was maintained or increased in non-sterile and semi-sterile soil, respectively, compared to the original inoculum load of P. aculeatum. In conclusion, our results underline the importance of C source addition for P. aculeatum if used as a biofertilizer. For this, cellulose seems to be a promising option promoting P. aculeatum growth and P solubilization also in non-sterilized soil.     

聚乙烯塑料生物降解研究进展

聚乙烯(polyethylene,PE)塑料是全球通用合成树脂中产量最丰富的品种,也是最难降解的塑料之一,其在环境中大量积累已造成严重的生态污染。传统的垃圾填埋、堆肥和焚烧处理技术难以满足生态环境的保护要求,生物降解是解决塑料污染问题的一种生态友好、成本低廉、前景可期的方法。本文对PE塑料的化学结构、降解微生物的种类、降解酶和代谢途径等方面进行了综述,结合国内外PE塑料生物降解的前沿和热点问题,建议重点开展高效降解菌株筛选、人工合成菌群构建、降解酶的挖掘与改造等方面的研究,为PE塑料生物降解研究提供路径选择和理论借鉴。     

Does apple replant disease affect the soil patch selection behaviour and population growth of Collembolans?

Apple replant disease (ARD) is common to all major apple-growing regions in the world. It occurs when new apple trees are replanted on sites where previously the same or closely related crop species were grown. Biotic (fungi, bacteria and nematodes) and abiotic soil factors (poor soil structure, nutrition) contribute to the development and severity of ARD. However, the aetiology of ARD and effects on higher trophic levels are still unknown. In that sense, Collembola might play an important role, since they are one of the dominant mesofauna groups in many soils. They act as decomposer, fungivores and predators, representing different trophic levels in soil food webs. Therefore, any effect of ARD on the occurrence of Collembola could have ecological impacts on the soil quality and health. Here, we examined the colonization behaviour of two Collembolan species, Folsomia candida and Sinella curviseta, in choice tests and population growth tests using Apple Replant Diseased soil (ARD) and non-ARD soil samples from different field sites and standardized laboratory bioassays. Additionally, Collembola behaviour was quantified by continuous video observations to investigate short-term behavioural changes. Results showed that both Collembolan species significantly preferred colonization of the non-ARD soils compared with ARD soils, independent of the origin of the soil samples or specific disinfection treatments. Moreover, the detailed video analysis of the foraging behaviour indicates rapid colonization of soil samples and low dispersal rates. Most likely, volatile compounds and to a lesser extent feeding stimulants play a vital role for the colonization process for both Collembolan species. Finally, results showed negative effects of ARD on population growth of both Collembolan species already after an 8-week period, implying strong nutritional deficiencies in ARD affected soils. The hypothesis that ARD causing microorganisms directly affected orientation, colonization and population development of Collembola is discussed.     

Global analysis of the perturbation effects of metal-based nanoparticles on soil nitrogen cycling

Although studies have investigated the effects of metal-based nanoparticles (MNPs) on soil biogeochemical processes, the results obtained thus far are highly variable. Moreover, we do not yet understand how the impact of MNPs is affected by experimental design and environmental conditions. Herein, we conducted a global analysis to synthesize the effects of MNPs on 17 variables associated with soil nitrogen (N) cycling from 62 studies. Our results showed that MNPs generally exerted inhibitory effects on N-cycling process rates, N-related enzyme activities, and microbial variables. The response of soil N cycling varied with MNP type, and exposure dose was the most decisive factor for the variations in the responses of N-cycling process rates and enzyme activities. Notably, Ag/Ag₂S and CuO had dose-dependent inhibitory effects on ammonia oxidation rates, while CuO and Zn/ZnO showed hormetic effects on nitrification and denitrification rates, respectively. Other experimental design factors (e.g., MNP size and exposure duration) also regulated the effect of MNPs on soil N cycling, and specific MNPs, such as Ag/Ag₂S, exerted stronger effects during long-term (>28 days) exposure. Environmental conditions, including soil pH, organic carbon, texture, and presence/absence of plants, significantly influenced MNP toxicity. For instance, the effects of Ag/Ag₂S on the ammonia oxidation rate and the activity of leucine aminopeptidase were more potent in acid (pH <6), organic matter-limited (organic carbon content ≤10 g kg⁻¹), and coarser soils. Overall, these results provide new insights into the general mechanisms by which MNPs alter soil N processes in different environments and underscore the urgent need to perform multivariate and long-term in situ trials in simulated natural environments.     

Seed coating with beneficial microorganisms for precision agriculture

Seed coating is a technique of covering seeds with adhesive agents to improve seed performance and plant establishment while reducing production cost. To meet the needs of development of precision agriculture, seed coating has been widely used in agriculture as an effective means to alleviate biotic and abiotic stresses, thus enhancing crop growth, yield, and health. Plant growth promoting microorganisms (PGPM) are recognized as essential contributors to improving agricultural productivity via direct application to the rhizosphere and plant tissues, or seed inoculation. However, during conventional inoculation processes, several factors such as insufficient microbial survival, hindrance in the application of biocontrol inocula to the seeds and exposure to unsuitable temperature and light in subsequent seed storage, force us to explore efficient and reliable microbial application tools. Recently, biological seed coating with PGPM is proposed as an alternative to conventional seed treatment (such as fertilizer and protection products) due to its ecological safety and socio-economic aspects. In this review, microbial seed coating technology and its contribution to sustainable precision agriculture are well discussed and highlighted in the extensive table and elaborate schematic drawings.     

Carbon sink reduction by fruit removal triggers respiration but not nitrous oxide emissions from the root zone of cucumber

Root exudation of organic carbon (C) is generally believed to be the cause of positive effects of root activity on nitrous oxide (N₂O) emissions. We tested the effects of root exudation in an actual soil–plant system on N₂O emissions while excluding most other potential factors. The C source/sink ratio in cucumber was changed by removing fruits to increase root exudation. Root‐zone emissions of carbon dioxide (CO₂) and N₂O were monitored in complete stands of adult plants in a greenhouse. Whereas CO₂ emissions rapidly increased as a result of fruit removal the N₂O emissions were completely unaffected. After cutting the shoots CO₂ emissions decreased within 2 weeks in both the fruit removal treatment and the control to a value significantly lower than that before the start of the treatments. However, N₂O emissions immediately exhibited a short peak, which was significantly higher in the fruit removal treatment compared to the control. Thereafter N₂O emissions in both treatments remained on the same level but considerably higher than before shoot cutting. We concluded that in a well‐aerated root zone, a root exudation pulse does not necessarily increase N₂O emissions, because C substrates are quickly respired by microorganisms before they can support heterotrophic denitrification. The results further indicate the significance of dying/dead roots for the creation of denitrificaton hot‐spots, which likely result from providing C substrates as well as poorly aerated habitats.     

The micro-biota of a sub-surface monument the medieval chapel of St. Virgil (Vienna, Austria)

The medieval chapel of St. Virgil is located sub-surface beneath the square of the dome of St. Stephen, in the heart of Vienna. The walls of the chapel are in direct contact with the surrounding soil. The water migrating horizontally into the walls of the chapel carries a huge load of soluble salts which crystallize on the surface of the walls and within the material. This phenomenon is causing material losses and destruction of original medieval fineries and paintings. Moreover, the salt creates special living conditions for microbes growing on and in the walls which is characterized by a high osmotic stress. The diversity of the micro-biota was studied both by cultivation and molecular techniques [a combination of denaturing gradient gel electrophoresis (DGGE) of PCR-amplified DNA encoding 16S rRNA and the construction of clone libraries]. The fungal diversity was found to be relatively low, albeit cell counts show more than 10⁵ colony forming units per gram of wall material. In the contrary, the diversity of bacteria was found to be high (more than 8 different genera). Furthermore, a community of extremely halophilic archaea was detected consisting of different species of two predominant genera, i.e., Halococcus and Halobacterium.