Abstract:2014年10月在北京召开的“2014年中国生态学会微生物生态专业委员会暨国际学术研讨会”标志着我国微生物生态学研究专业学术组织已经走过了30年的历程。经过几代微生物生态学研究者的不懈努力，我国的微生物生态学从无到有，不断开拓和发展，使得我国微生物生态学研究的队伍不断壮大，在若干方向的研究水平处于国际前沿。为了展现我国微生物生态学研究的最新进展，《微生物学通报》针对本次研讨会组织出版了本期《微生物生态学专刊》，以期促进微生物生态学及相关交叉研究领域的发展。

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Abstract:[Objective] Little is known about the diversity and distribution of cyanobacteria in salinized soils. In this study, we determined soil properties (pH, salinity and water contents, ammonium, nitrite, nitrate, total organic carbon and nitrogen), and investigated the molecular diversity and distribution patterns of soil cyanobacteria at 12 sites near the mouth of Yellow River and in the southern coastal plain of Laizhou Bay (Shandong province), typical salinized coastal regions in China. Salinity gradients were devided into three ranges: low (0.63%?1.27%), medium (1.55%?2.00%), and high saline (2.39%?5.11%). [Methods] Automated ribosomal intergenic spacer analysis (ARISA), clone libraries and real-time quantitative PCR were used to determine the cyanobacterial community structure, composition and abundance, respectively. [Results] Based on ARISA fingerprints, we found cyanobacterial phylotype richness increased with salinity; multiple dimensional scaling and hypothesis testing (ANOSIM) indicated that the community structure of cyanobacteria generally clustered by salinity (P=0.03) more than by water content (P=0.09). Biota-Environment correlation (BEST) analysis further revealed that a combination of two factors, salinity and water content of soils, could mostly explain the changes in cyanobacterial community structure (P=0.02). Clone libraries of 16S rRNA gene were constructed for 3 representative samples. Sequencing and classification following phylogenetic analysis showed that Halomicronema and Acaryochloris dominated in the low saline samples, whereas Leptolyngbya was the most abundant in both medium and high saline soils. Another two taxa, Arthrospira and Geitlerinema, were only found in the samples of low salinity, while Oscillatoria was detected once from the high salinity. Cyanbacterial 16S rRNA genes were much more abundant in low salinity (2.14×105 copies/g dry soil) than in medium (1.25×105 copies/g dry soil) and high salinity samples (1.20×105 copies/g dry soil). [Conclusion] This study demonstrates that salinity shapes the diversity, community structure and abundance of cyanobacteria in the saline soils, which has implications for carbon and nitrogen cycling contributed by these microorganisms in coastal terrestrial ecosystems.

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Abstract:[Objective] To evaluate and compare two GeoChip data pre-processing methods, LnMR and RAln. [Methods] The rank-abundance curve, evenness indice, one-way ANOVA, Q-Q plot, α diversity indice and response ratio were used to evaluate the pre-processing methods of GeoChip data from two recently published studies, a summer grazing experiment in the Tibetan grassland and a field study on the mutual effects of soil transplant and maize cropping. [Results] Both methods are efficient in removing or diminishing extreme values, optimizing data distribution, reducing random errors, improving data normalization and manifesting experimental differences, which makes GeoChip data more suitable for further statistical analysis. In particular, LnMR is more suitable for detecting subtle differences of microbial community compositions among different treatments, whereas RAln is more efficient in removing systematic errors. [Conclusion] LnMR and RAln are two powerful GeoChip data pre-processing methods, and should be applied with caution.

Abstract:[Objective] To investigate the effect of crude oil concentrations on bacterial community structures and diversity, and attempt to elucidate the mechanism of this effect. [Methods] Seawater was sampled near a marine drilling platform and was treated with five different crude oil concentrations (0 to 10 g/l) for a week in the laboratory. Then the bacterial communities were detected using terminal restriction fragment length polymorphism (TRFLP) method. [Results] Some new findings were exhibited, such as the bacterial diversity did not simply decrease with the increase of oil concentrations, but decreased at first, then increased and decreased again. Bacterial communities of treatments with 0.1 g/L (M0.1) and 0.5 g/L (M0.5) crude oil, treatments with 2.5 g/L (M2.5) and 10 g/L (M10) crude oil were similar, respectively, and bacterial communities in the oil added groups (M0.1, M0.5, M2.5, M10) were significantly different from the control (M0). Classification results of the dominant terminal restriction fragments (TRFs) in the oil treatments mainly attached to Proteobacteria, Firmicutes and Bacteroidetes. Based on the relative ratios of TRFs in different treatments, the 52 TRFs could be divided into six types (I to VI): low (I)/middle (II)/high (III)/broad (IV)/narrow (V) concentrations of crude oil adapted bacteria and crude oil sensitive bacteria (VI). Furthermore, “Carbon & Energy sources-Toxicities” hypothesis was proposed to explain effects of oil pollution on bacterioplankton. [Conclusion] Impacts of crude oil pollutions on the marine bacterioplankton are closely related to the concentration of oil and the original bacterial communities in the seawater, these bacteria could be classified upon their adaptability to the crude oil. And the “Carbon & Energy sources-Toxicities” hypothesis could explain effects of oil pollution on bacterioplankton very well.

Abstract:[Objective] The soil microbial communities and N2O emissions were compared between soil samples from a vegetable greenhouse and outside farmland. [Methods] Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR were used to investigate the difference of soil microbial communities and functional gene abundance, respectively. A robotized incubation system was employed to analyze the gaseous products of denitrification and calculate the ratio of N2O/(N2+N2O+NO). [Results] Significant differences were observed in soil bacterial communities between the two soils. The total number of bacteria in the greenhouse soil was higher than that of farmland. However, relative abundance of functional genes (nirS and nosZ) of the two types of soil was no significant difference. There were lower N2O accumulation and N2O/(N2+N2O+NO) ratio in the farmland soil compared to the greenhouse soil. In addition, the patterns of gas emissions in the two soils were significantly different in the early stage of anaerobic incubation. DNRA might lead to the increase of ammonium nitrogen content after the anaerobic incubation. [Conclusion] The higher strength of fertilization in greenhouse soil resulted in significant changes in soil bacterial communities and higher active soil microbial mass, N2O accumulation and N2O/(N2+N2O+NO) ratio. The soils from a greenhouse and a farmland, of which the greenhouse soil came from, have distinct nitrate respiration property. DNRA may be responsible for certain amounts of N2O emissions in both soils.

Abstract:[Objective] Microbial electrolysis cells (MEC) have been newly developed by employing anodic respiring bacteria to degrade waste organics to electrons. And hydrogen is recovered directly on the cathode surface under a very small external voltage to apply between anode and cathode. Although MECs showed great potential on high efficiency both on organic removal and energy recovery, there is a limited factor to enrich high-efficiency functional communities for scaled up reactors. [Methods] microbial community structure and characteristic of electron transport were analyzed through single-strand conformation poly-morphism (SSCP). [Results] The results showed that MECs were successfully started up within 2 days with coulombic efficiency of 20%. The hydrogen was produced steadily after 7 days with a conversion yield of 30% and energy recovery rate of 90%. SSCP analysis indicated that Pseudomonas sp., Flavobacterium sp., Ochrobactrum sp. as the main bacterial community related to electron transfer when inoculating the anode biofilm from microbial fuel cell. While a higher diversity presented when inoculating the anode biofilm of former MECs, and the dominant bacteria were including Desulfovibrio, Pseudomonas, and Shewanella, which were reported high efficiency on electron transport. In addition, it was uncovered the important role of the co-existing bacteria related to anaerobic digestion or assistance to electron transfer, showing an important function to support a stable anodic biofilm structure. [Conclusion] The results illustrated that high reactor performances with higher microbial diversity can be obtained using MEC biofilms as inoculum for large MEC reactor setup.

Abstract:[Objective] To isolate a functional strain with the highly efficient of biological desulfurization and denitrification from EGSB-DSR reactor, and study the characterization of the strain. [Methods] In this study, using the Hungate anaerobic roll tube technique a strain with the function of desulfurization and denitrification, A2, was isolated from EGSB-DSR reactor. [Results] Identification based on 16S rRNA sequence indicates that the isolate has a homologous similarity of 99% with Azoarcus sp.. In metabolic of A2, sulfide was adopted for its electron donor and nitrate for electron acceptor. This is the first report about the function of Azoarcus sp. in the desulfurization and denitrification process. The desulfurization and denitrification characterization of the strain shows that strain A2 degraded acetate, nitrate and sulfate in 20 hours completely, with the S2– concentration of 200 mg/L, NO3– concentration of 87.5 mg/L and the Ac– concentration of 200 mg/L. The removal rate of sulfate, nitrate and acetate is 95%, 99% and 99%, respectively. [Conclusion] This result indicates that newly isolated strain A2 with a high capability of desulfurization and denitrification. Strain A2 is a potential microbiology resource for the efficiency improvement of simultaneous desulfurization and denitrification process.

Abstract:[Objective] To provide theoretical basis for production and application of mix cultivated bio-demulsifier, the optimal conditions of mixed cultivation of strains L1 and XH1 were studied in this research. [Methods] Response surface methodology (RSM) based on the central composite rotation design (CCRD) was used to optimize fermentation conditions, and the demulsifying ratio was used to evaluate the demulsifying ability of fermentation broth. [Results] According to the results of the model analysis and verification, the optimal conditions were as follow: 3:2 inoculum proportion (strain L1:XH1), 3.6% (v/v) liquid paraffin contents, feeding glucose on the 4th day, and 21 h continuous incubation after feeding glucose. [Conclusion] Compared with single strain culture, the compound bio-demulsifier produced by complex culture of L1 and XH1 exhibited less dose and shorter demulsifying time. The complex culture increased the utilization ratio of main nutrients in the medium.

Abstract:[Objective] Acanthamoeba spp. and Hartmannella vermiformis are free-living amoebae (FLA), which are widely ubiquitous in soils and various aquatic environments. Certain species in these two genus were recognized as potential opportunistic pathogenicity for human and animals. It has practical significance of developing a highly specific, sensitive and reproducible assay which based on real-time fluorescence quantitative PCR for identifying amoebae. [Methods] we employed a culture-independent method, the real-time quantitative PCR assays to detect 18S rRNA genes of Acanthamoeba spp. and H. vermiformis using BRYT Green? dye in different processes of rural domestic wastewater treatment plant. [Results] The results indicated that the most frequently amoebae discovered were Acanthamoeba spp. and H. vermiformis which appear in all treatment system stages. The concentrations of two amoebae genus were up to 8.70×105 and 1.84×106 copies/L in untreated wastewater, respectively. Compared with untreated wastewater, the abundance of amoebae in adjusting tank, aerobic tank and membrane tank decreased in one or two orders of magnitude, while Acanthamoeba spp. was one order of magnitude higher in treated wastewater than untreated wastewater. [Conclusion] Hence, it should be paid much attention to amoebae having health risk and it is necessary to use amoebae as an additional reference standard for domestic wastewater treatment.

Abstract:[Objective] The eutrophication of water body is one of pressing water environmental problems in China today. It is mainly caused by over-discharge of wastewater with high nitrogen. Aerobic denitrification bacteria are promising on simultaneous nitrification and denitrification process, presenting high advantages than conventional denitrification process. A high efficient aerobic denitrification strain was isolated and its nitrogen removal efficiency was optimized. [Methods] The aerobic denitrification strain was obtained in a SBR reactor, and response surface method was used to improve key factors influencing denitrification and total nitrogen removal efficiency. [Results] High efficiency aerobic denitrification strain of Pseudomonas T13 was selected from a SBR reactor. Based on response surface method, the highest nitrate removal rate was 95%, total nitrogen removal rate of 90% within 18 h, which were obtained by optimizing key factors of ratio of carbon and nitrogen, dissolved oxygen, pH, and temperature. The suitable temperature ranged from 25 °C to 30 °C. The optimal pH is neutral and the suitable COD/NO3?-N was over 4:1. The DO was around 2.5 mg/L. Pseudomonas T13 can use nitrate and nitrite as electron acceptor for nitrate respiration with 90% removal rate. [Conclusion] An aerobic strain with high efficient denitrification was identified as Pseudomonas T13 from a long-term running SBR reactor. Over 30% nitrate reductase were detected out of all denitrification enzyme genes from the strain. It is presenting a great potential on nitrate removal (>90%) to strengthen nitrogen removal process in wastewater treatment.

Abstract:[Objective] (1) To investigate the effect of Pb2+ and Mn2+ stress on the mycelium morphology, structure and vitality of Pholiota adiposa; (2) To compare the adaptability and resistance of P. adiposa to Pb2+ and Mn2+. [Methods] Mycelia in both plate medium and liquid medium were cultured. The morphological characteristics were studied via electron microscopy and the growth characteristics were recorded. Contents of Pb2+ and Mn2+ in mycelia were also determined by atomic absorption spectrometry. The production of exopolysaccharides by the mycelia in the liquid medium were measured with the phenol-sulfuric acid method as to validate the vitality of the mycelium. [Results] A significant reduction of clampconnection caused by Pb2+ and Mn2+ was observed, and meanwhile the clampconnection was found unevenly distributed with big differences in size under the stress. The mycelium appeared rugate and proteiform, suggesting the decrease of the mycelial vitality caused by Pb2+ and Mn2+ stresses. The colonies were larger than others when the concentration of Pb2+ or Mn2+ in the plate medium was 100 mg/L, while the growth was significantly inhibited when the concentration reached to or exceeded 500 mg/L. For the liquid culture, the fresh weight of mycelium and exopolysaccharide production reached to maximum when Pb2+ was 50 mg/L, or Mn2+ 300 mg/L. [Conclusion] High stress of Pb2+ and Mn2+ have a significant effect on the growth of the mycelium and the vitality of mycelium and morphology. The adaptability and resistance of P. adiposa to Mn2+ was higher than that to Pb2+.

Abstract:The development of high-throughput sequencing technology promoted the wide applications of omics in the study of environmental microbiology. Among all omics technologies, metagenomics is the most critical and widely used method at present, while bioinformatics plays a very important role in its applications. The bioinformatic technologies were involved in metagenomics data collection, storage, preprocess and analysis. Therefore, it is not only the key of metagenomic development, but also the bottleneck for its implementation. This paper introduces the commonly used bioinformatic pipelines in both shotgun metagenome and amplicon of high-throughput sequencing. In next few years, the decline in cost and the increase in depth of high-throughput sequencing will dramatically elevate the difficulty on the analysis of metagenomic data. It is imperative to pay more and more attentions to develop the bioinformatics tools and analysis pipelines. Nowadays, we should strengthen the construction of fundamental analysis and storage platform to facilitate the data mining for ordinary microbial researchers. Meanwhile, we should develop more bioinformatic algorithms and tools to overcome the current bottleneck in the analysis of metagenomics.

Abstract:In the post-genomic era, the exponential progress in sequencing technology evidently reduced the cost of sequencing. Meta-omics technology includes metagenomics, metatranscripteomics and metaproteomics, has emerged in this progress, which has promoted the in-depth study of the diversity, construction and potential functions of microbial communities. Lately, the dynamic changes and metabolic functions of microbial communities can be comprehensively analyzed with the integrated application of meta-omics, and this is becoming a new research trend of microbial ecology. This paper summarized latest advances and successful application using meta-omics technology to study of structure and function of microbe communities in various environments, such as ocean, lakes, deep-sea hydrothermal vents, human gut, bovine rumen, soil and compost.

Abstract:The direct or indirect interactions between bacteria and algae occur widely in nature environment, and impact greatly on the physiological functions, community structures, and stress responses of both partners. Vitamin B12 (VB12), a structurally complex and functionally important vitamin, is required for the growth of many eukaryotic algae. The fact that VB12 can only be formed by bacteria and archaea implies that VB12-producing prokaryotes play an important role for algae. In this review, we focus on the recent reseach of VB12-involved algal growth promotion, stress tolerance and gene expression regulatoin in the interaction between bacteria and algae. Based on the recent progroess, we also discuss the future research directions in the research mode of bacteria-algae interaction.

Abstract:Methane is a crucial green-house gas as well as a typical renewable biomass energy. About 70% of the current CH4 emission into the atmosphere is originated from methanogenic microbial processes. In methanogenic environments, the close coupling of methanogens with syntrophic bacteria overcomes the energetic barriers for the anaerobic oxidation of short-chain fatty acids and alcohols with CH4 and CO2 as end products. Interspecies electron transfer is a critical step of this process. Here we firstly overviewed the research significance of methane and the microbial processes of syntrophic methanogenesis by degrading organic matters. And secondly summarized the origins, developments, research status and questions to be solved of the three interspecies electron transfer mechanisms, which is interspecies hydrogen transfer (IHT), interspecies formate transfer (IFT) and direct interspecies electron transfer (DIET).

Abstract:Microorganisms capable of degrading cellulose are widely distributed in nature and diverse strategies are thus employed to achieve the efficient deploymerization of lignocellulose. Cytophaga hutchinsonii belonging to the phylum Bacteroidetes has a strong ability to hydrolyze cellulose, but the involved mechanism seems to be different either from the known extracellular noncomplexed cellulase system or from cellulosome system. It is speculated that it possesses a third mode of cellulose utilization with the degradation system tightly associated with cells. The present review will briefly introduce the potentially novel strategy employed by C. hutchinsonii to assimilate cellulose.

Abstract:With the wide use of tetracyclines in the livestock and poultry industries, animal manure has become an important reservoir for tetracyclines and tetracycline resistance genes. The direct application of untreated manure will shade great potential risks for ecological environment and human health. Composting processes (including aerobic composting, anaerobic digestion and anaerobic lagoon, etc.) are important technologies for biotreatment of animal manure. Recent process on studies of the removal effects of tetracyclines and resistance genes in animal manure by different composting processes, the microbial degradation mechanism of tetracyclines during composting and the microbial ecological mechanism and strategies for controlling the proliferation of tetracycline resistance genes by composting were reviewed. Finally, suggestion of controlling tetracycline and resistance genes by using thermal hydrolysis pretreatment and anaerobic composting processes and strategy of dynamically exploring the removal mechanism of resistance genes during composting using high-throughput techniques were proposed.

Abstract:Targeting on the widely existed hydrocarbon pollution problems in the environment, this paper summarized the research progress on microbial ecology during microbial degradation of petroleum hydrocarbons in the aspect of molecular ecology. The research methods on molecular ecology and degradation genes and gene chip related to petroleum hydrocarbon degradation were introduced, and at the same time, the existing problems and future research directions were summarized.