温州市境内城市河流底泥氨氧化菌富集培养物微生物群落结构分析

【背景】城市河流底泥含有丰富的微生物资源,底泥表面更是硝化作用的主要位点之一,其表面微生物在河流生态系统氮的转化过程中发挥着重要作用。【目的】以温州市境内的城市河流水系温瑞塘河茶山段舜岙河和横江河的4条河道作为采样点,比较分析4种不同环境下城市河流表层底泥氨氧化菌富集培养物的微生物群落结构。【方法】通过野外采样及室内培养对底泥中氨氧化功能菌进行富集培养,采用高通量测序技术分析微生物群落的组成、丰度和多样性。【结果】富集培养后主要优势类群为变形菌门(Proteobacteria)和拟杆菌门(Bacteroidetes)。4个样品共涉及氨氧化细菌3个属,分别为亚硝化单胞菌属(Nitrosomonas)、亚硝化螺菌属(Nitrosospira)、亚硝化球菌属(Nitrosococcus),涉及氨氧化古菌1个属为Nitrososphaera,其中所有样品均以Nitrosomonas为主。不同底泥富集样品氨氧化微生物可操作分类单元(Operational taxonomic unit,OTU)组成存在明显差异,栽种有水生植物的河道底泥样品DA2具有最高的氨氧化细菌OTU数量和相对丰度,而存在生活餐饮污染的河道底泥样品DA4具有最高的氨氧化古菌OTU数量和相对丰度;相较于滞留水体,采自相对流动水体的富集样品DA2、DA4具有更高的氨氧化微生物OTU数量和相对丰度。【结论】阐述了4种不同环境下城市河流底泥氨氧化菌富集培养物微生物群落结构的多样性,确定了富集培养之后的优势类群,为氨氧化微生物培养源的选择提供了参考,也为城市河流底泥中氨氧化菌进一步的筛选分离及其生理生态特征的研究提供了科学依据。     

应用高通量技术分析F446饱水木漆器中微生物群落结构多样性

【背景】饱水保藏木漆器的环境中,微生物数量多、种类丰富,木漆器易受到微生物的腐蚀。【目的】研究木漆器上的微生物群落结构,分析饱水木漆器的微生物病害信息。【方法】采用Illumina MiSeq高通量测序技术对木漆器和保藏水样中的细菌进行群落结构分析。【结果】木质样品与水样品中的微生物群落多样性较丰富并在分布上存在一定差异。门水平上,木质样品共有7个优势菌门(相对丰度1%),分别为Proteobacteria(64.00%)、Acidobacteria(14.70%)和Actinobacteria(3.83%)等;水样共有6个优势菌门,分别为Proteobacteria(61.26%)、Acidobacteria(8.25%)和Planctomycetes(4.88%)等。属水平上木质样品共有8个优势菌属(相对丰度1%),分别为Phenylobacterium(16.24%)、Acidobacteria-Gp6(9.68%)和Rhodoplanes(6.45%)等;水样共有10个优势菌属,分别为Naxibacter(9.03%)、Acidobacteria-Gp6(3.84%)和Nevskia(3.27%)等。未分类菌在门和属上,木质样品分别占8.70%和50.68%;水样品分别占12.83%和59.35%。【结论】木漆器饱水保藏环境中木质样品与水样品的微生物群落结构均比较丰富,在门和属水平上水样品比木质样品复杂。另外,被测样品中可能含有大量潜在新菌。     

餐厨垃圾厌氧消化处理主要过程的微生物群落结构分析

【背景】厌氧消化是我国餐厨垃圾处理的主要方法,微生物在其处理过程中起到关键作用,但是目前对其不同工艺单元微生物群落结构的研究较少。【目的】通过分析各工艺单元的微生物多样性与群落结构,为改进餐厨垃圾资源化处理技术、提高资源利用效率提供科学依据。【方法】采集某餐厨垃圾处理厂油水分离、厌氧发酵、沼渣脱水等3个工艺单元产生的废液样品,采用16S rRNA基因高通量测序技术,研究其菌群组成、丰度、优势菌群及其与环境因子的相关性。【结果】初始油水分离样品中的微生物群落种类相对较少,而经厌氧发酵和沼渣脱水处理后样品中的微生物群落种类较丰富。在门水平上,厚壁菌门(Firmicutes)在各单元样品中所占平均比例最高,为81.1%,其次为拟杆菌门(Bacteroidetes)和绿弯菌门(Chloroflexi),分别占15.81%和4.59%;在属水平上,相对丰度较高的菌属为乳酸菌属(Lactobacillus)、互营单胞菌属(Syntrophomonas)等。餐厨垃圾处理过程中的部分菌属可能具有资源-环境双重属性,例如在沼渣脱水单元相对丰度高达32.67%的假单胞菌属(Pseudomonas),该菌属中既存在少部分致病菌或条件致病菌,也具有生产聚羟基脂肪酸酯的功能菌。影响各组样品微生物群落组成结构最显著的因子是p H值,其次是总糖的含量。【结论】研究明确了典型餐厨垃圾厌氧消化处理工艺单元的微生物群落结构和多样性,并提出了优化处理工艺、强化资源利用效率的建议。     

江苏沿江地区出口产品仓储昆虫群落结构数量特征研究

对江苏沿江地区出口产品仓储昆虫进行调查,分析了5种出口产品仓储昆虫群落的优势种.利用群落物种的丰富度、生态优势度、多样性和均匀度等群落特征指数,研究了5种类型出口产品仓储昆虫群落结构的数量特征,并分析了它们的相似性.通过系统聚类分析将5种群落分为4类,草柳藤制品和羽绒制品仓储昆虫群落同属一类,其它3种产品仓储昆虫群落各属一类.除木制品群落结构相对合理外,其它群落结构都不合理,皮毛制品群落结构尤其不合理.     

汾河入黄口夏季微生物群落结构分析

【背景】河流交汇区日益成为流域生态治理的焦点和热点之一。【目的】探明汾河入黄口微生物群落结构及其主要环境影响因子。【方法】应用16S rRNA基因Illumina MiSeq高通量测序技术,分析了汾河入黄口夏季微生物群落结构,并利用典范对应分析(Canonical correspondence analysis,CCA)了解影响微生物群落的主要环境因子。【结果】多样性指数分析表明该区域微生物群落多样性较高。微生物多样性分析发现优势菌门为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria);在属分类水平上,相对丰度最高的菌属为芽孢杆菌属(Bacillus),其次为乳球菌属(Lactococcus)和hgcI_clade。Spearman相关性分析及典范对应分析表明环境因子对水体微生物群落结构具有显著影响。【结论】汾河与黄河微生物群落组成具有一定的差异,不同环境因子对不同微生物的影响程度不同,p H和溶解氧(Dissolved oxygen,DO)是汾河入黄口微生物群落结构的主要影响因子。     

Plant growth, community structure, and nutrient removal in monoculture and mixed constructed wetlands

The aim of this study was to compare the growth, community structure, and nutrient removal rates between monoculture and mixed wetlands, based on the hypothesis that it depends on the plant species used in the wetlands as to whether monoculture or mixed wetland is superior in plant growth and nutrient removal. Pilot-scale monoculture and mixed constructed wetlands were studied over 4 years. The monoculture wetland had a community height similar to the mixed wetland during the early years but a significantly lower height than the mixed wetland (P < 0.05) during the last year. The mixed wetland also displayed a higher plant density than the monoculture wetland (P < 0.05). The leaf area index in the monoculture wetland was significantly higher in the first year (P < 0.05) and significantly lower in the later years (P < 0.05) than that in the mixed wetland. The monoculture wetland had a similar vertical distribution of below-ground biomass over 4 years, while the mixed wetland showed a significant change in vertical distribution of below-ground biomass in the last 2 years. The monoculture wetland had a larger (P < 0.05) above-ground biomass and a similar leaf biomass in the first year, and a smaller above-ground biomass (P < 0.05) and a smaller leaf biomass (P < 0.05) than the mixed wetland during the latter 2 years. The amount of standing dead mass was smaller in the mixed wetland than in the monoculture wetland (P < 0.05). The mixed wetland exhibited a significantly lower NH₄-N removal rate in the first year (P < 0.05), and significantly higher NH₄-N removal rate in the last year, when compared to the monoculture wetland (P < 0.05). The study indicated that species competition and stubble growth resulted in significant differences between monoculture and mixed constructed wetlands in plant growth, community structure, and nutrient removal rates.     

Predator driven changes in community structure

Summary The zooplankton community of a small pond changed markedly with temporal variation in predation pressure. Long term changes in zooplankton community structure occurred following the replacement of planktivorous fish by phantom midge (Chaoborus americanus) larvae as the predominant predator of zooplankton. The interannual changes following the establishment of Chaoborus included the apparent or near extinction, of species ill adapted to the new predation pressure and the successful colonization of well adapted species. Seasonal changes in the species composition and size distribution of the zooplankton community correlate with temporal variation in predation intensity associated with temperature-activity patterns of the predator or changes in the stage structure of the predator population.     

Cd对土壤动物群落结构的影响

Cd污染对土壤动物影响的模拟实验结果表明,土壤动物群落结构的变化与Cd处理浓度的大小密切相关．在高浓度(99．48mg     

An examination of multiple factors affecting community structure in an aquatic amphibian community

Summary The potential effects of multiple factors structuring certain larval amphibian communities were studied using a pen experiment in a natural pond. Potential factors (predation and competition from other species) were allowed to act in a stepwise fashion such that their relative importance could be evaluated. Based on a previous study, it was hypothesized that predation by Ambystoma salamander larvae on other larval amphibian species would be the most important factor. Survival of Ambystoma jeffersonianum salamander larvae and Rana sylvatica tadpoles was significantly depressed only by Ambystoma opacum predation. Survival of Ambystoma maculatum salamander larvae was significantly greater in the absence of both A. opacum and A. jeffersonianum predators. The virtual elimination of Hyla chrysoscelis larvae in all treatments also can be largely attributed to Ambystoma predation. Thus, Ambystoma predation was the dominant factor determining larval survival of four amphibian prey species in the experimental communities.     

Scale-dependent interactions and community structure on cobble beaches

Recent theory suggests that scale-dependent interaction between facilitation and competition can generate spatial structure in ecological communities. The application of this hypothesis, however, has been limited to systems with little underlying heterogeneity. We evaluated this prediction in a plant community along an intertidal stress gradient on cobble beaches in Rhode Island, USA. Prior studies have shown that Spartina alterniflora facilitates a forb-dominated community higher in the intertidal by modifying the shoreline environment. We tested the hypothesis that, at a smaller scale, Spartina competitively excludes forb species, explaining their marked absence within the lower Spartina zone. Transplant experiments showed forb species grow significantly better in the Spartina zone when neighbours were removed. Removal of the Spartina canopy led to a massive emergence of annual forbs, showing that competition limits local occupation. These findings indicate that interaction of large-scale facilitation and small-scale competition drives plant zonation on cobble beaches. This study is the first to provide empirical evidence of scale-dependent interactions between facilitation and competition spatially structuring communities in heterogeneous environments.     

Changes in community structure and photosynthetic activities of total phytoplankton species during the growth,maintenance, and dissipation phases of a Prorocentrum donghaiense bloom

The potential interactions between the bloom-forming dinoflagellates and other phytoplankton during the algal bloom cycle are interesting, while the causes for the phytoplankton community changes were not fully understood. We hypothesized that phytoplankton community structure and photosynthetic activities of total phytoplankton have their special characteristics in different phases of the algal blooms. To test this hypothesis, a survey covering the process of a Prorocentrum donghaiense bloom in coastal waters between Dongtou and Nanji Islands was carried out from 9 to 20 May 2016, and the changes in the phytoplankton community and photosynthetic activities of total phytoplankton were determined. Surface seawater was sampled for microscopic analysis of phytoplankton composition and pulse amplitude modulated (PAM) chlorophyll fluorescence analysis of photosynthetic activities of the total phytoplankton species. A total of 25, 31, and 19 phytoplankton species were identified in its growth (9–12 May), maintenance (13–18 May) and dissipation phases (19–20 May), respectively. Diatoms were dominant in terms of species number while dinoflagellates were predominant at cell abundance. Dinoflagellates were the major dominant species during three phases of the bloom based on the dominance (Y) value, whereas the dominant species extended to dinoflagellates and diatoms including P. donghaiense, Coscinodiscus argus, Gonyaulax spinifera, Cyclotella sp. and Scrippsiella trochoidea in the dissipation phase. In the maintenance phase, the average cell abundances of the total phytoplankton and P. donghaiense were consistent with the chlorophyll a (Chla) concentration in the seawater; for the diversity indices of total phytoplankton species, Simpson index (C) was the highest while Shannon index (H′) and Pielou evenness index (J′) were the lowest. Furthermore, photosynthetic activities of the total phytoplankton species represented by the effective quantum yield (F_q'/F_m') and the maximum relative electron transport rate (rETR_max) in the maintenance phase were higher than those in the growth and dissipation phases. The results indicated that the characteristics of phytoplankton community structure and photosynthetic activities could be regarded as criteria in predicting the phases of algal blooms.     

三江源地区不同植被土壤固氮微生物的群落结构研究

利用PCR_RFLP和测序分析法对位于青藏高原腹地三江源自然保护区的高寒草甸、高寒草原和高山森林等不同植被类型的土壤固氮微生物的群落组成进行了探讨。经过PCR_RFLP分析固氮基因nifH ,在3个样品中共得到2 33个克隆和99个可操作分类单元(OTUs) ,NQ_1样地具有最多的克隆数和OTUs,多样性为4 9 74 % ,在所有样品中分别具有1～2个明显的优势种群(占总克隆数>15 % ) ,并且具有4个共同的OTUs。选取了2 6个克隆进行基因测序分析,通过DNAMAN比较表明,这些序列间具有6 6 %～98%的相似性,并且在GenBank数据库中没有发现完全匹配的序列,因此这些序列可能代表着新的固氮生物株系。最后利用ClustalW与Mega软件构建了系统发育树,结果发现,这些序列被分为4个不同的簇,部分序列与属于蛋白细菌(Proteobacteria)的已知细菌具有近的亲缘关系,但是更多的序列与已知细菌具有较远的亲缘关系,而且nifH基因序列的分布在样地间没有明显的聚类     

Microbial community structure and global trace gases

Global change can affect soil processes by either altering the functioning of existing organisms or by restructuring the community, modifying the fundamental physiologies that drive biogeochemical processes. Thus, not only might process rates change, but the controls over them might also change. Moreover, previously insignificant processes could become important. These possibilities raise the question ‘Will changes in climate and land use restructure microbial communities in a way that will alter trace gas fluxes from an ecosystem?’ Process studies indicate that microbial community structure can influence trace gas dynamics at a large scale. For example, soil respiration and CH₄ production both show ranges of temperature response among ecosystems, indicating differences in the microbial communities responsible. There are three patterns of NH₄⁺ inhibition of CH₄ oxidation at the ecosystem scale: no inhibition, immediate inhibition, and delayed inhibition; these are associated with different CH₄ oxidizer communities. Thus, it is possible that changes in climate, land-use, and disturbance regimes could alter microbial communities in ways that would substantially alter trace gas fluxes; we discuss the data supporting this conclusion. We also discuss approaches to developing research linking microbial community structure and activity to the structure and functioning of the whole ecosystem. Modern techniques allow us to identify active organisms even if they have not been cultivated; in combination with traditional experimental approaches we should be able to identify the linkages between these active populations and the processes they carry out at the ecosystem level. Finally, we describe scenarios of how global change could alter trace gas fluxes by altering microbial communities and how understanding the microbial community dynamics could improve our ability to predict future trace gas fluxes.     

城市供水系统对水中真菌数量和群落结构的影响

【背景】对于饮用水中的微生物污染,绝大多数研究集中在细菌、病毒及原虫和蠕虫。由于真菌中包含多种潜在致病菌,应当引起人们的关注。【目的】研究城市供水系统中真菌数量、群落组成变化及可能存在的潜在致病真菌。【方法】利用MEA和RB两种培养基,对供水系统中的原水和两个水厂净水工艺过程及不同供水模式用户龙头水样进行培养法计数统计。提取上述样本总DNA,并应用Illumina MiSeq平台进行ITS1区高通量测序。【结果】从15个样本中共获得有效序列579 470条,1 260个OTU,包含8个门26个纲67个目228个属的真菌。门水平上子囊菌门真菌为供水系统优势真菌,属水平上不同样本存在差异,但曲霉属和枝顶孢属真菌在所有样本中均存在;培养法和高通量测序结果共同显示,活性炭过滤出水真菌数量和物种丰富度均较前一工艺有所上升;氯化消毒对真菌数量、物种多样性及物种组成影响显著;经过供水管网输配和二次供水设施后,用户龙头水样本真菌数量和物种丰富度明显高于出厂水。【结论】供水系统中的优势真菌为子囊菌门(Ascomycota),该门真菌可穿透净水工艺过程的多级屏障;水厂净水工艺能有效去除水中可培养真菌,生物活性炭过滤工艺能够影响真菌数目及物种多样性;供水管网及二次供水设施是末端饮用水中真菌污染的重要来源;供水系统中存在潜在致病真菌。     

Variation in herbivore density among host plants and its consequences for community structure

Summary The densities of four species of gall-forming sawflies were found to vary significantly among willow host plant clones. Two of the speices varied among host plants at four sites in each of three years. The other two species varied in density among host plants at most of the sites in two of the three years. Total sawfly density also varied significantly among clones. Individual species densities on willow clones were significantly positively correlated between years when all sites were combined and frequently when sites were considered separately. Most pairwise species combinations were independent in density between years, but some negative correlations existed between the stem galler and the leaf galler. Gall-former densities also were largely independent among clones within years with all sites combined and with sites considered separately. The significant correlations were nearly all positive. At all four sites the combination of significant variation in sawfly densities among willow clones in the field and independence of species densities among clones resulted in significantly different communities (relative abundance of species) among willow clones in three years. Although sawfly abundances differed substantially among the four sites, this remained true. It is argued that the pattern of community structure among clones is the result of variation in host plant quality of clones. We propose an hypothesis to account for patterns of herbivore species associations based on intrapopulation host plant variation.     

A method for the estimation of bacterial biomass and community structure in mangrove-associated sediments

Many recent reports have proposed that certain monocarboxylic fatty acids found in sediments originate in the in situ bacterial population. In this study we have divided the acids derived from bacteria into nine subgroups, each characteristic of a distinct compositional group of bacteria. It is proposed that the abundance of selected marker acids from each bacterial subgroup (chemotype) can be used to estimate the biomass of that chemotype. Conversion factors from acid abundance to bacterial biomass have been estimated using literature data. Since this procedure results in nine biomass parameters, bacterial communities can be compared in terms of both total biomass and chemotype distribution, that is, biomass and community structure. The ability of this procedure to resolve community structure variations is illustrated with the interpretation of the fatty acid profiles of a spatially distributed set of mangrove-associated sediments.     

Extreme temperature events alter demographic rates,relative fitness,and community structure

The frequency and magnitude of extreme events are predicted to increase under future climate change. Despite recent advancements, we still lack a detailed understanding of how changes in the frequency and amplitude of extreme climate events are linked to the temporal and spatial structure of natural communities. To answer this question, we used a combination of laboratory experiments, field experiments, and analysis of multi‐year field observations to reveal the effects of extreme high temperature events on the demographic rates and relative dominance of three co‐occurrence aphid species which differ in their transmission efficiency of different agricultural pathogens. We then linked the geographical shift in their relative dominance to frequent extreme high temperatures through a meta‐analysis. We found that both frequency and amplitude of extreme high temperatures altered demographic rates of species. However, these effects were species‐specific. Increasing the frequency and amplitude of extreme temperature events altered which species had the highest fitness. Importantly, this change in relative fitness of species was consistent with significant changes in the relative dominance of species in natural communities in a 1 year long field heating experiment and 6 year long field survey of natural populations. Finally, at a global spatial scale, we found the same relationship between relative abundance of species and frequency of extreme temperatures. Together, our results indicate that changes in frequency and amplitude of extreme high temperatures can alter the temporal and spatial structure of natural communities, and that these changes are driven by asymmetric effects of high temperatures on the demographic rates and fitness of species. They also highlight the importance of understanding how extreme events affect the life‐history of species for predicting the impacts of climate change at the individual and community level, and emphasize the importance of using a broad range of approaches when studying climate change.     

Influence of the habitat change for birds on community structure

In order to study the influence of habitat change on the community structure of birds, the species and individual numbers in the lakeside developmental land of Thousand-Island Lake have been recorded since January 2009 till December 2010, A fixed sample line was set up in the studied area, and the primary data was obtained about twice a month. In 2009, 1814 individuals were observed belonging to 12 orders, 31 families and 78 species, among which 4 species (Milvus lineatus, Haliastur Indus, Circus cyaneus and Glaucidium cuculoides) are the rank II national key protected species. In 2010, 872 individuals were recorded belonging to 12 orders, 33 families and 77 species, among which 2 species (Milvus lineatus and Glaucidium cuculoides) are the rank II national key protected ones. The total individual number of birds reduced 51.9%. Concerning the species, although the total species number decreased rarely after the habitat change, 23 species fled away and 22 species entered indicating the population similarity index value of 0.55. Among the top 10 species with large number of individuals, 5 species (Spizixos semitorques, Pycnonotus xanthorrhous, Paradoxornis webbianus, Passer montanus and Carduelis sinica) were overlapped indicating the similarity index value of 0.5. Comparison of the data of the corresponding months between two years, the highest similarity (index value > 0.6) was from January to February; and the lowest (index value < 0.3) from March to May. From June to December, the similarity index value was rebounded to 0.35–0.52 might due to the food tempt. Among the 55 overlapped species, 17 species (Tachybaptus ruficollis, Egretta garzetta, Phasianus colchicus, Streptopelia orientalis, Hirundo rustica, Hirundo daurica, Motacilla alba, Spizixos semitorques, Pycnonotus xanthorrhous, Pycnonotus sinensis, Urocissa erythrorhyncha, Paradoxornis webbianus, Prinia inornata, Passer rutilans, Passer montanus, Lonchura punctulata and Carduelis sinica) showed significant differences in individual number between the unchanged habitat and the changed habitat, including 2 species of water birds and 15 species of forest birds, which indicate these two types of birds were more affected than the others. In other words, the birds living close to the human crowds suffered bigger effect than the birds living away from the crowds. This is considered that the vocals, vehicle and machinery noises, and artificial constructions contributing to habitat change might be one of the main factors. All these analysis suggest the great influence of habitat change caused by human on the bird community structure. The higher diversity, richness and evenness index values in 2010 than in 2009 suggests that environmental modification led to a certain degree of habitat amelioration. Therefore, human being can improve environment by making the plant community structure complexity to increase the habitat heterogeneity, and consequently enhancing the diversity of bird community, as long as the habitat is not fragmented.     

The community structure of human cellular signaling network

Living cell is highly responsive to specific chemicals in its environment, such as hormones and molecules in food or aromas. The reason is ascribed to the existence of widespread and diverse signal transduction pathways, between which crosstalks usually exist, thus constitute a complex signaling network. Evidently, knowledge of topology characteristic of this network could contribute a lot to the understanding of diverse cellular behaviors and life phenomena thus come into being. In this presentation, signal transduction data is extracted from KEGG to construct a cellular signaling network of Homo sapiens, which has 931 nodes and 6798 links in total. Computing the degree distribution, we find it is not a random network, but a scale-free network following a power-law of P(K) approximately K(-gamma), with gamma approximately equal to 2.2. Among three graph partition algorithms, the Guimera's simulated annealing method is chosen to study the details of topology structure and other properties of this cellular signaling network, as it shows the best performance. To reveal the underlying biological implications, further investigation is conducted on ad hoc community and sketch map of individual community is drawn accordingly. The involved experiment data can be found in the supplementary material.