Microbial genetic diversity and ciliate community structure along an environmental gradient in coastal soil

We investigated the microbial genetic diversity and ciliate community in coastal soil from five sites with an environmental gradient using denaturing gradient gel electrophoresis (DGGE), gene sequencing and the Ludox–QPS method. The analyses of both the 16S ribosomal RNA (rRNA) gene and 18S rRNA gene DGGE resulted in equal or even a higher number of bands found in the samples taken from the high-salinity sites IV and V than in those taken from the low-to-moderate-salinity sites I–III. Cluster analysis of both DGGE profiles classified the five sites into three main groups (sites I, II and III and IV and V), which corresponded well to the analysis of environmental factors. There were 13 species observed at site I, three species at site II and nine species at site III, while no active ciliates were observed at the high-salinity sites IV and V. By contrast, the ciliate-specific DGGE revealed a higher number of bands in the samples taken from the high-salinity soil. Furthermore, gene sequencing suggested that the ciliates in the high-salinity soil comprised forms originating not only from soil but also from marine environments. The data indicate that saline soil may maintain a high diversity of ciliates and soil salinity might be the most influential factor regulating the community structure of ciliates.     

Global patterns of diversity and community structure in marine bacterioplankton

Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.     

Spatial patterns of diatom diversity and community structure in ancient Lake Ohrid

For effective lakes’ management, high-frequent water quality data on a synoptic scale are essential. The aim of this study is to test the suitability of the latest generation of satellite sensors to provide information on lake water quality parameters for the five largest Italian subalpine lakes. In situ data of phytoplankton composition, chlorophyll-a (chl-a) concentration and water reflectance were used in synergy with satellite observations to map some algal blooms in 2016. Chl-a concentration maps were derived from satellite data by applying a bio-optical model to satellite data, previously corrected for atmospheric effects. Results were compared with in situ data, showing good agreement. The shape and magnitude of water reflectance from different satellite data were consistent. Output chl-a concentration maps, show the distribution within each lake during blooming events, suggesting a synoptic view is required for these events monitoring. Maps show the dynamic of bloom events with concentration increasing from 2 up to 7 mg m^?3 and dropping again to initial value in less than 20 days. Latest generation sensors were shown to be valuable tools for lakes monitoring, thanks to frequent, free of charge data availability over long time periods.     

Towards global patterns in the diversity and community structure of ectomycorrhizal fungi

Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.     

Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity

Next‐generation DNA sequencing has enabled a rapid expansion in the size of molecular fungal ecology studies employing the nuclear internal transcribed spacer (ITS) region. Many sequence‐processing pipelines and protocols require sequence clustering to generate operational taxonomic units (OTUs) based on sequence similarity as a step to reduce total data quantity and complexity prior to taxonomic assignment. However, the consequences of ITS sequence clustering in regard to sample taxonomic coverage have not been carefully examined. Here we demonstrate that typically used clustering thresholds for fungal ITS sequences result in statistically significant losses in taxonomic coverage. Analyses using environmentally derived fungal sequences indicated an average of 3.1% of species went undetected (P < 0.05) if the sequences were denoised and clustered at a 97% threshold prior to taxonomic assignment. Additionally, an in silico analysis using a reference fungal ITS database suggested that approximately 25% of species went undetected if the sequences were clustered prior to taxonomic assignment. Finally, analysis of sequences derived from pure‐cultured fungal isolates of known identity indicated sequence denoising and clustering were not critical in improving identification accuracy.     

四合木(Tetraenamongolica)林地昆虫群落的组成、结构及多样性特征

濒危植物四合木(Tetraena mongolica)为我国特有的蒺藜科单种属落叶小灌木.对四合木林地昆虫群落进行了调查,共得昆虫标本11363号,263种.隶属于67个科(或总科)11个目.同翅目的个体数量和优势度指数最高;膜翅目的物种丰富度和多样性指数最大;双翅目的均匀度最大.数量优势类群(＞10％)为木虱和叶蝉类,常见类群(1％～10％)是象甲、小蜂、粒脉蜡蝉、拟步甲、蚂蚁、蝽科、皮蝽、盲蝽、斑翅蝗科昆虫.营养结构中植食性类群在种类和数量上占绝对优势,其中的吸食类昆虫优势度最大;天敌昆虫以寄生性类群为主,多样性最高;捕食性和中性昆虫的种类和数量相对较少,但捕食者的均匀度最高.灌木层与草本层相比,灌木层昆虫群落的物种丰富度和个体数量明显占优;优势种的优势度大.而草本层昆虫群落的多样性和均匀度高.2层整体的相似性低.膜翅目的共有种最多.     

Macrofaunal diversity and habitat structure in intertidal boulder fields

Low-midshore boulder fields in Europe are increasingly subject to degradation related to beach fishing for crabs and abalones. The aim of the study was to better understand the structure and species diversity of macrofaunal assemblages living in a low-midshore boulder field in order to define conservation strategies for this biotope. Sampling strategy involved different spatial scales (macro- and microstrata) relative to the complexity and heterogeneity of the habitat. Assemblages of species and the corresponding habitats were identified by multifactorial analysis and compared by ANOVAs. The results show a hierarchical organization of the macrofauna within the boulder field, corresponding to three spatial levels of habitat structure: (i) eight microhabitats at the lowest level of spatial organization, each defined by a specific assemblage (subcommunity); (ii) three habitats at a middle level combining these microhabitats, each associated with a specific community (open rock, protected rock and sediment); and (iii) three macrohabitats at the uppermost level (corresponding to the scale of the entire boulder field and including the main geomorphological features of the beach), each defined by a specific assemblage of species (boulders on boulders, boulders on bedrock, and boulders on sediment). Two microhabitats with particularly high species diversity were regarded as the most important ecological units of the field in terms of conservation of specific and functional biodiversity. Comparison of habitat/community parameters showed (i) that habitat heterogeneity was not an accurate indicator of faunal diversity, and (ii) that habitat complexity enhanced the species richness of the fauna, but only above a threshold value. This enhancement was due to semi-sheltered microhabitats, which were found only in the most complex areas of the boulder field. It is likely that this complexity affects species richness qualitatively more than by the diversity of microhabitats. In other words, a cross-scale effect is apparent in which high habitat complexity on the middle spatial scale creates microhabitats on the lowest spatial scale that are characterized by stable semi-sheltered environmental conditions conducive to a maximum of species.     

长江河口浮游动物的种类组成、群落结构及多样性

于1999年枯水期(2—3月份)、丰水期(8月份)、2000年枯水期(2—3月份)对长江河口浮游动物采样调查,研究了长江河口浮游动物的种类组成、群落结构及多样性并初步探讨了三峡工程对长江河口浮游动物的影响及长江河口水环境的生物监测。调查共发现浮游动物87种,甲壳动物占绝对优势,共59种。在所有浮游动物中挠足类31种。其次为水母类,有9种,此外,枝角类、毛颚类各8种。3次采样浮游动物的优势种主要有河口半咸水种和近岸低盐种类如华哲水蚤(Sinocalanus sinensis)、火腿许水蚤(Schmackeria poplesia)、虫肢歪水蚤(Tortanus vermiculus),真刺唇角水蚤(Labidocera euchaeta)等,还有长江径流带到河口的淡水种如近领剑水蚤（Cyclops vicinus vicinus)、英勇剑水蚤（Cyclops strenuus）、透明溞（Daphnia hyalina)等。一些浮游动物可作为水系指示种,其分布、数量反映了不同水系分布变化,长江河口浮游动物有;类水系指示种。通过对长江河口浮游动物群落聚类分析发现。1999、2000年枯水期浮游动物群落结构相似。可分为河口类群、近岸类群和近外海类群。1999年丰水期只形成近岸和近外海类群。浮游动物种类数由口门内向口门外方向有逐渐增加的趋势。浮游动物种类数由北向南变化趋势一致。大潮与小潮、涨憩与落强等潮汐作用对浮游动物影响往往因采样时间与区域等的不同而不同。对长江河口3次采样的物种多样性指数和均匀度指数进行了计算,结果表明：浮游动物多样性指数1999年枯水期最低,1999年丰水期最高。     

覆盖模式对旱作农田土壤微生物多样性及群落结构的影响

土壤微生物是表征土壤质量的敏感指标,采用Illumina HiSep技术分析不同覆盖方式对半湿润易旱区农田土壤微生物群落结构及多样性的影响,以期从微生物的角度评价农田不同覆盖措施对土壤质量的影响。设3种覆盖模式：平作塑料薄膜覆盖（P）、平作秸秆覆盖（S）和垄膜沟播覆盖（R）,以平作不覆盖为对照（CK）,研究不同覆盖模式下土壤微生物群落变化,分析各土壤理化因子与微生物群落之间的关系。研究结果表明各覆盖处理显著改变了土壤微生物的群落结构和多样性。所有土壤样品中,细菌群落的优势菌门是变形菌门（Proteobacteria）、酸杆菌门（Acidobacteria）、放线菌门（Actinobacteria）,丰度分别为29.69%、28.28%和20.76%,CK处理下较高的土壤pH和低NO₃-N含量抑制了土壤中酸杆菌门（Acidobacteria）的生长繁殖,而放线菌门（Actinobacteria）相对丰度为所有处理中最高。真菌群落的优势菌门是子囊菌门（Ascomycota）、担子菌门（Basidiomycota）,丰度分别为59.65%和20.96%,S处理下过低的土壤温度抑制了担子菌门（Basidiomycota）生长和繁殖,其相对丰度为所有处理中最低。与CK相比,P和R处理显著提高土壤细菌的多样性和丰富度;S和R处理下土壤真菌多样性和丰富度显著增加,而P处理的土壤真菌多样性和丰富度均无显著差异。斯皮尔曼相关分析表明土壤细菌多样性主要受土壤含水量（SM）和硝态氮含量（NO₃-N）影响,而土壤真菌多样性主要受土壤温度（ST）、全氮（TN）和硝态氮含量（NO₃-N）影响;RDA分析表明微生物群落结构的变化主要受SM、ST、NO₃-N和TN含量的影响。总的来说,R处理下土壤细菌和真菌的多样性和丰富度较CK处理显著提高,该处理下土壤中担子菌门（Basidiomycota）和球囊菌（Glomeromycota）相对丰度为所有处理中最高,两者分别形成的外生菌根和从生菌根不但促进了根部养分的吸收,而且提高了作物的抗逆性,且结果证明该处理的作物产量为最高,因此在半湿润旱作区推荐采用垄膜沟播覆盖种植方式。     

Seasonal changes in community structure along a vertical gradient: patterns and processes in rocky intertidal sessile assemblages

Population Ecology - Here we considered two fundamental questions in community ecology regarding the relationship between seasonal changes in community structure and environmental gradients: (i)...     

生姜根系不同生态位细菌群落多样性特征、组成及结构差异

生姜作为常见的调味品和传统中药材,是我国重要的经济作物之一。作为取食部分的生姜块茎与根系直接相连,其产量、品质与根相关细菌群落密切相关。然而,关于生姜根系微环境中细菌群落的特点仍鲜有报道,土壤环境能否衍生出宿主特异性内生菌群落尚不清楚。以生姜根系不同生态位细菌群落为研究对象,采用高通量测序技术,对非根际、根际及根内细菌进行16S rRNA基因测序。结果表明,不同生态位细菌群落多样性存在显著差异,其中非根际及根际细菌群落多样性(Shannon index, Observed species, Faith′s PD)显著高于内生菌群落。同时,各生态位共现网络稳定性和复杂度表现为非根际>根际>根内细菌群落。而在组成上,细菌群落在不同生态位差异显著(R²=0.57,P=0.001)。其中变形菌门(Proteobacteria)是根内的优势门,该门类下假单胞菌属(Pseudomonas)、短波单胞菌属(Brevundimonas)、寡养单胞菌属(Stenotrophomonas)及泛菌属(Pantoea)在根内显著富集。在根际细菌中,拟杆菌门(Bacteroid...     

中街山列岛岩相潮间带大型底栖动物的群落格局

于2006年9月和2007年7月在中街山列岛4个有居民海岛岩相潮间带设立8个断面,对大型底栖动物的群落结构进行了调查。共获得大型底栖动物34种,其中腔肠动物1种,环节动物3种,甲壳动物10种,软体动物20种。优势种有日本笠藤壶(Tetraclita japonica)、紫贻贝(Mytilus edulis)和节蝾螺(Turb articulatus)等4种。以季节和站位为因子对多样性指数进行双因素方差分析,结果表明只有夏、秋季丰富度指数(P=0.028)存在显著差异,其他指数的方差分析没有显著差异(P>0.05)。3个潮带4个岛屿共12个站位的聚类分析和MDS标序分析表明,12个群落可分为3组(Ⅰ、Ⅱ和Ⅲ组)。大型底栖动物ABC曲线分析表明底栖动物群落尚未受到干扰。     

Planktonic ciliate community structure in shallow lakes of lowland Western Europe

Temperate shallow meso- to eutrophic lakes can exist in one of two alternative states with contrasting foodwebs, referred to as the clear-water and the turbid state. We describe the planktonic ciliate communities of such lakes based on a survey of 66 northwestern European lakes. Ciliates were enumerated and identified to species level according to the quantitative protargol staining technique. Ciliate biomass was on average twice as high in the turbid than in the clear-water lakes. The ciliate communities were dominated by oligotrichs and protostomatids, and no differences in functional composition or α-diversity could be detected between turbid and clear-water lakes, although β-diversity tended to be higher in the latter. At the species level, however, community structure strongly differed between turbid and clear-water lakes, and several indicator species could be identified for the different lake categories. Variation partitioning showed that nutrient status did not explain ciliate community structure independent of the alternative states, while lake area was identified as an additional structuring factor for the ciliate communities. These results stress the importance of the ecosystem structure in shaping ciliate communities in temperate shallow lakes and suggest that nutrient status has little direct effect on ciliate community structure in such lakes.     

Metazoan parasite diversity of the endemic South African intertidal klipfish,Clinus superciliosus: Factors influencing parasite community composition

The current trend in marine parasitology research, particularly in South Africa, is to focus on a specific parasite taxon and not on the total parasite community of a specific fish host. However, these records do not always reveal the ecological role of parasites in ecosystems. Thus, the present study aimed to determine which factors influence the parasite community composition of the endemic southern African intertidal klipfish, Clinus superciliosus (n = 75). Metazoan parasites were sampled from four localities (two commercial harbours - west coast; and two relatively pristine localities - southeast coast) along the South African coast. A total of 75 klipfish were examined for parasites, where 30 distinct taxa, representing seven taxonomic groups were found: Acanthocephala (4 taxa), Cestoda (2 taxa), Crustacea (5 taxa), Digenea (11 taxa), Hirudinea (2 taxa), Monogenea (1 taxon) and Nematoda (5 taxa). Results indicated that the main driver of diversity was locality, with the highest diversity on the southeast coast, most likely due to higher water temperatures and upwelling compared to the west coast. The parasite community composition of the klipfish was significantly influenced by water temperature and parasite life cycle. These results emphasise the importance of parasitological surveys including all parasite taxa in hosts from multiple localities and seasons, to better comprehend their ecological role.     

Microbial diversity and community structure in Fynbos soil

The Fynbos biome in South Africa is renowned for its high plant diversity and the conservation of this area is particularly important for the region. This is especially true in the case of endangered vegetation types on the lowlands such as Sand Fynbos, of which only small fragments remain. The question is thus whether the diversity of the above‐ground flora is mirrored in the below‐ground microbial communities. In order to determine the relationship of the above‐ and below‐ground communities, the soil community composition of both fungal and bacterial groups in Sand Fynbos was characterized over space and time. A molecular approach was used based on the isolation of total soil genomic DNA and automated ribosomal intergenic spacer analysis of bacterial and fungal communities. Soil from four different sites was compared to resolve the microbial diversity of eubacterial and fungal groups on a local (alpha diversity) scale as well as a landscape scale (beta diversity). The community structures from different sites were compared and found to exhibit strong spatial patterns which remained stable over time. The plant community data were compared with the fungal and the bacterial communities. We concluded that the microbial communities in the Sand Fynbos are highly diverse and closely linked to the above‐ground floral communities.     

土壤纤毛虫群落对不同退还模式生态恢复的响应

为了探究土壤纤毛虫群落对不同退还模式生态恢复的响应及利用其群落特征来评价退还效果,于2014年4月至2015年7月在甘肃省天祝藏族自治县朵什乡退耕还林区选取了3个不同退还林型样点(云杉、沙棘混交林A1,云杉林A2,沙棘林B1)和2个对照耕地样点(小麦地A0,豌豆地B0)为研究样地,采用"非淹没培养皿法"、活体观察法和培养直接计数法对土壤纤毛虫群落特征进行了研究,同时测定了各样点土壤的相关环境因子,并分析了不同恢复模式下土壤纤毛虫群落特征与植被群落参数、土壤环境因子间的相关性。研究共鉴定到125种土壤纤毛虫,隶属于9纲19目29科34属。结果显示:退还样点和对照样点的土壤纤毛虫群落结构特征存在明显差异(P0.05),退还样点间的物种相似性减小,群落组成复杂化;退还样点土壤纤毛虫物种数、密度、物种多样性指数、均匀度指数和丰富度指数均明显增高(P0.05),且各样点间表现为A1B1A2B0A0;各样点优势类群的演替趋势,由对照样点的肾形目演替为退还样点的散毛目。相关性分析和冗余分析结果表明,退耕还林后,对纤毛虫群落结构稳定影响最主要的是有机质、含水量和全氮的含量,不同林型间土壤纤毛虫群落组成差异较大,表明土壤纤毛虫群落结构可作为对退耕还林生态恢复的评价指标。     

The effect of wrack composition and diversity on macrofaunal assemblages in intertidal marine sediments

Wrack (dead, washed-up seaweed and seagrass) buried in soft substrata may increase the organic content and alter the physical structure of sediments. These effects may influence the composition and structure of macrofaunal assemblages in the sediment. Such influences can be expected to vary according to the type and amount of wrack as well as the presence of invasive seaweeds in the wrack. In this study, we deliberately buried different amounts of the invasive species Sargassum muticum in isolation or mixed to the native species Ulva sp. and Fucus vesiculosus, in two intertidal sandflats to test some hypotheses about the response of macrofaunal assemblages. We tested whether (1) diversity of detritus (i.e. different mixtures), and (2) the amount of detritus of S. muticum influenced the composition and the relative abundance of macrofaunal assemblages. We also assessed whether the sediment organic carbon and the biomass of benthic microalgae varied depending on the diversity of detritus and the amount of detritus of S. muticum. Finally, we tested if these effects of wrack were consistent across sites. Results indicated that buried wrack affected the composition and structure of macrofaunal assemblages in short-term (i.e. 4 weeks), but there were no differences depending on detritus diversity or the amount of S. muticum. In addition, sediment organic matter and microalgal biomass were not affected by the addition of wrack. They instead varied greatly among small spatial scales (i.e. plots). Wrack composition or abundance of the invasive species S. muticum played thus a small role in shaping the structure of macrofaunal assemblages or the biomass of benthic microalgae in these intertidal sediments, probably because these sediments are frequently affected by various inputs of organic matter and benthic assemblages are already adapted to organically enriched sediments.     

Ecological correlates between cladocerans and their endoparasites from permanent and rain pools: patterns in community composition and diversity

Water fleas (Cladocera) constitute a major component in freshwater food webs, with important ecosystem-level consequences. Their abundance and richness are strongly influenced by their ecology and coevolution with numerous endoparasites. We investigated how parasitism shapes cladoceran community structure and diversity. We surveyed 204 freshwater permanent and rain pools in Israel, identified all cladoceran specimens and screened them for infection. Daphniid species richness in this survey was lower than in previous surveys and the distribution pattern of the species was different, most likely due to local extinction and habitat loss. We recorded a total of 21 taxa of endoparasites, of which 13 are most likely species not yet described. Variation in parasite richness among hosts and sites could not be attributed to differences in host body size and behavioral feeding strategies. We extend the known host range and geographic distribution of eight parasites from Europe and North America (between latitudes 40° and 70°) to much southern areas (latitudes 31° and 32°) and to different climate zones (arid and semi-arid areas). In many infected populations we found co-occurrence of at least two endoparasites, and in most of these cases Daphnia individuals were found to be infected by several endoparasite species simultaneously. Such multiple infections may have important consequences for community structure as well as host?Cparasite coevolution.     

Extreme heatwave drives topography-dependent patterns of mortality in a bed-forming intertidal barnacle,with implications for associated community structure

Heatwave frequency and intensity will increase as climate change progresses. Intertidal sessile invertebrates, which often form thermally benign microhabitats for associated species, are vulnerable to thermal stress because they have minimal ability to behaviourally thermoregulate. Understanding what factors influence the mortality of biogenic species and how heatwaves might impact their ability to provide habitat is critical. Here, we characterize the community associated with the thatched barnacle, Semibalanus cariosus (Pallass, 1788), in British Columbia (BC), Canada. Then, we investigate what site-level and plot-level environmental factors explained variations in barnacle mortality resulting from an unprecedented regional heatwave in BC, Canada. Furthermore, we used a manipulative shading experiment deployed prior to the heatwave to examine the effect of thermal stress on barnacle survival and recruitment and the barnacle-associated community. We identified 50 taxa inhabiting S. cariosus beds, with variations in community composition between sites. Site-scale variables and algal canopy cover did not predict S. cariosus mortality, but patch-scale variation in substratum orientation did, with more direct solar irradiance corresponding with higher barnacle mortality. The shading experiment demonstrated that S. cariosus survival, barnacle recruitment, and invertebrate community diversity were higher under shades where substratum temperatures were lower. Associated community composition also differed between shaded and non-shaded plots, suggesting S. cariosus was not able to fully buffer acute thermal stress for its associated community. While habitat provisioning by intertidal foundation species is an important source of biodiversity, these species alone may not be enough to prevent substantial community shifts following extreme heatwaves. As heatwaves become more frequent and severe, they may further reduce diversity via the loss of biogenic habitat, and spatial variation in these impacts may be substantial.