金门岛北部海域浮游植物的季节变动及与环境的关联

采用2013—2014年四季度月在金门岛北部海域获取的浮游植物及环境因子监测数据, 分析该区浮游植物的群落结构和季节变化及其与温度、盐度、悬浮物、营养盐、叶绿素等的关系, 初步探讨涉海工程建设对浮游植物群落的潜在影响。结果显示, 鉴定出的浮游植物隶属3门43属82种(不含未定种), 群落构成以硅藻为主, 其次是甲藻, 蓝藻仅1种。物种组成的季节差异较大, 3月物种贫乏, 1月次之, 7月和11月最丰富。四季丰度平均为47.09×103 cells/L, 1月丰度最高, 7月次之, 11月最低, 3月高于11月少许。四季优势种均为硅藻, 13个优势种分别为柔弱几内亚藻(Guinardia delicatula)、短角弯角藻(Ecampia zoodicaus)、骨条藻(Skeletonema spp.)、具槽帕拉藻(Paralia sulcata)、微小海链藻(Thalassiosira exigua)、标志星杆藻(Asterionella notula)、旋链角毛藻(Chaetoceros curvisetus)、新月菱形藻(Nitzchia closterium)、派格棍形藻(Bacillaria paxillifera)、异常角毛藻(Chaetoceros abmormis)、小细柱藻(Leptocylindrus minutum)、宽角曲舟藻(Pleurosigma angulatum)和美丽曲舟藻(Pleurosigma formosum)。不同季节优势种有一定程度交错, 仅在单季占优的有6种, 有2/3在3个以上季节出现, 具槽帕拉藻、骨条藻为四季优势种。浮游植物物种多样性和均匀度总体较好, 群落结构稳定。与毗邻海区相比, 本区物种丰富度偏低, 丰度高于毗邻海区, 种类组成相似, 优势种却有较大差别。Pearson相关分析表明, 溶解无机氮及活性磷酸盐仅在1月与丰度存在极显著的正相关, 是促使丰度为四季最高的原因。涉海工程施工产生的悬浮物和冲击波是影响浮游植物群落的主要因素, 大量海洋工程建设案例表明, 施工期造成的浮游植物丰度下降趋势和优势种更替混乱在工程结束后能得以恢复。     

Herbivore regulation of plant abundance in aquatic ecosystems

Herbivory is a fundamental process that controls primary producer abundance and regulates energy and nutrient flows to higher trophic levels. Despite the recent proliferation of small‐scale studies on herbivore effects on aquatic plants, there remains limited understanding of the factors that control consumer regulation of vascular plants in aquatic ecosystems. Our current knowledge of the regulation of primary producers has hindered efforts to understand the structure and functioning of aquatic ecosystems, and to manage such ecosystems effectively. We conducted a global meta‐analysis of the outcomes of plant–herbivore interactions using a data set comprised of 326 values from 163 studies, in order to test two mechanistic hypotheses: first, that greater negative changes in plant abundance would be associated with higher herbivore biomass densities; second, that the magnitude of changes in plant abundance would vary with herbivore taxonomic identity. We found evidence that plant abundance declined with increased herbivore density, with plants eliminated at high densities. Significant between‐taxa differences in impact were detected, with insects associated with smaller reductions in plant abundance than all other taxa. Similarly, birds caused smaller reductions in plant abundance than echinoderms, fish, or molluscs. Furthermore, larger reductions in plant abundance were detected for fish relative to crustaceans. We found a positive relationship between herbivore species richness and change in plant abundance, with the strongest reductions in plant abundance reported for low herbivore species richness, suggesting that greater herbivore diversity may protect against large reductions in plant abundance. Finally, we found that herbivore–plant nativeness was a key factor affecting the magnitude of herbivore impacts on plant abundance across a wide range of species assemblages. Assemblages comprised of invasive herbivores and native plant assemblages were associated with greater reductions in plant abundance compared with invasive herbivores and invasive plants, native herbivores and invasive plants, native herbivores and mixed‐nativeness plants, and native herbivores and native plants. By contrast, assemblages comprised of native herbivores and invasive plants were associated with lower reductions in plant abundance compared with both mixed‐nativeness herbivores and native plants, and native herbivores and native plants. However, the effects of herbivore–plant nativeness on changes in plant abundance were reduced at high herbivore densities. Our mean reductions in aquatic plant abundance are greater than those reported in the literature for terrestrial plants, but lower than aquatic algae. Our findings highlight the need for a substantial shift in how biologists incorporate plant–herbivore interactions into theories of aquatic ecosystem structure and functioning. Currently, the failure to incorporate top‐down effects continues to hinder our capacity to understand and manage the ecological dynamics of habitats that contain aquatic plants.     

Strong influences of a dominant,ground‐nesting ant on recruitment,and establishment of ant colonies and communities

Many factors drive the organization of communities including environmental factors, dispersal abilities, and competition. In particular, ant communities have high levels of interspecific competition and dominance that may affect community assembly processes. We used a combination of surveys and nest supplementation experiments to examine effects of a dominant ground‐nesting ant (Pheidole synanthropica) on (1) arboreal twig‐nesting, (2) ground‐foraging, and (3) coffee‐foraging ant communities in coffee agroecosystems. We surveyed these communities in high‐ and low‐density areas of P. synanthropica over 2 years. To test for effects on twig ant recruitment, we placed artificial nesting resources on coffee plants in areas with and without P. synanthropica. The first sampling period revealed differences in ant species composition on the ground, in coffee plants, and artificial nests between high‐ and low‐density sites of P. synanthropica. High‐density sites also had significantly lower recruitment of twig ants and had species‐specific effects on twig ant species. Prior to the second survey period, abundance of P. synanthropica declined in the high‐density sites, such that P. synanthropica densities no longer differed. Subsequent sampling revealed no difference in total recruitment of twig ants to artificial nests between treatments. Likewise, surveys of ground and coffee ants no longer showed significant differences in community composition. The results from the first experimental period, followed by survey results after the decline in P. synanthropica densities suggest that dominant ants can drive community assembly via both recruitment and establishment of colonies within the community.     

The Plant Host Can Affect the Encapsidation of Brome Mosaic Virus (BMV) RNA: BMV Virions Are Surprisingly Heterogeneous

Brome mosaic virus (BMV) packages its genomic and subgenomic RNAs into three separate viral particles. BMV purified from barley, wheat, and tobacco have distinct relative abundances of the encapsidated RNAs. We seek to identify the basis for the host-dependent differences in viral RNA encapsidation. Sequencing of the viral RNAs revealed recombination events in the 3′ untranslated region of RNA1 of BMV purified from barley and wheat, but not from tobacco. However, the relative amounts of the BMV RNAs that accumulated in barley and wheat are similar and RNA accumulation is not sufficient to account for the difference in RNA encapsidation. Virions purified from barley and wheat were found to differ in their isoelectric points, resistance to proteolysis, and contacts between the capsid residues and the RNA. Mass spectrometric analyses revealed that virions from the three hosts had different post-translational modifications that should impact the physiochemical properties of the virions. Another major source of variation in RNA encapsidation was due to the purification of BMV particles to homogeneity. Highly enriched BMV present in lysates had a surprising range of sizes, buoyant densities, and distinct relative amounts of encapsidated RNAs. These results show that the encapsidated BMV RNAs reflect a combination of host effects on the physiochemical properties of the viral capsids and the enrichment of a subset of virions. The previously unexpected heterogeneity in BMV should influence the timing of the infection and also the host innate immune responses.     

环境中生物膜的菌群结构与污染物降解特性

生物膜是细菌最常见的生长方式。结构有序、功能分化的生物膜群落为内部细菌提供在不利环境中生存的庇护,其环境功效也日益受到关注。本文综述了多种环境中微生物与不同材料表面相互作用、进而发展为生物膜的机制;介绍了环境工程领域中生物膜的先锋菌种和菌群结构动态变化;介绍了生物膜在污染环境中的抗逆与降解特性。     

糜蛋白酶提高膜蛋白质谱分析序列覆盖率的胶内消化方法

近年来,质谱技术在膜蛋白结构与功能研究中被广泛应用。由于膜蛋白的跨膜结构域含有大量疏水性氨基酸,常常导致液质串联质谱检测的序列覆盖率较低,从而限制了质谱技术在膜蛋白结构与功能研究中的应用。文中利用人的整合膜蛋白维生素K环氧化物还原酶为模型,优化胶内消化条件,建立了一种稳定提高膜蛋白质谱序列覆盖率的糜蛋白酶胶内消化方法。通过探索钙离子浓度、pH值和缓冲体系对序列覆盖率、检测特异肽段的总数和类型以及特异肽段大小的影响,发现在5–10 mmol/L钙离子浓度、pH 8.0–8.5的Tris-HCl缓冲液中,可以兼顾序列覆盖率和肽段的多样性。该方法可以使膜蛋白的质谱覆盖率达到80%以上,将在膜蛋白结构与功能、膜蛋白相互作用位点的鉴定以及膜蛋白与小分子药物结合位点的鉴定等研究中具有广泛的应用价值。     

The ABC transporters in Candidatus Liberibacter asiaticus

Candidatus Liberibacter asiaticus (Ca. L. asiaticus) is a Gram‐negative bacterium and the pathogen of Citrus Greening disease (Huanglongbing, HLB). As a parasitic bacterium, Ca. L. asiaticus harbors ABC transporters that play important roles in exchanging chemical compounds between Ca. L. asiaticus and its host. Here, we analyzed all the ABC transporter‐related proteins in Ca. L. asiaticus. We identified 14 ABC transporter systems and predicted their structures and substrate specificities. In‐depth sequence and structure analysis including multiple sequence alignment, phylogenetic tree reconstruction, and structure comparison further support their function predictions. Our study shows that this bacterium could use these ABC transporters to import metabolites (amino acids and phosphates) and enzyme cofactors (choline, thiamine, iron, manganese, and zinc), resist to organic solvent, heavy metal, and lipid‐like drugs, maintain the composition of the outer membrane (OM), and secrete virulence factors. Although the features of most ABC systems could be deduced from the abundant experimental data on their orthologs, we reported several novel observations within ABC system proteins. Moreover, we identified seven nontransport ABC systems that are likely involved in virulence gene expression regulation, transposon excision regulation, and DNA repair. Our analysis reveals several candidates for further studies to understand and control the disease, including the type I virulence factor secretion system and its substrate that are likely related to Ca. L. asiaticus pathogenicity and the ABC transporter systems responsible for bacterial OM biosynthesis that are good drug targets. Proteins 2012. © 2012 Wiley Periodicals, Inc.     

Solution structure of the Mesorhizobium loti K1 channel cyclic nucleotide‐binding domain in complex with cAMP

Cyclic nucleotide‐sensitive ion channels, known as HCN and CNG channels, are crucial in neuronal excitability and signal transduction of sensory cells. HCN and CNG channels are activated by binding of cyclic nucleotides to their intracellular cyclic nucleotide‐binding domain (CNBD). However, the mechanism by which the binding of cyclic nucleotides opens these channels is not well understood. Here, we report the solution structure of the isolated CNBD of a cyclic nucleotide‐sensitive K⁺ channel from Mesorhizobium loti. The protein consists of a wide anti‐parallel β‐roll topped by a helical bundle comprising five α‐helices and a short 3₁₀‐helix. In contrast to the dimeric arrangement (‘dimer‐of‐dimers’) in the crystal structure, the solution structure clearly shows a monomeric fold. The monomeric structure of the CNBD supports the hypothesis that the CNBDs transmit the binding signal to the channel pore independently of each other.     

The more food webs change,the more they stay the same

Here, we synthesize a number of recent empirical and theoretical papers to argue that food-web dynamics are characterized by high amounts of spatial and temporal variability and that organisms respond predictably, via behaviour, to these changing conditions. Such behavioural responses on the landscape drive a highly adaptive food-web structure in space and time. Empirical evidence suggests that underlying attributes of food webs are potentially scale-invariant such that food webs are characterized by hump-shaped trophic structures with fast and slow pathways that repeat at different resolutions within the food web. We place these empirical patterns within the context of recent food-web theory to show that adaptable food-web structure confers stability to an assemblage of interacting organisms in a variable world. Finally, we show that recent food-web analyses agree with two of the major predictions of this theory. We argue that the next major frontier in food-web theory and applied food-web ecology must consider the influence of variability on food-web structure.