Comparative analysis of multiple protein-sequence alignment methods [published erratum appears in Mol Biol Evol 1994 Sep;11(5):811]

We have analyzed a total of 12 different global and local multiple protein-sequence alignment methods. The purpose of this study is to evaluate each method's ability to correctly identify the ordered series of motifs found among all members of a given protein family. Four phylogenetically distributed sets of sequences from the hemoglobin, kinase, aspartic acid protease, and ribonuclease H protein families were used to test the methods. The performance of all 12 methods was affected by (1) the number of sequences in the test sets, (2) the degree of similarity among the sequences, and (3) the number of indels required to produce a multiple alignment. Global methods generally performed better than local methods in the detection of motif patterns.      

嗜盐耐盐微生物抗盐胁迫相关离子转运蛋白研究进展

离子转运蛋白在维持细胞内pH稳态、离子动态平衡等方面发挥着重要作用。钠离子转运体和钾离子转运体在嗜盐耐盐微生物中广泛存在,其"保钾排钠"机制是微生物抗盐胁迫的两大策略之一。近年来,嗜盐耐盐微生物中许多新型钠、钾离子转运体被陆续发现,如RDD蛋白、UPF0118蛋白、DUF蛋白和KimA蛋白等;Fe³⁺、Mg²⁺等其他金属离子的转运蛋白也被证实可通过影响微生物胞内相容性溶质的合成起到渗透调节的作用。本文综述了嗜盐耐盐微生物中抗盐胁迫相关的各类离子转运蛋白,分析其分子结构和工作机理,并对这些蛋白在农业方面的应用进行了展望。继续发现新的离子转运蛋白,探究抗盐胁迫相关离子转运蛋白的结构和机理,解析各转运系统的协同作用及分子调控机制,将进一步加深对嗜盐耐盐微生物抗盐胁迫调控的认识,并为盐碱地农作物的改良等提供新的思路。     

Environmental DNA reveals a mismatch between diversity facets of Amazonian fishes in response to contrasting geographical,environmental and anthropogenic effects

Freshwater ecosystems are among the most endangered ecosystem in the world. Understanding how human activities affect these ecosystems requires disentangling and quantifying the contribution of the factors driving community assembly. While it has been largely studied in temperate freshwaters, tropical ecosystems remain challenging to study due to the high species richness and the lack of knowledge on species distribution. Here, the use of eDNA-based fish inventories combined to a community-level modelling approach allowed depicting of assembly rules and quantifying the relative contribution of geographic, environmental and anthropic factors to fish assembly. We then used the model predictions to map spatial biodiversity and assess the representativity of sites surveyed in French Guiana within the EU Water Framework Directive (WFD) and highlighted areas that should host unique freshwater fish assemblages. We demonstrated a mismatch between the taxonomic and functional diversity. Taxonomic assemblages between but also within basins were mainly the results of dispersal limitation resulting from basin isolation and natural river barriers. Contrastingly, functional assemblages were ruled by environmental and anthropic factors. The regional mapping of fish diversity indicated that the sites surveyed within the EU WFD had a better representativity of the regional functional diversity than taxonomic diversity. Importantly, we also showed that the assemblages expected to be the most altered by anthropic factors were the most poorly represented in terms of functional diversity in the surveyed sites. The predictions of unique functional and taxonomic assemblages could, therefore, guide the establishment of new survey sites to increase fish diversity representativity and improve this monitoring program.     

柬埔寨白蝶兰，中国兰科一新记录种

报道中国兰科白蝶兰属一新记录种——柬埔寨白蝶兰Pecteilis cambodiana (Gagnep.) Aver.,描述其特征并提供了彩色图片。凭证标本保存于福建农林大学林学院树木标本室(FJFC)。     

厌氧氨氧化菌驱动脱氮途径的研究进展

厌氧氨氧化菌(anaerobic ammonia-oxidizing bacteria, AnAOB)的代谢多样性,使得该菌群能够在海洋、湿地和陆地等不同的自然生态系统中广泛分布,甚至在一些极热和极寒环境中也检测到了该菌群的存在。本文回顾并总结了厌氧氨氧化菌在不同生态系统中的发现、分布及脱氮贡献等方面的研究,分析了厌氧氨氧化菌分布的主要环境影响因素。该综述将帮助我们更好地理解全球氮循环中厌氧氨氧化菌的实际角色和功能,并基于厌氧氨氧化(anaerobicammoniaoxidation,anammox)过程,探究能与其进行协作的新型生物脱氮工艺,以期为这些工艺的研发和推广提供生态学基础和新的思考,从而实现脱氮工艺的技术变革。     

一株耐盐碱乳酪短杆菌G20响应盐碱胁迫的差异代谢物分析

【目的】探究耐盐碱乳酪短杆菌G20响应盐碱胁迫的代谢物组成以及代谢物合成潜力,为潜在功能分子和盐碱诱导的快速稳定响应逻辑门基因线路的挖掘提供参考。【方法】利用液相色谱-质谱联用技术(LC-MS)检测乳酪短杆菌G20盐碱环境与正常环境下4个生长时期的代谢产物。着重对富含高差异变化倍数代谢物的适应期与指数期进行分析。【结果】乳酪短杆菌G20可以在pH 10.0、9%NaCl环境中正常生长,同时环境pH值会随菌株生长逐步下降。综合正负离子2种模式,乳酪短杆菌G20在盐碱环境下各生长时期间差异代谢物数量分别为正常环境的0.69、0.75和0.81倍。盐碱胁迫诱导下适应期与指数期差异代谢物主要为苯环型化合物、有机酸及其衍生物与有机杂环类化合物。其中上调的有机酸化合物吲哚-3-乙酸、犬尿酸和葡萄糖酸指数期质谱信号强度低于适应期。菌株中可能存在的渗透保护剂有L-瓜氨酸、L-脯氨酸、N-乙酰鸟氨酸和左旋肉碱等。适应期变化倍数较大或质谱信号强度较高的差异化合物有毛果芸香碱、植物鞘氨醇和柠檬酸等,指数期有组胺、L-脯氨酸和硫胺素等。菌株差异代谢通路集中在氨基酸代谢与碳水化合物代谢。菌株代谢物中存在甜菜碱和...     

内生真菌印度梨形孢诱导小麦抗根腐病作用研究

【目的】明确印度梨形孢(Piriformospora indica)诱导小麦对根腐病产生抗性的作用机制。【方法】用印度梨形孢悬液浸种,以无菌培养液为对照,用病原菌禾谷镰孢菌(Fusarium graminearum)侵染小麦,对其相关生理生化指标及转录组变化进行分析。【结果】禾谷镰孢菌能诱导小麦产生过氧化氢,降低细胞内水含量,破坏细胞膜的稳定性;根部定殖印度梨形孢的小麦细胞内抗氧化酶活性增强,活性氧自由基含量降低,胞内水含量提高,细胞膜稳定性增强;印度梨形孢定殖能改变由于病原菌引起的mRNA转录组变化,抗性相关基因的表达增强。综合表明印度梨形孢定殖能有效地提高小麦对禾谷镰孢菌的抗性。【结论】研究结果为深入理解植物与微生物互作、开发新型高效环保抗根腐病生物制剂提供理论和实验依据。     

The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.