Islands as model systems in ecology and evolution: prospects fifty years after MacArthur‐Wilson

The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, ‘An equilibrium theory of insular zoogeography’, was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit re‐assessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution – understanding ecosystem functioning, speciation and diversification – frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island‐based theory is continually being enriched, incorporating non‐equilibrium dynamics is identified as a major challenge for the future.     

Lung inflammatory pattern and antibiotic treatment in pneumonia

Background

In community-acquired pneumonia host inflammatory response against the causative microorganism is necessary for infection resolution. However an excessive response can have deleterious effects. In addition to antimicrobial effects, macrolide antibiotics are known to possess immunomodulatory properties.We aimed to evaluate inflammatory cytokine profiles – both locally (bronchoalveolar lavage) and systemically (blood) – in community-acquired pneumonia admitted patients after at least 72 hours of antibiotic treatment (with and without macrolide containing regimens) and requiring bronchoscopic examination for inadequate response due to infection progression and/or lack of clinical stability.

Methods

A prospective study was performed on 52 admitted patients who developed an inadequate response after 72 hours of antibiotic treatment - non-responders community-acquired pneumonia - (blood and bronchoalveolar lavage), and two control groups: 1) community-acquired pneumonia control (blood) and 2) non-infection control (blood and bronchoalveolar lavage). Cytokine profiles (interleukin (IL)-6, IL-8, IL-10), tumour necrosis factor α and clinical outcomes were assessed.

Results

Non–responders patients treated with macrolide containing regimens showed significantly lower levels of IL-6 and TNF-α in bronchoalveolar lavage fluid and lower IL-8 and IL-10 in blood than those patients treated with non-macrolide regimens. Clinical outcomes showed that patients treated with macrolide regimens required fewer days to reach clinical stability (p < 0.01) and shorter hospitalization periods (p < 0.01).

Conclusions

After 72 hours of antibiotic effect, patients who received macrolide containing regimens exhibited lower inflammatory cytokine levels in pulmonary and systemic compartments along with faster stabilization of infectious parameters.     

OTO: Ontology Term Organizer

Background

The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software.

Methods

OTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java.

Results

Ontology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts’ opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available.

Conclusion

OTO has been used to organize the terms extracted from thirty volumes of Flora of North America and Flora of China combined, in addition to some smaller datasets of different taxon groups. User feedback indicates that the tool is efficient and user friendly. Being open source software, the application can be modified to fit varied term organization needs for different domains.     

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。     

宁夏枸杞深色有隔内生真菌的侵染特征及多样性

【背景】枸杞是享誉中外的名贵药材,深色有隔内生真菌(Dark septate endophytes,DSE)是枸杞内生真菌的重要组成部分。【目的】从宁夏枸杞栽培品种和野生品种的根系分离获得DSE菌株,研究枸杞DSE的群落组成、物种多样性及在宿主植物内的侵染定殖情况。【方法】从宁夏枸杞栽培园采集栽培品种宁杞1号、宁杞3号、宁杞5号、宁杞6号、宁杞7号、宁杞8号以及野生品种黄果枸杞和黑果枸杞共8个枸杞品种的根系,分离DSE菌株,运用形态学特征、r DNA-ITS序列分析进行菌株鉴定,采用回接试验方法确定DSE真菌。【结果】DSE在枸杞根系能形成大量"微菌核"典型结构。从8个枸杞品种根系中共分离获得DSE菌株279株,分属于18个属,具有丰富的物种多样性。镰刀菌属(Fusarium)为各品种的共有属和优势属,相对频率最高达85%。Monosporascus、蓝状菌属(Talaromyces)和俄氏孔菌属(Earliella)为枸杞内首次报道的DSE。枸杞不同品种中DSE群落物种多样性指数、均匀度指数和Simpson指数差异显著。【结论】DSE在枸杞栽培品种及野生品种中具有丰富的生物多样性,能够与枸杞根系形成良好的共生关系,增强了枸杞对生态环境的适应性。     

Fish and nutrient enrichment effects on rotifers in a Mediterranean shallow lake: a mesocosm experiment

A mesocosm experiment was conducted “in situ” in a Chara dominated shallow lake near Valencia (Spain) to study top–down and bottom–up effects on rotifers by means of nutrient and fish additions. Both processes were important in determining rotifer abundance, biomass and diversity. A total of 36 mesocoms were established with triplicate treatment combinations of three fish levels (from no fish to 45 individuals of Gambusia holbrooki males) and four nutrient enrichment levels (from no additions to 10 mg l⁻¹ nitrate-N and 1 mg l⁻¹ phosphate-P). The main effect was a notable increase of planktonic and plant associated rotifers densities with fish. Rotifers benefited from mosquitofish predation on microcrustaceans and chironomids. The results showed a marked negative relationship between rotifer and cyclopoid abundances, indicating the importance of the predatory pressure of cyclopoids on rotifers. Effects on rotifer diversity were also evident, in general rotifer diversity decreased with nutrients and increased with fish. The effects of nutrients analysed at species level showed two contrasting density responses: an increase or a decrease with nutrients, which levelled off at high nutrient concentrations. High-level nutrient additions (from 5 mg l⁻¹ nitrate-N and 0.5 mg l⁻¹ phosphate-P) induced a switch to a turbid state with macrophyte disappearance. Most planktonic rotifer species, as well as plant associated ones, diminished when the turbid state was well established, especially in the mesocosms without fish. In the turbid mesocosms, relative abundance of plant-associated rotifers (as a whole) was higher than that of planktonic rotifers. The changes in rotifer species composition after the switch from a clear to a turbid water state are also described. Species of the genus Anuraeopsis, Trichocerca and Hexarthra, dominant in the clear water state, practically disappeared in the turbid water state, in which Proalides tentaculatus and Lecane nana were the main species. Guest editors: S. S. S. Sarma, R. D. Gulati, R. L. Wallace, S. Nandini, H. J. Dumont & R. Rico-Martínez Advances in Rotifer Research     

人类休闲活动对森林鸟类群落无有害影响

我们对西班牙马德里森林深处(未受到人类干扰)、森林小路沿线(间或有徒步旅行者经过)以及森林野餐区(有较持久干扰)的鸟类进行了调查,以查明人类休闲活动对该地区鸟类群落的分布和多度的影响.结合样方法对以上3类区域鸟类群落的总体特征(如:鸟类的多度、物种的丰富度和多样性)、不同鸟类群体的特征(如:鸦科鸟类的多度,营巢或者取食集团的特征)、各鸟种的多度等参数进行了比较.结果表明:小路沿线和野餐区样方内鸟类的多度和物种丰富度比森林深处更高,已查明14种鸟类的多度在人为干扰区域比森林深处高,只有5种鸟类的多度在森林深处更高一些;在树冠层筑巢的鸟类、在树干和地面觅食的鸟类及鸦科鸟类在休闲活动区有更高的多度;地巢性鸟类在休闲区的多度较低,这种差别尤以阔叶落叶林中加明显.而森林小路的鸟类群落结构与森林内部非常相似,说明人类休闲活动对这些林区鸟类群落的影响更多缘自野餐.原因是野餐区常常具有以下特点:具有高大的乔木、中层植被稀疏、有较多的洞和缝隙以及野餐后会遗留下一些垃圾.以上结论与研究的预期目标正好相反,人类的这些休闲活动可能会降低地巢性鸟类的适宜度,但是对大多数鸟的类栖息地没有不利影响.     

中国云南小兽体表革螨的群落相似性

运用系统聚类分析方法对中国云南省境内17种主要小型哺乳动物(小兽)体表革螨群落相似性进行研究,每一种小兽体表的所有外寄生革螨被定义为一个相应的革螨群落。运用SPSS11.5软件完成17种革螨群落的相似性比较。研究结果表明:小兽体表革螨群落结构复杂,物种多样性高;隶属同一个属的小兽体表的革螨群落相似程度高,在系统聚类分析中聚为一类;大多数革螨群落相似性大小与相应小兽宿主在动物分类上的近缘性高低呈现高度一致,但也有一些革螨群落是例外的。这说明小兽体表革螨群落不仅受小兽宿主分类地位的影响,可能还受宿主生境的影响     

长江口潮下带春季大型底栖动物的群落结构

2005年4月对长江口全区域潮下带共10个采样站位的大型底栖动物进行了调查。调查采获大型底栖动物38种,分属5个生态类型,种类数较少,河口外缘站位种类数多于口内站位。各站位大型底栖动物的平均丰度为32.9个/m2、平均生物量为5.035g/m2(湿重);与20世纪七八十年代相比,平均生物量显著降低;口外缘站位的总丰度和总生物量均高于口内站位。环境因子相关分析表明,盐度是决定长江口大型底栖动物种类分布最重要的环境因子。群落聚类、标序分析显示,春季长江口潮下带大型底栖动物群落结构空间分异明显,完全符合目前长江口支、港、槽“三级分汊”的空间格局。其中,北支的大型底栖动物以混合高盐水种类为主,而南支则以淡水和半咸水种类为主。南支的南北槽分界处内外站位的群落差异也由盐度决定,因为靠近口内的群落均受长江冲淡水影响较大;而口外站位群落则受咸淡水影响。南支的南北港分界点内外的群落差异则主要受长江来水的影响,原因在于处在港分界点以内的群落所在区域,直接受长江来水的冲刷,底质环境极不稳定;而港、槽分界点之间的群落所在区域由于河口上段的诸多明暗沙体的阻挡,水势较为稳定,所以底质环境较稳定,从而使得港、槽分界点之间的群落出现了更多的沙蚕等底质环境类型种类。