Large-scale processes and the Asian bias in species diversity of temperate plants

An important issue in the study of biodiversity is the extent to which global patterns of species richness reflect large-scale processes and historical contingencies. Ecological interactions in local assemblages may constrain the number of species that can coexist, but differences in diversity in similar habitats within different regions (diversity anomalies) suggest that this limit is not firm. Variation in rate of species production could influence regional and perhaps local diversity independently of the ecological capacity of an area to support coexisting species, thereby creating diversity anomalies. Temperate Zone genera of plants that are disjunct between similar environments in eastern Asia and eastern North America (EAS-ENA) have twice as many species in Asia as in North America. Because lineages of these genera in Asia and North America are mostly sister pairs, they share a common history of adaptation and ecological relationship before disjunction. Thus, the diversity anomaly in EAS-ENA genera is not an artefact of taxon or habitat sampling but reflects differences in the net diversification (speciation-extinction) of the lineages in each of the continents. Here we propose that the most probable cause of the EAS-ENA anomaly in diversity is the extreme physiographical heterogeneity of temperate eastern Asia, especially compared with eastern North America, which in conjunction with climate and sea-level change has provided abundant opportunities for evolutionary radiation through allopatric speciation.     

基于高通量测序对四川怀远特色发酵食品微生物群落结构分析

为了研究四川怀远特色传统发酵食品的微生物多样性,利用Illumina HiSeq 2500高通量测序平台,对当地豆腐帘子和冻糕的微生物群落结构进行了系统分析.结果表明,豆腐帘子的菌群主要隶属于变形菌门(Proteobacteria)和担子菌门(Basidiomycota),检测出40个细菌属和21个真菌属,主要优势微生物是Acinetobacter和Trichosporon.冻糕的菌群主要隶属于厚壁菌门(Firmicutes)和子囊菌门(Ascomycota),检测出36个细菌属和23个真菌属,主要优势微生物是Lactobacillus和Kazachstania.     

Spatial scale dictates the productivity-biodiversity relationship

The diversity of life is heterogeneously distributed across the Earth. A primary cause for this pattern is the heterogeneity in the amount of energy, or primary productivity (the rate of carbon fixed through photosynthesis), available to the biota in a given location. But the shape of the relationship between productivity and species diversity is highly variable. In many cases, the relationship is 'hump-shaped', where diversity peaks at intermediate productivity. In other cases, diversity increases linearly with productivity. A possible reason for this discrepancy is that data are often collected at different spatial scales. If the mechanisms that determine species diversity vary with spatial scale, then so would the shape of the productivity-diversity relationship. Here, we present evidence for scale-dependent productivity-diversity patterns in ponds. When the data were viewed at a local scale (among ponds), the relationship was hump-shaped, whereas when the same data were viewed at a regional scale (among watersheds), the relationship was positively linear. This dependence on scale results because dissimilarity in local species composition within regions increased with productivity.     

Coral communities are regionally enriched along an oceanic biodiversity gradient

Ecological communities are influenced by processes operating at multiple scales. Thus, a better understanding of how broad- as well as local-scale processes affect species diversity and richness is increasingly becoming a central focus in modern community ecology. Here, in a study of unprecedented geographical scope, we show significant regional and local variation in the species richness of coral assemblages across an oceanic biodiversity gradient. The gradient that we sampled extends 10,000 km eastwards from the world's richest coral biodiversity hotspot in the central Indo-Pacific. Local richness and the size of regional species pools decline significantly across 15 islands spanning the gradient. In addition, richness declines across three adjacent habitats (reef slopes, crests and flats). In each habitat, a highly consistent linear relationship between local and regional species richness indicates strong regional enrichment. Thus, even on the most diverse coral reefs in the world, local coral assemblages are profoundly affected by regional-scale processes. Understanding these historical and biogeographical influences is essential for the effective management and preservation of these endangered communities.     

污水生物处理功能微生物的多样性

综述了污水处理微生物学近期的研究现状,介绍了一些仍不能培养的细菌被鉴定为对污泥膨胀、提高生物学除磷、亚硝酸盐氧化和脱氮负责,而许多原来认为的优势群体却对污水处理不是最重要的.这些知识可以为微生物多样性、种群动态、生态稳定和特定微生物种群活性等提供新的视野,可以应用于污水生物反应器的设计和处理参数的控制,为改进污水处理厂的处理策略等提供更多的理论基础和依据.     

General patterns of taxonomic and biomass partitioning in extant and fossil plant communities

A central goal of evolutionary ecology is to identify the general features maintaining the diversity of species assemblages. Understanding the taxonomic and ecological characteristics of ecological communities provides a means to develop and test theories about the processes that regulate species coexistence and diversity. Here, using data from woody plant communities from different biogeographic regions, continents and geologic time periods, we show that the number of higher taxa is a general power-function of species richness that is significantly different from randomized assemblages. In general, we find that local communities are characterized by fewer higher taxa than would be expected by chance. The degree of taxonomic diversity is influenced by modes of dispersal and potential biotic interactions. Further, changes in local diversity are accompanied by regular changes in the partitioning of community biomass between taxa that are also described by a power function. Our results indicate that local and regional processes have consistently regulated community diversity and biomass partitioning for millions of years.     

微生物共培养产生新颖活性次生代谢产物的研究进展

微生物源天然产物是药物先导化合物的重要资源之一.近年来,利用微生物共培养产生各类天然产物的研究发展迅速.微生物共培养是一种通过模拟（微生物）栖息地/栖息环境以激活可能的沉默生物合成基因簇并进而诱导微生物产生新次生代谢物的有效方法.与菌株纯培养相比,共培养不仅增加了次级代谢产物的种类多样性,而且其生物活性及产量也得到了提高.文章就近5年来真菌与真菌、真菌与细菌、细菌与细菌等3种类型的微生物共培养研究成果进行了综述,同时简要介绍了用于分析共培养作用机制的多组学技术,并在此基础上探讨了微生物共培养相互作用机制研究的进展及挑战.综述旨在为微生物共培养的深入研究提供借鉴,并为微生物药物的开发提供新思路.     

16S rRNA sequences reveal numerous uncultured microorganisms in a natural community.

Microbiologists have been constrained in their efforts to describe the compositions of natural microbial communities using traditional methods. Few microorganisms have sufficiently distinctive morphology to be recognized by microscopy. Culture-dependent methods are biased, as a microorganism can be cultivated only after its physiological niche is perceived and duplicated experimentally. It is therefore widely believed that fewer than 20% of the extant microorganisms have been discovered, and that culture methods are inadequate for studying microbial community composition. In view of the physiological and phylogenetic diversity among microorganisms, speculation that 80% or more of microbes remain undiscovered raises the question of how well we know the Earth's biota and its biochemical potential. We have performed a culture-independent analysis of the composition of a well-studied hot spring microbial community, using a common but distinctive cellular component, 16S ribosomal RNA. Our results confirm speculations about the diversity of uncultured microorganisms it contains.     

Genetic diversity in Sargasso Sea bacterioplankton

Bacterioplankton are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities. Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques. Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species. We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction. The analysis indicates the presence of a novel microbial group, the SAR11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community. A second cluster of lineages related to the oxygenic phototrophs--cyanobacteria, prochlorophytes and chloroplasts--was also observed. However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats. The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors.     

内源激活剂驱油藏内微生物菌群结构变化分析

油藏内源功能微生物的激活能有效提高采油效率。其中激活后功能微生物的群落变化分析及相关代谢基因丰度的变化对内源激活剂的筛选及激活机理研究具有重要的指导意义。本实验利用高通量测序技术准确分析了内源激活剂注入井（WJW199.1）和对照井（WJW202）中内源微生物（包括古菌和细菌）基于门、纲、属水平的种群多样性和群落结构。结果表明采出水中Thaumarchaeota门的古菌占主导,而丰度最高的细菌属于Proteobacteria门和 Firmicutes门。不管对于古菌还是细菌,注入井中的微生物多样性都远高于对照井,说明激活剂的添加有效激活了其中的内源微生物,提高了群落结构多样性。尤其是Pseudomonas,Arcobacter等具有产表活剂能力的功能微生物。同时,硫酸盐还原菌脱硫弧菌属等有害菌被抑制,丰度降低。表明从微生物种群变化的程度来看内源激活剂的注入降低了有害菌的丰度,激活了功能微生物,增强了整体微生物的驱油能力。     

Geographic structure and dynamics of coevolutionary selection

Coevolution of species is one of the major processes organizing the Earth's biodiversity. Recent coevolutionary theory has indicated that the geographic structure of species has the potential to impose powerful and continuing effects on coevolutionary dynamics, if that structure creates selection mosaics and coevolutionary hotspots across landscapes. Here we confirm that current coevolutionary selection in interspecific interactions can be highly divergent across both narrow and broad geographic scales, thereby fueling continuing coevolution of taxa. Study of a widespread plant insect interaction across a broad range of habitats for several years showed that an insect functioning both as a pollinator and a floral parasite can be strongly mutualistic in some habitats but commensal or antagonistic in neighbouring habitats. The results for one of the habitats span seven years, demonstrating that the local structure of coevolutionary selection can remain stable across multiple generations. Conservation of the evolutionary processes maintaining long-term biological diversity may require preservation of the conditions that allow a long-term shifting geographic mosaic of coevolutionary hotspots and coldspots.     

Drought sensitivity shapes species distribution patterns in tropical forests

Although patterns of tree species distributions along environmental gradients have been amply documented in tropical forests, mechanisms causing these patterns are seldom known. Efforts to evaluate proposed mechanisms have been hampered by a lack of comparative data on species' reactions to relevant axes of environmental variation. Here we show that differential drought sensitivity shapes plant distributions in tropical forests at both regional and local scales. Our analyses are based on experimental field assessments of drought sensitivity of 48 species of trees and shrubs, and on their local and regional distributions within a network of 122 inventory sites spanning a rainfall gradient across the Isthmus of Panama. Our results suggest that niche differentiation with respect to soil water availability is a direct determinant of both local- and regional-scale distributions of tropical trees. Changes in soil moisture availability caused by global climate change and forest fragmentation are therefore likely to alter tropical species distributions, community composition and diversity.     

Positive feedbacks promote power-law clustering of Kalahari vegetation

The concept of local-scale interactions driving large-scale pattern formation has been supported by numerical simulations, which have demonstrated that simple rules of interaction are capable of reproducing patterns observed in nature. These models of self-organization suggest that characteristic patterns should exist across a broad range of environmental conditions provided that local interactions do indeed dominate the development of community structure. Readily available observations that could be used to support these theoretical expectations, however, have lacked sufficient spatial extent or the necessary diversity of environmental conditions to confirm the model predictions. We use high-resolution satellite imagery to document the prevalence of self-organized vegetation patterns across a regional rainfall gradient in southern Africa, where percent tree cover ranges from 65% to 4%. Through the application of a cellular automata model, we find that the observed power-law distributions of tree canopy cluster sizes can arise from the interacting effects of global-scale resource constraints (that is, water availability) and local-scale facilitation. Positive local feedbacks result in power-law distributions without entailing threshold behaviour commonly associated with criticality. Our observations provide a framework for integrating a diverse suite of previous studies that have addressed either mean wet season rainfall or landscape-scale soil moisture variability as controls on the structural dynamics of arid and semi-arid ecosystems.     

基于高通量测序的不同养殖系统下凡纳滨对虾肠道和水体中微生物的多样性

【目的】研究不同养殖系统对凡纳滨对虾肠道及水体微生物多样性的影响。【方法】以循环养殖系统和非养殖系统下凡纳滨对虾养殖水体及其肠道为研究对象,在养殖30d后采集样品,采用Illumina MiSeq高通量测序样品细菌16SrRNA基因V3+V4区,通过RDP11.3、Greengenes13.8、NCBI 16S Microbial和Customized batabase等数据库进行分析,阐述循环养殖系统的意义和微生物在其中的作用。【结果】养殖期间,不同养殖系统凡纳滨对虾均正常存活。将原始序列优化后对Clean序列进行分析,非循环系统下水体优质序列百分比约81%,肠道中约89%;循环系统下水体优质序列百分比为92%,肠道中为94%。两种养殖系统下水体和肠道细菌在纲水平占绝对优势的是变形菌纲,但各菌群丰度不同;不同的Alpha指数显示出物种间的差异性;通过系统发育树可以看出,不同养殖系统改变了凡纳滨对虾生境中的物种及发育关系,间接阐述微生物在养殖生境中的作用和意义。【结论】通过高通量测序揭示不同养殖系统中微生物菌群的差异以及多样性,对于凡纳滨对虾实际养殖具有指导作用,对阐述养殖过程中微生物和相关疾病的关系具有重要意义。     

A taxa-area relationship for bacteria

A positive power-law relationship between the number of species in an area and the size of that area has been observed repeatedly in plant and animal communities. This species-area relationship, thought to be one of the few laws in ecology, is fundamental to our understanding of the distribution of global biodiversity. However, such a relationship has not been reported for bacteria, and little is known regarding the spatial distribution of bacteria, relative to what is known of plants and animals. Here we describe a taxa-area relationship for bacteria over a scale of centimetres to hundreds of metres in salt marsh sediments. We found that bacterial communities located close together were more similar in composition than communities located farther apart, and we used the decay of community similarity with distance to show that bacteria can exhibit a taxa-area relationship. This relationship was driven primarily by environmental heterogeneity rather than geographic distance or plant composition.     

Resource-use efficiency and plant invasion in low-resource systems

No species can maximize growth, reproduction and competitive ability across all environments, so the success of invasive species is habitat-dependent. Nutrient-rich habitats often experience more invasion than resource-poor habitats, a pattern consistent with traits generally associated with successful invaders (high growth rates, early reproduction and many offspring). However, invaders do colonize resource-poor environments, and the mechanisms that allow their success in these systems are poorly understood. Traits associated with resource conservation are widespread among species adapted to resource-poor environments, and invasive species may succeed in low-resource environments by employing resource conservation traits such as high resource-use efficiency (RUE; carbon assimilation per unit of resource). We investigated RUE in invasive and native species from three habitats in Hawaii where light, water or nutrient availability was limiting to plant growth. Here we show that across multiple growth forms and broad taxonomic diversity invasive species were generally more efficient than native species at using limiting resources on short timescales and were similarly efficient when RUE measures were integrated over leaf lifespans. Our data challenge the idea that native species generally outperform invasive species under conditions of low resource availability, and suggest that managing resource levels is not always an effective strategy for invasive species control.     

遗传指纹图谱技术对微生物群落的分析

微生物培养技术无法获得自然生境中99％以上的微生物，而可培养的微生物也仅提供极少的形态学线索，鉴定和生理学特性经常是模糊的。分子生物学技术对不可培养微生物的研究，开启了探索微生物多样性和新资源的大门。DNA杂交、rRNA分子标记测序等已经成为研究分子微生物生态学的常规手段，可以鉴定和描述微生物群落的种群，但却不适于探索微生物复杂群落的动力学。遗传指纹图谱技术允许同时进行多样本的分析，可比较不同生境和随时间变化的微生物群落行为，是传统手段的有力补充。     

Evidence that decomposition rates of organic carbon in mineral soil do not vary with temperature

It has been suggested that increases in temperature can accelerate the decomposition of organic carbon contained in forest mineral soil (Cs), and, therefore, that global warming should increase the release of soil organic carbon to the atmosphere. These predictions assume, however, that decay constants can be accurately derived from short-term laboratory incubations of soil or that in situ incubations of fresh litter accurately represent the temperature sensitivity of Cs decomposition. But our limited understanding of the biophysical factors that control Cs decomposition rates, and observations of only minor increases in Cs decomposition rate with temperature in longer-term forest soil heating experiments and in latitudinal comparisons of Cs decomposition rates bring these predictions into question. Here we have compiled Cs decomposition data from 82 sites on five continents. We found that Cs decomposition rates were remarkably constant across a global-scale gradient in mean annual temperature. These data suggest that Cs decomposition rates for forest soils are not controlled by temperature limitations to microbial activity, and that increased temperature alone will not stimulate the decomposition of forest-derived carbon in mineral soil.     

中国东北条子河中微生物群落变化与锌砷污染的关系研究

研究目的：通过研究河流微生物与污染物的互作关系,为河流污染治理等相关研究提供新途径。创新要点：研究选择的目标河流是报道较少的辽河二级支流,该研究对于了解支流污染特别是东北地区河流污染有重要的意义。将分子生态学技术应用于分析不同污染程度的河流底泥微生物变化,建立微生物种群变化和污染物的互作关系。研究方法：选取沿条子河的8个代表性区段,分析河水和底泥中重金属和污染物的变化情况。通过变性梯度凝胶电泳（DGGE）技术分析不同河流区段内真核和原核微生物种群变化,解析河流中污染物对底泥微生物的影响,建立微生物种群变化和重金属污染的互作关系。重要结论：重金属污染物的存在能抑制底泥中微生物生长,仅少量具有较强抗性的微生物存活（见图4）;有机污染物的增加使对重金属有较强抗性的Limnodrilus hoffmeisteri 大量繁殖（见图2~4）,从而大量消耗溶解氧,导致好氧微生物死亡和河水自净能力退化,最终引起水质恶化。由此可见,微生物对环境污染物的变化有很敏感的响应,通过对环境中微生物的监测有助于进一步分析环境污染的变化。     

Environmental determinants of extinction selectivity in the fossil record

The causes of mass extinctions and the nature of biological selectivity during extinction events remain central questions in palaeobiology. Although many different environmental perturbations have been invoked as extinction mechanisms, it has long been recognized that fluctuations in sea level coincide with many episodes of biotic turnover. Recent work supports the hypothesis that changes in the areas of epicontinental seas have influenced the macroevolution of marine animals, but the extent to which differential environmental turnover has contributed to extinction selectivity remains unknown. Here I use a new compilation of the temporal durations of sedimentary rock packages to show that carbonate and terrigenous clastic marine shelf environments have different spatio-temporal dynamics and that these dynamics predict patterns of genus-level extinction, extinction selectivity and diversity among Sepkoski's Palaeozoic and modern evolutionary faunae. These results do not preclude a role for biological interactions or unusual physical events as drivers of macroevolution, but they do suggest that the turnover of marine shelf habitats and correlated environmental changes have been consistent determinants of extinction, extinction selectivity and the shifting composition of the marine biota during the Phanerozoic eon.