Two decades of describing the unseen majority of aquatic microbial diversity

Aquatic environments harbour large and diverse microbial populations that ensure their functioning and sustainability. In the current context of global change, characterizing microbial diversity has become crucial, and new tools have been developed to overcome the methodological challenges posed by working with microbes in nature. The advent of Sanger sequencing and now next-generation sequencing technologies has enabled the resolution of microbial communities to an unprecedented degree of precision. However, to correctly interpret microbial diversity and its patterns this revolution must also consider conceptual and methodological matters. This review presents advances, gaps and caveats of these recent approaches when considering microorganisms in aquatic ecosystems. We also discuss potentials and limitations of the available methodologies, from water sampling to sequence analysis, and suggest alternative ways to incorporate results in a conceptual and methodological framework. Together, these methods will allow us to gain an unprecedented understanding of microbial diversity in aquatic ecosystems.     

Diagnostic microbial microarrays in soil ecology

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.     

Wildlife population assessment: past developments and future directions

We review the major developments in wildlife population assessment in the past century. Three major areas are considered: mark-recapture, distance sampling, and harvest models. We speculate on how these fields will develop in the next century. Topics for which we expect to see methodological advances include integration of modeling with Geographic Information Systems, automated survey design algorithms, advances in model-based inference from sample survey data, a common inferential framework for wildlife population assessment methods, improved methods for estimating population trends, the embedding of biological process models into inference, substantially improved models for conservation management, advanced spatiotemporal models of ecosystems, and greater emphasis on incorporating model selection uncertainty into inference. We discuss the kind of developments that might be anticipated in these topics.     

Ecogeochemistry potential in deep time biodiversity illustrated using a modern deep-water case study

The fossil record provides the only direct evidence of temporal trends in biodiversity over evolutionary timescales. Studies of biodiversity using the fossil record are, however, largely limited to discussions of taxonomic and/or morphological diversity. Behavioural and physiological traits that are likely to be under strong selection are largely obscured from the body fossil record. Similar problems exist in modern ecosystems where animals are difficult to access. In this review, we illustrate some of the common conceptual and methodological ground shared between those studying behavioural ecology in deep time and in inaccessible modern ecosystems. We discuss emerging ecogeochemical methods used to explore population connectivity and genetic drift, life-history traits and field metabolic rate and discuss some of the additional problems associated with applying these methods in deep time.     

土壤原生动物在环境监测中的应用

土壤原生动物具有丰富的种类多样性和巨大的生物量,在土壤生态系统中具有十分重要的地位。因此,其种类和数量的变化可指示环境质量的状况及发展趋势。与其它土壤生物相比,原生动物的一些特征使其更利于成为监测生物。土壤原生动物各类群在环境监测中的作用是不同的。有壳肉足虫和纤毛虫更适合作为土壤环境的指示生物。土壤原生动物在农田生态系统、森林生态系统等环境监测中已经有了一些应用,但与在水体环境监测中获得广泛应用的水生原生动物相比,土壤原生动物用于环境监测才刚刚起步。土壤原生动物分类学研究的滞后和方法学上的欠缺是阻碍其作为监测生物的瓶颈。相信随着这些问题的逐步解决,土壤原生动物在环境监测中必将发挥越来越大的作用。     

Contemporary issues,current best practice and ways forward in soil protist ecology

Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.     

EFFECTS OF CLIMATE CHANGE ON GLOBAL SEAWEED COMMUNITIES

Seaweeds are ecologically important primary producers, competitors, and ecosystem engineers that play a central role in coastal habitats ranging from kelp forests to coral reefs. Although seaweeds are known to be vulnerable to physical and chemical changes in the marine environment, the impacts of ongoing and future anthropogenic climate change in seaweed‐dominated ecosystems remain poorly understood. In this review, we describe the ways in which changes in the environment directly affect seaweeds in terms of their physiology, growth, reproduction, and survival. We consider the extent to which seaweed species may be able to respond to these changes via adaptation or migration. We also examine the extensive reshuffling of communities that is occurring as the ecological balance between competing species changes, and as top‐down control by herbivores becomes stronger or weaker. Finally, we delve into some of the ecosystem‐level responses to these changes, including changes in primary productivity, diversity, and resilience. Although there are several key areas in which ecological insight is lacking, we suggest that reasonable climate‐related hypotheses can be developed and tested based on current information. By strategically prioritizing research in the areas of complex environmental variation, multiple stressor effects, evolutionary adaptation, and population, community, and ecosystem‐level responses, we can rapidly build upon our current understanding of seaweed biology and climate change ecology to more effectively conserve and manage coastal ecosystems.     

Biogeography and priority areas for the conservation of bats in the Brazilian Cerrado

In this study, we describe the distribution pattern of bat species and select priority areas for the conservation of the Cerrado based on a systematic planning approach. We estimated species richness and calculated the total beta diversity based on Sørensen’s dissimilarity index (βsor). We estimated the species turnover using Simpson’s dissimilarity index (βsim). We then evaluated the nesting (βsne) by the difference between the dissimilarity indices (βsor and βsim). Based on this analysis, we identified the priority areas for the conservation of bats in the Cerrado based on the zonation approach. We found that the species richness and beta diversity of bats in the Cerrado are concentrated primarily in the central and northern portions of the biome. We also discovered that the conservation units of the Cerrado are ineffective for the protection of species with a restricted distribution (≤ 150 grid cells), such as Vampyrum spectrum, for which we propose the creation of new conservation units that better cover the diversity patterns observed in the present study. By conserving this diversity, we will also be protecting local habitats, which will in turn enable the survival of a wide range of species, and provide the ecosystems with the capacity to respond adequately to future changes in the environment.     

Invertebrates and the complexity of tropical ecosystems

It has been estimated that there are seven million terrestrial arthropod species on Earth consisting of 6.1 million species of insects, 1.5 million of which are beetles. Tropical forests hold a majority of these species, yet few such places have been adequately sampled for alpha diversity, and there remains even more uncertainty about beta diversity. From an ecological point of view, it is the functional role of organisms within ecosystems that is the particular focus. It has been customary to classify invertebrates within ecosystems in terms of their trophic roles, but it is also useful to consider their roles in networks. In broad terms, we can classify these networks on the grounds of their basal resources. Those based directly on the photosynthetic products of plants are so-called “green” food webs, and those based on dead and dying plant material are “brown” food webs. Here, we principally discuss the diversity and functional roles of the invertebrates in tropical terrestrial ecosystems. New sampling and analytical techniques, an expanded set of focal taxa, and an enhanced concern with interactions and processes hold the promise of a productive future for invertebrate studies in the tropics. These will not only add to general understanding of the dynamics of tropical ecosystems but will also provide powerful tools for monitoring and responding to environmental change.     

Linking Earth Observation and taxonomic,structural and functional biodiversity: Local to ecosystem perspectives

Impacts of human civilization on ecosystems threaten global biodiversity. In a changing environment, traditional in situ approaches to biodiversity monitoring have made significant steps forward to quantify and evaluate BD at many scales but still, these methods are limited to comparatively small areas. Earth observation (EO) techniques may provide a solution to overcome this shortcoming by measuring entities of interest at different spatial and temporal scales.This paper provides a comprehensive overview of the role of EO to detect, describe, explain, predict and assess biodiversity. Here, we focus on three main aspects related to biodiversity − taxonomic diversity, functional diversity and structural diversity, which integrate different levels of organization − molecular, genetic, individual, species, populations, communities, biomes, ecosystems and landscapes. In particular, we discuss the recording of taxonomic elements of biodiversity through the identification of animal and plant species. We highlight the importance of the spectral traits (ST) and spectral trait variations (STV) concept for EO-based biodiversity research. Furthermore we provide examples of spectral traits/spectral trait variations used in EO applications for quantifying taxonomic diversity, functional diversity and structural diversity. We discuss the use of EO to monitor biodiversity and habitat quality using different remote-sensing techniques. Finally, we suggest specifically important steps for a better integration of EO in biodiversity research.EO methods represent an affordable, repeatable and comparable method for measuring, describing, explaining and modelling taxonomic, functional and structural diversity. Upcoming sensor developments will provide opportunities to quantify spectral traits, currently not detectable with EO, and will surely help to describe biodiversity in more detail. Therefore, new concepts are needed to tightly integrate EO sensor networks with the identification of biodiversity. This will mean taking completely new directions in the future to link complex, large data, different approaches and models.     

再论生物多样性与生态系统的稳定性

本文在简述生物多样性与生态系统稳定性研究动态的基础上,从生物多样性和稳定性的概念出发,指出忽视多样性和稳定性的生物组织层次可能是造成观点纷争的根源之一。特定生物组织层次的稳定性可能更多地与该层次的多样性特征相关,探讨多样性和稳定性的关系应从不同的生物组织层次上进行,抗动是生态系统多样性与稳定性关系悖论中的重要因子,如果根据扰动的性质,把生态系统（或其他组织层次）区分为受非正常外力干扰和受环境因子时间异质性波动干扰2类系统,稳定性的4个内涵可以理解为：对于受非正常外力干扰的系统而言,抵抗力和恢复力是稳定性适宜的测度指标;对于受环境因子时间异质性波动干扰和系统而言。利用持久性和变异性衡量系统的稳定性则更具实际意义。结合对群落和种群层次多样性与稳定性相关机制的初步讨论,本文认为;在特定的前提下,多样性可以导致稳定性。     

Soil microbial diversity: Methodological strategy, spatial overview and functional interest

Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modifications of the taxonomic diversity and functioning of the indigenous microbial communities. As a consequence, the functional significance of these losses/modifications of biodiversity, in terms of the capacity of ecosystems to maintain the functions and services on which humanity depends, is now of pivotal importance. In this context, one of the main challenges in soil microbial ecology is to better understand and predict the processes that drive soil microbial diversity and the link between diversity and ecosystem process. This review describes past, present and ongoing conceptual and methodological strategies employed to better assess and understand the distribution and evolution of soil microbial diversity with the aim of increasing our capacity to translate such diversity into soil biological functioning and, more widely, into ecosystem services.     

How do plants regulate the function, community structure, and diversity of mycorrhizal fungi?

In many semi-natural and natural ecosystems, mycorrhizal fungi are the most abundant and functionally important group of soil micro-organisms. They are almost wholly dependent on their host plants to supply them with photosynthate in return for which they enable the plant to access greater quantities of nutrients. Thus, there is considerable potential for plant communities to regulate the structure and function of mycorrhizal communities. This paper reviews some of the key recent developments that have enabled the influence of plant species richness, composition, and age on mycorrhizal communities in boreal forests and temperate grassland to be determined. It discusses the emerging evidence that, in some situations, plant species richness is related to mycorrhizal species richness, in contrast to previous thinking. The paper also includes some preliminary data on the effect of host stand age on root-associated basidiomycete communities. It concludes by highlighting some of the new methodological advances that promise to unravel the linkages between mycorrhizal diversity and their function in situ.     

海南岛淡水蟹类分布格局与多样性保护

热带岛屿生物多样性是全球生物多样性保护研究的热点之一。海南岛是中国面积最大的热带岛屿, 丰富独特的淡水蟹类是维持岛内淡水生态系统功能完整性的关键类群。本文通过多年野外调查, 综合历史及最新文献资料, 对海南岛淡水蟹类物种多样性及其现状进行调查和评估, 并对淡水蟹类物种多样性保护现状进行了分析讨论。研究发现, 海南岛淡水蟹类物种多样性分布中心位于中南部山地, 主要集中于中部的霸王岭、鹦哥岭和猕猴岭, 南部的五指山和吊罗山, 以及西南部的尖峰岭一带。其物种多样性整体上呈现中南部山地高、平原台地低的特点。根据《IUCN物种红色名录濒危等级和标准》对海南岛淡水蟹类物种现状的评估结果显示, 全岛受威胁淡水蟹类物种的占比为16.7%。基于分布区预测, 以海南热带雨林国家公园为主体的保护地对淡水蟹类潜在适宜分布区的覆盖度明显优于此前碎片化的各级保护区。本文研究结果显示, 海南岛淡水蟹类的总体生存状况良好, 但一部分山地或平原种类处于受胁状态。国家公园体制的建立有望为岛内淡水蟹类物种多样性保护提供前所未有的机遇。基于物种多样性分布格局开展淡水蟹类等淡水生物多样性监测, 有助于促进海南岛淡水生态系统完整性的长效保护与可持续发展。     

A metabolic view of the diversity-stability relationship

A theoretical analysis of the “portfolio effect” expressed in metabolic terms indicates that the coefficient of variation of total biomass in the ecosystem is influenced by three factors: metabolic diversity, total population size and organism biomass (body mass). The contribution of these factors to ecosystem stability depends on the power scaling of population size to its temporal variance: the Tilman's z. In natural populations, 1<z<2 both from a theoretical and an empirical background, and so a higher metabolic diversity, a larger population size and a bigger body mass are expected to increase ecosystem stability. The maximization of any of these factors will enhance ecosystem stability both at ecological (successional) and evolutionary timescales, which could explain a number of trends observed in ecosystems and in the history of life.     

Recognizing diversity in coral symbiotic dinoflagellate communities

A detailed understanding of how diversity in endosymbiotic dinoflagellate communities maps onto the physiological range of coral hosts is critical to predicting how coral reef ecosystems will respond to climate change. Species-level taxonomy of the dinoflagellate genus Symbiodinium has been predominantly examined using the internal transcribed spacer (ITS) region of the nuclear ribosomal array (rDNA ITS2) and downstream screening for dominant types using denaturing gradient gel electrophoresis (DGGE). Here, ITS2 diversity in the communities of Symbiodinium harboured by two Hawaiian coral species was explored using direct sequencing of clone libraries. We resolved sixfold to eightfold greater diversity per coral species than previously reported, the majority of which corresponds to a novel and distinct phylogenetic lineage. We evaluated how these sequences migrate in DGGE and demonstrate that this method does not effectively resolve this diversity. We conclude that the Porites spp. examined here harbour diverse assemblages of novel Symbiodinium types and that cloning and sequencing is an effective methodological approach for resolving the complexity of endosymbiotic dinoflagellate communities harboured by reef corals.     

Evolutionary adaptations by fish to ecotonal complexity in spatially variable landscapes — a perspective

In most types of freshwater ecosystems fish diversity depends greatly on land/inland water ecotones. So, to maintain biodiversity of fish communities in inland waters, management and restoration of aquatic terrestrial ecotones will be an important tool. However, to provide a scientific background for such conservation activities, it will be desirable to test the importance of different types of ecotones in structuring and maintaining the genetic diversity of fish populations. The relevance of population genetics data to ecotone studies can only be understood in an ecological context as evolution is a function of environment. We suggest that as ecotone complexity increases opportunities for survival of individuals, improving trophic conditions and spatial habitat heterogeneity, so the population size and variation increase with increased genetic diversity and vulnerability to environment changes decreases.     

Longitudinal patterns of plant diversity in the North American boreal forest

Spatial patterns of plant diversity in the North American boreal forest were examined according to three plant life forms (woody plants, herbaceous plants, and bryophytes) and two taxonomic levels (species and genus), using sixty 9-ha plots sampled in white spruce (Picea glauca (Moench) Voss) and black spruce (Picea mariana (P. Mill.) B.S.P.) ecosystems along a transcontinental transect from the Pacific coast eastwards to the Atlantic coast. The patterns of inventory diversity (represented by alpha diversity), differentiation diversity (represented by the similarity index, habitat-heterogeneity index, similarity decay rate, and length of the first axis in detrended correspondence analysis), and pattern diversity (represented by the mosaic diversity index) were assessed along the transect in both ecosystem types. At the stand level, central North America had the highest alpha diversity in terms of the number of species or genera, and western North America had a higher alpha diversity than eastern North America. At the continental scale, herbaceous plants had the highest beta diversity in terms of floristic change from the eastern to western North America, bryophytes had the lowest beta diversity, and woody plants were in the middle, regardless of ecosystem type and taxonomic level. Central North America had the lowest mosaic diversity across the boreal transect of North America. The white spruce ecosystems had a higher alpha diversity than the black spruce ecosystems regardless of plant life form, taxonomic level and geographic location. The white spruce ecosystems tended to have more bryophytes, less woody plants, and higher species:genus ratio than the black spruce ecosystems. In general, the white spruce and black spruce ecosystems shared the same patterns in diversity changes at different spatial scales, plant life forms, and taxonomic levels across the transect studied. The existing patterns of plant diversity in the North American boreal forest area resulted from a combination of ecological processes and spatial configuration.     

关于蝗虫多样性与草原生态系统可持续发展的若干科学问题

蝗虫多样性既是草原生态系统演化的产物 ,反过来也影响着草原生态系统的结构与功能。蝗虫多样性状况与草原生态系统的持续发展有着密切的关联 ,这其中的科学问题包括 :(1 )蝗虫多样性及其空间变异机理 ;(2 )蝗虫多样性对草原生态系统过程的影响 ;(3 )蝗虫多样性空间格局与草原生态系统演化中的自然和人文因素的关联 ;(4 )蝗虫种群暴发的多样性阈值与草原生态系统的调控 ;(5 )蝗虫多样性和稳定性与草原生态系统的健康等。深入发掘生物多样性所包含的科学内涵 ,将一个物种的多样性与生态系统的结构和功能耦合起来研究 ,从重要物种蝗虫的生物多样性入手 ,深入探讨草原生态系统的持续发展问题 ,将为减少或减轻我国西部草原蝗灾发生提供科学的支持