Global biogeography of highly diverse protistan communities in soil

Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.     

Increasing temperatures increase the risk of reproductive failure in a near threatened alpine ground-nesting bird,the Cape Rockjumper Chaetops frenatus

A major cause of reproductive failure in birds is nest predation. Predation risk depends on predator type, as predators vary in their ecology and sensory modalities (e.g. visual vs. olfactory). Snakes (generally olfactory predators) are a major nest predator for small birds, with predation strongly associated with higher temperatures. We investigated nest survival in a ground-nesting alpine species, the Cape Rockjumper Chaetops frenatus, endemic to alpine fynbos in southwestern South Africa. We collected 3 years of nest data, testing whether nest survival was related to (1) habitat stage (early post-fire vs. late post-fire habitat, ≤ 3 and > 3 years since fire respectively), (2) nest concealment and (3) temperature. We found that nests had better survival at lower temperatures, with snake predation (our main source of predation) increasing in higher temperatures.     

Effects of long‐term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

To understand the fine‐scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long‐term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae‐Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88 706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic‐ (farmyard manure), mineral‐ and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co‐occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels.     

生物炭对农田土壤微生物生态的影响研究进展

生物炭作为新型土壤改良剂在国内外环境科学等领域受到广泛的关注.关于生物炭对土壤理化性质的改良研究较早,目前虽然已深入到土壤微生物生态的领域,但是大多数将土壤理化性质与土壤微生物生态分开考虑,缺乏对二者相互作用的系统评述.本文总结了施用生物炭后土壤理化性质的改变与土壤微生物群落变化之间的相互关系:生物炭不仅能够提高土壤pH值、增强土壤的持水能力、增加土壤有机质等,而且会影响土壤微生物的群落结构、改变细菌和真菌的丰度;施用生物炭后,土壤环境和土壤微生物之间互相影响互相制约,共同促进了土壤微生物生态系统的改良.本文旨在为生物炭改良农田土壤微生态的深入研究提供新的思路,从生态系统的角度促进生物炭环境效应影响的研究,使生物炭的应用更具有科学性和有效性,并对生物炭在相关领域的应用进行了展望.     

The ecology of fear and inverted biomass pyramids

In inverted biomass pyramids (IBPs) prey are outnumbered by their predators when measured by biomass. We investigate how prey should behave in the face of danger from higher predator biomass, and how anti-predator behavior (in the form of vigilance) can, in turn, affect the predator–prey system. In this study, we incorporate anti-predator behaviors into a Lotka–Volterra predator–prey model in the form of fixed and facultative vigilance. Facultative vigilance models behavior as a dynamic foraging game, allowing us to assess optimal behavioral responses in the context of IBPs using a dynamical fitness optimization approach. We model vigilance as a tradeoff between safety and either the prey's maximum growth rate or its carrying capacity. We assess the population dynamics of predators and prey with fear responses, and investigate the role fear plays on trophic structure. We found that the ecology of fear plays an important role in predator–prey systems, impacting trophic structure and the occurrence of IBPs. Fixed vigilance works against IBP structure by always reducing the predator–prey biomass ratio at equilibrium with increasing levels of vigilance. Facultative vigilance can actually promote IBPs, as prey can now adjust their vigilance levels to cope with increased predation and the costs associated with vigilance. This is especially true when the effectiveness of vigilance is low and predators are very lethal. In general, these trends are true whether the costs of vigilance are felt on the prey's maximum growth rate or its carrying capacity. Just as the ecology of fear, when first introduced, was used to explain why top carnivores are rare in terrestrial systems, it can also be used to understand how big fierce predators can be common in IBPs.     

Predator pheromone elicits a temporally dependent non-consumptive effect in prey

1. The influence of predator cues on the behaviour of prey is well supported in the literature; however, a clear understanding of how predator cues affect prey in variable environmental conditions and over longer time scales is needed to better understand the underlying mechanisms. Here, we measure how predator odors affect herbivore colonization, abundance, oviposition, and plant damage across two growing seasons.
2. The study system consisted of Leptinotarsa decemlineata (Colorado potato beetle) as prey, and the aggregation pheromone of live Podisus maculiventris (spined soldier bug) as the predator cue in a potato field.
3. In 2016, the amount of feeding damage by early beetle colonists was lower in predator odor-treated plots, reducing plant damage by 22%. Larval abundance was also reduced in treated plots in 2016. Beetle abundance and damage in 2017 was similar in the treatment and control plots. Two mechanisms were investigated to better understand why prey response to the predator odor treatment weakened over the first season, including changes in predator odor cue strength and prey habituation. Predator odor cue strength emerged as a likely explanation, as dispensers, which released a synthetic predator pheromone over the entire season, reduced the probability of finding damage more consistently than the live predator treatment.
4. These results suggest that temporal patterns of predator cue release and strength may drive prey response across the season, underscoring the importance of cue release-rate and consistency in both species interactions and for the future application of modifying insect behaviour using non-consumptive effects in agricultural systems.

     

长期施肥和增水对半干旱草地土壤性质和植物性状的影响

本文对内蒙古多伦退化草地2005年建立的长期野外控制试验中施肥和增水对土壤性质和植物群落特征的影响进行了总结和综合评述.结果表明:加氮导致了表土酸化并降低酸缓冲容量,提高了表土中碳氮磷硫有效性及DTPA-浸提态铁锰铜含量,导致盐基离子钙镁钾钠总量的消耗,降低了土壤微生物群落多样性,促进了优势植物物种叶片对氮磷硫钾及锰铜锌的吸收,抑制植物叶片对铁的吸收,而对钙镁吸收无显著影响,增加了植物地上净初级生产力(ANPP),降低了植物物种多样性和群落稳定性.单独加磷增加了表土全磷和Olsen-P含量及真菌丰度,促进了植物叶片对氮、磷、硫的吸收,但对其他土壤基本化学性质及ANPP、物种多样性无显著影响.增水提高了植物群落对干旱的抵抗力,但对ANPP增长的贡献受到土壤氮有效性的限制.增水对于加氮导致的土壤酸化、植物和微生物多样性降低等具有一定的缓冲作用;加氮增水和加磷增水下,土壤微生物多样性及功能受地上植物群落结构及功能变化的影响.长期野外控制试验对于深入理解草地生态系统结构和功能对环境变化的响应具有重要意义,但单点的研究结果仍需与不同区域多点控制试验的联网研究相结合,深入开展地上与地下生态过程的关联研究,才能深入理解草地生态系统生态学的相关机制.     

Perennial grass bioenergy cropping systems: Impacts on soil fauna and implications for soil carbon accrual

Perennial grass energy crop production is necessary for the successful and sustainable expansion of bioenergy in North America. Numerous environmental advantages are associated with perennial grass cropping systems, including their potential to promote soil carbon accrual. Despite growing research interest in the abiotic and biotic factors driving soil carbon cycling within perennial grass cropping systems, soil fauna remain a critical yet largely unexplored component of these ecosystems. By regulating microbial activity and organic matter decomposition dynamics, soil fauna influence soil carbon stability with potentially significant implications for soil carbon accrual. We begin by reviewing the diverse, predominantly indirect effects of soil fauna on soil carbon dynamics in the context of perennial grass cropping systems. Since the impacts of perennial grass energy crop production on soil fauna will mediate their potential contributions to soil carbon accrual, we then discuss how perennial grass energy crop traits, diversity, and management influence soil fauna community structure and activity. We assert that continued research into the interactions of soil fauna, microbes, and organic matter will be important for advancing our understanding of soil carbon dynamics in perennial grass cropping systems. Furthermore, explicit consideration of soil faunal effects on soil carbon can improve our ability to predict changes in soil carbon following perennial grass cropping system establishment. We conclude by addressing the major knowledge gaps that should be prioritized to better understand and model the complex connections between perennial grass bioenergy systems, soil fauna, and carbon accrual.     

Revolution in food web analysis and trophic ecology: diet analysis by DNA and stable isotope analysis

Characterization of energy flow in ecosystems is one of the primary goals of ecology, and the analysis of trophic interactions and food web dynamics is key to quantifying energy flow. Predator‐prey interactions define the majority of trophic interactions and food web dynamics, and visual analysis of stomach, gut or fecal content composition is the technique traditionally used to quantify predator‐prey interactions. Unfortunately such techniques may be biased and inaccurate due to variation in digestion rates ( Sheppard & Hardwood 2005 ); however, those limitations can be largely overcome with new technology. In the last 20 years, the use of molecular genetic techniques in ecology has exploded ( King et al. 2008 ). The growing availability of molecular genetic methods and data has fostered the use of PCR‐based techniques to accurately distinguish and identify prey items in stomach, gut and fecal samples. In this month’s issue of Molecular Ecology Resources, Corse et al. (2010) describe and apply a new approach to quantifying predator‐prey relationships using an ecosystem‐level genetic characterization of available and consumed prey in European freshwater habitats ( Fig. 1a ). In this issue of Molecular Ecology, Hardy et al. (2010) marry the molecular genetic analysis of prey with a stable isotope (SI) analysis of trophic interactions in an Australian reservoir community ( Fig. 1b ). Both papers demonstrate novel and innovative approaches to an old problem – how do we effectively explore food webs and energy movement in ecosystems?

Figure 1 Open in figure viewer PowerPoint The aquatic habitats used for two studies of diet and trophic interactions that employed molecular genetic and stable isotope analyses. Panel a: Example of Rhone basin habitat (France) where fish diet was determined using PCR to classify prey to a series of ecological clades (photo by Emmanuel Corse). Panel b: A weir pool on the lower Murray River (Australia) where food web and prey use was evaluated using a combination of advanced molecular genetic and stable isotope analyses (photo credit: CSIRO).     

The Biology of Tiger Sharks, Galeocerdo Cuvier, in Shark Bay, Western Australia: Sex Ratio, Size Distribution, Diet, and Seasonal Changes in Catch Rates

Tiger sharks, Galeocerdo cuvier, are apex predators in a variety of nearshore ecosystems throughout the world. This study investigates the biology of tiger sharks in the shallow seagrass ecosystem of Shark Bay, Western Australia. Tiger sharks (n = 252) were the most commonly caught species (94%) compared to other large sharks. Tiger sharks ranged from 148–407cm TL. The overall sex ratio was biased towards females (1.8:1), but the sex ratio of mature animals (> 300cm TL) did not differ from 1:1. Contrary to previous accounts, tiger sharks were caught more often in all habitats during daylight hours than at night. Tiger shark catch rates were highly correlated with water temperature and were highest when water temperatures were above 19°C. The seasonal abundance of tiger sharks is correlated to both water temperature and the occurrence of their main prey: sea snakes and dugongs, Dugong dugon. Stomach contents analysis indicated that sea turtles and smaller elasmobranchs were also common prey. The importance of major seagrass grazers (dugongs and green sea turtles, Chelonia mydas) in the diet of tiger sharks suggests the possibility that these sharks are keystone predators in this ecosystem.     

Using ecological networks to answer questions in global biogeography and ecology

Ecological networks have classically been studied at site and landscape scales, yet recent efforts have been made to collate these data into global repositories. This offers an opportunity to integrate and upscale knowledge about ecological interactions from local to global scales to gain enhanced insights from the mechanistic information provided by these data. By drawing on existing research investigating patterns in ecological interactions at continental to global scales, we show how data on ecological networks, collected at appropriate scales, can be used to generate an improved understanding of many aspects of ecology and biogeography—for example, species distribution modelling, restoration ecology and conservation. We argue that by understanding the patterns in the structure and function of ecological networks across scales, it is possible to enhance our understanding of the natural world.     

The effects of taxonomy,diet, and ecology on the microbiota of riverine macroinvertebrates

Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3‐V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus‐, family‐, and order‐levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico‐chemical conditions.     

Not just the sum of its parts: Geographic variation and nonadditive effects of pyrazines in the chemical defence of an aposematic moth

Chemical defences often vary within and between populations both in quantity and quality, which is puzzling if prey survival is dependent on the strength of the defence. We investigated the within- and between-population variability in chemical defence of the wood tiger moth (Arctia plantaginis). The major components of its defences, SBMP (2-sec-butyl-3-methoxypyrazine) and IBMP (2-isobutyl-3-methoxypyrazine), are volatiles that deter bird attacks. We hypothesized that (1) variation in the chemical defences of male wood tiger moths reflects the local predation pressure; (2) observed differences in quantity and quality of defence among populations have a genetic basis; and (3) increasing concentrations of SBMP and IBMP will elicit greater aversive reactions in predators, with the two pyrazines having an additive effect on predators' avoidance. We found that (1) the chemical defence of wild moths partly reflects local predator selection: high predation pressure populations (Scotland and Georgia) had stronger chemical defences, but not lower variance, than the low-predation populations (Estonia and Finland). (2) Based on the common garden results, both genetic and environmental components seem to influence the strength of chemical defence in moth populations; and (3) IBMP alone did not provide protection against bird predators but worked against bird attacks only when combined with SBMP, and while SBMP was more effective at higher concentrations, IBMP was not. Altogether this suggests that, when it comes to pyrazine concentration, more is not always better, highlighting the importance of testing the efficacy of chemical defence and its components with relevant predators, as extrapolating from chemical data may be less than straightforward.     

米槁根际土壤真菌多样性及其与果实药用活性成分含量的相关性分析

为了解不同产地米槁Cinnamomum migao根际土壤真菌多样性及其差异,探讨米槁活性成分、土壤理化因子与其土壤真菌群落的联系。本文采用高通量测序技术对云南、贵州及广西的9个产点米槁根际土壤真菌群落组成和结构进行分析,测定不同产地米槁的主要活性成分及土壤理化因子,同时对米槁活性成分及其与土壤理化因子和根际土壤真菌种群多样性进行相关性分析。结果表明,米槁根际土壤真菌物种可归入8门、30纲、89目、200科、440属,优势类群为一未能分类的属,相对丰度为18.76%,其次为被孢霉属Mortierella（16.37%）等;不同产地米槁根际土壤真菌群落组成存在差异,最高多样性指数出现在贵州罗甸,随后依次为贵州望谟、广西乐业、广西天峨、贵州册亨、贵州荔波、云南富宁、云南那坡、贵州贞丰;总体而言,广西乐业、贵州望谟和广西天峨3地米槁果实样本活性成分1,8-桉叶素（1,8-cineole）、香桧烯（sabinene）、柠檬烯（limonene）和α-松油醇（α-terpineo）的含量均高于其他样本;冗余分析（redundancy analysis,RDA）结果表明,部分真菌类群与米槁药用活性成分呈正相关。     

Effects of aqueous extracts from leaves and leaf litter on the abundance and diversity of soil gymnamoebae in laboratory microcosm cultures

The distribution and abundance of microbiota in soil and litter may be significantly affected by the quality and quantity of localized patches of leaf organic matter. This study examined the relative effects of aqueous extracts of shed autumn leaves from American beech (Fagus grandifolia), sugar maple (Acer saccharum), red oak (Quercus rubra), and white oak (Quercus alba) on the density and diversity of gymnamoebae in laboratory cultures. Overall, the beech leaf extract produced the most growth of gymnamoebae followed by white oak with leaf extracts from maple and red oak producing least growth. Cultures using natural leaf litter from beneath beech trees had higher densities and diversity of gymnamoebae than leaf-litter cultures from a maple-oak stand. Soil microcosms confirmed that beech leaf extracts produced a higher density of gymnamoeba growth when added to soil cultures compared with maple and oak leaf extracts. Protein content, CHN (carbon and nitrogen content), and pH of the leaf extracts were assayed, but these alone were not sufficiently different to account for the effects. A dilution experiment indicated that some other concentration-dependent factor in the extract may produce the effects.     

Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology

Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.     

黄土高原不同土壤微生物量碳、氮与氮素矿化势的差异

以采自于黄土高原差异较大的25个农田石灰性耕层土壤为供试土样,对黄土高原主要类型土壤中微生物量碳(Bc)、微生物量氮(BN)和氮素矿化势(NO)的差异性进行了比较研究.结果表明,Bc、BN和NO在不同类型土壤间存在显著差异,由关中平原至陕北风沙区,BC、Bn和NO总体呈现下降趋势,其中以土垫旱耕人为土最高,简育干润均腐土最低,黄土正常新成土和干润砂质新成土居中:土垫旱耕人为土、简育干润均腐土、黄土正常新成土和干润砂质新成土等各土类平均BC分别为305.2μg·g-1,108.4μg·g-1,161.7μg·g-1和125.4μg·g-1,BN分别为43.8μg·g-1,20.3μg·g-1,26.0μg·g-1和30.6μg·g-1,NO分别为223μ·g-1,75μg·g-1,163μg·g-1和193μg·g-1.土壤氮素矿化速率(k)则以简育干润均腐土最大,干润砂质新成土最低,土垫旱耕人为土和黄土正常新成土居中:土垫旱耕人为土、简育干润均腐土、黄土正常新成土和干润砂质新成土的k分别为0.039w-1,0.044w-1,0.031w-1和0.019w-1.不同类型土壤BC、BN与NO的差异,主要与土壤形成过程、输入土壤的植物同化产物和土壤有机质的差异等有关,从较大尺度进一步证明了在黄土高原,土壤有机质是影响BC、BN的主要因子.研究结果对分析黄土高原土壤生产力形成过程具有一定参考价值.     

Transgenerational plasticity of inducible defences: Combined effects of grand‐parental,parental and current environments

Phenotypic plasticity can occur across generations (transgenerational plasticity) when environments experienced by the previous generations influenced offspring phenotype. The evolutionary importance of transgenerational plasticity, especially regarding within‐generational plasticity, is a currently hot topic in the plasticity framework. How long an environmental effect can persist across generations and whether multigenerational effects are cumulative are primordial—for the evolutionary significance of transgenerational plasticity—but still unresolved questions. In this study, we investigated how the grand‐parental, parental and offspring exposures to predation cues shape the predator‐induced defences of offspring in the Physa acuta snail. We expected that the offspring phenotypes result from a three‐way interaction among grand‐parental, parental and offspring environments. We exposed three generations of snails without and with predator cues according to a full factorial design and measured offspring inducible defences. We found that both grand‐parental and parental exposures to predator cues impacted offspring antipredator defences, but their effects were not cumulative and depended on the defences considered. We also highlighted that the grand‐parental environment did alter reaction norms of offspring shell thickness, demonstrating an interaction between the grand‐parental transgenerational plasticity and the within‐generational plasticity. We concluded that the effects of multigenerational exposure to predator cues resulted on complex offspring phenotypic patterns which are difficult to relate to adaptive antipredator advantages.