Notes on the soil ciliate biota (Protozoa, Ciliophora) from the Shimba Hills in Kenya (Africa): diversity and description of three new genera and ten new species

A very diverse ciliate community was found in nine soil samples from the Shimba Hills Nature Reserve in Kenya, equatorial Africa. The ciliates, respectively, their resting cysts, were re-activated from air-dried samples using the non-flooded Petri dish method. Species were determined from life and by silver impregnation. 34 (27%) of the 125 taxa identified had not yet been described in 1985, when the samples were collected and investigated. The richest samples, each containing 59 species, were those from a deciduous primary forest and a young secondary pine forest. The most remarkable species discovered in the Shimba Hills were Krassniggia auxiliaris, Bresslauides terricola, Gigantothrix herzogi, and Afrothrix darbyshirei. They are flagships with a very distinct morphology and easy to recognise due to their extraordinarily large body size. Krassniggia auxiliaris occurs also in Australia and probably has a restricted Gondwanan distribution, like some other ciliates. Bresslauides terricola was later found in soils from all main biogeographical regions, except for Antarctica. Gigantothrix herzogi and Afrothrix darbyshirei are still unique to the Shimba Hills. The following taxa are described in detail: Sikorops woronowiczae nov. gen., nov. spec., Arcuospathidium multinucleatum nov. spec., Dileptus similis Foissner, 1995, Plagiocampa bitricha nov. spec., Drepanomonas exigua exigua Penard, 1922, D. exigua bidentata nov. sspec., Parafurgasonia protectissima (Penard, 1922) nov. comb., P. terricola nov. spec., Brachyosoma brachypoda mucosa nov. sspec., Gigantothrix herzogi nov. gen., nov. spec., Afrothrix darbyshirei nov. gen., nov. spec., Oxytricha africana nov. spec., and O. elegans nov. spec.     

土壤生物多样性的研究概况与发展趋势

本文概括性地介绍了土壤生物类群的多样性及其在生态系统中的作用; 同时简要地回顾和比较了国内外在土壤生物学方面的研究动态, 分析了土壤生物学今后的发展趋势。鉴于土壤生物在生态系统中的重要性以及我国在土壤生物学研究方面的不足, 《生物多样性》本期刊登了一系列有关土壤生物的文章, 目的是为了使国内科学家对土壤生物多样性在生态系统中的作用有更好的认识, 并希望能够唤起更多的年轻学者加入到土壤生物学研究的行列, 以推动土壤生物学在我国的迅速发展并将土壤生物学的研究成果应用于国民经济的发展中。     

兰州市北山不同林地春夏季土壤纤毛虫群落特征

为了研究兰州市北山绿化工程的植被恢复状况,于2016年4月和7月,对北山罗九公路绿化工程区的人工林及荒坡、半荒坡共6个样点进行野外调查采样,分析土壤纤毛虫群落组成及其影响因素。研究结果表明:(1)春季有10纲21目34科44属80种,夏季10纲21目38科54属104种。春夏季的优势类群均为尖毛科(Plagiocampidae),优势种为膨胀肾形虫(Colpoda inflate)和盘状肾形虫(Colpoda patella)。(2)土壤纤毛虫的丰度、物种数和多样性指数夏季高于春季,且人工林样点的土壤纤毛虫的丰度、物种数和多样性指数均高于荒坡;(3)春季土壤有机碳、土壤温度和电导率是影响土壤纤毛虫物种数分布的主要环境因子;夏季土壤有机碳、土壤温度及pH是影响土壤纤毛虫物种数分布的主要因子。总体而言,人工林土壤恢复较荒坡、半荒坡好,而人工林中杨树林和侧柏林的土壤环境质量较优。     

Effects of soil and wood depletion on biodiversity

Human depletion of soil and wood resources is dramatically altering the biodiversity of both terrestrial and aquatic ecosystems. This paper provides an overview of the numerous linkages between the depletion of soil and wood resources and the loss of biodiversity. While some of these linkages are well documented, others remain speculative or unexplored. In order to understand the full ramifications of resource depletion on biodiversity, additional research is required.     

Assessing the functional implications of soil biodiversity in ecosystems

Soil communities are among the most species-rich components of terrestrial ecosystems. A major challenge for soil ecologists is to formulate feasible research strategies that will preserve and capitalize on the biodiversity resources of the soil. This article considers the role of soil organism diversity by concentrating on: (i) the relationship between soil biodiversity and ecosystem function; (ii) what issues need to be explored; (iii) studies carried out in the Ecotron controlled environment facility; and (iv) how stable isotope techniques can improve our understanding of the relationship between soil biodiversity and ecosystem function. It is advocated that: (i) the objective of any soil biodiversity study should always be the generation of general concepts, rather than local, system-specific observations; and (ii) any empirical study can be properly interpreted only within a quantitative ecological framework.     

Interactive effects of global change drivers as determinants of the link between soil biodiversity and ecosystem functioning

Biodiversity, both aboveground and belowground, is negatively affected by global changes such as drought or warming. This loss of biodiversity impacts Earth's ecosystems, as there is a positive relationship between biodiversity and ecosystem functioning (BEF). Even though soils host a large fraction of biodiversity that underlies major ecosystem functions, studies exploring the relationship between soil biodiversity and ecosystem functioning (sBEF) as influenced by global change drivers (GCDs) remain scarce. Here we highlight the need to decipher sBEF relationships under the effect of interactive GCDs that are intimately connected in a changing world. We first state that sBEF relationships depend on the type of function (e.g., C cycling or decomposition) and biodiversity facet (e.g., abundance, species richness, or biomass) considered. Then, we shed light on the impact of single and interactive GCDs on soil biodiversity and sBEF and show that results from scarce studies studying interactive effects range from antagonistic to additive to synergistic when two individual GCDs cooccur. This indicates the need for studies quantitatively accounting for the impacts of interactive GCDs on sBEF relationships. Finally, we provide guidelines for optimized methodological and experimental approaches to study sBEF in a changing world that will provide more valuable information on the real impact of (interactive) GCDs on sBEF. Together, we highlight the need to decipher the sBEF relationship in soils to better understand soil functioning under ongoing global changes, as changes in sBEF are of immediate importance for ecosystem functioning.     

Global soil ciliate (Protozoa, Ciliophora) diversity: a probability-based approach using large sample collections from Africa, Australia and Antarctica

Large sample collections from Africa (92 samples), Australia (157) and Antarctica (90) were investigated for soil ciliates using the non-flooded Petri dish method, which re-activates the ciliates' resting cysts from air-dried samples. Species were determined from life and by silver impregnation. The African samples were the richest, containing 507 species (240 undescribed,=47%), followed by the Australian (361 species, 154=43% undescribed) and the Antarctic (95 species, 14=15% undescribed) samples. The percentage of new species/sample was consistently low, viz. 4–8% on average, indicating that new species were considerably undersampled relative to described ones, very probably due to methodological shortcomings, i.e. usually only cysts of the more euryoecious species could be reactivated. Thus, a probability theory-based statistical approach was applied to the data sets to compensate for the underestimated number of undescribed species. This procedure indicated that, depending on the region, 70–80% of the soil ciliates are still unknown and global soil ciliate diversity amounts to at least 1330–2000 species. Several indicators, especially the constant rate at which new species have been found during a 20-year period of intensive research, suggest that this estimate is conservative. This revised version was published online in August 2006 with corrections to the Cover Date.     

Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil

Using cultivation-independent methods the ciliate communities of a clay-rich soil with a 90-year record of pollution by polycyclic aromatic hydrocarbons (PAH) (4.5 g kg(-1) PAH) were compared with that of a nonpolluted soil collected in its vicinity and with similar properties. A ciliate-specific set of 18S rRNA gene targeting primers was designed and used to amplify DNA extracted from both soils (surface and 20 cm depth). Four clone libraries were generated with PCR products that covered an 18S rRNA gene fragment of up to 670 bp. Comparative sequence analysis of representative clones proved that the primer set was highly specific for ciliates. Calculation of similarity indices based on operational taxonomic units after amplified ribosomal DNA restriction analysis of the clones showed that the community from the nonpolluted surface soil was highly dissimilar to the other communities. The presence of several taxa, namely sequences affiliated to the orders Phyllopharyngia, Haptoria, Nassophorea, Peniculida and Scuticociliatia in samples from nonpolluted soil, points to the existence of various trophic functional groups. In contrast, the 18S rRNA gene diversity was much lower in the clone libraries from the polluted soil. More than 90% of these sequences belonged to the class Colpodea, a well-known clade of mainly bacterivorous and r-selected species, thus potentially also indicating a lower functional diversity.     

甘南亚高寒草甸土壤纤毛虫群落结构变化对不同坡向的响应

土壤纤毛虫不但是土壤生态系统的重要组成部分,而且是生态系统物质循环、能量流动过程的重要驱动因子。为了查明甘南亚高寒草甸不同坡向土壤纤毛虫群落特征,于2015年7月21—26日对同一山头的阳坡、半阳坡、西坡、半阴坡、阴坡五个坡向进行了调查。结果表明:(1)经"非淹没培养皿法"鉴定得到纤毛虫142种,隶属于9纲18目32科55属,各坡向物种数、个体数大小关系呈现出西坡半阳坡阳坡半阴坡阴坡;优势类群有旋毛纲、裂口纲、寡膜纲、肾形纲其优势度依次为28.17%、19.72%、13.38%、12.68%。(2)不同坡向上土壤纤毛虫的物种数、个体数、Shannon指数均具有显著性差异(P0.05),表明甘南亚高寒草甸生态系统中的土壤纤毛虫对于坡向这一微气候环境的变化具有敏感性。(3)各坡向土壤纤毛虫的物种数、个体数都具有明显的表聚性。(4)利用皮尔森相关性分析得出,在所测得的土壤理化因子中对纤毛虫的物种数、个体数均具有显著正相关(P0.05)的是全氮、有机质。综合分析,影响甘南亚高寒草甸不同坡向上土壤纤毛虫群落结构变化的主要因素为全氮、土壤有机质以及地上植被状况。     

土壤生物多样性的研究内容及持续利用展望

土壤生物多样性是一个被忽视的研究领域,在该领域急需开展如下研究：（1）土壤生物多样性本底调查研究;（2）土壤生物多样性的功能与生理生态学过程研究;（3）土壤生物多样性的丧失机制与恢复研究;（4）土壤生物多样性的保护及其开发利用研究。同时,要适度地持续开发利用土壤资源生物（包括食用与药用土壤生物、天敌生物、根际微生物、微生物肥料及环境净化与指示生物）,这些领域都具有广阔的应用前景。     

土壤生物多样性对植物利用营养物质和水分的影响

土壤生物多样性影响土壤营养物质和水等自然资源的有效利用是农业生态系统的重要功能.有证据表明土壤微生物多样性可提高土壤营养物质和水的利用率.土壤动物对土壤营养物质和水的有效利用也产生了明显的影响,它主要是通过促进营养物质的转化和改善土壤水渗透率而间接实现的.从已有文献的报道来看,单从某一个方面来研究土壤生物多样性对土壤营养物质和水的有效利用的影响并不能全面地反应它们之间相互作用的规律.因此未来的研究应当把土壤生物多样性、土壤营养物质和水的供给与植物生物多样性、植物营养物质和水的利用率结合起来,这样才有可能从理论上对土壤生物多样性与营养物质和水的利用之间的关系有更加深刻的认识并运用到实践中.     

Litter and soil biodiversity jointly drive ecosystem functions

The decomposition of litter and the supply of nutrients into and from the soil are two fundamental processes through which the above- and belowground world interact. Microbial biodiversity, and especially that of decomposers, plays a key role in these processes by helping litter decomposition. Yet the relative contribution of litter diversity and soil biodiversity in supporting multiple ecosystem services remains virtually unknown. Here we conducted a mesocosm experiment where leaf litter and soil biodiversity were manipulated to investigate their influence on plant productivity, litter decomposition, soil respiration, and enzymatic activity in the littersphere. We showed that both leaf litter diversity and soil microbial diversity (richness and community composition) independently contributed to explain multiple ecosystem functions. Fungal saprobes community composition was especially important for supporting ecosystem multifunctionality (EMF), plant production, litter decomposition, and activity of soil phosphatase when compared with bacteria or other fungal functional groups and litter species richness. Moreover, leaf litter diversity and soil microbial diversity exerted previously undescribed and significantly interactive effects on EMF and multiple individual ecosystem functions, such as litter decomposition and plant production. Together, our work provides experimental evidence supporting the independent and interactive roles of litter and belowground soil biodiversity to maintain ecosystem functions and multiple services.     

The influence of biotic interactions on soil biodiversity

Belowground communities usually support a much greater diversity of organisms than do corresponding aboveground ones, and while the factors that regulate their diversity are far less well understood, a growing number of recent studies have presented data relevant to understanding how these factors operate. This review considers how biotic factors influence community diversity within major groups of soil organisms across a broad spectrum of spatial scales, and addresses the mechanisms involved. At the most local scale, soil biodiversity may potentially be affected by interactions within trophic levels or by direct trophic interactions. Within the soil, larger bodied invertebrates can also influence diversity of smaller sized organisms by promoting dispersal and through modification of the soil habitat. At larger scales, individual plant species effects, vegetation composition, plant species diversity, mixing of plant litter types, and aboveground trophic interactions, all impact on soil biodiversity. Further, at the landscape scale, soil diversity also responds to vegetation change and succession. This review also considers how a conceptual understanding of the biotic drivers of soil biodiversity may assist our knowledge of key topics in community and ecosystem ecology, such as aboveground–belowground interactions, and the relationship between biodiversity and ecosystem functioning. It is concluded that an improved understanding of what drives the diversity of life in the soil, incorporated within appropriate conceptual frameworks, should significantly aid our understanding of the structure and functioning of terrestrial communities.     

Global change, soil biodiversity, and nitrogen cycling in terrestrial ecosystems: three case studies

The relative contribution of different soil organism groups to nutrient cycling has been quantified for a number of ecosystems. Some functions, particularly within the N-cycle, are carried out by very specific organisms. Others, including those of decomposition and nutrient release from organic inputs are, however, mediated by a diverse group of bacteria, protozoa, fungi and invertebrate animals. Many authors have hypothesized that there is a high degree of equivalence and flexibility in function within this decomposer community and thence a substantial extent of redundancy in species richness and resilience in functional capacity. Three case studies are presented to examine the relationship between soil biodiversity and nitrogen cycling under global change in ecosystem types from three latitudes, i.e. tundra, temperate grassland and tropical rainforest. In all three ecosystems evidence exists for the potential impact of global change factors (temperature change, CO₂ enrichment, land-use-change) on the composition and diversity of the soil community as well as on various aspects of the nitrogen and other cycles. There is, however, very little unequivocal evidence of direct causal linkage between species richness and nutrient cycling efficiency. Most of the changes detected are shifts in the influence of major functional groups of the soil biota (e.g. between microflora and fauna in decomposition). There seem to be few data, however, from which to judge the significance of changes in diversity within functional groups. Nonetheless the soil biota are hypothesized to be a sensitive link between plant detritus and the availability of nutrients to plant uptake. Any factors affecting the quantity or quality of plant detritus is likely to change this link. Rigorous experimentation on the relationships between soil species richness and the regulation or resilience of nutrient cycles under global change thus remains a high priority.     

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

High‐throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well‐supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer‐mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well‐understood ecosystems, and will propel both theoretical and applied soil science.     

Terra incognita of soil biodiversity: unseen invasions under our feet

Whilst cartographers of the 19th century endeavoured to chart the last unknown lands, the great challenge for biologists in the 21st century is to fill the gaps on the biodiversity map of the Earth. And one of the largest gaps concerns the biodiversity of soils, a terra incognita right under our feet. The study of soil biodiversity, and particularly the complex communities of small invertebrates, has suffered from a severe ‘taxonomic impediment’ (Decaëns 2010 ) leading to great uncertainties about total species richness, phylogenetic diversity, geographical structure, temporal dynamics of soil organisms, and consequently about their role on ecosystem function (Bardgett & van der Putten 2014 ). However, the revolution in high‐throughput sequencing is now revealing the hidden biodiversity of the soil with unprecedented detail (e.g. Arribas et al. 2016 ). In a noteworthy from the Cover article in this issue of Molecular Ecology, Cicconardi et al. ( 2017 ) apply these new tools to study soil communities of Collembola in three distant oceanic islands of volcanic origin, obtaining a striking result: only 38 of 70 species (54%) are exclusively found in a single island, with the remaining shared among islands or with other distant regions, suggesting a massive recent introduction of soil species, whose impact is entirely unknown.     

Interpreting the 'selection effect' of biodiversity on ecosystem function

Experimental ecosystems often function differently than expected under the null hypothesis that intra‐ and interspecific interactions are identical. Recent theory attributes this to the ‘selection effect’ (dominance by species with particular traits), and the ‘complementarity effect’ (niche differentiation and/or facilitative interactions). Using the Price Equation, I show that the ‘selection effect’ only partially reflects dominance by species with particular traits at the expense of other species, and therefore is only partially analogous to natural selection. I then derive a new, tripartite partition of the difference between observed and expected ecosystem function. The ‘dominance effect’ is analogous to natural selection. ‘Trait‐independent complementarity’ occurs when species function better than expected, independent of their traits and not at the expense of other species. ‘Trait‐dependent complementarity’ occurs when species with particular traits function better than expected, but not at the expense of other species. I illustrate the application of this new partition using experimental data.     

Release of transgenic plants: biodiversity and population-level considerations

Many transgenic plant gene products introduced into soil are likely to degrade so quickly that they will have little impact upon the ecosystem. Some products, however, will be more recalcitrant and thus may exhibit potentially adverse effects upon the soil ecosystem. Potential changes in specific groups of organisms, functional groups of organisms and biodiversity are discussed. Methods to detect changes and the impact of changes are considered.     

三种纤毛虫对土壤微生物量和有效氮磷含量的影响

采用土壤培养方法研究了 3种纤毛虫对土壤微生物量及氮磷转化的影响 ,结果表明 ,向土壤接种肾形虫 ( Colopodia sp.)、尖毛虫 ( Oxytricna sp.)和澳毛虫 ( Australothrix sp.) ,特别是澳毛虫 ,显著地降低了土壤微生物碳。说明供试的原生动物与微生物之间存在消长关系。接种澳毛虫显著地降低了土壤有效磷含量 ,而肾形虫和尖毛虫对土壤有效磷含量影响很小 ,仅在培养后期显著地降低了土壤铵态氮含量 ,3种原生动物特别是澳毛虫 ,显著地降低了土壤氮矿化量和硝态氮含量 ,但提高了土壤铵态氮含量 ,说明 3种原生动物抑制了硝化作用 ,而增强了氨化作用。     

不同施肥条件下黄土麦地杂草生物多样性

采用倒置“W”9点取样法,研究了黄土区9种不同施肥处理长期肥料定位试验小麦田间杂草的生物多样性.结果表明,不同施肥条件下小麦田间杂草组成有一定差异,试验区共有杂草16种,隶属10科16属,约占陕西省麦田杂草种数的34%.随着土壤养分状况的改善,杂草的物种多样性逐渐减少,氮磷钾及其与有机物料配合施用处理（NPK、SNPK、M1NPK、M2NPK）的杂草种群为3～5个,对照及氮、氮磷、氮钾处理(CK、N、NP、NK)杂草种群为6～8个;不同施肥处理杂草相对丰度为0～73%,Shannon多样性指数为0.2～1.08,Shannon均匀度指数为0.05～0.26,Margalef物种丰富度指数为0.26～1.26.不平衡施肥处理的3个多样性指数都高于平衡施肥处理,且大部分达到显著水平.