Mock communities highlight the diversity of host‐associated eukaryotes

Host‐associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High‐throughput sequencing (HTS) tools have illuminated the vast diversity of host‐associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall‐Ngai et al. 2013 ). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al. 2011 ) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host‐associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host‐associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. 2014 ; Simon et al. 2015 ; de Vargas et al. 2015 ). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al. 2014 )]. In this issue of Molecular Ecology, Geisen et al. ( 2015 ) use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free‐living. By isolating the host‐associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high‐throughput sequencing (HTS) and reinforce the ubiquity of these host‐associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free‐living, but instead need to design studies that specifically enumerate the diversity and function of host‐associated eukaryotes. Doing so will allow the field to determine the role host‐associated eukaryotes play in soils and other environments and to evaluate hypotheses on assembly of host‐associated communities, disease ecology and more.     

土壤含水量驱动土壤病毒和细菌多度及其与土壤异养呼吸关系的变化

土壤微生物是维持陆地生态系统稳定性和功能的重要组成部分。病毒是地球上数量最多的生物实体,也是若干类型生境中微生物数量的重要调节者。因此,了解病毒与微生物的相互作用,对深入认识包括碳循环在内的生态系统过程具有重要意义。在实验室建立土壤微宇宙实验系统,跟踪调查恒定低含水量、恒定高含水量和波动含水量3种水分处理下土壤病毒和细菌多度的变化,以及土壤异养呼吸速率对土壤病毒-细菌相互作用的响应。相较于低水分处理,高水分处理显著增加了病毒多度（P<0.001）和病毒-细菌多度比（P=0.0026）,波动水分处理显著增加了病毒多度（P<0.001）。在高水分处理的土壤微宇宙中,细菌和病毒多度呈现出随时间动荡的信号,即细菌多度表现出增加-降低-增加的趋势,而病毒多度则表现出增加-降低的趋势,且其变化滞后于细菌。土壤异养呼吸速率与土壤含水量（P<0.001）、细菌多度（P=0.0045）和病毒多度（P<0.001）都具有显著的正相关关系。这些结果说明：病毒导致的下行控制可能是细菌多度的重要影响因子,在水分增加情形下,病毒有可能通过加速细菌的更新速率进而加速土壤呼吸。因此,病毒与细菌的相互作用可能是碳循环的重要决定因素。     

不同放牧强度下土壤氨氧化和反硝化微生物的变化特征

土壤硝化及反硝化功能微生物在氮素可利用性、硝酸盐淋溶和氧化亚氮温室气体排放等方面起着关键作用,在指示不同放牧强度对生态系统的影响及预测草地生态系统退化状况等方面具有重要意义。以内蒙古干旱半干旱草原不同放牧强度(轻度、中度和重度)的长期试验样地为对象,应用定量PCR和限制性末端片段长度多态性(Terminal restriction fragment length polymorphism,T-RFLP)的方法,研究土壤氨氧化古菌(ammonia-oxidizing archaea,AOA)、氨氧化细菌(ammonia-oxidizing bacteria,AOB)和反硝化细菌的丰度、群落结构和多样性对不同放牧强度的响应。结果表明,土壤p H和铵态氮含量分别在7.90—8.18和6.37—35.92 mg/kg之间,中度放牧处理显著增高了土壤pH(P=0.03),而铵态氮含量在重度放牧处理中最高(P=0.02)。不同放牧强度下土壤异养呼吸相比未放牧处理均显著降低(P=0.02)。土壤AOA-amoA和AOB-amoA基因丰度范围分别为每克干土(4.94—7.60)×10~9个拷贝数和(0.68—3.75)×10~6个拷贝数,放牧处理对AOA-amoA基因丰度无显著影响,中度放牧处理显著降低了AOB-amoA基因丰度(P=0.04);反硝化微生物nosZ基因丰度随在轻度放牧处理中最低(P=0.03)。土壤铵态氮含量是影响AOA-amoA和AOB-amoA基因丰度的主要因子,而nosZ基因丰度主要受反硝化底物含量及土壤通气状况的影响。冗余分析表明由放牧所引起的可利用性氮含量的变化是导致氨氧化和反硝化微生物群落结构显著变化的主要因素。     

Does weather affect biting fly abundance in avian nests?

Environmental factors may strongly affect avian‐biting fly interactions in different ways because insects are heterothermic organisms that depend greatly on environmental variables to activate their metabolism and behaviour. We studied the effects of weather on both blackfly (Simuliidae) and biting midge Culicoides (Ceratopogonidae) abundance in nests of three passerine species: blue tits Cyanistes caeruleus, great tits Parus major and pied flycatchers Ficedula hypoleuca, breeding in the same area. We controlled for different host‐related factors (hatching date, brood size and host species). Blackfly abundance was negatively related to minimum temperature. In addition, blackfly and biting midge abundances were negatively affected by wind speed measured at 07.00 h, but blackfly abundance was positively associated to wind speed at 18.00 h. We found higher blackfly and biting midge abundances in nests with larger broods breeding later in the season, and significantly higher biting midge abundance in pied flycatcher nests as compared to tit nests. These results represent, to our knowledge, the first report of both environmental and host‐related effects on haematophagous fly abundance in the nests of wild hole‐nesting birds.     

Taxonomic level, trophic biology and the regulation of local abundance

• 1 Taxocenes — monophyletic ecological assemblages — are a key focus of macroecology. Abundance (individuals per area) is a basic property of taxocenes but has received less attention than diversity, although the two are probably related. Abundance reflects a taxocene’s ability to harvest and sequester available energy and divide it among individuals. This paper explores how two properties of all taxocenes — trophic makeup and taxonomic level (e.g. genus, tribe, subfamily, family … ) — may contribute to patterns of local abundance at geographical scales.
• 2 Forty‐nine ground ant taxocenes, in habitats ranging from New World deserts to rain forests, were surveyed along a three‐orders of magnitude productivity gradient using transects of 30 1‐m² quadrats at each site. Abundance — the number of nests per transect — varied over two orders of magnitude.
• 3 Over 80% of the genera collected were omnivores. However, herbivore, omnivore, and predator taxa were added to ant taxocenes in roughly 1 order of magnitude steps up the productivity gradient. Specialist detritivores were added last.
• 4 Net primary productivity and mean monthly temperature both consistently entered regression models predicting abundance. However, while productivity was the dominant predictor of abundance for higher taxa (families, subfamilies), temperature was the dominant predictor of abundance for lower taxa (tribes, genera). The answer to the question ‘What regulates the abundance of a taxocene?’ is thus sensitive to the taxonomic level of analysis.
• 5 These data support the following scenario. Lower taxa are abiotic specialists given the insufficient number of genomes and generations required for the exploration of the entire abiotic envelope. Higher taxa, in contrast, consist of suites of abiotic specialists arrayed along the entire productivity gradient, with access to productivity everywhere the taxon occurs. If this scenario is true, individual species may respond to global changes in temperature; the higher taxa they belong to may most respond to global changes in productivity.

     

Why is liana abundance low in semiarid climates?

Lianas are abundant in seasonal tropical forests, where they avoid seasonal water stress presumably by accessing deep‐soil water reserves. Although lianas are favoured in seasonal environments, their occurrence and abundance are low in semiarid environments. We hypothesized that lianas do not tolerate the great water shortage in the soil and air characteristic of semiarid environments, which would increase the risk of embolism. We compared the rooting depth of coarse roots, leaf dynamics, leaf water potential (ψ_leaf), embolism resistance (P₅₀) and lethal levels of embolism (P₈₈) between congeneric lianas that occur with different abundances in two semiarid sites differing in soil characteristics and vapour pressure deficit in the air (VPD_air). Regardless of soil texture and depth, water availability was restricted to the rainy season. All liana species were drought deciduous and had superficial coarse roots (not deeper than 35 cm). P₅₀ varied from ?1.8 to ?2.49 MPa, and all species operated under narrow safety margins against catastrophic (P₅₀) and irreversible hydraulic failure (P₈₈), even during the rainy season. In short, lianas that occur in semiarid environments have lower resistance to cavitation and limit carbon fixation to the rainy season because of leaf fall in the early dry season. We suggest that leaf shedding and shallow roots impairing carbon gain and growth in the dry season may explain why liana abundance is lower in semiarid than in other seasonally dry environments.     

Seasonal abundance of anopheline mosquitoes and their association with rainfall and malaria along the Matapí River,Amapí, Brazil

Three communities separated by 1.5–7.0 km, along the Matapí River, Amapá State, Brazil, were sampled monthly from April 2003 to November 2005 to determine relationships between seasonal abundance of host‐seeking anophelines, rainfall and malaria cases. Out of the 759 821 adult female anophelines collected, Anopheles darlingi Root (Diptera: Culicidae) was the most abundant (56.2%) followed by An. marajoara Galvão & Damasceno (24.6%), An. nuneztovari Gabaldón (12.4%), An. intermedius (Chagas) (4.4%) and An. triannulatus (Neiva and Pinto) (2.3%). Vector abundance, as measured by human landing catches, fluctuated during the course of the study and varied in species‐specific ways with seasonal patterns of rainfall. Anopheles darlingi and An. triannulatus were more abundant during the wet‐dry transition period in June to August, whereas An. marajoara began to increase in abundance in February in two villages, and during the wet‐dry transition in the other village. Anopheles nuneztovari and An. intermedius increased in abundance shortly after the rains began in January to February. A generalized linear mixed model (GLMM) analysis of 32 consecutive months of collections showed significant differences in abundance for each species by village and date (P < 0.0001). Correlations between lagged rainfall and abundances also differed among species. A strong positive correlation of An. darlingi abundance with rainfall lagged by 4 and 5 months (Pearson's r = 0.472–0.676) was consistent among villages and suggests that rainfall may predict vector abundance. Significant correlations were detected between numbers of malaria cases and abundances of suspected vector species. The present study shows how long‐term field research may connect entomological and climatological correlates with malaria incidence.     

天然高寒草地转变为燕麦人工草地对土壤线虫群落的影响

为查明高寒草地上种植燕麦(Avena sativa)对土壤线虫群落的影响,于2014年7、9月用土钻法和湿漏斗法(Baermann法)对西南民族大学青藏高原畜牧业高科技研发示范基地内燕麦地(Oat grassland,OG)和天然草地(Natural grassland,NG)的土壤线虫群落进行调查。共分离土壤线虫10179条,隶属于2纲8目50科143属,平均密度477条/100g干土。燕麦地与天然草地土壤线虫群落结构具有明显差异,影响群落结构的主要类群为拟丽突属(Acrobeloides)、原杆属(Protorhabditis)、丝尾垫刃属(Filenchus)和盘旋属(Rotylenchus),但不同月份间存在差异。燕麦地的土壤线虫群落密度、食细菌线虫密度、食真菌线虫密度和自由生活线虫成熟度指数(MI)均显著高于天然草地(P0.01;P0.05;P0.001;P0.01),植物寄生线虫成熟度指数(PPI)则显著低于天然草地(P0.05)。两种草地7月份的土壤线虫群落类群数和香农多样性指数(H′)均显著低于9月(P0.05),仅燕麦地7月份的食细菌、食真菌线虫密度和Simpson优势度指数(C)显著高于9月(P0.05;P0.001;P0.01)。典范对应分析(Canonical correspondence analysis,CCA)及回归分析结果表明,土壤pH、有机质、全氮、速效磷和含水量是影响线虫群落的主要环境因子。研究结果表明,高寒草地种植燕麦后在短期内改变了线虫群落结构,增加了线虫群落密度以及食细菌和食真菌线虫在群落中的比例,以植物寄生线虫为主的群落营养结构转变为以食细菌线虫为主,同时也增加了线虫群落不同月份间的差异。     

Plant diversity and identity effects on predatory nematodes and their prey

There is considerable evidence that both plant diversity and plant identity can influence the level of predation and predator abundance aboveground. However, how the level of predation in the soil and the abundance of predatory soil fauna are related to plant diversity and identity remains largely unknown. In a biodiversity field experiment, we examined the effects of plant diversity and identity on the infectivity of entomopathogenic nematodes (EPNs, Heterorhabditis and Steinernema spp.), which prey on soil arthropods, and abundance of carnivorous non‐EPNs, which are predators of other nematode groups. To obtain a comprehensive view of the potential prey/food availability, we also quantified the abundance of soil insects and nonpredatory nematodes and the root biomass in the experimental plots. We used structural equation modeling (SEM) to investigate possible pathways by which plant diversity and identity may affect EPN infectivity and the abundance of carnivorous non‐EPNs. Heterorhabditis spp. infectivity and the abundance of carnivorous non‐EPNs were not directly related to plant diversity or the proportion of legumes, grasses and forbs in the plant community. However, Steinernema spp. infectivity was higher in monocultures of Festuca rubra and Trifolium pratense than in monocultures of the other six plant species. SEM revealed that legumes positively affected Steinernema infectivity, whereas plant diversity indirectly affected the infectivity of Heterorhabditis EPNs via effects on the abundance of soil insects. The abundance of prey (soil insects and root‐feeding, bacterivorous, and fungivorous nematodes) increased with higher plant diversity. The abundance of prey nematodes was also positively affected by legumes. These plant community effects could not be explained by changes in root biomass. Our results show that plant diversity and identity effects on belowground biota (particularly soil nematode community) can differ between organisms that belong to the same feeding guild and that generalizations about plant diversity effects on soil organisms should be made with great caution.