Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula,Mexico

Aim

Desert springs or oases are the only permanent mesic environments in highly water-limited arid regions. Oases have immense cultural, evolutionary and ecological importance for people and a high number of endemic and relic species. Nevertheless, they are also highly vulnerable ecosystems, with invasive species, overexploitation and climate change being the primary threats. We used the arthropod communities' spatiotemporal diversity and distribution patterns as a proxy to understand biodiversity dynamics in two geographically close but ecologically contrasting and highly threatened ecosystems: deserts and oases.

Location

Baja California Peninsula, Mexico.

Methods

Arthropod communities at five oases and surrounding desert scrub areas were sampled in two seasons. Using DNA metabarcoding and traditional taxonomic surveys, we tried to identify what biotic and abiotic characteristics of the habitat are important drivers of arthropod diversity and how these characteristics can change across spatial and temporal scales.

Results

Over 6200 individuals representing 23 orders were collected. In oasis samples, the community composition fluctuated more in space (i.e. among sites) than in time (i.e. seasons). Thus, seasonal changes did not affect oasis community diversity and composition, but the dissimilarity among sites increased with geographic distance. Moreover, anthropic activities negatively correlated with arthropod diversity in oases. On the other hand, the season, geography (e.g. latitude) and biotic characteristics of the habitat (e.g. sampled scrub species) significantly affected the diversity and composition of the desert arthropod communities.

Main Conclusions

Neutral dynamics (e.g. historical climatic events, dispersal limitation and spatial component) and human impact significantly influenced the biodiversity patterns of each oasis. In contrast, the habitat's seasonal variation and biotic characteristics were the most important variables influencing the diversity of the desert communities. Baja California oases harbour distinct invertebrate communities; therefore, each oasis should be conserved individually to preserve these unique assemblages.     

Boophilus microplus: characterization of larval phosphomonoesterases and isolation of subcellular fractions with high phosphatase activity.

Phosphomonoesterase activity was determined for a 115,000g pellet and soluble fractions resulting from a subcellular fractioning of a homogenate of larval Boophilus microplus. Both fractions showed maximum phosphatase activity at pH 5.5 and 10. Acid phosphatase (EC 3.1.3.2) activity was found to be greatest in the soluble fraction. When the reaction rate was plotted against homogenate concentration, the soluble acid phosphatase deviated from the linear relationship. For both fractions different thermostability patterns were obtained, inactlvation beginning for the alkaline phosphatase (EC 3.1.3.1) at 45–55 C. When the effect of substrate concentration on activity was studied, deviations from the typical hyperbolic behavior were observed. Homogenization of larvae with 5 mm EDTA buffer failed to yield a low-speed pellet with high alkaline phosphatase activity, as it is expected if absorptive structures sediment. Moreover, total alkaline phosphatase activity recovered by this method is significantly lower than activity recovered when homogenization is carried out without EDTA. Alternately, homogenization with 10 mM Tris buffer and 0.25 M sucrose gave 27,000g and 115,000g fractions with high phosphatase activity when fractioned by centrifugation. Alkaline treatment of the 115,000g fraction with 10 mM Tris buffer, pH 7.8, failed to separate endoplasmic reticulum contaminants without loss of phosphatase activity. When the 115,000g fraction was centrifuged in a sucrose density gradient, two activity peaks, coincident for both acid and alkaline phosphatases, were obtained. Antigenic analysis showed the existence of similar antigenic determinants in both peaks “immunologically” presented in different ways.     

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo‐mock community (33 arthropod taxa from 16 orders), and guano‐based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano‐based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one‐third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.     

皖北石灰岩山地植被对地表节肢动物组成及多样性的影响

调查皖北石灰岩山地退化生态系统不同植被恢复类型地表节肢动物群落组成、类群多样性以及功能群组成,揭示退化生态系统植被恢复进程中土壤地表节肢动物群多样性变化规律及其影响因素,为石灰岩山地植被恢复成效评价提供科学依据。采用陷阱法对皖北石灰岩山地侧柏+构树混交林、酸枣+牡荆灌丛和荩草+牡荆草灌丛样地地表节肢动物群落组成、多样性以及功能群进行调查。共采节肢动物个体数11601,隶属8纲14目44科。酸枣+牡荆灌丛样地采集到节肢动物37科,占所有类群的84.1%,荩草+牡荆草灌丛和侧柏+构树混交林采集到土壤节肢动物类群为35和26科,分别占总科数的79.6%和59.1%。在目的分类单元下,直翅目、等足目和鞘翅目类群相对多度较高,而科的分类单元下,潮虫科、金龟甲科、蚁科和蟋蟀科为皖北石灰岩山地优势地表节肢动物类群。酸枣+牡荆灌丛节肢动物类群丰富度和荩草+牡荆草灌丛多样性指数最高,侧柏+构树混交林两者均最低。3个样地地表节肢动物营养功能群均以植食性为主。不同植被恢复类型间群落相似性也有变化,酸枣+牡荆灌丛和荩草+牡荆草灌丛间相似性较高,而侧柏+构树混交林与其他2种类型之间相似度均较低。研究结果表明石灰岩山地生境不同植被群落组成、数量和结构及其驱动形成的土壤理化特性、表层的凋落物数量、质量和微生境条件的变异,引起地表节肢动物群落组成、结构和多样性和营养功能群的不同。     

A study on the energy source in the developing embryo of the mangrove horseshoe crab,Carcinoscorpius rotundicauda (Latreille)

The mangrove horseshoe crab, Carcinoscorpius rotundicauda, is an Asian species found in Malaysia. This ancient arthropod has a long incubational period during which it depends on various energy sources for both embryogenesis and organogenesis. This study describes the trend of energy utilization from the endogenous reserves by the developing embryos from 0 to 40 days of incubation (until the hatching of the larvae). The dry weight, insoluble protein, carbohydrate, glycogen and lipid showed a declining trend from 0 to 40 days of incubation, whereas the wet weight, water content, ash content and soluble protein showed an increasing trend. Selected micro-elements such as Cu²⁺, Fe²⁺ and Zn²⁺ also demonstrated an interesting trend in the developing eggs when the egg mass was subjected to inductively coupled plasma mass spectrometry analysis, where these elements showed a high correlation with the moulting stages and egg development. Maximum variations within the micro-elements were observed during the 1st (10 days after fertilization) and 2nd (35–36 days after fertilization) moulting stages within the developing eggs. This study clearly indicated that the moulting cycles of C. rotundicauda during embryonic development influence energy utilization in the form of carbohydrates, lipids, proteins, glycogen and other micro-elements.     

Lateral transfers of insertion sequences between Wolbachia,Cardinium and Rickettsia bacterial endosymbionts

Various bacteria live exclusively within arthropod cells and collectively act as an important driver of arthropod evolutionary ecology. Whereas rampant intra-generic DNA transfers were recently shown to have a pivotal role in the evolution of the most common of these endosymbionts, Wolbachia, the present study show that inter-generic DNA transfers also commonly take place, constituting a potent source of rapid genomic change. Bioinformatic, molecular and phylogenetic data provide evidence that a selfish genetic element, the insertion sequence ISRpe1, is widespread in the Wolbachia, Cardinium and Rickettsia endosymbionts and experiences recent (and likely ongoing) transfers over long evolutionary distances. Although many ISRpe1 copies were clearly expanding and leading to rapid endosymbiont diversification, degraded copies are also frequently found, constituting an unusual genomic fossil record suggestive of ancient ISRpe1 expansions. Overall, the present data highlight how ecological connections within the arthropod intracellular environment facilitate lateral DNA transfers between distantly related bacterial lineages.     

Bt水稻田重要非靶标节肢动物权露于Cry2Aa蛋白的程度分析

根据风险=危险×机露的原理,在实验室条件下评价转基因作物对非靶标节肢动物影响时,所选择的代表性非靶标生物通常是在农田系统中较高地关露于转基因外源杀虫蛋白的节肢动物种.为了弄清Bt稻田主要节肢动物暴露于Cry蛋白的程度,选择合适的非靶标节肢动物,用于转基因抗虫水稻的风险评价,本文采用酶联免疫技术检测了水稻不同生长期从转cry2Aa基因水稻田采集的不同节肢动物体内Cry2Aa蛋白的含量.结果表明:不同节肢动物种体内的Cry蛋白含量差异显著.一些节肢动物体内不合Cry蛋白,而一些节肢动物体内含有较高的Cry蛋白;相对于花期后采集的节肢动物,在Bt水稻花期采集的节肢动物,特别是捕食性节肢动物体内的Cry蛋白含量较高;寄生性节肢动物体内未检测到Cry蛋白.这为在实验室条件下评价转基因水稻对农田非靶标节肢动物的影响奠定了基础.     

转基因抗草甘膦抗虫棉对棉田冠层节肢动物群落的影响

【背景】随着转基因抗虫棉在我国的广泛种植,一种具有抗虫和耐除草剂（草甘膦）的双价棉被培育成功。这种转双价基因棉和转单价基因抗虫棉对棉田节肢动物群落结构的影响可能不同。因此,在该类转双价基因棉花进行环境释放之前,有必要研究其对棉田节肢动物群落的影响,评价其环境安全性。【方法】试验于2010年5月9日~9月23日和2011年5月10日~9月24日在河南省安阳市中国农业科学院棉花研究所试验农场进行,棉田类型有3种——转基因抗草甘膦抗虫棉田、转Bt棉田和常规棉田,每种棉田种植3个小区,每个小区面积为200 m2（8 m×25 m）。采用对角线5点取样方法,每5 d调查1次棉田的节肢动物群落,通过目测对节肢动物鉴定到属。【结果】抗草甘膦抗虫棉田、Bt棉田和常规棉田节肢动物群落、害虫亚群落和天敌亚群落的结构与组成无明显差异;抗草甘膦抗虫棉田害虫种群数量低于抗虫棉田和常规棉田,而其天敌种群数量与常规棉田相当,略低于Bt棉田;3种棉田节肢动物群落、害虫亚群落和天敌亚群落的多样性指数、均匀性指数均无明显差异。【结论与意义】种植转基因抗草甘膦抗虫棉花不会对棉田节肢动物群落组成造成显著影响。本研究为转基因抗草甘膦抗虫棉田的环境安全性评价提供了依据。     

Western myall groves (Acacia papyrocarpa) determine the fine‐scale distribution of soil Collembola in semi‐arid South Australia

Vegetation can exert a strong influence on the distribution and activity of biotic communities across a broad range of spatial scales, especially in arid and semi‐arid ecosystems. At fine spatial scales, patches created by individual plants can support different faunal and floral communities even at locations distant from the plant. These differences can have profound effects on a range of ecosystem processes, including seed dispersal, nutrient cycling and resource distribution. In semi‐arid Australia, areas surrounding groves of western myall (Acacia papyrocarpa) trees are largely devoid of vegetation, being referred to as ‘halos’. Here, we investigate the soil‐dwelling Collembola in groves of western myall trees, the surrounding halos and nearby chenopod shrubland. We also investigated whether the abundance of Collembola was influenced by soil depth (0–5 cm layer vs. 6–10 cm layer) in groves. We found that collembolan density was approximately nine times lower and taxonomic richness half that in a halo compared with the grove and chenopod vegetation. Furthermore, analyses at finer taxonomic levels indicate that vegetation patches differed in species composition, with some species restricted to or preferring particular patches. In the grove, we found a higher abundance of Collembola in the 0–5 cm soil layer compared with the 6–10 layer. Our results indicate vegetation patches strongly influence collembolan abundance and species composition in bare patches around western myall. As patches created by vegetation are a common feature of semi‐arid and arid regions, we suspect that these effects are widespread although seldom reported. Furthermore, as Collembola are involved in the decomposition process, Acacia papyrocarpa patches will be influencing nutrient cycling through their effects on the soil biota. Our results also emphasize that comprehensive fauna survey and management of woodland ecosystems need to consider fine‐scale processes.