A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

Targeted species‐specific and community‐wide molecular diagnostics tools are being used with increasing frequency to detect invasive or rare species. Few studies have compared the sensitivity and specificity of these approaches. In the present study environmental DNA from 90 filtered seawater and 120 biofouling samples was analyzed with quantitative PCR (qPCR), droplet digital PCR (ddPCR) and metabarcoding targeting the cytochrome c oxidase I (COI) and 18S rRNA genes for the Mediterranean fanworm Sabella spallanzanii. The qPCR analyses detected S. spallanzanii in 53% of water and 85% of biofouling samples. Using ddPCR S. spallanzanii was detected in 61% of water of water and 95% of biofouling samples. There were strong relationships between COI copy numbers determined via qPCR and ddPCR (water R² = 0.81, p < .001, biofouling R² = 0.68, p < .001); however, qPCR copy numbers were on average 125‐fold lower than those measured using ddPCR. Using metabarcoding there was higher detection in water samples when targeting the COI (40%) compared to 18S rRNA (5.4%). The difference was less pronounced in biofouling samples (25% COI, 29% 18S rRNA). Occupancy modelling showed that although the occupancy estimate was higher for biofouling samples (ψ = 1.0), higher probabilities of detection were derived for water samples. Detection probabilities of ddPCR (1.0) and qPCR (0.93) were nearly double metabarcoding (0.57 to 0.27 marker dependent). Studies that aim to detect specific invasive or rare species in environmental samples should consider using targeted approaches until a detailed understanding of how community and matrix complexity, and primer biases affect metabarcoding data.     

CTENO64 Is Required for Coordinated Paddling of Ciliary Comb Plate in Ctenophores

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Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis

Terrestrial predators on marine shores benefit from the inflow of organisms and matter from the marine ecosystem, often causing very high predator densities and indirectly affecting the abundance of other prey species on shores. This indirect effect may be particularly strong if predators shift diets between seasons. We therefore quantified the seasonal variation in diet of two wolf spider species that dominate the shoreline predator community, using molecular gut content analyses with general primers to detect the full prey range. Across the season, spider diets changed, with predominantly terrestrial prey from May until July and predominantly marine prey (mainly chironomids) from August until October. This pattern coincided with a change in the spider age and size structure, and prey abundance data and resource selection analyses suggest that the higher consumption of chironomids during autumn is due to an ontogenetic diet shift rather than to variation in prey abundance. The analyses suggested that small dipterans with a weak flight capacity, such as Chironomidae, Sphaeroceridae, Scatopsidae and Ephydridae, were overrepresented in the gut of small juvenile spiders during autumn, whereas larger, more robust prey, such as Lepidoptera, Anthomyidae and Dolichopodidae, were overrepresented in the diet of adult spiders during spring. The effect of the inflow may be that the survival and growth of juvenile spiders is higher in areas with high chironomid abundances, leading to higher densities of adult spiders and higher predation rates on the terrestrial prey next spring.     

Quantifying long‐term recurrence in planktonic microbial eukaryotes

How much temporal recurrence is present in microbial assemblages is still an unanswered ecological question. Even though marked seasonal changes have been reported for whole microbial communities, less is known on the dynamics and seasonality of individual taxa. Here, we aim at understanding microbial recurrence at three different levels: community, taxonomic group and operational taxonomic units (OTUs). For that, we focused on a model microbial eukaryotic community populating a long‐term marine microbial observatory using 18S rRNA gene data from two organismal size fractions: the picoplankton (0.2–3 µm) and the nanoplankton (3–20 µm). We have developed an index to quantify recurrence in particular taxa. We found that community structure oscillated systematically between two main configurations corresponding to winter and summer over the 10 years studied. A few taxonomic groups such as Mamiellophyceae or MALV‐III presented clear recurrence (i.e., seasonality), whereas 13%–19% of the OTUs in both size fractions, accounting for ~40% of the relative abundance, featured recurrent dynamics. Altogether, our work links long‐term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non‐recurrent changes characterize the dynamics of microbial assemblages.     

海洋真菌Arthrinium sp. UJNMF0008代谢产物的研究

为丰富海洋真菌的化学多样性,发现海洋真菌活性代谢产物,对海洋沉积物来源真菌Arthriniumsp.UJNMF0008的化学成分及其生物活性进行研究,采用硅胶柱色谱、凝胶柱色谱、反向柱色谱和高效液相色谱等方法从海洋沉积物来源真菌Arthriniumsp.UJNMF0008的发酵提取物中分离到5个化合物,通过核磁共振、质谱等方法,结合文献对照,鉴定了化合物的结构分别为arthoneF(1)、arthoneG(2)、sydoxanthoneC(3)、(3R,4R)-cis-4-hydroxymellein(4)和2-(2′S-hydroxypropyl)-5-methyl-7-hydroxychromone(5),其中化合物1和2是新化合物,化合物3首次从该属真菌中分离到。活性测试显示,化合物1~5在50μmoL/L的测试浓度下均没有表现出明显的抗氧自由基活性、抗菌活性以及NO释放抑制活性。     

海洋自然保护区生态保护补偿机制

在提炼生态保护补偿概念内涵的基础上,综合考虑政策目标、海洋环境自然属性、自然保护区区域特殊性以及我国制度环境,明确了海洋自然保护区生态保护补偿的思路;根据相关法律法规,结合生态系统服务分析,对海洋自然保护区生态保护补偿机制的主体、客体和补偿标准进行了讨论。研究结果表明,海洋自然保护区生态保护补偿应该以持续的生态效益供给为目标,以正外部性内部化为基本原理;海洋自然保护区生态保护补偿的主体是国家,由相关政府部门代表国家履行补偿责任;补偿客体为保护区周边居民和保护区管理机构,对周边居民的补偿标准以其为保护区牺牲的生态效益价值来确定,对管理机构的补偿标准以其使保护区增加的生态效益价值来确定。在构建补偿机制框架后,探讨了保护区运营资金支持和补偿标准公信力等问题,为后续的研究实践提供参考与借鉴。     

海州湾鱼类群落平均营养级和大型鱼类指数的变化特征

为探究近年来海州湾鱼类群落的变化特征,本研究根据2011年及2013-2017年春季(5月)和秋季(9-10月)在海州湾及其邻近海域进行的渔业资源底拖网调查,分析了海州湾鱼类群落平均营养级(MTL)和大型鱼类指数(LFI),对海州湾鱼类群落结构特征进行研究.结果表明:海州湾的优势鱼种主要有大泷六线鱼、方氏云鳚、尖海龙、小黄鱼、长蛇鲻等,且优势鱼种季节性变化明显.海州湾鱼类群落的平均营养级存在明显的年际和季节变化,总体上秋季的MTL高于春季,而且秋季MTL变化具有滞后性.LFI计算结果表明,近年来海州湾及其邻近海域大个体鱼类资源量有所减少,鱼类群落结构呈现出明显的小型化趋势.     

乳酸菌及其细菌素在海水鱼保鲜中应用的研究进展

随着人们对生鲜海水鱼产品需求的日益增加,其保鲜技术的研发成为热点。乳酸菌及其细菌素以其天然、强抗菌性及安全可靠等优势,在海水鱼保鲜方面有广阔的应用前景。综述了海水鱼中乳酸菌细菌素分类、分离纯化方法,分析了乳酸菌产生的有机酸、细菌素和H₂O₂的抑菌作用,概述了乳酸菌及其细菌素在海水鱼保鲜中的应用现状和监管问题,提出了在应用上存在的问题和今后的发展重点。进一步阐明了乳酸菌生物保鲜剂在海水鱼保鲜中的应用价值,以推动海水鱼保鲜技术的发展。     

Microplastic ingestion ubiquitous in marine turtles

Despite concerns regarding the environmental impacts of microplastics, knowledge of the incidence and levels of synthetic particles in large marine vertebrates is lacking. Here, we utilize an optimized enzymatic digestion methodology, previously developed for zooplankton, to explore whether synthetic particles could be isolated from marine turtle ingesta. We report the presence of synthetic particles in every turtle subjected to investigation (n = 102) which included individuals from all seven species of marine turtle, sampled from three ocean basins (Atlantic [ATL]: n = 30, four species; Mediterranean (MED): n = 56, two species; Pacific (PAC): n = 16, five species). Most particles (n = 811) were fibres (ATL: 77.1% MED: 85.3% PAC: 64.8%) with blue and black being the dominant colours. In lesser quantities were fragments (ATL: 22.9%: MED: 14.7% PAC: 20.2%) and microbeads (4.8%; PAC only; to our knowledge the first isolation of microbeads from marine megavertebrates). Fourier transform infrared spectroscopy (FT‐IR) of a subsample of particles (n = 169) showed a range of synthetic materials such as elastomers (MED: 61.2%; PAC: 3.4%), thermoplastics (ATL: 36.8%: MED: 20.7% PAC: 27.7%) and synthetic regenerated cellulosic fibres (SRCF; ATL: 63.2%: MED: 5.8% PAC: 68.9%). Synthetic particles being isolated from species occupying different trophic levels suggest the possibility of multiple ingestion pathways. These include exposure from polluted seawater and sediments and/or additional trophic transfer from contaminated prey/forage items. We assess the likelihood that microplastic ingestion presents a significant conservation problem at current levels compared to other anthropogenic threats.