The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.     

Environmental gradients in a southern Europe estuarine system: Ria de Aveiro,Portugal implications for soft bottom macrofauna colonization

Four seasonal sampling surveys were carried out between December 1985 and September 1986 in Canal de Mira (Ria de Aveiro, Portugal). A total of 40 sampling stations, distributed over 13 transects, was used. Salinity, temperature, dissolved oxygen and pH of the water mass were measured. Sediment temperature, and salinity and pH of interstitial water were determined. Sediment variables also included granulometric composition and organic matter contents. Bottom macrofauna samples were collected at each station. Ordination (PCA and MDS) and classification of the sampling stations were performed, using the physicochemical and the biological data sets separately. Average linkage cluster analysis using the unweighted paired-group method, arithmetic averages, was used for both sets of data. With a salinity range from 35.1‰ to 0.0‰, Canal de Mira behaves like a tidally and seasonally poikilohaline estuary. Water temperature (8.5–24.7°C) decreased along the channel towards its inner part during the cold season; an inverse and more pronounced trend was observed during the hot season. Dissolved oxygen contents was generally high during the day (50% to 240% saturation). Oversaturation was observed throughout the growing season, with peaks in areas with large amounts of rooted vegetation. The pH values, largely correlated with dissolved oxygen, ranged from 6.8 to 8.9. Four types of sediment were present in Canal de Mira, medium and muddy sands being dominant. Two major gradients were identified: (i) a typical longitudinal estuarine gradient, associated with distance from the mouth, representing physicochemical variables such as tidal amplitude, salinity and temperature; this gradient was accompanied by an upstream increase in dominance; the community composition changes were mainly related to salinity; (ii) a lateral gradient, related to current velocity, depth and sediment composition; the subtidal community had a comparatively low species richness and abundance. Groups of stations could be recognized along the environmental gradients. Benthic community changes, however, appeared to be gradual rather than marked by abrupt transitions.     

From aquatic science to ecosystem health: a philosophical perspective

The development of an ecosystem (social, economic, environmental) approach to water management is traced from its origins in the Great Lakes of North America. The focus on health and integrity of ecosystems is an outgrowth of the Lamarckian concept of The Biosphere as a global system of matter, life, and mind. The driving forces behind the development of an ecosystem approach have been negative feedback from excessive demotechnic growth and faith that we can maintain a healthy relationship with Mother Earth.     

A data-driven framework to model the organism–environment system

Organisms modify their development and function in response to the environment. At the same time, the environment is modified by the activities of the organism. Despite the ubiquity of such dynamical interactions in nature, it remains challenging to develop models that accurately represent them, and that can be fitted using data. These features are desirable when modeling phenomena such as phenotypic plasticity, to generate quantitative predictions of how the system will respond to environmental signals of different magnitude or at different times, for example, during ontogeny. Here, we explain a modeling framework that represents the organism and environment as a single coupled dynamical system in terms of inputs and outputs. Inputs are external signals, and outputs are measurements of the system in time. The framework uses time-series data of inputs and outputs to fit a nonlinear black-box model that allows to predict how the system will respond to novel input signals. The framework has three key properties: it captures the dynamical nature of the organism–environment system, it can be fitted with data, and it can be applied without detailed knowledge of the system. We study phenotypic plasticity using in silico experiments and demonstrate that the framework predicts the response to novel environmental signals. The framework allows us to model plasticity as a dynamical property that changes in time during ontogeny, reflecting the well-known fact that organisms are more or less plastic at different developmental stages.     

尖峰岭热带天然林不同土层细菌群落多样性和组成的海拔变异规律

土壤微生物群落结构沿海拔梯度的变异是微生物生物地理学分异和群落空间分布的重要内容,然而,热带森林土壤微生物多样性及其群落特征的海拔模式尚不明确。研究海南省尖峰岭自然保护区0—20cm和20—40cm土壤细菌多样性和群落组成沿海拔梯度(400—1410m)的变化及其与环境因子的关系。结果表明：在0—20cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高(峰顶降低)而增加,20—40cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高呈先升高后降低趋势;整体上,变形菌门、放线菌门、酸杆菌门、拟杆菌门、厚壁菌门在0—20cm中占优势,丰度总和占该层细菌总量的88.17%;变形菌门、放线菌门、酸杆菌门、厚壁菌门、绿弯菌门在20—40cm中占优势,丰度总和占该层细菌总量的90.82%;随海拔增加,0—20cm细菌多样性线性减少,20—40cm细菌多样性变化不显著;沿海拔梯度,0—20cm细菌群落组成可分为低(409—1018m),中(1018—1357m)和高(1410m)三个海拔聚集群落,20—40cm细菌群落组成随海拔无显著性变化;两土层细菌多样性与土壤pH显著正相关,土壤细菌群落组成在0...     

中国环境规制对旅游业碳排放强度影响的空间异质性

环境规制作为实现旅游低碳发展的重要动力之一,也是实现旅游业“碳达峰、碳中和”目标的有效路径。基于综合指数法和“自下而上”法,测度2005—2019年中国大陆30个省份(中国港澳台及西藏统计数据尚缺)的环境规制水平和旅游业碳排放强度,并借助面板回归模型和面板门槛模型探讨了环境规制对旅游业碳排放强度的影响及其区域异质性。结果表明：(1)研究期内,中国整体旅游业碳排放强度呈下降趋势;其中,中部地区下降趋势最为明显,其次分别为西部、东部和东北地区。(2)中国环境规制水平呈增长态势,其规制效应对胡焕庸线右侧的地区更为显著,并呈现出自东向西递减的梯度分布特征。(3)中国环境规制对旅游业碳排放强度存在明显的“倒逼减排”效应,但东北地区却存在一定的“绿色悖论”现象;环境规制对旅游业碳排放强度的影响存在单一阈值,当旅游能源强度小于阈值时,存在显著的“倒逼减排”效应,当旅游能源强度超过阈值时则存在“绿色悖论”效应。(4)东部地区环境规制未通过门槛效应检验;中部地区存在单个门槛值,环境规制有效促进旅游业碳排放强度的下降,不存在“绿色悖论”现象;西部和东北地区分别存在单、双门槛效应,环境规制对旅游业碳排放强度...     

环境DNA在两栖动物监测中的应用研究进展

两栖动物是我国受威胁程度最高的动物类群,加强两栖动物资源调查和多样性监测,是开展两栖动物保护和濒危物种拯救行动的关键性基础工作。传统的两栖动物监测主要以形态学和声学为基础,耗时费力,且难以发现一些隐蔽性较强的稀有物种。基于环境DNA(environmental DNA, eDNA)的调查方法以其快速、灵敏、高效、无创等独特优势,为两栖动物多样性监测及保护提供了新的工具。综述了eDNA在两栖动物多样性监测、外来入侵和珍稀濒危物种调查、物种丰度或生物量估测等研究领域的应用进展,分析了两栖动物eDNA产生、扩散、迁移和降解的动态变化特征及其关键影响因子,探讨了eDNA应用于两栖动物监测研究的局限性并提出了优化建议,同时对未来的研究方向进行了展望,以充分挖掘eDNA在两栖动物监测中的应用潜力,为两栖动物多样性保护和管理提供新的思路。     

新疆猪毛菜属植物多样性地理分布格局及其环境解释

猪毛菜属(Salsola)是新疆干旱区分布最为丰富的被子植物属之一,是盐碱和荒漠区的先锋种和建群种,对西北干旱区植被恢复与建设具有巨大生态价值。基于新疆自然分布的33种猪毛菜属物种共741个分布数据,整合利用点格局法和物种分布模型法构建了物种丰富度(SR)、加权特有性指数(WE)和校正加权特有性指数(CWE)的分布格局。选取环境能量、水分可获得性、气候季节性、生境异质性、土壤条件和历史气候变化共6类19种生态因子,利用地理加权回归模型(GWR)探究了环境异质性对猪毛菜属物种丰富度的影响。结果显示：(1)基于现实点位模型和物种分布模型构建的物种丰富度具有一致性,均呈北高南低、西高东低的破碎化分布趋势,但物种分布模型的结果在空间上比点格局法更连续,物种丰富度的高值区主要分布于准噶尔盆地南缘、准噶尔西部山地、天山西端和天山南脉南缘;(2)加权特有性指数和校正加权特有性指数的分布格局与物种丰富度分布格局具有一定差异,其最大值集中分布于准噶尔盆地南缘、伊犁河谷和塔里木盆地西南缘;(3)GWR模型结果表明,海拔变幅、土壤酸碱度和最干月降水量是制约新疆分布的猪毛菜属丰富度和特有性分布的最重要因素。     

大陈岛海域浮游动物群落季节变化及其影响因素

为探究大陈岛海域浮游动物群落的季节变化,于2020年9月（夏季）、11月（秋季）和2021年1月（冬季）、4月（春季）分别对大陈岛海域的浮游动物及环境因子进行了4个航次的调查。结果共鉴定浮游动物90种,包括浮游幼体15类,其中夏季种类数最多（68种）,冬季最少（20种）,常见的优势种有：百陶箭虫（Sagitta bedoti）、微刺哲水蚤（Canthocalanus pauper）、中华哲水蚤（Calanus sinicus）等12种（Y>0.02）。浮游动物的年平均丰度和生物量分别为（153.40±214.73）个/m³、（411.93±561.76） mg/m³,二者存在明显的季节变化,平均丰度为春季（380.17±296.14）个/m³>夏季（135.30±112.59）个/m³>秋季（67.88±90.52）个/m³>冬季（25.30±19.11）个/m³;平均生物量为夏季（895.01±802.54） mg/m³>春季（623.39±358.73） mg/m³>秋季（91.08±82.36） mg/m³>冬季（45.96±84.95） mg/m³。多样性指数（H''）和均匀度指数（J''）的年平均值分别为1.71±0.96和0.53±0.20,均表现出夏秋季较高、冬春季较低的特征。聚类分析结果表明调查海域的浮游动物可划分为夏季类群、秋季类群、冬季类群和春季类群4组类群。Pearson相关性分析和冗余分析（RDA）结果表明,海水温度、盐度、叶绿素a浓度是影响大陈岛海域浮游动物群落特征的重要环境因素。此外,夏季大陈岛海域水母类浮游动物暴发的现象值得关注。研究结果将为大陈岛海域的生物多样性保护及渔业资源可持续开发利用提供可参考的数据资料。