Functional Trait Database describing micro-phytoplankton diversity from the North-West French coast

The primary producers represent an essential link for the ecosystem functioning. Understanding the community structure through long-term monitoring is key to understand the impact of climate and environmental changes at both global and local scale. To better understand those communities, many national and international networks have been collecting samples for the study of micro-phytoplankton (20µm to 200µm) diversity. This correspond to larger organisms among phytoplankton that can be accessed through light microscopy. However, it is hard or impossible to access pico or nano-phytoplankton through microscopy only. Looking at functional group distribution and variations with microphytoplankton data could provide information on overall primary producers’ adaptation to climate change. For instance, modification on large and small cells ratio could impact coastal ecosystem functioning and affect zooplankton, larvae and shellfish of ecological or economical interest.

The phytoplankton diversity is widely explored through a taxonomical approach. Nevertheless, a more global approach that could enable to examine primary producers not through taxonomy but functional diversity – through their direct adaptation to environment variables – could provide insights into how phytoplankton community respond to environmental changes and better apprehend global effect on the ecosystem functioning.

Records of the coastal micro-phytoplankton diversity are available at a national scale thanks to the REPHY (REPHY – French Observation And Monitoring Program For Phytoplankton And Hydrology In Coastal Waters, 2021). Here, we present a trait database of micro-phytoplankton entities as seen through the monitoring program for the North-West of France (Lefran et al., 2022). It has been built for the purpose of studying the impacts of environmental changes in the Eastern English Channel through a functional approach. It contains description of 93 entities through morphological, physiological and behavioural traits.

The initial work of Ramond and collaborators (2018) enabled to gather most of the information contained in this database. Morphological traits were each revised with nordicmicroalgae.org to better correspond to organisms from the North-East Atlantic (by opposition to measures taken from tropical organisms). Indeed, size can vary a lot depending on the organism’s stage of life (diatoms) or its environment. Gaps and additional traits were filled through an extensive literature review.

The excel file is composed of 2 tabs:

·       The first tab contains the datatable with all relevant information as described in the table below. Certain boxes have a comment tag indicating the reference associated to the trait, especially when the trait was not found in the main literature sources or did not correspond to local observations and required further research. This tab can be converted in a csv file to be used for functional analysis.

·       The second tab lists the sources used to complete the table. Books and websites with large records on phytoplankton traits are listed above, followed by species specific literature information.

Column name

Description

Trait.s

Taxon

Taxonomical denomination as referred to in the REPHY program

Shortname

Short denomination used in analysis

Rank

Organism’s rank

Class.worms2019

Organism’s class as registered in WoRMS 2019 (www.marinespecies.org)

Ramond_nameref

Taxonomical denomination as referred to in (Ramond et al., 2018)

Size_min

Size_max

Length (µm) of the cells (minimum and maximum values estimation) from NordicMicroalgae.org

Numerical

Biovolume_min

Biovolume_max

Biovolume (µm3) of the cells (minimum and maximum values calculation based on the geometric shape) from nordicmicroalgae.org

Numerical

Surface_min

Surface_max

Surface (µm2) area of the cells (minimum and maximum values calculation based on the geometric shape) from nordicmicroalgae.org

Numerical

S/V_min

S/V_max

S/V_mean

Surface / Volume ratio (µm-1)

Numerical

Geometric_shape

Geometric shape approximation that best describe the cell morphological aspect from nordicmicroalgae.org

13 traits such as cylinder sphere, prism, cone etc…

Spine_or_Setae_presence

Presence of hard spines or soft setae around the cells

Spines

Setae

None

Cover

Structure composition of the external cover of cells

Siliceous

Organic

Naked

Shape

Binomial shape description of the cells

Round

Elongated

Colony

Cells’ capacity to form colonies and their final aspect (long straight lines or curved; ball/mass aspect)

Curved

Straight

None

Motility

Capability to induce movement

Floater

Swimmer

Glider

Diet

How does the organism collect or produce its energy?

Autotrophic

Mixotrophic

Heterotrophic

Habitat

Water column position preferences

Planktonic

Tychoplanktonic (bentho-planktonic cycle)

Benthic

Epiphytic

Harmful

Harmful potential description if any

None

Toxin producer

Fish Mortality

Physical

Anoxia

Slime

Discoloration

RestingStage

Resting stage / cyst form known to the organism

0 - no

1 - yes

Substance producer

HABs category

No

Toxic

Harmful

Credits:

This trait table has been created as part of the S3-Eurohab project (https://www.s3eurohab.eu). It has been reviewed with members of the REPHY program. We recognise that nordicmicroagale.org has been a vital source of information for the study of morpho-functional traits. This database would not be as thorough without the information they openly share. The morphological information is accurate to this date (2024) but could be subject to change with new research findings.

References:

Lefran, A., Françoise, S., Legendre, A., Hebert, P., Hernandez-Fariñas, T., Claquin, P., 2022. Dataset of micro-phytoplankton biodiversity in the Eastern Channel area from 1987 to 2019. https://doi.org/10.5281/zenodo.7496602

Ramond, P., Siano, R., Sourisseau, M., 2018. Functional traits of marine protists. https://doi.org/10.17882/51662

REPHY – French Observation And Monitoring Program For Phytoplankton And Hydrology In Coastal Waters, ., 2021. REPHY dataset - French Observation and Monitoring program for Phytoplankton and Hydrology in coastal waters. Metropolitan data. https://doi.org/10.17882/47248

初级生产者是维系生态系统功能运转的核心纽带。通过长期监测解析浮游植物群落结构，是理解全球与局地尺度气候变化与环境变化影响的关键所在。

为深入解析此类群落，诸多国家级与国际级监测网络已开展样本采集工作，以研究微型浮游植物（micro-phytoplankton，20μm至200μm）的多样性。微型浮游植物即浮游植物中体型较大的类群，可通过光学显微镜观测。然而，仅依靠显微镜技术，难以甚至无法观测到皮克浮游植物（pico-phytoplankton）与纳克浮游植物（nano-phytoplankton）。

基于微型浮游植物数据解析功能群的分布与变化特征，可揭示初级生产者整体对气候变化的适应机制。例如，细胞大小比例的改变会影响沿岸生态系统功能，并对具有生态与经济价值的浮游动物、幼体及贝类造成影响。

当前浮游植物多样性研究多基于分类学方法，但倘若采用更具普适性的研究路径——不依赖分类学，而是通过初级生产者对环境变量的直接适应特征来解析功能多样性——则可更深入地理解浮游植物群落对环境变化的响应机制，进而更好地把握全球变化对生态系统功能的影响。

得益于REPHY计划（法国沿岸浮游植物与水文观测监测计划，REPHY – French Observation And Monitoring Program For Phytoplankton And Hydrology In Coastal Waters, 2021），国家级尺度的沿岸微型浮游植物多样性记录已可获取。本研究基于法国西北部海域的长期监测数据，构建了微型浮游植物类群特征数据库（Lefran等，2022），旨在通过功能组学方法探究英吉利海峡东部海域的环境变化影响。该数据库收录了93个类群的形态学、生理学及行为学特征信息。

本数据库的多数信息源自Ramond及其合作者2018年的研究工作。所有形态学特征均通过北欧微藻数据库（nordicmicroalgae.org）进行了修订，以更贴合东北大西洋海域的物种特征（区别于基于热带物种的测量标准）。事实上，细胞大小会随物种的生长阶段（如硅藻）或所处环境发生显著变化。研究团队通过系统性文献检索补充了数据库中的缺失条目与额外特征项。

本数据集的Excel文件包含两个工作表：
· 第一个工作表为核心数据表，收录如下表格所述的全部相关信息。部分单元格附带注释标签，用于标注对应特征的引用来源，尤其适用于未在主要文献中记载、或与本地观测结果不符且需额外溯源的特征项。该工作表可导出为CSV格式文件，用于功能组学分析。
· 第二个工作表为参考文献列表，优先列出收录大量浮游植物特征信息的书籍与网站，随后为针对特定物种的文献资料。

### 数据表字段说明
| 列名 | 描述 | 数据类型 |
|------|------|----------|
| Trait.s | 特征项 | —— |
| Taxon | REPHY计划中所使用的分类学名 | —— |
| Shortname | 分析过程中使用的简称 | —— |
| Rank | 物种分类等级 | —— |
| Class.worms2019 | WoRMS 2019（世界海洋物种登记系统2019版，www.marinespecies.org）中登记的物种类群 | —— |
| Ramond_nameref | Ramond等（2018）文献中所使用的分类学名 | —— |
| Size_min、Size_max | 细胞长度（μm）的最小值与最大值（基于北欧微藻数据库的估算值） | 数值型 |
| Biovolume_min、Biovolume_max | 细胞体积（μm³）的最小值与最大值（基于几何形状计算所得，源自北欧微藻数据库） | 数值型 |
| Surface_min、Surface_max | 细胞表面积（μm²）的最小值与最大值（基于几何形状计算所得，源自北欧微藻数据库） | 数值型 |
| S/V_min、S/V_max、S/V_mean | 表面积/体积比值（μm⁻¹） | 数值型 |
| Geometric_shape | 最贴合细胞形态的几何形状近似描述（源自北欧微藻数据库），包含圆柱、球形、棱柱、锥形等共13种类型 | —— |
| Spine_or_Setae_presence | 细胞周围是否存在硬棘或软刚毛，可选值：棘刺、刚毛、无 | —— |
| Cover | 细胞外部覆盖结构的组成类型，可选值：硅质、有机质、裸露 | —— |
| Shape | 细胞形状的二项式描述，可选值：圆形、伸长形 | —— |
| Colony | 细胞形成群落的能力及群落形态（长直链状、弯曲链状、球状/团块状），可选值：弯曲、直连、无 | —— |
| Motility | 细胞运动能力，可选值：漂浮、游动、滑行 | —— |
| Diet | 生物体获取能量的方式，可选值：自养、混合营养、异养 | —— |
| Habitat | 生物体在水层中的偏好栖息位置，可选值：浮游生活、底栖浮游生活（底栖-浮游生活周期）、底栖生活、附生生活 | —— |
| Harmful | 物种的有害潜力描述，可选值：无、产毒、致鱼类死亡、物理伤害、缺氧、黏液、变色 | —— |
| RestingStage | 物种是否存在已知的休眠阶段/孢囊形式，0代表无，1代表有 | —— |
| Substance producer | 有害藻华（HABs，Harmful Algal Blooms）类别，可选值：无、有毒、有害 | —— |

致谢：
本特征数据表为S3-Eurohab项目（https://www.s3eurohab.eu）的研究成果之一，已由REPHY计划成员完成审核。本研究衷心感谢北欧微藻数据库（nordicmicroalgae.org）所提供的关键数据支撑，若无其公开共享的信息，本数据库无法达到如此详尽的程度。截至2024年，本数据库的形态学信息均保持准确，但后续可能因新的研究成果而更新。

参考文献：
1. Lefran A, Françoise S, Legendre A, 等. 1987-2019年英吉利海峡东部海域微型浮游植物生物多样性数据集[EB/OL]. https://doi.org/10.5281/zenodo.7496602.
2. Ramond P, Siano R, Sourisseau M. 2018. 海洋原生生物功能特征[EB/OL]. https://doi.org/10.17882/51662.
3. REPHY计划. 2021. 法国沿岸浮游植物与水文观测监测计划数据集[EB/OL]. https://doi.org/10.17882/47248.