Benthic Macroinvertebrate Communities Associated with an Artificial Giant Kelp (Macrocystis pyrifera) Forest in Lüderitz Bay, Namibia
Description
This dataset contains benthic macroinvertebrate abundance data collected from an artificial giant kelp (Macrocystis pyrifera) forest and reference habitats in Lüderitz Bay, Namibia, during June–July 2025. The dataset includes: Raw and cleaned data: -Sediments Raw Data – original counts from Van Veen grab and sediment cores -Sediments_Clean_Data – processed sediment data for analysis -SWB-INT Rocky Raw Data – original rocky intertidal counts (R1-R5) -Rocky_Data_Clean – processed rocky intertidal data -SWB-INT Rocky Field Data – field observations -SACFOR-based scale – semi-quantitative abundance categories used for rocky intertidal -Kelp holdfast – epifauna from M. pyrifera holdfast (qualitative) -Laminaria holdfast – epifauna from L. pallida holdfast (qualitative) Analysis outputs: -R Notebook Report (Report.html) – complete reproducible analysis with code, tables, and figures -Biodiversity indices (Species richness, Shannon diversity, Pielou's evenness) per sample -NMDS ordination scores -Statistical test results (Kruskal-Wallis, Dunn's post-hoc, PERMANOVA) Methods: Van Veen grab (subtidal), sediment cores (sandy intertidal), time-constrained active search (rocky intertidal). Identification to family level using standard taxonomic keys for the Benguela Current region. This study provides baseline data for artificial kelp forest biodiversity in the Benguela Upwelling System, comparing communities across a spatial gradient: offshore artificial kelp forest (AKF), nearshore shallow artificial kelp zone (NKZ), intertidal rocky shore with native kelps (INT-Rocky), and intertidal sandy shore (INT-Sandy).
Files
Steps to reproduce
1. Field sampling (June–July 2025) -Subtidal habitats (AKF, NKZ): Benthic samples were collected using a Van Veen grab (0.05 m²) deployed from a vessel. Three replicate grabs were pooled per site per sampling event. -Intertidal rocky shore (INT-Rocky): A time-constrained active search (5 minutes per site) was conducted. Abundance of high-density sessile organisms was estimated using SACFOR categories. -Intertidal sandy shore (INT-Sandy): Sediment cores (10 cm diameter × 15 cm depth) were collected from lower and mid-intertidal zones and pooled per site. 2. Sample processing -Samples were sieved through stacked sieves (4.75 mm, 1.18 mm, 600 µm) using seawater. -Organisms retained on the 600 µm sieve were sorted under a dissecting microscope. -Identification was done to family level using standard taxonomic keys for the Benguela Current region. -Specimens were preserved in 4% buffered formalin. 3. Data entry and cleaning -Counts were recorded in Microsoft Excel. -Data were cleaned and formatted for analysis (removing blanks, standardizing habitat names, fixing dates). 4. Statistical analysis -All analyses were performed in R version 4.3 (R Core Team, 2023). -Required R packages: tidyverse, vegan, rstatix, ggplot2, car, kableExtra, lubridate. -Biodiversity indices (Shannon diversity, species richness, Pielou's evenness) were calculated using the vegan package. -Normality was assessed using Shapiro-Wilk tests; homogeneity of variances using Levene's tests. -Habitat comparisons used Kruskal-Wallis tests followed by Dunn's post-hoc tests (Bonferroni-adjusted). -Community composition was visualized using NMDS ordination (Bray-Curtis distance, Hellinger-transformed data) and tested with PERMANOVA (999 permutations). -Figures and tables were generated using ggplot2 and kableExtra. 5. Reproducing the analysis -Download the dataset from Mendeley Data. -Open Article1_Script.R in RStudio. -Update the data_file path in Section 1 to point to the downloaded Excel file. -Run the script to reproduce all results. -View Report.html for a complete output with code, tables, and figures.
Institutions
- Namibia University of Science and TechnologyKhomas Region, Windhoek