Analysis of benthic food web structure in coastal vegetated habitats
Yansong Huang, IMBRSea Professional Practice 2021
Overview
During my professional practice, I focused on the reconstruction of trophic relationship in coastal vegetated habitats. The food web includes meiofauna, macrofauna, primary producers and other organic matter sources.
My work is divided into 2 parts: lab work of preparing the sample for chemical analysis; and analysis of stable isotope data using R programming.
Map of Gazi Bay. (Nyunja et al., 2009)
Gazi Bay - the study site
Gazi Bay is located about 50 km south of Mombasa on the Kenyan coast (4°25'S, 39°30‘E). The bay is a tropical lagoon with a fringing coral reef at the seaward side, and extensive seagrass beds in between the mangrove forest and the reefs. (Baran and Hambrey, 1998)
Stable Isotope - biological tracers
"You are what you eat." This saying also applies to macrofauna and meiofauna in coastal vegetated habitats. Their stable isotope signature (δ13C and δ15N) can reflect their diet and trophic level within the food web. Furthermore, the analysis can provide useful information on quantifying matter pathways in the ecosystem.
Sample preparation
Extraction
The initial sample included benthos, sediment grains, plant detritus and small screes etc. In order to seperate meiofauna from the sediment, I first sieved the sample with 1mm and 38μm sieves. Then I used Redox solution to suspend the sample and centrifuge to have the meiofauna in supernanant.
Sorting & Identification
I pick the meiofauna out and group them into embry disks. The organisms of the same taxonomy group tend to have a similar diet. Therefore, identification and grouping is essential to have precise results.
Cleaning & Counting
Since meiofauna are small in biomass. I need to put multiple individuals into each aluminiun cup to have a valid measurement. At the same time, I clean the sample with Milli-Q water to minimise the contamination of potential attached organic matter.
Weighing of 'Cups'
Meiofauna samples will be placed in alumium cups for stable isotope and biomass measurement. Weighing the cup before putting the sample and after drying the sample is delicate and important step to obtain data.
data analysis
I first explore the R package 'MixSIAR' and 'SIBER' using a meiofauna dataset from the sample collected in 2010-2011 at Mira estuary, Portugal. Then I applied the same method to a macrofauna dataset from the sample collected in 2019 at Gazi Bay, Kenya.
Data Cleaning & Exploration
I start by filtering the data for quality control and adapting the raw data to the format that fit into R packages. Next, I make the scatter plots to have a overview of the isotope value of consumer (in coloured dots) and food sources (in black dots with error bars). I also made box plots to compare different taxonomy groups or different habitats so see temporal, spatial or interspecies variation.
Mixing Stable Isotope Modelling
Based on the stable isotopic value of consumers and food sources, the Bayesian mixing model construct the diet composition of each group. The plots show the contribution of food sources to the diet of two nametode genera. Spirinia mainly feeds on seagrass, while Terschellingia obtains organic matter from symbiosis with chemoautotrophic bacteria.
Niche Plotting
The niche plotting enables us to compare the niche of different species. In the first plot, the ellipses show the niche range of each species of crab. The second plot compares the niche width of these species using the area of ellipses. The package can also calculate the percentage of niche overlap based on the stable isotope signature.
Food sources: CATB - chemoautotrophic bacteria, EP - epiphytes, MG - mangrove, MPB - microphytobenthos, SG - seagrass, SPOM - suspended particulate organic matter.
Sampling sites: M1&M2&M3 - mangrove site 1, 2 and 3, UV - unvegetated habitats with seagrass patches, W2 - river.
reflection
Things I learned from the professional practice:
Professional skills: communicate with others, respect the rules for public space & equipment.
R programming skills: format data, build up models, interpreting results.
Lab skills: benthos extraction, microscopic identification.
Research methods: hypothesis testing, critical thinking.
Photo Gallery of Field Sampling
Photo by Anna-Maria Vafeiadou, 2019.
References
Baran, E., Hambrey, J., 1998. Mangrove conservation and coastal management in southeast Asia: what impact on fishery resources? Marine Pollution Bulletin 37, 431–440.
Nyunja, J & Ntiba, M & Onyari, John & Mavuti, Kenneth & Soetaert, K. & Bouillon, Steven. (2009). Carbon sources supporting a diverse fish community in a tropical coastal ecosystem (Gazi Bay, Kenya). Estuarine Coastal and Shelf Science - ESTUAR COAST SHELF SCI. 83. 10.1016/j.ecss.2009.01.009.