Deep Water Ports and Sediment Microbiome Shifts in Coral Reefs

15 February 2023by Barış Özdinç


To evaluate the impact of ports on the biodiversity in their vicinity, a recent study collected coral reef sediment samples from the vicinity of Port Everglades in South Florida, and performed 16S rRNA sequencing on the samples. 


CosmosID analyzed the 16S rRNA gene-based microbiome community data to illustrate the impact of port activities on the coral microbiome. 


Read on to learn more about the study and its findings.


Port Everglades Inlet (PEI) is a massive and active South Florida cargo port catering to over 2 million people and is adjacent to coral reefs.


Microbial communities have important ecological and biogeochemical roles in ecosystems, including those of coral reefs. Consequently, microbial community analysis may serve as a valuable ecosystem health marker. 


When combined with the environmental metadata for water masses, microbial community variation may indicate water quality variation. Moreover, microbes may act as integral symbionts to most resident organisms in sediments, such as on sensitive ecosystems like coral reefs. 

What does the research say?

Recent evidence suggests that microbial symbionts positively affect and protect coral species. In this context, analyzing the microbial communities of coral reefs in the vicinity of ports may illustrate the extent of deterioration of the ecosystem in the vicinity of water ports.


To investigate this idea, the study collected sediment samples from different locations in the zone and vicinity of Port Everglades. 


Some samples were collected from the inlet of the port, and some from adjacent coral reefs. Additional samples were collected from ‘no dredging’ zones and others from dredging zones to answer research questions on the impact of the port and port-related activities on the coral and microbial ecosystem.


The researchers collected a total of 240 surface marine sediment samples from 40 different sites. After having characterized the environmental metadata associated with the sites, the sediment samples were subjected to 16S rRNA gene sequencing to profile microbial communities present in the samples. 


After extracting genomic content and sequencing the 16S rRNA gene, the resulting data was uploaded to the CosmosID-HUB for quality trimming, microbial profiling, relative abundance measurement, and microbiome analysis.


According to the results of the study, microbial communities from coral reefs and Port Everglades inlet were significantly distinct, regardless of proximity and tidal connections of the Port and coral reefs. 


Additionally, the findings of the study suggested that dredging, a common port-linked activity, increased trace metals and led to a decrease in cyanobacterial diversity. 


Although dredging was linked to a decrease in cyanobacterial diversity, it did not affect the diversity of coral or human pathogens present in the reef. 


To learn more about the recent study establishing the baseline port/dredging-associated microbiome, please check out the original paper.

How did CosmosID support this research?

CosmosID supported the researchers in terms of data analysis and characterization by:

  • Quality trimming raw 16S rRNA sequence reads.
  • Microbial profiling all the samples to identify taxonomic groups present in each sample.
  • Relative abundance calculation of the microbial counts, which enabled examination of changes in microbial diversity across samples.


Overall, CosmosID’s software platform was a valuable tool used by the researchers in understanding how port activities can impact coral reef microbial communities. The study findings provide actionable insights that may inform port management decisions.


With the increased scientific understanding of microbial communities, we can better understand and protect coral reefs.

Discover the benefits of using CosmosID for your research…

Looking for industry-leading Microbiome Sequencing and Analysis Services? CosmosID is the answer. Our platform provides you with microbial data insights at unprecedented levels of accuracy and speed, enabling you to make better research decisions faster than ever before.


Our optimized sequencing workflow captures a comprehensive view of your samples, providing in-depth analyses that offer valuable insight into microbial populations present within them. Plus, our advanced pipeline for sequence post-processing and microbial characterization, ensures that you have access to the best possible data.


Whether you’re researching microbial communities in coral reefs or analyzing human gut microbiomes, CosmosID has the tools to help you get the most out of your research. 


Enquire today and experience the power of CosmosID – designed with researchers like you in mind.


Barış Özdinç

Barış Özdinç analyzes microbiome research with his educational background in genetics and evolution. As a research analyst for CosmosID, he combines metagenomics and data analyses to identify microbial biomarkers in disease cohorts and evaluate microbiome research tools. His work involves curating microbiome data and creating interesting microbiome content for newsletters and blog posts. Barış Özdinç received his bachelor’s degree in genetics and master’s degree in biodiversity, evolution, and conservation from University College London (UCL). Currently, he lives in Istanbul, Turkey, where he lives with his cat, Delight, and mentors female students in their STEM career pursuits.