Biodiversity & biogeography of protists in coastal ecosystems across indonesia
Microbial eukaryotes, otherwise known as protists, exhibit an immense range of morphological and ecological diversity and are ubiquitous in the world's oceans. In these environments these organisms play important roles in biogeochemical cycling as primary producers and consumers throughout the microbial food web.
In recent decades, expeditions like Tara Oceans and Malaspina have greatly increased our understanding of the composition and structure of these communities on a global scale. However, the data available on these communities in the Indo-Pacific was largely limited to visual surveys, which vastly underestimate the diversity in these communities.
As a PhD student in Dr. Christopher Lane's lab at the University of Rhode Island, in collaboration with Dr. Austin Humphries lab also at URI and Dr. Hawis Madduppa's lab at Institut Pertanian Bogor, we used metabarcoding to characterize protist communities across Indonesia with sites specifically ranging from the Pacific to the Indian Ocean. Below is a summary of our work and publications resulting from this projects.
WHERE WE SAMPLED
From July 2018 - May 2019, we sampled a total of 70 sites across 4 sampling regions:
Lombok, Wakatobi, Misool, and Waigeo
What we did
Water collected at 5m depth and surface sediment collected at 10m by SCUBA at each site
Samples filtered with peristaltic pump over 2 filter sizes
Filters split in half and preserved in DNA RNA shield (Zymo Research)
V9 hypervariable region of 18S rDNA amplified by PCR using same primers as Tara Oceans
Amplicons sequenced on Illumina MiSeq
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What we found
RUBBLE FIELDS SHAPE PLANKTONIC PROTIST COMMUNITIES ON A LOCAL SCALE
E.M. Borbee, I. P. Ayu, P. Carvalho, F. Setiawan, E. Restiana, B. Subhan, A.T. Humphries, H. Madduppa, & C.E. Lane
Journal of Eukaryotic Microbiology, e12954
The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fields of coral rubble. While the impacts of disturbances in these ecosystems are well documented on metazoans, we have a poor understanding of their impact on microbial communities at the base of the food web. We use metabarcoding to characterize protist community composition in sites of varying fisheries management schemes and benthic profiles across the island of Lombok, Indonesia. Our study shows that rubble coverage and net primary productivity are the strongest explainers of variation in protist communities across Lombok. More specifically, rubble fields are characterized by increases in small heterotrophic protists, including ciliates and cercozoans. In addition to shifts in heterotrophic protist communities, we also observed increases in diatom relative abundance in rubble fields, which corresponded to sites with higher net primary productivity. These results are the first to characterize protist communities in tropical marine rubble fields and provide insight on environmental factors potentially driving these shifts on a local scale.
SURFACE CURRENTS SHAPE PROTIST COMMUNITY STRUCTURE ACROSS THE INDO-PACIFIC
E.M. Borbee, I. P. Ayu, F. Setiawan, E. Restiana, B. Subhan, A.T. Humphries, H. Madduppa, & C.E. Lane
Journal of Phycology, 2024;00:1-18
Biogeographic structure in marine protist communities is shaped by a combination of dispersal potential and environmental selection. High-throughput sequencing and global sampling efforts have helped better resolve the composition and functions of these communities in the world's oceans using both
molecular and visual methods. However, molecular barcoding data are critically lacking across the Indo-Pacific, a region widely considered the epicenter
of marine biodiversity. To fill this gap, we characterized protist communities in four sampling regions across Indonesia that represent the latitudinal, longitudinal, and human population gradients of the region: Lombok, Wakatobi, Misool, and Waigeo. We show high spatial structuring in marine protist communities across Indonesia, and biotic factors appear to play little role in driving this observed structure. Our results appear to be driven by abiotic factors linked to surface current patterns across the Indo-Pacific as a result of: (1) a choke point in circulation at the Indonesian Throughflow leading to low diatom diversity in Lombok, Wakatobi, and Misool; (2) an increase in nutrient availability at the edge of the Halmahera Eddy in Waigeo, leading to an increase in diatom diversity; and/or (3) seasonal variations in protist communities in line with shifts in velocity of the Indonesian Throughflow. Overall, our results highlight the importance of abiotic factors in shaping protist communities on broad geographic scales over biotic, top-down pressures, such as grazing from higher trophic levels.
