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Cycle 9 (2020 Deadline)

Assessment and comparison of recovery of biodiversity and carbon sequestration in Philippine mangroves among natural, replanted and naturally-recolonized mangrove stands

PI: Severino Salmo III (, University of the Philippines Diliman - Institute of Biology
U.S. Partner: Richard MacKenzie, United States Department of Agriculture/United States Forest Service
Project Dates: July 2021 - June 2023

Project Overview
9-379_Salmo mangroves
Planted mangrove sampling site in Oriental Mindoro. Photo credit: Dr. Salmo.
The capacity of mangroves to render ecosystem services depends on their spatial extent, ecosystem health, and forest development. Intact mangroves have high primary productivity that result in elevated carbon stores and provide food for mangrove-specialist fauna (e.g., crabs, shrimp). These are then fed upon by transient species that migrate into mangroves from adjacent ecosystems. When disturbed, mangroves lose/reduce their ecosystem functionality. In restored mangroves that have been replanted, the recovery of vegetation structure, productivity, carbon storage, and fauna are thought to follow a “chronosequence” where these ecosystem attributes increase with mangrove age/maturity. In the Philippines, most restoration projects have been ineffective, resulting in stunted growth and poor survival. It will take a longer period before these restored mangroves match the ecosystem attributes of an intact/healthy natural mangroves, or they can fail altogether. The recovery of naturally-recolonized abandoned fishponds may follow a similar chronosequence as replanted mangroves. Prior to fishpond creation, mangroves were clear cut and sediments excavated, resulting in total forest cover loss, massive losses of carbon stores, and reduced biodiversity. The sediments and water quality were degraded (e.g., high salinity, low dissolved oxygen). After peak productivity (approximately 25 years), fishponds are abandoned, leaving degraded conditions that can provide spaces for mangroves to colonize. As mangrove vegetation matures, carbon stores and sediment conditions also improve and may shift faunal assemblages from mangrove generalist-dominant to specialist-dominant.

This project will compare carbon sequestration, burial, sources, greenhouse gas emissions, and biodiversity among intact, replanted and mangrove-recolonized fishponds. The study will be conducted in the highly diverse Mindoro Oriental and Panay Islands, which have experienced massive mangrove losses from fishponds. Intact mangroves will be used as reference systems to examine the recovery trajectories of planted mangroves and mangrove-recolonized fishponds. Sediment samples will be tested to determine carbon source, age, and accumulation rate. Biodiversity assessments will be done using environmental DNA (eDNA) technology. The use of these approaches as a direct determinant of recovery trajectories and ecosystem services are pioneering efforts on studies of restoration ecology in Philippine mangroves.

The project will be implemented through science-community-policy linkage, in which technical research will be conducted in collaboration with community groups. Together with the U.S.-based collaborators, some undergraduate and graduate students will be trained in the assessment of carbon sequestration, carbon burial, and biodiversity across intact, replanted, and naturally-recolonized mangrove stands. Results from these technical studies will be translated into policy briefs and infographics to improve mangrove research and management at the local and national level in the Philippines. The project will facilitate proactive community engagement with fishers, youth, women, local schools, and local government officials as collaborators. The datasets generated from the project will be publicly shared online through a project-managed website. The project will encourage local government partners to institutionalize funding through a counterparting scheme and through local policy that will help sustain mangrove monitoring and management activities beyond the project’s duration.

Summary of Recent Activities

By the time the project had completed its first full year of operation and submitted its first annual report in early January 2023, the PI Dr. Salmo and his team had overcome several challenges related to procurement and permit delays, ongoing COVID-related travel and meeting restrictions, and security conditions.

Ms Elisa Gerona-Daga (PhD student and also a UP Faculty) assisted the PI in administrative and technical preparations. The project team had to be adaptive and creative in selecting sites that would not require air travel but at the same time would offer optimal field experimental conditions (primarily the presence of intact, recolonized, and planted mangroves). The project then decided to retain Mindoro and have Sorsogon (instead of Iloilo), which are both located in Luzon. Because Ms Gerona-Daga is based at the University of the Philippines Tacloban (in the Visayas), the project also added sites initially in Samar (but replaced by Ormoc City in Leyte province), which at that time had fewer travel restrictions.

Two research assistants were hired in January and February 2022: Mr. John Ryan Navidad and Ms. Camila Frances Naputo. Mr. Navidad is tasked to do the carbon analysis, while Ms. Naputo is tasked to do biodiversity. An additional laboratory assistant was hired in September 2022 to complement the project in the needed laboratory analyses. The project also engaged graduate and undergraduate students, not just from the University of the Philippines Diliman – Institute of Biology (UPD-IB), but also from other state universities and colleges (SUCs). Aside from Ms. Gerona-Daga (PhD Biology student), the project is also working with Mr. Renzo Kouji Suratos (MSc Microbiology student, UPD-IB). Ms. Gerona-Daga is studying the forest productivity, litter degradation, and physiology primarily in Ormoc but will also include Mindoro and Sorsogon sites. She received a one-meter sediment steel corer donated by Dr. Mackenzie (USFS). Mr. Suratos is assessing the microbial diversity and composition in Mindoro and Sorsogon. Three BS Biology thesis students are also working with the project with topics on litter production/decay (Ms. Precious Jacob), mollusc diversity (Ms. Jalyssa Fermo), and lichen diversity (Mr. Andre Jacques Fallaria). The UPD-IB students are complemented with the undergraduate thesis students from the Mindoro State University (MinSU) and the University of the Philippines Visayas Tacloban College (UPVTC).

On the field research side, coordination with local government units (LGU) at each site was conducted to secure sampling and export permits, a process that took some time. Preliminary site inspections were held prior to sampling in January (Sorsogon), March (Mindoro), and April (Ormoc) to confirm the presence of natural/intact, recolonized, and restored mangroves. The original sampling design and the targeted variables stated in the proposal were followed, and seven field sampling campaigns were conducted in 2022. Twenty-six plots were tagged/marked for consistent monitoring. All vegetation, sediment, and biodiversity monitoring will be conducted in these plots. The parameters measured include structure and productivity (for the vegetation), organic matter/carbon and bulk density (for the sediment), and pore water quality. In addition, the physiology and photosynthetic performance of seedlings were measured as part of dissertation of Ms. Gerona-Daga. Water samples were collected from Sorsogon and Mindoro for the eDNA metabarcoding analysis (in Okinawa, Japan). The team is already observing some interesting similarities and differences in the vegetation structure and productivity at their study sites, where more than 20 species of mangroves have already been identified.

As for sediment analysis, the 1-m samples collected from Ormoc have already been processed for bulk density and organic matter/organic carbon determination. However, the preparation and analysis of samples from the other sites has been delayed due to the lack of equipment in the institute. Samples will be sent to Medan, Indonesia, for carbon and nitrogen analyses, pending the signing of a memorandum of agreement. Another set of samples will be sent to the United States for nucleotide analysis to estimate age and determine rates of carbon sequestration.

Another element of the project involves eDNA analysis. The team has sampled eDNA in seawater samples using the 12S genetic markers (MiFish primer pair) from the Sorsogon seascape: open sea with coral reefs, coastal fringe with seagrass meadows, and coastal fringe with mangroves and seagrass. A total of 63 fish species from 33 families were detected. Twenty-four species were found in the Philippine’s list of economically important aquatic organisms as food for export while two (Oreochromis mossambicus and Acanthopagrus sivicolus, both exotic) were tagged as Vulnerable in IUCN’s Red List of Threatened Species. The team’s results serve as baseline data for the mangrove seascape of Prieto Diaz and the first obtained using this method in the Philippines. Despite some limitations, the researchers were able to demonstrate the usefulness of this technique in doing rapid fish biodiversity assessment in Philippine mangrove biodiversity that will ultimately contribute to conservation efforts.

With regard to microbial ecology, the collected surface (0-10 cm) and subsurface (10-20 cm) sediment samples were extracted using QIAGEN PowerSoil Kit. The researchers found good-quality DNA for both natural and recolonized mangrove sediments. The obtained sequences will be deposited in the MG-RAST database. Clear paired-end reads will be assembled using four assemblers – MEGAHIT, Velvet, SPAdes, and IBDA_UD – for further potential microbial functional profile analysis.

The team have a busy schedule of activities planned for 2023. Dr. Salmo and Ms. Elisa Gerona-Daga will travel to the University of Wisconsin in Milwaukee from March 21 to April 4 to do nucleotide analysis of sediment samples. They will work with staff from the university and the U.S. Forest Service to learn how to age mangrove sediment samples using the 210Pb method. Depending on availability of the eDNA sampling kits, there is also a possibility for Dr. Salmo and Ms. Camila Frances Naputo to travel to Hawaii for the training on eDNA analysis. If abstracts are accepted, the project team will also attend some international and national scientific conferences. These are the 6th Mangrove Macrobenthos and Management Meeting (MMMM) to be held in Cartagena, Colombia and the 17th Philippine Association of Marine Science (PAMS) Symposium to be held in Batangas City, Philippines. Both scientific conferences will be held in July. The third and four partners' meeting on the project will be held in April and November. One focus of the meetings will be the development and calibration of a web-based state of the mangrove monitoring and reporting form.


Gerona-Daga MEB and Salmo SG III. 2022. A systematic review of mangrove restoration studies in Southeast Asia: Challenges and opportunities for the United Nation’s Decade on Ecosystem Restoration. Frontiers in Marine Science 1865,

Kannan S, Balamurugan S, Ragavan P, Deivasigamani B, Wee AKS, Salmo SG III, Basyuni M, Kajita T. 2022. eDNA envisaged conservation of IUCN threatened taxa of the tropical mangrove ecosystems. IOP Conference Series: Earth and Environmental Science, Volume 1115, 4th International Conference on Natural Resources and Technology 29-30 August 2022 Sumatera Utara, Indonesia.

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