Benthic Foraminiferal-Based Ecological Indices to Monitor Coastal Habitat Health of Jobos Bay, Puerto Rico

The Jobos Bay National Estuarine Research Reserve (JBNERR) includes the largest bay on the southern coast of Puerto Rico. The reserve includes diverse habitats ranging from mangrove forests, shallow lagoons, seagrass beds, cays and coral reefs, with a broad range of environmental gradients between the populated coastal plain and the oligotrophic Caribbean Sea. As the only research reserve in the region, resource managers seek cost-effective and reliable processes to restore and promote ecosystem health in the reserve. Benthic foraminiferal assemblages are widely applied bioindicators for assessing coastal environments, notably coral reefs and seagrass ecosystems. This study evaluated the applicability of three indices, the FoRAM Index (FI), the Epiphytic FoRAM Index (FI′), and the Long vs. Short Life-Span Index (ILS), to assess bayside and reef habitats bordering three cays of Jobos Bay. Surficial sediment samples were collected in 2018 and 2019. Environmental data included sediment composition (e.g., texture, total organic content) and water quality (e.g., nutrients and pH). From a total of 57 samples, 4671 individuals were counted, representing 35 genera. Cluster analysis based on genus-level relative abundances revealed four main groups: Dominant (>10%), Common (5–10%), Occasional (1–4%), and Rare (<1%). Dominant genera included Quinqueloculina (24%) and Amphistegina (18%). Common taxa included smaller rotaliids such as Rotorbinella (6%) and miliolids such as Pyrgo (5%). Twelve genera were occasional, including Triloculina (4%) and Elphidium (3%). Tests of 16 genera occurred rarely (<1%), including agglutinated taxa such as Textularia and stress-tolerant forms like Bolivina. In total, FI values ranged from 1.3 to 9.6, FI′ from 1.9 to 9.7, and ILS from 0.5 to 30.6. Bayside samples scored generally lower compared to reef samples. In summary, foraminiferal assemblages and associated bioindices indicated that environmental conditions supported Foraminifera that host algal symbionts in the reef environments and the prevalence of macroalgae and seagrass in the bayside benthos.