Benthic meiofaunal and micro-eukaryotic inhabitation of extreme environments: Submerged caves and hydrocarbon seeps

Abstract

Benthic meiofauna and microbial eukaryotes comprise diverse taxa that influence biogeochemical cycling and food-web dynamics in aquatic ecosystems. Many inhabit “extreme” environments with steep gradients in parameters such as oxygen, salinity, and organic matter availability, serving as natural laboratories for studying community structure and resilience. This thesis integrates molecular, geochemical, and microscopy-based approaches to investigate the biodiversity, community structure, and cytology of benthic eukaryotes in two chemically stratified systems: submerged caves (Chapters 2 and 3) and hydrocarbon seeps (Chapter 4). Chapter 2 explores the community composition and ecological structuring of benthic meiofauna and microbial eukaryotes across environmental gradients in submerged cave systems of the Yucatan Peninsula and Cozumel Island, Mexico using metabarcoding analysis. Despite a large percentage of unidentified sequences, diverse protistan, metazoan, and fungal taxa were detected, spanning a range of feeding strategies, with community composition differing both between caves and within a single system. Chapter 3 focuses on benthic foraminiferal communities in submerged cave systems using traditional morphological identification and metabarcoding analysis. Living and total (i.e., dead plus living) assemblages of foraminifera in picked samples were compared using a fluorogenic probe to identify living specimens, and a non-vital stain to identify recently living individuals. Living foraminiferal assemblages were recovered in the two cave systems studied, one with anoxic to hypoxic conditions, and the other an oxygenated system. Metabarcoding of cave sediments using foraminifera-specific primers yielded coarse taxonomic resolution, highlighting the need for an improved molecular reference database. Chapter 4 examines the cellular ultrastructure of foraminifera inhabiting hydrocarbon seeps using Transmission Electron Microscopy (TEM). Two extant foraminiferal groups (monothalamids and miliolids) representing early-evolving lineages showed ultrastructural variability between species, with differing feeding strategies observed. Potential adaptations to seep conditions include lipid proliferation, extensive peroxisome-endoplasmic reticulum complexes, and abundant “empty” vacuoles. These studies offer new insights into benthic eukaryotic life in geochemically dynamic systems, highlighting community-level patterns (Chapters 2-3) and organism-level characteristics (Chapter 4). As anthropogenic stressors increasingly impact marine systems, potentially increasing the prevalence of hypoxic, acidic, and eutrophic conditions, understanding how meiofaunal and microbial communities respond will be critical for predicting ecosystem resilience and future biogeochemical change.