Integrating benthic nematode and bacterial communities to assess spatial-temporal dynamics and ecosystem functioning in estuarine sediments

Abstract

Coastal and estuarine ecosystems are important carbon reservoirs, processes such as recycling of nutrients and degradation of pollutants, occur in soft-sediment intertidal and subtidal habitats. Benthic communities dominated by microorganisms and metazoans play a central role in mediating biogeochemical processes and energy pathways being powerful bioindicators of sediment habitat condition. Strong nematode–bacteria interconnections have been documented, with nematodes stimulating microbial activity and bacteria providing adaptive responses under stressful and low-oxygen conditions. This study aimed to investigate the spatial and temporal interactions between these communities and sediment biogeochemical conditions in the Sado Estuary (Portugal). Combining morphological and molecular approaches, it was explored how biodiversity patterns reflect environmental gradients and ecosystem functioning. Distinct ecological responses between the two biological groups were obtained. Nematode assemblages showed strong spatial and temporal variability, responding rapidly to site-specific environmental changes, whereas bacterial communities were mainly structured by spatial variability directly liked with sediment biogeochemical properties. Combining different approaches bacterial and nematode communities proved to be powerful ecological indicators capable of capturing the dynamics of macrobenthic food webs of the Sado estuary. These relationships between community composition and environmental drivers highlighted that diversity patterns of benthic communities can be integrated to better understand sediment trophic conditions and the impact on energy pathways. The co-occurrence of nematode and bacterial communities can provide a powerful framework for linking biodiversity patterns with ecosystem functioning, improving the evaluation of blue carbon restoration trajectories. The predominance of specific metabolic processes may therefore indicate environmental conditions that favour carbon retention and long-term burial. Such functional insight can contribute to improving the evaluation of blue carbon ecosystems and provide a scientific basis for the development of future predictive frameworks that combine biodiversity data, metabolic pathway analyses, and advanced modelling approaches to assess carbon sequestration potential and support restoration and conservation strategies.

Coastal and estuarine ecosystems represent important carbon reservoirs where key processes such as nutrient recycling, organic matter degradation and pollutant transformation occur in soft-sediment intertidal and subtidal habitats. These environments host complex benthic communities dominated by microorganisms and meiofauna that regulate biogeochemical processes and energy pathways. Among them, benthic bacteria and nematodes are highly sensitive to habitat conditions being powerful ecological indicators of sediment status and functioning. Their interactions have been documented, nematodes stimulate microbial activity, while bacteria provide adaptive responses to nematodes under stressful and low-oxygen conditions. This study investigated the spatial and temporal relationships between nematode assemblages, bacterial communities through different sediment biogeochemical conditions in Sado Estuary (SW cost of Portugal). Combining morphological identification of nematodes assemblages with 16S rRNA metagenomic characterization of bacterial communities, was explored how environmental variations shape biodiversity patterns and ecosystem functioning across contrasting sediment habitats. Results revealed distinct and complementary ecological responses between both groups. Nematode assemblages exhibited strong spatial and temporal variability, responding rapidly to site-specific environmental changes and shifts in trophic conditions, whereas bacterial communities were mainly structured by spatial variability due to sediment properties such as organic matter, grain size and oxygen availability. Together, these communities captured key patterns in benthic ecosystem dynamics. Nematodes reflected short-term ecological responses in line with benthic food webs dynamics, while bacterial communities provided insights into the dominant metabolic pathways driving sediment biogeochemistry. The predominance of specific microbial processes, including aerobic organic matter degradation or anaerobic sulfur-reduction pathways, revealed how environmental conditions regulate energy flow and nutrient cycling in estuarine sediments. The integration of both communities’ diversity provides a powerful framework for linking biodiversity patterns with ecosystem functioning. Combining taxonomic diversity, trophic traits and microbial metabolic pathways, develop integrative ecological framework capable of describing sediment condition and trophic state. Such integrated approaches can support the development of predictive frameworks that evaluate restoration trajectories in blue carbon ecosystems, and estimate the potential for carbon sequestration and long-term carbon burial in coastal sediments. Coupling biodiversity indicators with metabolic and biogeochemical information offers a robust pathway or improving the monitoring and management of estuarine ecosystems, enabling a more comprehensive evaluation of sediment ecological status and their role in long-term carbon storage.