The research, published in the journal Microbial Ecology, was carried out by a team from the University of Padova and the National Biodiversity Future Centre in Italy. Led by Irene Gregori and corresponding author Alessandro Vezzi, the researchers sampled sediments from two salt marshes in the Venice Lagoon, a productive microtidal coastal ecosystem in the northern Adriatic. Rather than tracking the marshes across weeks or seasons, the team focused on a much finer timescale: a single summer diel cycle, with sampling at four carefully chosen moments: sunset, night, dawn and solar noon. This design allowed them to capture the most extreme short-term physicochemical oscillations that intertidal ecosystems experience, driven by the interplay of sunlight, tides and biological activity.

The physicochemical measurements confirmed just how dynamic these environments are. Temperature and dissolved oxygen concentrations showed pronounced oscillations over the sampled cycle, with oxygen levels in particular responding to the balance between photosynthetic production during daylight hours and continuous respiratory consumption around the clock. Such fluctuations are typical of productive intertidal systems, where mats of microalgae and aquatic plants flood the water with oxygen by day and leave it depleted by night. For organisms living in the sediment, these swings represent a genuine physiological challenge, because oxygen availability dictates which metabolic pathways are energetically feasible at any given moment.

To characterise the biological players, the team employed two complementary DNA-based approaches. Prokaryotic communities, encompassing bacteria and archaea, were profiled using metabarcoding of the 16S ribosomal RNA gene, a standard molecular fingerprinting technique that reveals which microbial taxa are present and in what relative abundances. Eukaryotic organisms, ranging from microscopic algae to fungi and protists, were similarly catalogued using the 18S rRNA gene. But the researchers went a step further than simple taxonomic inventories: they also applied metagenomics, sequencing the collective genomes of the prokaryotic communities to assess their functional potential, in other words, which genes and metabolic pathways the communities carried and could, in principle, deploy.

The results were striking for what they did not show. Despite the pronounced swings in temperature and dissolved oxygen, both the prokaryotic and eukaryotic communities displayed only minor shifts in taxonomic composition across the four sampling points of the diel cycle. The same microbial lineages dominated the sediments at sunset as at dawn, and the relative abundances of most taxa remained essentially unchanged from night to solar noon. In many aquatic ecosystems, particularly the open ocean, researchers have documented clear diel rhythms in microbial communities, with different taxa rising and falling in abundance as light and nutrient conditions change. The Venice Lagoon salt marsh sediments, by contrast, appear to host assemblages that simply do not need to restructure themselves on this timescale.

The metagenomic data help explain why. The prokaryotic communities proved to be functionally redundant and metabolically versatile, meaning that multiple different taxa carried out the same key processes and that individual organisms possessed a broad repertoire of metabolic capabilities. The communities were dominated by taxa involved in organic-matter degradation, the cycling of sulphur compounds, denitrification, which converts bioavailable nitrogen into gaseous forms, and sulphur-oxidising chemolithoautotrophic carbon fixation, a process in which microbes use chemical energy from oxidising sulphur compounds, rather than sunlight, to fix carbon dioxide into biomass. This functional breadth means that whatever the prevailing oxygen and temperature conditions at a given hour, some members of the community are equipped to keep the essential biogeochemical machinery running.

The authors conclude that modulating their activities, rather than undergoing compositional restructuring, is likely how these communities sustain key ecological processes relevant to carbon and nutrient cycling over the diel timescale. In practical terms, a sulphate-reducing bacterium that dominates the community at midnight, when oxygen has been exhausted, does not need to be replaced by a different species at noon; it can simply slow down or speed up its metabolic output as conditions permit. Similarly, chemolithoautotrophs that fix carbon using sulphur-derived energy can ramp up their activity when their substrates become available, without any change in who is present. Activity-level regulation is a faster and energetically cheaper strategy than community turnover, and the study suggests it is the dominant mode of short-term response in these sediments.

The findings carry broader significance for the conservation and restoration of salt marshes, which are globally threatened by anthropogenic pressures including land reclamation, pollution, nutrient loading and sea-level rise. Because restoration efforts are increasingly needed to recover the carbon sequestration capacity, water quality regulation and coastal protection that these habitats provide, understanding the stability and resilience of their microbial engines is essential. If sediment microbial communities are functionally robust in the face of strong short-term physicochemical fluctuations, this suggests a degree of intrinsic resilience that could help restored marshes establish functioning biogeochemical cycles relatively quickly. At the same time, the central role of sulphur cycling, denitrification and organic-matter degradation in these communities underscores how tightly salt marsh ecosystem services are coupled to microbial metabolism, and how disturbances that alter sediment chemistry could ripple through the entire system.

The study also highlights the value of combining fine-scale temporal sampling with functional genomics. Taxonomic metabarcoding alone might have led researchers to conclude that diel dynamics are unimportant in salt marsh sediments, but the metagenomic perspective reveals the hidden versatility that makes that stability possible. As sequencing costs continue to fall, similar integrated approaches are likely to be applied to other intertidal and coastal ecosystems, from mangrove sediments to seagrass meadows, where the same questions about short-term microbial dynamics and ecosystem function remain open. For now, the Venice Lagoon results provide a clear and somewhat reassuring message: beneath the mud, the microbial workforce keeps its composition steady through night and day, adjusting its activity to whatever the marsh throws at it, and in doing so quietly sustaining the processes on which these threatened coastal habitats depend.

Subject of Research: Diel stability of sediment microbial communities in Venice Lagoon salt marshes

Article Title: Night and day in the Salt Marshes: Sediment Microbial Communities Remain Stable Over a Summer Diel Cycle

Article References: Gregori, I., Mohamed, F., Barausse, A., Frizzo, R., Archetti, L., Martino, F., Zane, L., & Vezzi, A. (2026). Night and day in the Salt Marshes: Sediment Microbial Communities Remain Stable Over a Summer Diel Cycle. Microbial Ecology. https://doi.org/10.1007/s00248-026-02890-4

Image Credits: AI Generated

DOI: 10.1007/s00248-026-02890-4

Keywords: salt marshes, microbial ecology, metabarcoding, metagenomics, diel cycle, Venice Lagoon, biogeochemistry, sulphur cycling, denitrification, carbon sequestration, coastal ecosystems, prokaryotes