511Microphytobenthos (MPB), consisting of benthic phototrophs such as microalgae, cyanobacteria, and dinoflagellates, is the fundament of the trophic food web in coastal ecosystems. In shallow-water environments, such as intertidal flats and estuaries, MPB represents a considerable portion of the autotrophic biomass, accounting for up to 50% of the primary production Nozais et al. 2001;Spilmont et al. 2006). MPB is the predominant food source for many deposit-feeding organisms, and the activity and distribution of MPB profoundly affect nutrient fluxes across the sediment-water interface, sediment geochemistry, as well as sediment morphology and stability (Sundbäck et al. 1991;Montagna et al. 1995;Miller et al. 1996;Stal 2010).The spatio-temporal organization of a community is a prominent issue in ecology. Levin (1992) argued that analysis of large-scale (regional) patterns must integrate effects occurring at smaller scales. Generally, the distribution of MPB is affected by both abiotic processes (e.g., nutrient availability, hydrodynamic exposure, sediment type) and biotic processes (e.g., grazing, competition) through a complex network of interactions. In their reductionist approach to benthic ecology, Miller et al. (1996) argued that studies of interactions with a direct effect on the MPB distribution (so called "isolated first-order interactions") are required to disentangle the complex relationships between the sediment bed, infaunal organisms, and the water column, and for a comprehensive picture AbstractWe describe a novel, field-deployable hyperspectral imaging system, called Hypersub, that allows noninvasive in situ mapping of the microphytobenthos (MPB) biomass distribution with a high spatial (sub-millimeter) and temporal (minutes) resolution over areas of 1 × 1 m. The biomass is derived from a log-transformed and near-infrared corrected reflectance hyperspectral index, which exhibits a linear relationship (R 2 > 0.97) with the chlorophyll a (Chl a) concentration in the euphotic zone of the sediment and depends on the sediment grain size. Deployments of the system revealed that due to factors such as sediment topography, bioturbation, and grazing, the distribution of MPB in intertidal sediments is remarkably heterogeneous, with Chl a concentrations varying laterally by up to 400% of the average value over a distance of 1 cm. Furthermore, due to tidal cycling and diel light variability, MPB concentrations in the top 1 mm of sediments are very dynamic, changing by 40-80% over a few hours due to vertical migration. We argue that the high-resolution hyperspectral imaging method overcomes the inadequate resolution of traditional methods based on sedimentary Chl a extraction, and thus helps improve our understanding of the processes that control benthic primary production in coastal sediments.

We developed a novel integrated technology for diver-operated surveying of shallow marine ecosystems. The HyperDiver system captures rich multifaceted data in each transect: hyperspectral and color imagery, topographic profiles, incident irradiance and water chemistry at a rate of 15–30 m2 per minute. From surveys in a coral reef following standard diver protocols, we show how the rich optical detail can be leveraged to generate photopigment abundance and benthic composition maps. We applied machine learning techniques, with a minor annotation effort (<2% of pixels), to automatically generate cm-scale benthic habitat maps of high taxonomic resolution and accuracy (93–97%). The ability to efficiently map benthic composition, photopigment densities and rugosity at reef scales is a compelling contribution to modernize reef monitoring. Seafloor-level hyperspectral images can be used for automated mapping, avoiding operator bias in the analysis and deliver the degree of detail necessary for standardized environmental monitoring. The technique can deliver fast, objective and economic reef survey results, making it a valuable tool for coastal managers and reef ecologists. Underwater hyperspectral surveying shares the vantage point of the high spatial and taxonomic resolution restricted to field surveys, with analytical techniques of remote sensing and provides targeted validation for aerial monitoring.

The biotic and abiotic controls on major shifts in atmospheric oxygen and the persistence of low-oxygen periods over a majority of Earth’s history remain under debate. Explanations of Earth’s stepwise pattern of oxygenation have mostly neglected the effect of changing diel illumination dynamics linked to daylength, which has increased through geological time due to Earth’s rotational deceleration caused by tidal friction. Here we used microsensor measurements and dynamic modelling of interfacial solute fluxes in cyanobacterial mats to investigate the effect of changing daylength on Precambrian benthic ecosystems. Simulated increases in daylength across Earth’s historical range boosted the diel benthic oxygen export, even when the gross photosynthetic production remained constant. This fundamental relationship between net productivity and daylength emerges from the interaction of diffusive mass transfer and diel illumination dynamics, and is amplified by metabolic regulation and microbial behaviour. We found that the resultant daylength-driven surplus organic carbon burial could have shaped the increase in atmospheric oxygen that occurred during the Great and Neoproterozoic Oxidation Events. Our suggested mechanism, which links the coinciding increases in daylength and atmospheric oxygen via enhanced net productivity, reveals a possible contribution of planetary mechanics to the evolution of Earth’s biology and geochemistry.

We report primary production and respiration of Posidonia oceanica meadows determined with the non-invasive aquatic eddy covariance technique. Oxygen fluxes were measured in late spring at an open-water meadow (300 m from shore), at a nearshore meadow (60 m from shore), and at an adjacent sand bed. Despite the oligotrophic environment, the meadows were highly productive and highly autotrophic. Net ecosystem production (54 to 119 mmol m −2 d −1) was about one-half of gross primary production. In adjacent sands, net primary production was a tenth-to a twentieth smaller (4.6 mmol m −2 d −1). Thus, P. oceanica meadows are an oasis of productivity in unproductive surroundings. During the night, dissolved oxygen was depleted in the open-water meadow. This caused a hysteresis where oxygen production in the late afternoon was greater than in the morning at the same irradiance. Therefore, for accurate measurements of diel primary production and respiration in this system, oxygen must be measured within the canopy. Generally, these measurements demonstrate that P. oceanica meadows fix substantially more organic carbon than they respire. This supports the high rate of organic carbon accumulation and export for which the ecosystem is known.