Beach surface model construction: A strategy approach with structure from motion - multi-view stereo

In contrast to traditional beach profiling methods like topographic surveys and GNSS, which pose significant challenges in terms of cost and time, this research underscores the efficiency, cost-effectiveness, and simplicity of terrestrial photogrammetry employing the Structure from Motion-Multi View Stereo (SfM-MVS) method. Notably, this approach enables the utilization of commonplace devices such as smartphones for data capture. The methodology integrates a 12-megapixel camera for image acquisition, processed through Agisoft Metashape Professional software, and validated for accuracy using ground control points (GCPs) and checkpoints (CKPs) calibrated via GNSS. Findings reveal substantial disparities in positional accuracy according to the Ground Control Points distribution. The study underscores the critical role of strategically distributing GCPs and CKPs in effectively mapping coastal areas, thus affirming the potential of SfM-MVS as a powerful and accessible tool for coastal monitoring initiatives. This research contributes significantly to advancing the efficiency and accessibility of beach profile monitoring, offering invaluable insights for researchers and practitioners in coastal management and environmental conservation efforts.•A simplified beach profile modeling methodology is proposed.•The method is faster and more cost-effective than traditional surveys (RTK GNSS, lidar, RPA).•The study highlights the importance of GCP and CKP distribution in enhancing SfM-MVS accuracy for coastal mapping.

Benthic foraminifera as proxies for assessing the effects of a pier marina construction: A case study in the naturally stressed environment of the Saco da Ribeira (Flamengo Bay, SE Brazil)

Brazilian coastal areas have been exposed to various anthropic influences including physical alteration such as marina construction. To assess the impact of the pier marina construction in the Saco da Ribeira cove (Flamengo Bay, SE Brazil), sedimentological (grain size), geochemical (organic and trace elements) parameters and benthic foraminifera were analyzed on a 50-cm-long dated sediment core covering the last century. The multiproxy approach applied to a numerical hydrodynamic model shows that the circulation in the study area underwent an overall reduction (ca. 30 %) after the pier marina construction in the 1970s, promoting an increase of mud accumulation and higher concentrations of total organic carbon and trace elements (i.e., Enrichment Factor Cu from 0.80 to 1.4) as well as a shift in the benthic foraminiferal assemblages (i.e., foraminiferal density from 63 to 23.20 specimens per 10 cm3 and dominance from 0.13 to 0.73). On the basis of these integrated data, better environmental conditions occurred before the 1970s, then an overall increase in environmental stress took place after the pier's marina construction. Our results provide a baseline for future biomonitoring projects in a stressed region and exemplify the strong capability and reliability of benthic foraminifera as bioindicators of paleoenvironmental changes in coastal environments and for understanding how human pressure might induce such changes.

Machine learning sheds light on physical-chemical and biological parameters leading to Abrolhos coral reef microbialization

Microbes play a central role in coral reef health. However, the relative importance of physical-chemical and biological processes in the control of microbial biomass are unknown. Here, we applied machine learning to analyze a large dataset of biological, physical, and chemical parameters (N = 665 coral reef seawater samples) to understand the factors that modulate microbial abundance in the water of Abrolhos reefs, the largest and richest coral reefs of the Southwest Atlantic. Random Forest (RF) and Boosted Regression Tree (BRT) models indicated that hydrodynamic forcing, Dissolved Organic Carbon (DOC), and Total Nitrogen (TN) were the most important predictors of microbial abundance. The possible cumulative effects of higher temperatures, longer seawater residence time, higher nutrient concentration, and lower coral and fish biomass observed in coastal reefs resulted in higher microbial abundance, potentially impacting coral resilience against stressors.

Fluxes of the Amazon River plume nutrients and microbes into marine sponges

Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km² off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ¹³C and δ¹⁵N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.

The dynamics of plastic pellets on sandy beaches: A new methodological approach

Plastic found in the coastal zone is a result of waste mismanagement. This material comes directly from offshore disposal or by fishing debris, other marine activities, and by marine currents and winds, as well as urban drainage systems and estuaries. Specifically, in the case of plastic pellets, which are spheres with 2-5 mm that constitute the raw material for the manufacture of plastic products, the Santos Port and the plastic factories in Cubatão city (Brazilian southeastern coast), are considered the main local sources for the São Paulo state coast. Consequently, the beaches most affected by this pollutant are those near Santos estuary, like Enseada do Guarujá beach. However, some questions are still open, such as: what are the mechanisms which control the pellets deposition, and which locations are most favorable for deposition on the beach? To answer these questions, a four-step research was carried out at Enseada beach: 1) Plastic pellets geodetic survey based on GNSS positioning; 2) Beach geomorphometric parameters (altitude, aspect, and slope) derived by Digital Elevation Model (DEM); 3) Strandline altitude estimated through wave climate and tide height; and, 4) Plastic pellets deposition Suitability Index (PSI). The joint analysis of the altimetric, geomorphometric and meteoceanographic aspects showed that the beach areas with altitudes higher than those calculated for the strandline (>2.06 m), slope ~ 3° and facing the same direction of the higher energy waves (157.5-202.5°) were more susceptible to pellet deposition. This indicates that the accumulation of this pollutant on the beach is controlled not only by its physical characteristics, but mainly by storm surge events. Besides, surveys with geodetic reference (fixed, univocal, and relatively stable on time) bring up altimetric information as a result of all interactions and can be compared with other beaches anywhere on the planet - thus contributing to a standardization of the survey methodology.

Wave energy distribution at inlet channel margins as a function of ebb tidal delta morphology: Cananéia Inlet, São Paulo, Brazil

Wave energy gradients between and along the margins of inlet channels play an important role in defining the inlet margins' evolutionary processes, mainly those related to spit erosion or accretion, and inlet migration. The aim of this study is to understand the wave power distribution along the margins of a tidal inlet (Cananéia inlet, São Paulo, Brazil), its variation over time, and the influences of the ebb tidal delta morphology on the incoming waves. To evaluate changes in bathymetry and morphology of submersed features, we apply geoprocessing techniques to analyze nautical charts from the Brazilian Navy from 1939, 1971, 1985 and 2004. The numerical model MIKE21 SW was applied to assess wave propagation and nearshore wave power. Hence, wave energy levels along the inlet margins were assessed in terms of decadal morphological changes. The results indicate a dynamic behavior of the inlet and ebb tidal delta, pointing to the ebb tidal delta as the main transforming agent of the waves that reach the inner portion of the channel. The morphological changes of the ebb tidal delta over the last decades are critical to define the action of waves on the margins of the inlet.

Coastal vulnerability to wave impacts using a multi-criteria index: Santa Catarina (Brazil)

The damage of coastal infrastructure due to wave action has stimulated the need for vulnerability assessments for integrated coastal management. Vulnerability is described as the ability of people living in an area to anticipate, cope with, resist and recover from the impact produced by a coastal hazard. This study aims to develop a multi-criteria index to assess coastal vulnerability to waves. Therefore, we analyze the Santa Catarina State (southern Brazil) coastline vulnerability to the incident wave climate. The applied coastal vulnerability index (CVI) was obtained by integrating the adaptive capacity index (ACI), composed of socioeconomic and locational variables, and the susceptibility index (SI), composed of physical variables. The resulting coastal dynamics from nearshore wave processes were analyzed through numerical models and integrated with other variables in a geographic information system (GIS). The relevance of the variables to the index was obtained by the analytic hierarchy process (AHP). The variables and indices were hierarchized into five vulnerability classes and represented in the administrative sectors defined by the local State Coastal Management Plan. Based on the AHP results, the physical variables were considered more relevant than the socioeconomic and locational variables. In general, the southern portion of the state presented higher susceptibility degrees, a lower income per capita and a lower number of second residences than the northern portion. At the same time, the northern portion presented higher percentages of developed areas, which are predominantly situated along susceptible and vulnerable segments. The numerical modeling of wave propagation has a large impact on the vulnerability as a function of the higher weights assigned to the related variables by experts and the high variability of the significant wave height along the state's coastline. Our results emphasize the importance of the inclusion of physical variables, such as waves, when defining coastal management measures in coastal zones.

Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics

Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 μM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.

When time affects space: Dispersal ability and extreme weather events determine metacommunity organization in marine sediments

Community ecology has traditionally assumed that the distribution of species is mainly influenced by environmental processes. There is, however, growing evidence that environmental (habitat characteristics and biotic interactions) and spatial processes (factors that affect a local assemblage regardless of environmental conditions - typically related to dispersal and movement of species) interactively shape biological assemblages. A metacommunity, which is a set of local assemblages connected by dispersal of individuals, is spatial in nature and can be used as a straightforward approach for investigating the interactive and independent effects of both environmental and spatial processes. Here, we examined (i) how environmental and spatial processes affect the metacommunity organization of marine macroinvertebrates inhabiting the intertidal sediments of a biodiverse coastal ecosystem; (ii) whether the influence of these processes is constant through time or is affected by extreme weather events (storms); and (iii) whether the relative importance of these processes depends on the dispersal abilities of organisms. We found that macrobenthic assemblages are influenced by each of environmental and spatial variables; however, spatial processes exerted a stronger role. We also found that this influence changes through time and is modified by storms. Moreover, we observed that the influence of environmental and spatial processes varies according to the dispersal capabilities of organisms. More effective dispersers (i.e., species with planktonic larvae) are more affected by spatial processes whereas environmental variables had a stronger effect on weaker dispersers (i.e. species with low motility in larval and adult stages). These findings highlight that accounting for spatial processes and differences in species life histories is essential to improve our understanding of species distribution and coexistence patterns in intertidal soft-sediments. Furthermore, it shows that storms modify the structure of coastal assemblages. Given that the influence of spatial and environmental processes is not consistent through time, it is of utmost importance that future studies replicate sampling over different periods so the influence of temporal and stochastic factors on macrobenthic metacommunities can be better understood.

Unraveling the performance of the benthic index AMBI in a subtropical bay: The effects of data transformations and exclusion of low-reliability sites

We investigated the relationship between the AMBI index and different contamination proxies in an urbanized bay in South America (SE Brazil), and the effect of (a) abundance data transformation and (b) exclusion of low-reliability sites (high SD; low N) on the index' performance. Poor ecological quality and opportunistic species were related to an increase in contaminants concentrations and mud content. Good ecological status and sensitive species (EG I) were mainly related to increased hydrodynamics. Data transformation caused minimal changes to the overall relationships, but exclusion of low-reliability sites improved the relationship between ecological groups and contamination proxies. Our results show that AMBI is robust in detecting effects of different contaminants in the area and reinforce the importance of the index as a tool for coastal management, but local joint efforts are needed to improve and adjust local species classification in ecological groups to improve the index' performance.

Storm effects on intertidal invertebrates: increased beta diversity of few individuals and species

Climate change is predicted to lead to more extreme weather events, including changes to storm frequency, intensity and location. Yet the ecological responses to storms are incompletely understood for sandy shorelines, the globe’s longest land-ocean interface. Here we document how storms of different magnitude impacted the invertebrate assemblages on a tidal flat in Brazil. We specifically tested the relationships between wave energy and spatial heterogeneity, both for habitat properties (habitat heterogeneity) and fauna (β-diversity), predicting that larger storms redistribute sediments and hence lead to spatially less variable faunal assemblages. The sediment matrix tended to become less heterogeneous across the flat after high-energy wave events, whereas β-diversity increased after storms. This higher β-diversity was primarily driven by species losses. Significantly fewer species at a significantly lower density occurred within days to weeks after storms. Negative density and biomass responses to storm events were most prominent in crustaceans. Invertebrate assemblages appeared to recover within a short time (weeks to months) after storms, highlighting that most species typical of sedimentary shorelines are, to some degree, resilient to short-term changes in wave energy. Given that storm frequency and intensity are predicted to change in the coming decades, identifying properties that determine resilience and recovery of ecosystems constitute a research priority for sedimentary shorelines and beyond.

Circulation and suspended sediment dynamics in a tropical estuary under different morphological setting

Estuarine processes are directly related to the interaction of its forcing conditions with the local morphology. In this study we assess the implications of the opening of a new inlet on the hydrodynamics and suspended sediment concentration (SSC). A set of physical parameters have been measured in the Itanhém river estuary, a small, shallow and mangrove fringed tropical estuary in Northeastern Brazil. Field surveys have been conducted in August 2007 and January 2008, separated by an important morphological change. Our observations show that even shortening the lower estuary channel in 2 km, the inlet opening did not imply in changes in the estuarine circulation. However, SSC increased after the inlet opening. General estuarine circulation showed synodical modulation of tidal asymmetry and residual suspended sediment transport. The estuary showed flood dominance at spring tide and ebb dominance at neap tide. Although not directly changing the estuarine hydrodynamics, the morphological change resulted in an important increase in SSC. This increase might be related to a facilitated import of inner shelf sediment through a shorter channel, having important implications for the estuarine sedimentation processes.

An extensive reef system at the Amazon River mouth

Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20% of the global riverine discharge to the ocean, generating up to a 1.3 × 10(6)-km(2) plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume's eastward retroflection, conditions the existence of this extensive (~9500 km(2)) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth-ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes.

Frequency, Magnitude, and Possible Causes of Stranding and Mass-Mortality Events of the Beach Clam Tivela mactroides (Bivalvia: Veneridae)

Stranding combined with mass-mortality events of sandy-beach organisms is a frequent but little-understood phenomenon, which is generally studied based on discrete episodes. The frequency, magnitude, and possible causes of stranding and mass-mortality events of the trigonal clam Tivela mactroides were assessed based on censuses of stranded individuals, every four days from September 2007 through December 2008, in Caraguatatuba Bay, southeastern Brazil. Stranded clams were classified as dying (closed valves did not open when forced) or dead (closed valves were easily opened). Information on wave parameters and the living intertidal clam population was used to assess possible causes of stranding. This fine-scale monitoring showed that stranding occurred widely along the shore and year-round, with peaks interspersed with periods of low or no mortality. Dead clams showed higher mean density than dying individuals, but a lower mean shell length, attributed to a higher tolerance to desiccation of larger individuals. Wave height had a significant negative relationship to the density of dying individuals, presumed to be due to the accretive nature of low-energy waves: when digging out, clams would be more prone to be carried upward and unable to return; while larger waves, breaking farther from the beach and with a stronger backwash, would prevent stranding in the uppermost areas. This ecological finding highlights the need for refined temporal studies on mortality events, in order to understand them more clearly. Last, the similar size structure of stranded clams and the living population indicated that the stranded individuals are from the intertidal or shallow subtidal zone, and reinforces the ecological and behavioral components of this process, which have important ecological and socioeconomic implications for the management of this population.

BaMBa: towards the integrated management of Brazilian marine environmental data

A new open access database, Brazilian Marine Biodiversity (BaMBa) (https://marinebiodiversity.lncc.br), was developed in order to maintain large datasets from the Brazilian marine environment. Essentially, any environmental information can be added to BaMBa. Certified datasets obtained from integrated holistic studies, comprising physical-chemical parameters, -omics, microbiology, benthic and fish surveys can be deposited in the new database, enabling scientific, industrial and governmental policies and actions to be undertaken on marine resources. There is a significant number of databases, however BaMBa is the only integrated database resource both supported by a government initiative and exclusive for marine data. BaMBa is linked to the Information System on Brazilian Biodiversity (SiBBr, http://www.sibbr.gov.br/) and will offer opportunities for improved governance of marine resources and scientists' integration. Database URL: http://marinebiodiversity.lncc.br.