Benthic Macrofauna Research Articles

Rapid, detrimental response of estuarine benthic macrofauna communities to pollution by littered cigarette filters and e-liquid

Cigarette butts are amongst the most littered single-use plastics on coasts, yet their impacts on marine ecosystems, especially on a community level, are not well understood. Recently, e-cigarettes have become popular and are a novel litter item in marine habitats. Preliminary research indicates that e-liquid can harm individual organisms, but few studies have been done and none on a community level. In a mesocosm experiment, we tested the impacts of cigarette butts (0.25, 1 butt L−1) or e-liquid (1 mL L−1) on infaunal invertebrate communities using intact sediment cores. After two weeks, the abundance of polychaetes, bivalves, and gastropods was significantly reduced in mesocosms with 1 cigarette butt L−1 compared with controls. Exposure to e-liquid resulted in severe oxygen depletion (<1 mg L−1) and almost complete mortality of sediment infauna after just four days. As litter, cigarette butts and disposable e-cigarettes both pose a threat to estuarine biodiversity.

The Core of the Matter-Importance of Identification Method and Biological Replication for Benthic Marine Monitoring.

Benthic macrofauna are important and widely used biological indicators of marine ecosystems as they have limited mobility and therefore integrate the effects of local environmental stressors over time. Recently, environmental DNA (eDNA) analysis has provided a potentially more resource-efficient approach for benthic biomonitoring than traditional morphology-based methods. Several studies have compared eDNA with morphology-based monitoring, but few have compared the two approaches using the exact same sediment cores. In addition, the meiofauna and pelagic organisms obtained as 'bycatch' using eDNA have largely been disregarded from comparisons. Here, we address these shortcomings through comparative invertebrate analyses of six sediment sample replicates from each of four stations in Denmark, using eDNA metabarcoding and morphological identification. Our results revealed large variation between the six replicates for both methods and little overlap in taxon compositions between methods. While the morphological dataset was dominated by molluscs and annelids, the eDNA dataset was dominated by arthropods and annelids. Using community composition data, we found that sampling stations could be distinguished both with eDNA and morphology. Finally, we inferred expected total richness from extrapolated accumulation curves of detected taxa from each method. This indicated that eDNA metabarcoding requires less replication than morphology for maximum coverage of diversity to be reached. However, both methods required high levels of replication, and our results on taxonomic composition add to the evidence that morphological and eDNA-based methods should preferably be used as complimentary tools for marine bioassessment.

Benthic habitat mapping of the glass sponge (Vazella pourtalesii), and associated community composition on Sambro Bank, Scotian Shelf, Canada

Sponges have been identified as ecosystem engineers, providing habitat structure for many other benthic organisms, but are vulnerable to the impacts of bottom contact fishing. The Sambro Bank Sponge Conservation Area (SBSCA) protects a globally unique aggregation of the glass sponge (Vazella pourtalesii) off the east coast of Canada. Here, we present the first comprehensive, high-resolution mapping study of this site. Multispectral multibeam echosounder (MBES) mapping at three operating frequencies and benthic drop camera surveys were conducted at the SBSCA in 2022. Video data were analysed to quantify the abundance and location of V. pourtalesii and all associated benthic fauna and sediment characteristics. Using the MBES data as predictor variables, the study created a generalized linear mixed model of V. pourtalesii presence in the SBSCA, with 90.1% accuracy. Four seafloor benthoscape classes were identified from the video imagery, with statistically distinct benthic macrofaunal communities associated with each class. The study creates a baseline assessment of the current community composition and habitat characteristics of the site, which can be used for future ecological monitoring and management.

Spatial distribution and composition of benthic macro-invertebrate in upper Awash River, below and upper Ginchi town, West Shoa Zone, Ethiopia

The composition and distribution of macro-invertebrates of benthic species can be influenced by water quality. The primary objective of this study was to understand the spatial distribution and composition of macro-invertebrates of benthic nature in the upper Awash River below and above Ginchi Town. The study was carried out for a period of three months from February 2020 to April 2020, and macro-invertebrates samples were collected from three stations using Surber sampler with 500 μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\upmu$$\\end{document}m/mesh size and 25 cm × 25 cm (0.0625 m2) of sampling area coverage. The present study showed that, in the study area, there was a low density of macro-invertebrates and species richness in general with a comparative difference between the pool riffle habitats in density and family richness. And the total abundance of benthic macro-invertebrates showed a positive correlation with NO3-N, dissolved oxygen, and total phosphorus, while a negative correlation with all the other physicochemical parameters measured during the study period. Spatial and monthly variations in the diversity and richness of benthic macro-invertebrates were attributed to the effects of human action and changes in environmental factors. So, the water shade management system should be applied to control pollution factors that can affect the macro-benthic fauna community.

Seagrass space occupation efficiency is key for their role as ecosystem engineers and ecological indicators

Studies for the preservation of seagrass beds biotopes have met difficulties in establishing appropriate methods assessing their health. We tested the efficiency of space occupation by seagrasses scattered worldwide (dgrass index), which proved to be dependent on clonal growth form and morphometric plasticity. dgrass correlated with the above-ground to below-ground biomass ratio. However, the latter was misleading when high ratios resulted from low below-ground biomass. Nutrient Posphate-limitations were revealed in situations of theoretical Nitrogen-limitation. Enhanced nutrient supply benefitted seagrasses only up to a threshold after which it became detrimental. Better nurtured, healthier meadows with denser canopies increased the organic matter in the sediment and had associated greater abundances of benthic macrofauna. Hence, seagrass biotopes could benefit from moderate anthropogenic nutrient additions. However, organic matter above ≈6% and/or reduced riverine discharges (dams upstream and climate-change-related droughts) were detrimental to healthy meadows, jeopardizing ecosystem services such as macrofauna abundances and carbon sinks.

Invasive mussels reduce community bioturbation but do not affect oxygen penetration or nutrient fluxes in organic‐poor Great Lakes sediments

Abstract Invasive zebra and quagga (dreissenid) mussels have disrupted nutrient cycling and benthic macrofauna communities in the Laurentian Great Lakes and other invaded ecosystems. Dreissenids are now the dominant benthic macroinvertebrate in the Great Lakes, replacing the formerly dominant native bioturbating amphipod Diporeia spp. Dreissenids and Diporeia interact with their environment in fundamentally different ways, and the consequences of this functional shift in benthic community structure on benthic–pelagic coupling are not well understood, particularly in unproductive offshore lake regions. To determine how functional biology and benthic community structure impact sediment mixing and biogeochemistry in low particulate organic matter (POM) lake regions, we conducted a 6‐week sediment microcosm experiment with dreissenids, Diporeia and oligochaete worms—the second most common Great Lakes benthic macroinvertebrate. We found that sediment mixing rate and depth varied significantly among the taxa. Diporeia mixed sediment the deepest and strongest, followed by oligochaetes, while dreissenids did not appreciably mix sediment. Despite these differences, we found no significant variations among treatments in sediment oxygen penetration depth, sediment respiration (oxygen uptake) or nutrient dynamics. Our results suggest that dreissenids mix sediment less than native Great Lakes taxa, but that differential mixing rates may not measurably affect nutrient and oxygen dynamics in low‐POM sediments. Therefore, mussel effects in these areas may be manifested more through direct mechanisms rather than via altered sediment geochemistry.

Profile of Pangpang Bay (Banyuwangi, Indonesia) based on water, sediment type, and macrobenthic diversity

Pangpang Bay is a wetland with mangrove forests, covering an area of more than 3,000 ha, which has been designated as an Indonesian Essential Ecological Area to maintain its high floral and faunal diversity. However, land-use changes and anthropogenic pressure from surrounding areas have caused changes in its biodiversity and community structures, including those of macrobenthic fauna. This study was conducted to determine the current environmental characteristics of Pangpang Bay and their influence on indicator organisms, such as macrobenthos. Eight stations were selected based on their geographical locations, macrobenthic fauna, physicochemical parameters, heavy metal concentrations, and sediment types to represent the entire Pangpang Bay. Results revealed that Pangpang Bay was strongly influenced by the sea. There were no significant differences among the sediment characteristics at all stations, which were all mud. Polychaetes were dominant at stations with muddy characteristics. Furthermore, the physicochemical parameters of water affected macrobenthic diversity and dominance. In contrast, the concentrations of heavy metals, such as Pb, Cu, Cd, and Fe were below the threshold values at all stations. Therefore, they did not affect macrobenthic diversity.

A diversity baseline of benthic macrofauna along the northwestern slope of Cuba (Gulf of Mexico)

The Gulf of Mexico (GoM) is a unique ecosystem due to its physical characteristics, being influenced by the Mississippi River in the north and the Loop Current from the south, resulting in a gradient of organic to carbonate sediment composition from north to south. The continental slope of the northern and southwestern portions of the GoM are generally well studied; however, less is known about the southeastern GoM along the slope of Cuba. To fill this knowledge gap, sediment cores were collected in 2017 at nine stations (974–1580 m depth) to determine abiotic controls on the deep-sea benthic macrofauna community. Oceanographic data indicated a stratified water column typical of an oligotrophic ocean and no evidence of hypoxia. Sediment texture and composition indicated a west-east gradient likely determined by downslope transport of terrigenous material in the eastern part with a high proportion of carbonate in the west. Heavy metals (Cu, Hg, Pb, and Zn) at concentrations known to cause adverse benthic effects were present in the east near the city of Havana, with the macrofauna community showing characteristics indicative of environmental stress. Overall, this region supported a diverse community of macrofauna families of low abundance, typically only 1–2 animals, and high variability among replicates within stations. Rarefaction curves revealed higher biodiversity per number of individuals in the samples from Cuba compared to those from the nGoM at similar depths, though more samples would be needed to better reveal the true diversity. The major factors influencing macrofauna communities in the continental slope off northwestern Cuba are most likely the lack of organic-rich sediment and low sediment deposition rates, both of which can be attributed to the strong currents and lack of major terrigenous input, along with the regular natural disturbances which prevents domination.

How restoration engineering measures can enhance the ecological value of intertidal flats

Restoration engineering measures, such as managed realignments or building groins, modify the environmental characteristics of coastal intertidal ecosystems. Creating physical modifications that are beneficial to an intertidal system's ecology necessitates an in‐depth understanding of the relationships between the abiotic and biotic components of a given intertidal habitat. In this study, we evaluate how hydrodynamics and sediment characteristics drive the development of the benthic macrofauna community during the first 5 years following engineering measures to enhance benthic macrofauna diversity at three locations. The creation of low‐energy habitats through groins (Knuitershoek and Baalhoek) and a managed realignment dike breach (Perkpolder) led to the accumulation of fine sediments in all three impact sites. Biomass of benthic macrofauna quickly increased between 2016 and 2020, with successional processes being more important in Perkpolder, where the habitat was started completely from scratch due to a managed realignment, than at Knuitershoek or Baalhoek, where habitat conditions were improved by adding groins. In addition, the density of benthos‐eating birds, especially oystercatchers, increased at some of the modified sites. While a low‐energy habitat may harbor more diverse assemblages of benthic macrofauna than a highly dynamic one, the extremely high silt content, which is typical for low‐energy habitats, may slow benthic community development. The observed increase of biomass at our impact sites highlights the value of the interventions, while the delays in the response of the benthic macrofauna community emphasizes the need for extensive monitoring both in time and space and the identification of underlying abiotic–biotic mechanisms.

Seasonal Variability in the Influence of Coastal Aquaculture Operation on Benthic–Pelagic Coupling Processes in Shallow Aquatic Ecosystems

Coastal shellfish aquaculture can influence benthic–pelagic-coupled systems because cultured species consume phytoplankton in the water column and return the captured organic matter and nutrients to the environment as biodeposits, which fall to the seafloor, affecting local sediment characteristics and the benthic community. In 2023, we conducted monthly field surveys to characterize the relationships between shellfish aquaculture and the surrounding environment by examining a range of physical and biological variables along the benthic–pelagic gradient at multiple sampling locations in relation to their distances from the aquaculture facilities in Onagawa Bay, Japan. The abundances of benthic macrofauna were dominated by polychaetes (86.3%), followed by gastropods (4.7%), malacostracans (2.7%), ophiuroids (2.1%), and bivalves (1.5%). Both benthic biomass and biodiversity were markedly higher, but the chlorophyll-a concentration of the water column and the sediment organic matter content were significantly lower at the closest proximity to the aquaculture facilities. Although the physical presence of shellfish aquaculture may effectively enhance pelagic–benthic energy fluxes, such processes may also pose a new challenge under the influence of recent global warming, causing widespread hypoxic conditions due to increased stratification in the water column accompanied by excess organic inputs from the aquaculture.

Using macrobenthic community structure and biotic indices to assess the ecological status of Wulan Estuary, Demak, Indonesia

Abstract. Hartati R, Widianingsih W, Zainuri M, Wardianto Y. 2024. Using macrobenthic community structure and biotic indices to assess the ecological status of Wulan Estuary, Demak, Indonesia. Biodiversitas 25: 3073-3087. Estuaries provide critical habitats for species, and they are valued commercially, recreationally, and culturally. They also filter for sediments and pollutants from rivers before entering the ocean, providing cleaner waters for marine biota. This study presents a unique approach to assessing the ecological status of an estuary using microbenthic community structure and biotic indices with a case study of Wulan Estuary, Demak District, Central Java Province, Indonesia. AZTI’s Marine Biotic Index (AMBI) community structure and biotic indices were used to assess ecological quality at eleven stations and determine the marine macrobenthic fauna's sensitivity to disturbances in two periods, i.e. August 2021 and 2022. A distinct spatial and temporal variation was evident in the macrobenthic community structure, where higher species richness and density were observed in 2022, with some species being more dominant in 2022. The trophic structure analysis showed the dominance of deposit-feeding bivalves in the fine sediments during those sampling intervals. These trophic groups, however, were dispersed less uniformly in the sandy substratum. Compared to the previous year, the density of herbivorous grazers and suspension feeders was higher in 2022. It is also shown by AMBI values that Wulan Estuary belonged to the good (slightly disturbed) to the high (undisturbed) condition, along with other biotic indices, which showed an enhanced habitat quality for benthic organisms. This result revealed the comparative ecological quality of related estuary ecosystems in Indonesia.

Bioaccumulation of Cadmium and Copper in Different Areas of The Eastern Part of The Gulf of Finland

The Gulf of Finland (with the estuary of the Neva River) is located in the northeastern part of the Baltic Sea and plays a key role in the formation of biological resources and the quality of the natural environment of the entire Baltic Sea. Along with eutrophication, its ecosystem is subject to anthropogenic pollution with toxic elements, including heavy metals. In this work, we analyzed the content of cadmium and copper in bottom sediments of the Gulf of Finland and in the tissues of the dominant species of benthic macrofauna — the deposit-feeder polychaete Marenzelleria arctia and the predatory isopod Saduria entomon. Significant variability was found in the spatial distribution of these elements in both environments. The average concentrations of cadmium (0.67±0.1 mg/kg of dry matter) in bottom sediments were correspondingly two times higher, and copper (34.4±4.0 mg/ kg) 1.5 times lower than the threshold levels established for the Baltic Sea. A significantly higher content of these metals was found in the tissues of isopods than polychaetes; in some locations it is an order of magnitude higher in isopods than in polychaetes. The factor of trophic transfer of metals in the Gulf food web showed biomagnification, i. e. accumulation of metals during the transition from low-level consumers (M. arctia) to predatory consumers (S. entomon), cadmium by 3.7 times and copper by 8.7 times. Thus, both species of benthic animals have high accumulative activity in relation to cadmium and copper, which contributes to the active transport of both metals from bottom sediments to marine biota, and, ultimately, transfer to the higher levels of the food web (fish, birds and mammals).

A revision of Rhombuniopsis Haas, 1920 (Unionida, Unionidae) endemic to the ancient lakes of Yunnan, China, with descriptions of two new species

Freshwater mussels are an important component of the macrobenthic fauna but due to modern environmental pollution and destruction, the abundance of freshwater mussels has declined rapidly, and this fauna is one of the most threatened animal groups in the world. China is the country with the second highest diversity of freshwater mussels in the world. Rhombuniopsis is a genus of freshwater mussels endemic to the ancient lakes and surrounding area in Yunnan Province, China. Species in this genus are threatened with extinction and have not been recorded alive for many years. We present a revision of Rhombuniopsis based on the morphological study of the museum materials and newly collected specimens, and propose two species new to science: Rhombuniopsis linan sp. nov. and Rhombuniopsis songmeng sp. nov. The two new species are considered extinct because the lakes they inhabited were completely dried up due to human activity. We compare our recent data with the historical studies to trace the population change of the Rhombuniopsis species in different lakes. We revise the distribution and assess the conservation status for each species. The present work confirms the importance of conservation of molluscs in the ancient lakes of Yunnan and suggest that several species are already extinct.

Diversity, distribution and knowledge gaps of Polychaeta on the continental shelf of southern Namibia

This study investigated the diversity, composition and distribution patterns of polychaete macrofauna inhabiting unconsolidated sediments on the continental shelf of southern Namibia. During the austral summer of 2021, 910 Van Veen grab samples were collected from 91 sites in water depths ranging between 43 and 146 m. All benthic macrofauna (> 1 mm) were extracted, identified, enumerated and weighed. Polychaetes were the most abundant taxon, equating to 66% of total abundance and 37% of total biomass. A total of 83 712 polychaete specimens comprising 112 species, 80 genera and 33 families were collected. Several taxa identified were listed as putative cosmopolitans (19 taxa) or have known wide local distributions (10 taxa). Voucher specimens were collected for DNA barcoding to improve reference sequence libraries for the region. Hierarchical cluster analyses using both abundance and biomass data were undertaken to determine spatial distribution patterns in polychaete communities. Both datasets yielded similar results with polychaete assemblages divided into inshore and offshore communities, that were further subdivided at a local scale. Investigation of physical and chemical drivers suggested that polychaete communities in southern Namibia are structured to varying degrees by water depth, latitude, sediment composition, redox potential and organic content. Deeper stations comprised the highest diversity of polychaeta fauna. Species adapted to hypoxic conditions (e.g. Sigambra parva, Pararionospio pinnata, Diopatra cf. monroi and Nepthys cf. hombergii) dominated an area known as the mudbelt, where organically enriched silts and clays originating from the Orange River are deposited on the mid-shelf between the 40 and 120 m isobaths.

Damage assessment on the discarded macro-benthic fauna in the Italian striped venus clam (Chamelea gallina) fisheries

The striped venus clam fishery in Italy is carried out by means of hydraulic dredges and it is one of the most important socio- economic activities in the Italian fisheries sector. Dredging has traditionally been considered among fishing activities with the greatest impact at the ecosystem level. Here, therefore, we investigated the disturbance level exerted by dredging on the studied area. Also, damage and mortality rates exerted by dredging on the discarded macro-benthic fauna living associated with Chamelea gallina during the summer season were investigated using a four-level damage scale, given three different haul time duration (3, 6 and 9 minutes). Despite the fact that macro-benthic fauna represented on average only 4.4% of the total catch, the most represented taxa in terms of both abundance and number were Malacostraca, Bivalvia, and Echinoidea. The analysis of the macro-benthic communities’ structure between hauls revealed that the species composition was very similar, and ABC plots together with the Warwick Statistics (W) revealed a moderately disturbed macro-benthic community. No significant difference was found in damage and mortality rates between hauls duration when stratified at taxon or species level. Overall, 61.0% of individuals of the catch were undamaged, whereas 16.1%, 3.7%, and 19.2% displayed slight, intermediate, and severe damage, respectively. We found that soft-shelled or soft-bodied species were the most affected by the harvesting process, whereas thick-shelled or thick-bodied species suffered the slightest damage. In particular, the species suffering major (severe) damage were the sea urchin Echinocardium cordatum (84.6%), the bivalves Mactra stultorum and Polititapes aureus (32.5% and 20.0%, respectively), the crab Liocarcinus vernalis (4.0%), and the sea star Astropecten irregularis (4.8%). The overall mortality rate of all discarded individuals was 22.9%, with E. cordatum showing the highest mortality rate of 96.0%. These findings highlight the importance of guaranteeing the integrity of the entire ecosystem through the adoption of suitable management plans and actions.

What has Changed in 20 Years? Structure and Function of Soft-sediment Macrofauna in a Subarctic Embayment, Newfoundland (Canada)

Understanding how natural and anthropogenic disturbances affect the structure and functioning of marine ecosystems is central to predicting future dynamics. Placentia Bay is an Ecologically and Biologically Significant Area (EBSA) in the North Atlantic exposed to multiple stressors (e.g., rising sea surface temperatures, tanker traffic, and aquaculture). To investigate changes in the community and functional structure of soft-sediment macrofauna as well as environmental drivers of observed variation, we compared contemporary (2019–2020) and historical (1998) samples at eight stations (n = 77) collected 21 years apart. Although community and functional structure differed between these time points, functional traits were maintained (i.e., no loss of 36 trait modalities). Overall, 37% of species/taxa were only observed in either the historical or contemporary community, and the contemporary community exhibited lower macrofaunal density but had similar richness, resulting in higher evenness and diversity. Highly tolerant subsurface deposit feeders having small body sizes (< 10 mm) and direct development dominated the historical community. The contemporary community had nearly equal proportions of surface and subsurface deposit feeders with small to medium body sizes (< 10–50 mm) with pelagic larvae, and the proportion of highly tolerant species/taxa was reduced. These changes likely reflect the reduction in polychaetes (91 vs. 58%) and increased bivalves (4 vs. 25%) relative to the historical time point. Community variation was driven by changes in the sedimentary habitat. Contemporary versus historical sediments were ~ 4.5x coarser (possibly due to storms) with higher levels of sedimentary organic matter. This work contributes to advancing the understanding of relationships between benthic macrofauna, functional traits, and the sedimentary habitat in coastal environments.

Habitat Provision Differs Across Subtidal Reefs Varying in Location Within the Estuarine Landscape

Although position within the estuarine landscape is known to influence structural characteristics and ecological functioning of many habitats, the influence of position on subtidal oyster reef characteristics and functioning is relatively understudied. This study assessed habitat provision by oysters and benthic macrofauna on subtidal bar and patch oyster reefs within the northwestern Gulf of Mexico estuary. Bar reefs had greater and more variable oyster density, biomass, and volume, as well as dead shell material, compared to patch reefs. Benthic macrofaunal community composition differed between reef types, with bar reefs hosting 11× and 30× higher biomass of Porcellanidae and Ampithoidae crustaceans, and patch reefs supporting 34× and 47× higher biomass of Eunicidae annelids and Leptocheliidae crustaceans. The environmental variables most highly correlated with macrofaunal communities on both bar and patch reefs were sediment chlorophyll-a, volume of dead oyster shells, and depth. Despite differences in structural characteristics and position within the estuarine landscape, subtidal oyster reefs are often managed as a single habitat type. Our findings emphasize the importance of considering location in oyster reef conservation and restoration efforts to better predict and optimize faunal provision outcomes.

Biodiversity and functioning of benthic macrofauna associated with natural and artificial hard substrate in the Gulf of Gdańsk (Baltic sea)

Biodiversity and functioning of benthic macrofauna associated with natural and artificial hard substrate in the Gulf of Gdańsk (Baltic sea)

Functional diversity of benthic macrofauna during and after an el niño event in a subtropical estuary

Bioturbation promoted by benthic macrofauna impacts the biogeochemical processes in the sediment and water column, being an important process in estuaries, which are depositional ecosystems of high ecological importance. Functional diversity provides clear connections between biota and environmental variables, enabling researchers to comprehend the structure and functioning of ecosystems. The functional approach is still an emerging field of studies for estuaries, especially in the context of weather events such as the ENSO – El Niño. We investigated the functional diversity on a sandflat in the Patos Lagoon Estuary, regarding the bioturbation related traits of the benthic macrofauna, during and following the 2002/2003 El Niño event. Our study evidenced that the decrease in salinity caused by the high precipitation during the El Niño was the most influential factor affecting the functional diversity of the macrofauna. This led to assemblages with less potential for bioturbation, decreased stability, and higher prevalence of opportunistic traits. We also found that despite using bioturbation related traits for our analysis, the proportions of sand, silt, and clay in the sediment were not the main drivers of changes in the functional indices or trait composition, presenting less influence than the seasonal variation of temperature.

Baseline Inventory of Benthic Macrofauna in German Marine Protected Areas (2020-2022) before Closure for Bottom-Contact Fishing.

The response of benthic habitats and organisms to bottom-contact fishing intensity is investigated in marine protected areas (MPAs) of the German EEZ in the North and Baltic Seas. We examined the current state of macrofauna biodiversity in 2020-2022. Comparative analysis for macrofauna (in- and epifauna) inhabiting nine Natura 2000 MPAs constitutes a baseline to assess the effects of bottom-contact fishing exclusion in the future. Aspects of spatial and temporal variability are briefly summarized and discussed. We provide a species list for each region, including 481 taxa, of which 79 were found in both regions, 183 only in the North Sea, and 219 only in the Baltic Sea. The Baltic Sea dataset surprisingly included higher numbers of taxa and revealed more Red List species. The share of major taxonomic groups (polychaetes, bivalves and amphipods) in species richness showed peculiar commonalities between the two regions. In the North Sea, multivariate analysis of community structure revealed significantly higher within-similarity and stronger separation between the considered MPAs compared to the Baltic MPAs. Salinity, temperature and sediment fractions of sand were responsible for over 60% of the variation in the North Sea macrofauna occurrence data. Salinity, mud fraction and bottom-contact fishing were the most important drivers in the Baltic Sea and, together with other considered environmental drivers, were responsible for 53% of the variation. This study identifies aspects of macrofauna occurrence that may be used to assess (causes of) future changes.