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Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays

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A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Marine Biology".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 26238

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Dr. Mayya Gogina

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Guest Editor

Biological Oceanography, Leibniz-Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
Interests: marine benthic ecology; species distribution modelling and habitat mapping; macrofauna communities of the Baltic Sea; biogeographic comparisons; ecosystem functioning; biological traits; bioturbation and bioirrigation; biodiversity and its response to environment, climate change and bottom trawl fishing

Dr. Judith Piontek

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Guest Editor

Biological Oceanography, Leibniz-Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
Interests: marine microbiology; structure and function of pelagic and benthic bacterial communities; microbially mediated biogeochemical processes in marine ecosystems; bacterial carbon remineralization

Special Issue Information

Dear Colleagues,

Benthic biodiversity plays an important regulatory role in marine ecosystem functioning, including the transport of energy, solutes and materials within sediments and across the sediment–water interface. Biological interactions within and between components often expose co-structure and may superimpose on the relationships between biodiversity and its abiotic drivers, potentially masking or even reversing them. Due to limited accessibility, the seafloor environment still hides many of its inhabitants and their functions from us, even in the most studied regions.

Progress made in global and regional analyses has revealed the potential controlling mechanisms of large-scale benthic biodiversity patterns. Changes in benthic communities along natural gradients have been the focus of ecological research for decades; however, with a strong bias on macrozoobenthos and biogeochemical elemental cycling. The structure and function of other organism groups living in and on sediment, including prokaryotes, protists, microphytobenthos and meiofauna, are largely understudied. Particularly, the monitoring of benthic habitats is necessary to expand our insights into the underlying mechanisms of spatial and temporal variability. Elucidating the interactions between different components of the benthic biota and parameterizing the implications of biodiversity changes for ecosystem functions along natural gradients and in response to anthropogenic disturbance remains a continuing challenge.

This Special Issue aims to explore how changes in the diversity of benthic communities, from prokaryotes to macrofauna, and the link between them impact community metabolism, biogeochemical fluxes and transport processes. Observational, experimental and modelling studies that showcase the latest developments in the field, particularly those tackling interactions between multiple biological compartments, are highly encouraged.

Dr. Mayya Gogina
Dr. Judith Piontek
Guest Editors

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Keywords

benthic organisms
biological response
ecosystems
natural gradients
anthropogenic pressures
biological interactions
macrofauna
meiofauna
protists
prokaryotes
microbial mediated biogeochemical processes
nutrient fluxes
sediment biogeochemistry

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Published Papers (12 papers)

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Research

30 pages, 3927 KiB

Open AccessArticle

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

by Mayya Gogina, Sarah Joy Hahn, Ramona Ohde, Angelika Brandt, Stefan Forster, Ingrid Kröncke, Martin Powilleit, Katharina Romoth, Moritz Sonnewald and Michael L. Zettler

Biology 2024, 13(6), 389; https://doi.org/10.3390/biology13060389 - 28 May 2024

Viewed by 1388

Abstract

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. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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33 pages, 11775 KiB

Open AccessArticle

Habitats and Biotopes in the German Baltic Sea

by Denise Marx, Agata Feldens, Svenja Papenmeier, Peter Feldens, Alexander Darr, Michael L. Zettler and Kathrin Heinicke

Biology 2024, 13(1), 6; https://doi.org/10.3390/biology13010006 - 21 Dec 2023

Cited by 2 | Viewed by 2142

Abstract

To maintain or enhance biodiversity and sea floor integrity, mapping benthic habitats is a mandatory requirement in compliance with the Marine Strategy Framework Directive (MSFD). The EU Commission Decision distinguishes between Broad Habitat Types (BHTs) and Other Habitat Types (OHTs). At the regional level, biotopes in the Baltic Sea region are classified according to the HELCOM underwater biotope and habitat classification (HUB). In this study, the habitats and their benthic communities were mapped for the entire German Baltic Sea at a high spatial resolution of 1 km. In two nature conservation areas of the Exclusive Economic Zone (EEZ) as well as selected focus areas in the coastal waters, the resolution we provide is even more detailed at 50 × 50 m. Hydroacoustic data recording and benthological surveys (using bottom grabs, underwater towing camera technology, and diver sampling) helped identify biotopes in high resolution. Based on these data, together with additional data acquired since 2010 (a total of over 7000 stations and transect sections), we were able to spatially delineate benthic biotopes and their communities via predictive habitat modelling. The results are provided as full-coverage maps each for BHT, OHT, and HUB (9 classes of BHTs, 5 classes of OHTs, and 84 classes of HUB) with a level of spatial detail that does not yet exist for the Baltic Sea, and they form an essential basis for future monitoring, status assessments, and protection and management measures. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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21 pages, 2051 KiB

Open AccessArticle

Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts

by Florian Baletaud, Gaël Lecellier, Antoine Gilbert, Laëtitia Mathon, Jean-Marie Côme, Tony Dejean, Mahé Dumas, Sylvie Fiat and Laurent Vigliola

Biology 2023, 12(11), 1446; https://doi.org/10.3390/biology12111446 - 17 Nov 2023

Cited by 3 | Viewed by 2435

Abstract

Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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19 pages, 3910 KiB

Open AccessArticle

Benthic Heterotrophic Protist Communities of the Southern Baltic Analyzed with the Help of Curated Metabarcoding Studies

by Maria Sachs, Manon Dünn and Hartmut Arndt

Biology 2023, 12(7), 1010; https://doi.org/10.3390/biology12071010 - 15 Jul 2023

Cited by 4 | Viewed by 1628

Abstract

Heterotrophic protists are key components of marine ecosystems. They act as controllers of bacterial and microphytobenthos production and contribute significantly to the carbon flux to higher trophic levels. Still, metabarcoding studies on benthic protist communities are much less frequent than for planktonic organisms. Especially in the Baltic Sea, representing the largest brackish water environment on earth, so far, no extensive metabarcoding studies have been conducted to assess the diversity of benthic protists in this unique and diverse habitat. This study aims to give first insights into the diversity of benthic protist communities in two different regions of the Baltic Sea, Fehmarnbelt, and Oderbank. Using amplicon sequencing of the 18S rDNA V9 region of over 100 individual sediment samples, we were able to show significant differences in the community composition between the two regions and to give insights into the vertical distribution of protists within the sediment (0–20 cm). The results indicate that the differences in community composition in the different regions might be explained by several abiotic factors such as salinity and water depth, but are also influenced by methodological aspects such as differences between DNA and RNA results. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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13 pages, 1145 KiB

Open AccessArticle

The Relationship between Lifespan of Marine Bivalves and Their Fatty Acids of Mitochondria Lipids

by Aleksandra Anatolyevna Istomina, Avianna Fayazovna Zhukovskaya, Andrey Nikolaevich Mazeika, Ekaterina Andreevna Barsova, Victor Pavlovich Chelomin, Marina Alexandrovna Mazur, Olesya Alexandrovna Elovskaya, Andrey Alexandrovich Mazur, Nadezda Vladimirovna Dovzhenko, Yuliya Vladimirovna Fedorets and Alexander Alexandrovich Karpenko

Biology 2023, 12(6), 837; https://doi.org/10.3390/biology12060837 - 9 Jun 2023

Cited by 3 | Viewed by 1692

Abstract

Marine bivalves belonging to the Mytilidae and Pectinidae Families were used in this research. The specific objectives of this study were: to determine the Fatty Acids (FAs) of mitochondrial gill membranes in bivalves with different lifespans, belonging to the same family, and to calculate their peroxidation index; to compare the levels of ROS generation, malondialdehyde (MDA), and protein carbonyls in the mitochondria of gills, in vitro, during the initiation of free-radical oxation; to investigate whether the FAs of mitochondria gill membranes affect the degree of their oxidative damage and the maximum lifespan of species (MLS). The qualitative membrane lipid composition was uniform in the studied marine bivalves, regardless of their MLS. In terms of the quantitative content of individual FAs, the mitochondrial lipids differed significantly. It is shown that lipid matrix membranes of the mitochondria of long-lived species are less sensitive to in vitro-initiated peroxidation compared with the medium and short-lived species. The differences in MLS are related to the peculiarities of FAs of mitochondrial membrane lipids. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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16 pages, 2817 KiB

Open AccessArticle

Substrate Heterogeneity as a Trigger for Species Diversity in Marine Benthic Assemblages

by Katharina Romoth, Alexander Darr, Svenja Papenmeier, Michael L. Zettler and Mayya Gogina

Biology 2023, 12(6), 825; https://doi.org/10.3390/biology12060825 - 6 Jun 2023

Cited by 4 | Viewed by 2169

Abstract

Many studies show that habitat complexity or habitat diversity plays a major role in biodiversity throughout different spatial scales: as structural heterogeneity increases, so does the number of available (micro-) habitats for the potential species inventory. The capability of housing species (even rare species) increases rapidly with increasing habitat heterogeneity. However, habitat complexity is not easy to measure in marine sublittoral sediments. In our study, we came up with a proposal to estimate sublittoral benthic habitat complexity using standard underwater video techniques. This tool was subsequently used to investigate the effect of habitat complexity on species richness in comparison to other environmental parameters in a marine protected area situated in the Fehmarn Belt, a narrow strait in the southwestern Baltic Sea. Our results show that species richness is significantly higher in heterogeneous substrates throughout all considered sediment types. Congruently, the presence of rare species increases with structural complexity. Our findings highlight the importance of the availability of microhabitats for benthic biodiversity as well as of the study area for regional ecosystem functioning. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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17 pages, 8220 KiB

Open AccessArticle

A Highly Diverse Olenekian Brachiopod Fauna from the Nanpanjiang Basin, South China, and Its Implications for the Early Triassic Biotic Recovery

by Huiting Wu, Yang Zhang, Anfeng Chen and Thomas L. Stubbs

Biology 2023, 12(4), 622; https://doi.org/10.3390/biology12040622 - 19 Apr 2023

Cited by 1 | Viewed by 1960

Abstract

As one of the predominant benthic organisms in the Palaeozoic, brachiopod was largely eliminated in the Permian–Triassic boundary mass extinction, and then highly diversified in the Middle Triassic. Since fossil data from the Early Triassic are rarely reported, the recovery patterns of Early Triassic brachiopods remain unclear. This study documents a well-preserved fauna that is the most diverse Olenekian brachiopod fauna so far (age constrained by conodont biostratigraphy) from the Datuguan section of ramp facies in South China. This fauna is composed of 14 species within nine genera, including six genera (Hirsutella, Sulcatinella, Paradoxothyris, Dioristella, Neoretzia and Isocrania) found in the Early Triassic for the first time and three new species, including Paradoxothyris flatus sp. nov., Hirsutella sulcata sp. nov. and Sulcatinella elongata sp. nov. The Datuguan fauna indicates that the diversity of Olenekian brachiopod fauna has been underestimated, which can be caused by a combination of reduced habitats (in geographic size and sedimentary type) compared with the end-Permian, great bed thickness making it difficult to find fossils and most species in the fauna having low abundance. Based on the faunal change in the Datuguan section and environmental changes in South China, it can be inferred that brachiopod recovery in the studied section occurred in the latest Spathian rather than the Smithian when the environment started to ameliorate. Global brachiopod data also indicates that the initial recovery of brachiopods happened in the Spathian, and many genera that widely occurred in the Middle or Late Triassic had originated in the Olenekian. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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14 pages, 1792 KiB

Open AccessArticle

Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

by Sichen Zheng, Tianshi Zhang, Kang Tu, Li Li, Zhihong Liu, Biao Wu, Liqing Zhou and Xiujun Sun

Biology 2023, 12(4), 557; https://doi.org/10.3390/biology12040557 - 6 Apr 2023

Cited by 7 | Viewed by 2171

Abstract

The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (N_e). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (H_o) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (H_e) was calculated to be varying from 0.587 to 0.700. F_st values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all F_st values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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22 pages, 5995 KiB

Open AccessArticle

Role of Macrofaunal Communities in the Vistula River Plume, the Baltic Sea—Bioturbation and Bioirrigation Potential

by Natalia Anna Miernik, Urszula Janas and Halina Kendzierska

Biology 2023, 12(2), 147; https://doi.org/10.3390/biology12020147 - 18 Jan 2023

Cited by 3 | Viewed by 1913

Abstract

Macrozoobenthos plays a key role in the transformation of inputs from rivers to the sea, such as nutrients, organic matter, or pollutants, and influences biogeochemical processes in the sediments through bioturbation and bioirrigation activity. The purpose of our study was to determine the structure of benthic communities, their bioturbation (BP_C) and bioirrigation potential (IP_C), and the vertical distribution of macrofauna in the Gulf of Gdańsk. The study revealed changes in the structure of benthic communities and, consequently, in the bioturbation and bioirrigation potential in the study area. Despite the presence of diverse and rich communities in the coastal zone, BP_C and IP_C values, although high, were formed by a few species. Both indices were formed mainly by the clam Macoma balthica and polychaetes, although the proportion of polychaetes in IP_C was higher than in BP_C. In the deepest zones, the communities became poorer until they eventually disappeared, along with all macrofaunal functions. Both indices changed similarly with distance from the Vistula River mouth, and there was a very strong correlation between them. We also demonstrated that the highest diversity of the macrofauna was observed in the upper first cm of the sediment, but the highest biomass was observed in deeper layers—at a depth of up to 6 cm, and single individuals occurred even below 10 cm. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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19 pages, 1187 KiB

Open AccessArticle

Estimating Effects of Sea Level Rise on Benthic Biodiversity and Ecosystem Functioning in a Large Meso-Tidal Coastal Lagoon

by Olivia Dixon, Johanna Gammal, Dana Clark, Joanne I. Ellis and Conrad A. Pilditch

Biology 2023, 12(1), 105; https://doi.org/10.3390/biology12010105 - 10 Jan 2023

Cited by 2 | Viewed by 2903

Abstract

Estuaries are among the world’s most productive ecosystems, but due to their geographic location, they are at the forefront of anthropogenic pressures. Sea level rise (SLR) is one major consequence of climate change that poses a threat to estuaries with extensive intertidal habitats. The ecological implications of intertidal habitat loss have been largely overlooked despite their likely significance. We aimed to address this knowledge gap by investigating how benthic macroinvertebrate communities and their contributions to ecosystem function are likely to respond to SLR. Based on a spatially extensive dataset (119 sites) from a large coastal lagoon, depth, sediment chlorophyll concentrations, mud content, and average current speed were identified as the main drivers of community compositional turnover. Shifts in benthic community structure and associated functional implications were then evaluated using depth as a proxy for SLR. Three main macrofaunal groups representing intertidal, shallow subtidal, and deep subtidal habitats were identified. Functional trait analysis indicated low functional redundancy for a key intertidal suspension-feeding bivalve (Austrovenus stutchburyi) and the lack of a shallow subtidal functional replacement should intertidal habitats become inundated. These findings strongly suggest SLR and the associated environmental changes will alter estuarine macroinvertebrate communities, with implications for future ecosystem function and resilience. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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13 pages, 1902 KiB

Open AccessArticle

Linking Species Functional Traits to Specific Biogeochemical Processes under Trawling Pressure

by Irini Tsikopoulou, Christopher J. Smith, Konstantia Nadia Papadopoulou and Melanie C. Austen

Biology 2022, 11(10), 1378; https://doi.org/10.3390/biology11101378 - 21 Sep 2022

Cited by 8 | Viewed by 1842

Abstract

The impact of otter trawling on the relationship between functional traits of benthic invertebrates and specific biogeochemical processes were investigated in the oligotrophic Cretan Sea. The fishery is managed through a seasonal closure during the summer. During two seasons (winter and summer) replicate samples were taken from the field from a commercial trawl ground and an adjacent control area. Environmental parameters related to sediment biogeochemistry were measured including particulate organic carbon, sedimentary organic carbon, bottom water and sedimentary chlorophyll a and phaeopigment concentrations as well as benthic oxygen consumption. A significant impact of trawling was recorded only for bottom water chlorophyll and sedimentary organic carbon. Furthermore, the links between species traits and specific ecosystem processes were affected by trawling, highlighting the importance of unique functional modalities on ecosystem functioning. The traits that mostly influenced benthic biogeochemistry in the control sites were related to bioturbation and burrowing activities. In contrast, in the trawled sites, the associated traits were related to more opportunistic lifestyles and deposit feeding species that do not act as bioturbators. Thus, under trawling disturbance, this shift can decouple the species-sediment relations and affect nutrient cycling. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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17 pages, 2531 KiB

Open AccessArticle

Benthic Macrofauna Community Bioirrigation Potential (BIPc): Regional Map and Utility Validation for the South-Western Baltic Sea

by Mayya Gogina, Judith Rahel Renz, Stefan Forster and Michael L. Zettler

Biology 2022, 11(7), 1085; https://doi.org/10.3390/biology11071085 - 20 Jul 2022

Cited by 5 | Viewed by 2113

Abstract

Benthic community bioirrigation potential (BIPc), an index developed to quantify the anticipated capacity of macrofauna to influence the solute exchange at the sediment–water interface, was calculated for the south-western Baltic Sea. This index can be regarded as an effect trait that is useful for predicting ecosystem processes impacted by animal burrow ventilation. The special feature, and presumably an advantage, of BIPc, compared to alternative recently developed benthic macrofauna-based bioirrigation indices, lies in its ability to distinguish the taxa-specific score values between diffusion- and advection-dominated sediment systems. The usefulness of the BIPc index was compared against the estimates of the well-established community bioturbation potential index (BPc). The BIPc index displayed a moderately but significantly stronger correlation with estimates of irrigation rates derived from tracer experiments. Using a random forest machine learning approach and a number of available relevant environmental predictor layers, we have modelled and mapped the spatial differences in this ecosystem functioning expression. The key species contributing to bioirrigation potential in the study area were identified. The interannual variation in BIPc was assessed on a small exemplary dataset. The scores required to calculate the index, that were assigned to 120 taxa dominating abundance and biomass in the region, are provided for reuse. The utility, temporal variability and uncertainty of the distribution estimate are discussed. Full article

(This article belongs to the Special Issue Benthic Biodiversity from Microbes to Multicellular Organisms and Its Functional Interplays)

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