Passive concentration dynamics incorporated into the library IB2d, a two-dimensional implementation of the immersed boundary method

In this paper, we present an open-source software library that can be used to numerically simulate the advection and diffusion of a chemical concentration or heat density in a viscous fluid where a moving, elastic boundary drives the fluid and acts as a source or sink. The fully- coupled fluid-structure interaction problem of an elastic boundary in a viscous fluid is solved using Peskin’s immersed boundary method. The addition or removal of the concentration or heat density from the boundary is solved using an immersed boundary-like approach in which the concentration is spread from the immersed boundary to the fluid using a regularized delta function. The concentration or density over time is then described by the advection-diffusion equation and numerically solved. This functionality has been added to our software library, IB2d, which provides an easy-to-use immersed boundary method in two dimensions with full implementations in MATLAB and Python. We provide four examples that illustrate the usefulness of the method. A simple rubber band that resists stretching and absorbs and releases a chemical concentration is simulated as a first example. Complete convergence results are presented for this benchmark case. Three more biological examples are presented: (1) an oscillating row of cylinders, representative of an idealized appendage used for filter-feeding or sniffing, (2) an oscillating plate in a background flow is considered to study the case of heat dissipation in a vibrating leaf, and (3) a simplified model of a pulsing soft coral where carbon dioxide is taken up and oxygen is released as a byproduct from the moving tentacles. This method is applicable to a broad range of problems in the life sciences, including chemical sensing by antennae, heat dissipation in plants and other structures, the advection-diffusion of morphogens during development, filter-feeding by marine organisms, and the release of waste products from organisms in flows.

New fossil assemblages from the Early Ordovician Fezouata Biota

The Fezouata Biota (Morocco) is an exceptionally well-preserved fossil community of Early Ordovician age and although its oldest units are comparable with Burgess Shale-type localities of the Cambrian Explosion, little attention has been paid to the younger units despite potential to reveal the conditions of the Ordovician Radiation. Herein, we describe a new middle to upper Floian Fezouata locality (Taichoute) encompassing an assemblage dominated by large bivalved euarthropods and giant filter-feeding radiodonts, which were transported and preserved in concretions associated with density-flow deposits. Taichoute captures the closing of the taphonomic window that characterizes exceptional fossil preservation during the Cambrian Explosion (i.e., carbonaceous compressions) as well as the faunal transition to assemblages dominated by typical Palaeozoic taxa.

Ecological features of the accumulation of carotenoids in the Black Sea molluscs

The analysis of carotenoids of three species of bivalve filter feeding molluscs: Cerastoderma glaucum, Chamelea galina and Polititapis aureus, inhabiting the same ecotope, in the innermost part of the bay of the Sevastopol city, has been carried out. The dynamics of total carotenoid content (TCC) in these species had shown during 4 seasons of the year. The composition of carotenoids is presented in C. glaucum and P. aureus by 8 carotenoids, and Ch. galina - 11 carotenoids. However, in P. aureus, only 75% of the TCC were analyzed. The TCC of all 3 species of molluscs contained to 75% of the total (identical) carotenoids. Each species of molluscs retained their specific carotenoids. Comparative analysis of carotenoids between Black Sea mollusks and their species analogues from other regions of the World Ocean showed differences in the composition of carotenoids. Thus, changing environmental conditions of the same type of filter-feeding mollusk lead to the implementation of adaptation mechanisms in the body, as a result of which the qualitative composition of carotenoids changes.

Dataset of Oyster Virome and the Remarkable Virus Diversity in Filter-Feeding Oysters

Background:Viruses are the most abundant biological entities, and they play critical roles in entire ecosystems. Nevertheless, current knowledge about them is no more than 1% of the estimated diversity of the Earth’s virosphere. Oysters are filter-feeding molluscan bivalves and are ideal sentinels for marine virus exploration and viral ecology studies. Results: Here we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit (vOTU) contigs and 3,473 high-quality viral genomes, enabling the first comprehensive overview of viral communities in oysters. As in other marine viromes, families Siphoviridae, Podoviridae, and Myoviridae are dominant in the DOV. However, Circoviridae is the most abundant family among the high-quality genomes, indicating that oysters may be their potential hotspots. Despite performing target amplification for RNA genomes, the diversity of RNA viruses was much lower than the diversity of DNA viruses. Notably, most of the vOTUs in the DOV were previously undescribed viruses and could not be clustered with any sequences in three reference datasets. Three approaches (based on references, vOTUs, and auxiliary metabolic genes) consistently showed that host health status, location, and sampling date had potential impacts on virome structures. Conclusions: This study highlights the practicality of oysters for marine virus exploration and provides a new direction to understand the relationship between marine bivalves and the environment.

Next-generation sequencing-based Actinobacteria community associated with Callyspongia sp. from Kepulauan Seribu Marine National Park, Jakarta, Indonesia

Retnowati D, Solihin DD, Ghulamahdi M, Lestari. 2021. Next-generation sequencing-based Actinobacteria community associated with Callyspongia sp. from Kepulauan Seribu Marine National Park, Jakarta, Indonesia. Biodiversitas 22: 3702-3708. Sponges are sessile benthic filter-feeding animals, which harbor numerous microbes. The enormous community and abundance of sponge-associated actinobacteria envisage sponges as hot spots of microbes. The metagenomic approach with Next Generation Sequencing (NGS) technology was used to investigate the actinobacteria community of Callyspongia sp. collected from Kepulauan Seribu Marine National Park, Indonesia. Fourteen actinobacteria families were found associated with the sponge. Among them, Microbacteriaceae was the most dominant family. The community of actinobacteria was higher than that of the culturable method from our previous study. The research showed that a metagenomic approach using NGS technology reveals better information regarding the actinobacteria community associated with Callyspongia sp.

Interactions between Filter-Feeding Bivalves and Toxic Diatoms: Influence on the Feeding Behavior of Crassostrea gigas and Pecten maximus and on Toxin Production by Pseudo-nitzschia

Among Pseudo-nitzschia species, some produce the neurotoxin domoic acid (DA), a source of serious health problems for marine organisms. Filter-feeding organisms—e.g., bivalves feeding on toxigenic Pseudo-nitzschia spp.—are the main vector of DA in humans. However, little is known about the interactions between bivalves and Pseudo-nitzschia. In this study, we examined the interactions between two juvenile bivalve species—oyster (Crassostrea gigas) and scallop (Pecten maximus)—and two toxic Pseudo-nitzschia species—P. australis and P. fraudulenta. We characterized the influence of (1) diet composition and the Pseudo-nitzschia DA content on the feeding rates of oysters and scallops, and (2) the presence of bivalves on Pseudo-nitzschia toxin production. Both bivalve species fed on P. australis and P. fraudulenta. However, they preferentially filtered the non-toxic Isochrysis galbana compared to Pseudo-nitzschia. The presence of the most toxic P. australis species resulted in a decreased clearance rate in C. gigas. The two bivalve species accumulated DA in their tissues (up to 0.35 × 10−3 and 5.1 × 10−3 µg g−1 for C. gigas and P. maximus, respectively). Most importantly, the presence of bivalves induced an increase in the cellular DA contents of both Pseudo-nitzschia species (up to 58-fold in P. fraudulenta in the presence of C. gigas). This is the first evidence of DA production by Pseudo-nitzschia species stimulated in the presence of filter-feeding bivalves. The results of this study highlight complex interactions that can influence toxin production by Pseudo-nitzschia and accumulation in bivalves. These results will help to better understand the biotic factors that drive DA production by Pseudo-nitzschia and bivalve contamination during Pseudo-nitzschia blooms.

Semi-Intrinsic Luminescence in Marine Organisms

Light emission is widespread in the oceans, with over three quarters of all observed marine species exhibiting bioluminescence. Several organisms such as the copepod Metridia pacifica and the ostracod Vargula hilgendorfii have been proven to synthesise their luciferin and luciferase to facilitate light emission. However, many luminescent species lack the capability to do this and instead it is possible that they acquire some of the components for their luminescence through predation or filter feeding on organisms that produce luciferins or precursors to these molecules. This has resulted in many organisms using certain luciferins, such as coelenterazine, as their substrate without possessing a clear mechanism to synthesise these. This chapter will review several examples of these semi-intrinsic luminescent systems and how the substrates and enzymes can be obtained for these reactions. Moreover, it will look at why particular luciferins, such as coelenterazine, are more widespread and utilised in this manner compared to other substrates.

Effects of the Filter-Feeding Benthic Bivalve Corbicula fluminea on Plankton Community and Water Quality in Aquatic Ecosystems: A Mesocosm Study

The influence of filter-feeding bivalves on plankton communities, nutrients, and water quality in a given aquatic ecosystem is so profound that they can be considered ecosystem engineers. In a 70-day mesocosm experiment, we tested the hypothesis that Corbicula fluminea would change plankton community structure by reducing small zooplankton and large phytoplankton and improve water quality by reducing nutrients. We monitored levels of nitrogen and phosphorus, organic suspended solids (OSS), and light at the sediment surface. Within the plankton, phytoplankton biomass (as Chl a, >0.45 μm), the biomass of microphytoplankton (>20 μm), nanophytoplankton (2–20 μm), picophytoplankton (0.2–2 μm), and zooplankton were determined. Compared with the controls, C. fluminea reduced the abundance of rotifers and the biomass of phytoplankton, and picophytoplankton, thereby modifying the plankton community structure. We did not observe reductions in TN and TP concentration, but OSS concentrations were reduced, and light intensity at the sediment surface was increased as a result of the improved water transparency. Our research shows that colonization by C. fluminea may modify plankton community structure and improve water quality of eutrophic shallow lakes, shedding further light on the ecological roles of filter-feeding bivalves in aquatic ecosystems.