nov., isolated from gut of marine sandworm (Alitta virens) and emended description of the genus Alkalimarinus

A novel, Gram-stain-negative, aerobic, motile, catalase- and oxidase-negative bacterial strain, designated A2M4T, was isolated from the gut contents of a marine sandworm Alitta virens, collected from the eastern coast of the Republic of Korea. Strain A2M4T formed translucent circular colonies and showed rod-shaped cells with peritrichous flagella. Optimal growth of strain A2M4T occurred at 25 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain A2M4T was closely related to Alkalimarinus sediminis FA028T, with the highest sequence similarity of 98.9 %. The complete genome sequence of strain A2M4T was 4.25 Mbp in size and the genomic G+C content, calculated from the genome sequence, was 43.2 mol%. A comparison between the genome sequence of strain A2M4T and that of its closest relative, A. sediminis FA028T, showed an average nucleotide identity value of 76.63 % and a digital DNA-DNA hybridization value of 22.2 %. Strain A2M4T contained Q-9 as the sole respiratory isoprenoid quinone and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids of strain A2M4T were C14 : 0, C16 : 0 and summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c). Based on its phenotypic, chemotaxonomic and genomic characteristics, strain A2M4T represents a novel species of the genus Alkalimarinus, for which the name Alkalimarinus alittae sp. nov. is proposed. The type is strain A2M4T (=KCTC 92030T=JCM 35924T). The description of the genus Alkalimarinus has also been emended.

The genome sequence of the King Ragworm, Alitta virens (Sars, 1835)

We present a genome assembly from an individual Alitta virens (the King Ragworm; Annelida; Polychaeta; Phyllodocida; Nereididae). The genome sequence is 671.2 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.83 kilobases in length.

Interlaboratory Comparison of Three Sediment Bioaccumulation Tests

Standard bioaccumulation tests are commonly conducted using Macoma nasuta (clam), and Alitta virens (polychaete) for marine tests, and Lumbriculus variegatus (an oligochaete) for freshwater tests. Because the interlaboratory variability associated with these tests is unknown, four experienced laboratories conducted standard 28-day bioaccumulation tests with the above species using sediments contaminated with polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs). Chemical analysis of tissue samples was performed by a single laboratory. The intralaboratory variance among replicates was relatively low for PCB tissue concentrations, with coefficients of variation (CVs) ranging from 9% to 28% for all laboratories and species, with the exception of one laboratory reporting higher variability for L. variegatus (CV = 51%). Intralaboratory variance for PCB tissue concentrations was higher than interlaboratory variance for A. virens and L. variegatus, and the magnitude of difference (MOD) for laboratory means ranged from 1.4 to 2.0 across species. Intralaboratory variability was also low for lipid content, and lipid normalization of PCB and PAH body residues generally had little impact on variability. In addition to variability across bioassay laboratories, analytical variability was evaluated by different laboratories measuring the concentration of PCBs and total lipids in a subsample of tissue homogenate of sediment-exposed test organisms. Variability associated with tissue analysis was higher than bioassay laboratory variability only in tests with L. variegatus. Statistical differences between samples may be observed due to the low intralaboratory variability; however, the biological significance of these differences may be limited because the MOD is low. Considering the MOD when comparing bioaccumulation across treatments accounts for uncertainty related to inherent variability of the test in the interpretation of statistically significant results. Environ Toxicol Chem 2022;41:1260-1275. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Bioaccumulation in Functionally Different Species: Ongoing Input of PCBs with Sediment Deposition to Activated Carbon Remediated Bed Sediments

Activated carbon-amended bed sediments reduced total polychlorinated biphenyl (PCB) accumulation in 3 functionally different marine species, sandworms (Alitta virens), hard clams (Mercenaria mercenaria), and sheepshead minnows (Cyprinodon variegatus), during both clean and contaminated ongoing sediment inputs. Mesocosm experiments were conducted for 90 d to evaluate native, field-aged bed sediment PCBs, and ongoing input PCBs added 3 times a week. Simulated in situ remediation applied an activated carbon dose equal to the native organic carbon content that was premixed into the bed sediment for 1 mo. The highest bioaccumulation of native PCBs was in worms that remained in and directly ingested the sediment, whereas the highest bioaccumulation of the input PCBs was in fish that were exposed to the water column. When periodic PCB-contaminated sediment inputs were introduced to the water column, the activated carbon remedy had minimal effect on the input PCBs, whereas the native bed PCBs still dominated bioaccumulation in the control (no activated carbon). Therefore, remediation of only the local bedded sediment in environmental systems with ongoing contaminant inputs may have lower efficacy for fish and other pelagic and epibenthic organisms. While ongoing inputs continue to obscure remedial outcomes at contaminated sediment sites, the present study showed clear effectiveness of activated carbon amendment remediation on native PCBs despite these inputs but no remediation effectiveness for the input-associated PCBs (at least within the present study duration). Environ Toxicol Chem 2019;38:2326-2336. Published 2019 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities

Given concerns of increasing rates of species extinctions, the relationship between biodiversity and ecosystem functioning has become a major research focus over the past two decades. Many studies have shown that biodiversity per se (e.g. species richness) or species-specific traits may be good predictors of changes in ecosystem function. Although numerous studies on this subject have focused on terrestrial systems, few have evaluated benthic marine systems. We used the Limecola balthica community as a model to test whether the number or identity of three well-studied macrofaunal species influence the sediment bacterial compartment, which drives important biogeochemical processes and influence ecosystem functioning. We also investigated the poorly known role of meiofauna in the interactions between macrofauna and bacteria. Eight combinations of 0-3 species were maintained in microcosms for 34 days in the presence or absence of meiofauna. The abundance and composition of the bacterial community, defined by the relative percentage of cells with a high (HNA) vs low (LNA) nucleic acid content, were measured. Species identity of macrofauna was a better indicator of changes in the microbial compartment than was species richness per se. In particular, the gallery-diffuser behaviour of the polychaete Alitta virens likely induced strong changes in sediment physical and geochemical properties with a major impact on the bacterial compartment. Moreover, the presence of meiofauna modulated the influence of macrofauna on bacterial communities. This study provides evidence that species identity provides greater explanatory power than species richness to predict changes in the bacterial compartment. We propose that multi-compartment approaches to describe interactions amongst different size classes of organisms and their ecological roles should be further developed to improve our understanding of benthic ecosystem functioning.

Palaeoecological implications of the preservation potential of soft-bodied organisms in sediment-density flows: testing turbulent waters

Interpreting how far organisms within fossil assemblages may have been transported and if they all originated from the same location is fundamental to understanding whether they represent true palaeocommunities. In a three-factorial experimental design, we used an annular flume to generate actualistic sandy sediment-density flows that were fast (2 ms^-1) and fully turbulent in order to test the effects of flow duration, sediment concentration, and grain angularity on the states of bodily damage experienced by the freshly euthanized polychaete Alitta virens. Results identified statistically significant effects of flow duration and grain angularity. Increasing sediment concentration had a statistically significant effect with angular sediment but not with rounded sediment. Our experiments demonstrate that if soft-bodied organisms such as polychaetes were alive and then killed by a flow then they would have been capable of enduring prolonged transport in fast and turbulent flows with little damage. Dependent upon sediment concentration and grain angularity, specimens were capable of remaining intact over flow durations of between 5 and 180 min, equating to transport distances up to 21.6 km. This result has significant palaeoecological implications for fossil lagerstätten preserved in deposits of sediment-density flows because the organisms present may have been transported over substantial distances and therefore may not represent true palaeocommunities.