Mitogenome features and phylogenetic analysis of red algae, Grateloupia cornea (Rhodophyta, Halymeniales).

The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of Grateloupia cornea Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other Grateloupia species, it has a group II intron in the cox1 gene. Maximum likelihood and maximum parsimony analyses showed that G. cornea is more closely related to G. asiatica. This shows that the group II intron in the cox1 ORF present in most species of Grateloupia was present in their common ancestor, and uniquely lost in G. asiatica. The seven Grateloupia species with known mitogenome sequences remain monophyletic, with the genus Polyopes as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the cox1 intron in Rhodophyta as well as phylogenetic analysis.

Complete Mitochondrial Genome and Its Phylogenetic Position in Red Algae Fushitsunagia catenata from South Korea.

The mitogenome is an important tool in taxonomic and evolutionary studies. Only a few complete mitogenomes have been reported for red algae. Herein, we reported the complete mitochondrial genome sequence of Fushitsunagia catenata (Harvey) Filloramo, G.V. and Saunders, G.W. 2016, a monospecific genus. The genome was 25,889 bp in circumference and had a strongly biased AT of 70.4%. It consisted of 2 rRNAs, 23 tRNAs, and 24 protein-coding genes (PCGs). nad5 (1986 bp) was the largest and atp9 (231 bp) was the smallest PCG. All PCGs used ATG as an initiation codon and TAA as a termination codon, except TAG, which was the termination codon used in the sdh3, rps3, and rps11 genes. The general structure and gene content of the present findings were almost identical to those of other red algae genomes, particularly those of the Rhodymeniales order. The maximum likelihood analysis showed that F. catenata was closely related to Rhodymenia pseudopalmata. The mitochondrial genome data presented in this study will enhance our understanding of evolution in Rhodophyta species.

Long-term effects of chromium from red mud (bauxite residue) ocean dumping on the benthic environment in South Korea.

Between 1999 and 2009, 344,000 m3 of red mud was released into the red mud dumping zone in the East Sea-Byeong ocean dumping site in South Korea. This study aimed to assess the impacts before and after the 2010 red mud dumping ban. We quantified total Cr concentrations by depth from core sediment samples at the red mud dumping station and evaluated benthic communities in 2004, 2009, 2012, 2017, and 2019. At the dumping station DB-085, the Cr content in the upper layer (0-10 cm) exceeded the effect range median criteria in all study years and decreased with time. Geochemical fraction studies using sequential extraction methods from core sediment samples in 2004, 2009, and 2017 showed high ratios of non-residual fractions (anthropogenic inputs), indicating persistent potential long-term risk after the 2010 ban. Additionally, we confirmed that Thyasira tokunagai, an opportunistic and contamination-stress-resistant species, dominated the study station.

Complete Mitogenome Sequencing, Annotation, and Phylogeny of Grateloupia turuturu, a Red Alga with Intronic cox1 Gene.

The mitochondrial genome (mitogenome) is essential for identifying species and tracing genetic variation, gene patterns, and evolutionary studies. Here, the mitogenome of Grateloupia turuturu was sequenced on the Illumina sequencing platform. This circular mitogenome (28,265 bp) contains 49 genes, including three rRNAs, twenty transfer RNAs (tRNAs), and twenty-six protein-coding genes (PCGs). Nucleotide composition indicates biased AT (68.8%) content. A Group II intronic sequence was identified between two exons of the cox1 gene, and this sequence comprises an open reading frame (ORF) that encodes a hypothetical protein. The gene content, annotation, and genetic makeup are identical to those of Halymeniaceae members. The complete mitogenome sequences of the Grateloupia and Polyopes species were used in a phylogenetic analysis, which revealed that these two genera are monophyletic and that G. turuturu and G. elliptica are closely related. This newly constructed mitogenome will help us better understand the general trends in the development of cox1 introns in Halymeniaceae, as well as the evolution of red algal mitogenomes within the Rhodophyta and among diverse algal species.

Field experiments on chemical and biological changes of thin-layer oyster shells capping sediments in dense aquaculture area.

Thin-layer oyster shell capping has been proposed as a method for improving contaminated coastal environments. Field experiments were conducted to investigate the effects of oyster shell capping on nutrient concentrations, microorganisms, and macrobenthic communities. The concentration of PO4-Pin the experimental area decreased by approximately 38% more than in the control, due to phosphorus fixation of oyster shells and the presence of Proteobacteria. Ammonia-oxidizing bacteria such as the order Pirellulales (phylum Planctomycetes) were related to the low ratio of NH3-N found in dissolved inorganic nitrogen in the experimental area, indicating nitrification promotion. The reduction in annular benthic organisms observed in the experimental area indicates a decline in sediment organic matter, which could potentially mitigate eutrophication. Oyster shell capping was confirmed to be an effective material for restoring coastal sediments by improving their chemical and biological properties.

The complete sequence of the mitochondrial DNA and phylogenetic analysis of the marine red alga Grateloupia elliptica (Rhodophyta: Halymeniales).

Grateloupia elliptica (Holmes, 1896) is a red alga belonging to the order Halymeniales and phylum Rhodophyta. In this study, the complete mitochondrial DNA (mtDNA) of G. elliptica has been described. The complete circular mtDNA of G. elliptica was 28,503 bp in length, with an A + T content of 68.78%; it encoded a total of 49 genes, including 20 tRNA, three rRNA, and 26 protein-coding (CDS) genes. Phylogenetic analysis based on complete mitochondrial genomes revealed that G. elliptica was most closely related to G. angusta. The complete mitochondrial sequence of G. elliptica will enrich the mitochondrial genome database and provide useful resources for population genetics and evolution analyses.

Field-portable seawater toxicity monitoring platform using lens-free shadow imaging technology.

The accidental spill of hazardous and noxious substances (HNSs) in the ocean has serious environmental and human health consequences. Assessing the ecotoxicity of seawater exposed to various HNS is challenging due to the constant development of new HNS or mixtures, and assessment methods are also limited. Microalgae viability tests are often used among the various biological indicators for ecotoxicity testing, as they are the primary producers in aquatic ecosystems. However, since the conventional cell growth rate test measures cell viability over three to four days using manual inspection under a conventional optical microscope, it is labor- and time-intensive and prone to subjective errors. In this study, we propose a rapid and automated method to evaluate seawater ecotoxicity by quantification of the morphological changes of microalgae exposed to more than 30 HNSs. This method was further validated using conventional growth rate test results. Dunaliella tertiolecta, a microalgae species without rigid cell walls, was selected as the test organism. Its morphological changes in response to HNS exposure were measured at the single cell level using a custom-developed device that uses lens-free shadow imaging technology. The ecotoxicity evaluation induced by the morphological change could be available in as little as 5 min using the proposed method and device, and it could be effective for 20 HNSs out of 30 HNSs tested. Moreover, the test results of six selected HNSs with high marine transport volume and toxicity revealed that the sensitivity of the proposed method extends to half the maximum effective concentration (EC50) and even to the lowest observed effective concentration (LOEC). Furthermore, the average correlation index between the growth inhibition test (three to four days) and the proposed morphology changes test (5 min) for the six selected HNSs was 0.84, indicating great promise in the field of various point-of-care water quality monitoring. Thus, the proposed equipment and technology may provide a viable alternative to traditional on-site toxicity testing, and the potential of rapid morphological analysis may replace traditional growth inhibition testing.

Complete mitochondrial genome and phylogenetic analysis of the marine red alga Polyopes affinis (Rhodophyta: Halymeniales).

Polyopes affinis ((Harvey) Kawaguchi & Wang, 2002) is a red alga in the order Halymeniales of the phylum Rhodophyta. The entire mitogenome of P. affinis was sequenced and compared to related Halymeniales species. The entire circular-mitogenome is 25,988 bp long, has 27.59% GC content, and comprises 25 protein-coding genes (CDS), 23 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. In terms of gene synteny and tRNA composition, the P. affinis mitogenome differs significantly from that of P. lancifolius. Phylogenetic analysis shows P. affinis mitogenome in a branch sister to P. lancifolius, indicating a close relationship with other Halymeniales species.

Distribution and assessment of heavy metal concentrations in the East Sea-Byeong ocean dumping site, Korea.

Sediment cores were collected from three sites, the Control, Dumping, and Resting sites in the East Sea-Byeong ocean dumping site, Korea, and the enrichment and degree of accumulation of heavy metals were investigated. Further, to assess the level of heavy metal pollution and understand the potential effects of the ocean dumping activities that began in 1993, the results obtained corresponding to the different sampling sites were compared, and various criteria were employed. Indices, including the enrichment factor and the modified contamination degree, demonstrated that the sediments were contaminated with various heavy metals at different contamination levels. The results also indicated a significant upward enrichment in heavy metals, with the uppermost 0-10 cm sediment layer showing relatively high concentrations. Overall, this study confirmed that anthropogenic heavy metal contamination at the study sites, and the implementation of continuous monitoring, alongside the application of proper management tools, is recommended.

Initial environmental risk assessment of hazardous and noxious substances (HNS) spill accidents to mitigate its damages.

In this study, a system was established to perform an initial environmental risk assessment of hazardous and noxious substances (HNS) spill accidents. Initial environmental risk assessment was performed using exposure and hazard assessments. An integrated hydrodynamic and chemical fate model was used to predict HNS concentrations at harbors, taking into account local environmental conditions. To consider the worst case HNS spill accident, the spill amount of 10,000 tonnages, was used for this study. The results show that highly soluble HNS are fatal to marine organisms during the neap tide. The results were based on a hypothetical worst case HNS spill accident and, not any specific actual HNS spill accident. Nevertheless, the method and system developed in this study, which includes the physical/chemical properties of 158 priority HNS, can be readily used to perform an initial environmental risk assessment for future HNS spill accidents.

Thyasira tokunagai as an ecological indicator for the quality of sediment and benthic communities in the East Sea-Byeong, Korea.

The biomass and abundance of molluscan species were identified to evaluate the ecological quality of the surface sediment at the East Sea-Byeong ocean dumping site, Korea. To identify the dominant molluscan species, sediment samples were collected at nine selected stations during five expeditions in 2009, 2012, 2013, 2014, and 2015. In total, 16 molluscan species, including Aplacophora, Gastropoda, Bivalvia, and Scaphopoda, were observed. The bivalve Thyasira tokunagai was the dominant species, accounting for 82.6% of the total abundance of all identified species. This species was also the dominant benthic molluscan in sediments rich in organic matter and with a low manganese content. In addition, environmental variables, including sediment grain size, water depth, total organic carbon, and heavy metals, were found to be critical drivers affecting the spatial distribution of molluscan species.