Coastal Sediment Samples Research Articles

The Antibacterial Efficacy of a Compound Extracted from Marine Sediment Bacterium Enterococcus Lactis (S-2): A Comparative Analysis Through In-Vitro and In-Silico Assessments.

Marine sediment bacteria have been generating considerable attention lately due to their potential as valuable reservoirs of novel antimicrobial agents. In vitro and in silico antibacterial activities of antibacterial compounds isolated from the marine sediment bacterium Enterococcus Lactis (S-2). Coastal sediment samples were collected from Rameswaram, Ramnathapuram District, Tamil Nadu, India. Bacteria were isolated using the crowded plate method, and their phenotypic and genotypic characteristics were studied. Purified bacteria were cultured in large volumes, secondary metabolites were extracted, and novel antibacterial agents were isolated from the aqueous extract. Novel compound antibacterial activity was studied through in-silico and invitro. The mechanism activity of antibacterial activity was confirmed by a high-resolution transmission electron microscope. Genotypic analysis confirmed that the isolated S-2 bacteria were Enterococcus lactis, and the aqueous extract showed antibacterial activity against Staphylococcus aureus (17 mm zone of inhibition) and Proteus mirabilis (12 mm zone of inhibition). A bioactive molecule, 13- hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4dioxapentacyclo[10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa- 1(20),5,7,12,14(19), 16-hexane-18-one, was isolated from aqueous extracts of the S-2 bacterium. Chromatography and spectroscopic analysis confirmed the identity of the isolated compound. Novel compound potential antibacterial activity showing against S. aureus (18 mm zone of inhibition) and MIC 250 μg/mL, which was confirmed by tetrazolium staining. The antibacterial activity mechanism was confirmed by transmission electron microscopy. Molecular docking studies show good binding (-9.9 kcal/mol) of the compound with 3U2D, while molecular dynamic simulation studies confirm the conformationally stable structure of the complex between 3U2D and 13-hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4-dioxapentacyclo [10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa-1(20),5,7,12,14(19), 16-hexane-18-one. It has been observed from the docking study of 3U2D with standard drug ciprofloxacin that the lower affinity is compared to the test ligand, which has a docking score of 7.3 kcal/mol. Out of interacting residues of protein 3U2D residue, Thr173 and Ile86 formed conventional hydrogen bonds. Marine bacterium E. lactis produces a novel antibacterial compound (13-hydroxy- 9-(1-hydroxyethyl)-11-methoxy-2,4-dioxapentacyclo[10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa- 1(20),5,7,12,14(19),16-hexane-18-one), which shows antibacterial activity against clinical S. aureus, confirmed by in vitro and in silico analysis. This molecule can used as a lead molecule for antibacterial activity.

Environmental health risk of brine disposal for reverse osmosis water desalination plants: A case study in Bandar Abbas city, Iran

Reverse osmosis desalination brine (RODB) is a concentrated by-product containing higher salinity and turbidity and chemicals added to the raw water. As the RODB discharge has caused many environmental concerns, this case-control study investigated the (RODB) impact on the coastal environment. Five RODB Receiving beaches and one control point were selected, 84 samples of RODB, seawater, and coastal sediments were taken then chemical, physical, and biological parameters were measured. As well as environmental risk was assessed. The seawater salinity and turbidity on the RODB-receiving beaches were higher than the control point, and the population and diversity of plankton were lower. The content of some heavy metals was higher in the sediments affected by RODB. Low to moderate degrees of heavy metal-related environmental threat was calculated. The discharge of RODB leads to changes in the coastal ecosystem quality and can be an environmental hazard, therefore, it requires serious monitoring and control programs.

Lutimonas zeaxanthinifaciens sp. nov., a zeaxanthin-producing marine bacterium isolated from coastal sediment.

A Gram-stain-negative, yellow-pigmented, strictly aerobic, non-flagellated, motile by gliding, rod-shaped bacterium, designated strain YSD2104T, was isolated from a coastal sediment sample collected from the southeastern part of the Yellow Sea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain YSD2104T was closely related to three type strains, Lutimonas vermicola IMCC1616T (97.4 %), Lutimonas saemankumensis SMK-142T (96.9 %), and Lutimonas halocynthiae RSS3-C1T (96.8 %). Strain YSD2104T has a single circular chromosome of 3.54 Mbp with a DNA G+C content of 38.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain YSD2104T and the three type strains (L. vermicola IMCC1616 T, L. saemankumensis SMK-142T, and L. halocynthiae RSS3-C1T) were 74.0, 86.2 and 73.6 %, and 17.9, 30.3 and 17.8 %, respectively. Growth was observed at 20-30 °C (optimum, 30 °C), at pH 6.5-8.5 (optimum, pH 7.0), and with NaCl concentrations of 1.5-3.5 % (optimum, 2.5 %). The major carotenoid was zeaxanthin, and flexirubin-type pigment was not produced. The major respiratory quinone was menaquinone-6. The major fatty acids (>10 %) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), and summed feature 9 (iso-C17 : 1 ω9c and/or 10-methyl C16 : 0). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids, and eight unidentified lipids. Conclusively, based on this polyphasic approach, we classified strain YSD2104T (=KCTC 102008T=JCM 36287T) as representing a novel species of the genus Lutimonas and proposed the name Lutimonas zeaxanthinifaciens sp. nov.

Non-negligible contribution from coastal erosion to sedimentation around the archipelago: A case study of Miaodao Archipelago

The Miaodao Archipelago, located in the southern Bohai Strait, serves as a major route for the exchange of energy and materials between the Yellow and Bohai seas and is distinguished by a complicated hydrodynamic environment and provenance. Based on the grain size and elemental data of 107 surface sediment samples from the archipelago waters, and 58 coastal erosional sediment and bedrock samples, this study investigated the factors influencing the geochemical elemental distribution, discusses the provenance of the surface sediments and relative contributions, as well as proposes a sediment source–sink model for the region. The distribution of major and trace elements in the surface sediments, typically characterized by “high in the north, low in the south” patterning (except for SiO2, Ba, and Sr), with their contents primarily controlled by the input of terrestrial materials. The surface sediments in the study area are separated into the geochemical subdivisions of north and south. The main provenances of the study area include the Yellow River, the nearshore Miaodao Archipelago, and the north side of nearshore Penglai, whose sediments were transported under the combined action of the Shandong Peninsula's tidal current, waves, and longshore current. Deposition occurred under the capturing action of the archipelago. The relative contributions of the three provenance areas were 74.7%, 15.5%, and 9.8%, respectively; the relative contribution of coastal erosion reaches 1/3 of the river. Studies have demonstrated that the contribution of coastal erosion provenances to sea surface sediments is non-negligible, and in fact, it may even be quite important; thus, in the context of decreasing riverine inputs to the sea and enhanced coastal erosion processes, the contribution of coastal erosion requires special attention.

Metagenomics reveals the influence of small microplastics on microbial communities in coastal sediments

The ecological impact of microplastics (MPs) in coastal environments has been widely studied. However, the influence of small microplastics in the actual environment is often overlooked due to measurement challenges. In this study, Hangzhou Bay (HZB), China, was selected as our study area. High-throughput metagenomic sequencing and micro-Raman spectrometry were employed to analyze the microbial communities and microplastics of coastal sediment samples, respectively. We aimed to explore the ecological impact of MPs with small sizes (≤ 100 μm) in real coastal sediment environments. Our results revealed that as microplastic size decreased, the environmental behavior of MPs underwent alterations. In the coastal sediments, no significant correlations were observed between the detected MPs and the whole microbial communities, but small MPs posed potential hazards to eukaryotic communities. Moreover, these small MPs were more prone to microbial degradation and significantly affected carbon metabolism in the habitat. This study is the first to reveal the comprehensive impact of small MPs on microbial communities in a real coastal sediment environment.

Co-occurrence of toxic metals, bacterial communities and metal resistance genes in coastal sediments from Bohai bay

Sediment heavy metal contamination poses substantial risks to microbial community composition and functional gene distribution. Bohai Bay (BHB), the second-largest bay in the Bohai Sea, is subject to severe anthropogenic pollution. However, to date, there have been no studies conducted to evaluate the distribution of metal resistance genes (MRGs) and bacterial communities in the coastal sediments of BHB. In this study, we employed high-throughput sequencing based on 16S rRNA genes and real-time quantitative PCR (qPCR) to provide a comprehensive view of toxic metals, MRGs, and bacterial communities in BHB's coastal sediment samples across two seasons. We detected high levels of Cd in the summer samples and As in the autumn samples. The metal content in most autumn samples and all summer samples, based on ecological indices, indicated low ecological risk. Proteobacteria dominated all samples, followed by Desulfobacterota, Bacteroidota and Campilobacterota. Bacterial community variability was higher between autumn sampling sites but more stable in summer. We detected 9 MRG subtypes in all samples, with abundances ranging from 4.58 × 10−1 to 2.25 copies/16S rRNA copies. arsB exhibited the highest relative abundance, followed by acr3, czcA and arrA. The efflux mechanism is a common mechanism for sediment resistance to metal stress in Bohai Bay. Procrustes analysis indicated that bacterial community composition may be a determinant of MRGs composition in BHB sediments. Network analysis suggested that eight classes could be potential hosts for six MRGs. However, this type of correlation requires further validation. To summarize, our study offers preliminary insights into bacterial community and MRG distribution patterns in heavy metal-exposed sediments, laying the groundwork for understanding microbial community adaptations in multi-metal polluted environments and supporting ecological restoration efforts.

A holistic approach on the impact of microplastic discharge from WWTPs to the neighboring environment in Southeast Spain

The present study investigated the release of microplastics (MPs) from wastewater treatment plants (WWTPs) to the neighboring environment, including marine and coastal sediments, and fish. Here, we comprehensively investigated MP abundance in 34 samples of marine sediment, corresponding to 5,530.5 g of sediment (d.w.) collected at –8.0 m, –12.5 m, and –24.0 m, 69 samples of coastal sediment, accounting for 13,617.4 g (d.w.) from 17 different beaches from Mar Menor, and stomach and intestine of 17 fish samples of Sparus aurata, in the vicinity of Cartagena, a port city in Southeast Spain. The results showed that MPs were detected in all marine sediment samples, with an average abundance of 19.4 ± 2.4 items/kg (d.w.), in coastal sediments, with an average abundance of 52.5 ± 5.3 items/kg (d.w.), and fish samples, with an average of 8.2 ± 1.4 items per individual. The contribution of MPs from WWTPs to marine sediments is expected to be slow, as effluents were mostly dominated by fiber and film shapes, and by polymers less dense than seawater. There were no significant variations in the MP abundance of marine sediments after the atmospheric phenomenon named DANA, although a significant smaller MP size was reported, indicating a high mobility for tiny sizes. The same results were revealed for coastal sediment, although variations after DANA were statistically significant. Coastal sediment samples closer to WWTPs and agricultural fields with plastic mulching displayed higher MP concentrations, and an increase in the removal rate of MPs from WWTP effluents was negatively correlated with a decrease in MPs from fish collected. This study highlights the importance of sewage treatment plants in transporting MPs to the aquatic and terrestrial surrounding environment, which warrants further research on human health risks associated to MP pollution.

Description of Flavimaribacter sediminis gen. nov., sp. nov., a New Member of the Family Rhizobiaceae Isolated from Marine Sediment.

A novel Gram-staining-negative, aerobic and rod-shaped bacterium, designated WL0058T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51' 13″ E, 32° 6' 26″ N) in October 2020. Strain WL0058T was found to grow at 4-37°C (optimum, 28°C) with 1.5-4.0% NaCl (optimum, 4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0-10.0 (optimum, pH 6.0). Phylogenetic trees constructed based on 16S rRNA gene sequence indicated that strain WL0058T is a member of the family Rhizobiaceae, shared the highest similarity with "Hoeflea prorocentri" CCTCC AB 2016294T (97.7%) and constituted a sub-cluster within the family with it, while the similarity with others in the family Rhizobiaceae was lower than 97.0%. The G + C content of genomic DNA was 59.5mol%. Polar lipids profile of strain WL0058T included phosphatidylcholine (PC), phosphatidylethanolamine (PE), and glycolipid (GL), phosphatidylmonomethylethanolamine (PME) and two unidentified polar lipids (L). The major isoprenoid quinone was determined to be Q-10 and the major fatty acids were C16:0, C18:0, summed features 4 (iso-C17:1 and/or anteiso-C17:1), and summed features 8 (C18:1ω6c and/or C18:1ω7c). As inferred from the morphology, physiology, and biochemical analysis, genotypic characteristics, and the phylogenetic trees, strain WL0058T ought to be recognized as a novel genus in the family Rhizobiaceae, for which the name Flavimaribacter sediminis gen. nov., sp. nov. The type strain of Flavimaribacter sediminis gen. nov., sp. nov. is WL0058T (= MCCC 1K06063T = JCM 34659T = GDMCC 1.2448T).

Microbial Dimethylsulfoniopropionate Cycling in Deep Sediment of the Mariana Trench.

Dimethylsulfoniopropionate (DMSP) and related organic sulfur compounds play key roles in global sulfur cycling. Bacteria have been found to be important DMSP producers in seawater and surface sediments of the aphotic Mariana Trench (MT). However, detailed bacterial DMSP cycling in the Mariana Trench subseafloor remains largely unknown. Here, the bacterial DMSP-cycling potential in a Mariana Trench sediment core (7.5 m in length) obtained at a 10,816-m water depth was investigated using culture-dependent and -independent methods. The DMSP content fluctuated along the sediment depth and reached the highest concentration at 15 to 18 cm below the seafloor (cmbsf). dsyB was the dominant known DMSP synthetic gene, existing in 0.36 to 1.19% of the bacteria, and was identified in the metagenome-assembled genomes (MAGs) of previously unknown bacterial DMSP synthetic groups such as Acidimicrobiia, Phycisphaerae, and Hydrogenedentia. dddP, dmdA, and dddX were the major DMSP catabolic genes. The DMSP catabolic activities of DddP and DddX retrieved from Anaerolineales MAGs were confirmed by heterologous expression, indicating that such anaerobic bacteria might participate in DMSP catabolism. Moreover, genes involved in methanethiol (MeSH) production from methylmercaptopropionate (MMPA) and dimethyl sulfide (DMS), MeSH oxidation, and DMS production were highly abundant, suggesting active conversions between different organic sulfur compounds. Finally, most culturable DMSP synthetic and catabolic isolates possessed no known DMSP synthetic and catabolic genes, and actinomycetes could be important groups involved in both DMSP synthesis and catabolism in Mariana Trench sediment. This study extends the current understanding of DMSP cycling in Mariana Trench sediment and highlights the need to uncover novel DMSP metabolic genes/pathways in extreme environments. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is an abundant organosulfur molecule in the ocean and is the precursor for the climate-active volatile gas dimethyl sulfide. Previous studies focused mainly on bacterial DMSP cycling in seawater, coastal sediment, and surface trench sediment samples, but DMSP metabolism in the Mariana Trench (MT) subseafloor sediments remains unknown. Here, we describe the DMSP content and metabolic bacterial groups in the subseafloor of the MT sediment. We found that the tendency for vertical variation of the DMSP content in the MT was distinct from that of the continent shelf sediment. Although dsyB and dddP were the dominant DMSP synthetic and catabolic genes in the MT sediment, respectively, both metagenomic and culture methods revealed multiple previously unknown DMSP metabolic bacterial groups, especially anaerobic bacteria and actinomycetes. The active conversion of DMSP, DMS, and methanethiol may also occur in the MT sediments. These results provide novel insights for understanding DMSP cycling in the MT.

Tsuneonella litorea sp. nov., a novel carotenoid-producing bacterium isolated from coastal sediment.

A Gram-stain-negative, aerobic, non-motile and pleomorphic bacterium designated as YG55T was isolated from a coastal sediment sample. Growth was found to occur at 10-37 °C (optimum, 28 °C), at pH 6-9 (optimum, pH 8) and in 0-6 % NaCl (optimum, 1 %). The results of 16S rRNA gene-based analysis showed that strain YG55T was related to the members of the genus Tsuneonella and shared the highest identity of 99.4 % with Tsuneonella dongtanensis GDMCC 1.2307T, followed by Tsuneonella troitsensis JCM 17037T (98.4 %). The phylogenomic results indicated that strain YG55T formed an independent branch distinct from the reference type strains. The 22.7 and 21.8 % digital DNA-DNA hybridization (dDDH) values and 83.0 and 81.8 % average nucleotide identity (ANI) values between strain YG55T and the two relatives were below the species definition thresholds of 70 % (dDDH) and 95-96 % (ANI), indicating that the strain represents a novel genospecies. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain YG55T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C14 : 0 2OH and C16 : 0; the main polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid; the respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.03 Mbp and 66.98 %. The strain contained carotenoid biosynthesis genes and could produce carotenoids. Based on its genotypic and phenotypic characteristics, strain YG55T is concluded to represent a novel species of the genus Tsuneonella, for which the name Tsuneonella litorea sp. nov. is proposed. The type strain is YG55T (=GDMCC 1.2590 T=KCTC 82812T).

Selective extraction of levoglucosan and its isomers from complex matrices using ligand exchange-solid phase extraction for analysis by liquid chromatography-electrospray ionization-tandem mass spectrometry

The analysis of trace quantities of monosaccharide anhydrides (MAs) in sediments is complicated by the lack of fast and reliable technologies to selectively extract these water-soluble non-ionic compounds from samples of complex composition. Here we describe a solid phase extraction method that takes advantage of the affinity between monosaccharide anhydrides (MAs) and immobilized Na+ ions related to ligand-exchange processes (LE-SPE). The capacity factor of LE-SPE columns was enhanced by using non-aqueous mobile phases such as DCM/MeOH mixtures. We have used the unique properties of LE-SPE columns to selectively extract MAs from lacustrine, coastal, and deep-sea oceanic sediment samples. The analytical procedure produces extracts with low ion suppression effects (0-20%), resulting in ideal conditions for MAs quantification with LC-ESI-MS/MS systems irrespective of the sedimentary matrix and MAs concentration. The analytical method yields repeatable concentration values (RSD of 9-23% for levoglucosan and 15-34% for mannosan and galactosan) and an IS recovery of 45-70%. The instrumental dynamic range is 10-10000 pg injected, but in practice, the methodological lower limit of quantification is constrained by sample contamination during processing. The combination of LE-SPE and LC-ESI-MS/MS has the potential to produce sensitive and reliable technologies to analyze saccharides and amino acids in environmental and biological samples.

Potentially toxic elements (PTEs) in coastal sediments of Bandar Abbas city, North of Persian Gulf: An ecological risk assessment

ABSTRACT The concentration of potentially toxic elements (PTEs; Lead (Pb), Nickel (Ni), and Cadmium (Cd) Pb, Ni, and Cd), using flame atomic absorption spectrometry (FAAS) was measured in fifty surface coastal sediment samples collected from 5 points coastal sediment of Bandar Abbas city, Iran besides the potential ecological risk index (RI) estimated the environmental health risk. The rank order of PTEs was Pb (52.090 ± 4.113 mg/kg dry weight) > Ni (34.940 ± 8.344 mg/kg dry weight) > Cd (2.944 ± 0.013 mg/kg dry weight). RI due to PTEs in sediments for A, B, C, D, and E points were 187.655, 190.542, 191.079, 189.496, and 192.053, respectively. RI for sampling points A to E was at moderate risk (150 ≤ RI < 300). Therefore, it is recommended to carry out control programs to reduce the amount of PTEs in the coastal sediment of the Persian Gulf.

Industrial effluents boosted antibiotic resistome risk in coastal environments

Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP’s effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.

Bisphenol analogues in water and sediment from the Beibu Gulf, South China Sea: Occurrence, partitioning and risk assessment

Bisphenol analogues (BPs) have gained increasing attention in recent years due to their ubiquitousness in the environment, potential endocrine disrupting properties and ecological impacts. However, very little information is available on the occurrence, partitioning and ecological risks of BPs in marine environments. In the present study, six BPs were investigated in surface water and sediment samples from the Beibu Gulf, South China Sea. Results showed that bisphenol A (BPA) was the predominant BP in both water and sediment samples with levels ranging from 5.26 to 12.04 ng/L in water and 0.56 to 5.22 ng/g dw in sediment samples, followed by bisphenol AF (BPAF: 0.44–0.60 ng/L in water and 0.08–0.66 ng/g dw in sediment samples, respectively) and bisphenol S (BPS: 0.07–0.63 ng/L in water and not detected (ND) to 0.19 ng/g dw in sediment samples, respectively). There is no significant spatial difference of BPs levels between riverine sediment samples and coastal sediment samples. Compared with other studies, the concentrations of BPs from the Beibu Gulf were relatively low. The mean log-transformed sediment-seawater partitioning coefficients (log Koc) ranged from 4.4 (DHBP) to 5.2 (BPAF) and the log Koc values for all the target BPs were generally higher than those reported in freshwater environments. The present study firstly reported the field-based log Koc values for BPB (mean: 4.5) and DHBP (mean: 4.4). The estimated risk quotient (RQ) and 17β-estradiol (E2) equivalent quotient (EEQ) values indicated that the ecological and human health impacts were negligible associated with target BPs. The present study provided reliable and detailed data for completely evaluating contamination level and environmental behaviors of BPs in the Beibu Gulf.

Hyphomonas sediminis sp. nov., isolated from marine sediment.

A Gram-staining-negative, aerobic and pear-shaped bacterial strain, designated WL0036T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51' 13″ E, 32° 6' 26″ N) in October 2020. Strain WL0036T was found to grow at 20-37°C (optimum, 28°C) with 0-9.0% NaCl (optimum, 2.5-4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0-10.0 (optimum, pH 7.0-8.0). The polar lipids profile of strain WL0036T included phosphatidylcholine, phosphatidylethanolamine, glycolipid and an unidentified lipid. The major isoprenoid quinone was determined to be Q-11 and the major fatty acids were C16:0, 11-methyl-C18:1ω7c, and summed features 8 (C18:1ω6c and/or C18:1ω7c). The G + C content of genomic DNA was 61.8%. Phylogenetic trees constructed based on 16S rRNA gene sequence and bac120 gene set (a collection of 120 single-copy protein sequences prevalent in bacteria) indicted that strain WL0036T clustered with strains Hyphomonas neptunium ATCC 15444T and H. polymorpha PS728T. The average nucleotide identities between strain WL0036T and strains H. neptunium ATCC 15444T and H. polymorpha PS728T were 80.7% and 81.2%, respectively. Strain WL0036T showed 22.8% and 23.2% of digital DNA-DNA hybridization identities with H. neptunium ATCC 15444T and H. polymorpha PS728T, respectively. As inferred from the phenotypic and genotypic characteristics and the phylogenetic trees, strain WL0036T ought to be recognized as a novel species in genus Hyphomonas, for which the name Hyphomonas sediminis sp. nov. is proposed. The type strain is WL0036T (= MCCC 1K05843T = JCM 34658T = GDMCC 1.2413T).

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

Marine sediments are a sink for antibiotic resistance genes (ARGs) and antibiotic-resistant microbes (ARMs). Wastewater discharge into the aquatic environment is the dominant pathway for pharmaceuticals reaching aquatic organisms. Hence, the characterization of ARGs is a priority research area. This baseline study reports the presence of ARGs in 12 coastal sediment samples covering the urban coastline of Kuwait through whole-genome metagenomic sequencing. The presence of 402 antibiotic resistance genes (ARGs) were recorded in these samples; the most prevalent were patA, adeF, ErmE, ErmF, TaeA, tetX, mphD, bcrC, srmB, mtrD, baeS, Erm30, vanTE, VIM-7, AcrF, ANT4-1a, tet33, adeB, efmA, and rpsL, which showed resistance against 34 drug classes. Maximum resistance was detected against the beta-lactams (cephalosporins and penam), and 46% of genes originated from the phylum Proteobacteria. Low abundances of ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sps., and Escherichia coli) were also recorded. Approximately 42% of ARGs exhibited multiple drug resistance. All the ARGs exhibited spatial variations. The major mode of action was antibiotic efflux, followed by antibiotic inactivation, antibiotic target alteration, antibiotic target protection, and antibiotic target replacement. Our findings supported the occurrence of ARGs in coastal marine sediments and the possibility of their dissemination to surrounding ecosystems.

Characterization of Kordiimonas marina sp. nov. and Kordiimonas laminariae sp. nov. and Comparative Genomic Analysis of the Genus Kordiimonas, A Marine-Adapted Taxon

Two novel rod-shaped and Gram-negative bacterial strains, designated A6E486T and 5E331T, were isolated from a coastal sediment sample taken from Xiaoshi Island, Weihai, China, and a fresh kelp sample collected from a kelp culture area, Rongcheng, China, respectively. Growth of strain A6E486T occurred at 20°C–43°C (optimum, 33°C–35°C) at pH 5.5–7.5 (optimum, 6.5) and in the presence of 1.0%–5.5% (w/v) NaCl (optimum, 2.5%–3.0%). Strain 5E331T grew with 1.5%–5.0% (w/v) NaCl (optimum, 3.0%) at 15°C–40°C (optimum, 33°) and pH 6.0–8.5 (optimum, 7.0). The similarity of 16S rRNA gene sequence between the two strains was 95.2%. The phylogenetic analysis based on 16S rRNA gene sequence showed that strains A6E486T and 5E331T belong to the genus Kordiimonas, sharing the highest similarity to the genus Kordiimonas (94.6%–96.8%, 94.9%–96.1%, respectively). Strains A6E486T and 5E331T had percentage of conserved protein (POCP) values of 56.0%–67.3% and average nucleotide identity (ANI) values of 68.8%–73.1% to members of the genus Kordiimonas. The major polar lipids detected in the two strains were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and unidentified glycolipids, aminolipids, and lipids. The predominant respiratory quinone of the two strains was Q-10. Based upon the results presented in this study, strains A6E486T and 5E331T represent two novel species of the genus Kordiimonas, for which the names Kordiimonas marina and Kordiimonas laminariae are proposed with the type strains A6E486T (= KCTC 82758T = MCCC 1H00470T) and 5E331T (= KCTC 92199T = MCCC 1H00515T), respectively. Comparative genomic analysis showed that seven species of the genus Kordiimonas shared 1,258 core genes and had differences in carbohydrate metabolism, energy metabolism, and cofactor and vitamin metabolism. The pan-genome of the genus Kordiimonas was open. The prediction of secondary metabolites showed that most strains of the genus Kordiimonas had the ability to produce homoserine lactones, one of the most important signal molecules in the quorum-sensing system of Gram-negative bacteria. Additionally, numerous genes involved in bacterial defense, motility and chemotaxis, cold adaptation, and environment stress response were found in the genus Kordiimonas, indicating the marine-adapted lifestyle of members of the genus Kordiimonas.

Enhanced Terrestrial Carbon Export From East Antarctica During the Early Eocene

AbstractTerrestrial organic carbon (TerrOC) acts as an important CO2 sink when transported via rivers to the ocean and sequestered in coastal marine sediments. This mechanism might help to modulate atmospheric CO2 levels over short‐ and long‐ timescales (103–106 years), but its importance during past warm climates remains unknown. Here we use terrestrial biomarkers preserved in coastal marine sediment samples from Wilkes Land, East Antarctica (∼67°S) to quantify TerrOC burial during the early Eocene (∼54.4–51.5 Ma). Terrestrial biomarker distributions indicate the delivery of plant‐, soil‐, and peat‐derived organic carbon (OC) into the marine realm. Mass accumulation rates of plant‐ (long‐chain n‐alkane) and soil‐derived (hopane) biomarkers dramatically increase between the earliest Eocene (∼54 Ma) and the early Eocene Climatic Optimum (EECO; ∼53 Ma). This coincides with increased OC mass accumulation rates and indicates enhanced TerrOC burial during the EECO. Leaf wax δ2H values indicate that the EECO was characterized by wetter conditions relative to the earliest Eocene, suggesting that hydroclimate exerts a first‐order control on TerrOC export. Our results indicate that TerrOC burial in coastal marine sediments could have acted as an important negative feedback mechanism during the early Eocene, but also during other warm climate intervals.

Complete Genome Sequence of Methanobacterium electrotrophus Strain YSL, Isolated from Coastal Riverine Sediments.

ABSTRACTMethanobacterium electrotrophus strain YSL was isolated from enriched microbial aggregates from a coastal riverine sediment sample from Shandong Province, China. The genome of YSL was sequenced with the PacBio Sequel platform and contained three plasmids in addition to the chromosome. A total of 2,521 protein-coding genes and 58 RNA genes were predicted.

Validation of an analytical technique, distribution, and risk assessment of aliphatic and polycyclic aromatic hydrocarbons in surface sediments of the coastal and selected estuaries of Sarawak

This study explains a validation of an analytical technique, monitoring, and risk evaluation of hydrocarbons in surface sediments of the coastal and selected estuaries of Sarawak, Malaysia. The performance of an analytical methodology was validated for the evaluation of hydrocarbons in coastal and estuaries sediment samples. After the clean-up and separation process, GC-FID and GC-MS were used to quantify aliphatic and polycyclic aromatic hydrocarbon extracts, respectively. The suggested methodology is able to measure aliphatic and polycyclic aromatic hydrocarbons in samples at lower concentrations for example 10 ng/g. The precision of the technique was satisfactory as compared to 15% for most of the analytes. This method gives information concerning the distribution and characteristics of hydrocarbon contaminants in the coastal environment. In regard to monitoring and risk assessment, total n-alkane concentrations (C10–C33) varied from 96.63 to 367.28 ng/g dw. The lowest and highest n-alkane content is observed at Santubong estuary (CZ10) and the coastal site CZ2, respectively. Simultaneously, the contents of ∑PAHs varied from 12.54 to 21.20 ng/g dw. The highest ∑PAH content is reported in the sediments of coastal site CZ8 (21.20 ng/g dw), whereas the lowest content is recorded in the sediments of coastal site CZ3 (12.54 ng/g dw). The outcome of the risk assessment suggested that there is no risk in all the studied locations. The findings from this study will help to understand the sources and possible risks of hydrocarbons in the coastal and estuary settings, and provide information for safeguarding human health and aquatic bodies in the studied area.