Deep-sea Sediment Samples Research Articles

Albusamides A-G: Hydroxylated Fatty Amine Derivatives from the Deep-Sea-Derived Actinomycete Streptomyces albus 228DD-066 and Their Cytotoxic Activity.

A series of new hydroxylated fatty amine derivatives, albusamides A-G (1-7), along with four known compounds (8-11), which are reported for the first time from a natural source, were isolated from the culture broth of Streptomyces albus 228DD-066 derived from a deep-sea sediment sample gathered off the coast of Dokdo Island, Republic of Korea. Their structures were elucidated through the comprehensive analysis of 1D and 2D NMR spectra and HRESIMS, and absolute configurations were determined using the modified Mosher's method. Biological evaluations against solid and blood cancer cell lines revealed that these new metabolites have moderate to strong cytotoxic activity. Compound 3 exhibited high cytotoxic activity with GI50 values ranging from 0.4 to 0.6 μM against solid cancer cell lines and exhibited the strongest cytotoxicity (GI50 value = 0.2 μM) against the WSU-DLCL2 blood cancer cell line.

Chemical constitutents and chemotaxonomic research of the deep-sea-derived fungus Talaromyces minioluteus W19

Talaromyces minioluteus W19 was isolated from a deep-sea sediment sample of the western Pacific Ocean. A systematic investigation of its chemical constituents led to the isolation of nine compounds, including one new macrolactin (1), three citrinin (2−4), one sesquiterpene ester (5), one steroid (6), two fatty acid analogues (7 and 8), and one glyceride (9). Compounds 2, 4, and 6−9 were isolated from the genus Talaromyces for the first time. Fusarimone A (3) could be ideal chemotaxonomic marker for T. minioluteus. Drimane sesquiterpenoid-amino acid hybrid is potent chemotaxonomic marker for the genus Talaromyces.

2,3-Dimethoxycinnamic Acid from a Marine Actinomycete, a Promising Quorum Sensing Inhibitor in Chromobacterium violaceum.

An ethyl acetate extract of a marine actinomycete strain, Nocardiopsis mentallicus SCSIO 53858, isolated from a deep-sea sediment sample in the South China Sea, exhibited anti-quorum-sensing (QS) activity against Chromobacterium violaceum CV026. Guided by the anti-QS activity, a novel active compound was isolated and purified from the extract and was identified as 2,3-dimethoxycinnamic acid (2,3-DCA) through spectral data analysis. At a concentration of 150 μg/mL, 2,3-DCA exhibited robust inhibitory effects on three QS-regulated traits of C. violaceum CV026: violacein production, swarming motility, and biofilm formation, with inhibition rates of 73.9%, 65.9%, and 37.8%, respectively. The quantitative reverse transcription polymerase chain reaction results indicated that 2,3-DCA can disrupt the QS system in C. violaceum CV026 by effectively suppressing the expression of QS-related genes, including cviR, vioA, vioB, and vioE. Molecular docking analysis revealed that 2,3-DCA hinders the QS system by competitively binding to the same binding pocket on the CviR receptor as the natural signal molecule N-hexanoyl-L-homoserine lactone. Collectively, these findings suggest that 2,3-DCA exhibits promising potential as an inhibitor of QS systems, providing a potential solution to the emerging problem of bacterial resistance.

Microbacterium abyssi sp. nov. and Microbacterium limosum sp. nov., two new species of the genus Microbacterium, isolated from deep-sea sediment samples.

Two Gram-positive, non-motile, short rod-shaped actinomycete strains, designated as A18JL241T and Y20T, were isolated from deep-sea sediment samples collected from the Southwest Indian Ocean and Western Pacific Ocean, respectively. Both of the isolates were able to grow within the temperature range of 5-40 °C, NaCl concentration range of 0-7 % (w/v) and at pH 6.0-12.0. The two most abundant cellular fatty acids of both strains were anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipid contents of the two strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified glycolipid. These two strains shared common chemotaxonomic features comprising MK-10 and MK-12 as the respiratory quinones. The genomic DNA G+C contents of the two strains were 68.1 and 70.4 mol%, respectively. The 16S rRNA gene phylogeny showed that the novel strains formed two distinct sublines within the genus Microbacterium. Strain A18JL241T was most closely related to the type strain of Microbacterium tenebrionis KCTC 49593T (98.8 % sequence similarity), whereas strain Y20T formed a tight cluster with the type strain of Microbacterium schleiferi NBRC 15075T (99.0 %). The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the type strains of related Microbacterium species were in the range of 74.1-89.1 % and 19.4-36.9 %, respectively, which were below the recognized thresholds of 95-96 % ANI and 70 % dDDH for species definition. Based on the results obtained here, it can be concluded that strains A18JL241T and Y20T represent two novel species of the genus Microbacterium, for which the names Microbacterium abyssi sp. nov. (type strain A18JL241T=JCM 33956T=MCCC 1A16622T) and Microbacterium limosum sp. nov. (type strain Y20T=JCM 33960T=MCCC 1A16747T) are proposed.

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity.

Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.

Antifungal profile against Candida auris clinical isolates of tyroscherin and its new analog produced by the deep-sea-derived fungal strain Scedosporium apiospermum FKJ-0499.

A new antifungal compound, named N-demethyltyroscherin (1), was discovered from the static fungal cultured material of Scedosporium apiospermum FKJ-0499 isolated from a deep-sea sediment sample together with a known compound, tyroscherin (2). The structure of 1 was elucidated as a new analog of 2 by MS and NMR analyses. The absolute configuration of 1 was determined by chemical derivatization. Both compounds showed potent in vitro antifungal activity against clinically isolated Candida auris strains, with MIC values ranging from 0.0625 to 4 µg ml-1.

Mesonia profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench.

A Gram-stain-negative, aerobic, rod-shaped, non-flagellated, non-gliding bacterial strain, designated MT50T, was isolated from a deep-sea sediment sample collected from the Mariana Trench. Optimal growth of strain MT50T was observed at 25 °C, pH 7.0-7.5 and in the presence of 3-5 % (w/v) NaCl. The strain was positive for oxidase and catalase. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain MT50T is affiliated with the genus Mesonia, showing the highest sequence similarity (98.5 %) to the type strain of Mesonia ostreae. The digital DNA-DNA hybridization and average nucleotide identity values between strain MT50T and four closely related type strains of known Mesonia species (14.1-54.8 % and 72.7-86.8 %, respectively) were all below the threshold values to discriminate bacterial species, indicating that strain MT50T is affiliated with a novel species within the genus. The genomic G+C content deduced from the genome of strain MT50T was 36.2 mol%. The major fatty acids of strain MT50T were iso-C15 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0. The predominant respiratory quinone of the strain was MK-6. The polar lipids of strain MT50T included phosphatidylethanolamine and two unidentified lipids. Based on the polyphasic data presented in this study, strain MT50T represents a novel species of the genus Mesonia, for which the name Mesonia profundi sp. nov. is proposed. The type strain is MT50T (=MCCC 1K07833T=KCTC 92380T).

Experimental investigation of the inhibition of deep-sea mining sediment plumes by polyaluminum chloride

Deep-sea sediment disturbance may occur when collecting polymetallic nodules, resulting in the creation of plumes that could have a negative impact on the ecological environment. This study aims to investigate the potential solution of using polyaluminum chloride (PAC) in the water jet. The effects of PAC are examined through a self-designed simulation system for deep-sea polymetallic nodule collection and sediment samples from a potential deep-sea mining area. The experimental results showed that the optimal PAC dose was found to be 0.75 g/L. Compared with the test conditions without the addition of PAC, the presence of PAC leads to a reduction in volume, lower characteristic turbidity, smaller diffusion velocity, and shorter settling time of the plume. This indicates that PAC inhibits the entire development process of the plume. The addition of PAC leads to the flocculation of mm-sized particles, resulting in the formation of cm-sized flocs. The flocculation of particles decreases the rate of erosion on the seabed by around 30%. This reduction in erosion helps to decrease the formation of plumes. Additionally, when the size of suspended particles increases, it reduces the scale at which they diffuse. Furthermore, the settling velocity of flocs (around 10−2 m/s) is much higher that of compared to sediment particles (around 10−5 m/s), which effectively reduces the amount of time the plume remains in suspension.

Taxonomic identification and temperature stress tolerance mechanisms of Aequorivita marisscotiae sp. nov

The deep sea harbours microorganisms with unique life characteristics and activities due to adaptation to particular environmental conditions, but the limited sample collection and pure culture techniques available constrain the study of deep-sea microorganisms. In this study, strain Ant34-E75 was isolated from Antarctic deep-sea sediment samples and showed the highest 16 S rRNA gene sequence similarity (97.18%) with the strain Aequorivita viscosa 8-1bT. Strain Ant34-E75 is psychrotrophic and can effectively increase the cold tolerance of Chlamydomonas reinhardtii (a model organism). Subsequent transcriptome analysis revealed multiple mechanisms involved in the Ant34-E75 response to temperature stress, and weighted gene co-expression network analysis (WGCNA) showed that the peptidoglycan synthesis pathway was the key component. Overall, this study provides insights into the characteristics of a deep-sea microorganism and elucidates mechanisms of temperature adaptation at the molecular level.

Nocardioides cremeus sp. nov., Nocardioides abyssi sp. nov. and Nocardioides oceani sp. nov., three actinobacteria isolated from Western Pacific Ocean sediment.

Three Gram-stain-positive, non-motile, short rod-shaped, catalase-positive and oxidase-negative actinomycete strains (SOB44T, SOB72T and SOB77T) were isolated from a deep-sea sediment sample collected from the Western Pacific Ocean. Cells of the three strains showed optimum growth at 30 °C and pH 7.0. Strains SOB44T, SOB72T and SOB77T could tolerate up to 10, 9 and 9 % (w/v) NaCl concentration and grow at pH 5.0-12.0, 5.0-11.0 and 5.0-11.0, respectively. Phylogenetic results based on 16S rRNA gene sequences showed that the three isolates belonged to the genus Nocardioides and were identified as representing three novel species based on 78.0-93.1 % average nucleotide identity and 21.3-50.0 % DNA-DNA hybridization values with closely related reference strains. Strains SOB44T, SOB72T and SOB77T showed highest 16S rRNA gene sequence similarity to Nocardioides salarius CL-Z59T (99.2 %), Nocardioides deserti SC8A-24T (99.2 %) and Nocardioides marmotae zg-579T (98.5 %), respectively. All three strains had MK-8(H4) as the respiratory quinone, iso-C16 : 0 as the major fatty acid, and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the major polar lipids. The diagnostic diamino acid in the cell-wall peptidoglycan of all three isolates was ll-diaminopimelic acid. The DNA G+C contents of strains SOB44T, SOB72T and SOB77T were 71.1, 72.9 and 72.9 mol%, respectively. Based on the phenotypic, phylogenetic and genotypic data, strains SOB44T, SOB72T and SOB77T clearly represent three novel taxa within the genus Nocardioides, for which the names Nocardioides cremeus sp. nov. (type strain SOB44T=JCM 35774T= MCCC M28400T), Nocardioides abyssi sp. nov. (type strain SOB72T=JCM 35775T=MCCC M28318T) and Nocardioides oceani sp. nov. (type strain SOB77T=JCM 35776T=MCCC M28544T) are proposed.

Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean.

Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.

Antibacterial polyketides and ascochlorins from deep-sea cold-seep-derived fungus Furcasterigmium furcatum (syn. Acremonium furcatum)

Three new secondary metabolites, including a new polyketide, acrefurcatone A (1), a new ascochlorin analogue, acremochlorin N (2), and 3-phenylcyclopentane-1,2-diol (±-3), a pair of new naturally occurring enantiomers, along with nine known ascochlorins (4–12), were identified from Furcasterigmium furcatum CS-280 (syn. Acremonium furcatum CS-280), a fungus isolated from the deep-sea cold-seep sediment samples collected in the South China Sea. Their structures were determined by detailed interpretation of NMR spectroscopic and mass spectrometric data. The relative configurations of compounds 1–3 were assigned by NOESY correlations combined with gauge-independent atomic orbital (GIAO) NMR shift calculations and DP4+ probability analysis, while their absolute configurations were assigned by time-dependent density functional (TDDFT) ECD calculations and specific rotation calculations. Compound 1 exhibited potent activity against the human pathogenic bacterium Pseudomonas aeruginosa, with a minimum inhibitory concentration (MIC) value of 8 μg/mL. The isolated ascochlorins also showed potent activities against aquatic bacteria, especially for Vibrio harveyi and V. alginolyticus, with MIC values comparable to chloramphenicol. Analysis of the structure-activity relationship indicated that the cinnamate derivative, such as compound 1, or the presence of chlorine atom in ascochlorin derivatives, such as compounds 4, 6, and 7, significantly enhanced the antibacterial activities. This is the first report of anti-Vibrio activities for ascochlorin derivatives.

Biocontrol potential of two deep-sea microorganisms against gray blight disease of tea

BackgroundGray blight is among the most destructive diseases that affect tea plants worldwide. In this study, microorganisms from deep-sea sediment samples for those with antagonistic effects were screened against gray blight caused by Pestalotiopsis theae.ResultsThirty-two and twenty-eight morphologically different deep-sea bacteria and fungi were isolated, respectively. Isolates B5 and A65 clearly inhibited the pathogens in vitro and were prepared as wettable agent powders for evaluation in micro-plot field trials. Foliar application of the 48-h culture of B5 (1 × 108, 2 × 107, 1 × 107 colony-forming units (CFU)/ml) significantly reduced the incidence of gray blight disease. Compared to the untreated control, spraying with B5 inhibited gray blight disease by 78.57%. Isolate B5 was identified as Bacillus subtilis B5 in morphological and 16S rDNA sequence analyses. The foliar application of 7-day cultures of A65 (1 × 108, 2 × 107, 1 × 107 CFU/ml) significantly reduced the incidence of gray blight disease. A65 (108 CFU/ml) inhibited gray blight disease by 75.46% and was identified as Paecilomyces lilacinus A65 in morphologically and internally transcribed spacer sequence analyses.ConclusionsThese candidate microbial pesticides may inhibit gray wilt in tea, replace chemical pesticides’ use without causing environmental pollution, and promote the development of green agriculture.

Salinimicrobium profundisediminis sp. nov., isolated from deep-sea sediment of the Mariana Trench.

A Gram-stain-negative, aerobic, rod-shaped, non-gliding bacterial strain, designated as MT39T, was isolated from a deep-sea sediment sample collected from the Mariana Trench. Strain MT39T grew optimally at 35°C and pH 7.0, and could tolerate up to 10% (w/v) NaCl. The strain was positive for catalase and negative for oxidase. The genome of strain MT39T was 4 033 307 bp, with a 41.1 mol % genomic G+C content and 3514 coding sequences. Phylogenetic analysis based on 16S rRNA gene sequences placed strain MT39T within the genus Salinimicrobium, showing the highest 16S rRNA gene sequence similarity to Salinimicrobium terrea CGMCC 1.6308T (98.1%). The average nucleotide identity and in silico DNA-DNA hybridization values between strain MT39T and the type strains of seven Salinimicrobium species were all less than the threshold values to discriminate bacterial species, indicating that strain MT39T is affiliated with a novel species within the genus. The major cellular fatty acids of strain MT39T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. Polar lipids of strain MT39T included phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. Menaquinone-6 was the only respiratory quinone in strain MT39T. On the basis of the polyphasic data present in this study, strain MT39T represents a novel species of the genus Salinimicrobium, for which the name Salinimicrobium profundisediminis sp. nov. is proposed, with type strain being MT39T (=MCCC 1K07832T=KCTC 92381T).

Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota.

Benefiting from the rapid developments and wide applications of high-throughput sequencing, great advancements have been made in investigating microbiota, which are highly diverse and play key roles in both element cycling and the energy flow of ecosystems. There have been inherent limitations of amplicon sequencing that could introduce uncertainty and raise concerns about the accuracy and reproducibility of this technology. However, studies focusing on the reproducibility of amplicon sequencing are limited, especially in characterizing microbial communities in deep-sea sediments. To evaluate reproducibility, 118 deep-sea sediment samples were used for 16S rRNA gene sequencing in technical replicates (repeated measurements of the same sample) that demonstrate the variability of amplicon sequencing. The average occurrence-based overlaps were 35.98% and 27.02% between two and among three technical replicates, respectively, whereas their abundance-based overlaps reached 84.88% and 83.16%, respectively. Although variations of alpha and beta diversity indices were found between/among technical replicates, alpha diversity indices were similar across samples, and the average beta diversity indices were much smaller for technical replicates than among samples. Moreover, clustering methods (i.e., operational taxonomic units [OTUs] and amplicon sequence variants [ASVs]) were shown to have little impact on the alpha and beta diversity patterns of microbial communities. Taken together, although there are variations between/among technical replicates, amplicon sequencing is still a powerful tool with which to reveal diversity patterns of microbiota in deep-sea sediments. IMPORTANCE The reproducibility of amplicon sequencing is vital for whether the diversities of microbial communities could be accurately estimated. Thus, reproducibility influences the drawing of sound ecological conclusions. Nevertheless, few studies have focused on the reproducibility of microbial communities that are characterized by amplicon sequencing, and studies focusing on microbiota in deep-sea sediments have been especially lacking. In this study, we evaluated the reproducibility of amplicon sequencing targeting microbiota in deep-sea sediments of cold seep. Our results revealed that there were variations between/among technical replicates and that amplicon sequencing was still a powerful tool with which to characterize the diversities of microbial communities in deep-sea sediments. This study provides valuable guidelines for the reproducibility evaluation of future work in experimental design and interpretation.

Environmental viromes reveal global virosphere of deep-sea sediment RNA viruses

IntroductionViruses are the most abundant and diverse life forms on the earth. Both DNA viruses and RNA viruses play important roles in marine ecosystems via regulating biogeochemical cycles. ObjectivesHowever, the virome of marine RNA viruses has been rarely explored so far. In this study, therefore, the environmental viromes of deep-sea sediment RNA viruses were characterized on a global scale to reveal the global virosphere of deep-sea RNA viruses. MethodsThe viral particles were purified from each of 133 deep-sea sediment samples and then characterized based on metagenomes of RNA viruses. ResultsIn this study, we established the global virome dataset of deep-sea RNA viruses purified from 133 sediment samples that were collected from typical deep-sea ecosystems of three oceans. A total of 85,059 viral operational taxonomic units (vOTUs) were identified, of which only 1.72% were hitherto known, indicating that the deep-sea sediment is a repository of novel RNA viruses. These vOTUs were classified into 20 viral families, including prokaryotic (7.09%) and eukaryotic (65.81%) RNA viruses. Furthermore, 1,463 deep-sea RNA viruses with complete genomes were obtained. The differentiation of RNA viral communities was driven by the deep-sea ecosystems as opposed to geographical region. Specifically, the virus-encoded metabolic genes took great effects on the differentiation of RNA viral communities by mediating the energy metabolism in the deep-sea ecosystems. ConclusionsTherefore, our findings indicate that the deep sea is a vast reservoir of novel RNA viruses for the first time, and the differentiation of RNA viral communities is driven by the deep-sea ecosystems through energy metabolism.

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.

On New Species of Three Genera of Zosimeidae Seifried, 2003 (Copepoda: Harpacticoida) from the Deep Sea of the Gulf of California and Gulf of Mexico, with Notes on the Phylogeny of the Family and on the Species Groups of Zosime Boeck, 1873

Thirty-one nominal species of the benthic harpacticoid family Zosimeidae Seifried, 2003 are known from several coastal systems less than 200 m depth and the deep sea. Several copepods of the family Zosimeidae were found in deep-sea sediment samples from the Gulf of Mexico and the Gulf of California (Mexico). The Mexican material represents new species of the genera Zosime Boeck, 1873, Peresime Dinet, 1974, Heterozosime Kim and Lee, 2021, and Acritozosime Kim and Lee, 2021. Standardized and complete descriptions for these new species are provided. Previous studies have shown that the genus Zosime can be subdivided into two species groups. We performed phylogenetic analyses (88 characters and 42 taxa) to test the naturalness of such subdivision, to subdivide these groupings further, and to shed some light on the phylogenetic relationships among the zosimeid genera and their species. Our results confirmed (i) the monophyly of previous subdivisions of the genus Zosime, and (ii) that the genus Zosime can be further subdivided into two major subgroups composed of several subordinate clades. Additionally, some comments on the phylogenetic hypotheses amongst the species of each genus reported here, are provided.

Emestrin-type thiodiketopiperazines from Aspergillus nidulans SD-531, a fungus obtained from the deep-sea sediment of cold seep in the South China Sea

Three new emestrin-type thiodiketopiperazines including didethio-11a-methylthioemestrin (1), 7′-epi-didethio-11a-methylthioemestrin (2), and 2″-desmethyl-MPC1001F (3), along with three known analogues emestrin (4), dethiosecoemestrin (5), and emestrin H (6), were isolated and identified from the culture extract of Aspergillus nidulans SD-531, a fungus obtained from the deep-sea cold seep sediment sample collected from the South China Sea. Their structures and absolute configurations were determined by spectroscopic analysis and TDDFT-ECD calculations. Compounds 3–6 showed antimicrobial activity against some of the tested strains, while compounds 3–5 had cytotoxic activity against the tumor cell line Huh 7.5. Compound 4 exhibited the strongest cytotoxic activity with an IC50 value of 0.25 μM, which was better than that of the positive control sorafenib.

Complete genome sequence of the denitrifying Pseudomonas sp. strain DNDY-54 isolated from deep-sea sediment of ninety east ridge.

Pseudomonas sp. strain DNDY-54, a denitrifying bacterium, was isolated from a deep-sea sediment sample from Ninety East Ridge in the Indian Ocean. Here, we show that the complete genome of DNDY-54 has one circular chromosome of 4,412,895bp with mean 60.57% GC content. The complete genome contains 4111 predicted protein-coding genes, 59 tRNAs, and 4 rRNA operons as 16S-23S-5S rRNA. On the basis of the annotation results, we identified genes that encode 27 proteins related to nitrogen metabolism, including enzymes that make up a complete denitrifying pathway. This work will improve the understanding of nitrogen cycling in the deep biosphere and provides a new candidate for protection of the environment and applications in waste water disposal.