Chromosome-level genome assembly of the silver pomfret Pampus argenteus.

Pampus argenteus (Euphrasen, 1788) is one of the major fishery species in coastal China. Pampus argenteus has a highly specialized morphology, and its declining fishery resources have encouraged massive research efforts on its aquacultural biology. In this study, we reported the first high-quality chromosome-level genome of P. argenteus obtained by integrating Illumina, PacBio HiFi, and Hi-C sequencing techniques. The final size of the genome was 518.06 Mb, with contig and scaffold N50 values of 20.47 and 22.86 Mb, respectively. The sequences were anchored and oriented onto 24 pseudochromosomes based on Hi-C data corresponding to the 24-chromatid karyotype of P. argenteus. A colinear relationship was observed between the P. argenteus genome and that of a closely related species (Scomber japonicus). A total of 24,696 protein-coding genes were identified from the genome, 98.9% of which were complete BUSCOs. This report represents the first case of high-quality chromosome-level genome assembly for P. argenteus and can provide valuable information for future evolutionary, conservation, and aquacultural research.

Two new species of Promonhystera Wieser, 1956 (Nematoda: Monhysterida: Xyalidae) from the South China Sea.

Two new species of free-living marine nematodes from the littoral sediment of the South China Sea are described as Promonhystera papilla sp. nov. and Promonhystera fluctispicula sp. nov. Both new species are characterized by striated cuticle; circular amphideal fovea; anterior sensilla in two circles, inner labial sensilla setiform; funnel-shaped buccal cavity; elongated spicules and conico-cylindrical tail. P. papilla sp. nov. is different from all known species of the genus by longer body length (more than 2.1mm versus less than 1.5 mm in other species), longer spicules (sp/a.b.d. = 4.14.6 versus 2.7) and males with three papilliform precloacal supplements and one small postcloacal papilla (versus absence) and gubernaculum boot-shaped. P. fluctispicula sp. nov. is similar to P. tricuspidata Wieser, 1956 in having similar waved spicules but differs from the latter species by tail conico-cylindrical (versus conical) and simple plate-like gubernaculum without tooth (versus gubernaculum with four distal teeth).

Distribution patterns of six metals and their influencing factors in M4 seamount seawater of the Western Pacific.

Metals are crucial to the stability of marine ecosystems, and it is important to analyze their spatial heterogeneity. This study examined the distribution and influencing factors of six metals such as manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu) and cadmium (Cd) in M4 seamount of the Western Pacific. The results showed that the factors affecting the distribution of metals are complex. The concentration ranges of Mn, Fe, Co, Ni, Cu, and Cd in the M4 seamount were 0-0.05, 0-0.44, 0-0.0014, 0-0.082, 0.12-0.16, and 0-0.013 µg/L, respectively, roughly equivalent to those of other open seas, however, there were also some differences. Specifically, the distribution of ferromanganese nodules and Co-rich crusts, resulted in a significant increase in the concentration of metals such as Mn, Fe, and Co in the bottom. This study will significantly contribute to our understanding of the spatial heterogeneity of metals in seamount areas.

Studies on western Pacific gorgonians (Anthozoa: Octocorallia, Chrysogorgiidae). Part 1: a review of the genus Chrysogorgia, with description of a new genus and three new species.

Members of Chrysogorgia Duchassaing & Michelotti, 1864, known as golden corals, are distributed in the deep sea worldwide. Based on specimens obtained from the tropical western Pacific and an integrated morphological-molecular approach, we established a new genus Parachrysogorgia, which includes 13 species separated from Chrysogorgia, and described nine species of Chrysogorgia including three new species C. arboriformis sp. nov., C. cylindrata sp. nov. and C. tenuis sp. nov., and two new combinations of Parachrysogorgia. The genus differs from Chrysogorgia by possessing a bare, sclerite-free area at the base of each tentacle and eight distinct projections beneath tentacles. Chrysogorgia cylindrata sp. nov. is distinguished by a slender bottlebrush-shaped colony in adults, elongate and lobed scales in coenenchyme, and warty and thick sclerites near the polyp mouth area. Chrysogorgia arboriformis sp. nov. is characterized by a tree-shaped colony with a long unbranched stem, slender and thin scales usually with large warts in coenenchyme. Chrysogorgia tenuis sp. nov. can be separated by a broad bottlebrush-shaped colony, long interbranch distance, elongate scales with broad lobes in polyp body wall. In contrast to the intraspecific variation of colony form, branch internodes, branching sequence and polyps, the sclerite forms and arrangement in different parts can be viewed as the most important character to separate Chrysogorgia species. For convenient identification, we divided the Chrysogorgia species into 12 morphological groups and divided Parachrysogorgia into three groups based on their sclerite forms and arrangement.

Morphology and molecular phylogeny of Pleurosigmapacificum sp. nov. (Pleurosigmataceae), a new tropical pelagic species from the Western Pacific Ocean.

A new species of pelagic diatom, Pleurosigmapacificumsp. nov., is described from the tropical Western Pacific Ocean. It has the typical features of Pleurosigma, including a slightly sigmoid raphe, intersected transverse and oblique striae, and loculate areolae with external opening slits and internal poroids. Morphologically, P.pacificum belongs to a species group of Pleurosigma with lanceolate valves, including P.atlanticum Heiden & Kolbe, P.nubecula W. Smith, P.indicum Simonsen, and P.simonsenii Hasle. However, P.pacificum differs by its smaller lanceolate valve and smaller intersection angle as well as elliptical areolae without a silica bar. The SSU rDNA and rbcL sequence data place P.pacificum in a basal position relative to other species of Pleurosigma. Our molecular phylogenetic analyses did not support the monophyly of lanceolate and slightly sigmoid species. Thus, the sigmoidality of valve outline cannot be considered as a criterion to define the species group.

itol.toolkit accelerates working with iTOL (Interactive Tree of Life) by an automated generation of annotation files.

SUMMARY: iTOL is a powerful and comprehensive phylogenetic tree visualization engine. However, adjusting to new templates can be time-consuming, especially when many templates are available. We developed an R package namely itol.toolkit to help users generate all 23 types of annotation files in iTOL. This R package also provides an all-in-one data structure to store data and themes, accelerating the step from metadata to annotation files of iTOL visualizations through automatic workflows. AVAILABILITY AND IMPLEMENTATION: The manual and source code are available at https://github.com/TongZhou2017/itol.toolkit.

Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration.

The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.

Autoinduction AND Gate Inhibits Cell Lysis to Enhance Protein Production in Bacillus subtilis Controlled by Population Density and Cell Physiological State.

The extracellular protease-deficient strain Bacillus subtilis WB600 is commonly used as a chassis cell for the production of industrial proteins. However, B. subtilis WB600 exhibits an increased susceptibility to cell lysis and a reduction in biomass. Inhibition of cell lysis by knocking out lytic genes will impair physiological function. Here, we dynamically inhibited cell lysis in B. subtilis WB600 to balance the impairment of physiological function with the accumulation of biomass. First, the inducible protein degradation systems (IPDSs) were constructed and used to investigate the effects of inhibiting cell lysis on biomass, cell morphology, and protein production at different times (using pullulanase as a test). The highest pullulanase activity was obtained at 20 h of inhibiting cell lysis, 184.8 U/mL, which was 44% higher than the activity of B. subtilis WB600. Then, to avoid addition of inducers, we introduced orthogonal quorum sensing and constructed autoinduction protein degradation systems (AIPDSs). The optimized AIPDS showed similar pullulanase activity to the optimal IPDS (20 h), 181.3 U/mL. Next, we constructed dual-signal input autoinduction protein degradation systems (DSI-AIPDSs) via AND gate to further address two deficiencies of AIPDS, one-time activation and damage to new cells. These DSI-AIPDSs were controlled by quorum sensing and stationary phase promoters that respond to population density and single-cell physiological state, respectively. Finally, the OD600 and pullulanase activity of the strain with optimal DSI-AIPDS were 51% and 115% higher than those of B. subtilis WB600 in pullulanase production, respectively. We provided a B. subtilis chassis strain with considerable potential for biomass accumulation and enhanced protein production.

The effects of seawater thermodynamic parameters on the oxygen minimum zone (OMZ) in the tropical western Pacific Ocean.

The continuous expansion of the oxygen minimum zone (OMZ) is a microcosm of marine hypoxia problem. Based on a survey in M4 seamount area of Tropical Western Pacific Ocean, the effects of thermodynamic parameters on OMZ were discussed. The study showed thermodynamic parameters mainly affect the upper oxycline of OMZ. The increase in temperature aggravates seawater stratification, which not only shallows oxycline but also increases the strength of DO stratification, promoting the expansion of OMZ. Based on relationships between thermodynamic parameters, water mass and DO, OMZ in this area is defined as follows: the water layer with low DO between the lower boundary of high-salt area and 1000 m. Moreover, the study showed that though there is no "seamount effect" on a scale of 3000 m, low-value areas of DO form at the bottom of seamount. This study will provide an evidence for expansion of OMZ exacerbated by global warming.

Phylogeny and Evolution of Cocconeiopsis (Cocconeidaceae) as Revealed by Complete Chloroplast and Mitochondrial Genomes.

The genus Cocconeiopsis was separated from Navicula, but its systematic position is in debate. We sequenced the complete chloroplast and mitochondrial genome of Cocconeidaceae for the first time with Cocconeiopsis kantsiensis and investigated its phylogeny and evolutionary history. Results showed that the plastid genome was 140,415 bp long with 167 genes. The mitochondrial genome was 43,732 bp long with 66 genes. Comparative analysis showed that the plastid genome structure of C. kantsiensis was most similar to those of three Navicula species and Halamphora americana, and its size was significantly smaller than that of a monoraphid species. Its mitochondrial genome was similar to that of related species except for Phaeodactylum tricornutum. The multigene phylogeny reconstruction showed that Cocconeiopsis was sister to Didymosphenia but distant from Naviculaceae. The two-gene phylogenetic analysis containing 255 species showed Cocconeiopsis was sister to Cocconeis, and distant from Naviculaceae as well. Divergence time estimation indicates the common ancestor of cocconeid species occurred about 62.8 Ma and Cocconeiopsis diverged with monoraphid Cocconeis about 58.9 Ma. Our results support the assignment of Cocconeiopsis to Cocconeidaceae and that monoraphid cocconeids were likely evolved from the lineage of Cocconeiopsis.

Autoinduction Expression Modules for Regulating Gene Expression in Bacillus subtilis.

Although quorum sensing (QS) promoters that can autonomously activate gene expression have been identified and engineered in Bacillus subtilis, researchers focus on quantifying individual promoters while ignoring the interaction between other genetic regulatory elements. Here, we constructed the autoinduction expression modules consisting of promoters responsive to QS ComQXPA, ribosome binding sites (RBSs), and terminators. Using superfolder green fluorescent protein (sfGFP) as a reporter gene, three individual element libraries were generated from 945 promoters, 12,000 RBSs, and 425 terminators by random mutation, de novo design, and database mining strategies, respectively. Then, the efficiency of three libraries in regulating gene expression was further enhanced by engineering the core region of each optimal element. After hybridizing the element libraries, the generated expression modules exhibited a 627-fold range in regulating gene expression without significantly affecting the autoinduction initiation. Here, the hybrid modules with broad expression strength may benefit the application of QS-based autoinduction systems in B. subtilis.

Bacteria, Protists, and Fungi May Hold Clues of Seamount Impact on Diversity and Connectivity of Deep-Sea Pelagic Communities.

The topography and hydrography around seamounts have a strong influence on plankton biogeography. The intrinsic properties of various biological taxa inherently also shape their distribution. Therefore, it is hypothesized that different pelagic groups respond differently to effects of seamounts regarding their distribution and connectivity patterns. Herein, bacterial, protist, and fungal diversity was investigated across the water column around the Kocebu Guyot in the western Pacific Ocean. A higher connectivity was detected for bacteria than for protists and an extremely low connectivity for fungi, which might be attributed to parasitic and commensal interactions of many fungal taxa. The seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced protist connectivity along horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification. All the bacterial, protist, and fungal communities were more strongly affected by deterministic than stochastic processes. Drift appeared to have a more significant role in influencing the fungal community than other groups. Our study indicates the impact of seamounts on the pelagic community distribution and connectivity and highlights the mechanism of horizontally restricted dispersal combined with vertical mixing, which promotes the diversification of eukaryotic life.

Morphology, molecular phylogeny and systematics of the diatom genus Fallacia (Sellaphoraceae), with descriptions of three new species1.

Fallacia is distinguished morpho-anatomically from Navicula sensu lato based on the possession of an H-shaped chloroplast, lateral sterna and a finely porous conopeum, but whether this genus is monophyletic is still in question. Three new Fallacia species are described based on morphology and SSU rRNA and rbcL gene sequences: Fallacia tateyamensis sp. nov., Fallacia bosoensis sp. nov. and Fallacia laevis sp. nov. We performed the first comprehensive molecular and morphological phylogenetic analyses of 31 Fallacia species based on 11 new sequences from six species and 23 morphological characters. We also documented the detailed morphogenesis of Fallacia for the first time. Fallacia is not monophyletic. Both morphological and DNA sequence data supported the separation of Rossia from Fallacia, while the phylogenetic position of Pseudofallacia is uncertain. We recognized four morphogroups in Fallacia by morphological and molecular phylogenetic analyses. Ancestral character reconstruction indicated that diatoms in Sellaphoraceae evolved from the possession of two lateral narrow parallel depressions covered by narrow nonporous conopea, to lyre-shaped canals covered by wide porous conopea. Lanceolate canals and the presence of areolae in canals evolved multiple times independently.

A dark-tolerant diatom (Chaetoceros) cultured from the deep sea.

Although the extreme conditions of the deep sea are typically not suitable for the growth of photosynthetic algae, accumulating evidence indicates that there are diverse healthy phytoplankton living in this environment. However, living phytoplankton from the deep sea have rarely been isolated and cultivated, and so our understanding of where they come from and how they adapt to (or tolerate) the extreme deep-sea environment is limited. Here, under long-term dark stress and subsequent light treatment, we successfully isolated a diatom from a depth of 1,000 m in the Western Pacific Ocean. Morphological observations and molecular phylogenetic analysis revealed that it is affiliated to the genus Chaetoceros, and thus, we tentatively named it Chaetoceros sp. DS1. We observed that the chloroplast genome of this species, is most closely related to that of Chaetoceros simplex. It was shown to have a strong tolerance to darkness in that it maintained its morphological integrity and vitality for up to 3 months in complete darkness at room temperature. We also demonstrated that Chaetoceros sp. DS1 presented a facultative heterotrophic function. Its growth was promoted by many organic carbon sources (e.g., glycerine, ethanol, and sodium acetate) under low light conditions. However, under dark and high light conditions, the growth promotion effect of organic carbon was not obvious. Indeed, Chaetoceros sp. DS1 grew best under low light conditions, indicating that it likely came from the deeper layer of the euphotic zone. The facultative heterotrophic function of this diatom and tolerance to darkness may help it survive in these conditions or enter a dormant period in the deep sea.

Biological Response of Planktic Foraminifera to Decline in Seawater pH.

Understanding the way in which a decline in ocean pH can affect calcareous organisms could enhance our ability to predict the impacts of the potential decline in seawater pH on marine ecosystems, and could help to reconstruct the paleoceanographic events over a geological time scale. Planktic foraminifera are among the most important biological proxies for these studies; however, the existing research on planktic foraminifera is almost exclusively based on their geochemical indices, without the inclusion of information on their biological development. Through a series of on-board experiments in the western tropical Pacific (134°33'54″ E, 12°32'47″ N), the present study showed that the symbiont-bearing calcifier Trilobatus sacculifer-a planktic foraminifer-responded rapidly to a decline in seawater pH, including losing symbionts, bleaching, etc. Several indices were established to quantify the relationships between these biological parameters and seawater pH, which could be used to reconstruct the paleoceanographic seawater pH. We further postulated that the loss of symbionts in planktic foraminifera acts as an adaptive response to the stress of low pH. Our results indicate that an ongoing decline in seawater pH may hinder the growth and calcification of planktic foraminifera by altering their biological processes. A reduction in carbonate deposition and predation could have profound effects on the carbon cycle and energy flow in the marine food web.

Two new species of nematodes from shallow and deep-water sediments in the South China Sea.

Two new species of free-living marine nematodes from the South China Sea are described: Gomphionema setiforme sp. nov. from intertidal sediment and Paracomesoma longissimum sp. nov. from upper continental slope sediment. Gomphionema setiforme sp. nov. is characterized by the punctated cuticle without lateral differentiation and cuticular pores; short cephalic setiform sensilla; spiral amphideal fovea with 4 turns close to the anterior body extremity; large cuticularized buccal cavity with a massive dorsal tooth; pharynx with a large posterior bulb; short, curved spicules; knife-like gubernaculum without apophyses and 11 cup-shaped precloacal supplements. Paracomesoma longissimum sp. nov. is characterized by cuticle with transverse rows of fine punctuations without lateral differentiation; buccal cavity with three teeth; lateral outer labial setiform sensilla 1.5 times as long as the other four outer labial setiform sensilla; spiral amphideal fovea with 2.5 turns; spicules 350360 m long or 15.716 times cloacal body diameter; plate-like gubernaculum without apophyses and 2528 papilliform precloacal supplements.

Metabarcoding Analysis of Harmful Algal Bloom Species in the Western Pacific Seamount Regions.

The Western Pacific is the most oligotrophic sea on Earth, with numerous seamounts. However, the plankton diversity and biogeography of the Western Pacific in general and the seamount regions in particular remains largely unexplored. In this project, we quantitatively analyzed the composition and distribution patterns of plankton species in the Western Pacific seamount regions by applying metabarcoding analysis. We identified 4601 amplicon sequence variants (ASVs) representing 34 classes in seven protist phyla/divisions in the Western Pacific seamount regions, among which Dinoflagellata was by far the most dominant division. Among the 336 annotated phytoplankton species (including species in Dinoflagellata), we identified 36 harmful algal bloom (HAB) species, many of which displayed unique spatial distribution patterns in the Western Pacific seamount regions. This study was the first attempt in applying ASV-based metabarcoding analysis in studying phytoplankton and HAB species in the Western Pacific seamount regions, which may facilitate further research on the potential correlation between HABs in the Western Pacific seamount regions and coastal regions.

Efficient, Flexible Autoinduction Expression Systems with Broad Initiation in Bacillus subtilis.

Low expression levels and inflexible induction initiation have been the main obstacles to produce proteins using bacterial quorum sensing (QS). The typical QS system in Bacillus subtilis, ComQXPA, activates the promoter PsrfA using ComX and ComA as an auto-inducer and a promoter activator, respectively. Here, we developed a series of flexible autoinduction expression systems in B. subtilis WB600 based on ComQXPA using a super-folder green fluorescent protein as the reporter. The -35 region of PsrfA was replaced with corresponding conserved sequences of σA-dependent promoters, yielding P1 with 85% enhanced strength. We then applied a semi-rational design within the spacer between the -35 and -15 regions of P1 to generate the QS promoter PS1E, which generated 8.22-fold more expression than PsrfA. Based on PS1E, we finally obtained three types of autoinduction expression systems with initiation ranging from 1.5-9.5 h by optimizing the combination of the promoters for ComX and ComA. The yield of Bacillus deramificans pullulanase generated using autoinduction expression systems in B. subtilis reached 80.2 U/mL, which was 36% more than that of the most powerful constitutive promoter P566. Flexible autoinduction expression systems with diverse dynamic features have considerable potential for improving protein expression and metabolite production in B. subtilis.

Morphological and Molecular Characterization of Five Species Including Three New Species of Golden Gorgonians (Cnidaria: Octocorallia) from Seamounts in the Western Pacific.

Members of genus Iridogorgia Verrill, 1883 are the typical deep-sea megabenthos with only seven species reported. Based on an integrated morphological-molecular approach, eight sampled specimens of Iridogorgia from seamounts in the tropical Western Pacific are identified as three new species, and two known species I. magnispiralis Watling, 2007 and I. densispicula Xu, Zhan, Li and Xu, 2020. Iridogorgia flexilis sp. nov. is unique in having a very broad polyp body base with stout and thick scales. Iridogorgia densispiralis sp. nov. can be distinguished by rods present in both polyps and coenenchyme, and I. verrucosa sp. nov. is characterized by having numerous verrucae in coenenchyme and irregular spindles and scales in the polyp body wall. Phylogenetic analysis based on the nuclear 28S rDNA indicated that I. densispiralis sp. nov. showed close relationships with I. splendens Watling, 2007 and I. verrucosa sp. nov., and I. flexilis sp. nov. formed a sister clade with I. magnispiralis. In addition, due to Rhodaniridogorgia fragilis Watling, 2007 nested into the Iridogorgia clade in mtMutS-COI trees and shared highly similar morphology to the latter, we propose to eliminate the genus Rhodaniridogorgia by establishing a new combination Iridogorgia fragilis (Watling, 2007) comb. nov. and resurrecting I. superba Nutting, 1908.

Patterns and drivers of microeukaryotic distribution along the North Equatorial Current from the Central Pacific Ocean to the South China Sea.

Microeukaryotes have been recognized as highly abundant and diverse both in form and function, however, data on their diversity and distribution along marine currents remain scarce. Herein, the distribution of microeukaryotes in surface seawaters was analyzed along a 9000 km stretch of the North Equatorial Current (NEC) and its bifurcation using high throughput DNA sequencing. Significant distance-decay patterns were detected, and the microeukaryote communities were further divided into Central Pacific Ocean (CPO), Western Pacific Ocean (WPO), and South China Sea (SCS) groups. Statistical analyses suggested that the microeukaryotic assembly in the WPO is maintained by the CPO community transported via the NEC. Environmental selection contributed more to community variations than spatial processes did. Temperature and salinity were the two most important environmental factors to shape the examined communities. Altogether, characterizing the microeukaryotic diversity and distribution along the NEC provided an insight into the drivers of their distribution in open oceans.