Different Responses of Bacteria and Microeukaryote to Assembly Processes and Co-occurrence Pattern in the Coastal Upwelling.

Upwelling may generate unique hydrological and environmental heterogeneity, leading to enhanced diffusion to reshape microbial communities. However, it remains largely unknown how different microbial taxa respond to highly complex and dynamic upwelling systems. In the present study, geographic patterns and co-occurrence network of different microbial communities in response to upwelling were examined. Our results showed that coastal upwelling shaped prokaryotic and eukaryotic microbial community and decreased their diversity. In addition, bacteria and microeukaryote had similar biogeographical patterns with distinct assembly mechanisms. The impact of stochastic processes on bacteria was significantly stronger compared with microeukaryote in upwelling. Lower network complexity but more frequent interaction was found in upwelling microbial co-occurrence. However, the upwelling environment increased the robustness and modularity of bacterial network, while eukaryotic network was just the opposite. Co-occurrence networks of bacteria and microeukaryote showed significant distance-decay patterns, while the bacterial network had a stronger spatial variation. Temperature and salinity were the strongest environmental factors affecting microbial coexistence, whereas the topological characteristics of bacterial and eukaryotic networks had different responses to the upwelling environment. These findings expanded our understanding of biogeographic patterns of microbial community and ecological network and the underlying mechanisms of different microbial taxa in upwelling.

Genome-wide identification of PEBP gene family members in potato, their phylogenetic relationships, and expression patterns under heat stress.

BACKGROUND: The phosphatidylethanolamine-binding protein (PEBP) gene family is involved in regulating many plant traits. Genome-wide identification of PEPB members and knowledge of their responses to heat stress may assist genetic improvement of potato (Solanum tuberosum). METHODS AND RESULTS: We identified PEBP gene family members from both the recently-updated, long-reads-based reference genome (DM v6.1) and the previous short-reads-based annotation (PGSC DM v3.4) of the potato reference genome and characterized their heat-induced gene expression using RT-PCR and RNA-Seq. Fifteen PEBP family genes were identified from DM v6.1 and named as StPEBP1 to StPEBP15 based on their locations on 6 chromosomes and were classified into FT, TFL, MFT, and PEBP-like subfamilies. Most of the StPEBP genes were found to have conserved motifs 1 to 5. Tandem or segmental duplications were found between StPEBP genes in seven pairs. Heat stress induced opposite expression patterns of certain FT and TFL members but involving different members in leaves, roots and tubers. CONCLUSION: The long-reads-based genome assembly and annotation provides a better genomic resource for identification of PEBP family genes. Heat stress tends to decrease FT gene activities but increases TFL gene activities, but this opposite expression involves different FT/TFL pairs in leaves, roots, and tubers. This tissue-specific expression pattern of PEBP members may partly explain why different potato organs differ in their sensitivities to heat stress. Our study provides candidate PEBP family genes and relevant information for genetic improvement of heat tolerance in potato and may help understand heat-induced responses in other plants.

Organelle DNA contents and starch accumulation in potato tubers.

KEY MESSAGE: Starch contents were found to be positively correlated with organelle/nuclear DNA ratios, suggesting that these ratios are involved in starch accumulation and may serve as a target trait in genetic engineering and a biomarker in breeding for improving the dry matter and starch production in potato. Starch is the main dry matter component of various staple food crops, including potato. Starch synthesis and accumulation is in plastids, uses sugar, consumes cellular energy, and requires active expression of starch synthesis genes. We hypothesized that the plastid/nuclear DNA ratios and mitochondrial/nuclear DNA ratios are involved in this accumulation. We analyzed the dry mater, starch, plastid DNA, mitochondrial DNA, and nuclear DNA in tuber stem ends and tuber bud ends in two potato cultivars and verified the results using whole tubers in nine potato cultivars. Dry matter contents (DMC) and organelle/nuclear DNA ratios increased rapidly during tuber bulking. DMC and starch contents were greater at the tuber stem ends than at the tuber bud ends. Both the comparisons between tuber ends and among whole tubers indicated that DMC and starch contents were positively correlated with both plastid/nuclear DNA ratios and mitochondrial/nuclear DNA ratios. The results suggest that pt/nuc and mt/nuc DNA ratios are important and may serve as a biomarker in selection, genetic engineering, and cytoplasm manipulation, for dry matter and starch accumulation in potato.

A Steroid-Type Antioxidant Targeting the Keap1/Nrf2/ARE Signaling Pathway from the Soft Coral Dendronephthya gigantea.

Four new steroids, named 7-dehydroerectasteroid F (1), 11α-acetoxyarmatinol A (2), 22,23-didehydroarmatinol A (3), and 3-O-acetylhyrtiosterol (4), together with 11 previously described analogues, were isolated from a South China Sea collection of the soft coral Dendronephthya gigantea. The structures of the new steroids were elucidated by comprehensive spectroscopic analysis and by comparison with previously reported data. Compound 1 showed potent protection against H2O2-induced oxidative damage in neuron-like PC12 cells by promoting nuclear translocation of Nrf2 and enhancing the expression of HO-1. 1 represents the first steroid-type antioxidant from marine organisms.

Structurally Diverse Metabolites from the Soft Coral Sinularia verruca Collected in the South China Sea.

Nineteen metabolites with diverse structures, including the rare pyrroloindoline alkaloid verrupyrroloindoline (1), the unprecedented highly fused benzosesquiterpenoid verrubenzospirolactone (2), the new asteriscane-type sesquiterpenoid 10-deoxocapillosanane D (3), and the two new cyclopentenone derivatives (4S*,5S*)-4-hydroxy-5-(hydroxymethyl)-2,3-dimethyl-4-pentylcyclopent-2-en-1-one (4) and (S)-4-hydroxy-5-methylene-2,3-dimethyl-4-pentylcyclopent-2-en-1-one (5), were isolated from a South China Sea collection of the soft coral Sinularia verruca. Eleven previously described marine metabolites (7-15, 18, and 19) were also obtained as well as three new EtOH-adduct artifacts (6, 16, and 17). The structures of the new compounds were elucidated by extensive spectroscopic analysis and by comparison with previously reported data. Compounds 4, 5, and 16 showed protection against the cytopathic effects of HIV-1 infection with EC50 values of 5.8-34 µM, and 4, 6, and 16 exhibited inhibition against LPS-induced NO production with IC50 values of 24-28 µM.

Cembranoids from a Chinese Collection of the Soft Coral Lobophytum crassum.

Ten new cembrane-based diterpenes, locrassumins A-G (1-7), (-)-laevigatol B (8), (-)-isosarcophine (9), and (-)-7R,8S-dihydroxydeepoxysarcophytoxide (10), were isolated from a South China Sea collection of the soft coral Lobophytum crassum, together with eight known analogues (11-18). The structures of the new compounds were determined by extensive spectroscopic analysis and by comparison with previously reported data. Locrassumin C (3) possesses an unprecedented tetradecahydrobenzo[3,4]cyclobuta[1,2][8]annulene ring system. Compounds 1, 7, 12, 13, and 17 exhibited moderate inhibition against lipopolysaccharide (LPS)-induced nitric oxide (NO) production with IC50 values of 8-24 µM.

Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater.

Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.

Four New 7,8-epoxycembranoids from a Chinese soft coral Lobophytum sp.

Four new 7,8-epoxycembranoids, namely (2S*,7S*,8S*,12R*,1Z,3E,10E)-7,8:2,16-diepoxycembra-1(15),3,10-trien-12-ol (1), (2S*,7S*,8S*,11R*,1Z,3E)-7,8:2,16-diepoxycembra-1(15),3,12(20)-trien-11-ol (2), (4S*,7S*,8S*,1Z,2E,11E)-16-acetoxy-7,8-epoxycembra-1(15),2,11-trien-4-ol (3), and (7S*,8S*,15S*,1E,3E,11E)-7,8-epoxycembra-1,3,11-trien-15,16-diol (4) were isolated from a Chinese soft coral Lobophytum sp., together with eleven known analogues 5-15. The structures of the new compounds were determined by extensive spectroscopic data analysis. All compounds were tested for the inhibitory effect on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in mouse peritoneal macrophages (PEMΦ).

Consistent responses of coral microbiome to acute and chronic heat stress exposures.

Frequent and intense heat waves lead to bleaching and even death of reef-building corals, and the thermal tolerance ultimately depends on the genetic composition of the holobiont. Here, we compared the effects of acute and chronic heat stress exposures on coral Porites cylindrica holobiont. Regardless of the temperature treatment, corals at 33 °C showed signs of bleaching and a significant decrease in photochemical efficiency (Fv/Fm). However, Symbiodiniaceae communities were relatively stable and all dominated by the same genus Cladocopium (C15). The relative abundanbce of core microbiome varied significantly, and they may provide several functions important to holobiont fitness. Both heat stress exposures induced the significant structural reorganization of coral-associated bacteria, with bacterial diversity and community heterogeneity significantly increasing with the temperature treatment. The modified stochasticity ratio (MST) revealed that stochastic processes dominated bacterial community assembly in thermally stressed corals. Certain core bacterial members that were hypothesized to fulfil functional niche decreased significantly, with the enrichment of potentially pathogenic and opportunistic bacteria in heat stress exposures. Thermally stressed corals had more positive correlation, higher network complexity and tighter associations among microbial taxa, relative to healthy corals. Overall, the coral microbiome exhibits similar responses to acute and chronic heat stress, and our study provides new insights about the deleterious impacts of complex warming oceans on coral holobiont.

Symbiotic relationship of Comaster schlegelii (Crinoidea: Comatulidae) And Gymnolophus obscura (Ophiuroidea: Ophiotrichidae) derived from stable isotope and fatty acid analyses.

Coral reef community exhibit high species diversity and a broad range of biological relationships including widespread symbiosis and complex food utilization patterns. In our study, we investigated the symbiotic relationship between the commonly crinoid host Comaster schlegelii and its ophiuroid obligatory symbiont Gymnolophus obscura. Using a combination of fatty acid biomarkers and stable isotopic compositions, we explored differences in their organic matter utilization strategies and nutritional relationships. The result of stable isotopes revealed that G. obscura had higher δ15N values than its crinoid host. Particulate organic matter and phytoplankton were identified as the primary food sources for both species, however C. schlegelii showed a higher proportional contribution from benthic microalgae. Fatty acid markers showed that C. schlegelii was more dependent on benthic microalgae such as diatoms, and less on debritic organic matter and bacteria than G. obscura. Elevated δ15N values of G. obscura and similar food source contribution rates between the host and symbiont suggest that ophiuroid feeds on materials filtered by crinoids and have similar diet to the host. Our results provide insights into the symbiotic patterns of crinoids and ophiuroids, while also supplying foundational data on how symbiotic reef species select organic matter utilization strategies to adapt to their environment.

Response of coral bacterial composition and function to water quality variations under anthropogenic influence.

Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.

New cembrane diterpenoids from a Hainan soft coral Sinularia sp.

Five new cembrane diterpenoids, named sinuflexibilins A-E (1-5), along with nine other known diterpenoids (6-14), have been isolated from the organic extract of a Hainan soft coral Sinularia sp. Their structures were determined on the basis of extensive spectroscopic analyses and by comparison of their spectral data with those of related metabolites. Compound 13, flexibilide, exhibited significant inhibitory activity of NF-κB activation using the cell-based HEK293 NF-κB luciferase reporter gene assay.

Polyoxygenated sterols from the South China Sea soft coral Sinularia sp.

Chemical investigation of the ethanol extract of soft coral Sinularia sp. collected from the South China Sea led to the isolation of three new polyoxygenated sterols, (3S,23R,24S)-ergost-5-ene-3ß,23α,25-triol (1), (24S)-ergostane-6-acetate-3ß,5α,6ß,25-tetraol (2), (24S)-ergostane-6-acetate-3ß,6ß,12ß,25-tetraol (3) together with three known ones (4-6). The structures, including relative configurations of the new compounds (1-3), were elucidated by detailed analysis of spectroscopic data (IR, UV, NMR, MS) and by comparison with related reported compounds. The absolute configuration of 1 was further determined by modified Mosher's method. Compound 5 exhibited moderate cytotoxicity against K562 cell line with an IC(50) value of 3.18 µM, but also displayed strong lethality toward the brine shrimp Artemia salina with a LC(50) value of 0.96 µM.

Responses of Symbiodiniaceae Shuffling and Microbial Community Assembly in Thermally Stressed Acropora hyacinthus.

Although the importance of coral holobionts is widely accepted, the relationship between the flexibility of the microbial structure and the coral host is very complicated. Particularly, the community dynamics of holobionts and the stability of host-microbe interactions under different thermal stresses remain largely unknown. In the present study, we holistically explored the physiology and growth of Acropora hyacinthus in response to increased temperatures (from 26 to 33°C). We observed that bleaching corals with loss of algal symbionts reduced lipids and proteins to maintain their survival, leading to decreased tissue biomass and retarded growth. The diversity of Symbiodiniaceae and symbiont shuffling in the community structure was mainly caused by alterations in the relative abundance of the thermally sensitive but dominant clade C symbionts and low abundance of "background types." Bacterial diversity showed a decreasing trend with increasing temperature, whereas no significant shifts were observed in the bacterial community structure. This finding might be attributed to the local adjustment of specific microbial community members that did not affect the overall metabolic state of the coral holobiont, and there was no increase in the proportion of sequences identified as typically pathogenic or opportunistic taxa. The Sloan neutral community model showed that neutral processes could explain 42.37-58.43% of bacterial community variation. The Stegen null model analysis indicates that the stochastic processes explain a significantly higher proportion of community assembly than deterministic processes when the temperature was elevated. The weak effect of temperature on the bacterial community structure and assembly might be related to an increase in stochastic dominance. The interaction of bacterial communities exhibits a fluctuating and simplistic trend with increasing temperature. Moreover, temperature increases were sufficient to establish the high stability of bacterial networks, and a non-linear response was found between the complexity and stability of the networks. Our findings collectively provide new insights into successive changes in the scleractinian coral host and holobionts in response to elevated seawater temperatures, especially the contribution of the community assembly process and species coexistence patterns to the maintenance of the coral-associated bacterial community.

Oxidative stress, apoptosis, and transcriptional responses in Acropora microphthalma under simulated diving activities.

This study simulated the effects of diving activities on the physiology, enzymatic, and transcriptional responses of Acropora microphthalma. Touching had less impact on Fv/Fm, but a few zooxanthellae were decreased and minor MDA was elevated. Caspase 3 was activated to remove damaged cells, and SOD was increased to alleviate oxidative damage. Under double or triple diving stress, we observed mass loss of zooxanthellae and Fv/Fm, a significant increase in MDA, and SOD, CAT was activated in response to oxidative stress. Transcriptome analyses showed that corals activated immune signaling pathways, anti-oxidation pathways, lysosomal, phagosomal, and cellular autophagy pathways to manage oxidation stress. Moreover, it up-regulated carbohydrate metabolisms, as well as lipopolysaccharide metabolism, glycosphingolipid biosynthesis, photorespiration, amino acid metabolism, and fatty acid beta-oxidation, but down-regulated fatty acid biosynthesis to answer energy insufficiency. This research supported that even in a short time, improper diving activities could have a serious impact on coral health.

Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress.

Global change and local stressors are simultaneously affecting the nearshore corals, and microbiome flexibility may assist corals in thriving under such multiple stressors. Here, we investigated the effects of various environmental variables on Galaxea fascicularis holobiont from nearshore and offshore reefs. These nearshore reefs were more turbid, eutrophic, and warm than offshore reefs. However, coral physiological parameters did not differ significantly. Corals under stressful nearshore environments had low symbiont diversity and selected more tolerant Symbiodiniaceae. The bacterial diversity of offshore corals was significantly higher, and their community composition varied obviously. Diffusion limitations and environmental heterogeneity were essential in structuring microbial communities. Functional annotation analysis demonstrated significant differences between nearshore and offshore corals in bacterial functional groups. Environmental stress significantly reduced the complexity and connectivity of bacterial networks, and the abundances of keystone taxa altered considerably. These results indicated that corals could thrive nearshore through holobiont plasticity to cope with multiple environmental stresses.

Steroids with aromatic A-rings from the Hainan soft coral Dendronephthya studeri Ridley.

Eight new marine steroids, characterized by either the presence of an aromatic ring or a cross-conjugated dienone system in ring A, were isolated from the Hainan soft coral Dendronephthya studeri Ridley. Their structures were elucidated on the basis of detailed spectroscopic analysis and by comparison of their NMR data with those reported in the literature.

Bioactive 11,20-epoxy-3,5(16)-diene briarane diterpenoids from the South China Sea gorgonian Dichotella gemmacea.

Seven new briarane diterpenoids, gemmacolides G-M (1-7), were isolated together with two known analogues, juncin O and junceellolide C, from the South China Sea gorgonian Dichotella gemmacea. The structures of the new compounds were elucidated by detailed analysis of spectroscopic data and comparison with reported data. In an in vitro bioassay, these compounds exhibited different levels of growth inhibition activity against A549 and MG63 cells. In particular, compound 4 was more active than the positive control adriamycin against A549 cells. Compounds 4 and 7 also exhibited weak antimicrobial activity against the bacterium Bacillus megaterium and the fungus Septoria tritici, respectively.

Tritoniopsins A-D, cladiellane-based diterpenes from the South China Sea nudibranch Tritoniopsis elegans and its prey Cladiella krempfi.

Four diterpenes, tritoniopsins A-D (1-4), have been isolated from the South China Sea nudibranch Tritoniopsis elegans and its prey, the soft coral Cladiella krempfi. They display an unprecedented pyran ring in the cladiellane framework, thus representing a novel cladiellane-based diterpene family. Their structures have been mainly characterized by NMR and mass spectrometric techniques, whereas the relative configuration of compound 1 was secured by X-ray analysis. Antiproliferative assays on tumor and nontumor cell lines have been carried out for the main metabolite, tritoniopsin B (2).

Diterpenes from the Hainan soft coral Lobophytum cristatum Tixier-Durivault.

Two new prenylgermacrane-type diterpenoids, lobophytumins A and B (1 and 2), two new prenyleudesmane-type diterpenoids, lobophytumins C and D (3 and 4), and two new spatane-type diterpenoids, lobophytumins E and F (5 and 6), were isolated from the Hainan soft coral Lobophytum cristatum Tixier-Durivault. Their structures, including relative configuration, were elucidated by detailed analysis of spectroscopic data and by comparison with related known compounds. In addition, the absolute configuration of lobophytumin C (3) was tentatively assigned by comparing its specific rotation with that of the closely related model compound (-)-ß-selinene (8). On the basis of biogenetic considerations, the absolute configurations of lobophytumins A, B, and D-F were also tentatively suggested. This is the first report of spatane-type diterpenoids from a soft coral source. The present work supports Faulkner's proposal of prenylgermacrene as the precursor of many diterpenes. In a bioassay, lobophytumins C and D (3 and 4) showed weak in vitro cytotoxicities against the tumor cell lines A-549 and HCT-116.