A genomic and epigenomic atlas of prostate cancer in Asian populations.

Prostate cancer is the second most common cancer in men worldwide1. Over the past decade, large-scale integrative genomics efforts have enhanced our understanding of this disease by characterizing its genetic and epigenetic landscape in thousands of patients2,3. However, most tumours profiled in these studies were obtained from patients from Western populations. Here we produced and analysed whole-genome, whole-transcriptome and DNA methylation data for 208 pairs of tumour tissue samples and matched healthy control tissue from Chinese patients with primary prostate cancer. Systematic comparison with published data from 2,554 prostate tumours revealed that the genomic alteration signatures in Chinese patients were markedly distinct from those of Western cohorts: specifically, 41% of tumours contained mutations in FOXA1 and 18% each had deletions in ZNF292 and CHD1. Alterations of the genome and epigenome were correlated and were predictive of disease phenotype and progression. Coding and noncoding mutations, as well as epimutations, converged on pathways that are important for prostate cancer, providing insights into this devastating disease. These discoveries underscore the importance of including population context in constructing comprehensive genomic maps for disease.

HPS6 Deficiency Leads to Reduced V-ATPase and Impaired Biogenesis of Lamellar Bodies in Alveolar Type II Cells.

Lamellar body (LB) is a tissue-specific lysosome-related organelle in type II alveolar cells, which is the main site for the synthesis, storage and secretion of pulmonary surfactants. Defects in pulmonary surfactants lead to a variety of respiratory and immune-related disorders. LB biogenesis is closely related to its function, but the underlying regulatory mechanism is largely unclear. Here, we found that deficiency of HPS6, a subunit of BLOC-2 (biogenesis of lysosome-related organelles complex-2), led to the reduction of the steady-state level of V-ATPase and the increase of luminal pH of LB. Furthermore, we observed increased LB size, accumulated surfactant proteins, and altered lipid profiling of lung tissue and bronchoalveolar lavage fluid due to HPS6 deficiency. These findings suggest that HPS6 regulates the distribution of V-ATPase on LBs to maintain its luminal acidity and LB homeostasis. This may provide new insights into the LB pathology.

Comprehensive Evolutionary Analysis of the SMXL Gene Family in Rosaceae: Further Insights into Its Origin, Expansion, Diversification, and Role in Regulating Pear Branching.

SMXL genes constitute a conserved gene family that is ubiquitous in angiosperms and involved in regulating various plant processes, including branching, leaf elongation, and anthocyanin biosynthesis, but little is known about their molecular functions in pear branching. Here, we performed genome-wide identification and investigation of the SMXL genes in 16 angiosperms and analyzed their phylogenetics, structural features, conserved motifs, and expression patterns. In total, 121 SMXLs genes were identified and were classified into four groups. The number of non-redundant SMXL genes in each species varied from 3 (Amborella trichopoda Baill.) to 18 (Glycine max Merr.) and revealed clear gene expansion events over evolutionary history. All the SMXL genes showed conserved structures, containing no more than two introns. Three-dimensional protein structure prediction revealed distinct structures between but similar structures within groups. A quantitative real-time PCR analysis revealed different expressions of 10 SMXL genes from pear branching induced by fruit-thinning treatment. Overall, our study provides a comprehensive investigation of SMXL genes in the Rosaceae family, especially pear. The results offer a reference for understanding the evolutionary history of SMXL genes and provide excellent candidates for studying fruit tree branching regulation, and in facilitating pear pruning and planting strategies.

The hepatoprotective effects of plant-based foods based on the "gut-liver axis": a prospective review.

The importance of the "gut-liver axis" in the pathogenesis of liver diseases has been revealed recently; which promotes the process of developing preventive and therapeutic strategies. However, considering that there are still many challenges in the medical treatment of liver diseases, potential preventive dietary intervention may be a good alternative choice. Plant-based foods have received much attention due to their reported health-promoting effects in targeting multiple pathways involved in the pathogenesis of liver diseases as well as the relative safety for general use. Based on the PubMed and Web of Science databases, this review emphatically summarizes the plant-based foods and their chemical constituents with reported effects to impact the LPS/TLR4 signaling pathway of gut-liver axis of various liver diseases, reflecting their health benefits in preventing/alleviating liver diseases. Moreover, some plant-based foods with potential gut-liver effects are specifically analyzed from the reported studies and conclusions. This review intends to provide readers an overview of the current progress in the field of this research topic. We expect to see more hepatoprotective measures for alleviating the current prevalence of liver diseases.

Seagrass Thalassia hemprichii and associated bacteria co-response to the synergistic stress of ocean warming and ocean acidification.

Seagrass meadows play vital ecological roles in the marine ecosystem. Global climate change poses considerable threats to seagrass survival. However, it is unclear how seagrass and its associated bacteria will respond under future complex climate change scenarios. This study explored the effects of ocean warming (+2 °C) and ocean acidification (-0.4 units) on seagrass physiological indexes and bacterial communities (sediment and rhizosphere bacteria) of the seagrass Thalassia hemprichii during an experimental exposure of 30 days. Results demonstrated that the synergistic effect of ocean warming and ocean acidification differed from that of one single factor on seagrass and the associated bacterial community. The seagrass showed a weak resistance to ocean warming and ocean acidification, which manifested through the increase in the activity of typical oxidoreductase enzymes. Moreover, the synergistic effect of ocean warming and ocean acidification caused a significant decrease in seagrass's chlorophyll content. Although the bacterial community diversity exhibited higher resistance to ocean warming and ocean acidification, further bacterial functional analysis revealed the synergistic effect of ocean warming and ocean acidification led to significant increases in SOX-related genes abundance which potentially supported the seagrass in resisting climate stress by producing sulfates and oxidizing hydrogen sulfide. More stable bacterial communities were detected in the seagrass rhizosphere under combined ocean warming and ocean acidification. While for one single environmental stress, simpler networks were detected in the rhizosphere. In addition, the observed significant correlations between several modules of the bacterial community and the physiological indexes of the seagrass indicate the possible intimate interaction between seagrass and bacteria under ocean warming and ocean acidification. This study extends our understanding regarding the role of seagrass associated bacterial communities and sheds light on both the prediction and preservation of the seagrass meadow ecosystems in response to global climate change.

Evaluation of the Different Nutritional and Environmental Parameters on Microbial Pyrene Degradation by Mangrove Culturable Bacteria.

Mangrove ecosystems play curial roles in providing many ecological services and alleviating global climate change. However, they are in decline globally, mainly threatened by human activities and global warming, and organic pollutants, especially PAHs, are among the crucial reasons. Microbial remediation is a cost-effective and environmentally friendly way of alleviating PAH contamination. Therefore, understanding the effects of environmental and nutritional parameters on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) is significant for the bioremediation of PAH contamination. In the present study, five bacterial strains, designated as Bp1 (Genus Rhodococcus), Sp8 (Genus Nitratireductor), Sp13 (Genus Marinobacter), Sp23 (Genus Pseudonocardia), and Sp24 (Genus Mycolicibacterium), have been isolated from mangrove sediment and their ring hydroxylating dioxygenase (RHD) genes have been successfully amplified. Afterward, their degradation abilities were comprehensively evaluated under normal cultural (monoculture and co-culture) and different nutritional (tryptone, yeast extract, peptone, glucose, sucrose, and NPK fertilizer) and environmental (cetyl trimethyl ammonium bromide (CTAB), sodium dodecyl sulfate (SDS)) parameters, as well with different co-contaminants (phenanthrene and naphthalene) and heavy metals (Cd2+, Cu2+, Fe3+, Ni2+, Mg2+, Mn2+, and Co2+). The results showed that strain Sp24 had the highest pyrene degradation rate (85%) in the monoculture experiment after being cultured for 15 days. Adding nitrogen- and carbon-rich sources, including tryptone, peptone, and yeast extract, generally endorsed pyrene degradation. In contrast, the effects of carbon sources (glucose and sucrose) on pyrene degradation were distinct for different bacterial strains. Furthermore, the addition of NPK fertilizer, SDS, Tween-80, phenanthrene, and naphthalene enhanced the bacterial abilities of pyrene removal significantly (p < 0.05). Heavy metals significantly reduced all bacterial isolates' degradation potentials (p < 0.05). The bacterial consortia containing high bio-surfactant-producing strains showed substantially higher pyrene degradation. Moreover, the consortia of three and five bacterial strains showed more degradation efficiency than those of two bacterial strains. These results provide helpful microbial resources for mangrove ecological remediation and insight into optimized culture strategies for the microbial degradation of PAHs.

Superconductivity Induced by Site-Selective Arsenic Doping in Mo5Si3.

Arsenic doping in silicides has been much less studied compared with phosphorus. In this study, superconductivity is successfully induced by As doping in Mo5Si3. The superconducting transition temperature (Tc) reaches 7.7 K, which is higher than those in previously known W5Si3-type superconductors. Mo5Si2As is a type-II BCS superconductor with upper and lower critical fields of 6.65 T and 22.4 mT, respectively. In addition, As atoms are found to selectively take the 8h sites in Mo5Si2As. The emergence of superconductivity is possibly due to the shift of Fermi level as a consequence of As doping, as revealed by the specific heat measurements and first-principles calculations. Our work provides not only another example of As doping but also a practical strategy to achieve superconductivity in silicides through Fermi level engineering.

METTL16 promotes hepatocellular carcinoma progression through downregulating RAB11B-AS1 in an m6A-dependent manner.

BACKGROUND: The molecular mechanisms driving hepatocellular carcinoma (HCC) remain largely unclear. As one of the major epitranscriptomic modifications, N6-methyladenosine (m6A) plays key roles in HCC. The aim of this study was to investigate the expression, roles, and mechanisms of action of the RNA methyltransferase methyltransferase-like protein 16 (METTL16) in HCC. METHODS: The expression of METTL16 and RAB11B-AS1 was determined by RT-qPCR. The regulation of RAB11B-AS1 by METTL16 was investigated by RNA immunoprecipitation (RIP), methylated RIP (MeRIP), and RNA stability assays. In vitro and in vivo gain- and loss-of-function assays were performed to investigate the roles of METTL16 and RAB11B-AS1. RESULTS: METTL16 was upregulated in HCC, and its increased expression was correlated with poor prognosis of HCC patients. METTL16 promoted HCC cellular proliferation, migration, and invasion, repressed HCC cellular apoptosis, and promoted HCC tumoral growth in vivo. METTL16 directly bound long noncoding RNA (lncRNA) RAB11B-AS1, induced m6A modification of RAB11B-AS1, and decreased the stability of RAB11B-AS1 transcript, leading to the downregulation of RAB11B-AS1. Conversely to METTL16, RAB11B-AS1 is downregulated in HCC, and its decreased expression was correlated with poor prognosis of patients with HCC. Furthermore, the expression of RAB11B-AS1 was negatively correlated with METTL16 in HCC tissues. RAB11B-AS1 repressed HCC cellular proliferation, migration, and invasion, promoted HCC cellular apoptosis, and inhibited HCC tumoral growth in vivo. Functional rescue assays revealed that overexpression of RAB11B-AS1 reversed the oncogenic roles of METTL16 in HCC. CONCLUSIONS: This study identified the METTL16/RAB11B-AS1 regulatory axis in HCC, which represented novel targets for HCC prognosis and treatment.

MicroRNA-145-5p targeting of TRIM2 mediates the apoptosis of retinal ganglion cells via the PI3K/AKT signaling pathway in glaucoma.

BACKGROUND: There is accumulating evidence to suggest that microRNAs (miRNAs) are associated with the progressive optic neuropathy including glaucoma. Apoptosis of retinal ganglion cells (RGCs) is a hallmark of glaucoma. The present study focused on the effects of miR-145-5p on RGC apoptosis in glaucoma. METHODS: We established a glaucoma rat model by intraocular injection of N-methyl-d-aspartic acid (NMDA). RGCs were isolated from newborn rats and treated with NMDA. Hematoxylin and eosin staining was performed to detect morphological changes in the retinas of rats. The expression of miR-145-5p and tripartite motif-containing 2 (TRIM2) in RGCs was measured by RT-qPCR. The viability of RGCs was measured by MTT assay. Flow cytometry analysis and TUNEL assays were conducted to assess the apoptosis of RGCs. The interaction between miR-145-5p and TRIM2 was investigated using a luciferase reporter assay. RESULTS: Rats injected with NMDA showed a thinner ganglion cell layer (GCL) and inner plexiform layer (IPL) as well as increased expression of miR-145-5p. Silencing of miR-145-5p significantly increased the GCL and IPL in the glaucoma rat model. Moreover, miR-145-5p expression was upregulated in RGCs ex vivo in response to NMDA. Silencing of miR-145-5p promoted cell viability and suppressed apoptosis in NMDA-treated RGCs. Mechanistically, miR-145-5p targeted the TRIM2 3' untranslated region to suppress its expression. TRIM2 was upregulated in NMDA-treated RGCs and protected RGCs against NMDA-induced apoptosis. Furthermore, miR-145-5p suppressed the PI3K/AKT pathway by downregulating TRIM2 in NMDA-treated RGCs. CONCLUSIONS: Suppression of miR-145-5p inhibited the apoptosis of RGCs via TRIM2-mediated activation of the PI3K/AKT signaling pathway in NMDA-induced glaucoma.

Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium.

BACKGROUND: The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the ability of this host to cope with complex and changing marine environments. In this study, the coral Pocillopora damicornis was inoculated with a beneficial microorganisms for corals (BMC) consortium to investigate how the coral host and its associated microbial community would respond. RESULTS: High-throughput 16S rRNA gene sequencing revealed no significant differences in bacterial community α-diversity. However, the bacterial community structure differed significantly between the BMC and placebo groups at the end of the experiment. Addition of the BMC consortium significantly increased the relative abundance of potentially beneficial bacteria, including the genera Mameliella and Endozoicomonas. Energy reserves and calcification rates of the coral host were also improved by the addition of the BMC consortium. Co-occurrence network analysis indicated that inoculation of coral with the exogenous BMC consortium improved the physiological status of the host by shifting the coral-associated microbial community structure. CONCLUSIONS: Manipulating the coral-associated microbial community may enhance the physiology of coral in normal aquarium conditions (no stress applied), which may hypothetically contribute to resilience and resistance in this host.

Effect of pyrene and phenanthrene in shaping bacterial communities in seagrass meadows sediments.

Polycyclic aromatic hydrocarbons (PAHs), originating from anthropogenic and natural sources, are highly concerned environmental pollutants. This study investigated the impact of two model PAHs (pyrene and phenanthrene) on bacterial community succession in the seagrass meadows sediment in a lab-scale microcosm. Halophila ovalis sediment slurry microcosms were established, one group was placed as a control, and the other two were treated with pyrene and phenanthrene. Bacterial community succession in response to respective PAHs was investigated by 16S rRNA amplicon sequencing. The results demonstrated that bacterial diversity decrease in each microcosm during the incubation process; however, the composition of bacterial communities in each microcosm was significantly different. Proteobacteria (37-89%), Firmicutes (9-41%), and Bacteroides (7-21%) were the predominant group at the phylum levels. Their abundance varies during the incubation process. Several previously reported hydrocarbon-degrading genera, such as Pseudomonas, Spinghobium, Sphingobacterium, Mycobacterium, Pseudoxanthomonas, Idiomarina, Stenotrophomonas, were detected in higher abundance in pyrene- and phenanthrene-treated microcosms. However, these genera were distinctly distributed in the pyrene and phenanthrene treatments, suggesting that certain bacterial groups favorably degrade different PAHs. Statistical analyses, such as ANOSIM and PERMANOVA, also revealed that significant differences existed among the treatments' bacterial consortia (P < 0.05). This work showed that polycyclic aromatic hydrocarbon significantly affects bacterial community succession, and different PAHs might influence the bacterial community succession differently.

Effect of PAHs on nitrogen-fixing and sulfate-reducing microbial communities in seagrass Enhalus acoroides sediment.

Seagrass meadows are vital ecosystems with high productivity and biodiversity and often in the oligotrophic area. Nitrogen usually limits productivity in this ecosystem as the main nutrient factor. Biological nitrogen fixation by diazotrophs in the rhizosphere sediment can introduce "new" nitrogen into the ecosystem. Previous studies revealed that most sulfate-reducing bacteria (SRB) can also fix nitrogen like the nitrogen-fixing bacteria (NFB). Moreover, both sulfate reduction and nitrogen fixation were affected by the organic pollutant. However, rare information is available regarding the NFB and SRB community composition and their temporal response to the pollutant. The quantitative real-time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis have been used to analyze NFB and SRB communities' shifts under different PAHs concentrations. They both experienced a dramatic shift under PAHs stress but exhibited different patterns. SRB could use the low and high concentration PAHs at the early stage of the incubation, while only the low concentration of PAHs could stimulate the growth of NFB through the whole incubation period. The predominant species of NFB communities were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria; while for SRB communities were class Epsilonproteobacteria. Redundancy analysis indicated the significant environmental factors for the two communities were both ammonium and pH (P < 0.05). There existed nifH sequences related to known nitrogen fixing SRB Desulfatibacillum alkenivorans, which confirmed that microbial N2 fixation and sulfate reduction were coupled in the seagrass ecosystem by molecular technique. Our investigation provides new insight into the NFB and SRB community in the seagrass meadow.

Diversity and abundance of diazotrophic communities of seagrass Halophila ovalis based on genomic and transcript level in Daya Bay, South China Sea.

Seagrass ecosystems are among the most productive marine ecosystems, and diazotrophic communities play a crucial role in sustaining the productivity and stability of such ecosystems by introducing fixed nitrogen. However, information concerning both total and active diazotrophic groups existing in different compartments of seagrass is lacking. This study comprehensively investigated the diversity, structure, and abundance of diazotrophic communities in different parts of the seagrass Halophila ovalis at the DNA and RNA level from clone libraries and real-time quantitative PCR. Our results indicated that nearly one-third of existing nitrogen-fixing bacteria were active, and their abundance might be controlled by nitrogen to phosphorus ratio (N:P). Deltaproteobacteria and Gammaproteobacteria were dominant groups among the total and active diazotrophic communities in all samples. These two groups accounted for 82.21% and 70.96% at the DNA and RNA levels, respectively. The genus Pseudomonas and sulfate-reducing bacteria (genera: Desulfosarcina, Desulfobulbus, Desulfocapsa, and Desulfopila) constituted the significant fraction of nitrogen-fixing bacteria in the seagrass ecosystem, playing an additional role in denitrification and sulfate reduction, respectively. Moreover, the abundance of the nitrogenase gene, nifH, was highest in seawater and lowest in rhizosphere sediments from all samples. This study highlighted the role of diazotropic communities in the subtropical seagrass ecosystem.

Coacervation of Spherical Polyelectrolyte Brushes with Additional Polyelectrolytes Bearing Positive or Negative Charges.

By combining small-angle X-ray scattering, wide-angle X-ray scattering, and rheology, the effect of additional polyelectrolyte chains on interactions among spherical polyelectrolyte brushes (SPB) was systematically investigated both on microscopic and macroscopic levels. The negatively charged poly(acrylic acid) (PAA) chains and positively charged poly(dimethyl diallyl ammonium chloride) (PDDA) chains were used as additional polyelectrolyte chains to investigate the local ordered structure and the "polyelectrolyte peak" among SPB. Interestingly, coacervation appeared in the SPB emulsion while introducing additional free polyelectrolyte chains. The addition of excess positively charged PDDA chains would lead to the transformation of the SPB emulsion from the coacervation to the aggregation, while it has not been observed in the case of PAA chains. Moreover, it was further confirmed that the specific local ordered structure was caused by the electrostatic interaction among polyelectrolyte chains of adjacent SPB. This work could enrich our understanding of polyelectrolyte assembly in concentrated SPB, thereby greatly broadening the application fields of SPB.

Whole-body MRI-based multivariate prediction model in the assessment of bone metastasis in prostate cancer.

PURPOSE: A whole-body MRI (WB-MRI) including T1, short time inversion recovery (STIR), diffusion-weighted imaging (high b value) was applied in our center for the detection of bone metastasis in prostate cancer (PCa) patients. We intended to assess the diagnostic performance of this examination. METHODS: 547 cases of PCa patients with higher risk of metastasis were referred to bone scintigraphy with SPECT/CT (BS + SPECT/CT) and whole-body MRI in Shanghai Changhai Hospital. Best valuable comparator (BVC) was applied for the final diagnosis of metastasis. A panel of radiologists interpreted the results. Decision curve analysis (DCA) and receiver operating characteristic curve (ROC) analysis were applied. RESULTS: Bone metastasis was diagnosed in 110 cases, and others were non-metastatic by BVC. The area under the receiver operating characteristic curve (AUC) was higher in WB-MRI (0.778) than BS + SPECT/CT (0.634, p < 0.001). A WB-MRI-based prediction model was established with AUC of 0.877. Internal validation showed that the predictive model was well-calibrated. The DCA demonstrated that the model had higher net benefit than the BS + SPECT/CT-based model. CONCLUSION: WB-MRI is more effective in identifying metastasis in PCa patients than BS + SPECT/CT. The prediction model combined WB-MRI with clinical parameters may be a promising approach to the assessment of metastasis.

Insight into Bacterial Community Responses to Polycyclic Aromatic Hydrocarbons and the Degradation Potentials of Three Bacterial Isolates in Seagrass Halophila ovalis Sediments.

Seagrass meadows constitute a prestigious ecosystem in the marine environment, providing valuable ecological and commercial services. Among the various causes, pollutions are considered one of the significant reasons for seagrass decline globally. This study investigates the impacts of polycyclic aromatic hydrocarbons mixture (pyrene, phenanthrene, and fluorene) on bacterial communities in Halophila ovalis sediments. The seagrass sediment bacterial microbiome was evaluated in a batch culture experiment by Illumina MiSeq sequencing. Culture-able bacterial strains were isolated and characterized by 16S rRNA gene sequencing. The results demonstrated an excellent alpha diversity in the original sediments with a Shannon index of (8.078) compared to the subsequent control group (5.908) and PAH-treated group (PAH-T) (4.916). Three phyla, Proteobacteria, Firmicutes, and Bacteroidetes, were detected in high abundance in the control and PAH-T groups. However, a significant difference (P < 0.05) was observed at the genus level between control and PAH-T group bacterial consortia. Pseudomonas, Mycobacterium, Idiomarina, Hydrogenophaga, Alteromonas, Sphingobacterium, and several others were highly abundant in PAH-T groups. Most of the culture-able isolates recovered in this study showed the closest resemblance to previously identified hydrocarbon-degrading bacteria. Among the three strains, Mix-16 (Citricoccus yambaruensis) and Mix-20 (Gordonia rubripertincta) showed a higher degradation of PAHs than Mix-19 (Isoptericola halotolerans) in the monoculture experiment. The most increased degradation of PAHs was recorded in the co-culture experiment. The present work revealed that PAHs could act as environmental stress and can influence bacterial community succession. Moreover, the co-culture strategy significantly enhanced the biodegradation of PAHs.

The diversity and metabolic potential of the microbial functional gene associated with Porites pukoensis.

Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.

Microbial community structure shifts and potential Symbiodinium partner bacterial groups of bleaching coral Pocillopora verrucosa in South China Sea.

The community structure of coral associated microorganisms will change greatly in coral bleaching. However, the relationship between specific bacteria groups and Symbiodinium, which is easy to be found in the bleaching process, has been ignored for a long time. In this study, the changes of coral microbial community during a natural bleaching event in the South China Sea were studied by 16S rRNA gene high-throughput sequencing. The microbial community composition of bleached corals was significantly different from that of normal corals (P < 0.001). OTUs belong to Bacillus, Exiguobacterium, Oceanobacillus, Saccharibacteria and Ostreobiaceae was significantly increased in the bleaching corals. The relative abundance of 30.9% OTUS changed significantly during coral bleaching. The relative abundance of potential coral pathogenic groups was not significantly different between normal and bleaching corals. Symbiodinium positively correlated bacterial groups accounted for 6.9% and 4.3% in the normal corals and bleached corals, respectively. The dominated groups of potential Symbiodinium-partner bacteria are Lactococcus and Bacillus. The potential Symbiodinium-partner bacterial groups in bleached corals were significantly lower than that in the normal corals, which further showed their coexistence with Symbiodinium. This study provides insight into the role of potential Symbiodinium-partner bacterial groups in the coral bleaching process and supports the theory of beneficial microorganisms for corals.

The diversity of alkane-degrading bacterial communities in seagrass ecosystem of the South China Sea.

Seagrass meadows are one of the most important marine ecosystems. Alkanes are the common hydrocarbon contaminants that can affect seagrass growth. In this study, a large spatial-scale investigation has been carried out on the alkane-degrading bacterial community structure in the rhizosphere and non-rhizosphere sediments of two seagrass species (Thalassia hemprichii and Halophila ovalis). AlkB gene was employed as a biomarker gene to study the alkane-degrading bacterial community structure. The results showed that the alpha diversity of the alkane-degrading bacterial community in T. hemprichii non-rhizosphere sediments was higher than that of its rhizosphere sediments. However, the alpha diversity of the alkane-degrading bacterial community in H. ovalis rhizosphere sediments was higher than that of its non-rhizosphere sediments in the open sea, but the result was contrast in the coast area. In addition, the alpha diversity of alkane-degrading bacterial communities in the coast area was higher than that of far away from the coast in the T. hemprichii rhizosphere and non-rhizosphere sediments. The phylogenetic analysis result revealed that the alkB sequences from the seagrass ecosystem were mainly affiliated with the class Alphaproteobacteria, and had the two novel lineages. Genus Agrobacterium was the most predominant alkane-degrading bacteria. These results contributed to disclose the geographical distribution pattern of alkane-degrading bacteria in the seagrass ecosystem of the South China Sea.

Identification of three seagrass species in coral reef ecosystem by using multiple genes of DNA barcoding.

Seagrasses constitute a significant part of coral reef ecosystems, representing high primary productivity and one of the most important coastal habitats in marine ecosystems. Though seagrasses possess irreplaceable ecological services to the marine environment, taxonomical ambiguity still exists due to similar morphological characters and phenotypic plasticity. As an emerging technology, DNA barcoding can effectively identify cryptic species using a short orthologous DNA region. In this study, we collected samples from five different locations (Daya Bay, Xincun Bay, Sanya Bay, Xisha Islands, and Nansha Islands), and three seagrass species Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis was evaluated. Moreover, ITS, matK and rbcL genes were used as DNA barcodes. The results indicated that single ITS and concatenated ITS/matK/rbcL both conducted better species resolution than single matK and rbcL. Nevertheless, single ITS was more convenient. Furthermore, in all the four topology trees, three species resolved as 3 clusters as well H. ovalis and T. hemprichii grouped as sister clade. In the meantime, differentiation lay in intra-species based on the result of single ITS and three-locus analysis. Within H. ovalis and T. hemprichii separately, individuals from Xisha Islands first group together, then grouped with individuals from Nansha Islands and/or Xincun Bay and/or Sanya Bay and/or Daya Bay, which indicated that geographical distribution influenced population evolution. However, intra-species differentiation did not emerge in the tree of matK or rbcL.