Planktonic eukaryotes in the Chesapeake Bay: contrasting responses of abundant and rare taxa to estuarine gradients.

Phytoplankton are important drivers of aquatic ecosystem function and environmental health. Their community compositions and distributions are directly impacted by environmental processes and human activities, including in the largest estuary in North America, the Chesapeake Bay. It is crucial to uncover how planktonic eukaryotes play fundamental roles as primary producers and trophic links and sustain estuarine ecosystems. In this study, we investigated the detailed community structure and spatiotemporal variations of planktonic eukaryotes in the Chesapeake Bay across space and time for three consecutive years. A clear seasonal and spatial shift of total, abundant, and rare planktonic eukaryotes was evident, and the pattern recurred interannually. Multiple harmful algal species have been identified in the Bay with varied distribution patterns, such as Karlodinium, Heterosigma akashiwo, Protoperidinium sp., etc. Compared to abundant taxa, rare subcommunities were more sensitive to environmental disturbance in terms of richness, diversity, and distribution. The combined effects of temporal variation (13.3%), nutrient availability (10.0%), and spatial gradients (8.8%) structured the distribution of eukaryotic microbial communities in the Bay. Similar spatiotemporal patterns between planktonic prokaryotes and eukaryotes suggest common mechanisms of adjustment, replacement, and species interaction for planktonic microbiomes under strong estuarine gradients. To our best knowledge, this work represents the first systematic study on planktonic eukaryotes in the Bay. A comprehensive view of the distribution of planktonic microbiomes and their interactions with environmental processes is critical in understanding the underlying microbial mechanisms involved in maintaining the stability, function, and environmental health of estuarine ecosystems. IMPORTANCE: Deep sequencing analysis of planktonic eukaryotes in the Chesapeake Bay reveals high community diversity with many newly recognized phytoplankton taxa. The Chesapeake Bay planktonic eukaryotes show distinct seasonal and spatial variability, with recurring annual patterns of total, abundant, and rare groups. Rare taxa mainly contribute to eukaryotic diversity compared to abundant groups, and they are more sensitive to spatiotemporal variations and environmental filtering. Temporal variations, nutrient availability, and spatial gradients significantly affect the distribution of eukaryotic microbial communities. Similar spatiotemporal patterns in prokaryotes and eukaryotes suggest common mechanisms of adjustment, substitution, and species interactions in planktonic microbiomes under strong estuarine gradients. Interannually recurring patterns demonstrate that diverse eukaryotic taxa have well adapted to the estuarine environment with a long residence time. Further investigations of how human activities impact estuarine planktonic eukaryotes are critical in understanding their essential ecosystem roles and in maintaining environmental safety and public health.

Depth shapes microbiome assembly and network stability in the Mariana Trench.

IMPORTANCE: Exploring microbial interactions and their stability/resilience from the surface to the hadal ocean is critical for further understanding of the microbiome structure and ecosystem function in the Mariana Trench. Vertical gradients did not destabilize microbial communities after long-term evolution and adaption. The uniform niche breadth, diversity, community complexity, and stability of microbiomes in both upper bathypelagic and hadal waters suggest the consistent roles of microbiomes in elemental cycling and adaptive strategies to overcome extreme environmental conditions. Compared with microeukaryotes, bacteria and archaea play a pivotal role in shaping the stability of the hadal microbiome. The consistent co-occurrence stability of microbiomes across vertical gradients was observed in the Mariana Trench. These results illuminate a key principle of microbiomes inhabiting the deepest trench: although distinct microbial communities occupy specific habitats, the interactions within microbial communities remain consistently stable from the upper bathypelagic to the hadal waters.

Dynamic Susceptibility Contrast-Enhanced Perfusion-Weighted Imaging in Differentiation Between Recurrence and Pseudoprogression in High-Grade Glioma: A Meta-analysis.

INTRODUCTION: In glioma patients that have undergone surgical tumor resection, the ability to reliably distinguish between pseudoprogression (PsP) and a recurrent tumor (RT) is of key clinical importance. Accordingly, this meta-analysis evaluated the utility of dynamic susceptibility contrast-enhanced perfusion-weighted imaging as a means of distinguishing between PsP and RT when analyzing patients with high-grade glioma. MATERIALS AND METHODS: The PubMed, Web of Science, and Wanfang databases were searched for relevant studies. Pooled analyses of sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR) values were conducted, after which the area under the curve (AUC) for summary receiver operating characteristic curves was computed. RESULTS: This meta-analysis ultimately included 21 studies enrolling 879 patients with 888 lesions. Cerebral blood volume-associated diagnostic results were reported in 20 of the analyzed studies, and the respective pooled sensitivity, specificity, PLR, and NLR values were 86% (95% confidence interval [CI], 0.81-0.89), 83% (95% CI, 0.77-0.87), 4.94 (95% CI, 3.61-6.75), and 0.18 (95% CI, 0.13-0.23) for these 20 studies. The corresponding AUC value was 0.91 (95% CI, 0.88-0.93), and the publication bias risk was low ( P = 0.976). Cerebral blood flow-related diagnostic results were additionally reported in 6 of the analyzed studies, with respective pooled sensitivity, specificity, PLR, and NLR values of 85% (95% CI, 0.78-0.90), 85% (95% CI, 0.76-0.91), 5.54 (95% CI, 3.40-9.01), and 0.18 (95% CI, 0.12-0.26). The corresponding AUC value was 0.92 (95% CI, 0.89-0.94), and the publication bias risk was low ( P = 0.373). CONCLUSIONS: The present meta-analysis results suggest that dynamic susceptibility contrast-enhanced perfusion-weighted imaging represents an effective diagnostic approach to distinguishing between PsP and RT in high-grade glioma patients.

Elevated Homocysteine Levels and Hypertension Relate to Cognitive Impairment via Increased White Matter Hyperintensity Volume.

BACKGROUND: Recent studies have identified a relationship between elevated homocysteine levels and hypertension (HTN) with Alzheimer's disease (AD), but its pathogenesis remains unclear. OBJECTIVE: To evaluate elevated homocysteine levels and HTN as risk factors for cognitive impairment (CI) and determine their relationship with white matter hyperintensity (WMH) volume. METHODS: A total of 521 subjects were selected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database and divided into two groups according to the diagnostic criteria of the ADNI database. The CI group included 370 subjects, consisting of 122 with AD and 248 with mild CI, while the cognitively normal (CN) group contained 151 subjects. The history of HTN, homocysteine levels, WMH volume and Mini-Mental State Examination (MMSE) scores were analyzed. RESULTS: The study found that patients with CI had higher homocysteine levels than those with CN. Additionally, WMH volume was significantly correlated with homocysteine levels in CI patients, and MMSE scores decreased as WMH volume increased. Further analysis revealed that CI patients with HTN had significantly higher homocysteine levels than those without HTN. Furthermore, the correlation between WMH volume and homocysteine levels was significant only in CI patients with HTN and not in those without HTN. In CN patients, there was no correlation between WMH volume and homocysteine levels in either the HTN or non-HTN groups, and no difference was observed in homocysteine levels. CONCLUSIONS: It is indicated that elevated homocysteine levels in conjunction with HTN are associated with the increased volume of WMHs and CI.

Environmental gradients shape microbiome assembly and stability in the East China sea.

Microbiomes play a key role in marine ecosystem functioning and sustainability. Their organization and stability in coastal areas, particularly in anthropogenic-influenced regions, however, remains unclear compared with an understanding of how microbial community shifts respond to marine environmental gradients. Here, the assembly and community associations across vertical and horizontal gradients in the East China Sea are systematically researched. The seawater microbial communities possessed higher robustness and lower fragmentation and vulnerability compared to the sediment microbiomes. Spatial gradients act as a deterministic filtering factor for microbiome organization. Microbial communities had lower phylogenetic distance and higher niche breadth in the nearshore and offshore areas compared to intermediate areas. The phylogenetic distance of microbiomes decreased from the surface to the bottom but the niche breadth was enhanced in surface and bottom environments. Vertical gradients destabilized microbial associations, while the community diversity was enhanced. Multivariate regression tree analysis and canonical correspondence analysis indicated that depth, distance from shore, nutrient availability, temperature, salinity, and chlorophyll a, affected the distribution and co-occurrence of microbial groups. Our results highlight the crucial roles of environmental gradients in determining microbiome association and stability. These results improve our understanding of the survival strategies/adaptive mechanisms of microbial communities in response to environmental variation and provide new insights for protecting the ecosystems and maintaining the sustainability of ecological functions.

Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae.

The marine bacterial family Oceanospirillaceae, is well-known for its ability to degrade hydrocarbons and for its close association with algal blooms. However, only a few Oceanospirillaceae-infecting phages have been reported thus far. Here, we report on a novel Oceanospirillum phage, namely, vB_OsaM_PD0307, which has a 44,421 bp linear dsDNA genome and is the first myovirus infecting Oceanospirillaceae. A genomic analysis demonstrated that vB_OsaM_PD0307 is a variant of current phage isolates from the NCBI data set but that it has similar genomic features to two high-quality, uncultured viral genomes identified from marine metagenomes. Hence, we propose that vB_OsaM_PD0307 can be classified as the type phage of a new genus, designated Oceanospimyovirus. Additionally, metagenomic read mapping results have further shown that Oceanospimyovirus species are widespread in the global ocean, display distinct biogeographic distributions, and are abundant in polar regions. In summary, our findings expand the current understanding of the genomic characteristics, phylogenetic diversity, and distribution of Oceanospimyovirus phages. IMPORTANCE Oceanospirillum phage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae, and it represents a novel abundant viral genus in polar regions. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral genus, namely Oceanospimyovirus.

Assembly and Network Stability of Planktonic Microorganisms under the Influence of Salinity Gradient: an Arctic Case Study from the Lena River Estuary to the Laptev Sea.

The diversity and primary productivity in the Arctic ecosystem are rapidly changing due to global warming. Microorganisms play a vital role in biogeochemical cycling. However, the diversity of planktonic microorganism communities in the Laptev Sea, one of the most important marginal seas of the Western Arctic Ocean, have not been studied sufficiently in depth. The diversity and community structure of the planktonic microorganisms in the surface water were investigated at 20 stations on the Lena River flowing into the Laptev Sea. Multivariate statistical analyses demonstrated clear spatial patterns in the α diversity and community structure for microorganisms under different salinity levels. Co-occurrence networks of microbial communities revealed that spatial variation promoted differentiation of the characteristics and stability of microbial networks in the Laptev Sea. Contrary to expectations, abundant taxa were found to not have a large influence on the stability and resilience of microbial interactions in the region. On the contrary, less-abundant taxa were found to have far greater influence. The stability and resilience of the prokaryotic and microeukaryotic networks in the Lena River estuary and the continental shelf provided valuable insights into the impact of freshwater and land inflow disturbances on microbial assemblage. Overall, these results enhance our understanding of the composition of microbial communities and provide insights into how spatial changes of abundant versus rare species alter the nature and stability of microbial networks from the Lena River estuary to the Laptev Sea. In addition, this study explored microbial interactions and their ability to resist future disturbances. IMPORTANCE The regime of the Laptev Sea depends closely on the runoff of the Lena River. Microorganisms are essential components of aquatic food webs and play a significant role in polar ecosystems. In this study, we provided a basic microbial data set as well as new insights into the microbial networks from the Lena River estuary to the Laptev Sea, while exploring their potential to resist future disturbances. A comprehensive and systematic study of the community structure and function of the planktonic microorganisms in the Laptev Sea would greatly enhance our understanding of how polar microbial communities respond to the salinity gradient under climate warming.

Characterization and genomic analysis of a novel Synechococcus phage S-H9-2 belonging to Bristolvirus genus isolated from the Yellow Sea.

Cyanophages are known to influence the population dynamics and community structure of cyanobacteria and thus play an important role in biogeochemical cycles in aquatic ecosystems. In this study, a novel Synechococcus phage S-H9-2 infecting Synechococcus sp. WH 8102 was isolated from the coastal water of the Yellow Sea. Synechococcus phage S-H9-2 contains a 187,320 bp genome of double-stranded DNA with a G + C content of 40.3%, 202 potential open reading frames (ORFs), and 15 tRNAs. Phylogenetic analysis and nucleotide-based intergenomic similarity suggest that Synechococcus phage S-H9-2 belongs to the Bristolvirus genus under the family Kyanoviridae. Homologs of the S-H9-2 open reading frame can be found in a variety of marine environments, as shown by the results of mapping the genome sequence of S-H9-2 to the Global Ocean Viromes 2.0 dataset. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as phylogenetic relationships based on complete genome sequences, reflect the mechanism of phage-host interaction and host-specific strategies for adaptation to environmental conditions. This study enriches the current genomic database of cyanophage and contributed to our understanding of the virus-host interactions and their adaption to the environment.

Spatiotemporal Dynamics of Coastal Viral Community Structure and Potential Biogeochemical Roles Affected by an Ulva prolifera Green Tide.

The world's largest macroalgal green tide, caused by Ulva prolifera, has resulted in serious consequences for coastal waters of the Yellow Sea, China. Although viruses are considered to be one of the key factors in controlling microalgal bloom demise, understanding of the relationship between viral communities and the macroalgal green tide is still poor. Here, a Qingdao coastal virome (QDCV) time-series data set was constructed based on the metagenomic analysis of 17 DNA viromes along three coastal stations of the Yellow Sea, covering different stages of the green tide from Julian days 165 to 271. A total of 40,076 viral contigs were detected and clustered into 28,058 viral operational taxonomic units (vOTUs). About 84% of the vOTUs could not be classified, and 62% separated from vOTUs in other ecosystems. Green tides significantly influenced the spatiotemporal dynamics of the viral community structure, diversity, and potential functions. For the classified vOTUs, the relative abundance of Pelagibacter phages declined with the arrival of the bloom and rebounded after the bloom, while Synechococcus and Roseobacter phages increased, although with a time lag from the peak of their hosts. More than 80% of the vOTUs reached peaks in abundance at different specific stages, and the viral peaks were correlated with specific hosts at different stages of the green tide. Most of the viral auxiliary metabolic genes (AMGs) were associated with carbon and sulfur metabolism and showed spatiotemporal dynamics relating to the degradation of the large amount of organic matter released by the green tide. IMPORTANCE To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.

C/EBPß/AEP is age-dependently activated in Parkinson's disease and mediates α-synuclein in the gut and brain.

Parkinson's disease (PD) is the most common neurodegenerative motor disorder, and its pathologic hallmarks include extensive dopaminergic neuronal degeneration in the Substantia nigra associated with Lewy bodies, predominantly consisting of phosphorylated and truncated α-Synuclein (α-Syn). Asparagine endopeptidase (AEP) cleaves human α-Syn at N103 residue and promotes its aggregation, contributing to PD pathogenesis. However, how AEP mediates Lewy body pathologies during aging and elicits PD onset remains incompletely understood. Knockout of AEP or C/EBPß from α-SNCA mice, and their chronic rotenone exposure models were used, and the mechanism of α-Syn from the gut that spread to the brain was observed. Here we report that C/EBPß/AEP pathway, aggravated by oxidative stress, is age-dependently activated and cleaves α-Syn N103 and regulates Lewy body-like pathologies spreading from the gut into the brain in human α-SNCA transgenic mice. Deletion of C/EBPß or AEP substantially diminished the oxidative stress, neuro-inflammation, and PD pathologies, attenuating motor dysfunctions in aged α-SNCA mice. Noticeably, PD pathologies initiate in the gut and progressively spread into the brain. Chronic gastric exposure to a low dose of rotenone initiates Lewy body-like pathologies in the gut that propagate into the brain in a C/EBPß/AEP-dependent manner. Hence, our studies demonstrate that C/EBPß/AEP pathway is critical for mediating Lewy body pathology progression in PD.

Time-resolved transcriptome analysis of Scenedesmus obliquus HTB1 under 10% CO2 condition.

Certain microalgal species can grow under high CO2 concentrations providing potential for mitigating CO2 pollution in flue gas produced by power plants. Microalga Scenedesmus obliquus strain HTB1 was isolated from the Chesapeake Bay and grow rapidly in a high level of CO2 . However, little is known about the molecular responses of HTB1 to high CO2 levels. Here, we investigated how HTB1 responds to 10% CO2 using the time-resolved transcriptome analysis. Gene expression profiles indicated that HTB1 responds quickly (in 2 h) and becomes adaptive within 12 h when exposed to 10% CO2 . Interestingly, certain genes of light-harvesting, chlorophyll synthesis and carbon fixation (i.e. rbcS) were up-regulated at 10% CO2 , and these functional responses are consistent with the increased photosynthesis efficiency and algal biomass under 10% CO2 . Nitrate assimilation was strongly enhanced, with amino acid biosynthesis and aminoacyl tRNA biosynthesis genes being markedly up-regulated, indicating that HTB1 actively takes up nitrogen and accelerates protein synthesis at 10% CO2 . Carbon metabolism including fatty acid biosynthesis and TCA cycle was enhanced at 10% CO2 , supporting the earlier observation of increased lipid content of Scenedesmus sp. under high CO2 levels. Interestingly, key genes like RuBisCO (rbcL) and carbonic anhydrase in carboxysomes did not respond actively to 10% CO2 , implying that exposure to 10% CO2 has little impact on the carbon concentrating mechanisms and CO2 fixation of the Calvin cycle. It appears that HTB1 can grow rapidly at 10% CO2 without significant metabolic changes in carbon fixation and ATP synthesis.

Speech silence character as a diagnostic biomarker of early cognitive decline and its functional mechanism: a multicenter cross-sectional cohort study.

BACKGROUND: Language deficits frequently occur during the prodromal stages of Alzheimer's disease (AD). However, the characteristics of linguistic impairment and its underlying mechanism(s) remain to be explored for the early diagnosis of AD. METHODS: The percentage of silence duration (PSD) of 324 subjects was analyzed, including patients with AD, amnestic mild cognitive impairment (aMCI), and normal controls (NC) recruited from the China multi-center cohort, and the diagnostic efficiency was replicated from the Pitt center cohort. Furthermore, the specific language network involved in the fragmented speech was analyzed using task-based functional magnetic resonance. RESULTS: In the China cohort, PSD increased significantly in aMCI and AD patients. The area under the curve of the receiver operating characteristic curves is 0.74, 0.84, and 0.80 in the classification of NC/aMCI, NC/AD, and NC/aMCI+AD. In the Pitt center cohort, PSD was verified as a reliable diagnosis biomarker to differentiate mild AD patients from NC. Next, in response to fluency tasks, clusters in the bilateral inferior frontal gyrus, precentral gyrus, left inferior temporal gyrus, and inferior parietal lobule deactivated markedly in the aMCI/AD group (cluster-level P < 0.05, family-wise error (FWE) corrected). In the patient group (AD+aMCI), higher activation level of the right pars triangularis was associated with higher PSD in in both semantic and phonemic tasks. CONCLUSIONS: PSD is a reliable diagnostic biomarker for the early stage of AD and aMCI. At as early as aMCI phase, the brain response to fluency tasks was inhibited markedly, partly explaining why PSD was elevated simultaneously.

Microstate feature fusion for distinguishing AD from MCI.

Electroencephalogram (EEG) microstates provide powerful tools for identifying EEG features due to their rich temporal information. In this study, we tested whether microstates can measure the severity of Alzheimer's disease (AD) and mild cognitive impairment (MCI) in patients and effectively distinguish AD from MCI. We defined two features using transition probabilities (TPs), and one was used to evaluate between-group differences in microstate parameters to assess the within-group consistency of TPs and MMSE scores. Another feature was used to distinguish AD from MCI in machine learning models. Tests showed that there were between-group differences in the temporal characteristics of microstates, and some kinds of TPs were significantly correlated with MMSE scores within groups. Based on our newly defined time-factor transition probabilities (TTPs) feature and partial accumulation strategy, we obtained promising scores for accuracy, sensitivity, and specificity of 0.938, 0.923, and 0.947, respectively. These results provide evidence for microstates as a neurobiological marker of AD.

Diagnostic Performance of Dynamic Susceptibility Contrast-Enhanced Perfusion-Weighted Imaging in Differentiating Recurrence From Radiation Injury in Postoperative Glioma: A Meta-analysis.

PURPOSE: It is important to differentiate between radiation injury (RI) and tumor recurrence (TR) in patients with glioma after surgery and radiotherapy. Our objective was to evaluate the use of dynamic susceptibility contrast-enhanced perfusion-weighted imaging to distinguish between TR and RI in patients with glioma. METHODS: Relevant studies published until October 2021 were identified in the PubMed, Embase, and Cochrane Library databases. Stata v12.0 and RevMan 5.3 were used for meta-analysis. RESULTS: In total, the meta-analysis incorporated 13 retrospective studies that included 513 patients with 522 lesions. Among the 522 lesions, 329 lesions were TRs and 193 lesions were RIs. The pooled relative cerebral blood volume value was significantly greater in the TR group ( P < 0.00001) with significant heterogeneity ( I2 = 88%). The pooled sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR) were 83% (95 confidence interval [CI], 77%-88%), 85% (95 CI, 77%-91%), 5.60 (95 CI, 3.61-8.70), and 0.20 (95% CI, 0.14-0.27), respectively. The heterogeneity of sensitivity ( I2 = 33.18%), specificity ( I2 = 24.01%), PLR ( I2 = 0.00%), and NLR ( I2 = 6.68%) is not significant. The area under the receiver operating characteristic curve was 0.91 (95% CI, 0.88-0.93). The 3.0 T magnetic resonance imaging, high-grade glioma, and Europe/America patient subgroups showed PLR greater than 5 and NLR less than 0.2. There was no significant indication of publication bias in the analysis ( P = 0.496). CONCLUSIONS: It is concluded that dynamic susceptibility contrast-enhanced perfusion-weighted imaging is effective for the diagnostic differentiation between TR and RI in patients with glioma.

Characterization and Genomic Analysis of ssDNA Vibriophage vB_VpaM_PG19 within Microviridae, Representing a Novel Viral Genus.

Vibrio parahaemolyticus, a widespread marine bacterium, is responsible for a variety of diseases in marine organisms. Consumption of raw or undercooked seafood contaminated with V. parahaemolyticus is also known to cause acute gastroenteritis in humans. While numerous dsDNA vibriophages have been isolated so far, there have been few studies of vibriophages belonging to the ssDNA Microviridae family. In this study, a novel ssDNA phage, vB_VpaM_PG19 infecting V. parahaemolyticus, with a 5,572 bp ssDNA genome with a G+C content of 41.31% and encoded eight open reading frames, was isolated. Genome-wide phylogenetic analysis of the total phage isolates in the GenBank database revealed that vB_VpaM_PG19 was only related to the recently deposited vibriophage vB_VpP_WS1. The genome-wide average nucleotide homology of the two phages was 89.67%. The phylogenetic tree and network analysis showed that vB_VpaM_PG19 was different from other members of the Microviridae family and might represent a novel viral genus, together with vibriophage vB_VpP_WS1, named Vimicrovirus. One-step growth curves showed that vB_VpaM_PG19 has a short incubation period, suggesting its potential as an antimicrobial agent for pathogenic V. parahaemolyticus. IMPORTANCE Vibriophage vB_VpaM_PG19 was distant from other isolated microviruses in the phylogenetic tree and network analysis and represents a novel microviral genus, named Vimicrovirus. Our report describes the genomic and phylogenetic features of vB_VpaM_PG19 and provides a potential antimicrobial candidate for pathogenic V. parahaemolyticus.

Variations in Marine Bacterial and Archaeal Communities during an Ulva prolifera Green Tide in Coastal Qingdao Areas.

Green tides caused by Ulva prolifera occur annually in the Yellow Sea, potentially influencing the marine microorganisms. Here, we focused on the variations in marine bacterial and archaeal communities during an U. prolifera green tide in coastal Qingdao areas with Illumina high-throughput sequencing analysis. Our results revealed that the diversity and structure of bacterial and archaeal communities, as well as the organization and structure of microbial co-occurrence networks, varied during the green tide. The decline phase may be favorable to the bacterial and archaeal diversity and richness. The bacterial community, as well as the archaeal community, showed clear variations between the outbreak and decline phases. A simpler and less connected microbial co-occurrence network was observed during the outbreak phase compared with the decline phase. Flavobacteriales and Rhodobacterales separately dominated the bacterial community during the outbreak and decline phase, and Marine Group II (MGII) dominated the archaeal community during the green tide. Combined with microbial co-occurrence network analysis, Flavobacteriales, Rhodobacterales and MGII may be important organisms during the green tide. Temperature, chlorophyll a content and salinity may have an important impact on the variations in bacterial and archaeal communities during the green tide.

CircATXN7 contributes to the progression and doxorubicin resistance of breast cancer via modulating miR-149-5p/HOXA11 pathway.

Breast cancer is a frequent tumor threatening the health of women. Circular RNAs (circRNAs) play vital roles in cancer progression and chemoresistance. Herein, we mainly investigate the role and potential mechanism of circRNA ataxin 7 (circATXN7; circ_0066436) in breast cancer. RNA expression levels were detected via quantitative real-time PCR (qPCR), western blot and immunohistochemistry. Cell viability and half inhibitory concentration (IC50) of doxorubicin were assessed by cell counting kit-8 (CCK-8) method. Cell proliferation, migration and invasion were determined by CCK-8, 5-ethynyl-2'-deoxyuridine, colony formation and transwell assays. The binding relationship between microRNA-149-5p (miR-149-5p) and circATXN7 or homeobox A11 (HOXA11) was validated via dual-luciferase reporter assay and RNA immunoprecipitation assay. Xenograft assay was conducted to analyze the effect of circATXN7 on doxorubicin resistance of breast cancer. CircATXN7 and HOXA11 levels were enhanced, whereas miR-149-5p level was declined in breast cancer tissues and cells. CircATXN7 silencing suppressed breast cancer development and doxorubicin resistance. Additionally, circATXN7 upregulated HOXA11 via absorbing miR-149-5p, thereby inducing breast cancer cell progression and reducing doxorubicin sensitivity. Besides, depletion of circATXN7 enhanced doxorubicin sensitivity in vivo. Interference of circATXN7 inhibited breast cancer progression and doxorubicin resistance via mediating miR-149-5p/HOXA11 axis, which might provide a possible biomarker for breast cancer therapy.

Estuarine gradients dictate spatiotemporal variations of microbiome networks in the Chesapeake Bay.

BACKGROUND: Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradients in the estuaries. RESULTS: Here, we constructed co-occurrence networks on prokaryotic microbial communities in the CB, which included seasonal samples from seven spatial stations along the salinity gradients for three consecutive years. Our results showed that spatiotemporal variations of planktonic microbiomes promoted differentiations of the characteristics and stability of prokaryotic microbial networks in the CB estuary. Prokaryotic microbial networks exhibited a clear seasonal pattern where microbes were more closely connected during warm season compared to the associations during cold season. In addition, microbial networks were more stable in the lower Bay (ocean side) than those in the upper Bay (freshwater side). Multivariate regression tree (MRT) analysis and piecewise structural equation modeling (SEM) indicated that temperature, salinity and total suspended substances along with nutrient availability, particulate carbon and Chl a, affected the distribution and co-occurrence of microbial groups, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. Interestingly, compared to the abundant groups (such as SAR11, Saprospiraceae and Actinomarinaceae), the rare taxa including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), and NS11-12 marine group (Bacteroidetes) contributed greatly to the stability of microbial co-occurrence in the Bay. Modularity and cluster structures of microbial networks varied spatiotemporally, which provided valuable insights into the 'small world' (a group of more interconnected species), network stability, and habitat partitioning/preferences. CONCLUSION: Our results shed light on how estuarine gradients alter the spatiotemporal variations of prokaryotic microbial networks in the estuarine ecosystem, as well as their adaptability to environmental disturbances and co-occurrence network complexity and stability.

Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus.

Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCEAlteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.

Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria.

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from -20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.