Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea.

This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.

Biogeochemical controls on methylmercury distribution in a subtropical wetland ecosystem.

Wetlands are widely regarded as biogeochemical hotspots of mercury methylation but little is known regarding such roles of mangrove forests. Here, we examined the detailed depth profile of mercury, methylmercury, and organic matter in surface sediments within an estuarine pond at Mai Po Nature Reserve in Hong Kong, China. There is a progressive enrichment of organic matter in sites closer to mangrove forests, and methylmercury showed a significantly positive correlation with organic matter content (p < 0.001). Methylmercury in sediments is significantly (p < 0.05) higher in the summertime when the temperature is elevated but salinity is reduced. Further, sediments at or near the mangrove forest have lower carbon to nitrogen ratio, which may imply more labile organic matter in these organic-rich sediments that can promote microbial mercury methylation. In summary, mangrove forests can enhance net methylmercury production and increase the risk to the migratory birds overwintering in this internationally important wetland.

Exploring the Microbial Mosaic: Insights into Composition, Diversity, and Environmental Drivers in the Pearl River Estuary Sediments.

River estuaries are dynamic and complex ecosystems influenced by various natural processes, including climatic fluctuations and anthropogenic activities. The Pearl River Estuary (PRE), one of the largest in China, receives significant land-based pollutants due to its proximity to densely populated areas and urban development. This study aimed to characterize the composition, diversity, and distribution patterns of sediment microbial communities (bacteria, archaea, and eukaryotes) and investigated the connection with environmental parameters within the PRE and adjacent shelf. Physicochemical conditions, such as oxygen levels, nitrogen compounds, and carbon content, were analyzed. The study found that the microbial community structure was mainly influenced by site location and core depth, which explained approximately 67% of the variation in each kingdom. Sites and core depths varied in sediment properties such as organic matter content and redox conditions, leading to distinct microbial groups associated with specific chemical properties of the sediment, notably C/N ratio and NH4+ concentration. Despite these differences, certain dominant taxonomic groups were consistently present across all sites: Gammaproteobacteria in bacteria; Bathyarchaeia, Nitrososphaeria, and Thermoplasmata in archaea; and SAR in Eukaryota. The community diversity index was the highest in the bacteria kingdom, while the lowest values were observed at site P03 across the three kingdoms and were significantly different from all other sites. Overall, this study highlights the effect of depth, core depth, and chemical properties on sediment microbiota composition. The sensitivity and dynamism of the microbiota, along with the possibility of identifying specific markers for changes in environmental conditions, is valuable for managing and preserving the health of estuaries and coastal ecosystems.

Quantification of Polyphosphate in Environmental Planktonic Samples Using a Novel Fluorescence Dye JC-D7.

Polyphosphate (polyP) is found in plankton of diverse aquatic ecosystems and is important for plankton ecology and biogeochemical cycling. However, our knowledge of polyP in aquatic environments is hindered by a lack of data due to the limitations of quantification methods. The estimate of polyP in model organisms using phenol-chloroform extraction followed by enzymatic hydrolysis is complicated and fails for environmental samples. The commonly used 4',6-diamidino-2-phenylindole (DAPI) fluorescence method for environmental studies, on the contrary, severely overestimates polyP due to interference. In this paper, we develop a plankton lysis buffer to extract polyP and a quantification method using a novel polyP-specific fluorescence dye JC-D7. We test the methods using cultured algae and bacteria, as well as natural samples from marine and freshwater environments. We show that our plankton lysis extracts polyP with high recovery while requiring substantially less time and effort. Subsequent polyP quantification using JC-D7 fluorescence overcomes the interference encountered by the DAPI method and provides an accurate measurement of polyP down to <0.5 µmol L-1. This novel method enables more accurate quantification of polyP in aquatic environments and will profoundly enhance our knowledge of polyP, plankton ecology, and biogeochemistry.

DeepCBA: A deep learning framework for gene expression prediction in maize based on DNA sequences and chromatin interactions.

Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome, which has an important impact on gene expression, transcriptional regulation, and phenotypic traits. To date, several methods have been developed for predicting gene expression. However, existing methods do not take into consideration the effect of chromatin interactions on target gene expression, thus potentially reducing the accuracy of gene expression prediction and mining of important regulatory elements. In this study, we developed a highly accurate deep learning-based gene expression prediction model (DeepCBA) based on maize chromatin interaction data. Compared with existing models, DeepCBA exhibits higher accuracy in expression classification and expression value prediction. The average Pearson correlation coefficients (PCCs) for predicting gene expression using gene promoter proximal interactions, proximal-distal interactions, and both proximal and distal interactions were 0.818, 0.625, and 0.929, respectively, representing an increase of 0.357, 0.16, and 0.469 over the PCCs obtained with traditional methods that use only gene proximal sequences. Some important motifs were identified through DeepCBA; they were enriched in open chromatin regions and expression quantitative trait loci and showed clear tissue specificity. Importantly, experimental results for the maize flowering-related gene ZmRap2.7 and the tillering-related gene ZmTb1 demonstrated the feasibility of DeepCBA for exploration of regulatory elements that affect gene expression. Moreover, promoter editing and verification of two reported genes (ZmCLE7 and ZmVTE4) demonstrated the utility of DeepCBA for the precise design of gene expression and even for future intelligent breeding. DeepCBA is available at http://www.deepcba.com/ or http://124.220.197.196/.

Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment.

Previous studies have deciphered the genomic basis of host-symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae-a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep-sea and shallow-water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free-living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well-adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen-adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves.

A Hierarchical SnO2@Ni6MnO8 Composite for High-Capacity Lithium-Ion Batteries.

Semiconductor-based composites are potential anodes for Li-ion batteries, owing to their high theoretical capacity and low cost. However, low stability induced by large volumetric change in cycling restricts the applications of such composites. Here, a hierarchical SnO2@Ni6MnO8 composite comprising Ni6MnO8 nanoflakes growing on the surface of a three-dimensional (3D) SnO2 is developed by a hydrothermal synthesis method, achieving good electrochemical performance as a Li-ion battery anode. The composite provides spaces to buffer volume expansion, its hierarchical profile benefits the fast transport of Li+ ions and electrons, and the Ni6MnO8 coating on SnO2 improves conductivity. Compared to SnO2, the Ni6MnO8 coating significantly enhances the discharge capacity and stability. The SnO2@Ni6MnO8 anode displays 1030 mAh g-1 at 0.1 A g-1 and exhibits 800 mAh g-1 under 0.5 A g-1, along with high Coulombic efficiency of 95%. Furthermore, stable rate performance can be achieved, indicating promising applications.

Characterization of internal phosphorus loading in the sediment of a large eutrophic lake (Lake Taihu, China).

Lake Taihu suffers from severe algal blooms every year, which is attributed primarily to the release of sediment phosphorus (P), namely the internal P loading. However, the overall internal P loading and the P hotspots in sediment have not been fully studied. This paper presents several methods, including sequential P extraction, the use of diffusive gradient in thin film (DGT), and intact core incubation to give a detailed investigation of sediment internal P loading as well as its roles in algal dominated zones (ADZs) and grass dominated zones (GDZs) in Lake Taihu. Sediment microbial composition was also analyzed to investigate its relationship with P fractions. The results indicate that the total P and the mobile P fraction in the ADZ sediments are generally higher than those of the GDZ sediments. The percentage of sediment mobile P to TP is similar to the mobile P in their distributions. In contrast, calcium bound P accounts for most of the TP in GDZ, while mobile P contributes the most to TP in ADZ. Overall, sediment can release 256 tons of TP and 217 tons of soluble reactive phosphorus (SRP) over a period of six months in the warmer seasons. Similarly, a high concentration of DGT-measured P was observed in ADZs that are recognized as P hotspots in Lake Taihu. Sediments in ADZ and GDZ was dominated by the bacteria Firmicutes and Proteobacteria, respectively and which were closely related with mobile P and calcium bound P in sediment, respectively. GZD seems to be able to retain more P in sediments, thereby reducing its contribution to of internal P loading. These results indicate that the difference in sediment composition between ADZ and GDZ affects their roles in sediment internal P loading, therefore, different management strategies should be used to combat sediment internal P loads in the two zones.

Copper-Catalyzed [4 + 1] Annulation of Enaminothiones with Indoline-Based Diazo Compounds.

A concise synthetic route to spiroindoline-fused S-heterocycles was developed through copper-catalyzed [4 + 1] annulation using enaminothiones as donor-acceptor synthons. Both 3-diazoindolin-2-imines and 3-diazooxindoles were amenable to work as effective C1 building blocks. The reaction proceeds via a copper-catalyzed cascade process involving the in situ generation of copper(I) carbene and C-S/C-C bond formation. This synthetic protocol features the use of readily available substrates, diverse substituent tolerance, and good to excellent yields.

Immunological functional differentiation of two transmembrane variants of Dscam in Chinese mitten crab.

Down syndrome cell adhesion molecule (Dscam), also called hypervariable Dscam (Dscam-hv), is an important player in arthropod alternative splicing that connects neurons and immune regulation, acting as a pathogen-specific recognition molecule. Dscam-hv has two forms: transmembrane (TM) Dscam (mDscam) and soluble Dscam (sDscam). Herein, we investigated two transmembrane variants of mDscam resulting from alternative splicing of the transmembrane domain, focusing on differences in their immune regulation. We characterized the Dscam[TM1] and Dscam[TM2] genes of Chinese mitten crab (Eriocheir sinensis) through bioinformatics analysis. Both genes are expressed in the gill, intestine, and other immune tissues. Following gram-positive and gram-negative bacteria stimulation, EsDscam[TM1] and EsDscam[TM2] mRNA expression levels increased significantly in hemocytes. Sequencing showed that EsDscam[TM1] was more abundant in hemocytes than EsDscam[TM2]. Additionally, the two subtypes differ in their regulation of antimicrobial peptides, the proportion of exon 33 carried, and bacterial phagocytosis.

Phosphorus internal loading and sediment diagenesis in a large eutrophic lake (Lake Chaohu, China).

Sediment phosphorus (P) release and retention are important in controlling whole-system P dynamics and budget in eutrophic lakes. Here we combine short- (seasonal) and long-term (years to decades) studies to quantify the internal P loading and P release potential in the sediments of Lake Chaohu and explore their controlling mechanisms. In the west region of the lake, short-term P diffusive fluxes ranged from 0.2 mg/m2·d-1 to 6.69 mg/m2·d-1 (averaged 2.76 mg/m2·d-1) and long-term net P release ranged from 2.25 mg/m2·d-1 to 8.94 mg/m2·d-1 (averaged 5.34 mg/m2·d-1); in the east region, short-term P diffusive fluxes varied from 0.73 mg/m2·d-1 to 1.76 mg/m2·d-1 (averaged 1.05 mg/m2·d-1) and long-term P release ranged from 0.13 mg/m2·d-1 to 4.15 mg/m2·d-1 (averaged 1.3 mg/m2·d-1). Both short- and long-term P releases were in the same order of magnitudes as the external P inputs (3.56 mg/m2·d-1). Comparison of the long-term and short-term sediment P release indicates that while the high summer P release in the east might only represent a snapshot value, the sediments in the west contribute to large P release for years or even decades, impeding water quality recovery under lake management. Mobilization of surface sediment legacy P accounted for 81% of short-term P release. The long-term release was dominated by remobilization of iron bond P (BD-P) (average 52.1%) at all sites, while Aluminium-bound P (NaOH-rP) exhibited partly reactive and potentially mobile, releasing P to the water column in most sites in the west. Our study demonstrates the importance of sediments as P sources in lake Chaohu. The combination of short- and long-term P release studies can help understand the roles of sediments in regulating the water quality and eutrophication.

Correlational research on facial and clinical characteristics of adolescents with obsessive-compulsive disorder.

BACKGROUND: The neurodevelopmental model of obsessive-compulsive disorder (OCD) suggests that the neurodevelopmental changes in the ventral striatal circuit of the prefrontal lobe are associated with the initial symptoms of OCD. Facial morphology is one of the most consistent anatomical phenotypes of neurodevelopmental disorders, which can reflect brain structure and function. Facial deformity, an easily measured index of brain malformation, can reflect abnormal brain structure and function. Therefore, this study aims to explore the relationship between clinical features and neurodevelopment of adolescents with OCD through facial morphology. METHODS: The enrolled study sample comprised 40 adolescents diagnosed with OCD using the Obsessive Compulsive Inventory-Child Version (OCI-CV) and 38 healthy controls (HCs). Facial photos, 21 facial diameters, and 9 facial angles were collected using image software. RESULTS: In males, lower lip red height was significantly lower in OCD patients than in HCs (P < 0.025); no significant differences were observed in other facial indicators (all P > 0.025). In females, the nasolabial angle was smaller in OCD patients than in HCs (P < 0.025); no significant differences were observed in other facial indicators (all P > 0.025). The difference in lower lip red height between the OCD group and HC group was positively correlated with neutralizing symptoms (r = 0.401, P < 0.05). CONCLUSIONS: Male OCD patients had a thinner lower lip and female OCD patients had smaller nasolabial angles. The facial features of adolescents with OCD were positively correlated with lower lip redness and neutralizing symptoms.

DeepLearnMOR: a deep-learning framework for fluorescence image-based classification of organelle morphology.

The proper biogenesis, morphogenesis, and dynamics of subcellular organelles are essential to their metabolic functions. Conventional techniques for identifying, classifying, and quantifying abnormalities in organelle morphology are largely manual and time-consuming, and require specific expertise. Deep learning has the potential to revolutionize image-based screens by greatly improving their scope, speed, and efficiency. Here, we used transfer learning and a convolutional neural network (CNN) to analyze over 47,000 confocal microscopy images from Arabidopsis wild-type and mutant plants with abnormal division of one of three essential energy organelles: chloroplasts, mitochondria, or peroxisomes. We have built a deep-learning framework, DeepLearnMOR (Deep Learning of the Morphology of Organelles), which can rapidly classify image categories and identify abnormalities in organelle morphology with over 97% accuracy. Feature visualization analysis identified important features used by the CNN to predict morphological abnormalities, and visual clues helped to better understand the decision-making process, thereby validating the reliability and interpretability of the neural network. This framework establishes a foundation for future larger-scale research with broader scopes and greater data set diversity and heterogeneity.

Benthic invaders control the phosphorus cycle in the world's largest freshwater ecosystem.

The productivity of aquatic ecosystems depends on the supply of limiting nutrients. The invasion of the Laurentian Great Lakes, the world's largest freshwater ecosystem, by dreissenid (zebra and quagga) mussels has dramatically altered the ecology of these lakes. A key open question is how dreissenids affect the cycling of phosphorus (P), the nutrient that limits productivity in the Great Lakes. We show that a single species, the quagga mussel, is now the primary regulator of P cycling in the lower four Great Lakes. By virtue of their enormous biomass, quagga mussels sequester large quantities of P in their tissues and dramatically intensify benthic P exchanges. Mass balance analysis reveals a previously unrecognized sensitivity of the Great Lakes ecosystem, where P availability is now regulated by the dynamics of mussel populations while the role of the external inputs of phosphorus is suppressed. Our results show that a single invasive species can have dramatic consequences for geochemical cycles even in the world's largest aquatic ecosystems. The ongoing spread of dreissenids across a multitude of lakes in North America and Europe is likely to affect carbon and nutrient cycling in these systems for many decades, with important implications for water quality management.

Application of deep learning in genomics.

In recent years, deep learning has been widely used in diverse fields of research, such as speech recognition, image classification, autonomous driving and natural language processing. Deep learning has showcased dramatically improved performance in complex classification and regression problems, where the intricate structure in the high-dimensional data is difficult to discover using conventional machine learning algorithms. In biology, applications of deep learning are gaining increasing popularity in predicting the structure and function of genomic elements, such as promoters, enhancers, or gene expression levels. In this review paper, we described the basic concepts in machine learning and artificial neural network, followed by elaboration on the workflow of using convolutional neural network in genomics. Then we provided a concise introduction of deep learning applications in genomics and synthetic biology at the levels of DNA, RNA and protein. Finally, we discussed the current challenges and future perspectives of deep learning in genomics.

Picoplankton accumulate and recycle polyphosphate to support high primary productivity in coastal Lake Ontario.

Phytoplankton can accumulate polyphosphate (polyP) to alleviate limitation of essential nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain elusive. Previously reported polyP enrichment in low-phosphorus oligotrophic marine waters contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay of Lake Ontario, planktonic polyP is controlled by multiple mechanisms and responds strongly to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under acute P stress. Low phosphorus also triggers enrichment of polyP that can be preferentially recycled to attenuate P lost. We discover that picoplankton, despite their low production rates, are responsible for the dynamic polyP metabolisms. Picoplankton store and liberate polyP to support the high primary productivity of blooming algae. PolyP mechanisms enable efficient P recycling on ecosystem and even larger scales.

A Cytosolic Bypass and G6P Shunt in Plants Lacking Peroxisomal Hydroxypyruvate Reductase.

The oxygenation of ribulose 1,5-bisphosphate by Rubisco is the first step in photorespiration and reduces the efficiency of photosynthesis in C3 plants. Our recent data indicate that mutants in photorespiration have increased rates of photosynthetic cyclic electron flow around photosystem I. We investigated mutant lines lacking peroxisomal hydroxypyruvate reductase to determine if there are connections between 2-phosphoglycolate accumulation and cyclic electron flow in Arabidopsis (Arabidopsis thaliana). We found that 2-phosphoglycolate is a competitive inhibitor of triose phosphate isomerase, an enzyme in the Calvin-Benson cycle that converts glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. This block in metabolism could be overcome if glyceraldehyde 3-phosphate is exported to the cytosol, where cytosolic triose phosphate isomerase could convert it to dihydroxyacetone phosphate. We found evidence that carbon is reimported as glucose-6-phosphate, forming a cytosolic bypass around the block of stromal triose phosphate isomerase. However, this also stimulates a glucose-6-phosphate shunt, which consumes ATP, which can be compensated by higher rates of cyclic electron flow.

Dynamic polyphosphate metabolism in cyanobacteria responding to phosphorus availability.

Despite the crucial role of polyphosphate (polyP) in aquatic environments, its metabolism in cyanobacteria responding to nutrients is poorly understood. We investigate polyP in three cyanobacteria species, specifically unicellular picocyanobacteria, under various nutritional conditions. Our experiments show that the accumulation of polyP in cyanobacteria is strongly dynamic, depending on phosphate levels and growth stages. 'Overplus' uptake of phosphorus (P) during the lag phase leads to the rapid accumulation of polyP, followed by lower polyP quotas during the exponential growth stage as a result of competing 'luxury' P uptake and polyP utilization to support rapid cell division. Cyanobacteria are capable of P deficiency responses that preferentially maintain polyP. However, preferential utilization of polyP occurs under severe P stress, suggesting the crucial role of polyP as P reserve to support cellular survival. Strong variability was observed among different species of cyanobacteria in their ability to accumulate polyP, and likely in the threshold P levels at which preferential polyP degradation occurs. This suggests that some cyanobacteria may be more adaptive to P-stressed or P-fluctuating conditions. Our results explain and provide important insights into the variability of polyP observed in aquatic environments where picocyanobacteria are the dominant primary producers.

Photometric screens identified Arabidopsis peroxisome proteins that impact photosynthesis under dynamic light conditions.

Plant peroxisomes function collaboratively with other subcellular organelles, such as chloroplasts and mitochondria, in several metabolic processes. To comprehensively investigate the impact of peroxisomal function on photosynthesis, especially under conditions that are more relevant to natural environments, a systematic screen of over 150 Arabidopsis mutants of genes encoding peroxisomal proteins was conducted using the automated Dynamic Environment Photosynthesis Imager (DEPI). Dynamic and high-light (HL) conditions triggered significant photosynthetic defects in a subset of the mutants, including those of photorespiration (PR) and other peroxisomal processes, some of which may also be related to PR. Further analysis of the PR mutants revealed activation of cyclic electron flow (CEF) around photosystem I and higher accumulation of hydrogen peroxide (H2 O2 ) under HL conditions. We hypothesize that impaired PR disturbs the balance of ATP and NADPH, leading to the accumulation of H2 O2 that activates CEF to produce ATP to compensate for the imbalance of reducing equivalents. The identification of peroxisomal mutants involved in PR and other peroxisomal functions in the photometric screen will enable further investigation of regulatory links between photosynthesis and PR and interorganellar interaction at the mechanistic level.

Novel anammox bacteria and nitrogen loss from Lake Superior.

Anaerobic ammonium oxidizing (anammox) bacteria own a central position in the global N-cycle, as they have the ability to oxidize NH4+ to N2 under anoxic conditions using NO2-. They are responsible for up to 50% of all N2 released from marine ecosystems into the atmosphere and are thus indispensible for balancing the activity of N-fixing bacteria and completing the marine N-cycle. The contribution, diversity, and impact of anammox bacteria in freshwater ecosystems, however, is largely unknown, confounding assessments of their role in the global N-cycle. Here we report the activity and diversity of anammox bacteria in the world's largest freshwater lake-Lake Superior. We found that anammox performed by previously undiscovered bacteria is an important contributor to sediment N2 production. We observed striking differences in the anammox bacterial populations found at different locations within Lake Superior and those described from other locations. Our data thus reveal that novel anammox bacteria underpin N-loss from Lake Superior, and if more broadly distributed across inland waters would play an important role in continental N-cycling and mitigation of fixed nitrogen transfer from land to the sea.