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Background: As one of the most common autoimmune diseases, myasthenia gravis (MG) severely affects the quality of life of patients. Therefore, exploring the role of dysregulated genes between MG and healthy controls in the diagnosis of MG is beneficial to reveal new and promising diagnostic biomarkers and clinical therapeutic targets.Methods: The GSE85452 dataset was downloaded from the Gene Expression Omnibus (GEO) database and differential gene expression analysis was performed on MG and healthy control samples to identify differentially expressed genes (DEGs). The functions and pathways involved in DEGs were also explored by functional enrichment analysis. Significantly associated modular genes were identified by weighted gene co-expression network analysis (WGCNA), and MG dysregulated gene co-expression modular-based diagnostic models were constructed by gene set variance analysis (GSVA) and least absolute shrinkage and selection operator (LASSO). In addition, the effect of model genes on tumor immune infiltrating cells was assessed by CIBERSORT. Finally, the upstream regulators of MG dysregulated gene co-expression module were obtained by Pivot analysis.Results: The green module with high diagnostic performance was identified by GSVA and WGCNA. The LASSO model obtained NAPB, C5orf25 and ERICH1 genes had excellent diagnostic performance for MG. Immune cell infiltration results showed a significant negative correlation between green module scores and infiltration abundance of Macrophages M2 cells.Conclusion: In this study, a diagnostic model based on the co-expression module of MG dysregulated genes was constructed, which has good diagnostic performance and contributes to the diagnosis of MG.

Supplementing exogenous carbon sources is a practical approach to improving shrimp health by manipulating the microbial communities of aquaculture systems. However, little is known about the microbiological processes and mechanisms of these systems. Here, the effects of glucose addition on shrimp growth performance and bacterial communities of the rearing water and the shrimp gut were investigated to address this knowledge gap. The results showed that glucose addition significantly improved the growth and survival of shrimp. Although the α-diversity indices of both bacterioplankton communities and gut microbiota were significantly decreased by adding glucose, both bacterial communities exhibited divergent response patterns to glucose addition. Glucose addition induced a dispersive bacterioplankton community but a more stable gut bacterial community. Bacterial taxa belonging to Ruegeria were significantly enriched by glucose in the guts, especially the operational taxonomic unit 2575 (OTU2575), which showed the highest relative importance to the survival rate and individual weight of shrimp, with the values of 43.8 and 40.6%, respectively. In addition, glucose addition increased the complexity of interspecies interactions within gut bacterial communities and the network nodes from Rhodobacteraceae accounted for higher proportions and linked more with the nodes from other taxa in the glucose addition group than that in control. These findings suggest that glucose addition may provide a more stable gut microbiota for shrimp by increasing the abundance of certain bacterial taxa, such as Ruegeria.

Salt marshes are potentially one of the most efficient carbon (C) sinks worldwide and perform important ecosystem functions, but sea level rise alters marsh sediments properties and thus threatens microbial roles in ecosystem functioning. Yet, the mechanisms of interactions of biochemical processes with microorganisms and their functions are still not fully understood. Here, this study investigated metagenomic taxonomic and functional profiling from the water-land conjugation up to about 300 m, 1000 m, and 2500 m in three parallel transects, respectively, in Hangzhou Bay, China. The results showed that soil physicochemical factors drove metagenomic taxonomic and functional genes in the 2500-m transect significantly different from other sites. The 2500-m transect had a greater abundance of Chloroflexi and Acidobacteria but lower in Proteobacteria. The metagenomic functional genes related to Phosphorus Metabolism (PHO) and Potassium Metabolism (POT) increased in the 2500 m. Additionally, nutrient-cycling functions and the genera of Anaeromyxobacter, Roseiflexus, and Geobacter related to PHO, POT at 2500 m were significantly greater than those of other transects. Carbon cycling functions within Carbohydrates (CHO) also differed significantly across transects. These research results demonstrated that the relative abundance of metagenomic microorganisms and their functional genes were significantly separated across the three transects. The vegetation type, salinity, and soil properties might be among the influencing factors.

Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters.

To understand the evolution of the Miocene gravity flow deposits in the Lower Cong—Congo Fan Basin, this paper documents the Miocene sequence stratigraphic framework, the depositional characteristics and the controlling factors of the gravity flow system. Based on the establishment of high-resolution sequence stratigraphic framework, lithofacies characteristics and sedimentary units of the gravity flow deposits in the region are identified by using seismic, well logging and core data comprehensively, and the sedimentary evolution process is revealed and the controlling factors are discussed. The Miocene can be divided into four 3rd-order sequences (SQ1—SQ4). The gravity flow deposits mainly include siliciclastic rock and pelite. The main sedimentary units include slumping deposits, mass transport deposits (MTD), channel fills, levee-overbank deposits, and frontal lobes. In the Early Miocene (SQ1), mainly gull-wing, weakly restricted to unrestricted depositional channel-overbank complexes and lobes were formed. In the early Middle Miocene (SQ2), W-shaped and weakly restricted erosional-depositional channels (multi-phase superposition) were subsequently developed. In the late Middle Miocene (SQ3), primarily U-shaped and restricted erosional channels were developed. In the Late Miocene (SQ4), largely V-shaped and deeply erosional isolated channels were formed in the study area. Climate cooling and continuous fall of the sea level made the study area change from toe of slope-submarine plain to lower continental slope, middle continental slope and finally to upper continental slope, which in turn affected the strength of the gravity flow. The three times of tectonic uplifting and climate cooling in the West African coast provided abundant sediment supply for the development of gravity flow deposits. Multistage activities of salt structures played important roles in redirecting, restricting, blocking and destroying the gravity flow deposits. Clarifying the characteristics, evolution and controlling factors of the Miocene gravity flow deposits in the Lower Congo—Congo Fan Basin can provide reference for deep-water petroleum exploration in this basin.

Lithology prediction is a fundamental problem because the outcome of lithology prediction is the critical underlying data for some basic geological work, e.g., establishing stratigraphic framework or analyzing distribution of sedimentary facies. As the geological formation generally consists of many different lithologies, the lithology prediction is always viewed as a tough work by geologists. Probabilistic neural network (PNN) shows high efficiency when solving pattern recognition problem since learning data do not need to do any pre-training of learning data and calculation results are universally reliable, and then, this model could be considered as an effective solution. However, there are two factors that seriously limit the PNN’s performance: One is existence of the interference variables of learning samples, and the other is selection of the window length of probability density distribution. In view of adverse impact of those two factors, two techniques, mean impact value (MIV) and particle swarm optimization (PSO), are introduced to improve the PNN’s calculation capability. Thus, a new prediction method referred as MIV–PSO–PNN is proposed in this paper. The proposed method is validated by three well-designed experiments, and the corresponding experiment data are recorded by two cored wells of the LULA oilfield. For the three experiments, prediction accuracies of the results provided by the proposed method are 81.67%, 73.34% and 88.34%, respectively, all of which are higher than those provided by other comparative approaches including backpropagation (BP), PNN, and MIV-PNN. The experiment results strongly demonstrate that the proposed method is capable to predict complex lithology.

Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a ~ 200 km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4+-N, NO3−-N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.

Sucrose is an effective carbon source for creating more reliable and environmentally friendly conditions for shrimp growth by regulating bacteria in biofloc-based culture systems. However, the influence of sucrose addition on the interaction, co-occurrence networks, and assembly mechanisms of bacterial communities in biofloc-based culture systems remains largely unknown. Here, we comprehensively investigated the effects of sucrose addition on bacterial communities in three habitats (water, bioflocs, and gut). The bacterial community structures and compositions of these three habitats became more similar in groups with sucrose addition, compared with those in controls. More than 50% gut bacterial communities were mainly derived from water and biofloc communities in the sucrose addition groups, but only about 33% bacterial communities migrated from water and biofloc to the gut in the control culture system. Sucrose addition accordantly enriched core taxa belonging to the phylum Actinobacteria and the families Rhodobacteraceae and Flavobacteriaceae in water, biofloc, and gut habitats. These core taxa were important for maintaining bacterial network stability in the sucrose addition culture systems and some were identified as keystone taxa for improving shrimp growth. Furthermore, after sucrose addition, gut bacterial community assembly from water and biofloc was dominated by the heterogeneous select with the ratios of 55–91% and 67–83%, respectively, indicating that sucrose addition can directionally shape the bacterial assembly of the shrimp culture system. These results provide a basis for selectively regulating certain beneficial taxa to improve shrimp growth in culture systems.

In this study, we aimed to determine the complete mitochondrial genome of blacktip shark

Heat cooking of meat gives it a specific taste and flavor which are favored by many consumers. While the characteristic taste components of chicken, duck, pig, and seafood have been studied, there is a lack of information about the molecular components that give donkey meat its unique taste. Here, the characterization profiles of raw donkey meat (RDM) and cooked donkey meat (CDM) meat by metabonomics and lipidomics. The results showed that a total of 186 metabolites belonging to 8 subclasses were identified in CDM and RDM, including carbohydrates (27.42%), amino acids (17.20%), lipids (13.44%), and nucleotides (9.14%). In total, 37 differential metabolites were identified between CDM and RDM. Among these, maltotriose, L-glutamate, and L-proline might predominantly contribute to the unique umami and sweet taste of donkey meat. Comprehensive biomarker screening detected 9 potential metabolite markers for the discrimination among RDM and CDM, including L-glutamate, gamma-aminobutyric acid, and butane-1, 2, 3, 4-tetrol. Moreover, a total of 992 and 1,022 lipids belonging to 12 subclasses were identified in RDM and CDM, respectively, mainly including triglycerides (TGs) and glycerophospholipids (GPs). Of these lipids, 116 were significantly different between CDM and RDM. The abundances of 61 TGs rich in saturated and monounsaturated fatty acids were retained in CDM, whereas the abundances of 37 GPs rich in polyunsaturated fatty acids were reduced, suggesting that TGs and GPs might be the predominant lipids for binding and generating aroma compounds, respectively. A total of 13 lipids were determined as potential markers for the discrimination among RDM and CDM, including PC(O-16:2/2:0), LPE(22:5/0:0), and PC(P-16:0/2:0). In conclusion, this study provided useful information about the metabolic and lipid profiles of donkey meat which may explain its unique taste and flavor, which could serve as a basis for the development and quality control of donkey meat and its products.

Critical-sized bone defects caused by trauma, tumor resection or serious infection represent one of the most challenging problems faced by orthopedic surgeons. However, the construction of bone grafts with good osteointegration and osteoinductivity is a clinical challenge. It has been elaborated that the nail bed tissue is an essential element for digit tip regeneration, suggesting that the nail bed may serve as a new material to manipulate bone regeneration. Herein, it was found that human nail bed extracellular matrix derived from amputated patients stimulates macrophage polarization toward a pro-healing phenotype and the expression of BMP2, to facilitate the osteogenic differentiation of bone marrow stromal cells (BMSCs) in vitro. The in vivo osteogenic capacity of decellularized nail bed scaffolds was then confirmed using a rat model of critical-sized calvarial defects. The in-depth analysis of immune responses to implanted scaffolds revealed that macrophage polarization toward the pro-regenerative M2 phenotype directs osteogenesis, as confirmed by macrophage depletion. A combination of proteomics analysis and RNA interference verified that the JAK2/STAT3 pathway is the positive regulator of macrophage polarization initiated by the decellularized nail bed during the promoted osteogenesis process. Thus, the decellularized human nail bed scaffold developed in this work is a promising biomaterial for bone regeneration.

Diatom blooms can significantly influence the dynamics of microbial communities, yet little is known about the interaction and assembly mechanisms of abundant and rare taxa during bloom process. Here, using 16S rRNA gene amplicon sequencing, we investigated the co-occurrence patterns and assembly processes of abundant and rare microbial communities during an early spring diatom bloom in Xiangshan bay. Our results showed that α-diversity indices in the rare subcommunity (RS) were significantly higher than those in the abundant and common subcommunities. β-Diversity of the RS was the highest among three subcommunities, and the variation of β-diversity in the three subcommunities was mainly induced by species turnover, which was also the highest in the RS. The assembly of microbial communities was mainly driven by the neutral processes, but the roles of neutral processes might differ in each subcommunity. Co-occurrence network analysis revealed that abundant and common operational taxonomic units were more often located in central positions within the network. Most of the modules in the network were specific to a particular bloom stage, owing to the succession of Skeletonema costatum. Overall, these findings expand current understanding of the microbial interaction and assembly mechanisms in marine environment suffering harmful algal bloom disturbance.

Tight oil sandstones have complex pore structure due to multiple pore types and multiscale pore size ranging from several nanometers to dozens of microns. In this study, petrophyiscal properties of tight oil sandstones were quantified based on microscale X-ray computed tomography (μXCT) imaging techniques. The pore types in gray scale images were identified; porosity, pore size distribution (PSD), and pore connectivity were analyzed from segmented image stacks; and their permeability was calculated by representative elementary volume (REV) scale lattice Boltzmann method (LBM). Three types of pores including residual interparticle pores, grain dissolution pores and micro fractures were identified. A multi-threshold segmentation algorithm was applied to segment the image stacks into three constituents, namely, pore, matrix, and clay. The calculated volumetric fraction of the pore constituent from the segmented image stacks was smaller than experimental porosity, because a certain amount of porosity was also contributed by clay constituent. The PSD of the samples was found to be unimodal in the range of 3–69 μm, with the peak at around 10–15 μm. The clay constituent led to the increase in the overall connectivity of the images stacks, indicating that clays bridged the isolated pores. By assigning appropriate porosity and permeability to the clay constituent, calculated permeability of the samples using REV scale LBM well matched the experimental data. This study provides new insight into characterization of pore structure of tight oil sandstones by μXCT technique.

The gut microbiota is closely related to shrimp growth and health. However, the response patterns of gut bacterial communities to environmental stresses (such as cold) in distinct shrimp strains and their association with host status are still unclear. In this study, stress tolerance and its potential association with the gut microbiota in two white shrimp Litopenaeus vannamei strains (ZT and PM) were investigated using 16S rRNA gene amplicon sequencing. The stable body weight of PM relative to the obvious weight loss of ZT after both were subjected to cold stress (at the adult life stage) suggests that PM possess stronger tolerance to cold stress. Meanwhile, the α-diversity indices of PM gut bacteria were significantly higher than those of ZT, and the bacterial community structure in the PM gut was more stable as well. Furthermore, cold stress led to domination of the bacterial composition in the ZT gut by the families Erysipelotrichaceae, Mycoplasmataceae, and Vibrionaceae, which have potential pathogenic members. On the other hand, the relative abundances of 18 discriminatory families, represented by Rhodobacteraceae (33.8%), in the PM gut were significantly higher than those in the ZT gut, suggesting that distinct gut bacterial assemblages may reflect the stress resistance potential of shrimp. The taxonomic signature of gut microbiota of the cold-resistant strain could be a guidance for isolation of novel probiotics from bacterial groups such as Rhodobacteraceae, which could be potentially applied to reduce the influence of cold stress in white shrimp.

Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.

Understanding how species interaction and assembly processes structure the abundant and rare bacterial biospheres in soils is crucial for predicting how biodiversity influences ecosystem functioning. Here, we profiled the bacterial communities across a salt marsh ecosystem gradient to investigate the co-occurrence patterns across taxa and the relative influence of ecological processes mediating the assembly of the abundant and rare biospheres in soil. Our results revealed abundant taxa to be ubiquitous across all sites, whereas the distributions of the rare taxa were relatively more site specific. The α-diversity indices and β-diversity of rare subcommunities were significantly higher than those of the abundant subcommunities. Besides, both the taxonomic and functional composition of soil bacterial communities differed significantly between the two biospheres. Furthermore, the influence of stochasticity differed in each subcommunity. In particular, stochastic processes were relatively more important in constraining the assembly of rare taxa. Co-occurrence network analysis revealed that a few abundant taxa occupy central nodes within the networks, possibly indicating crucial roles as keystone taxa. Collectively, these findings suggest that abundant and rare bacterial biospheres have distinct distributions underpinned by a dynamic interplay of ecological processes and taxon co-occurrence patterns. IMPORTANCE Estuarine salt marshes are highly productive ecosystems subjected to regular disturbances by hydrodynamic exchange. However, little is known about how distinct assembly processes and co-occurrence of taxa influence the structure of the abundant and rare bacterial biospheres in these soil systems. This study aims at unravelling these intricacies by studying a typical estuarine salt marsh located in Hangzhou Bay, China. Our study provides important pieces of evidence on the diverse distribution of rare and abundant bacterial biospheres. We show that a few abundant taxa are central nodes in species co-occurrence, potentially playing important roles as keystone species in the system. In addition, we highlight a dynamic interplay of assembly processes structuring these two subcommunities.

Wulong geese are renowned for their egg-laying and reproductive abilities. This work investigated the potential of using body size traits in the selection and breeding of high-yielding Wulong geese. A total of forty 479day-old female geese (high-yielding geese, n = 20; low-yielding geese, n = 20) were selected to evaluate the relationship between body weight, body size trait indicators, serum reproductive hormones, and biochemical indicators. The results showed that serum estradiol (E2), glucose (GLU), and triglyceride (TG) concentrations, together with pubic spacing and abdominal circumference were significantly higher in high-yielding geese (P < 0.01), whereas the opposite was true for neck circumference, neck length, and tibial circumference. In addition, the serum testosterone (T) concentration and body weight were higher in high-yielding geese (P < 0.05). Neck circumference and neck length were negatively correlated with E2 and TG (P < 0.01); while pubic spacing and abdominal circumference were positively correlated with E2, GLU, and TG (P < 0.01), the highest correlation coefficient was 0.777 between TG and pubic spacing; T was also strongly associated with neck circumference (P < 0.01). In conclusion, high-yielding Wulong geese can be selected through neck circumference, neck length, pubic spacing, and abdominal circumference.

Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors affect bacterial community diversity and structure. We used 16S rRNA gene pyrosequencing to investigate the spatial variation in bacterial community composition (BCC) across five sites on a coast-offshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not differ across sites, except that richness and phylogenetic diversity were lower in the offshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-a being the main factor. BCCs generally clustered into coastal and offshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical (5.7%) or spatial (8.5%) variables. Nutrients (particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families (primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-offshore gradient, with phytoplankton abundance increasing in the offshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.

Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between-domain differences in underlying mechanism are largely unassessed. Using a high-coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria archaea) and relative abundance (bacteria archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism-dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism-stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism-vs.-stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.

Additional file 2: Figure S1. Experimental design and sampling schedules. Figure S2. Dynamics of bacterial α-diversity and evenness indices of shrimp larvae and water across developmental stages. Figure S3. Linear discriminant analysis taxonomic cladogram showing discriminatory taxa at each developmental stage of shrimp larvae. Figure S4. Dynamics of bacterial community similarity among larvae samples and between larvae and water samples. Figure S5. The relationship between larval shrimp and water bacterial communities. Figure S6. Heatmaps showing the predicted function potentials of larval shrimp bacterial communities across the developmental stages.

Additional file 1: Table S1. Pairwise similarity test of bacterial communities between larval shrimp developmental stages. Table S2. Analysis of Similarity (ANOSIM) testing the differences between larval shrimp and rearing water bacterial communities.

Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P

Shiga toxin-producing Escherichia coli (E. coli) O157:H7 is recognized as a hazardous microorganism in the environment. Its longer survival might contribute to higher contamination risk. In this study, E. coli O157:H7 survival in estuarine sediments collected from south Hangzhou Bay was investigated. The survival time of E. coli O157:H7 in estuarine sediments increased with the distance to the water-land junction. Sediment pH was the most important factor in regulating E. coli O157:H7 survival in estuarine sediments. In addition, sediment nutrients and texture also played significant roles in the survival of E. coli O157:H7 in the sediments. On the other hand, bacterial diversity as determined by the alpha-diversity index had no significant effect on E. coli O157:H7 survival. However, specific families of bacteria were closely associated with E. coli O157:H7 survival in the sediments. Remarkably, some potential bacterial groups, e.g., the Desulfobacteraceae, Desulfobulbaceae and Desulfarculaceae families, which are mainly involved in the sulfur cycle, showed significant negative correlation with the E. coli O157:H7 survival in the sediments. On the whole, abiotic factors showed greater effects on E. coli O157:H7 survival in the test sediments than the bacterial community. Our findings provide a comprehensive understanding of E. coli O157:H7 survival and regulatory factors in estuarine sediments, establishing foundation for the prevention of pathogen contamination.

Among hand trauma, nail bed is the most involved tissue in hospital emergency departments, resulting in the loss of nail plate, which leads to a disturbance of hand grasp function, long-lasting digit tip pain, hyperpathia, and disesthesia. Treatment of nail bed defects is a significant clinical challenge due to the lack of uniform nail bed thickness and distinct regenerative ability. In this study, it is shown that the extracellular matrix of decellularized nail bed scaffolds can play an important role in inducing bone mesenchymal stem cells to differentiate into nail epithelial cells. Using decellularized nail bed scaffolds combined with bone mesenchymal stem cells, it is revealed that the engineered nail bed can promote nude mouse nail plate regeneration ectopically. The natural extracellular matrix of decellularized nail bed scaffolds can serve as a 3D structural template for bone mesenchymal stem cell differentiation into nail-associated cells, initiating the nail plate regeneration. These results not only provide a proof-of-principle for the generation of transplantable nail grafts based on decellularized nail bed scaffolds derived from clinically wasted amputated fingers but also provide important considerations for clinical treatment for digit tip trauma.

Carbonate karst is one of the research highlights in the field of carbonate reservoir geology. High porosity zones can develop in carbonate rocks which are modified by the karst. However, the carbonate porosity development and its evolution process in a polyphase paleokarst are rarely reported in the geological record. Here, the paper focuses on this point from the Precambrian Upper Sinian carbonate in the north Tarim basin, northwest China. Five outcrops and two wells reveal that the karstic porosity development of Upper Sinian carbonate was petrography-controlled of microbial dolostone and grain dolostone. The karstic porosities were in relation to three paleokarst phases: (1) eogenetic karst during depositional environment, (2) telogenetic karst at the end of late Sinian, and (3) hydrothermal karst in the early Permian. Eogenetic karst was related to frequent and short sea-level fluctuation, and was characterized by selective dissolution of intragranular dissolution porosity, moldic porosity, bird’s eye porosity, and intergranular dissolution porosity. Telogenetic karst was related to tectonic uplift, and was characteristic of non-selective dissolution of vugs and cavities with karst intensity increasing upward. Hydrothermal karst was related to geothermal events, and was featured by highly solution-enlarged porosities which mainly overprinted earlier telogenetic and eogenetic karst porosities. The suggested paleokarst model, combined with the related karstic porosity evolution process, will perfectly reveal its porosity development.

Coastal ecosystems are receiving elevated loads of nitrogen (N) from anthropogenic sources. Understanding how excessive N loading affects bacterioplankton communities is critical to predict the biodiversity of marine ecosystems under conditions of eutrophic disturbance. In this study, oligotrophic coastal water microcosms were perturbed with nitrate in two loading modes: 1) one-off loading at the beginning of the incubation period; and 2) periodic loading every two days for 16 days. Turnover in the bacterioplankton community was investigated by 16S rDNA gene amplicon sequencing. The alpha diversity of the bacterioplankton community showed great temporal variability and similar responses to the different treatments. Bacterioplankton community composition was influenced remarkably by time and N loading mode. The effects of N loading on bacterioplankton community structure showed obvious temporal variation, probably because of the great temporal variation in environmental parameters. This study provides insights into the effects of N pollution in anthropogenically perturbed marine environments.

Phytoplankton bloom has imposed ecological concerns worldwide; however, few studies have been focused on the successional trajectories of bacterioplankton community over a complete phytoplankton bloom cycle. Using 16S pyrosequencing, we investigated how the coastal bacterioplankton community compositions (BCCs) respond to a phytoplankton bloom in the Xiangshan Bay, East China Sea. The results showed that BCCs were significantly different among the pre-bloom, bloom, and after-bloom stages, with the lowest bacterial diversity at the bloom phase. The BCCs at the short-term after-bloom phase showed a rapid but incomplete recovery to the pre-bloom phase, evidenced by 69.8% similarity between pre-bloom and after-bloom communities. This recovery was parallel with the dynamics of the operational taxonomic units (OTUs) affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Alphaproteobacteria and Gammaproteobacteria, whose abundance enriched when bloom occur, and decreased after-bloom, and vice versa. Collectively, the results showed that the BCCs were sensitive to algal-induced disturbances, but could recover to a certain extent after bloom. In addition, OTUs which enriched or decreased during this process are closely associated with this temporal pattern, thus holding the potential to evaluate and indicate the succession stage of phytoplankton bloom.

Phosphorus (P), primarily as phosphate, is considered as a key trophic factor of eutrophication in coastal environments. Information on the response of bacterial community to excess phosphate loading in oligotrophic coastal water could provide insights into the micro-ecological effects on the expanding trend of nutrient-enrichment in coastal water. In this study, temporal dynamic of bacterioplankton community composition was investigated using 16S Illumina MiSeq sequencing technique in oligotrophic seawater microcosms manipulated with no perturbation (control) and a certain level of phosphate by two loading modes: 1) one-off loading at the beginning of incubation; and 2) periodic loadings every two days over a 16-day duration. The results showed that overall bacterial alpha-diversity temporally changed and achieved the lowest value in phosphate loading (P-loading) microcosms at day 8; phosphate-addition increased the Shannon index and Pielou's evenness compared with those of the control at day 16. Bacterioplankton community turnover across all the treatments showed a similar temporal pattern. P-loading significantly affected bacterioplankton community composition with negative correlations of Methylophilaceae and Flavobacteriaceae and positive correlation of Saprospiraceae. Periodic loading treatments demonstrated a greater effect on community variation than one-off loading treatments did. Moreover, excess P-loading accelerated the temporal succession of the bacterioplankton community composition. These results provide insights into the pattern of bacterioplankton community phylogenetically responding to excess P-loading in the manipulated oligotrophic coastal system.

The common shrimp disease, acute hepatopancreatic necrosis disease (AHPND), has caused extensive damage to the shrimp farming industry due to its rapid spread and high mortality rates. However, the alterations in gastrointestinal microbiota (GM) ecosystem in subadult shrimps (Litopenaeus vannamei) with AHPND occurrence are still unclear. This study identified AHPND according to clinical symptoms and the existence of the toxin gene pirAVP, analyzed the microbiome dynamics of healthy and diseased subadult shrimps, and built an ecological model for quantitative evaluation of the GM imbalance. The results showed that the GM community diversity in diseased shrimps was significantly lower than that in healthy ones. The structural composition, dysbiosis-related indices, and assembly processes of the GM community were also evidently changed in diseased shrimps. The different operational taxonomic units (OTUs) in GM of diseased shrimps were mainly composed of Vibrio spp. with a relative abundance >90%, the majority of these were neutrally distributed in the neutral model of AHPND occurrence. Of 39 biomarkers for predicting AHPND occurrence, nine belonging to Vibrio were overrepresented in diseased shrimps, whereas biomarkers such as Rhodobacteraceae OTU3427, Candiadatus aysiosphaera OTU1041, KD4-96 OTU4963, and Rhodobacter OTU3366 were enhanced in healthy shrimps. Functional prediction showed that the gene abundances of the NOD receptor signaling pathway (p = .04), Vibrio infection (p

Microbial fermentation can increase the water-soluble protein (WSP) contents of soybean meal, but the microbial community compositions and its functions remain unclear during the fermentation of soybean meal. In this study, the soybean meal was naturally fermented and the dynamics of bacterial community structure were determined. The results showed that natural fermentation can significantly increase the WSP content and digestive enzyme activities of soybean meal. The bacterial diversity indexes of soybean meal were increased and the community structure was significantly changed after fermentation. The bacterial community composition mainly consisted of Pseudomonas before fermentation, but it was almost completely replaced by Bacillus after 24 h of fermentation. The key operational taxonomic unit (OTU) for fermentation was screened as OTU161 from Bacillus, and its candidate strain was isolated from the fermented soybean meal and identified as Bacillus amyloliquefaciens ZB. Bioaugmented inoculation of ZB significantly increased the WSP content by 110.0%, 47.2%, and 473.7%, respectively, after 24, 72, and 96 h of fermentation and digestive enzyme activities by 16.1–41.8% during 24–48 h of fermentation, and shorten the fermentation time, compared to natural fermentation.

Microplastics have emerged as a new anthropogenic substrate that can readily be colonized by microorganisms. Nevertheless, microbial community succession and assembly among different microplastics in nearshore mariculture cages remains poorly understood. Using an in situ incubation experiment, 16S rRNA gene amplicon sequencing, and the neutral model, we investigated the prokaryotic communities attached to polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) in a mariculture cage in Xiangshan Harbor, China. The α-diversities and compositions of microplastic-attached prokaryotic communities were significantly distinct from free-living and small particle-attached communities in the surrounding water but relatively similar to the large particle-attached communities. Although a distinct prokaryotic community was developed on each type of microplastic, the communities on PE and PP more closely resembled each other. Furthermore, the prokaryotic community dissimilarity among all media (microplastics and water fractions) tended to decrease over time. Hydrocarbon-degrading bacteria Alcanivorax preferentially colonized PE, and the genus Vibrio with opportunistically pathogenic members has the potential to colonize PET. Additionally, neutral processes dominated the prokaryotic community assembly on PE and PP, while selection was more responsible for the prokaryotic assembly on PET. The assembly of Planctomycetaceae and Thaumarchaeota Marine Group I taxa on three microplastics were mainly governed by selection and neutral processes, respectively. Our study provides further understanding of microplastic-associated microbial ecology in mariculture environments.

Terminating harmful algal blooms by using algicidal agents is a strong disturbance event in marine environment, which has powerful structural influences on microbial ecosystems. But, the response of microbial ecosystem to algicidal agent is largely unknown. Here, we conducted Phaeocystis globosa microcosms to investigate the dynamics, assembly processes, and co-occurrence patterns of microbial communities in response to algicidal process induced by a highly efficient algicidal agent, prodigiosin, by using 16S rRNA gene amplicon sequencing. The α-diversity of microbial community showed no obvious changes during the algicidal process in P. globosa microcosm treated with prodigiosin (group PD). Rhodobacteraceae increased significantly (P 0.05) during algicidal process in PD, and this was mainly due to the lysis of P. globosa cells. Compared to the control group, the temporal turnover rates of common and rare taxa in PD were significantly higher because of the lysis of P. globosa induced by prodigiosin. Neutral processes mainly drove the assembly of microbial communities in all microcosms, even though the algicidal process induced by prodigiosin had no effect on the assembly processes. In addition, the time-decay relationship and co-occurrence network analysis indicate that rare taxa play important roles in maintaining microbial community stability in response to the algicidal process, rather than prodigiosin. These findings suggest that prodigiosin cannot affect the dynamics of microbial communities directly; however, future investigations into the function of microbial communities in response to prodigiosin remain imperative.

Seasonal succession in bacterioplankton is a common process in marine waters. However, seasonality in their spatial turnover is largely unknown. Here, we investigated spatial turnover of surface bacterioplankton along a nearshore-to-offshore gradient in the East China Sea across four seasons. Although seasonality overwhelmed spatial variability of bacterioplankton composition, we found significant spatial turnover of bacterioplankton along the gradient as well as overall seasonal consistency in biogeographic patterns (including distance&ndash, decay relationship and covariation of community composition with distance to shore) with subtle changes. Bacterioplankton assembly was consistently dominated by deterministic mechanisms across seasons, with changes in specific processes. We found overall seasonal consistency in abiotic factors (mainly salinity and nitrogen and phosphorus nutrients) shaping bacterioplankton composition, while phytoplankton showed a similar influence as abiotic factors only in spring. Although key taxa responsible for bacterioplankton spatial turnover showed certain season-specificity, seasonal switching between closely related taxa occurred within most dominant families. Moreover, many close relatives showed different responding patterns to the environmental gradients in different seasons, suggesting their differences in both seasonally climatic and spatially environmental preferences. Our results provide insights into seasonal consistency and variability in spatial turnover of bacterioplankton in terms of biogeographic patterns, ecological processes, and external and internal drivers.

Oyster (Crassostrea gigas) shell-loading in aquaculture systems can regulate water quality, a critical factor for Litopenaeus vannamei growth. However, the effects of oyster shell-loading on the bacterial community composition and their interactions during shrimp culture processes remain elusive. Here, 16S rRNA gene amplicon sequencing was used to investigate the dynamics and co-occurrence patterns of bacterial communities in L. vannamei culture systems loaded with oyster shells. The results indicated that oyster shell-loading significantly improved both shrimp survival and water quality. Oyster shell-loading was found to cause a significant increase in the relative abundance of Alphaproteobacteria (P

Biofloc technology (BFT) has been widely studied and applied in aquaculture, but the bacterial community compositions (BCCs) of bioflocs with different sizes and their associations with the shrimp gut microbiota remain unclear. In this study, bacterial communities of shrimp gut and the bioflocs with three different size-fractions (BS, 100 μm) were investigated by MiSeq sequencing technique. Significantly different bacterial communities were observed between the large (> 20 μm) and small ( 20 μm). A majority of these taxa were strongly correlated with shrimp health or water environmental parameters. However, some candidate pathogens (i.e., Vibrionaceae, Mycoplasmataceae and Pseudoalteromonadaceae) were overrepresented in small-sized bioflocs (

The interaction and assembly processes of microeukaryotic community compositions (MECs) are rarely elucidated in environment with strong disturbance such as harmful algal blooms. To fill this gap, we analyzed changes of MECs induced by a diatom bloom using 18S rRNA gene amplicon sequencing. The MECs were mainly dominated by Cercozoa (average relative abundance, 49.2%), Diatom (25.5%) and Dinoflagellata (15.6%). MECs changed significantly (ANOSIM P

Marine Archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~200 km by 16S rRNA gene amplicon sequencing. Total archaeal communities were extremely dominated by MGI and/or MGII (98.9% in average relative abundance). Niche partitioning between MGI and MGII or within each group was found across multiple environmental gradients. "Selection" was more important than "dispersal limitation" in governing biogeographic patterns of total archaeal, MGI, and MGII communities, and basic abiotic parameters (such as salinity) and inorganic/organic resources as a whole could be the main driver of "selection". While "homogenizing dispersal" also considerably governed their biogeography. MGI-Nitrospira assemblages were speculatively responsible for complete nitrification. MGI taxa commonly had negative correlations with members of Synechococcus but positive correlations with members of eukaryotic phytoplankton, suggesting that competition or synergy between MGI and phytoplankton depends on specific MGI-phytoplankton assemblages. MGII taxa showed common associations with presumed (photo)heterotrophs including members of SAR11, SAR86, SAR406, and Candidatus Actinomarina. This study sheds light on ecological processes and drivers shaping archaeal biogeography and many strong MGI/MGII-bacterial associations across complex subtropical coastal waters. Future efforts should be made on seasonality of archaeal biogeography and biological, environmental, or ecological mechanisms underlying these statistical microbial associations.

Increasing evidence has emerged supporting a tight link between gut bacterial community and shrimp health. However, the knowledge about the variation of gut bacterial community, especially with different disease onset time, remains elusive. Here, healthy and diseased shrimps were collected at 3 disease-outbreak times (day 70, 80 and 85) to investigate the variation of gut bacterial community and its underlying ecological process with 16S rRNA gene amplicon sequencing. The gut bacterial community of diseased shrimp was distinct from the healthy one and temporally less stable, characterized by decreased alpha-diversity and dispersive structure. And its dominant ecological process experienced a transition with disease onset time, although deterministic process mainly governed the healthy gut bacterial assembly. In addition, the core microbiota of healthy shrimp gut harbored more diverse bacterial taxa with more cooperative interactions, while the diseased core microbiota showed opposite pattern with significantly higher abundance of opportunistic pathogens as well. These findings indicate that shrimp heath is highly relevant to the homeostasis of its gut bacterial community. Preservation and restoration of the bacterial community equilibrium could represent an effective strategy for shrimp disease prevention. Electronic supplementary material The online version of this article (10.1186/s13568-018-0644-x) contains supplementary material, which is available to authorized users.

Contrasting temperature Bacterial community Turnover rate Temperature relationship Indicator species A B S T R A C T Soil microbial communities potentially mediate the feedbacks to climate change, and thus, the understanding of microbial ecology is central to predict future global warming. However, the direct warming effects on microbial communities are uncertain due to the confounding effects of plant traits and soil heterogeneities. Here, we exposed alpine meadow soil microcosms to temperature between 10 and 40 � C for 28 days, to evaluate the temperature relationship of the bacterial community structure and microbial functions. Our results showed that sustained exposure to contrasting temperature produced compositionally and functionally distinct microbial communities. The degree of these changes was dependent on the magnitude of warming, as shown by a consistent increase in the dissimilarities and a shift of the carbon (C) use pattern along the temperature gradient. We found that the bacterial community temporal dynamics followed a gradual process of succession, and the turnover rate was substantially accelerated (P = 0.012) by warmer temperatures; every 1 � C elevation in soil temperature was estimated to increase the turnover by 0.001. Consistently, contrasting temperature was found to be the dominant factor explained 6.1% of the total variation of the microbial community structures; however, the incubation duration and the interaction between incubation temperature and duration explained 5.4% and 4.1% of the variation, respectively. As anticipated, the shift in bacterial community rapidly translated to a similar change in enzymes activities and C utilization. In addition, potential indicator species were screened; these species characterized the temperature gradient. Collectively, our findings indicate that direct warming effects on soil bacterial community could substantially alter certain function and that contrasting temperatures would accelerate the bacterial community turnover– temperature relationship in this alpine meadow soil.