Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench.

BACKGROUND: The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes. RESULTS: In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench. CONCLUSIONS: Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.

Removal of Cu (II) by ion exchange resin and its re-utilization of the residual solution from the distilled Lycium barbarum wine.

In order to re-utilize the residual from the distillation of the Chinese wolfberry wine and reduce the environmental pollution, the residual is firstly filtered by the ceramic membrane of 50 nm, then the Cu (II) has transferred from the distillation is removed using the ion exchange resin, and the treated solution is recombined with the distilled liquor to make the Chinese wolfberry brandy and the comparison has conducted on the physicochemical properties, antioxidant activity and flavor compounds between the recombined brandy and the finished brandy. The results indicate that the Cu (II) was effectively removed by ceramic membrane combined with the D401 resin. Compared with finished brandy, the recombined brandy contains high contents of polysaccharides, phenols and flavonoids, thus contributing to the improvement of antioxidant capacity. The gas chromatography-ion mobility spectrometry (GC-IMS) reveals that 25 volatile compounds like esters and alcohols have identified in the brandy samples, and the differences are significant between the recombined and the finished brandy. In summary, the distilled residual from the Chinese wolfberry wine might be re-used after the appropriate treatment so as to reduce the discharge and environmental pollution.

Naoxueshu Oral Liquid Accelerates Post-Craniotomy Hematoma Absorption in Patients: An Open-Label, Multicenter, and Randomized Controlled Trial.

OBJECTIVE: To investigate whether Naoxueshu Oral Liquid (NXS) could promote hematoma absorption in post-craniotomy hematoma (PCH) patients. METHODS: This is an open-label, multicenter, and randomized controlled trial conducted at 9 hospitals in China. Patients aged 18-80 years with post-craniotomy supratentorial hematoma volume ranging from 10 to 30 mL or post-craniotomy infratentorial hematoma volume less than 10 mL, or intraventricular hemorrhage following cranial surgery were enrolled. They were randomly assigned at a 1:1 ratio to the NXS (10 mL thrice daily for 15 days) or control groups using a randomization code table. Standard medical care was administered in both groups. The primary outcome was the percentage reduction in hematoma volume from day 1 to day 15. The secondary outcomes included the percentage reduction in hematoma volume from day 1 to day 7, the absolute reduction in hematoma volume from day 1 to day 7 and 15, and the change in neurological function from day 1 to day 7 and 15. The safety was closely monitored throughout the study. Moreover, subgroup analysis was performed based on age, gender, history of diabetes, and etiology of intracerebral hemorrhage (ICH). RESULTS: A total of 120 patients were enrolled and randomly assigned between March 30, 2018 and April 15, 2020. One patient was lost to follow-up in the control group. Finally, there were 119 patients (60 in the NXS group and 59 in the control group) included in the analysis. In the full analysis set (FAS) analysis, the NXS group had a greater percentage reduction in hematoma volume from day 1 to day 15 than the control group [median (Q1, Q3): 85% (71%, 97%) vs. 76% (53%, 93%), P<0.05]. The secondary outcomes showed no statistical significance between two groups, either in FAS or per-protocol set (P>0.05). Furthermore, no adverse events were reported during the study. In the FAS analysis, the NXS group exhibited a higher percentage reduction in hematoma volume on day 15 in the following subgroups: male patients, patients younger than 65 years, patients without diabetes, or those with initial cranial surgery due to ICH (all P<0.05). CONCLUSIONS: The administration of NXS demonstrated the potential to promote the percentage reduction in hematoma volume from day 1 to day 15. This intervention was found to be safe and feasible. The response to NXS may be influenced by patient characteristics. (Registration No. ChiCTR1800017981).

Enhancement of electron transfer via magnetite in nitrite-dependent anaerobic methane oxidation system.

Nitrite-dependent anaerobic methane oxidation (n-DAMO) is a novel denitrification process that simultaneously further removes and utilizes methane from anaerobic effluent from wastewater treatment plants. However, the metabolic activity of n-DAMO bacteria is relative low for practical application. In this study, conductive magnetite was added into lab-scale sequencing batch reactor inoculated with n-DAMO bacteria to study the influence on n-DAMO process. With magnetite amendment, the nitrogen removal rate could reach 34.9 mg N·L-1d-1, nearly 2.5 times more than that of control group. Magnetite significantly facilitated the interspecies electron transfer and built electrically connected community with high capacitance. Enzymatic activities of electron transport chain were significantly elevated. Functional gene expression and enzyme activities associated with nitrogen and methane metabolism had been highly up-regulated. These results not only propose a useful strategy in n-DAMO application but also provide insights into the stimulating mechanism of magnetite in n-DAMO process.

Multimodal image fusion-assisted endoscopic evacuation of spontaneous intracerebral hemorrhage.

PURPOSE: Although traditional craniotomy (TC) surgery has failed to show benefits for the functional outcome of intracerebral hemorrhage (ICH). However, a minimally invasive hematoma removal plan to avoid white matter fiber damage may be a safer and more feasible surgical approach, which may improve the prognosis of ICH. We conducted a historical cohort study on the use of multimodal image fusion-assisted neuroendoscopic surgery (MINS) for the treatment of ICH, and compared its safety and effectiveness with traditional methods. METHODS: This is a historical cohort study involving 241 patients with cerebral hemorrhage. Divided into MINS group and TC group based on surgical methods. Multimodal images (CT skull, CT angiography, and white matter fiber of MRI diffusion-tensor imaging) were fused into 3 dimensional images for preoperative planning and intraoperative guidance of endoscopic hematoma removal in the MINS group. Clinical features, operative efficiency, perioperative complications, and prognoses between 2 groups were compared. Normally distributed data were analyzed using t-test of 2 independent samples, Non-normally distributed data were compared using the Kruskal-Wallis test. Meanwhile categorical data were analyzed via the Chi-square test or Fisher's exact test. All statistical tests were two-sided, and p < 0.05 was considered statistically significant. RESULTS: A total of 42 patients with ICH were enrolled, who underwent TC surgery or MINS. Patients who underwent MINS had shorter operative time (p < 0.001), less blood loss (p < 0.001), better hematoma evacuation (p = 0.003), and a shorter stay in the intensive care unit (p = 0.002) than patients who underwent TC. Based on clinical characteristics and analysis of perioperative complications, there is no significant difference between the 2 surgical methods. Modified Rankin scale scores at 180 days were better in the MINS than in the TC group (p = 0.014). CONCLUSIONS: Compared with TC for the treatment of ICH, MINS is safer and more efficient in cleaning ICH, which improved the prognosis of the patients. In the future, a larger sample size clinical trial will be needed to evaluate its efficacy.

Effect of different hydrogen evolution rates at cathode on bioelectrochemical reduction of CO2 to acetate.

Microbial electrosynthesis (MES) offers a promising approach for converting CO2 into valuable chemicals such as acetate. However, the relative low conversion rate severely limits its practical application. This study investigated the impact of different hydrogen evolution rates on the conversion rate of CO2 to acetate in the MES system. Three potentials (-0.8 V, -0.9 V and -1.0 V) corresponding to various hydrogen evolution rates were set and analyzed, revealing an optimal hydrogen evolution rate, yielding a maximum acetate formation rate of 1410.9 mg/L and 73.5 % coulomb efficiency. The electrochemical findings revealed that an optimal hydrogen evolution rate facilitated the formation of an electroactive biofilm. The microbial community of the cathode biofilm highlighted key genera, including Clostridium and Acetobacterium, which played essential roles in electrosynthesis within the MES system. Notably, a low hydrogen evolution rate failed to provide sufficient energy for the electrochemical reduction of CO2 to acetate, while a high rate led to cathode alkalinization, impeding the reaction and causing significant energy wastage. Therefore, maintaining an appropriate hydrogen evolution rate is crucial for the development of mature electroactive biofilms and achieving optimal performance in the MES system.

Riboflavin-loaded carbon cloth aids the anaerobic digestion of cow dung by promoting direct interspecies electron transfer.

Cow dung generates globally due to increased beef and milk consumption, but its treatment efficiency remains low. Previous studies have shown that riboflavin-loaded conductive materials can improve anaerobic digestion through enhance direct interspecies electron transfer (DIET). However, its effect on the practical anaerobic digestion of cow dung remained unclear. In this study, carbon cloth loaded with riboflavin (carbon cloth-riboflavin) was added into an anaerobic digester treating cow dung. The carbon cloth-riboflavin reactor showed a better performance than other two reactors. The metagenomic analysis revealed that Methanothrix on the surface of the carbon cloth predominantly utilized the CO2 reduction for methane production, further enhanced after riboflavin addition, while Methanothrix in bulk sludge were using the acetate decarboxylation pathway. Furthermore, the carbon cloth-riboflavin enriched various major methanogenic pathways and activated a large number of enzymes associated with DIET. Riboflavin's presence altered the microbial communities and the abundance of functional genes relate to DIET, ultimately leading to a better performance of anaerobic digestion for cow dung.

Granular activated carbon enhances volatile fatty acid production in the anaerobic fermentation of garden wastes.

Garden waste, one type of lignocellulosic biomass, holds significant potential for the production of volatile fatty acids (VFAs) through anaerobic fermentation. However, the hydrolysis efficiency of garden waste is limited by the inherent recalcitrance, which further influences VFA production. Granular activated carbon (GAC) could promote hydrolysis and acidogenesis efficiency during anaerobic fermentation. This study developed a strategy to use GAC to enhance the anaerobic fermentation of garden waste without any complex pretreatments and extra enzymes. The results showed that GAC addition could improve VFA production, especially acetate, and reach the maximum total VFA yield of 191.55 mg/g VSadded, which increased by 27.35% compared to the control group. The highest VFA/sCOD value of 70.01% was attained in the GAC-amended group, whereas the control group only reached 49.35%, indicating a better hydrolysis and acidogenesis capacity attributed to the addition of GAC. Microbial community results revealed that GAC addition promoted the enrichment of Caproiciproducens and Clostridium, which are crucial for anaerobic VFA production. In addition, only the GAC-amended group showed the presence of Sphaerochaeta and Oscillibacter genera, which are associated with electron transfer processes. Metagenomics analysis indicated that GAC addition improved the abundance of glycoside hydrolases (GHs) and key functional enzymes related to hydrolysis and acidogenesis. Furthermore, the assessment of major genera influencing functional genes in both groups indicated that Sphaerochaeta, Clostridium, and Caproicibacter were the primary contributors to upregulated genes. These findings underscored the significance of employing GAC to enhance the anaerobic fermentation of garden waste, offering a promising approach for sustainable biomass conversion and VFA production.

Ecological function and interaction of different bacterial groups during alginate processing in coastal seawater community.

The degradation of high molecular weight organic matter (HMWOM) is a core process of oceanic carbon cycle, which is determined by the activity of microbial communities harboring hundreds of different species. Illustrating the active microbes and their interactions during HMWOM processing can provide key information for revealing the relationship between community composition and its ecological functions. In this study, the genomic and transcriptional responses of microbial communities to the availability of alginate, an abundant HMWOM in coastal ecosystem, were elucidated. The main degraders transcribing alginate lyase (Aly) genes came from genera Alteromonas, Psychrosphaera and Colwellia. Meanwhile, some strains, mainly from the Rhodobacteraceae family, did not transcribe Aly gene but could utilize monosaccharides to grow. The co-culture experiment showed that the activity of Aly-producing strain could promote the growth of Aly-non-producing strain when alginate was the sole carbon source. Interestingly, this interaction did not reduce the alginate degradation rate, possibly due to the easily degradable nature of alginate. This study can improve our understanding of the relationship between microbial community activity and alginate metabolism function as well as further manipulation of microbial community structure for alginate processing.

Transcriptomic analysis reveals hub genes and pathways in response to acetic acid stress in Kluyveromyces marxianus during high-temperature ethanol fermentation.

The thermotolerant yeast Kluyveromyces marxianus is known for its potential in high-temperature ethanol fermentation, yet it suffers from excess acetic acid production at elevated temperatures, which hinders ethanol production. To better understand how the yeast responds to acetic acid stress during high-temperature ethanol fermentation, this study investigated its transcriptomic changes under this condition. RNA sequencing (RNA-seq) was used to identify differentially expressed genes (DEGs) and enriched gene ontology (GO) terms and pathways under acetic acid stress. The results showed that 611 genes were differentially expressed, and GO and pathway enrichment analysis revealed that acetic acid stress promoted protein catabolism but repressed protein synthesis during high-temperature fermentation. Protein-protein interaction (PPI) networks were also constructed based on the interactions between proteins coded by the DEGs. Hub genes and key modules in the PPI networks were identified, providing insight into the mechanisms of this yeast's response to acetic acid stress. The findings suggest that the decrease in ethanol production is caused by the imbalance between protein catabolism and protein synthesis. Overall, this study provides valuable insights into the mechanisms of K. marxianus's response to acetic acid stress and highlights the importance of maintaining a proper balance between protein catabolism and protein synthesis for high-temperature ethanol fermentation.

Fast Lithium Ion Transport Pathways Constructed by Two-Dimensional Boron Nitride Nanoflakes in Quasi-Solid-State Polymer Electrolyte.

Quasi-solid-state electrolytes (QSSEs) are gaining huge popularity because of their significantly improved safety performance over nonaqueous liquid electrolytes and superior process adaptability over all-solid-state electrolytes. However, because of the existence of liquid molecules, QSSEs typically have low lithium ion transference numbers and compromised thermal stability. In this work, we present the fabrication of a well-rounded QSSE by introducing hexagonal boron nitride nanoflakes (BNNFs) as an inorganic filler in a poly(vinylene carbonate) matrix. BNNFs, in contrast to most inorganic fillers used as anion trappers, are used to build fast lithium ion transport pathways directly on their two-dimensional surfaces. We confirm the attractive coupling between lithium ions and BNNFs, and we confirm that with the help of BNNFs, lithium ions can migrate with less damping and a lower transport energy barrier. As a result, the designed electrolyte exhibits good ion transportability, promoted fire retardancy, and good compatibility with lithium metal anodes and commercial cathodes.

Comparison study on enhancement of phosphorus recovery from low-strength wastewater treated with different magnesium-based electrochemical constructed wetland.

Phosphorus (P) recovery from wastewaters treated with constructed wetlands (CWs) could alleviate the current global P crisis but has not received sufficient attention. In this study, P transformation in different magnesium-based electrochemical CWs, including micro-electrolysis CW (M-CW), primary battery CW (P-CW), and electrolysis CW (E-CW), was thoroughly examined. The results revealed that the P removal efficiency was 53.0%, 75.8%, and 61.9% in the M-CW, E-CW, and P-CW, respectively. P mass balance analysis showed that P electrode deposition was the main reason for the higher P removal in the E-CW and P-CW. Significant differences were found between the E-CW and P-CW, P was distributed primarily on the magnesium plate in the P-CW but was distributed on the carbon plate in the E-CW. The E-CW had excellent P recovery capacity, and struvite was the major P recovery product. More intense magnesium plate corrosion and alkaline environment increased struvite precipitation in the E-CW, with the proportion of 61.6%. The results of functional microbial community analysis revealed that the abundance of electroactive bacteria was positively correlated with the deposition of struvite. This study provided an essential reference for the targeted electrochemical regulation of electric field processes and microorganisms in CWs to enhance P recovery.

Application of artificial intelligence-based methods in bioelectrochemical systems: Recent progress and future perspectives.

Bioelectrochemical Systems (BESs) leverage microbial metabolic processes to either produce electricity by degrading organic matter or consume electricity to assist metabolism, and can be used for various applications such as energy production, wastewater treatment, and bioremediation. Given the intricate mechanisms of BESs, the application of artificial intelligence (AI)-based methods have been proposed to enhance the performance of BESs due to their capability to identify patterns and gain insights through data analysis. This review focuses on the analysis and comparison of AI algorithms commonly used in BESs, including artificial neural network (ANN), genetic programming (GP), fuzzy logic (FL), support vector regression (SVR), and adaptive neural fuzzy inference system (ANFIS). These algorithms have different features, such as ANN's simple network structure, GP's use in the training process, FL's human-like thought process, SVR's high prediction accuracy and robustness, and ANFIS's combination of ANN and FL features. The AI-based methods have been applied in BESs to predict microbial communities, products or substrates, and reactor performance, which can provide valuable information and improve system efficiency. Limitations of AI-based methods for predicting and optimizing BESs and recommendations for future development are also discussed. This review demonstrates the potential of AI-based methods in optimizing BESs and provides valuable information for the future development of this field.

Clinical Characteristics and Early Diagnosis of Spontaneous Fungal Peritonitis/Fungiascites in Hospitalized Cirrhotic Patients with Ascites: A Case-Control Study.

BACKGROUND: Spontaneous fungal peritonitis (SFP) and fungiascites is less well-recognized and described in patients with liver cirrhosis. The aims of this study were to determine the clinical characteristics, prognosis, and risk factors of cirrhotic patients with SFP/fungiascites and to improve early differential diagnosis with spontaneous bacterial peritonitis (SBP). METHODS: This was a retrospective case-control study of 54 cases of spontaneous peritonitis in cirrhotic patients (52 SFP and 2 fungiascites) with fungus-positive ascitic culture. Fifty-four SBP cirrhotic patients with bacteria-positive ascitic culture were randomly enrolled as a control group. A nomogram was developed for the early differential diagnosis of SFP and fungiascites. RESULTS: Hospital-acquired infection was the main cause of SFP/fungiascites. Of the 54 SFP/fungiascites patients, 31 (57.41%) patients carried on with the antifungal treatment, which seemed to improve short-term (30-days) mortality but not long-term mortality. Septic shock and HCC were independent predictors of high 30-day mortality in SFP/fungiascites patients. We constructed a predictive nomogram model that included AKI/HRS, fever, (1,3)-ß-D-glucan, and hospital-acquired infection markers for early differential diagnosis of SFP/fungiascites in cirrhotic patients with ascites from SBP, and the diagnostic performance was favorable, with an AUC of 0.930 (95% CI: 0.874-0.985). CONCLUSIONS: SFP/fungiascites was associated with high mortality. The nomogram established in this article is a useful tool for identifying SFP/fungiascites in SBP patients early. For patients with strongly suspected or confirmed SFP/fungiascites, timely antifungal therapy should be administered.

Enhancement of carbon sequestration via MIL-100(Fe)@PUS in bacterial-algal symbiosis treating municipal wastewater.

Bacterial-algal symbiosis (BAS) is a promising carbon neutrality technology to treat municipal wastewater. However, there are still non-trivial CO2 emissions in BAS due to the slow diffusion and biosorption of CO2. Aiming to reduce CO2 emissions, the inoculation ratio of aerobic sludge to algae was further optimized at 4:1 on the base of favorable carbon conversion. MIL-100(Fe) served as CO2 adsorbents was immobilized on polyurethane sponge (PUS) to increase the interaction with microbes. When MIL-100(Fe)@PUS was added to BAS in the treatment of municipal wastewater, zero CO2 emission was achieved and the carbon sequestration efficiency was increased from 79.9% to 89.0%. Most genes related to metabolic function were derived from Proteobacteria and Chlorophyta. The mechanism of enhanced carbon sequestration in BAS could be attributed to both enrichment of algae (Chlorella and Micractinium) and increased abundance of functional genes related to PS I, PS II and Calvin cycle in photosynthesis.

Enhancement of nitrogen removal in coupling Anammox and DAMO via Fe-modified granular activated carbon.

Anaerobic ammonium oxidation (Anammox) coupled with Denitrifying anaerobic methane oxidation (DAMO) is an attractive technology to simultaneously remove nitrogen and mitigate methane emissions from wastewater. However, its nitrogen removal rate is usually limited due to the low methane mass transfer efficiency, low metabolic activity and slow growth rate of functional microorganisms. In this study, GAC and Fe-modified GAC (Fe-GAC) were added into Anammox-DAMO process to investigate their effects on nitrogen removal rates and then reveal the mechanism. The results showed that after 80-day experiments, the total nitrogen removal rate was slightly improved in the presence of GAC (3.94 mg L-1·d-1), while it reached high as 16.66 mg L-1·d-1 in the presence of Fe-GAC, which was ca.17 times that of non-amended control group (0.96 mg L-1·d-1). The addition of Fe-GAC stimulated the secretion of extracellular polymeric substance (EPS), improved the electron transfer capability and promoted the production of Cytochrome C. Besides, the key functional enzyme activities (HZS, HDH and NAR) were highest in the Fe-GAC group, which were approximately 1.06-1.56 times higher than those of GAC-amended and blank control groups. Microbial community analysis showed that the abundance of the DAMO archaea (Candidatus Methanoperedens) and Anammox bacteria (Candidatus Brocadia) were remarkably increased with the addition of Fe-GAC. Functional genes associated with nitrogen removal and methane oxidation in Fe-GAC system were up-regulated. This study provides a promising strategy for achieving high rate of nitrogen removal upon Anammox-DAMO process.

Carbon-defect-driven persulfate activation for highly efficient degradation of extracellular DNA contaminant: Radical oxidation and electron transfer pathways.

Extracellular DNA (eDNA), as a dynamic repository for antibiotic-resistant genes (ARGs), is a rising threat to public health. This work used a ball-milling method to enhance defect structures of activated carbon, and carbon defects exhibited an excellent capacity in persulfate (PS) activation for model eDNA and real ARGs degradation. The eDNA removal by defect-rich carbon with PS was 2.3-fold higher than that by unmilled activated carbon. The quenching experiment, electrochemical analysis and thermodynamic calculation showed that carbon defects could not only enhance the generation of SO4•- and •OH, but formed an electron transfer bridge between eDNA and PS, leading to the non-radical oxidation of eDNA. According to molecular calculations, the nitrogenous bases of DNA were the easiest sites to be oxidized by electron transfer pathway. This research offers a new way using defective carbon materials as PS activator for eDNA pollutants, and an insight into the non-radical mechanism of eDNA degradation.

Genomic analysis of Marinimicrobium sp. C6131 reveals its genetic potential involved in chitin metabolism.

Marinimicrobium sp. C6131, which had the ability to degrade chitin, was isolated from deep-sea sediment of the southwest Indian Ocean. Here, the genome of strain C6131 was sequenced and the chitin metabolic pathways were constructed. The genome contained a circular chromosome of 4,207,651 bp with a G + C content of 58.50%. A total of 3471 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction showed that strain C6131 possessed genes and two metabolic pathways involved in chitin catabolism: the hydrolytic chitin utilization pathway initiated by chitinases and the oxidative chitin utilization pathway initiated by lytic polysaccharide monooxygenases. Chitin is the most abundant polysaccharide in the ocean. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. The genomic information of strain C6131 revealed its genetic potential involved in chitin metabolism. The strain C6131 could grow with colloidal chitin as the sole carbon source, indicating that these genes would have functions in chitin degradation and utilization. The genomic sequence of Marinimicrobium sp. C6131 could provide fundamental information for future studies on chitin degradation, and help to improve our understanding of the chitin degradation process in deep-sea environments.

Integrated analysis of transcriptomic and protein-protein interaction data reveals cadmium stress response in Geobacter sulfurreducens.

Bacteria have evolved several mechanisms to resist Cd toxicity, which are crucial for Cd detoxication and have the potential to be used for bioremediation of Cd. Geobacter species are widely found in anaerobic environments and play important roles in natural biogeochemical cycles. However, the transcriptomic response of Geobacter sulfurreducens under Cd stress have not been fully elucidated. Through integrated analysis of transcriptomic and protein-protein interaction (PPI) data, we uncovered a global view of mRNA changes in Cd-induced cellular processes in this study. We identified 182 differentially expressed genes (|log2(fold change)| > 1, adjusted P < 0.05) in G. sulfurreducens exposed to 0.1 mM CdCl2 using RNA sequencing (RNA-seq). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that CdCl2 significantly affected sulfur compound metabolic processes. In addition, through PPI network analysis, hub genes related to molecular chaperones were identified to play important role in Cd stress response. We also identified a Cd-responsive transcriptional regulator ArsR2 (coded by GSU2149) and verified the function of ArsR2-ParsR2 regulatory circuit in Escherichia coli. This study provides new insight into Cd stress response in G. sulfurreducens, and identified a potential sensor element for Cd detection.