Metaexoproteomics Reveals Microbial Behavior in the Ocean's Interior.

The proteins present in the extracellular environment of cells, named the "exoproteome," are critical for microbial survival, growth, and interaction with their surroundings. However, little is known about microbial exoproteomes in natural marine environments. Here, we used a metaproteomic approach to characterize the exoprotein profiles (10 kDa-0.2 µm) throughout a water column in the South China Sea. Viruses, together with Alpha- and Gammaproteobacteria were the predominant contributors. However, the exoprotein-producing microbial communities varied with depth: SAR11 in the shallow waters, Pseudomonadales and Nitrososphaeria in the mesopelagic layer, and Alteromonadales, Rhizobiales, and Betaproteobacteria in the bathypelagic layer. Besides viral and unknown proteins, diverse transporters contributed substantially to the exoproteomes and varied vertically in their microbial origins, but presented similar patterns in their predicted substrate identities throughout the water column. Other microbial metabolic processes subject to vertical zonation included proteolysis, the oxidation of ammonia, nitrite and carbon monoxide, C1 metabolism, and the degradation of sulfur-containing dissolved organic matter (DOM). Our metaexoproteomic study provides insights into the depth-variable trends in the in situ ecological traits of the marine microbial community hidden in the non-cellular world, including nutrient cycling, niche partitioning and DOM remineralization.

Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics.

Understanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-021-00119-6.

In Situ Aliovalent Nickle Substitution and Acidic Modification of Nanowalls Promoted Proton Conductivity in InOF with 1D Helical Channel.

Proton-conductive materials have attracted increasing attention because of their broad explorations in chemical sensors, water electrolysis, fuel cells, and biological systems. Especially, metal-organic frameworks (MOFs) have been demonstrated to be extremely promising candidates as proton-exchange membrane (PEM) fuel cells. Compared with other configurations, MOFs with one-dimensional (1D) channels have the characteristics of enhancing the host-guest interaction and promoting the anisotropic motion of proton carriers in restricted volume, which are beneficial for acquiring rich proton sources and forming successive hydrogen bonds to improve proton conductivity. We are endeavored to screen and find a helical three-dimensional (3D) framework InOF-1, namely, [In2(OH)2(BPTC)]·6H2O (BPTC4- = 3,3',5,5'-biphenyl tetracarboxylate), as a typical 1D-channel MOF, which is pristinely grafted with spirally distributed -OH groups on the channel surface. Accompanied by an aliovalent substitution Ni(II) for In(III), isostructural NiOF-1 ([Ni2(BPTC)(HCOOH)2]·3H2O) is successfully prepared and massive formic acids are anchored at interior walls, which are interacted with adsorbed water molecules via the formation of stronger O-H···O bonds. This interaction between host-guest molecules and dynamics of lattice water has already led to a remarkable conductivity of InOF-1 (σ = 7.86 × 10-3 S/cm at 328 K under 95% RH). The synergistic effect of the acidic-modified nanowall, contracted volume, and enhanced adsorption of water molecules in the NiOF-1 channel contributes to a high conductivity value of 3.41 × 10-2 S/cm (at 328 K under 95% RH). Moreover, the proton conduction mechanism is further visually presented by molecular dynamic (MD) simulation. In contrast to InOF-1, aliovalent-substituted and acidic-modified NiOF-1 has a stronger host-guest interaction and more abundant hydrogen-bond networks, resulting in shorter proton migration distances and more frequent proton hopping, in agreement with the experimental results.

Illuminating Key Microbial Players and Metabolic Processes Involved in the Remineralization of Particulate Organic Carbon in the Ocean's Twilight Zone by Metaproteomics.

The twilight zone (from the base of the euphotic zone to the depth of 1,000 m) is the major area of particulate organic carbon (POC) remineralization in the ocean, and heterotrophic microbes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity directly associated with POC remineralization in this chronically understudied realm. Here, we characterized the microbial community proteomes of POC samples collected from the twilight zone of three contrasting sites in the Northwest Pacific Ocean using a metaproteomic approach. The particle-attached bacteria from Alteromonadales, Rhodobacterales, and Enterobacterales were the primary POC remineralizers. Hydrolytic enzymes, including proteases and hydrolases, that degrade proteinaceous components and polysaccharides, the main constituents of POC, were abundant and taxonomically associated with these bacterial groups. Furthermore, identification of diverse species-specific transporters and metabolic enzymes implied niche specialization for nutrient acquisition among these bacterial groups. Temperature was the main environmental factor driving the active bacterial groups and metabolic processes, and Enterobacterales replaced Alteromonadales as the predominant group under low temperature. This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The ocean's twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) is remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of microbial community structure and metabolic activity is still lacking. This study unveiled microbial communities and metabolic activities of POC samples collected from the twilight zone of three contrasting environments in the Northwest Pacific Ocean using a metaproteomic approach. Alteromonadales, Rhodobacterales, and Enterobacterales were the major remineralizers of POC. They excreted diverse species-specific hydrolytic enzymes to split POC into solubilized POC or dissolved organic carbon. Temperature played a crucial role in regulating the community composition and metabolism. Furthermore, niche complementarity or species substitution among bacterial groups guaranteed the efficient remineralization of POC in the twilight zone.

Metaproteomics Reveals Similar Vertical Distribution of Microbial Transport Proteins in Particulate Organic Matter Throughout the Water Column in the Northwest Pacific Ocean.

Solubilized particulate organic matter (POM) rather than dissolved organic matter (DOM) has been speculated to be the major carbon and energy sources for heterotrophic prokaryotes in the ocean. However, the direct evidence is still lack. Here we characterized microbial transport proteins of POM collected from both euphotic (75 m, deep chlorophyll maximum DCM, and 100 m) and upper-twilight (200 m and 500 m) zones in three contrasting environments in the northwest Pacific Ocean using a metaproteomic approach. The proportion of transport proteins was relatively high at the bottom of the euphotic zone (200 m), indicating that this layer was the most active area of microbe-driven POM remineralization in the water column. In the upper-twilight zone, the predicted substrates of the identified transporters indicated that amino acids, carbohydrates, taurine, inorganic nutrients, urea, biopolymers, and cobalamin were essential substrates for the microbial community. SAR11, Rhodobacterales, Alteromonadales, and Enterobacteriales were the key contributors with the highest expression of transporters. Interestingly, both the taxonomy and function of the microbial communities varied among water layers and sites with different environments; however, the distribution of transporter types and their relevant organic substrates were similar among samples, suggesting that microbial communities took up similar compounds and were functionally redundant in organic matter utilization throughout the water column. The similar vertical distribution of transport proteins from the euphotic zone to the upper twilight zone among the contrasting environments indicated that solubilized POM rather than DOM was the preferable carbon and energy sources for the microbial communities.

Metaproteomics reveals the molecular mechanism underlying bloom maintenance of a marine dinoflagellate under low ambient CO2 and inorganic nutrients.

Dinoflagellate blooming periods are paradoxically characterized by high biomass growth rate and low ambient dissolved CO2 and inorganic nutrients, however, the underlying mechanisms linking cell growth and nutrient acquisition are poorly understood. Here, we compared metaproteomes of non-bloom, mid-blooming and late-blooming cells of a marine dinoflagellate Prorocentrum donghaiense. Cell division, metabolism of carbon, nitrogen, phosphorus, lipid, porphyrin and chlorophyll were more active in blooming cells than in non-bloom cells. Up-regulation of carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase II, and C4-cycle proteins enhanced CO2 assimilation of P. donghaiense. Proteins participating in external organic nutrient acquisition and conversion, such as transporters for fatty acids, peptides and amino acids, external- and internal-phosphomonoester hydrolase, and diverse peptidases and amino acid transaminases, exhibited higher expression in blooming cells relative to non-bloom cells. Interestingly, dissolved organic nitrogen (DON) such as urea and aspartate significantly down-regulated expression and activity of carbon assimilation proteins except for RuBisCO form II, suggesting that DON provided sufficient carbon source which reduced the need to concentrate internal CO2. This study demonstrates that coupling of efficient CO2 assimilation with DON utilization are essential for bloom maintenance of P. donghaiense, and future efforts should be devoted to dissolved organic nutrients for prevention and management of dinoflagelllate blooms.

Enhanced Proton Conductivity by Aliovalent Substitution of Cadmium for Indium in Dimethylaminium-Templated Metal Anilicates.

Metal-organic frameworks (MOFs) with excellent proton conducting ability are crucial to fuel cells, chemical sensors, and redox flow batteries, but achieving them remain a challenge because of the difficulty in simultaneous fulfillment of large number of proton carriers, high mobility of protons, and long-term durable proton conduction. To explore a simple, efficient, and general route toward highly proton-conducting MOFs, we propose herein an aliovalent substitution metal strategy for isostructural aminium-templated MOFs which benefit the acquisition of rich proton sources without modifying ligands or exchanging protic organic molecules. This idea is verified by 100-fold enhancement of conductivity in compounds (Me2NH2)2[Cd(mdhbqdc)2] (Cd-BQ) and (Me2NH2) (Me2NH)[In(mdhbqdc)2] (In-BQ) (H2mdhbqdc = dimethyl 3,6-dihydroxy-2,5-benzoquinone-1,4-dicarboxylic acid) that feature three-dimensional diamond-like structures with two-dimensional intersected channels. Accompanied by the in situ formation of an anilicate ligand, a great number of -OH groups are grafted onto the inner wall of pores, which interact with neutral Me2NH and/or protonated Me2NH2+ cations via N-H···O hydrogen bonds. The high concentration of protons and dynamics of protic amines in the porous framework readily leads to a moderate conductivity of In-BQ (2.10 × 10-4 S cm-1, at 303 K under 95% RH) and an activation energy of 0.73 eV (95% RH). It should be noted that the aliovalent substitution of Cd(II) for In(III) results in the doubling of dimethylaminium proton carriers in Cd-BQ, indicating more frequent hopping and multiple proton-transfer pathways. This indication is supported by a very high protonic conductivity of 2.30 × 10-2 S cm-1 and a reduced activation energy of 0.48 eV under the same conditions. Molecular dynamics simulations visually elucidate the fact that compared with In-BQ, aliovalent-substituted Cd-BQ has shorter proton-migration distances, which in combination with more proton numbers results in more frequent hopping and sliding of protons, in agreement with the experimental results.

Functional Differences in the Blooming Phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense Revealed by Comparative Metaproteomics.

Phytoplankton blooms are natural phenomena in the ocean, which are the results of rapid cell growth of some phytoplankton species in a unique environment. However, little is known about the molecular events occurring during the bloom. Here, we compared metaproteomes of two phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense in the coastal East China Sea. H. akashiwo and P. donghaiense accounted for 7.82% and 4.74% of the phytoplankton community protein abundances in the nonbloom sample, whereas they contributed to 60.13% and 78.09%, respectively, in their individual blooming samples. Compared with P. donghaiense, H. akashiwo possessed a significantly higher abundance of light-harvesting complex proteins, carbonic anhydrasem and RuBisCO. The blooming H. akashiwo cells expressed more proteins related to external nutrient acquisition, such as bicarbonate transporter SLC4, ammonium transporter, nitrite transporter, and alkaline phosphatase, while the blooming P. donghaiense cells highly expressed proteins related to extra- and intracellular organic nutrient utilization, such as amino acid transporter, 5'-nucleotidase, acid phosphatase, and tripeptidyl-peptidase. The strong capabilities of light harvesting, as well as acquisition and assimilation of inorganic carbon, nitrogen, and phosphorus, facilitated the formation of the H. akashiwo bloom under the high turbidity and inorganic nutrient-sufficient condition, whereas the competitive advantages in organic nutrient acquisition and reallocation guaranteed the occurrence of the P. donghaiense bloom under the inorganic nutrient-insufficient condition. This study highlights the power of metaproteomics for revealing the underlying molecular behaviors of different coexisting phytoplankton species and advances our knowledge on the formation of phytoplankton blooms.IMPORTANCE A deep understanding of the mechanisms driving bloom formation is a prerequisite for effective bloom management. Metaproteomics was applied in this study to reveal the adaptive and responsive strategies of two coexisting phytoplankton species, H. akashiwo and P. donghaiense, during their bloom periods. Metabolic features and niche divergence in light harvesting, as well as carbon, nitrogen, and phosphorus acquisition and assimilation likely promoted the bloom occurrence under different environments. The molecular behaviors of coexisting bloom-causing species will give clues for bloom monitoring and management in the oceans.

[Factors affecting recovery of consciousness in patients with disorders of consciousness following brain trauma: a logistic regression analysis].

OBJECTIVE: To explore the factors that affect the recovery of consciousness in patients with disorders of consciousness following brain trauma. METHODS: We analyzed the data of 114 patients with disorders of consciousness following brain trauma admitted for rehabilitation. Bilateral logistic regression analysis was used to explore the factors that affected the recovery of the patients' consciousness. A logistic regression model was established and the ROC curve was drawn to obtain the optimal threshold of the prognostic model. RESULTS: Univariate analysis showed that vegetative state duration (P<0.001), CRS-R scores (P<0.001), hydrocephalus (P=0.037), hypertonia (P=0.034), central fever (P=0.035), paroxysmal sympathetic hyperactivity (PSH) (P=0.004), and epilepsy seizures were correlated with the recovery of consciousness. Logistic multivariate analysis showed that central fever (OR=3.493, P=0.044), vegetative state duration (OR=1.016, P=0.008), PSH (OR=4.223, P=0.034) and CRS-R scores (OR=0.640, P=0.002) all significantly affected the recovery of consciousness. The χ2 value of the Hosmer-Lemeshow test was 10.214 (P=0.250), and the goodness of fit of this model indicated an outstanding fitting (c=0.91). CONCLUSIONS: The presence of PSH is the one of the most important factor followed by centric fever to affect the outcome of patients with disorders of consciousness. A lower CRS-R score and a longer duration of vegetative state also predict a poor recovery of consciousness in these patients.

Electrochemical sensors using gold submicron particles modified electrodes based on calcium complexes formed with alizarin red S for determination of Ca(2+) in isolated rat heart mitochondria.

A simple glassy carbon electrode (GCE) modified with gold submicron particles (AuSPs), characterized by a mean diameter of about0.15-0.20µm has been developed. Herein, the complexation reaction of Ca(2+) with alizarin red S (ARS), in 0.1M KOH, has been followed by electrochemical methods using the modified electrode which is able to catalyze the electro-reduction of ARS. When the stoichiometry ratio of Ca(2+) and ARS is 1:2, a new reduction peak at a higher negative potential of -0.975V appeared, and the peak of ARS at -0.815V disappeared. The peak current of ARS in alkaline solution is proportional to the concentration of Ca(2+) in the range 6.0×10(-7)-1.2×10(-4)M with a limit of detection (LOD) of 5.1×10(-7)M. Furthermore, the complex site of Ca(2+) with ARS was analysized by the experimental UV-vis and infrared spectrums and those calculated electronic and vibrational spectroscopies with density functional theory (DFT). The good accordance between theoretical and experimental data confirms that chelation of calcium ion preferentially occurs at the deprotonated catechol site. Then, we implemented an electrochemical assay for the investigation of Ca(2+) in preparations of isolated rat heart mitochondria, which demonstrates the submicron particles modified electrode is a simple and rapid sensor for determining the Ca(2+) in the biological samples.

Thermodynamic and kinetic analysis of the interaction between hepatitis B surface antibody and antigen on a gold electrode modified with cysteamine and colloidal gold via electrochemistry.

Hepatitis B surface antibody (HBsAb) was immobilized to the surface of a gold electrode modified with cysteamine and colloidal gold as matrices to detect hepatitis B surface antigen (HBsAg). Differential pulse voltammetry (DPV) method was used for the investigation of the specific interaction between the immobilized HBsAb and HBsAg in solution, which was followed as a change of peak current in DPV with time. With the modified gold electrode, the differences in affinity of HBsAb with HBsAg at the temperatures of 37 and 40 degrees C were easily distinguished and the kinetic rate constants (k(ass) and k(diss)) and kinetic affinity constant K were determined from the curves of current versus time. In addition, the thermodynamic constants, DeltaG, DeltaH and DeltaS, of the interaction at 37 degrees C were calculated, which were -56.65, -64.54 and -25.45 kJ mol(-1), respectively.