Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients.

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.

Inhibitory effect of α-ketoglutaric acid on α-glucosidase: integrating molecular dynamics simulation and inhibition kinetics.

The inhibition of α-glucosidase is used as a key clinical approach to treat type 2 diabetes mellitus and thus, we assessed the inhibitory effect of α-ketoglutaric acid (AKG) on α-glucosidase with both an enzyme kinetic assay and computational simulations. AKG bound to the active site and interacted with several key residues, including ASP68, PHE157, PHE177, PHE311, ARG312, TYR313, ASN412, ILE434 and ARG439, as detected by protein-ligand docking and molecular dynamics simulations. Subsequently, we confirmed the action of AKG on α-glucosidase as mixed-type inhibition with reversible and rapid binding. The relevant kinetic parameter IC50 was measured (IC50 = 1.738 ± 0.041 mM), and the dissociation constant was determined (Ki Slope = 0.46 ± 0.04 mM). Regarding the relationship between structure and activity, a high AKG concentration induced the slight modulation of the shape of the active site, as monitored by hydrophobic exposure. This tertiary conformational change was linked to AKG inhibition and mostly involved regional changes in the active site. Our study provides insight into the functional role of AKG due to its structural property of a hydroxyphenyl ring that interacts with the active site. We suggest that similar hydroxyphenyl ring-containing compounds targeting key residues in the active site might be potential α-glucosidase inhibitors. AbbreviationsAKGalpha-ketoglutaric acidpNPG4-nitrophenyl-α-d-glucopyranosideANS1-anilinonaphthalene-8-sulfonateMDmolecular dynamics.Communicated by Ramaswamy H. Sarma.

The inhibitory effect of pyrogallol on tyrosinase activity and structure: Integration study of inhibition kinetics with molecular dynamics simulation.

Pyrogallol is naturally found in aquatic plant and has been proposed as a substrate of tyrosinase. In this study, we evaluated the dual effect of pyrogallol on tyrosinase as an inhibitor in the presence of L­DOPA simultaneously via integrating methods of enzyme kinetics and computational molecular dynamics (MD) simulations. Pyrogallol was found to be a reversible inhibitor of tyrosinase in the presence of L­DOPA and its induced mechanism was the parabolic non-competitive inhibition type (IC50 = 0.772 ±â€¯0.003 mM and Ki = 0.529 ±â€¯0.022 mM). Kinetic measurements by real-time interval assay showed that pyrogallol induced rapid inactivation process composing with slight activations at the low dose. Spectrofluorimetry studies showed that pyrogallol mainly induced regional changes in the active site of tyrosinase accompanying with hydrophobic disruption at high dose. The computational MD simulations further revealed that pyrogallol could interact with several residues near the tyrosinase active site pocket such as HIS61, HIS85, HIS259, ASN260, HIS263, VAL283, and ALA296. Our study provides insight into the mechanism by which hydroxyl group composing pyrogallol inhibit tyrosinase and pyrogallol is a potential natural anti-pigmentation agent.

Carnobacterium antarcticum sp. nov., a psychrotolerant, alkaliphilic bacterium isolated from sandy soil in Antarctica.

A novel, alkaliphilic, psychrotolerant, facultative anaerobe, designated CP1T, was isolated from sandy soil near the Davis Station in Antarctica. The short-rod-shaped cells displayed Gram-positive staining and did not form spores. Strain CP1T was able to grow at temperatures between 4 and 36 °C, pH 6.0-9.5, and in the presence of up to 5.0 % (w/v) NaCl. 16S rRNA gene and multilocus (pheS, rpoA, and atpA) sequence analysis revealed Carnobacterium mobile DSM 4848T and Carnobacterium iners LMG 26642T as the closest relatives (97.4 and 97.1 % 16S rRNA gene sequence similarity, respectively). The genomic G+C content was 38.1 mol%, and DNA-DNA hybridization with DSM 4848T revealed 32.4±3.4 % similarity. The major fatty acid components were C14 : 0 and C16 : 1ω9c. The cell wall contained meso-diaminopimelic acid and was of peptidoglycan type A1γ. Based on physiological, genotypic and biochemical characteristics, strain CP1T represents a novel species of the genus Carnobacterium for which the name Carnobacterium antarcticum sp. nov. is proposed. The type strain is CP1T (=DSM 103363T=CGMCC 1.15643T).

Microeukaryotic biogeography in the typical subtropical coastal waters with multiple environmental gradients.

The determinants of microeukaryotic biogeography in coastal waters at a regional scale remain largely unclear. The coastal northern Zhejiang (in the East China Sea) is a typical subtropical marine ecosystem with multiple environmental gradients that has been extensively perturbed by anthropogenic activities. Thus, it is a valuable region to investigate the key drivers that shape microbial biogeography. We investigated microeukaryotic communities in surface waters from 115 stations in this region using 18S ribosomal RNA gene amplicon sequencing. The microeukaryotic communities were mainly comprised of Dinoflagellata, Ciliophora, Protalveolata, Rhizaria, Stramenopiles and Cryptophyceae. The top abundant operational taxonomic units (OTUs) were highly specific for distinct habitat types, exhibiting significant environment-conditioned features; however, the cosmopolitan OTUs were not strongly correlated with the measured environmental variables. Total phosphorus and suspended particles were major environmental determinants of microeukaryotic α-diversity. Environmental variables, particularly temperature, salinity, pH and silicate concentration, were strongly associated with the microeukaryotic community composition. Overall, environmental and spatial factors explained 55.92% of community variation in total with 34.03% of the variation shared, suggesting that spatially structured environmental variations mainly conditioned the microeukaryotic biogeography in this region. Additionally, dispersal limitation, as indicated by the great pure spatial effect and distance-decay pattern, was another important factor. In summary, our results reveal that spatially structured environmental variation and dispersal limitation mainly conditioned the microeukaryotic biogeography. The results may provide useful distribution patterns of microeukaryotes to determine sources of microbes from marine ecosystems that may facilitate the utilization of coastal resources.

Inhibitory effect of raspberry ketone on α-glucosidase: Docking simulation integrating inhibition kinetics.

Inhibition of α-glucosidase is directly associated with treatment of type 2 diabetes. In this regard, we conducted enzyme kinetics integrated with computational docking simulation to assess the inhibitory effect of raspberry ketone (RK) on α-glucosidase. RK bound to the active site of α-glucosidase and interacted with several key residues such as ASP68, TYR71, HIS111, PHE157, PHE158, PHE177, GLN181, ASP214, THR215, ASP349, ASP408, and ARG439, as detected by protein-ligand docking simulation. Subsequently, we confirmed the action of RK on α-glucosidase as the non-competitive type of inhibition in a reversible and rapidly binding manner. The relevant kinetic parameters were IC50=6.17±0.46mM and Ki=7.939±0.211mM. Regarding the structure-activity relationship, the higher concentration of RK induced slight modulation of the shape of the active site as monitored by hydrophobic exposure. The tertiary conformational change was linked to RK inhibition, and mostly involved regional changes of the active site. Our study provides insight into the functional role of RK due to its structural property of a hydroxyphenyl ring that interacts with the active site of α-glucosidase. We suggest that similar hydroxyphenyl ring compounds targeting the key residues of the active site might be potential α-glucosidase inhibitors.

A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria.

Anaerobic digestion is a complicated microbiological process that involves a wide diversity of microorganisms. Acetate is one of the most important intermediates, and interactions between acetate-oxidizing bacteria and archaea could play an important role in the formation of methane in anoxic environments. Anaerobic digestion at thermophilic temperatures is known to increase methane production, but the effects on the microbial community are largely unknown. In the current study, stable isotope probing was used to characterize acetate- and lactate-oxidizing bacteria in thermophilic anaerobic digestion. In microcosms fed 13C-acetate, bacteria related to members of Clostridium, Hydrogenophaga, Fervidobacterium, Spirochaeta, Limnohabitans, and Rhodococcus demonstrated elevated abundances of 13C-DNA fractions, suggesting their activities in acetate oxidation. In the treatments fed 13C-lactate, Anaeromyxobacter, Desulfobulbus, Syntrophus, Cystobacterineae, and Azospira were found to be the potential thermophilic lactate utilizers. PICRUSt predicted that enzymes related to nitrate and nitrite reduction would be enriched in 13C-DNA fractions, suggesting that the acetate and lactate oxidation may be coupled with nitrate and/or nitrite reduction. Co-occurrence network analysis indicated bacterial taxa not enriched in 13C-DNA fractions that may also play a critical role in thermophilic anaerobic digestion.

Thermal discharge-created increasing temperatures alter the bacterioplankton composition and functional redundancy.

Elevated seawater temperature has altered the coupling between coastal primary production and heterotrophic bacterioplankton respiration. This shift, in turn, could influence the feedback of ocean ecosystem to climate warming. However, little is known about how natural bacterioplankton community responds to increasing seawater temperature. To investigate warming effects on the bacterioplankton community, we collected water samples from temperature gradients (ranged from 15.0 to 18.6 °C) created by a thermal flume of a coal power plant. The results showed that increasing temperatures significantly stimulated bacterial abundance, grazing rate, and altered bacterioplankton community compositions (BCCs). The spatial distribution of bacterioplankton community followed a distance similarity decay relationship, with a turnover of 0.005. A variance partitioning analysis showed that temperature directly constrained 2.01 % variation in BCCs, while temperature-induced changes in water geochemical and grazing rate indirectly accounted for 4.03 and 12.8 % of the community variance, respectively. Furthermore, the relative abundances of 24 bacterial families were linearly increased or decreased (P < 0.05 in all cases) with increasing temperatures. Notably, the change pattern for a given bacterial family was in concert with its known functions. In addition, community functional redundancy consistently decreased along the temperature gradient. This study demonstrates that elevated temperature, combined with substrate supply and trophic interactions, dramatically alters BCCs, concomitant with decreases in functional redundancy. The responses of sensitive assemblages are temperature dependent, which could indicate temperature departures.

Pseudoalteromonas gelatinilytica sp. nov., isolated from surface seawater.

Three Gram-stain-negative, rod-shaped bacteria, designated strains NH153T, F-2-11 and M-1-78, were isolated from surface seawater of the South China Sea and the East China Sea. The three isolates were able to grow at 15-45 °C (optimum 28-37 °C), but no growth occurred at 4 or 50 °C. The pH range for growth was pH 5.5-9.5 (optimum pH 7.5-8.5). The isolates required sea salts for growth and growth occurred in the presence of 0-10 % (w/v) NaCl (optimum 3-5 %); no growth occurred in the presence of 12.0, 15.0 or 20.0 % (w/v) NaCl. They were positive for hydrolysis of gelatin and Tween 80. The sole respiratory quinone was ubiquinone-8 (Q-8). The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipid components were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain NH153T was 41.4 mol%. Based on 16S rRNA gene sequence analysis, the isolates were closely related to the type strain of Pseudoalteromonas shioyasakiensis (98.0-98.6 % sequence similarity). The 16S rRNA gene sequence similarities between the three isolates were 98.8-99.7 %. Phylogenetic analysis indicated that they formed a distinct lineage and clustered with P. shioyasakiensis and Pseudoalteromonas arabiensis. The level of DNA-DNA relatedness among the three isolates was 78.0-85.5 %. Strain NH153T exhibited average nucleotide identity values of 93.4 and 84.2 % with respect to P. shioyasakiensisJCM 18891T and P. arabiensisJCM 17292T, respectively. The genome-to-genome distance analysis revealed that strain NH153T shared 52.4 % DNA relatedness with P. shioyasakiensisJCM 18891T and 28.1 % with P. arabiensisJCM 17292T. On the basis of the phenotypic, genotypic and chemotaxonomic characterizations, as well as phylogenetic inference obtained in this study, strains NH153T, F-2-11 and M-1-78 represent a novel species within the genus Pseudoalteromonas, for which the name Pseudoalteromonasgelatinilytica sp. nov. is proposed. The type strain is NH153T (=CGMCC 1.15370T=DSM 100951T), and F-2-11 (=CGMCC 1.15364=DSM 100953) and M-1-78 (=CGMCC 1.15365=DSM 100952), are additional strains of the species.

[Bacterial diversity in deep-sea sediments from two stations in the east Pacific polymetallic nodule province].

Objective: The objective of this study was to assess bacterial diversity in sediment samples from two stations (WBC1305 and WBC1316A) in the Pacific polymetallic nodule province. Methods: The environmental total DNAs were extracted, and 6 bacterial 16S rRNA gene libraries were generated from 6 sediment layers. The Shannon diversity index and Simpson dominance index were calculated for each bacterial community and then compared. The bacterial community structure of each sediment sample was analyzed, and the results were used to construct phylogenetic trees. Results: In total, 533 bacterial clones were obtained from 6 bacterial clone libraries. Among these 533 clones, 472 clones could be assigned to 16 phylogenetic groups (Acidobacteria, Actinobacteria, Alpha, Beta, Delta, gamma-Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Elusimicrobia, Hydrogenedentes, Chlorobi, and Nitrospinae), whereas the remaining 61 clones could not be classified into any known groups. Conclusion: The bacterial communities in sediments from WBC1305 are dominated mainly by gamma-Proteobacteria and from WBC1316A by Firmicutes. In addition, the bacterial community structure at WBC1316A is more abundant and complex than that at WBC1305.

[Studies of on-site night soil and kitchen garbage treatment].

The biological treatment technique of collection at source and disposition on-site of night soil and kitchen garbage were presented. By design project of overall technics, the lab-scale experiments were performed. It was revealed that water consumption of vacuum closestool was about 1 L/time. It consumed 0.4- 0.6L water to shred 1 kg kitchen garbage. Night soil covered 40%, kitchen garbage covered 60% in the influent. Water was controlled at about 93%, the C:N ratio was about 25:1, pH was between 6.2 and 7.3, the optical blend frequency was 6h/d and the overall solid retention time was 28 days in anaerobic digestion reactor. The COD removal rate of mixed supernatant was 91% in anaerobic baffled reactor. It was identified that these phosphorus strains and potassium strains were Bacillus. sp, and biological activated fertilizer was obtained by mixed these strains with digestion sludge which had been dehydrated and deodorized. These strains ability of forming phosphorus and potassium were determined, and the concentration of phosphorus increased 67.5%, potassium increased 33.4%.