Improvement of phenolic acid autotoxicity in tea plantations by Pseudomonas fluorescens ZL22.

Accumulation of phenolic acids, such as p-hydroxybenzoic acid (PHBA), 3,4 dihydroxybenzoic acid (PA), and cinnamic acid (CA) causes a decline in tea plantation soil quality. Bacterial strains that can balance phenolic acid autotoxicity (PAA) in tea tree rhizosphere soil are used to improve tea plantation soil. In this study, the effects of Pseudomonas fluorescens ZL22 on soil restoration and PAA regulation in tea plantations were investigated. ZL22 carries a complete pathway for degrading PHBA and PA to acetyl coenzyme A. ZL22 can colonise and reduce PHBA by 96% and PA by 98% in tea rhizosphere soil within 30 days. The cooccurrence of ZL22 and low CA levels further promotes lettuce seed growth and substantially increases tea production. ZL22 effectively regulates PAA to a safe level in rhizospheric soil, alleviating the inhibition of microbiota by PAA, increases the abundance of genera associated with soil N, C, and S cycling, and creates optimum pH (approximately 4.2) and organic carbon (approximately 25 g/kg), and available N (approximately 62 mg/kg) contents for secondary metabolite accumulation in tea leaves. The application of P. fluorescens ZL22 controls PAA, which synergistically improves plant growth and soil nutrition, thereby promoting tea production and quality.

Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas.

Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.

Synthesis and antimicrobial activities of chitosan/polypropylene carbonate-based nanoparticles.

Antibiotic resistance is an emerging threat to public health. The development of a new generation of antimicrobial compounds is therefore currently required. Here we report a novel antimicrobial polymer of chitosan/polypropylene carbonate nanoparticles (CS/PPC NPs). These were designed and synthesized from readily available chitosan and a reactive oligomer polypropylene carbonate (PPC)-derived epoxy intermediate. By employing a simple and efficient functionalized strategy, a series of micelle-like chitosan-graft-polypropylene carbonate (CS-g-PPC) polymers and chitosan-polypropylene carbonate (CS-PPC) microgels were prepared by reacting mono-/bis-epoxy capped PPC with chitosan. The chemical structure, particle size, and surface charge of the newly synthesized polymers were characterized by infrared (IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and zeta potential measurements. The antimicrobial activities of these nanoparticles were determined in both Gram-positive bacteria (S. aureus) and Gram-negative bacteria (E. coli). Minimum inhibitory concentration (MIC), the nanoparticle concentration needed to completely inhibit the bacterial growth, was found at 128 µg mL-1 to 1024 µg mL-1, strongly depending both on the nature of the epoxy-imine network formed from the functional groups (mono- or bis-capped epoxy groups reacting with amine groups) and the feed ratio of the functional groups (-epoxy/-NH2) between the functionalized PPC and chitosan. No hemolysis was observed at concentrations well in excess of the effective bacteria-inhibiting concentrations. These findings provide a novel strategy to fabricate a new type of nanoantibiotic for antimicrobial applications.

Influences of organic nitrogen on the removal of inorganic nitrogen from complicated marine aquaculture water by Marichromatium gracile YL28.

The sediment-water interface is not only an important location for substrate conversion in a mariculture system, but also a major source of eutrophication. This study aimed to clarify the characteristics of inorganic nitrogen (ammonia, nitrite and nitrate) removal by Marichromatium gracile YL28 in the presence of both organic nitrogen and inorganic nitrogen. The results showed that, in the presence of peptone or urea, seaweed oligosaccharides (SOS) effectively enhanced the ammonia removal capacity of YL28 (6.42 mmol/L) and decreased the residual rate by 54.04% or 8.17%, respectively. With increasing peptone or urea concentrations, the removal of both ammonia and nitrate was gradually inhibited, and the residual rates of ammonia and nitrate reached 22.56-34.36% and 12.03-15.64% in the peptone system and 20.65-24.03% and 12.20-13.21% in the urea system, respectively. However, in the control group the residual rates of ammonia and nitrate reached 11.97% and 5.12%, respectively. In addition, the concentrations of peptone and urea did not affect nitrite removal, and YL28 displayed better cell growth and nitrogen removal activity in the presence of bait and SOS. Overall, the ability of YL28 to remove inorganic nitrogen was enhanced in the presence of organic nitrogen.

Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems.

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the ß-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

Effects of Marichromatium gracile YL28 on the nitrogen management in the aquaculture pond water.

Nitrogen pollution in aquaculture needs the efficient and cost-effective in-situ technology. This study aims to apply Marichromatium gracile YL28 to in-situ bioremediation and test its ability to maintain the nitrogen balance in aquaculture. In laboratory aquaculture system, approximately 99.96% of nitrite (1 mg/L) was removed within 7 d through denitrification coupled with assimilatory nitrate reduction. Ammonium (3.5 mg/L) of 95.6% was directly assimilated by YL28 within 7 d. Moreover, in zero exchange water from shrimp (Penaeus vannamei) aquaculture field trials (20 days), YL28 significantly reduced the ammonium accumulation (0.6 mg/L) and 99.3% of nitrite (1.25 mg/L). Toxicological studies with the Institute of Cancer Research (ICR) mice and Oryzias melastigma indicated that M. gracile YL28 can be safely applied in aquatic ecosystems. All results demonstrate that strain YL28 has high promise for future applications of removing inorganic nitrogen and maintaining the nitrogen balance from in-situ aquaculture.

Comparative genome analysis of marine purple sulfur bacterium Marichromatium gracile YL28 reveals the diverse nitrogen cycle mechanisms and habitat-specific traits.

Mangrove ecosystems are characteristic of the high salinity, limited nutrients and S-richness. Marichromatium gracile YL28 (YL28) isolated from mangrove tolerates the high concentrations of nitrite and sulfur compounds and efficiently eliminates them. However, the molecular mechanisms of nitrite and sulfur compounds utilization and the habitat adaptation remain unclear in YL28. We sequenced YL28 genome and further performed the comparative genome analysis in 36 purple bacteria including purple sulfur bacteria (PSB) and purple non-sulfur bacteria (PNSB). YL28 has 6 nitrogen cycle pathways (up to 40 genes), and possibly removes nitrite by denitrification, complete assimilation nitrate reduction and fermentative nitrate reduction (DNRA). Comparative genome analysis showed that more nitrogen utilization genes were detected in PNSB than those in PSB. The partial denitrification pathway and complete assimilation nitrate reduction were reported in PSB and DNRA was reported in purple bacteria for the first time. The three sulfur metabolism genes such as oxidation of sulfide, reversed dissimilatory sulfite reduction and sox system allowed to eliminate toxic sulfur compounds in the mangrove ecosystem. Several unique stress response genes facilitate to the tolerance of the high salinity environment. The CRISPR systems and the transposon components in genomic islands (GIs) likely contribute to the genome plasticity in purple bacteria.