Wenxuan Zhang

Coastal sediment bacteria mediate essential biogeochemical cycles, yet their functional gene potential to anthropogenic stress gradients remains insufficiently understood. This study presents a comparative analysis of sediment bacterial communities and carbon, nitrogen, phosphorus, and sulfur (C/N/P/S) cycling genes between the west and east coasts of Shenzhen, China, a region exemplifying sharp contrasts between intensive urbanization and relatively pristine marine environments. We integrated 16S rRNA gene high-throughput sequencing with QMEC (Quantitative Microbial Element Cycling), a high-throughput quantitative PCR chip to profile both bacterial taxonomic composition and quantitatively measured gene abundances across C/N/P/S biogeochemical pathways. Western sediments, under strong terrestrial input, exhibited higher ammonium and organic carbon, while eastern sediments had higher salinity. Bacterial alpha diversity was significantly higher in the west, and community structure differed markedly between regions (ANOSIM R = 0.334, p = 0.001). Although dominant phyla (Pseudomonadota, Bacteroidota, and Planctomycetota) were shared, genus-level taxa diverged: Sulfurovum (sulfur cycling) was enriched in the west, while organic-degrading Burkholderia-Caballeronia-Paraburkholderia and Phaeodactylibacter prevailed in the east. Notably, functional gene abundance for all four biogeochemical cycles was an order of magnitude higher in western sediments, with denitrification genes dominating there and nitrification genes in the east. Redundancy analysis (RDA) and the Mantel test identified nitrate as the primary environmental driver of bacterial variation (r = 0.574, p = 0.001), alongside salinity, temperature, ammonium, and total organic carbon. These findings reveal distinct bacterial adaptations to contrasting anthropogenic pressures and demonstrate that sediment bacterial functional gene profiles can serve as sensitive indicators of ecosystem health, providing a quantitative microbiological basis for targeted pollution management in urbanized coastal zones.

The investigation of metabolic pathways and regulatory mechanisms in newly discovered species can offer valuable insights into the nitrogen removal function of heterotrophic nitrification–aerobic denitrification (HN-AD) bacteria. To investigate the nitrogen removal mechanism of a new genus, Delftia, we analyzed the complete genome, metabolic pathways, and the related genes of Delftia sp. B7. We further examined the nitrogen removal capacity of Delftia sp. B7 under various nitrogen sources and real wastewater. Our results demonstrate the presence of several genes in Delftia sp. B7, including narGHI, nasAB, nirK, nirS, nirBD, norBC, nosZ, nxrAB, gdhA, glnA, gltBD, amt, and nrt. These genes encode enzymes that facilitate ammonia assimilation, assimilatory nitrate reduction to nitrite, HN-AD, and dissimilatory nitrate reduction (DNRA) in Delftia sp. B7. Specifically, we propose an HN-AD pathway in Delftia sp. B7, NH₄⁺-N → NH₂OH → NO₂⁻-N → NO₃⁻-N → NO₂⁻-N → NO → N₂O → N₂, which accounts for the majority of nitrogen removal. Here, the transformation of NH₄⁺-N to NO₂⁻-N was achieved by unknown enzymes or by another pathway. When treating municipal wastewater, Delftia sp. B7 was able to remove 45.62 ± 1.29% of TN. These findings provide a theoretical basis for utilizing microbial resources to mitigate nitrogen contamination.

Nitrogen removal through heterotrophic nitrification–aerobic denitrification (HN–AD) has been acknowledged as one of the most efficient and cost-effective nitrogen removal processes. This study involved the isolation of a novel HN–AD bacterium (Rhodococcus sp. S2) from landfill leachate. Rhodococcus sp. S2 exhibited high nitrogen removal performance under aerobic conditions without the accumulation of nitrite as an intermediate. The maximum removal efficiencies for NH₄⁺-N, NO₂⁻-N, and NO₃⁻-N were found to be 99.97 ± 0.3%, 99.79 ± 0.14%, and 83.53 ± 0.31%, respectively. Additionally, Rhodococcus sp. S2 demonstrated simultaneous nitrifying and denitrifying capabilities and showed a preference for utilizing NH₄⁺-N in mixed nitrogen sources. The optimal nitrogen removal conditions for Rhodococcus sp. S2 were as follows: sodium acetate as a carbon source, a C/N ratio of 16, a shaking speed of 200 rpm, a pH of 9, and a temperature of 35 °C. Genome sequencing results revealed the presence of nitrate reductases (NarG), nitrate oxidoreductase (NxrA), and nitrite reductase (NirBD) in Rhodococcus sp. S2, providing further evidence of its HN–AD capability. In treating raw wastewater under the aforementioned experimental conditions, S2 achieved a maximum TN removal efficiency of 57.16 ± 0.52% with the addition of sodium acetate as a carbon source. These results suggest that Rhodococcus sp. S2 might be a promising candidate for wastewater nitrogen removal.

The marine waters in semi-enclosed bays are highly dynamic and strongly influenced by different levels of anthropogenic activity. This study explored the bacterial community composition and diversity in two typical urbanized coastal bay areas (Shenzhen Bay (S) and Dapeng Bay (D)) in Shenzhen, China, based on Illumina NovaSeq sequencing. Seawater analysis showed that coastal area S experienced a higher level of pollution, with higher nutrient concentrations observed. Alpha diversity analysis showed a higher bacterial diversity and richness in coastal area S than D. Taxonomic analysis revealed that the phylum Proteobacteria showed the highest abundance in all samples. Other dominant phyla were Firmicutes, Cyanobacteria, Tenericutes, and Actinobacteria. The bacterial community compositions were significantly different between the two coastal areas. A significant community difference was also found between the sampling sites of coastal area S. However, the difference between sampling sites in coastal area D was not significant. Physicochemical factors showed a more significant effect on bacterial community composition than nutrients. Pearson correlation tests and Network analysis further confirmed that salinity/conductivity, pH, and nitrate were the key factors driving the community difference. PICRUSt analysis revealed a higher degree of functional pathways in coastal area S relating to carbohydrate metabolism, membrane transport, and xenobiotics biodegradation. Our results provide in-depth insights into the bacterial community compositions in typical polluted coastal bays. They may provide information on underlying factors of the assembly process in microbial communities in the coastal zone.