Bacterial community response to chronic heavy metal contamination in marine sediments of the East China Sea

Ecofriendly biosynthesis of copper nanoparticles from novel marine S. rhizophila species for enhanced antibiofilm, antimicrobial and antioxidant potential

Marine microorganisms offer a promising avenue for the eco-friendly synthesis of nanoparticles due to their unique biochemical capabilities and adaptability to various environments. This study focuses on exploring the potential of a marine bacterial species, Stenotrophomonas rhizophila BGNAK1, for the synthesis of biocompatible copper nanoparticles and their application for hindering biofilms formed by monomicrobial species. The study begins with the isolation of the novel marine S. rhizophila species from marine soil samples collected from the West coast region of Kerala, India. The isolated strain is identified through 16S rRNA gene sequencing and confirmed to be S. rhizophila species. Biosynthesis of copper nanoparticles using S. rhizophila results in the formation of nanoparticles with size of range 10-50 nm. The nanoparticles exhibit a face-centered cubic crystal structure of copper, as confirmed by X-Ray Diffraction analysis. Furthermore, the synthesized nanoparticles display significant antimicrobial activity against various pathogenic bacteria and yeast. The highest inhibitory activity was against Staphylococcus aureus with a zone of 27 ± 1.00 mm and the least activity was against Pseudomonas aeruginosa with a zone of 22 ± 0.50 mm. The zone of inhibition against Candida albicans was 16 ± 0.60 mm. The antibiofilm activity against biofilm-forming clinical pathogens was evidenced by the antibiofilm assay and SEM images. Additionally, the copper nanoparticles exhibit antioxidant activity, as evidenced by their scavenging ability against DPPH, hydroxyl, nitric oxide, and superoxide radicals, as well as their reducing power in the FRAP assay. The study highlights the potential of the marine bacterium S. rhizophila BGNAK1 for the eco-friendly biosynthesis of copper nanoparticles with diverse applications. Synthesized nanoparticles exhibit promising antibiofilm, antimicrobial, and antioxidant properties, suggesting their potential utility in various fields such as medicine, wastewater treatment, and environmental remediation.

Influence of cadmium and zinc contamination on the sediment microbiome of estuarine and coastal ecosystems in the Southwest Coast of India

Metals and their nanoparticles can induce toxicities that influence the survival of both microorganisms and macroorganisms. The current study reports on the impact of heavy metal pollution on the microbiome of estuarine and coastal sediments, where the settling and final remineralization of organic matter occur. Sediment samples collected from the Cochin estuary along the southwest coast of India and its adjacent coast showed high concentrations of cadmium (Cd) and zinc (Zn). The contamination factor (CF), calculated by comparing the concentration of metals in each station with that of shale value for Cd and Zn, ranged from 5.2 to 8.7 and 1.5 to 2.0 respectively, in the estuarine and coastal stations. Microbiome analysis revealed that bacteria were common across all stations but varied in relative abundance. Proteobacteria, Chloroflexi, Actinobacteria, Desulfobacteria, and Acidobacteria were the major bacterial phylum found in all stations. More than 70% of the bacteria were tolerant to 1 mM concentration of Cd. The findings of our study suggest that metal pollution can influence the microbiome of sediments in the estuaries and coasts. Bacteria with metal tolerance may dominate in polluted areas, but their participation in remineralization may be impaired, as evident in our previous reports. This impairment could ultimately influence the dynamics of the food web and the biogeochemical cycling of nutrients, necessitating further research.

The abundance and pathogenicity of microbes in automobile air conditioning filters across the typical cities of China and Europe

Bioaerosols are widely distributed in urban air and can be transmitted across the atmosphere, biosphere, and anthroposphere, resulting in infectious diseases. Automobile air conditioning (AAC) filters can trap airborne microbes. In this study, AAC filters were used to investigate the abundance and pathogenicity of airborne microorganisms in typical Chinese and European cities. Culturable bacteria and fungi concentrations were determined using microbial culturing. High-throughput sequencing was employed to analyze microbial community structures. The levels of culturable bioaerosols in Chinese and European cities exhibited disparities (Analysis of Variance, P < 0.01). The most dominant pathogenic bacteria and fungi were similar in Chinese (Mycobacterium: 18.2-18.9 %; Cladosporium: 23.0-30.2 %) and European cities (Mycobacterium: 15.4-37.7 %; Cladosporium: 18.1-29.3 %). Bartonella, Bordetella, Alternaria, and Aspergillus were also widely identified. BugBase analysis showed that microbiomes in China exhibited higher abundances of mobile genetic elements (MGEs) and biofilm formation capacity than those in Europe, indicating higher health risks. Through co-occurrence network analysis, heavy metals such as zinc were found to correlate with microorganism abundance; most bacteria were inversely associated, while fungi exhibited greater tolerance, indicating that heavy metals affect the growth and reproduction of bioaerosol microorganisms. This study elucidates the influence of social and environmental factors on shaping microbial community structures, offering practical insights for preventing and controlling regional bioaerosol pollution.

Bacterial community in the metal(loid)-contaminated marine vertical sediments of Jinzhou Bay: Impacts and adaptations

Metal(loid) discharge has led to severe coastal contamination; however, there remains a significant knowledge gap regarding its impact on sediment profiles and depth-resolved bacterial communities. In this study, geochemical measurements (pH, nutrient elements, total and bioavailable metal(loid) content) consistently revealed decreasing nitrogen, phosphorus, and metal(loid) levels with sediment depth, accompanied by reduced alpha diversity. Principal coordinate analysis indicated distinct community compositions with varying sediment depths, suggesting a geochemical influence on diversity. Ecological niche width expanded with depth, favoring specialists over generalists, but both groups decreased in abundance. Taxonomic shifts emerged, particularly in phyla and families, correlated with sediment depth. Microbe-microbe interactions displayed intricate dynamics, with keystone taxa varying by sediment layer. Zinc and arsenic emerged as key factors impacting community diversity and composition using random forest, network analysis, and Mantel tests. Functional predictions revealed shifts in potential phenotypes related to mobile elements, biofilm formation, pathogenicity, N/P/S cycles, and metal(loid) resistance along sediment profiles. Neutral and null models demonstrated a transition from deterministic to stochastic processes with sediment layers. This study provides insights into the interplay between sediment geochemistry and bacterial communities across sediment depths, illuminating the factors shaping these ecosystems.

Relationships between high-concentration toxic metals in sediment and evolution of microbial community structure and carbon-nitrogen metabolism functions under long-term stress perspective

Microorganisms are highly sensitive to toxic metal pollution and play an important role in the material cycling and energy flow of the water ecosystem. Herein, 13 sediment samples from Junchong Reservoir (Guangxi Province, China) were collected in December 2021. The spatial distribution of pollution levels for toxic metals and the effects of toxic metals on the composition, functional characteristics, and metabolism of microorganisms were investigated. The results demonstrated that the area is a proximate area to industrial zones with severity of toxic metal pollution. Their mean concentrations of As, Cu, Zn, and Pb were up to 128.79 mg/kg, 57.62 mg/kg, 594.77 mg/kg, and 97.12 mg/kg respectively. There was a strong correlation between As, Cu, Zn, and Pb, with the highest correlation coefficient reaching 0.94. As the level of toxic metal pollution increases, the diversity and abundance of microorganisms gradually decrease. Compared to those with lower pollution levels, the Shannon index in regions with higher pollution levels decreases by up to 0.373, and the Chao index decreases by up to 143.507. However, the relative abundance of Bacteroidota, Patescibacteria, and Chloroflexi increased by 23%, 20%, and 5%, respectively, indicating their higher adaptability to toxic metals. Furthermore, microbial carbon and nitrogen metabolism were also affected by the presence of toxic metals. FAPROTAX analysis demonstrated an abundant reduction of ecologically functional groups associated with carbon and nitrogen transformations under high toxic metal pollution levels. KEGG pathway analysis indicated that carbon fixation and nitrogen metabolism pathways were inhibited with increasing toxic metal concentrations. These findings would contribute to a better understanding of the effects of toxic metal pollution on sediment microbial communities and function, shedding light on the ecological consequences of toxic metal contamination.

Seasonal and distance-decay patterns of surface sediments microbial nitrogen and sulfur cycling linkage in the eastern coast of China

The surface sediments as a repository of pelagic environment changes and microbial community structural succession tend to have a profound effect on global and local nitrogen and sulfur cycling. In this study, analysis of sediment samples collected from the Bohai Sea, Yellow Sea, and north of the East China Seas (BYnECS) revealed longitude, latitude, depth, and chlorophyll had the strongest influence on microbial community structure (p-values < 0.005). A clear distance-decay pattern was exhibited in BYnECS. The result of co-occurrence network modularization implied that the more active pathway in winter was thiosulfate reduction and nitrate reduction, while in summer it was nitrification. The potential functional genes were predicted in microbial communities, and the most dominant genes were assigned to assimilatory sulfur reduction, denitrification, and dissimilatory nitrate reduction. This study innovatively explored the potential relationships between nitrogen and sulfur cycling genes of these three sea regions in the China Sea.

Divergent adaptation strategies of abundant and rare bacteria to salinity stress and metal stress in polluted Jinzhou Bay

Understanding how abundant (AT) and rare (RT) taxa adapt to diverse environmental stresses is vital for assessing ecological processes, yet remains understudied. We collected sediment samples from Liaoning Province, China, representing rivers (upstream of wastewater outlet), estuaries (wastewater outlets), and Jinzhou Bay (downstream of wastewater outlets), to comprehensively evaluate AT and RT adaptation strategies to both natural stressors (salinity stress) and anthropogenic stressors (metal stress). Generally, RT displayed higher α- and β-diversities and taxonomic groups compared to AT. Metal and salinity stresses induced distinct α-diversity responses in AT and RT, while β-diversity remained consistent. Both subcommunities were dominated by Woeseia genus. Metal stress emerged as the primary driver of diversity and compositional discrepancies in AT and RT. Notably, AT responded more sensitively to salinity stress than RT. Stress increased topological parameters in the biotic network of AT subcommunities while decreasing values in RT subcommunities, concurrently loosening interactions of AT with other taxa and strengthening interactions of RT with others in biotic networks. RT generally exhibited greater diversity of metal resistance genes compared to AT. Greater numbers of genes related to salinity tolerance was observed for the RT than for AT. Compared to AT, RT demonstrated higher diversity of metal resistance genes and a greater abundance of genes associated with salinity tolerance. Additionally, deterministic processes governed AT community assembly, reinforced by salinity stress. However, the opposite trend was observed in the RT, where the importance of stochastic process gradually increased with metal stresses. The study is centered on exploring the adaptation strategies of both AT and RT to environmental stress. It underscores the importance of future research incorporating diverse ecosystems and a range of environmental stressors to draw broader and more reliable conclusions. This comprehensive approach is essential for gaining a thorough understanding of the adaptive mechanisms employed by these microorganisms.

Unveiling the impact and mechanisms of Cd-driven ecological assembly and coexistence of bacterial communities in coastal sediments of Yellow Sea

The microbial community assembly processes and underlying mechanisms in response to heavy metal accumulation in coastal sediments remain underexplored. In this study, the heavy metal concentration in samples were found below the marine sediment quality standards. Through partial Mantel tests and linear regression analysis, Cd was identified as the major influencing factor, displaying strongest correlation with the bacterial community in the sediments. The class Desulfuromonadia was identified as a biomarker which showed enrichment in the sediments with high Cd content. Additionally, the results of null model and the neutral community model demonstrated the prominent role of stochastic processes in the assembly of bacterial community. However, with the increase in Cd concentration, the influence of selection processes intensified, resulting in a decline in species migration rate and subsequent reduction in ecological niche width. Furthermore, the intensified competition and an increase in keystone species among bacterial populations further enhanced the stability of the microbial co-occurrence network in response to high Cd concentration. This study offers an insight into the effects of heavy metal on microbial assembly and coexistence, which are conducive to marine ecosystem management and conservation.

Impact of different industrial activities on heavy metals in floodplain soil and ecological risk assessment based on bioavailability: A case study from the Middle Yellow River Basin, northern China

Understanding the impact of different industrial activities on heavy metals and conducting scientific ecological risk assessments are critical to the management of heavy metal pollution. The present study compared soils affected by different industrial activities in three types of industrial cities (coal city, oil-gas city, and economic city) to control samples and examined the ecological risk based on bioavailability in the Middle Yellow River Basin. The findings revealed that the impact characteristics of different industrial activities on soil heavy metals in the research area were different. Both coal-based and oil-gas industry activities had a minor impact on soil heavy metals, whereas economic industry activities in the southern part had a major impact, as evidenced by significant enrichment of Cd, Hg, Cu, Pb, and Zn. In principal component analysis, the soil heavy metals affected by economic industry activities designated a distinct source from the control samples, particularly the anthropogenic sources represented by Hg and Cd. In the context of heavy metals in chemical form, three types of industrial activities all had an effect on bioavailability (0.72-24.27%) and could increase migratory activity in the environment. Furthermore, both traditional and improved assessments, based on total content and bioavailability, showed a low ecological risk near coal cities and oil-gas cities in the middle and northern parts, while there was a medium-high ecological risk near economically developed cities in the south, particularly Tianshui, Baoji, Qishan, Xianyang, Xi'an, and Tongchuan. In comparison, improved risk assessment based on bioavailability tends to not only compensate for an overestimation in traditional risk assessment from the perspective of total content, but additionally achieve a more reasonable, effective, and advanced assessment of heavy metal risks in scientific research. The outcome of this study has significance for the ecological conservation and high-quality development of the Yellow River Basin.

Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils

Both heavy metals and antibiotics exert selection pressure on bacterial resistance, and as they are commonly co-contaminated in the environment, they may play a larger role in bacterial resistance. This study examined how breeding cycles affect antibiotic resistance genes (ARGs) in chicken manure and the surrounding topsoils at 20, 50, 100, 200, and 300 m from twelve typical laying hen farms in the Ningxia Hui Autonomous Region of northwest China. Six antibiotics, seven heavy metals, ten mobile genetic elements (MGEs), and microbial community affected the ARGs profile in chicken dung and soil samples. Tetracycline antibiotic residues were prevalent in chicken manure, as were relatively high content of aureomycin during each culture period. Zinc (Zn) content was highest among the seven heavy metals in chicken feces. Chicken dung also enriched aminoglycosides, MLSB, and tetracycline ARGs, notably during brooding and high production. The farm had a minimal influence on antibiotics in the surrounding soil, but its effect on ARGs and MGEs closer to the farm (50 m) was stronger, and several ARGs and MGEs increased with distance. Manure microbial composition differed dramatically throughout breeding cycles and sampling distances. ARGs were more strongly related with antibiotics and heavy metals in manure than soil, whereas MGEs were the reverse. Antibiotics, heavy metals, MGEs, and bacteria in manure accounted 12.28%, 22.25%, 0.74%, and 0.19% of ARGs composition variance, respectively, according to RDA and VPA. Bacteria (2.89%) and MGEs (2.82%) only affected soil ARGs composition. These findings showed that heavy metals and antibiotics are the main factors affecting faecal ARGs and bacteria and MGEs soil ARGs. This paper includes antibiotic resistance data for large-scale laying hen husbandry in northwest China and a theoretical framework for decreasing antibiotic resistance.

Biochar loaded with bacteria enhanced Cd/Zn phytoextraction by facilitating plant growth and shaping rhizospheric microbial community

Biochar and metal-tolerant bacteria have been widely used in the remediation of heavy metal contaminated soil. However, the synergistic effect of biochar-functional microbes on phytoextraction by hyperaccumulators remains unclear. In this study, the heavy metal-tolerant strain Burkholderia contaminans ZCC was selected and loaded on biochar to produce biochar-resistant bacterial material (BM), and the effects of BM on Cd/Zn phytoextraction by Sedum alfredii Hance and rhizospheric microbial community were explored. The results showed that, BM application significantly enhanced the Cd and Zn accumulation of S. alfredii by 230.13% and 381.27%, respectively. Meanwhile, BM alleviated metal toxicity of S. alfredii by reducing oxidative damage and increasing chlorophyll and antioxidant enzyme activity. High-throughput sequencing revealed that BM significantly improved soil bacterial and fungal diversity, and increased the abundance of genera with plant growth promoting and metal solubilizing functions such as Gemmatimonas, Dyella and Pseudarthrobacter. Co-occurrence network analysis showed that BM significantly increased the complexity of the rhizospheric bacterial and fungal network. Structural equation model analysis revealed that soil chemistry property, enzyme activity and microbial diversity contributed directly or indirectly to Cd and Zn extraction by S. alfredii. Overall, our results suggested that biochar- B. contaminans ZCC was able to enhance the growth and Cd/Zn accumulation by S. alfredii. This study enhanced our understanding on the hyperaccumulator-biochar-functional microbe interactions, and provided a feasible strategy for promoting the phytoextraction efficiency of heavy metal contaminated soils.

Effect of antibiotic and/or heavy metal on nitrogen cycle of sediment-water interface in aquaculture system: Implications from sea cucumber culture

Antibiotics and heavy metals can have a negative impact on the nitrogen (N) cycle and microbial metabolism in coastal aquaculture environment. An indoor simulated culture experiment was conducted to explore how sulfadiazine and lead influence the N cycling in aquatic environment. Specifically, the experiment involved adding sulfadiazine (SDZ), lead (Pb), a combination of SDZ and Pb (SP), and a control group (CK). The fluxes and contents of ammonia nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N) and nitrite nitrogen (NO₂^--N) in sediment-water interface and sediments, the abundance of N cycle function genes (amoA_AOB, hzsA, nar, nirK, nirS, norB and nosZ) and microbiota in sediments were analyzed. The results showed that the presence of SDZ and Pb inhibited the nitrification function gene and nitrifiers abundance in surface sediment, and thus leading to more accumulation of NH₄⁺ and NO₂^- in overlying water. Pb exposure increased the abundances of denitrifying bacteria stimulated the first three steps of denitrification in the sediment, resulting in more removal of NO₃^- from the sediment, but possibly had the risk of releasing more greenhouse gas N₂O. Conversely, the presence of SDZ ultimately inhibited denitrification and anammox bacterial activities in the sediment. This study revealed how heavy metal and antibiotic impair the microbial communities and N cycling function gene expression, leading to the deterioration of typical coastal aquaculture environments.

Cascading effects of Pb on the environmental and symbiotic microbiota and tadpoles' physiology based on field data and laboratory validation

Heavy metal pollution poses a serious threat to ecosystems. Currently, there is a lack of field data that would enable us to gain a systematic understanding of the influences of heavy metals on aquatic ecosystems, especially the interactions between environments and animals. We studied the relationships between the variations in heavy metal concentrations (10 species including Pb in sediments and surface water), the community structure of environmental and symbiotic microbiota, and the gut traits of Bufo gargarizans tadpoles across 16 sampling sites on the Chengdu Plain through rigorous statistical analysis and laboratory validation. The results show that heavy metal concentrations, especially the Pb concentration of the sediment, are linked to the variations in sediment and tadpoles' gut microbiomes but not to water microbiota. For the sediment microbiota, Pb causes a trade-off between the proportions of Burkholderiales and Verrucomicrobiae and affects the methane, sulfide, and nitrate metabolisms. For tadpoles, a high sediment Pb content leads to a low abundance of gut aerobic bacteria and a large relative gut weight under both field and laboratory conditions. In addition, Pb promotes the growth of B. gargarizans tadpoles under laboratory conditions. These effects seem to be beneficial to tadpoles. However, a high Pb content leads to a low abundance of probiotic bacteria (e.g., Verrucomicrobiae, Eubacteriaceae, and Cetobacterium) and a high abundance of pathogenic bacteria in the gut and environment, suggesting potential health risks posed by Pb. Interestingly, there is a causal relationship between Pb-induced variations in sediment and symbiotic microbiotas, and the latter is further linked to the variation in relative gut weight of tadpoles. This suggests a cascading effect of Pb on the ecosystem. In conclusion, our results indicate that among the heavy metals, the Pb in sediment is a critical factor affecting the aquatic ecosystem through an environment-gut-physiology pathway mediated by microbiota.

Bioaerosols in an industrial park and the adjacent houses: Dispersal between indoor/outdoor, the impact of air purifier, and health risk reduction

Inhaling airborne pathogens may cause severe epidemics showing huge threats to indoor dwellings residents. The ventilation, environmental parameters, and human activities would affect the abundance and pathogenicity of bioaerosols in indoor. However, people know little about the indoor airborne microbes especially pathogens near the industrial park polluted with organics and heavy metals. Herein, the indoor bioaerosols' community composition, source and influencing factors near an electronic waste (e-waste) industrial park were investigated. Results showed that the average bioaerosol level in the morning was lower than evening. Bioaerosol concentration and activity in indoor (1936 CFU/m³ and 7.62 × 10⁵ ng/m³ sodium fluorescein in average) were lower than the industrial park (4043 CFU/m³ and 7.77 × 10⁵ ng/m³ sodium fluorescein), and higher microbial viability may be caused by other pollutants generated during e-waste dismantling process. Fluorescent biological aerosol particles occupied 17.6%-23.7% of total particles, indicating that most particles were non-biological. Bacterial communities were richer and more diverse than fungi. Furthermore, Bacillus and Cladosporium were the dominant indoor pathogens, and pathogenic fungi were more influenced by environmental factors than bacteria. SourceTracker analysis indicates that outdoor was the main source of indoor bioaerosols. The hazard quotient (<1) of airborne microbes through inhalation was negligible, but long-term exposure to pathogens could be harmful. Air purifiers could effectively remove the airborne fungi and spheroid bacteria than cylindrical bacteria, but open doors and windows would reduce the purification efficiency. This study is great important for risk assessments and control of indoor bioaerosols near industrial park.

Impact of environmental factors on the ammonia-oxidizing and denitrifying microbial community and functional genes along soil profiles from different ecologically degraded areas in the Siding mine

Ammonia oxidizers (ammonia-oxidizing bacteria (AOB amoA) and ammonia-oxidizing archaea (AOA amoA)) and denitrifiers (encoded by nirS, nirK and nosZ) in the soil nitrogen cycle exist in a variety of natural ecosystems. However, little is known about the contribution of these five N-related functional genes to nitrification and denitrification in the soil profile in severely ecologically degraded areas. Therefore, in the present study, the abundance, diversity and community composition of AOA, AOB, nirS, nirK and nosZ were investigated in the soil profiles of different ecologically degraded areas in the Siding mine. The results indicated that, at the phylum level, the dominant archaea were Crenarchaeota and Thaumarchaeota and the dominant bacteria were Proteobacteria. Heavy metal contents had a great impact on AOA amoA, nirS and nirK gene abundances. AOA amoA contributed more during the ammonia oxidation process and was better adapted for survival in heavy metal-contaminated environments. In addition to heavy metals, the soil organic matter (SOM) content and C/N ratio had strong effects on the AOA and AOB community diversity and structure. In addition, variations in the net ammonification and nitrification rates were proportional to AOA amoA abundance along the soil profile. The soil C/N ratio, soil available phosphorus content and soil moisture influenced the denitrification process. Both soil available phosphorus and moisture were more strongly related to nosZ than to nirS and nirK. In addition, nosZ presented a higher correlation with the nosZ/(nirS + nirK) ratio. Moreover, nosZ/(nirS + nirK) was the key functional gene group that drove the major processes for NH₄⁺-N and NO₃^--N transformation. This study demonstrated the role and importance of soil property impacts on N-related microbes in the soil profile and provided a better understanding of the role and importance of N-related functional genes and their contribution to soil nitrification and denitrification processes in highly degraded areas in the Siding mine.