Characteristics of Bacterial Community and Function in Paddy Soil Profile around Antimony Mine and Its Response to Antimony and Arsenic Contamination

Characterizing the metabolome and microbiome at giant panda scent marking sites during the mating season

Scent marking sites served as a primary means of chemical communication for giant pandas, enabling intraspecific communication. We integrated metabolomics and high-throughput sequencing techniques to examine the non-targeted metabolome and microbial community structure of scent marking sites and feces in the field. Integrative analysis revealed a more comprehensive array of chemical compounds compared to previous investigations, including ketones, acids, heterocycles, alcohols, and aldehydes. Notably, specific compounds such as 2-decenal, (E)-, octanal, decanal, L-α-terpineol, vanillin, and nonanal emerged as potential key players in scent signaling. Intriguingly, our study of the microbial domain identified dominant bacterial species from the Actinobacteria, Bacteroidetes, and Proteobacteria phyla, likely orchestrating metabolic processes at scent marking sites. Comparative analyses showed, for the first time, that feces do not share the same functions as scent markers, indicating distinct functional roles. This research deepens scientific understanding of chemical communication in wild pandas.

Arsenic pollution from human activities drives changes in soil microbial community characteristics

Soil arsenic (As) pollution not only decreases plant productivity but also soil quality, in turn hampering sustainable agricultural development. Despite the negative effects of As contamination on rice yield and quality being reported widely, the responses of microbial communities and co-occurrence networks in paddy soil to As pollution have not been explored. Here, based on high-throughput sequencing technologies, we investigated bacterial abundance and diversity in paddy soils with different levels of As contamination, and constructed associated microbial co-occurrence networks. As pollution reduced soil bacterial diversity significantly (p < 0.001). In addition, bioavailable As concentrations were negatively correlated with Actinobacteria and Acidobacteria relative abundance (p < 0.05). Conversely, As pollution had a positive relationship with Chloroflexi, Betaproteobacteria, and Bacteroidetes relative abundance (p < 0.05). Firmicutes relative abundance decreased with an increase in total As concentration. The ecological clusters and key groups in bacterial co-occurrence networks exhibited distinct trends with an increase in As pollution. Notably, Acidobacteria play an important role in maintaining microbial networks in As contaminated soils. Overall, we provide empirical evidence that As contamination influences soil microbial community structure, posing a threat to soil ecosystem health and sustainable agriculture.

Rhizosphere bacteria regulated arsenic bioavailability and accumulation in the soil-Chinese cabbage system

The accumulation of arsenic (As) in Chinese cabbage (Brassica rapa ssp. pekinensis) has recently been a source of concern for a potential risk to human health. It is unknown whether natural variations of As accumulation in different genotypes of Chinese cabbage are related to rhizobacterial characteristics. Experiments were conducted to investigate the mechanisms of rhizobacteria involving in As fates in a soil-Chinese cabbage system using various genotypes using high-throughput sequencing and quantitative PCR. There were significant differences in As accumulation in cabbage leaves between 32 genotypes, and genotypes of low-As-accumulation (LSA) and high-As-accumulation (HSA) were identified. The As concentrations in the shoots of LSA were 23.25 %, 24.19 %, 15.05 %, and 70.69 % lower than those of HSA in seedling stage (SS), rosette stage (RS), heading stage (HS), and mature stage (MS), respectively. Meanwhile, the relative abundances of phyla Patescibacteria (in RS), Acidobacteria and Rokubacteria (in HS) in the rhizosphere of LSA were 60.18 %, 28.19 %, and 45.38 % less than those of HSA, respectively. Additionally, both shoot-As and As translocation factor had significantly positive or negative correlations with the relative abundances of Rokubacteria or Actinobacteria. In LSA rhizosphere, the relative abundances of genera Flavobacterium (in SS), Ellin6055 and Sphingomonas (in HS) were 128.12 %, 83.69 % and 79.50 % higher than those of HSA, respectively. This demonstrated that rhizobacteria contribute to the accumulation and translocation of As in HSA and LSA. Furthermore, the gene copies of aioA and arsM in LSA rhizosphere were 25.54 % and 16.13 % higher than those of HSA, respectively, whereas the gene copies of arsC in LSA rhizosphere were 26.36 % less than those of HSA in MS, indicating that rhizobacteria are involved in As biotransformation in the soil. These results provide a comprehensive understanding of the relationship between characteristics of rhizobacterial communities and As variations in Chinese cabbage genotypes.

Evaluation of Pollution Level, Spatial Distribution, and Ecological Effects of Antimony in Soils of Mining Areas: A Review

The first global-scale assessment of Sb contamination in soil that was related to mining/smelting activities was conducted based on 91 articles that were published between 1989 and 2021. The geographical variation, the pollution level, the speciation, the influencing factors, and the environmental effects of Sb that were associated with mining/smelting-affected soils were analyzed. The high Sb values mainly occurred in developed (Poland, Italy, Spain, Portugal, New Zealand, Australia) and developing (China, Algeria, Slovakia) countries. Sb concentrations of polluted soil from mining areas that were reported in most countries significantly exceeded the maximum permissible limit that is recommended by WHO, except in Turkey and Macedonia. The soil Sb concentrations decreased in the order of Oceania (29,151 mg/kg) > North Africa (13,022 mg/kg) > Asia (1527 mg/kg) > Europe (858 mg/kg) > South America (37.4 mg/kg). The existing extraction methods for Sb speciation have been classified according to the extractant, however, further research is needed in the standardization of these extraction methods. Modern analytical and characterization technologies, e.g., X-ray absorption spectroscopy, are effective at characterizing chemical speciation. Conditional inference tree (CIT) analysis has shown that the clay content was the major factor that influenced the soil Sb concentration. Non-carcinogenic risks to the public from soil Sb pollution were within the acceptable levels in most regions. An Sb smelter site at the Endeavour Inlet in New Zealand, an abandoned open-pit Sb mine in Djebel Hamimat, Algeria, an old Sb-mining area in Tuscany, Italy, and Hillgrove mine in Australia were selected as the priority control areas. Cynodon dactylon, Boehmeria, Pteris vittata, and Amaranthus paniculatus were found to be potential Sb accumulators. All of the values of bioaccumulation factors for the crops were less than one. However, ingestion of Sb through crop consumption posed potential non-carcinogenic health risks, which should not be neglected. The soil variables (pH, Eh, total sulfur, carbon nitrogen ratio, total organic carbon, and sulfate), the total Sb and the bioavailable Sb, and heavy metal(loid)s (As, Pb, and Fe) were the major parameters affecting the microbial community compositions.

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

Marine sediments act as a sink for various heavy metals, which may have profound impact on sedimentary microbiota. However, our knowledge about the collaborative response of bacterial community to chronic heavy metal contamination remains little. In this study, concentrations of seven heavy metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) in sediments collected from the East China Sea were analyzed and Illumina Miseq 16 S rRNA sequencing was applied to characterize the structure of bacterial community. Microbiota inhabiting sediments in the East China Sea polluted with heavy metals showed different community composition from relatively pristine sites. The response of bacterial community to heavy metal stress was further interrogated with weighted correlation network analysis (WGCNA). WGCNA revealed ten bacterial modules exhibiting distinct co-occurrence patterns and among them, five modules were related to heavy metal pollution. Three of them were positively correlated with an increase in at least one heavy metal concentration, hubs (more influential bacterial taxa) of which were previously reported to be involved in the geochemical cycling of heavy metals or possess tolerance to heavy metals, while another two modules showed opposite patterns. Our research suggested that ecological functional transition might have occurred in East China Sea sediments by shifts of community composition with sensitive modules majorly involved in the meaningful global biogeochemical cycling of carbon, sulfur, and nitrogen replaced by more tolerant groups of bacteria due to long-term exposure to low-concentration heavy metals. Hubs may serve as indicators of perturbations of benthic bacterial community caused by heavy metal pollution and support monitoring remediation of polluted sites in marine environments.

Fate and Transformation of 6:2 Fluorotelomer Sulfonic Acid Affected by Plant, Nutrient, Bioaugmentation, and Soil Microbiome Interactions

6:2 Fluorotelomer sulfonic acid (6:2 FTSA) is a dominant per- and poly-fluoroalkyl substance (PFAS) in aqueous film-forming foam (AFFF)-impacted soil. While its biotransformation mechanisms have been studied, the complex effects from plants, nutrients, and soil microbiome interactions on the fate and removal of 6:2 FTSA are poorly understood. This study systematically investigated the potential of phytoremediation for 6:2 FTSA byArabidopsis thalianacoupled with bioaugmentation ofRhodococcus jostiiRHA1 (designated as RHA1 hereafter) under different nutrient and microbiome conditions. Hyperaccumulation of 6:2 FTSA, defined as tissue/soil concentration > 10 and high translocation factor > 3, was observed in plants. However, biotransformation of 6:2 FTSA only occurred under sulfur-limited conditions. Spiking RHA1 not only enhanced the biotransformation of 6:2 FTSA in soil but also promoted plant growth. Soil microbiome analysis uncovered Rhodococcus as one of the dominant species in all RHA1-spiked soil. Different nutrients such as sulfur and carbon, bioaugmentation, and amendment of 6:2 FTSA caused significant changes in - microbial community structure. This study revealed the synergistic effects of phytoremediation and bioaugmentation on 6:2 FTSA removal. and highlighted that the fate of 6:2 FTSA was highly influced by the complex interactions of plants, nutrients, and soil microbiome.

Accumulation, regional distribution, and environmental effects of Sb in the largest Hg-Sb mine area in Qinling Orogen, China

In this study, knowledge gaps on Sb concentration in rocks, ores, tailings, soil, river water, sediments, and crops of mine areas were identified and discussed in terms of contamination levels, spatial distribution, and environmental effects. Accordingly, Xunyang Hg-Sb mine, the largest Hg-Sb deposit in China as research region in this study, field sampling and laboratory analysis were conducted. The results showed elevated concentrations of Sb in the soil, sediment, and river water. The X-ray diffraction analysis indicated that the main minerals of the rocks were quartz, dolomite, calcite, and margarite. Based on the TESCAN integrated mineral analyzer analysis, the main ore minerals in the Gongguan mine were dolomite (93.97%), cinnabar (2.50%), stibnite (2.48%), calcite (0.38%), and quartz (0.38%). The μ-XRF analysis indicated that Sb distribution was similar to those of S and O, instead of those of Hg and As. The clear spatial variation of Sb concentration in environmental media, mines, tailings, and settling ponds affected Sb accumulation. Actinobacteriota, Proteobacteria, Acidobacteriota, and Chloroflexi were the dominant phyla in the soil. Patescibacteria, Proteobacteria, and Bdellovibrionota were negatively correlated with Sb in the soil (p < 0.05). Exposure to Sb through maize grain and cabbage consumption poses serious non-carcinogenic health risk for residents. This work provides a scientific basis for the environmental quality assessment of Sb mine areas and development of applicable guidelines.

Distribution characteristics and risk of heavy metals and microbial community composition around the Wanshan mercury mine in Southwest China

The Wanshan mercury (Hg) mine in Guizhou Province is one of the main Hg-producing mines in China, resulting in serious Hg pollution in soil and wastewater. Therefore, the present study is mainly aimed to investigate the current degree of heavy metal pollution and compared the microbial diversity in the Wanshan Hg mine and its surrounding environment. The results showed the distribution of the pollution load index values was low in the west and high in the east. The northwestern (Aozhai River), northern (Meizi Stream), and southwestern parts of the study area and the area surrounding Erkeng did not reach moderate pollution. Mercury accounted for the majority of the potential ecological risk index values, reaching 67.62%, while the proportions of Cd and As were 15.75% and 10.75%, respectively. Mercury was found mainly in a residual state, which had an average proportion of 71.09%. In the three regions, Proteobacteria and Actinobacteria had the highest relative abundances. According to linear discriminant analysis effect size, the indicator species in the Hg mining area, woodland and cultivated land was f__67-14 (belonging to a family of Solirubrobacterales), Reyranellales and Reyranellaceae, Intrasporangiaceae, respectively. In summary, this study for the very first time estimated that the higher Hg, Cd and As pollution existed in Wanshan Hg mine since their concentration in the all soil samples totally exceeded the standard value (GB15618-2018), while Cd and As pollution in soil was commonly ignored by the previous study. The cultivated land had higher community richness than the mercury mining district and woodland. Our results suggested that the relevant local departments need to take more active measures to solve the problem of high levels of Hg, Cd, and As in the local soil, and prevent their adverse effects on humans.

Evaluating the Heavy Metal Risk in Spinacia oleracea L. and Its Surrounding Soil with Varied Biochar Levels: A Pot Experiment

Spinacia oleracea L., as the most widely cultivated green leafy vegetable in China, can threaten human health in cases of its excessive heavy metal content, especially in mining areas of karst landforms. Therefore, the present study mainly investigates whether biochar is useful for remediating heavy metal pollution in soil and S. oleracea and the degree of this improvement in karst areas. The effects of heavy metal exposure on the health of children and adults in S. oleracea and rhizosphere lime soil with six biochar levels are evaluated by a health risk assessment, namely, 4000 g of lime soil (C-0), 160 g of biochar + 3840 g of lime soil (C-160), 240 g of biochar + 3760 g of lime soil (C-240), 320 g of biochar + 3680 g of lime soil (C-320), 400 g of biochar + 3600 g of lime soil (C-400) and 800 g of biochar + 3200 g of lime soil (C-800). The results show that the pH values of the lime soil were positively correlated with Pb, P and K contents and negatively correlated with As, Cr, Hg, Cd and N contents in S. oleracea. The assessments of the potential ecological risk index show that the soil samples for the C-0 and C-160 levels pose moderate ecological hazards, while the soil samples for the C-320, C-800, C-400 and C-240 levels constitute mild ecological hazards. The single noncarcinogenic risks, total noncarcinogenic risk indexes, single carcinogenic risks and total carcinogenic risks values indicate that exposure to heavy metals in lime soil and S. oleracea poses a serious threat to human health. It also presents an unacceptable cancer risk and children are more threatened than adults. Our results suggest that heavy metal pollution of S. oleracea and its rhizosphere lime soil in karst areas still poses a threat to human health after adding biochar, and the relevant local departments need to implement more active measures to solve the excessive heavy metal contents in the local soil and vegetables of this karst regions.

Microbial community structure and metabolome profiling characteristics of soil contaminated by TNT, RDX, and HMX

This experiment was conducted to evaluate the ecotoxicity of typical explosives and their mechanisms in the soil microenvironment. Here, TNT (trinitrotoluene), RDX (cyclotrimethylene trinitramine), and HMX (cyclotetramethylene tetranitramine) were used to simulate the soil pollution of single explosives and their combination. The changes in soil enzyme activity and microbial community structure and function were analyzed in soil, and the effects of explosives exposure on the soil metabolic spectrum were revealed by non-targeted metabonomics. TNT, RDX, and HMX exposure significantly inhibited soil microbial respiration and urease and dehydrogenase activities. Explosives treatment reduced the diversity and richness of the soil microbial community structure, and the microorganisms able to degrade explosives began to occupy the soil niche, with the Sphingomonadaceae, Actinobacteria, and Gammaproteobacteria showing significantly increased relative abundances. Non-targeted metabonomics analysis showed that the main soil differential metabolites under explosives stress were lipids and lipid-like molecules, organic acids and derivatives, with the phosphotransferase system (PTS) pathway the most enriched pathway. The metabolic pathways for carbohydrates, lipids, and amino acids in soil were specifically inhibited. Therefore, residues of TNT, RDX, and HMX in the soil could inhibit soil metabolic processes and change the structure of the soil microbial community.

Effects of different antimony contamination levels on paddy soil bacterial diversity and community structure

To clarify the response mechanism of paddy soil microorganisms to contamination caused by antimony (Sb) alone, we added K(SbO)C₄H₄O₆.1/2 H₂O with different contents to uncontaminated paddy soil and carried out related studies. 16S rRNA was sequenced in V3-V4 regions of paddy soil bacteria with different Sb contamination levels. Then, α diversity and species enrichment and separation of paddy soil microorganisms were analyzed. The biochemical behavior and the influences of Sb fractions on bacterial communities and ecological function were explored in paddy soil with different contamination levels. The results showed that the contents of Sb_tot and Sb(V) increased with the increase of contamination level, and the difference was significant among the groups. For Sb_exe and Sb_srp there were slight differences between S100 and S200 groups, but significant differences among other groups. The diversity index increased with the increase of Sb concentration, which reached the maximum value in S200 group and the minimum value in control group (SC). The relative importance analysis demonstrated that Sb(III) and Sb_srp were the main Sb fractions affecting the diversity index of bacterial community. In addition, the results of principal coordinate analysis (PCoA) showed that there were significant differences between the bacterial communities in SC and in the soil with different Sb contamination levels. Based on diversity analysis, it was found that Proteobacteria, Actinobacteria and Bacteroidetes were the main dominant phyla in paddy soil with different Sb concentrations, and their enrichment and separation were greater than those of other dominant phyla. Though the Static Bayesian network inference, it was shown that Sb_tot affected Sphingomonadaceae, and Sb_srp affected Burkholderiaceae, Xanthomonadaceae and Acidobacteriale to further affect bacterial communities, while Sb(V) mainly affected Flavobacteriaceae, Rhodopirillaceae and Acidobacteriale. The above results provide a scientific basis for the biochemical restoration potential of paddy soils with different Sb contamination levels.

Effects of antimony contamination on bioaccumulation and gut bacterial community of earthworm Eisenia fetida

Antimony (Sb) contamination has brought great environmental problems to the surrounding soils. However, few studies focused on the response of bacterial communities in earthworm gut to Sb. Eisenia fetida was cultured in four soils with Sb contents (5,25,50,100 mg•kg^-1) to investigate the distribution of Sb species in earthworm gut and the response mechanism of bacterial communities to Sb contamination. The results showed that Sb accumulated in the gut and tissues of earthworms, and the mortality of earthworms showed a dose-response relationship with the increase of Sb content. Sb(III) and Sb_exe were the major species in gut, whereas Sb(V) and Sb_srp were predominant in surrounding soil. There were significant differences in bacterial diversity between earthworm gut and soil, but there was no significant between the two with different Sb content. The network constructed by gut bacterial community of earthworm was less stable and more sensitive to Sb species than that in soil. Sb(III) had the greatest influence on the gut bacterial community of earthworm, which not only directly affected the community through Xanthomonadaceae, Rhodomicrobiaceae and Anaerolineaceae, but also indirectly influenced through Chthoniobacteraceae. This study fills a research gap on the effect of Sb contamination on the gut bacterial community of earthworm.

Arsenic and antimony co-contamination influences on soil microbial community composition and functions: Relevance to arsenic resistance and carbon, nitrogen, and sulfur cycling

Microorganisms can mediate arsenic (As) and antimony (Sb) transformation and thus change the As and Sb toxicity and mobility. The influence of As and Sb on the innate microbiome has been extensively characterized. However, how microbial metabolic potentials are influenced by the As and Sb co-contamination is still ambiguous. In this study, we selected two contrasting sites located in the Shimen realgar mine, the largest realgar mine in Asia, to explore the adaptability and response of the soil microbiome to As and Sb co-contamination and the impact of co-contamination on microbial metabolic potentials. It is observed that the geochemical parameters, including the As and Sb fractions, were the driving forces that reshaped the community composition and metabolic potentials. Bacteria associated with Bradyrhizobium, Nocardioides, Sphingomonas, Burkholderia, and Streptomyces were predicted to be tolerant to high concentrations of As and Sb. Co-occurrence network analysis revealed that the genes related to C fixation, nitrate/nitrite reduction, N fixation, and sulfate reduction were positively correlated with the As and Sb fractions, suggesting that As and Sb biogeochemical cycling may interact with and benefit from C, N, and S cycling. The results suggest that As and Sb co-contamination not only influences As-related genes, but also influences other genes correlated with microbial C, N, and S cycling.

Soil bacterial community composition in rice-fish integrated farming systems with different planting years

The high productivity and efficient nutrient utilization in rice–fish integrated farming system are well reported. However, the characteristics of soil bacterial communities and their relationship with soil nutrient availability in rice–fish field remain unclear. In this study, we selected three paddy fields, including a rice monoculture field and two rice–fish fields with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the soil properties were significantly different among different rice farming systems. The soil bacterial community composition in the rice–fish field was significantly different from that in the rice monoculture field. Five of the top 15 phyla were observed with significant differences and Nitrospirae was the most significant one. However, no taxa observed with significance between the rice planting area and aquaculture area no matter in the 1st or 5th year of rice–fish field. RDA analysis showed that the soil bacterial community differentiation in the 5th year of rice–fish field was positively correlated with soil properties, such as AN and OM contents, EC and pH value. Although the rice yields in rice–fish field decreased, the net economic benefit of the rice–fish system enhanced obviously due to the high value of aquaculture animals.