Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach

Hemmat-Jou, Mohammad Hossein; Sinegani, Ali Akbar Safari; Mirzaie-Asl, Asghar; Tahmourespour, Arezoo

doi:10.1007/s10646-018-1981-x

Cited by 108 publications

(35 citation statements)

References 71 publications

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“…These results were consistent with previous studies conducted in urban ecosystems, indicating that the dominant phyla of bacterial communities in urban soils may be similar (Ramirez et al, 2014;Wang, Wu & Kumari, 2018;Xu et al, 2014;Zhalnina et al, 2015). Moreover, it has been reported that the bacterial phyla Proteobacteria, Acidobacteriota, and Actinobacteriota were also predominant in agricultural soils, forest soils, and even in heavy metal polluted soils (Hemmat-Jou et al, 2018;Sul et al, 2013;Zhang et al, 2017). Thus, the similar relative abundances of these bacterial phyla in urban and suburban park soils may be due to the fact that these phyla can well adapt to various environments.…”

Section: Differences In Microbial Community Composition and Ecologicasupporting

confidence: 92%

Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China

Zhang

Han

et al. 2021

PeerJ

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Background The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils. Methods In this study, the community variations of bacteria and fungi in urban and suburban park soils were investigated in Shanghai, China. Real-time PCR and high-throughput Illumina sequencing were used to examine the microbial abundance and community composition, respectively. Results The results showed that soil molecular biomass and fungal abundance in urban park soils were significantly higher than those in suburban park soils, while no significant difference was observed in the bacterial abundance between urban and suburban park soils. The alpha diversity of soil microbes in urban and suburban park soils was similar to each other, except for Chao1 index of fungal communities. The results of similarity analysis (ANOSIM) revealed remarkable differences in the composition of bacterial and fungal communities between urban and suburban park soils. Specifically, park soils in urban areas were enriched with the phyla Methylomirabilota and Verrucomicrobiota, while the relative abundance of Gemmatimonadota was higher in suburban park soils. Moreover, the fungal class Eurotiomycetes was also enriched in urban park soils. Compared with suburban park soils, nodes and average paths of the bacterial and fungal networks were higher in urban park soils, but the number of module hubs and connectors of the bacterial networks and negative interactions among bacterial taxa were lower. Compared with suburban park soils, Acidobacteriota bacterium and Mortierellomycota fungus played more important roles in the ecological networks of urban park soils. Soil available zinc (Zn), available nitrogen (N), pH, and total potassium (K) significantly affected fungal community composition in park soils in Shanghai. Soil available Zn was also the most important factor affecting the bacterial community composition in this study. Conclusion There were significant differences in the soil molecular biomass, fungal abundance, and the community composition and co-occurrence relations of both soil bacterial and fungal communities between urban and suburban park soils. Soil available Zn played an important part in shaping the structures of both the bacterial and fungal communities in park soils in Shanghai.

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Section: Differences In Microbial Community Composition and Ecologicasupporting

confidence: 92%

Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China

Zhang

Han

et al. 2021

PeerJ

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“…As seen, Proteobacteria (42.8–79.5%), Acidobacteria (1.8–16.5%), Firmicutes (0.9–41.9%), and Chloroflexi (1.0–10.6%) were dominant phyla with high relative abundances in all of the soil sample, which was consistent with the results shown in LEfSe analysis. These predominant phyla also obtained in other metal(loid)s contaminated soil, such as paddy soil, mining sites, and sediment [ 37 , 38 , 39 , 40 ], which indicated these phyla might be closely related to metal(loid)s-contaminated soil. For example, Liu et al also found that Proteobacteria (33.0–96.7%), Actinobacteria (0.3–6.9%), Firmicutes (0.0–5.8%), and Chloroflexi (0.0–13.1%) dominated the indigenous soil microbial communities at a chromium salt factory [ 41 ].…”

Section: Resultsmentioning

confidence: 78%

Spatial Distribution of Toxic Metal(loid)s and Microbial Community Analysis in Soil Vertical Profile at an Abandoned Nonferrous Metal Smelting Site

Yang

Wang

Guo

et al. 2020

IJERPH

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In this study soils at different depths were collected in a Zn smelting site located in Zhuzhou City, China, in order to understand toxic metal(loid)s distribution and microbial community in vertical soil profile at a smelting site. Except Soil properties and metal(loid)s content, the richness and diversity of microbial communities in soil samples were analyzed via high-throughput Illumina sequencing of 16s rRNA gene amplicons. The results showed that the content of As, Pb, Cu, Cd, Zn, and Mn was relatively high in top soil in comparison to subsoil, while the concentration of Cr in subsoil was comparable with that in top soil due to its relative high background value in this soil layer. The bioavailability of Cd, Mn, Zn, and Pb was relative higher than that of As, Cr, and Cu. The diversity of soil microbial communities decreased with increasing depth, which might be ascribed to the decrease in evenness with increase in depth duo to the influence by environmental conditions, such as pH, TK (total potassium), CEC (cation exchange capacity), ORP (oxidation reduction potential), and Bio-Cu (bioavailable copper). The results also found Acidobacteria, Proteobacteria, Firmicutes, and Chloroflexi were dominant phyla in soil samples. At the genus level, Acinetobacter, Pseudomonas, and Gp7 were dominant soil microorganism. Besides, Environmental factors, such as SOM (soil organic matter), pH, Bio-Cu, Bio-Cd (bioavailable cadmium), and Bio-Pb (bioavailable lead), greatly impacted microbial community in surface soil (1–3 m), while ORP, TK, and AN concentration influenced microbial community in the subsoil (4–10 m).

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“…Interestingly, the decrease of richness and diversity indexes observed in soil between successive cultivation years is less marked in the case of inoculated plants, suggesting that mycorrhizal symbiosis is likely to improve the resilience of the plant and its associated microbial communities against biotic and abiotic stresses (Bi et al, 2018). In previous studies, the mycorrhizal symbiosis was also highlighted to result in changes in the host plant metabolism and hence in the root exudation profile, further modifying and shaping the bacterial communities, in both TE-contaminated and uncontaminated conditions (Harrison, 1999;Hause and Fester, 2005;Ferrol et al, 2016;Iffis et al, 2017). In addition, the exudation of carbohydrates and citric acid, detected in AMF hyphal exudates, and their quantitative and qualitative patterns were brought forward as potential key drivers in the changes of the soil bacterial communities as well (Lioussanne et al, 2010;Iffis et al, 2016;Qin et al, 2016).…”

Section: Mitigated Effects Of Amf Inoculation In Shaping Bacterial Comentioning

confidence: 98%

The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial

et al. 2020

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To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb – 394 ppm, Zn – 443 ppm, and Cd – 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn’t observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.

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Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach

Cited by 108 publications

References 71 publications

Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China

Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China

Spatial Distribution of Toxic Metal(loid)s and Microbial Community Analysis in Soil Vertical Profile at an Abandoned Nonferrous Metal Smelting Site

The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial

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