Changes in the Composition of the Soil Bacterial Community in Heavy Metal-Contaminated Farmland

Tseng, Shu-chun; Liang, Chen-Jui; Chia, Taipau; Ton, Shanshin

doi:10.3390/ijerph18168661

Cited by 18 publications

(6 citation statements)

References 45 publications

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“…This result was expected, since variations in soil pH are related to changes in bacterial communities (Lauber et al, 2009;Mandakovic et al, 2018). In addition, our results show that the relative abundance of bacterial families in this extreme environment is rather low, confirming the results of microbial diversity in acid mine drainages (Baker and Banfield, 2003;Tyson et al, 2004), or in heavy metal-contaminated soils (Li et al, 2017;Tseng et al, 2021). Additionally, the soil micronutrient composition or other environmental factors, such as temperature or oxygen availability, could explain the low relative abundance of some bacteria (Landesman et al, 2014;Freedman and Zack, 2015).…”

Section: Microbiome Abundance and Diversitysupporting

confidence: 88%

Co-occurrence Interaction Networks of Extremophile Species Living in a Copper Mining Tailing

et al. 2022

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Copper mining tailings are characterized by high concentrations of heavy metals and an acidic pH, conditions that require an extreme adaptation for any organism. Currently, several bacterial species have been isolated and characterized from mining environments; however, very little is known about the structure of microbial communities and how their members interact with each other under the extreme conditions where they live. This work generates a co-occurrence network, representing the bacterial soil community from the Cauquenes copper tailing, which is the largest copper waste deposit worldwide. A representative sampling of six zones from the Cauquenes tailing was carried out to determine pH, heavy metal concentration, total DNA extraction, and subsequent assignment of Operational Taxonomic Units (OTUs). According to the elemental concentrations and pH, the six zones could be grouped into two sectors: (1) the “new tailing,” characterized by neutral pH and low concentration of elements, and (2) the “old tailing,” having extremely low pH (~3.5) and a high concentration of heavy metals (mainly copper). Even though the abundance and diversity of species were low in both sectors, the Pseudomonadaceae and Flavobacteriaceae families were over-represented. Additionally, the OTU identifications allowed us to identify a series of bacterial species with diverse biotechnological potentials, such as copper bioleaching and drought stress alleviation in plants. Using the OTU information as a template, we generated co-occurrence networks for the old and new tailings. The resulting models revealed a rearrangement between the interactions of members living in the old and new tailings, and highlighted conserved bacterial drivers as key nodes, with positive interactions in the network of the old tailings, compared to the new tailings. These results provide insights into the structure of the soil bacterial communities growing under extreme environmental conditions in mines.

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Section: Microbiome Abundance and Diversitysupporting

confidence: 88%

Co-occurrence Interaction Networks of Extremophile Species Living in a Copper Mining Tailing

et al. 2022

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“…Other important phyla observed in this study are, Actinobacterota, Planctomycetota, Acidobacteriota, Gemmatimonadota, Myxococcota, and Halobacteriota (Archaea) as the most abundant. All the abundant microbial phyla obtained in this study have been documented previously in other metal-contaminated environments, such as sediments (Lee et al, 2021;Rajeev et al, 2021;Yi et al, 2021;Custodio et al, 2022), iron tailing pond (Li et al, 2021), mining soils (Cao et al, 2017;Hemmat-Jou et al, 2018;Liu et al, 2021a), paddy soils (Tseng et al, 2021), arid loess region (Zeng et al, 2020), and electric waste soils (Jiang et al, 2019), this suggests that these phyla are associated with metal-polluted sediment.…”

Section: B a Figure 10supporting

confidence: 84%

Exploring the diversity and structural response of sediment-associated microbiota communities to environmental pollution at the siangshan wetland in Taiwan using environmental DNA metagenomic approach

et al. 2022

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One of the most crucial struggles for the aquatic ecosystem and modern society is environmental pollution. New approaches, such as the environmental DNA Metagenomic approach, have become a powerful tool to investigate the abundance and diversity of sediment-associated microbiota communities. Nevertheless, information on the response of microbial populations to heavy metals (HMs) in the coastal sediments of Taiwan is scarce. 44 sediment samples were collected from the Siangshan wetland in Taiwan (Taiwan Strait) at two different depths (surface and sub-surface) to measure various environmental variables viz., heavy metals, total organic matters, and sediment composition. Moreover, the abundance and structure of sediment-associated microbiota were examined using high-throughput 16S rRNA gene (V3-V4) next-generation sequencing, to explore the response of the microbiota community to environmental variables. According to the computed pollution indices viz., sediment quality guidelines (SQGs), enrichment factor (EF), geo-accumulation index (Igeo), pollution index (PI), and pollution load index (PLI), the studied sites were classified as unpolluted, moderately polluted, and extremely polluted. Our results revealed that the majority of high-quality reads were assigned to bacteria (~ 95.05%), Archaea (~ 4.83%), and 0.13% were unclassified. Study sites were dominated largely by Proteobacteria with a total of 38.02% across all sediment samples, followed by Bacteroidota (7.18%), Desulfobacterota (6.97%), Actinobacterota (6.68%), Cyanobacteria (5.84%), Chloroflexota (4.18%), Planctomycetota (4.16%), and Firmicutes (3.69%). Beta diversity (Non-metric dimensional scaling analysis, nMDS) explained that surface and sub-surface groups had significantly different microbial community compositions (p = 0.01). Meanwhile, polluted sites exhibited more richness and diversity than unpolluted sites. Redundancy analysis (RDA) illustrated that Mn, Cu, Al, Co, Ni, Sand, and Cr had a sizable effect on the structure of microbiota communities (at the class level). This work highlights the potential responsibility of environmental variables in shaping the sedimentary microbiota of the Siangshan wetland via integrating various ecological variables with alteration of the microbiota composition.

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“…A significant proportion of bacterial community variation was explained by metals and pH value in farmland [52]. The heavy metal may cause a shift in the bacteria composition.…”

Section: Contributions Of Factors To Bacterial Community and Argsmentioning

confidence: 99%

Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil

Yuan

Zhang²,

Sun

et al. 2022

IJERPH

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The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant phyla, while aadA, tetL, sul1, and sul2 were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the intI gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.

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Changes in the Composition of the Soil Bacterial Community in Heavy Metal-Contaminated Farmland

Cited by 18 publications

References 45 publications

Co-occurrence Interaction Networks of Extremophile Species Living in a Copper Mining Tailing

Co-occurrence Interaction Networks of Extremophile Species Living in a Copper Mining Tailing

Exploring the diversity and structural response of sediment-associated microbiota communities to environmental pollution at the siangshan wetland in Taiwan using environmental DNA metagenomic approach

Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil

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