An Attempt to Quantify Cu-Resistant Microorganisms in a Paddy Soil from Jiaxing, China

doi:10.1016/S1002-0160(12)60006-X

Pedosphere

Volume 22, Issue 2, April 2012, Pages 201-205

https://doi.org/10.1016/S1002-0160(12)60006-X Get rights and content

Abstract

Understanding the mechanisms of Cu pollution-induced community tolerance (PICT) in soil requires the characterization of Cu-resistant microorganisms at a community level using modern molecular tools. A primer pair (copAF2010 (5′-TGCAC CTGAC VGGSC AYAT-3′)/copAR2333 (5′-GVACT TCRCG GAACA TRCC-3′)) tentatively targeting Pseudomonas-like Cu-resistant microorganisms was designed in this study. The specification of the primers was tested through conventional polymerase chain reaction (PCR) and the construction of a Pseudomonas-like copA gene fragment library, and then the primers were used to quantify the Cu-resistant microorganisms using quantitative PCR technique. A significant increase of Cu-resistant microorganisms targeted by the primers was observed in a paddy soil from Jiaxing, China which has been exposed to one-year Cu contamination. The results provided direct evidence for Cu PICT in the soil, and the quantification method developed in this study has the potential to be used as a molecular assay for soil Cu pollution.

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Cited by (18)

Co-occurrence of toxic metals, bacterial communities and metal resistance genes in coastal sediments from Bohai bay
2023, Environmental Pollution
Sediment heavy metal contamination poses substantial risks to microbial community composition and functional gene distribution. Bohai Bay (BHB), the second-largest bay in the Bohai Sea, is subject to severe anthropogenic pollution. However, to date, there have been no studies conducted to evaluate the distribution of metal resistance genes (MRGs) and bacterial communities in the coastal sediments of BHB. In this study, we employed high-throughput sequencing based on 16S rRNA genes and real-time quantitative PCR (qPCR) to provide a comprehensive view of toxic metals, MRGs, and bacterial communities in BHB's coastal sediment samples across two seasons. We detected high levels of Cd in the summer samples and As in the autumn samples. The metal content in most autumn samples and all summer samples, based on ecological indices, indicated low ecological risk. Proteobacteria dominated all samples, followed by Desulfobacterota, Bacteroidota and Campilobacterota. Bacterial community variability was higher between autumn sampling sites but more stable in summer. We detected 9 MRG subtypes in all samples, with abundances ranging from 4.58 × 10⁻¹ to 2.25 copies/16S rRNA copies. arsB exhibited the highest relative abundance, followed by acr3, czcA and arrA. The efflux mechanism is a common mechanism for sediment resistance to metal stress in Bohai Bay. Procrustes analysis indicated that bacterial community composition may be a determinant of MRGs composition in BHB sediments. Network analysis suggested that eight classes could be potential hosts for six MRGs. However, this type of correlation requires further validation. To summarize, our study offers preliminary insights into bacterial community and MRG distribution patterns in heavy metal-exposed sediments, laying the groundwork for understanding microbial community adaptations in multi-metal polluted environments and supporting ecological restoration efforts.
Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure
2023, Aquatic Toxicology
Chemical contamination is a common threat to biota thriving in estuarine and coastal ecosystems. Of particular importance is that trace metals tend to accumulate and exert deleterious effects on small invertebrates such as zooplankton, which are essential trophic links between phytoplankton and higher-level consumers in aquatic food webs. Beyond the direct effects of the contamination, we hypothesized that metal exposure could also affect the zooplankton microbiota, which in turn might further impair host fitness. To assess this assumption, copepods (Eurytemora affinis) were sampled in the oligo-mesohaline zone of the Seine estuary and exposed to dissolved copper (25 µg.L⁻¹) over a 72-hour time period. The copepod response to copper treatment was assessed by determining transcriptomic changes in E. affinis and the alteration of its microbiota. Unexpectedly, very few genes were differentially expressed in the copper-treated copepods compared to the controls for both male and female samples, while a clear dichotomy between sex was highlighted with 80% of the genes showing sex-biased expression. In contrast, copper increased the taxonomic diversity of the microbiota and resulted in substantial compositional changes at both the phyla and genus levels. Phylogenetic reconstruction of the microbiota further suggested that copper mitigated the phylogenetic relatedness of taxa at the basal tree structure of the phylogeny, whereas it strengthened it at the terminal branches. Increased terminal phylogenetic clustering in the copper-treated copepods coincided with higher proportions of bacterial genera previously identified as copper resistant (e.g., Pseudomonas, Acinetobacter, Alkanindiges, Colwellia) and a higher relative abundance of the copA_ox gene encoding a periplasmic inducible multi-copper oxidase. The enrichment in micro-organisms likely to perform copper sequestration and/or enzymatic transformation processes, underlines the need to consider the microbial component during evaluation of the vulnerability of zooplankton to metallic stress.
Zero-valent iron drives the passivation of Zn and Cu during composting: Fate of heavy metal resistant bacteria and genes
2023, Chemical Engineering Journal
Citation Excerpt :
Representative HMRGs in composting were copA, a chromosomal encoded p-ATPase that has been shown to be involved in Cu resistance in a variety of gram-positive bacteria [27]. Previous reports have shown a positive correlation between copA and Cu levels in soils exposed to Cu contamination [53]. cueO is a periplasmic multi-copper oxidase that can oxidize Cu+ to low-toxicity Cu2+ [54].
Livestock and poultry manures usually contain substantial heavy metals, especially Cu and Zn, which may induce the enrichment of heavy metal resistant genes (HMRGs) and heavy metal resistant bacteria (HMRB). This study aims to clarify the relationship among heavy metal bioavailability, HMRB and HMRGs during composting, so as to assess and alleviate potential ecological risks of manure application to land. In this study, zero-valent iron (ZVI) was used as passivator, and HMRGs and their host microorganisms were investigated by metagenomic analysis. The results showed that ZVI effectively promoted the passivation of Zn and Cu, and the bioavailability of Zn and Cu decreased by 8.25% and 19.84%, respectively. Proteobacteria was the main HMRB in composting, among which Escherichia, Pseudomonas and Salmonella contained abundant HMRGs, and the succession of these bacteria was closely related to the fate of HMRGs. Spearman correlation analysis showed that metal exchangeable and reducible fractions were positively correlated with the abundance of most HMRGs. Furthermore, structural equation model showed that heavy metal passivation can also indirectly reduce the abundance of HMRGs by regulating the succession of HMRB. These results suggested that the fate of HMRGs is closely related to the chemical speciation of heavy metals in composting habitats.
Sewage sludge in agriculture – the effects of selected chemical pollutants and emerging genetic resistance determinants on the quality of soil and crops – a review
2021, Ecotoxicology and Environmental Safety
Citation Excerpt :
As a result, metals can exert stronger selective pressure on microorganisms than antibiotics (J. Song et al., 2017). Wu et al. (2018) identified genes encoding resistance to SAs (sul), aminoglycosides (aph, aac), tetracyclines (tet), and heavy metals (arsB, copB, ruvB), whereas Besaury et al. (2013) and Li et al. (2012) reported positive correlations between the content of heavy metals and the presence of HMRGs in soils and sewage sludge. Zhao et al. (2018) identified metals that potentially co-select for ARGs, and found 24 significant positive correlations between them, and no significant negative correlations.
In line with sustainable development principles and in order to combat climate change, which contributes to progressive soil depletion, various solutions are being sought to use treated sewage sludge as a soil amendment to improve soil quality and enrich arable soils with adequate amounts of biogenic compounds. This review article focuses on the effects of the agricultural use of biosolids on the environment. The article reviews the existing knowledge on selected emerging contaminants in treated sewage sludge and describes the impact of these pollutants on the environment and living organisms based on 183 publications selected from over 16,000 papers on related topics published over the last ten years. This study deals not only with chemical contaminants but also genetic determinants of resistance to these compounds. Current research has questioned the agricultural use of biosolids due to the presence of mutual interactions between antibiotics, heavy metals, the genetic determinants of resistance (antibiotic resistance genes - ARGs and heavy metal resistance genes - HMRGs) and non-steroidal anti-inflammatory drugs as well as the risks associated with their transfer to the environment. This study emphasizes the need for more extensive legal regulations that account for other pollutants of environmental concern (PEC), particularly in countries where sewage sludge is applied in agriculture most extensively. Future research should focus on more effective methods of eliminating PEC from sewage sludge, especially from the sludge that is used to fertilize agricultural land, because even small amounts of these micropollutants can have serious implications for the health and life of humans and animals.
Changes in sediment microbial diversity following chronic copper-exposure induce community copper-tolerance without increasing sensitivity to arsenic
2020, Journal of Hazardous Materials
Citation Excerpt :
A previous study designed and used primers for copA quantification in sediment (Roosa et al., 2014), but we failed to amplify any specific fragment with this procedure. Alternatively, copA abundance could have been quantified using the protocol published by Li et al. (2012) and successfully used by other authors (Kang et al., 2018; Zhang et al., 2019; Yin et al., 2017) or using the protocol published by Chen et al. (2020). However, many other mechanisms can be involved in Cu resistance in Gram-negative bacteria (Alquethamy et al., 2019), among which the CDF family of transport proteins (Moore et al., 2005), the periplasmic multi-copper oxidase CueO (Grass and Rensing, 2001), CopB, an outer membrane protein (Cha and Cooksey, 1991), CopD, an inner membrane protein coupled with the CopC copper-binding protein (Cha and Cooksey, 1993; Hu et al., 2009; Lawton et al., 2016), and also the MerR-family regulator CueR, and CopRS, a two-component regulatory system (Stoyanov et al., 2001; Quintana et al., 2017).
Sediment microbial communities were exposed for 21 days to an environmental concentration of copper to assess Cu-induced composition changes and resulting effects on microbial sensitivity to acute Cu and As toxicity. Chronic Cu exposure reduced the diversity of the bacterial and archaeal communities from Day 0 to Day 21. The pollution-induced community tolerance concept (PICT) predicts that loss of the most sensitive taxa and gain of more tolerant ones should increase the capacity of Cu-exposed communities to tolerate acute Cu toxicity. Although diversity loss and functional costs of adaptation could have increased their sensitivity to subsequent toxic stress, no increased sensitivity to As was observed. PICT responses varied according to heterotrophic activity, selected as the functional endpoint for toxicity testing, with different results for Cu and As. This suggests that induced tolerance to Cu and As was supported by different species with different metabolic capacities. Ecological risk assessment of contaminants would gain accuracy from further research on the relative contribution of tolerance acquisition and co-tolerance processes on the functional response of microbial communities.
The toxic factor of copper should be adjusted during the ecological risk assessment for soil bacterial community
2020, Ecological Indicators
The toxic factor (TF) is a key parameter commonly used to evaluate the potential ecological risk index (RI) of heavy metals. However, it remains largely unknown whether this traditional TF is applicable to the ecological risk assessment of heavy metal to soil microorganisms, which are essential to ecological functions and ecosystem sustainability. Here, based on the TF values of 5 and 30 for copper (Cu) and cadmium (Cd), respectively, we constructed soil microcosms to establish a gradient of ecological risk levels, and different combinations of Cu and Cd concentrations were used at each ecological risk level. We found that bacterial abundance and functional diversity significantly decreased and the metal resistance gene (MRG) abundances increased with the increasing RI level. At the same RI level, the bacterial abundance and functional diversity decreased while MRG abundances increased with increasing Cu concentrations, suggesting that the ecological risk to soil bacterial community was more relevant to Cu, rather than Cd. The traditional TF of Cu used to calculate the RI might be underestimated if it is used for evaluation of the risk to soil bacteria. Our calibration analysis revealed that the TF of Cu should be adjusted to 6 during the assessment of the RI for soil bacterial community in heavy-metal contaminated area.

View all citing articles on Scopus

: Supported by the International Copper Association, Rio Tinto Limited, the Nickel Producers Environmental Research Association, the Key International S&T Cooperation Projects of China (No. 2009DFB90120), and the National Natural Science Foundation of China (No. 31070101).

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Pedosphere

Abstract

References (23)

Characterization of copper-resistant bacterial community in rhizosphere of highly copper-contaminated soil

Eur. J. Soil Biol.

Indigenous Plasmids in Pseudomonas syringae pv. tomato: conjugative transfer and role in copper resistance

J. Bacteriol.

Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the field

Lett. Appl. Microbiol.

A critical review of procedures and approaches used for assessing pollution-induced community tolerance (PICT) in biotic communities

Hum. Ecol. Risk. Assess.

Resistance and resilience of Cu-polluted soil after Cu perturbation, tested by a wide range of soil microbial parameters

FEMS Microbiol. Ecol.

Development of metal tolerance in soil bacterial communities exposed to experimentally increased metal levels

Appl. Environ. Microbiol.

Tolerance of nitrifying bacteria to copper and nickel

Environ. Toxicol. Chem.

Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar

Environ. Microbiol.

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices

Environ. Microbiol.

Prevalence of copper resistant salmonellae in India

Indian J. Med. Res.

Copper resistance in Desulfovibrio strain R2

A. Van Leeuw.

Cited by (18)

Co-occurrence of toxic metals, bacterial communities and metal resistance genes in coastal sediments from Bohai bay

Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure

Zero-valent iron drives the passivation of Zn and Cu during composting: Fate of heavy metal resistant bacteria and genes

Sewage sludge in agriculture – the effects of selected chemical pollutants and emerging genetic resistance determinants on the quality of soil and crops – a review

Changes in sediment microbial diversity following chronic copper-exposure induce community copper-tolerance without increasing sensitivity to arsenic

The toxic factor of copper should be adjusted during the ecological risk assessment for soil bacterial community