Dynamics of microbial community during bioremediation of phenanthrene and chromium(VI)-contaminated soil microcosms

Sphingobium sp. SJ10-10 encodes a not-yet-reported chromate reductase and the classical Rieske dioxygenases to simultaneously degrade PAH and reduce chromate

Both polycyclic aromatic hydrocarbons (PAHs) and heavy metals persist in the environment and are toxic to organisms. Their co-occurrence makes any of them difficult to remove during bioremediation and poses challenges to environmental management and public health. Microorganisms capable of effectively degrading PAHs and detoxifying heavy metals concurrently are required to improve the bioremediation process. In this study, we isolated a new strain, Sphingobium sp. SJ10-10, from an abandoned coking plant and demonstrated its capability to simultaneously degrade 92.6 % of 75 mg/L phenanthrene and reduce 90 % of 3.5 mg/L hexavalent chromium [Cr(VI)] within 1.5 days. Strain SJ10-10 encodes Rieske non-heme iron ring-hydroxylating oxygenases (RHOs) to initiate PAH degradation. Additionally, a not-yet-reported protein referred to as Sphingobium chromate reductase (SchR), with low sequence identity to known chromate reductases, was identified to reduce Cr(VI). SchR is distributed across different genera and can be classified into two classes: one from Sphingobium members and the other from non-Sphingobium species. The widespread presence of SchR in those RHO-containing Sphingobium members suggests that they are excellent candidates for bioremediation. In summary, our study demonstrates the simultaneous removal of PAHs and Cr(VI) by strain SJ10-10 and provides valuable insights into microbial strategies for managing complex pollutant mixtures.

Synergistic effects of a functional bacterial consortium on enhancing phenanthrene biodegradation and counteracting rare earth biotoxicity in liquid and slurry systems

The biodegradation of polycyclic aromatic hydrocarbons (PAHs) by microorganisms in the environment is often inhibited by coexisting metal ions. The aim of this work is to study a bacterial consortium for enhancing phenanthrene biodegradation under the inhibition effect of the rare earth (RE) ions Ce³⁺ and Y³⁺ . This bacterial consortium was composed of two bacteria, namely, the RE-adsorbing Bacillus subtilis MSP117 and the phenanthrene-degrading Moraxella osloensis CFP312. Ce³⁺ and Y³⁺ at the concentration of 1.15 mmol L^-1 inhibited CFP312 from degrading phenanthrene but not glucose. Using glucose as a co-substrate could promote the proliferation of CFP312 but decreased phenanthrene degradation. Adsorption experiments and electron microscopy imaging showed that CFP312 had no RE ions adsorption capacity for RE ions and that RE elements could not be observed on its cell surfaces. MSP117 could adsorb 0.14 and 0.12 mmol g^-1 wet cells of Ce³⁺ and Y³⁺ in aqueous solution, respectively, thus demonstrating considerable adsorption capacity. The MSP117 cell surface immobilized part of the free RE ions and reduced their bioaccessibility, thereby alleviating their biotoxic effect on phenanthrene degradation by CFP312. In liquid and slurry systems, glucose, which was used as the co-substrate of the bacterial consortium, must be kept at a low level to avoid the catabolism repression of phenanthrene degradation by CFP312.

Insights into the vertical distribution of the microbiota in steel plant soils with potentially toxic elements and PAHs contamination after 60 years operation: Abundance, structure, co-occurrence network and functionality

Both potentially toxic elements (PTEs) and polycyclic aromatic hydrocarbons (PAHs) are widely present in soil contaminated by steel industries. This study assessed the vertical variation (at 20 cm, 40 cm, 60 cm, 80 cm, 120 cm, and 150 cm depth) of bacterial abundance, community structure, functional genes related to PAHs degradation, and community co-occurrence patterns in an old steel plant soils which contaminated by PTEs and PAHs for 60 years. The excessive PAHs and PTEs in steel plant soils were benzo (a) pyrene, benzo (b) fluoranthene, dibenzo (a, h) anthracene, indeno (1,2,3-c, d) pyrene, and lead (Pb). The abundance and composition of bacterial community considerably changed with soil depth in two study areas with different pollution degrees. The results of co-occurrence network analysis indicated that the top genera in blast furnace zone identified as the potential keystone taxa were Haliangium, Blastococcus, Nitrospira, and Sulfurifustis. And in coking zone, the top genera were Gaiella. The predictions of bacterial metabolism function using PICRUSt showed that the PAHs-PTEs contaminated soil still had the potential for PAHs degradation, but most PTEs negatively correlated with PAHs degradation genes. The total sulfur (TS), acenaphthene (ANA), and Zinc (Zn) were the key factors to drive development of bacterial communities in the steel plant soils. As far as we know, this is the first investigation of vertical distribution and interaction of the bacterial microbiota in the aging soils of steel plant contaminated with PTEs and PAHs.

Simultaneous degradation of trichlorfon and removal of Cd(II) by Aspergillus sydowii strain PA F-2

Co-contamination with heavy metals and pesticides is a severe environmental problem, but little information is available regarding the simultaneous removal of these pollutants. In this study, we showed that Aspergillus sydowii strain PA F-2 isolated from soil contaminated with heavy metal and pesticides can simultaneously degrade trichlorfon (TCF) and adsorb Cd(II) from mineral salt medium. The maximum removal rates for TCF and Cd(II) were 55.52% and 57.90%, respectively, in the treatment containing 100 mg L^-1 TCF and 2 mg L^-1 Cd(II). As the initial Cd(II) concentration increased (2, 5, and 10 mg L^-1), the PA F-2 biomass, TCF degradation rate, and Cd(II) adsorption efficiency decreased, whereas the Cd(II) adsorption capacity by PA F-2 increased. The addition of exogenous glucose and sucrose significantly increased the PA F-2 biomass as well as the removal of TCF and Cd(II). Moreover, the TCF degradation pathway and Cd(II) adsorption mechanism were investigated by gas chromatography-mass spectrometry, scanning electron microscopy, and Fourier transform infrared spectroscopy. These results suggest that PA F-2 has potential applications in the bioremediation of TCF and Cd(II) co-contamination.

Remediation potential of immobilized bacterial consortium with biochar as carrier in pyrene-Cr(VI) co-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) and potentially toxic trace elements (PTEs) soil contamination have become areas of concern. Bioaugmentation is regarded as an effective bioremediation method, however it is difficult to simultaneously degrade organic compounds and remove PTEs with individual microbial strains. Therefore, the objective of this study was to evaluate the feasibility of using immobilized microbial consortia, including two PAH-degrading bacterial strains (W1 and W2) and a Cr(VI)-reducing bacterium (Y2), for the remediation of pyrene-Cr(VI) co-contaminated soil. Three immobilization methods were investigated: (1) bacterial consortium adsorption onto biochar (BC), (2) bacterial consortium entrapment in alginate beads (AC), (3) bacterial consortium adsorption on biochar and sequential entrapment in alginate beads (BAC). In addition, a free bacterial consortium (FC) was also used for comparison. Ten treatments were designed to illustrate the bioremediation efficiency of the free and immobilized consortia. The results show that treatments AC and BAC resulted in more efficient Cr(VI) removal compared with BC and FC. Pyrene levels in AC and BAC microcosms were reduced from 42.33 ± 3.82 to 11.56 ± 1.37 and 7.48 ± 0.39 mg kg^-1, respectively. Bioavailable Cr (VI) in AC and BAC was significantly lower than that in other microcosms after 28 days' incubation. Both AC and BAC microcosms exhibited a higher level of dehydrogenase and fluorescein diacetate hydrolysis activity. Furthermore, soil microbial diversity was higher in AC and BAC microcosms compared with the others. Thus, the entrapped consortia may be useful for bioremediation of pyrene and Cr (VI) without compromising soil ecology.

The naphthalene catabolic protein NahG plays a key role in hexavalent chromium reduction in Pseudomonas brassicacearum LZ-4

Soil contamination by PAH and heavy metals is a growing problem. Here, we showed that a new isolate, Pseudomonas brassicacearum strain LZ-4, can simultaneously degrade 98% of 6 mM naphthalene and reduce 92.4% of 500 μM hexavalent chromium [Cr (VI)] within 68 h. A draft genome sequence of strain LZ-4 (6,219,082 bp) revealed all the genes in the naphthalene catabolic pathway and some known Cr (VI) reductases. Interestingly, genes encoding naphthalene pathway components were upregulated in the presence of Cr (VI), and Cr (VI) reduction was elevated in the presence of naphthalene. We cloned and expressed these naphthalene catabolic genes and tested for Cr (VI) reduction, and found that NahG reduced 79% of 100 μM Cr (VI) in 5 minutes. Additionally, an nahG deletion mutant lost 52% of its Cr (VI) reduction ability compared to that of the wild-type strain. As nahG encodes a salicylate hydroxylase with flavin adenine dinucleotide (FAD) as a cofactor for electron transfer, Cr (VI) could obtain electrons from NADH through NahG-associated FAD. To the best of our knowledge, this is the first report of a protein involved in a PAH-degradation pathway that can reduce heavy metals, which provides new insights into heavy metal-PAH contamination remediation.

Characterisation of the phenanthrene degradation-related genes and degrading ability of a newly isolated copper-tolerant bacterium

A copper-tolerant phenanthrene (PHE)-degrading bacterium, strain Sphingobium sp. PHE-1, was newly isolated from the activated sludge in a wastewater treatment plant. Two key genes, ahdA1b-1 encoding polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDɑ) and xyLE encoding catechol-2,3-dioxygenase (C23O), involved in the PHE metabolism by strain PHE-1 were identified. The PAH-RHD gene cluster showed 96% identity with the same cluster of Sphingomonas sp. P2. Our results indicated the induced transcription of xylE and ahdA1b-1 genes by PHE, simultaneously promoted by Cu(II). For the first time, high concentration of Cu(II) is found to encourage the expression of PAH-RHDɑ and C23O genes during PHE degradation. Applying Sphingomonas PHE-1 in PHE-contaminated soils for bioaugmentation, the abundance of xylE gene was increased by the planting of ryegrass and the presence of Cu(II), which, in turn, benefited ryegrass growth. The best performance of PHE degradation and the highest abundance of xylE genes occurred in PHE-copper co-contaminated soils planted with ryegrass.

A novel Pseudomonas gessardii strain LZ-E simultaneously degrades naphthalene and reduces hexavalent chromium

Combined pollutants with polycyclic aromatic hydrocarbons (PAHs) and heavy metals have been identified as toxic and unmanageable contaminates. In this work, Pseudomonas gessardii strain LZ-E isolated from wastewater discharge site of a petrochemical company degrades naphthalene and reduces Cr(VI) simultaneously. 95% of 10mgL(-1) Cr(VI) was reduced to Cr(III) while 77% of 800mgL(-1) naphthalene was degraded when strain LZ-E was incubated in BH medium for 48h. Furthermore, naphthalene promotes Cr(VI) reduction in strain LZ-E as catechol and phthalic acid produced in naphthalene degradation are able to reduce Cr(VI) abiotically. An aerated bioreactor system was setup to test strain LZ-E's remediation ability. Strain LZ-E continuously remediated naphthalene and Cr(VI) at rates of 15mgL(-1)h(-1) and 0.20mgL(-1)h(-1) of 800mgL(-1) naphthalene and 10mgL(-1) Cr(VI) addition with eight batches in 16days. In summary, strain LZ-E is a potential applicant for combined pollution remediation.

Impact of Zn, Cu, Al and Fe on the partitioning and bioaccessibility of (14)C-phenanthrene in soil

This investigation considered the effects of Zn, Cu, Al and Fe (50 and 500 mg kg(-1)) on the loss, sequential extractability, using calcium chloride (CaCl2), hydroxypropyl-β-cyclodextrin (HPCD) and dichloromethane (DCM) and biodegradation of (14)C-phenanthrene in soil over 63 d contact time. The key findings were that the presence of Cu and Al (500 mg kg(-1)) resulted in larger amounts of (14)C-phenanthrene being extracted by CaCl2 and HPCD. Further, the CaCl2 + HPCD extractions directly predicted the biodegradation of the PAH in the presence of the metals, with the exception of 500 mg kg(-1) Cu and Zn. The presence of high concentrations of some metals can impact on the mobility and accessibility of phenanthrene in soil, which may impact on the risk assessment of PAH contaminated soil.

Mixtures of environmental pollutants: effects on microorganisms and their activities in soils

Soil is the ultimate sink for most contaminants and rarely has only a single contaminant. More than is generally acknowledge, environmental pollutants exist as mixtures (organic-organic, inorganic-inorganic, and organic-inorganic). It is much more difficult to study chemical mixtures than individual chemicals, especially in the complex soil environment. Similarly, understanding the toxicity of a chemical mixture on different microbial species is much more complex, time consuming and expensive, because multiple testing designs are needed for an increased array of variables. Therefore, until now, scientific enquiries worldwide have extensively addressed the effects of only individual pollutants toward nontarget microorganisms. In this review, we emphasize the present status of research on (i) the environmental occurrence of pollutant mixtures; (ii) the interactions between pollutant mixtures and ecologically beneficial microorganisms; and (iii) the impact of such interactions on environmental quality. We also address the limitations of traditional cultivation based methods for monitoring the effects of pollutant mixtures on microorganisms. Long-term monitoring of the effects of pollutant mixtures on microorganisms, particularly in soil and aquatic ecosystems, has received little attention. Microbial communities that can degrade or can degrade or can develop tolerance to, or are inhibited by chemical mixtures greatly contribute to resilience and resistance in soil environments. We also stress in this review the important emerging trend associated with the employment of molecular methods for establishing the effects of pollutant mixtures on microbial communities. There is currently a lack of sufficient cogent toxicological data on chemical mixtures for making informed decision making in risk assessment by regulators. Therefore, not only more toxicology information on mixtures is needed but also there is an urgent need to generate sufficient, suitable, and long-term modeling data that have higher predictability when assessing pollutant mixture effects on microorganisms. Such data would improve risk assessment at contaminated sites and would help devise more effective bioremediation strategies.