A poplar short-chain dehydrogenase reductase plays a potential key role in biphenyl detoxification

Contreras, Ángela; Merino, Irene; Álvarez, Enrique Alarcón; Bolonio, David; Ortiz, José-Eugenio; Oñate-Sánchez, Luis; Gómez, Luis

doi:10.1073/pnas.2103378118

Cited by 8 publications

(4 citation statements)

References 52 publications

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“…For the higher levels of contamination encountered at brownfield sites, phytoremediation performance can be enhanced by the addition of mobilizing reagents to the soil 69 . More efficient phytoremediation technologies based on new molecular mechanisms of plant-specific detoxification pathways and genetic modification are under development 70,71 . However, the bioremediation effect of plants is limited to the rhizosphere, making it difficult to use plants alone to remediate brownfields whose contaminants usually reach much deeper.…”

Section: Low-impact Bioremediationmentioning

confidence: 99%

Sustainable remediation and redevelopment of brownfield sites

Hou

Al‐Tabbaa

O’Connor

et al. 2023

Nat Rev Earth Environ

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Widespread pollution from industrial activities has driven land degradation with detrimental human health effects, especially in urban areas. Remediation and redevelopment of the estimated 5 million brownfield sites globally is needed to support the sustainable transition and increase urban ecosystem services, but many traditional strategies are often environmentally harmful. In this Review, we outline sustainable remediation strategies for the clean-up of contaminated soil and groundwater at brownfield sites. Conventional remediation strategies, such as dig and haul, or pump and treat, ignore secondary environmental burdens and socioeconomic impacts; over their life cycle, some strategies are more detrimental than taking no action. Sustainable remediation technologies, such as sustainable immobilization, low-impact bioremediation, new forms of in-situ chemical treatment and innovative passive barriers, can substantially reduce the environmental footprint of remediation and maximize overall net benefits. Compared with traditional methods, they can typically reduce the life-cycle greenhouse gas emissions by ~50-80%. Integrating remediation with redevelopment through nature-based solutions and sustainable energy systems could further increase the socioeconomic benefit, while providing carbon sequestration or green energy. The long-term resilience of these systems still needs to be understood, and ethics and equality must be quantified, to ensure that these systems are robust and just. Nature Reviews Earth & Environment Review articleoften hindered by high costs, cumbersome administrative processes and uncertain remediation performance 12 . Sustainable remediation has the potential to accelerate BRR 13 through accounting for three factors: adverse life-cycle impacts of traditional remediation, institutional pressures exerted by new industrial norms, and stakeholder demand for sustainable practices 13 . Yet there are also concerns that businesses will use this concept for 'green washing' (claiming a remediation project or technology is sustainable, without robust evidence 14 ) or to reduce project costs by undertaking less remediation 15 . Thus, it is vital to better understand the holistic impacts of remediation and redevelopment to support the implementation of sustainable practices.In this Review, we outline sustainable strategies for BRR. We begin with a discussion of the primary, secondary and tertiary impacts of traditional practices over the life cycle of remediation. Then, we summarize promising sustainable strategies, namely, innovative in-situ soil and groundwater remediation technologies and strategies that integrate remediation with redevelopment. We end by identifying challenges and future research directions. Life-cycle impactsTraditional brownfield remediation was long considered inherently sustainable because it removes toxic chemicals from the environment, frees up contaminated land for reuse and reduces urban sprawl. However, holistic sustainability assessments and life-based approaches have exposed...

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Section: Low-impact Bioremediationmentioning

confidence: 99%

Sustainable remediation and redevelopment of brownfield sites

Hou

Al‐Tabbaa

O’Connor

et al. 2023

Nat Rev Earth Environ

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“…Additionally, some SDR enzymes are involved in detoxifying harmful compounds such as pollutants and oxidants in terrestrial environments 104 , which can help airbreathing catfishes survive in these harsh conditions.…”

Section: Positive Selection In Airbreathing Clariasmentioning

confidence: 99%

Haplotype-resolved assembly of the African catfish (Clarias gariepinus) provides insights for semi-terrestrial adaptation of airbreathing catfishes

Nguinkal

Zoclanclounon

Brunner

et al. 2023

Preprint

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Airbreathing catfishes (clariids) are a group of stenohaline freshwater fish that can withstand various environmental conditions and farming practices, including the ability to breathe atmospheric oxygen. This unique ability has allowed them to thrive in semi-terrestrial habitats. However, the underlying genomic and adaptive mechanisms remain poorly investigated. Here, we sequenced the genome of the African catfish Clarias gariepinus, one of the most commonly farmed clariids, and generated a gapless telomere-to-telomere (T2T) chromosome-level assembly with high-resolution haplotypes, by integrating long-range sequencing (Hi-C) with PacBio single-molecule (HiFi), Oxford Nanopore, and Illumina sequencing data. The diploid genome assembly yielded 58 contigs with a total length of 969.72 Mb and a contig N50 of 33.71 Mb. We report 25,655 predicted protein-coding genes and 49.94% repetitive elements in the African catfish genome. Our genome assembly provides the first comprehensive gene annotation and haplotype information, such as the male-specific haplotype, enabling us to identify putative genes and molecular mechanisms underlying amphibious traits and terrestrial adaptation of airbreathing catfishes. Several gene families involved in ion transport, osmoregulation, oxidative stress response, and muscle metabolism were expanded or positively selected in clariids, suggesting a potential role in their transition to terrestrial life. The reported findings expand our understanding of the genomic mechanisms underpinning the resilience and adaptive mechanisms of C. gariepinus to adverse ecological conditions. They will serve as a valuable resource for future studies in elucidating these unique biological traits in related teleosts and leverage these insights for aquaculture improvement.

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“…The regulation, biochemical, genetic and structural analysis of these genes in the biphenyl pathway have been reported in previous studies (Furusawa et al ., 2004; Parnell et al ., 2010; Chakraborty and Das, 2016; Kour et al ., 2019; Contreras et al ., 2021; Hirose et al ., 2021); however, the evolutionary research about this pathway is rare. Meanwhile, the evolutionary impetus for the microbes to evolve this new pathway in such a little time (about 100 years after the appearance of PCBs in nature) could be an excellent model to investigate the possible evolutionary mechanisms of new pathways evolution.…”

Section: Introductionmentioning

confidence: 99%

Micro‐synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway

Ullah

Zhu

Nawaz

et al. 2022

Environ Microbiol Rep

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Phenolic compounds have been enlisted by the United States Environmental Protection Agency (USEPA) and the European Union (EU) as pollutants of priority concern. The biphenyl degradation pathway plays an essential role in prokaryote polychlorinated biphenyls degradation. Our understanding of prokaryotic pathways and their evolution has dramatically increased in recent years with the advancements in prokaryotic genome sequencing and analysis tools. In this work, we applied bioinformatics tools to study the evolution of the biphenyl degradation pathway focusing on the phylogeny and initiation of four representative species (Burkholderia xenovorans LB400, Polaromonas naphthalenivorans CJ2, Pseudomonas putida F1 and Rhodococcus jostii RHA1). These species contained partial or full concatenated genes from bph gene cluster (i.e. bphRbphA1A2A3A4BCKHJID). The aim was to establish this pathway's origin and development mode in the prokaryotic world. Genomic screening revealed that many bacterial species possess genes for the biphenyl degradation pathway. However, the micro-synteny conservation analysis indicated that massive gene recruitment events might have occurred during the evolution of the biphenyl degradation pathway. Combining with the phylogenetic positions, this work points to the evolutionary process of acquiring the biphenyl degradation pathway by different fragments through horizontal gene transfer in these bacterial groups. This study reports the first-ever evidence of the birth of this pathway in the represented species.

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A poplar short-chain dehydrogenase reductase plays a potential key role in biphenyl detoxification

Cited by 8 publications

References 52 publications

Sustainable remediation and redevelopment of brownfield sites

Sustainable remediation and redevelopment of brownfield sites

Haplotype-resolved assembly of the African catfish (Clarias gariepinus) provides insights for semi-terrestrial adaptation of airbreathing catfishes

Micro‐synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway

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