Challenges in bioremediation: from lab to land

Nandy, Sampurna; Andraskar, Jayanta; Lanjewar, Krutika; Kapley, Atya

doi:10.1016/b978-0-12-820524-2.00023-7

Cited by 9 publications

(3 citation statements)

References 81 publications

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“…Simultaneously, although microorganisms isolated through RACS-SIP exhibited lower degradation capacity on culture medium compared with conventionally isolated strains, they demonstrated significantly greater PHE removal capacities in native soil ( P < .05). Previous research has highlighted the obstacles encountered by many microorganisms, particularly non-native functional strains, in achieving effective remediation when introduced into real-world environments [ 3 , 50 , 51 ]. These challenges are related to the intricate nature of the in situ milieu, including competition with indigenous microbial populations, limited nutrient availability, and the presence of inhibitory compounds [ 41 , 51 ].…”

Section: Discussionmentioning

confidence: 99%

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders

Li,

Luo,

Cai

et al. 2024

The ISME Journal

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Soil microbial flora constitutes a highly diverse and complex microbiome on Earth, often challenging to cultivation, with unclear metabolic mechanisms in situ. Here, we present a pioneering concept for the in situ construction of functional microbial consortia (FMCs) and introduce an innovative method for creating FMCs by utilising phenanthrene as a model compound to elucidate their in situ biodegradation mechanisms. Our methodology involves single-cell identification, sorting, and culture of functional microorganisms, resulting in the formation of a precise in situ FMC. Through RACS-SIP, we identified and isolated phenanthrene-degrading bacterial cells from Achromobacter sp. and Pseudomonas sp., achieving precise and controllable in situ consortia based on genome-guided cultivation. Our in situ FMC outperformed conventionally designed functional flora when tested in real soil, indicating its superior phenanthrene degradation capacity. We revealed that microorganisms with high degradation efficiency isolated through conventional methods may exhibit pollutant tolerance but lack actual degradation ability in natural environments. This finding highlights the potential to construct FMCs based on thorough elucidation of in situ functional degraders, thereby achieving sustained and efficient pollutant degradation. Single-cell sequencing linked degraders with their genes and metabolic pathways, providing insights regarding the construction of in situ FMCs. The consortium in situ comprising microorganisms with diverse phenanthrene metabolic pathways might offer distinct advantages for enhancing phenanthrene degradation efficiency, such as the division of labour and cooperation or communication among microbial species. Our approach underscores the importance of in situ, single-cell precision identification, isolation, and cultivation for comprehensive bacterial functional analysis and resource exploration, which can extend to investigate MFCs in archaea and fungi, clarifying FMC construction methods for element recycling and pollutant transformation in complex real-world ecosystems.

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Section: Discussionmentioning

confidence: 99%

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders

Li,

Luo,

Cai

et al. 2024

The ISME Journal

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“…Similar issues in biotechnology are numerous. Scaling bioremediation beyond the lab remains challenging due to the complexity of microbial communities in natural environments [108]. Phage therapy is often less effective than expected due to the presence of biofilms and the interaction with the human immune system [118].…”

Section: Novelty Before Fitnessmentioning

confidence: 99%

Open-endedness in synthetic biology: a route to continual innovation for biological design

Stock¹,

Gorochowski²

2023

Preprint

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Design in synthetic biology is typically goal-oriented: aiming to repurpose and optimize existing biological functions for new contexts, augmenting biology with new-to-nature capabilities, or creating life-like systems from scratch. While the field has seen many advances over the past two decades, bottlenecks in the complexity of the systems built are emerging and designs that function in the lab often fail when used in real-world contexts. Here, we propose an open-ended approach to biological design that aims to continuously generate innovative solutions capable of overcoming such hurdles. The fundamental principle we put forward is that the novelty of designed biology, be it a protein, genetic construct or organism, is at least as important as how well it fulfils its goal. Designing with novelty in mind, rather than a sole focus on optimization towards a single ``best'' design, may allow us to move beyond the diminishing returns we see in performance for most engineered biology to date. Research from the artificial life and evolutionary computing communities has demonstrated that embracing novelty can allow for the automatic generation of innovative and surprising solutions to challenging problems that move us beyond local optima. Synthetic biology now offers the ideal playground to test these ideas in living systems and explore more creative approaches to biological design.

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“…Long-term exposure generates modifications in species richness and diversity, with metal-resistant strains becoming dominant, albeit fewer in number [ 36 ]. Non-native microbial communities are in competition with the native microbiota and face difficulties in surviving in a polluted environment [ 37 ], whereas native strains develop tolerance over time through several extracellular and intracellular mechanisms, thus being more efficient in bioremediation [ 38 , 39 , 40 ]. Pollution-induced community tolerance (PICT) was proposed for the first time in 1988 by Blanck et al [ 41 ], which suggests that microbial communities exposed to xenobiotic compounds for a sufficient period of time could develop selective resistance as well as suffer modifications in species composition.…”

Section: Introductionmentioning

confidence: 99%

Microbial Removal of Heavy Metals from Contaminated Environments Using Metal-Resistant Indigenous Strains

Firincă,

Zamfir,

Constantin

et al. 2023

JoX

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Contamination of soil with heavy metals has become a matter of global importance due to its impact on agriculture, environmental integrity, and therefore human health and safety. Several microbial strains isolated from soil contaminated by long-term chemical and petrochemical activities were found to manifest various levels of tolerance to Cr, Pb, and Zn, out of which Bacillus marisflavi and Trichoderma longibrachiatum exhibited above-moderate tolerance. The concentrations of target heavy metals before and after bioremediation were determined using electrochemical screen-printed electrodes (SPE) modified with different nanomaterials. The morpho-structural SEM/EDX analyses confirmed the presence of metal ions on the surface of the cell, with metal uptake being mediated by biosorption with hydroxyl, carboxyl, and amino groups as per FTIR observations. T. longibrachiatum was observed to pose a higher bioremediation potential compared to B. marisflavi, removing 87% of Cr and 67% of Zn, respectively. Conversely, B. marisflavi removed 86% of Pb from the solution, compared to 48% by T. longibrachiatum. Therefore, the fungal strain T. longibrachiatum could represent a viable option for Cr and Zn bioremediation strategies, whereas the bacterial strain B. marisflavi may be used in Pb bioremediation applications.

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Challenges in bioremediation: from lab to land

Cited by 9 publications

References 81 publications

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders

Open-endedness in synthetic biology: a route to continual innovation for biological design

Microbial Removal of Heavy Metals from Contaminated Environments Using Metal-Resistant Indigenous Strains

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