Enrichment of novel Actinomycetales and the detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula

Ramalingam, Vidhya; Cupples, Alison M.

doi:10.1007/s00253-020-10376-7

Cited by 19 publications

(4 citation statements)

References 62 publications

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“…The high symbiotic capacity of bacteria in the consortium resulted in a lesser impact on community alpha diversity by the DTE method, indicating that DTE provides more information than directly isolated degraders on agar plates. The phylum Proteobacteria carrying order Rhizobiales remained the most dominant microbiota in all consortia, owing to their adaptation and utilization towards 1,4-dioxane ( 48 , 49 ) (Fig. S5).…”

Section: Discussionmentioning

confidence: 99%

Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing

Tian,

Zhang,

Chen

et al. 2023

Microbiol Spectr

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Assembling a functional consortium and identifying novel degraders from contaminated environments are still challenging due to the large diversity of microorganisms and the difficulty in isolating pure cultures. Here, we constructed a relatively simple functional consortium by enriching 1,4-dioxane-degrading-consortia using a culture-dependent dilution-to-extinction (DTE) method and reported a new key dioxane-degrader Shinella sp. Our results showed that serial dilution and reculture led to a divergence in the degradation ability of each consortium. Next-generation sequencing data revealed that the divergence in degradation performance was due to the reassembly of microbiota in the DTE process, which occurred most notably in 10 −8 and 10 −9 dilutions. The shift in community structure at 10 −9 prevented the recovery of 1,4-dioxane degradation capacity, and the newly dominant taxa, Xanthobacter and Acinetobacter , struggled to replace the original dominant genus Shinella for 1,4-dioxane biodegradation. Combining differential analysis of community structure and metabolic function, we confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, we verified our findings using our isolated dioxane-degrading bacteria, Shinella yambaruensis , resulting in the rapid recovery of degradation performance of a 10 −9 dilution consortium with Xanthobacter and Acinetobacter as the dominant microbiota. Taken together, this study provides a strategy for self-assembling functional consortiums and identifying the key degraders to explore the underlying biological mechanisms of enriched contaminant-degrading consortia. IMPORTANCE Assembling a functional microbial consortium and identifying key degraders involved in the degradation of 1,4-dioxane are crucial for the design of synergistic consortia used in enhancing the bioremediation of 1,4-dioxane-contaminated sites. However, due to the vast diversity of microbes, assembling a functional consortium and identifying novel degraders through a simple method remain a challenge. In this study, we reassembled 1,4-dioxane-degrading microbial consortia using a simple and easy-to-operate method by combining dilution-to-extinction and reculture techniques. We combined differential analysis of community structure and metabolic function and confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, a new dioxane-degrading bacterium was isolated, Shinella yambaruensis , which verified our findings. These results demonstrate that DTE and reculture techniques can be used beyond diversity reduction to assemble functional microbial communities, particularly to identify key degraders in contaminant-degrading consortia.

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Section: Discussionmentioning

confidence: 99%

Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing

Tian,

Zhang,

Chen

et al. 2023

Microbiol Spectr

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“…Possible mechanisms of cooperation between degrader ZM13 and its cooperators Overall, the above results indicated that although the key degrading bacteria are essential for biodegradation, community members involved in intermediate degradation and environmental adaptation are also indispensable for the e cient degradation. Genera Xanthobacter and Mesorhizobium have been identi ed in multiple consortia that had 1,4-dioxanedegrading capability [23,53], suggesting potentially important roles of these two bacteria in the cooperation of 1,4-dioxane degradation. However, because of the slow growth rate of Mesorhizobium even at the optimum medium [54] and the di culty of nding the optimum medium for cultivating Xanthobacter, as well as the tight interspecies collaboration in the community, these two strains were not successfully isolated.…”

Section: Discussionmentioning

confidence: 99%

Network And Meta-Omics Reveal The Key Degrader And Cooperation Patterns In An Efficient 1,4-Dioxane-Degrading Microbial Community

Dai

Wang

et al. 2021

Preprint

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Background: 1,4-dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mix cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial community CH1.Results: The 1,4-dioxane degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and proved to be the key degrader because of the high relative abundance, highly expressed toluene monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium were proved to be involved in the intermediate metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) upregulated. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators of CH1 cooperated with ZM13 in the way of providing amino acids or fatty acids and relieving environmental stresses to promote biodegradation.Conclusions: This study revealed the biodiversity, community structure, microbial functions and interactions in a microbial community CH1 during the efficient 1,4-dioxane degradation and proved the degrader Ancylobacter polymorphus ZM13 that isolated from CH1 was the key degrading bacterium. These results provide new insights into our understanding of how the key degrading bacterium interacted with cooperators in a 1,4-dioxane-degrading community, and has important implications for predicting microbial cooperation and constructing highly efficient synthetic 1,4-dioxane-degrading communities.

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“…Multiple investigations of mixed microbial communities capable of 1,4-dioxane degradation have revealed population shifts over time and substantially enhanced Mycobacterium populations (Nam et al 2016;He et al 2018;Xiong et al 2020;Ramalingam and Cupples 2020a;Miao et al 2021), suggesting that these microorganisms are particularly well suited to the process. However, Nam et al (2016) also demonstrated that uncharacterized, and hard to characterize, microorganisms may play a substantial role in 1,4-dioxane degradation in some cases.…”

Section: Evolution In Understanding Of 14-dioxane Biodegradationmentioning

confidence: 99%

“…2018; Xiong et al. 2020; Ramalingam and Cupples 2020a; Miao et al. 2021), suggesting that these microorganisms are particularly well suited to the process.…”

Section: Evolution In Understanding Of 14‐dioxane Biodegradationmentioning

confidence: 99%

Advances in Remediation Solutions: New Developments and Opportunities in 1,4‐Dioxane Biological Treatment

Divine,

Bell,

Heintz

et al. 2024

Groundwater Monitoring Rem

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Enrichment of novel Actinomycetales and the detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula

Cited by 19 publications

References 62 publications

Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing

Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing

Network And Meta-Omics Reveal The Key Degrader And Cooperation Patterns In An Efficient 1,4-Dioxane-Degrading Microbial Community

Advances in Remediation Solutions: New Developments and Opportunities in 1,4‐Dioxane Biological Treatment

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