Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

Kim, Jinha; Hwangbo, Myung; Shih, Chih-Hsuan; Chu, Kung-Hui

doi:10.1016/j.wroa.2023.100187

Cited by 7 publications

(6 citation statements)

References 136 publications

(188 reference statements)

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“…More broadly, the last decade has seen an explosion of methods for quantifying community dynamics and metabolism from transcriptomic and metagenomic measurements [57][58][59] to single-cell metabolomics [60] and quantitative stable isotope probes [61][62][63]. The challenge is to synthesize these data to achieve insights into dynamics and function.…”

Section: Functional Phases As Guides For Understanding Complex Omics ...mentioning

confidence: 99%

Functional regimes define the response of the soil microbiome to environmental change

Lee,

Liu,

Crocker

et al. 2024

Preprint

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A major challenge in microbiome research is understanding how natural communities respond to environmental change. The ecological, spatial, and chemical complexity of soils makes understanding how these communities respond metabolically to perturbations particularly challenging. Here we measure the dynamics of respiratory nitrate utilization in >1,500 soil microcosms from 20 soil samples subjected to pH perturbations. Despite the complexity of the soil microbiome a minimal mathematical model with two parameters, the quantity of active biomass and the availability of a limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. The model reveals three distinct functional phases that encode the low-dimensional dynamics of nitrate utilization in response to short and long-term pH perturbations: a phase where acidic perturbations induce cell death that limits metabolic activity, a nutrient-limiting phase where nitrate utilization is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth phase in basic conditions, where nutrients are in excess and rare taxa rapidly outgrow dominant populations. The underlying functional mechanism of each phase is revealed by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. The long-term pH of the soil determines the size of pH changes necessary to drive transitions between functional phases. Our results unify decades of previous studies on nitrogen utilization and pH in soils under a single quantitative framework. A minimal mathematical formalism reveals the existence of a few qualitative phases that capture the mechanisms and dynamics of a community responding to environmental change.

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Section: Functional Phases As Guides For Understanding Complex Omics ...mentioning

confidence: 99%

Functional regimes define the response of the soil microbiome to environmental change

Lee,

Liu,

Crocker

et al. 2024

Preprint

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“…were previously identified as consumers of dead biomass derived from E. coli [60]; however, among them, only Lysobacter is known as a facultative predator [61]. This fact, together with the late incorporation of labelled biomass, suggests that the enrichment of bacteria may have resulted from cross-feeding [38]. It has been recently suggested that the role of predatory bacteria may be underestimated and that they could play a major role in the soil food web [7,11].…”

Section: Bacillus)mentioning

confidence: 99%

“…Stable isotope probing (SIP) of DNA can assess trophic linkages between microbes or identify their contributions to specific functions in the environment [28]. SIP has been widely applied to trace carbon transfer in soil food webs [29][30][31][32], and to identify microbial degraders in bioremediation processes [33][34][35][36][37][38]. Most commonly, a labelled substrate is added to the soil to follow its fate as it is consumed by the soil biota.…”

Section: Introductionmentioning

confidence: 99%

Analysis of predation-driven inoculum loss and carbon flow in bioaugmented soils through DNA-SIP

Nieto,

Jurburg,

Steinbach

et al. 2024

Preprint

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Bioaugmentation is considered as a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to modified enrichment factor calculation. Inoculation effectively increased PAH removal in short-term polluted soils but not in long-term polluted soils. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. Our results showed differences in the inoculum establishment and predator community behaviours, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies.

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“…For example, advancing the performance of biological wastewater treatment through processes like anammox, granular sludge, and enhanced biological phosphorus removal ( An et al, 2023 ; Nguyen et al, 2023 ; Wen et al, 2023 ; Yin et al, 2023 ; Zhang et al, 2024 ; Zheng et al, 2023 ) reflect the need for wastewater plants to do more. Wastewater treatment advancements also benefit from understanding the interactions of microbial communities ( Gao et al, 2023 ; Kim et al, 2023 ), and research on underexplored areas such as microbial predation and parasitism ( Kuroda et al, 2023 ). In addition to centralized wastewater treatment, decentralized treatment also needs innovative solutions, such as stormwater and rainwater harvesting and nutrient recovery from waste streams ( Keller, 2023 ).…”

mentioning

confidence: 99%

Research stories along the urban water cycle

Boyer,

Gernjak

2024

Water Research X

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Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

Cited by 7 publications

References 136 publications

Functional regimes define the response of the soil microbiome to environmental change

Functional regimes define the response of the soil microbiome to environmental change

Analysis of predation-driven inoculum loss and carbon flow in bioaugmented soils through DNA-SIP

Research stories along the urban water cycle

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