Simulation of Microbial Response to Accidental Diesel Spills in Basins Containing Brackish Sea Water and Sediment

Yan, Lijuan; Hui, Nan; Simpanen, Suvi; Tudeer, Laura; Romantschuk, Martin

doi:10.3389/fmicb.2020.593232

Cited by 9 publications

(3 citation statements)

References 74 publications

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“…We excluded datasets for which raw sequencing data were not publicly available and stopped data collection in October 2020. In all, datasets from 29 studies matched our criteria [ 14 , 23 , 31 – 54 ], see Table S 1 for all datasets). We grouped these time series into three environmental categories: aquatic, mammal-associated, and soil microbiomes (including rhizosphere microbiomes).…”

Section: Methodsmentioning

confidence: 99%

Synthesis of recovery patterns in microbial communities across environments

Jurburg,

Blowes,

Shade

et al. 2024

Microbiome

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Background Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. Results To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. Conclusions This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective.

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Section: Methodsmentioning

confidence: 99%

Synthesis of recovery patterns in microbial communities across environments

Jurburg,

Blowes,

Shade

et al. 2024

Microbiome

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“…Amplification was conducted using 2.0 μL of diluted DNA (dilution of 1:100), 10 μL of 2X DYNAMO Master Mix, 1 μL of each primer (10 μM), and 6 μl of sterile distilled water. The thermal cycling conditions followed were similar to those described by Yan et al ( 2020 ). A negative control (ddH 2 O) was included, and all samples were run in triplicate.…”

Section: Methodsmentioning

confidence: 99%

Meat and bone meal stimulates microbial diversity and suppresses plant pathogens in asparagus straw composting

Liu

Li²,

Hua³

et al. 2022

Front. Microbiol.

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Meat and bone meal (MBM), as slaughterhouse waste, is a potential biostimulating agent, but its efficiency and reliability in composting are largely unknown. To access the MBM application to the composting process of asparagus straw rice, we followed the composting process for 60 days in 220-L composters and another 180 days in 20-L buckets in treatments applied with MBM or urea. The microbial succession was investigated by high-throughput sequencing. Compared with urea treatments, MBM addition stabilized pH and extended the thermophilic phase for 7 days. The germination index of MBM treatments was 24.76% higher than that of urea treatments. MBM also promoted higher microbial diversity and shifted community compositions. Organic matter and pH were the most significant factors that influence the bacterial and fungal community structure. At the genus level, MBM enriched relative abundances of organic matter-degrading bacteria (Alterococcus) and lignocellulose-degrading fungi (Trichoderma), as well as lignocellulolytic enzyme activities. Notably, MBM addition decreased sum abundances of plant pathogenic fungi of Phaeoacremonium, Acremonium, and Geosmithia from 17.27 to 0.11%. This study demonstrated the potential of MBM as an effective additive in asparagus straw composting, thus providing insights into the development of new industrial aerobic fermentation.

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“…In the case of readily biodegradable organic compounds such as PHC, mineralization of the contaminant is largely dictated by bacteria (Romantschuk et al, 2000;Mukherjee et al, 2015;Simpanen et al, 2016a), but recent research shows that Archaea may also be involved (Yan et al, 2018(Yan et al, , 2020. To facilitate bioremediation in such cases, soil conditions need to be optimized for bacterial activity and proliferation, which will accelerate removal of the pollutant.…”

Section: Microbial Bioremediation -Forms Prerequisites and Conditionsmentioning

confidence: 99%

Bioremediation of contaminated soil and groundwater by in situ biostimulation

Romantschuk,

Lahti-Leikas,

Kontro

et al. 2023

Front. Microbiol.

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Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.

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Simulation of Microbial Response to Accidental Diesel Spills in Basins Containing Brackish Sea Water and Sediment

Cited by 9 publications

References 74 publications

Synthesis of recovery patterns in microbial communities across environments

Synthesis of recovery patterns in microbial communities across environments

Meat and bone meal stimulates microbial diversity and suppresses plant pathogens in asparagus straw composting

Bioremediation of contaminated soil and groundwater by in situ biostimulation

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