Beyond taxonomy: Validating functional inference approaches in the context of fish‐farm impact assessments

Laroche, Olivier; Pochon, Xavier; Wood, Susanna A.; Keeley, Nigel

doi:10.1111/1755-0998.13426

Cited by 14 publications

(9 citation statements)

References 91 publications

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“…In the deep sea, eDNA analysis has focused on the sediments to survey the benthic communities (e.g., Guardiola et al, 2016;Sinniger et al, 2016;Laroche et al, 2021). On the other hand, a few surveys of aquatic communities in the deep sea have been conducted (Fraija-Fernańdez et al, 2020;McClenaghan et al, 2020;Merten et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Yoshida

Kawato²,

Fujiwara³

et al. 2023

Front. Mar. Sci.

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Deep-sea ecosystems present difficulties in surveying and continuous monitoring of the biodiversity of deep-sea ecosystems because of the logistical constraints, high cost, and limited opportunities for sampling. Environmental DNA (eDNA) metabarcoding analysis provides a useful method for estimating the biodiversity in aquatic ecosystems but has rarely been applied to the study of deep-sea fish communities. In this study, we utilized pumped deep-sea water for the continuous monitoring of deep-sea fish communities by eDNA metabarcoding. In order to develop an optimum method for continuous monitoring of deep-sea fish biodiversity by eDNA metabarcoding, we determined the appropriate amount of pumped deep-sea water to be filtered and the practical number of filtered sample replicates required for biodiversity monitoring of deep-sea fish communities. Pumped deep-sea water samples were filtered in various volumes (5–53 L) at two sites (Akazawa: pumping depth 800 m, and Yaizu: pumping depth 400 m, Shizuoka, Japan) of deep-sea water pumping facilities. Based on the result of evaluations of filtration time, efficiency of PCR amplification, and number of detected fish reads, the filtration of 20 L of pumped deep-sea water from Akazawa and filtration of 10 L from Yaizu were demonstrated to be suitable filtration volumes for the present study. Fish biodiversity obtained by the eDNA metabarcoding analyses showed a clear difference between the Akazawa and Yaizu samples. We also evaluated the effect of the number of filter replicates on the species richness detected by eDNA metabarcoding from the pumped deep-sea water. At both sites, more than 10 sample replicates were required for the detection of commonly occurring fish species. Our optimized method using pumped deep-sea water and eDNA metabarcoding can be applied to eDNA-based continuous biodiversity monitoring of deep-sea fish to better understand the effects of climate change on deep-sea ecosystems.

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Section: Introductionmentioning

confidence: 99%

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Yoshida

Kawato²,

Fujiwara³

et al. 2023

Front. Mar. Sci.

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“…Within a microbial community, diverse and multiple species can perform similar catabolic functions that affect the microbial community structure over time or in response to stimuli. To evaluate the functional capacity of the soil microbiome in sandy soil and rhizosphere sandy soil that received different treatments, Tax4Fun2 was used to predict functional features based on the 16S rRNA gene sequencing data. − Our previous study reported desulfonation and defluorination enzymes involved in 6:2 FTSA biodegradation by RHA1 . So, the analysis was focused on these known desulfonation and defluorination enzymes.…”

Section: Resultsmentioning

confidence: 99%

Fate and Transformation of 6:2 Fluorotelomer Sulfonic Acid Affected by Plant, Nutrient, Bioaugmentation, and Soil Microbiome Interactions

Shan

Chu

2022

Environ. Sci. Technol.

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Fluorotelomer sulfonic acid (6:2 FTSA) is a dominant per-and poly-fluoroalkyl substance (PFAS) in aqueous film-forming foam (AFFF)-impacted soil. While its biotransformation mechanisms have been studied, the complex effects from plants, nutrients, and soil microbiome interactions on the fate and removal of 6:2 FTSA are poorly understood. This study systematically investigated the potential of phytoremediation for 6:2 FTSA byArabidopsis thalianacoupled with bioaugmentation ofRhodococcus jostiiRHA1 (designated as RHA1 hereafter) under different nutrient and microbiome conditions. Hyperaccumulation of 6:2 FTSA, defined as tissue/ soil concentration > 10 and high translocation factor > 3, was observed in plants. However, biotransformation of 6:2 FTSA only occurred under sulfur-limited conditions. Spiking RHA1 not only enhanced the biotransformation of 6:2 FTSA in soil but also promoted plant growth. Soil microbiome analysis uncovered Rhodococcus as one of the dominant species in all RHA1-spiked soil. Different nutrients such as sulfur and carbon, bioaugmentation, and amendment of 6:2 FTSA caused significant changes in -microbial community structure. This study revealed the synergistic effects of phytoremediation and bioaugmentation on 6:2 FTSA removal. and highlighted that the fate of 6:2 FTSA was highly influced by the complex interactions of plants, nutrients, and soil microbiome.

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“…These tools use hidden-state prediction (HSP) algorithms, which allow the estimation of metabolic functions based on representative genomic content from a well-described bacterial community. A key problem in using such databases is the relatively low correlation between the relative abundance of their specific functions [ 106 ] and the high population variability, limiting these tools in applications with defined cohorts.…”

Section: Focus On Bacterial Communitiesmentioning

confidence: 99%

Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

Purushothaman

Meola

Egli

2022

IJMS

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Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.

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Beyond taxonomy: Validating functional inference approaches in the context of fish‐farm impact assessments

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 14 publications

References 91 publications

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Fate and Transformation of 6:2 Fluorotelomer Sulfonic Acid Affected by Plant, Nutrient, Bioaugmentation, and Soil Microbiome Interactions

Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

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