Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing

Heyde, Mieke van der; Bunce, Michael; Dixon, Kingsley W.; Wardell‐Johnson, Grant; White, Nicole E.; Nevill, Paul

doi:10.1016/j.scitotenv.2020.142262

Cited by 41 publications

(32 citation statements)

References 69 publications

(103 reference statements)

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“…DNA metabarcoding further allows assessing soil microbial biodiversity (also in terms of phylogenetic relatedness), and to compare soil communities subjected to experimental conditions or geographical distance. It is also a cost-effective method for biomonitoring as DNA metabarcoding is more frequently used for monitoring agricultural practices, restoration efforts or forensics [9][10][11][12]. Presently, it represents the most used molecular approach to characterize microbiota in environmental samples.…”

Section: Introductionmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

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Section: Introductionmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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“…While many different approaches have been proposed to evaluate "soil health" to inform restoration (Hart et al 2020), including in a mining context (Kumaresan et al 2017;van der Heyde et al 2020), a key test of soil quality for restoration purposes is the ability to support plant growth. Longterm monitoring of restored vegetation is necessary for evaluating the ability of soils to support selfsustaining plant communities, and monitoring data from one site can inform future restoration projects.…”

Section: Introductionmentioning

confidence: 99%

Stockpiling disrupts the biological integrity of topsoil for ecological restoration

et al. 2021

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Purpose Biotic and abiotic properties of soils can hinder or facilitate ecological restoration, and management practices that impact edaphic factors can strongly influence plant growth and restoration outcomes. Salvaged topsoil is an invaluable resource for mine-site restoration, and a common practice is topsoil transfer from mined areas to restoration sites. However, direct transfer is often not feasible, necessitating storage in stockpiles. We evaluated the effects of topsoil stockpiling on plant performance across diverse ecosystems impacted by mining throughout Western Australia. Methods We conducted a bioassay experiment using a widespread native Acacia species to assess how topsoil storage might impact plant growth, physiology, and nodulation by N-fixing bacteria using soils from native reference vegetation and stockpiled soils from six mine sites across Western Australia. Results Plant responses varied across mine sites, but overall plants performed better in soils collected from native vegetation, exhibiting greater biomass, more root nodules, and higher water-use efficiency compared to those grown in stockpiled soils. Soil physiochemistry showed few and minor differences between native soils and stockpiles. Conclusion Results strongly suggest observed differences in plant performance were biotic in nature. This study highlights the negative effects of topsoil storage on the biological integrity of soil across diverse ecosystems, with important implications for mine-site restoration; our results show that topsoil management can strongly influence plant performance, and stockpiled soils are likely inferior to recently disturbed topsoil for restoration purposes. We also use this study to illustrate the utility of bioassays for assessing soil quality for ecological restoration.

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“…Investigations of these systems are breaking boundaries between disciplines (i.e., biogeochemistry, genetics, hydrology) but yet public awareness of their key role to humankind is lacking and this deficiency needs to be addressed [4]. DNA metabarcoding is widely employed as an ecological tool in many contexts and ecosystems (i.e., groundwater [5,6], marine [7,8], terrestrial [9,10] and freshwater [11,12]), and it is gaining prominence as an effective, robust and reliable biomonitoring technique [13].…”

Section: Introductionmentioning

confidence: 99%

Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia)

Saccò

White

Campbell

et al. 2021

Water

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Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.

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Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing

Cited by 41 publications

References 69 publications

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

Stockpiling disrupts the biological integrity of topsoil for ecological restoration

Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia)

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