Tracking functional bacterial biomarkers in response to a gradient of contaminant exposure within a river continuum

Reid, Thomas; Droppo, Ian G.; Weisener, Christopher G.

doi:10.1016/j.watres.2019.115167

Cited by 21 publications

(10 citation statements)

References 26 publications

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“…The broader field of aquatic environmental science is clearly facing the paradigm shift toward post-genomic approaches, already revealing the potential to contribute to regulatory and policy decisions. These datasets have the not over-promized ability to improved sensitivity of biomarker selection (Pomfret et al, 2019), aid in earlier and more precise detection and modeling of ecosystem perturbations (Reid et al, 2020;Hipsey et al, 2020), and improved risk assessment frameworks that includes functional characteristics of microbial behavior (Cocolin et al, 2018). This type of data also stands to revolutionize the time and expense-consuming (and oftenneglected) pursuit of microbial cultivation that is required for experimental and ecological validation of gene annotations and activities.…”

Section: Discussionmentioning

confidence: 99%

“…), are beginning to be augmented and even replaced by "postgenomic" techniques, and for good reason (Beale et al, 2017). For instance, metatranscriptomics, which directly measures the gene expression of entire microbial communities, has provided novel insights into actual microbial activity and functionality in various aquatic environments (Lamendella et al, 2014;Falk et al, 2019;Bergsveinson et al, 2020;Reid et al, 2020). While this type of data presents us with an understanding of differential gene expression and "shifts" in activities undertaken by a community at a given time, further enhancement of these studies with metabolomics-the characterization of the low-weight molecular compounds, substrates, and enzymatic by-products within a sample matrix-that cumulatively allow for potential linkages between organism(s) genetic transcription, metabolic output, and the metabolite signature of a given environment.…”

Section: Introductionmentioning

confidence: 99%

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How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Reid

Bergsveinson

2021

Front. Mol. Biosci.

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Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Reid

Bergsveinson

2021

Front. Mol. Biosci.

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“…However the review by Poursat et al (2019) showed that adaptation can be induced under certain laboratory conditions, even with persistent or inherently biodegradable compounds. Among all techniques used to trigger adaptation events, pre-exposure of microorganisms present in the soil of croplands to STP effluent before cultivating crops seems to be the best candidate to optimize the biotransformation in SSI (Poursat et al 2019;Reid et al 2020;Wang et al 2020).…”

Section: Enhanced Biotransformationmentioning

confidence: 99%

Natural Purification Through Soils: Risks and Opportunities of Sewage Effluent Reuse in Sub-surface Irrigation

Narain-Ford

Bartholomeus

Dekker

et al. 2020

Reviews of Environmental Contamination and Toxicology

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At global level there are several guidelines, i.e., non-mandatory recommendations, available concerning water reuse (Table 1). In 2006 the World Health Organization (WHO) published guidelines on the safe use of wastewater, intended as a tool for decision-makers and regulators to provide a consistent level of health protection in different settings. The guidelines can be adapted for implementation under specific environmental, sociocultural, and economic conditions at a national level (WHO 2006). The United States Environmental Protection Agency issued the last version of the "Guidelines for Water Reuse" (USEPA 2012). These guidelines include a wide range of reuse applications (e.g., agricultural irrigation and aquifer recharge) and apply similar approaches as described by the WHO (2006) and the Australian Government Initiative (2006) for controlling health and environmental risks. The most recent global guidelines for STP effluent reuse in agricultural irrigation were published in 2015 by the International Organization for Standardization (ISO 2015). These ISO guidelines include water quality requirements for CoECs. Remarkably, the State of California overtakes these global guidelines with specific regulations for CoECs (California Water Boards 2019). Consequently, these California water reuse regulations are being used as a global benchmark for the development of water reuse regulations worldwide. Noteworthy, California recently signed the Senate Bill No. 996 (Legislative Counsel Bureau 2018), which encourages communities to reuse STP effluent on-site. 2.2 Europe At European level the need to address management of water resources to prevent scarcity and droughts was acknowledged in the EU's Blueprint to safeguard Europe's water resources (Table 1). In this Blueprint the need to use STP effluent as an alternative water resource for irrigation purposes is re-emphasized (European Commission 2012). Six EU Member States

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“…There are a variety of niches of riverine ecosystems that may harbour specific microbial communities, including: planktonic, sediment, flocs, biofilms, as well as those associated with suspended sediments or the suspended load (sediment particles maintained in suspension). The taxonomic profile of riverine bacterioplanktonic communities (Portillo et al 2012;Staley et al 2013Staley et al , 2014 and sediment bacterial communities (Drury et al 2013;Reid et al 2019Reid et al , 2020 have been previously examined. The influence of a variety of physical and chemical factors on these communities (Portillo et al 2013;Fortunato et al 2012) including pollution gradients and land use (Staley et al 2014) has also been assessed.…”

Section: Introductionmentioning

confidence: 99%

“…This is of utility for riverine systems impacted by anthropogenic activities. For instance, a few studies have applied genomic approaches to assess the bed and suspended sediments in Athabasca River tributaries (Reid et al 2020;Yergeau et al 2012), demonstrating that there were changes in the microbial processes of bed and suspended sediments associated with increasing polycyclic aromatic compound concentrations resulting from Oil Sands mining activities (Reid et al 2020). The utility of exploring the diversity of different microbial niches within and between sample sites as a reliable indicator of anthropogenic effects is unclear, given the potential stability and response to environmental parameters of each niche community.…”

Section: Introductionmentioning

confidence: 99%

Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River

et al. 2021

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Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilm, suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the level of phyla, different niche communities were highly similar to one another and across locations. However, there were significant differences in the abundance of specific genera amongst different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though “suspended load” communities collected by any means remained stably diverse across locations. Though there was influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.

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Tracking functional bacterial biomarkers in response to a gradient of contaminant exposure within a river continuum

Cited by 21 publications

References 26 publications

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Natural Purification Through Soils: Risks and Opportunities of Sewage Effluent Reuse in Sub-surface Irrigation

Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River

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