Analysis of viral and bacterial communities in groundwater associated with contaminated land

Costeira, Ricardo; Doherty, Rory; Allen, Christopher C. R.; Larkin, Michael J.; Kulakov, Leonid

doi:10.1016/j.scitotenv.2018.11.429

Cited by 20 publications

(12 citation statements)

References 104 publications

(104 reference statements)

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“…For instance, the "piggy-back-the-winner" model was born from observations that showed lysogeny is more prevalent at higher host cell densities [115,116]. In this study, the prevalence of lysogenic phages may also be due to the composition of the host taxa, as the dominant bacterial phyla of the pond, Actinobacteria, and Proteobacteria, have been previously reported in some environments to be ideal hosts for temperate phages [117].…”

Section: Discussionmentioning

confidence: 69%

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Chopyk

Nasko

Allard

et al. 2020

Environmental Microbiome

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Background Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

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Section: Discussionmentioning

confidence: 69%

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Chopyk

Nasko

Allard

et al. 2020

Environmental Microbiome

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“…Phage associated genes have been found to be more abundant in oil-contaminated seawater compared with uncontaminated water (Lu, Deng et al 2012). A recent study showed that phages that infect known degraders can be highly abundant in hydrocarbon polluted water (Costeira, Doherty et al 2019). Taxonomic analysis of the viral contigs at the species level showed abundance of the uncultured Mediterranean phage uvMED, abundant in the marine environment (Mizuno, Rodriguez-Valera et al 2013, Garin-Fernandez, Pereira-Flores et al 2018.…”

Section: Dominant Functions Reflect the "Tank Effect"mentioning

confidence: 99%

Discovery of functional gene markers of bacteria for monitoring hydrocarbon pollution in the marine environment - a metatranscriptomics approach

Knapik

Bagi

Królicka

et al. 2019

Preprint

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The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, day 4 and day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ringdegrading enzymes (e.g. ben, box, and dmp clusters) were observed on day 4 in both control and oil tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus, were significantly enriched in the oil-treated tank in comparison to control, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.

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“…Collectively, these studies revealed a large diversity of viruses specific to and/or mostly identified in freshwater ecosystems, mostly phages with double-stranded DNA (dsDNA) genomes, but also including eukaryotic viruses and phages with single-stranded DNA (ssDNA) and RNA genomes ( 16 – 18 ). Comparatively, viral diversity in groundwater systems has been much less studied, but recent metagenomic studies suggested that groundwater viral communities were clearly distinct from other freshwater environments, that their diversity and structure reflected changes in environmental parameters, including especially pH level and the presence of contaminants, and that viruses may significantly influence groundwater microbe dynamics ( 19 , 20 ). The Oak Ridge Field Research Center (ORFRC) ( 21 – 23 ) is a well-studied U.S. Department of Energy site that includes groundwater areas with and without metal contamination, referred to as the contaminated and background sites, respectively.…”

Section: Introductionmentioning

confidence: 99%

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

et al. 2021

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To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications.

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Analysis of viral and bacterial communities in groundwater associated with contaminated land

Cited by 20 publications

References 104 publications

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Discovery of functional gene markers of bacteria for monitoring hydrocarbon pollution in the marine environment - a metatranscriptomics approach

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

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