Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment

Abstract

During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels impact upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically-diverse microbial community played in this transition. In particular, aerobes dominated in the first day followed by an increase of facultative anaerobes/denitrifiers at day four. Towards the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.ImportanceThe role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility.Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solidiron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically-diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.

Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences

“…Additional metadata is provided as derived from MGnify or the original studies. The column 'Reference' indicates the source study, corresponding to references (Simon et al, 20162009;Eiler et al, 20162014;Nielsen et al, 20172014;Staley et al, 20182014;Brown et al, 2015;Hugerth et al, 2015;Sunagawa et al, 2015;Yan et al, 2015;Bendall et al, 2016;Meziti et al, 2016;Seitz et al, 2016;Toyama et al, 2016;Tsementzi et al, 2016;Vázquez-Campos et al, 2017;Linz et al, 2018), or 'Unpublished' corresponding to data publicly available in the SRA/ENA databases but not currently linked to publications. Table S5: Correlation tests performed between genomospecies features and ecologic breadth metrics.…”

“…In addition to the metagenomes sequenced as part of our study, we used previously reported metagenomes from other sites and environments for comparisons. These metagenomes, derived from previous studies (Simon et al, 2009;Eiler et al, 2014;Nielsen et al, 2014;Staley et al, 2014;Brown et al, 2015;Hugerth et al, 2015;Sunagawa et al, 2015;Yan et al, 2015;Bendall et al, 2016;Meziti et al, 2016;Seitz et al, 2016;Toyama et al, 2016;Tsementzi et al, 2016;Vázquez-Campos et al, 2017;Linz et al, 2018), or recovered via MGnify (Mitchell et al, 2016), are described in Table S4. The raw reads were obtained from the European Nucleotide Archive (EBI ENA) and processed as described above.…”

Comparison of Microbiomes and Resistomes in Two Karst Groundwater Sites in Chongqing, China

“…Next Generation Sequencing‐based metagenomics and metatranscriptomics have revolutionized the methodologies to decipher the diversity of microorganisms, community characteristics, and metabolic activity in different environments (Tringe et al ; Ventosa et al ) by obviating the need for the isolation and culture of microorganisms (Handelsman et al ; Chen and Pachter ). Both metagenome and metatranscriptome contribute significantly to appreciate the microbial processes and community functionalities in biogeochemistry, including groundwater (Einsiedl and Mayer ; Long et al ; Coutinho et al ; Vazquez‐Campos et al ). In comparison with DNA microarrays or qPCR, high throughput metagenome and metatranscriptome profiling can also capture more comprehensive picture of resistome in the groundwater (Luo and Angelidaki ; Li et al ).…”

Genomic insights into the Archaea inhabiting an Australian radioactive legacy site

“…Since its closure, the periodic occurrence of intense rainfall events leads to the filling of the former trenches with surface waters, which, depending on preceding conditions, can result in the trench water discharging into the surface and near-surface soils in a ‘bath-tub’-like mechanism (Payne et al, 2013, 2020). Aside from providing a mechanism enabling the export of contaminants from the legacy trenches (Payne et al, 2013), the periodic influx of oxic waters into these natural reducing zones results in transitory microbial population shifts associated with pronounced elemental cycling (Vázquez-Campos et al, 2017; Kinsela et al, 2021). Our previous research showed that the archaeal community in the LFLS waste trenches, while constituting a minor portion of the whole microbial community, included a number of potentially interesting members, either in terms of phylogeny and/or functionality (Vázquez-Campos et al, 2017).…”