Community dynamics and functional characteristics of naphthalene‐degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater

Abstract

Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.

A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures

“…As the novelty of our method lies in the recovery of proteins from the phenol phase, typically discarded in the protocol of Griffiths et al (), we further demonstrate that our biomolecule co‐extraction is suitable for metaproteomics analysis of other soil types with varying clay contents. Indeed, the DNA and RNA co‐extraction protocol from Griffiths et al () has been cited to date by over 1,250 papers including many reporting on downstream high‐throughput sequencing, including 16SrRNA and ITS amplicon analysis (Haas et al, ; Morawe et al, ; Sayer et al, ; Whitman et al, ), metagenomics (Malik, Thomson, Whiteley, Bailey, & Griffiths, ; Soares et al, ; Wilhelm, Hanson, Chandra, & Madsen, ) and metatranscriptomics (Alessi et al, ; de Menezes, Clipson, & Doyle, ; Hesse et al, ). Here, 16S rRNA profiling from DNA and cDNA was performed on three samples corresponding to three biological replicates from one soil type (with a clay content of 11.1%) while metaproteomics was conducted for nine samples corresponding to three biological replicates from three soil types (with clay content of 11.1%, 19.4% and 35.1%).…”

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

“…Currently, the genetic basis of the catabolic pathways of the various PAHs remains poorly understood. Thus, the use of recent approaches as meta-taxonomics and metagenomics offers great potential to contribute with information to elucidate PAH degradation pathways ( Brennerova et al, 2009 ; Nyyssönen et al, 2009 ; Abbai and Pillay, 2013 ; Uhlik et al, 2013 ; Mason et al, 2014 ; Xu et al, 2014 ; El Amrani et al, 2015 ; Loviso et al, 2015 ; Ma B. et al, 2015 ; Techtmann and Hazen, 2016 ; Zafra et al, 2016 ; Duarte et al, 2017 ; Muangchinda et al, 2018 ; Tiralerdpanich et al, 2018 ; Wilhelm et al, 2018 ; Xu et al, 2018 ; Hidalgo et al, 2019 ). From now on, we will present the information available from several studies carried out to explore PAH biodegradation in natural or impacted environments rich in hydrocarbons.…”

“…A long-term coal-tar contaminated groundwater called “Site 24” located in the state of New York, is one of the best characterized fields in terms of PAH contamination and has served as a model for natural attenuation during almost three decades ( Madsen et al, 1991 ; Bakermans et al, 2002 ; Yagi et al, 2010 ). Wilhelm et al (2018) executed a study in “Site 24” to evaluate the natural attenuation process in the affected area. They used a polyphasic approach based on SIP with 13C-napthalene, 16S rRNA gene and shotgun metagenomic sequencing to identify genes and taxa specialized in the naphthalene degradation under oxic (DO < 2.0 mgL –1 ) and hypoxic/suboxic conditions (DO < 0.2 mgL –1 ).…”

“…Genes for sulfate and iron reduction were not found in any MAG. Two ring-cleaving dioxygenases (2,3-dihydroxybiphenyl 1,2 dioxygenase and 3-hydrixyanthranilate 3,4-dioxygenase) were present in some MAGs ( Wilhelm et al, 2018 ). The study contributed to gain information about undescribed taxa and metabolic potential associated to the natural attenuation process in the polluted subsurface environment ( Wilhelm et al, 2018 ).…”

“…There are many complete or almost complete sequenced genomes of cultured microorganisms which have functional potential metabolism for hydrocarbon degradation ( Ghosal et al, 2016 ). Nevertheless, scientists have long known that only about 1% of the total microbial communities has been cultivated ( Hugenholtz and Pace, 1996 ; Hugenholtz et al, 1998 ) and advances in the use of -omics techniques, like genomics, proteomics and metabolomics, in bioremediation studies have helped to improve the understanding of biodegradation processes ( Brennerova et al, 2009 ; Nyyssönen et al, 2009 ; Abbai and Pillay, 2013 ; Uhlik et al, 2013 ; Mason et al, 2014 ; Xu et al, 2014 , 2018 ; El Amrani et al, 2015 ; Loviso et al, 2015 ; Ma B. et al, 2015 ; Techtmann and Hazen, 2016 ; Zafra et al, 2016 ; Duarte et al, 2017 ; Muangchinda et al, 2018 ; Tiralerdpanich et al, 2018 ; Wilhelm et al, 2018 ; Hidalgo et al, 2019 ). Sequencing metagenomes from diverse contaminated environments (soils, aquifers, seawater) can help to providing insights into the ecology of the dominant and rare members and their functional potential for transformation of pollutant molecules such as PAHs and other hydrocarbons ( Blow, 2008 ; Ghosal et al, 2016 ).…”