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Article ; Online: Data on the characterization of phthalate-degrading bacteria from Asian carp microbiomes and riverine sediments

Steven A. Kolb / Edward J. O'Loughlin / Timothy C. Gsell

Data in Brief, Vol 25, Iss , Pp - (2019)

2019

Abstract: Datasets presented here were employed in the main work “Characterization of phthalate-degrading-bacteria from Asian carp microbiomes and riverine sediments” (Kolb et al., 2019a). The carcinogenic compounds dimethyl phthalate (DMP), diethyl phthalate (DEP) ...

Abstract	Datasets presented here were employed in the main work “Characterization of phthalate-degrading-bacteria from Asian carp microbiomes and riverine sediments” (Kolb et al., 2019a). The carcinogenic compounds dimethyl phthalate (DMP), diethyl phthalate (DEP), and dibutyl phthalate (DBP) are ubiquitous in the environment due to widespread production and distribution which can be taken up by aquatic organisms. Asian carp species silver (Hypophthalmichthys molitrix) and bighead (Hypophthalmichthys nobilis) are exposed to phthalates by ingestion and absorption. This article presents data on the characterization of phthalate-degrading bacteria isolated from Asian carp microbiomes and riverine sediments by means of sample collection, enrichment, and isolation. Graphical data presents substrate utilization profiles of consortium SK-1 and Rhodococcus ruber derived from the gut microbiome of H. molitrix. Additionally, phthalate-degrading microbes were isolated from the gut and scale microbiomes of Asian carp where scanning electron microscopy images show the morphology from samples of final enrichment cultures and isolates. Consortium SK-1 was subjected to amplicon sequencing where community data shows the distribution of taxa while enriched with 500 mg L−1 DMP, DEP, and DBP combined. The data presented can provide insights to future research since other phthalate-degrading isolates and consortia can potentially be isolated from the microbiomes of aquatic organisms. Keywords: Biodegradation, Phthalates, Asian carp, Microbiomes, Bacteria, Isolation
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	550
Language	English
Publishing date	2019-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: U(VI) Reduction by Biogenic and Abiotic Hydroxycarbonate Green Rusts: Impacts on U(IV) Speciation and Stability Over Time

Yan, Sen / Bhoopesh Mishra / Edward J. O’Loughlin / Kenneth M. Kemner / Maxim I. Boyanov

Environmental science & technology. 2018 Apr. 09, v. 52, no. 8

2018

Abstract: Green rusts (GRs) are redox active FeII–FeIII minerals that form in the environment via various biotic and abiotic processes. Although both biogenic (BioGR) and abiotic (ChemGR) GRs have been shown to reduce UVI, the dynamics of the transformations and ... ...

Abstract	Green rusts (GRs) are redox active FeII–FeIII minerals that form in the environment via various biotic and abiotic processes. Although both biogenic (BioGR) and abiotic (ChemGR) GRs have been shown to reduce UVI, the dynamics of the transformations and the speciation and stability of the resulting UIV phases are poorly understood. We used carbonate extraction and XAFS spectroscopy to investigate the products of UVI reduction by BioGR and ChemGR. The results show that both GRs can rapidly remove UVI from synthetic groundwater via reduction to UIV. The initial products in the ChemGR system are solids-associated UIV–carbonate complexes that gradually transform to nanocrystalline uraninite over time, leading to a decrease in the proportion of carbonate-extractable U from ∼95% to ∼10%. In contrast, solid-phase UIV atoms in the BioGR system remain relatively extractable, nonuraninite UIV species over the same reaction period. The presence of calcium and carbonate in groundwater significantly increase the extractability of UIV in the BioGR system. These data provide new insights into the transformations of U under anoxic conditions in groundwater that contains calcium and carbonate, and have major implications for predicting uranium stability within redox dynamic environments and designing approaches for the remediation of uranium-contaminated groundwater.
Keywords	anaerobic conditions ; calcium ; groundwater ; minerals ; nanocrystals ; prediction ; remediation ; spectroscopy ; uranium
Language	English
Dates of publication	2018-0409
Size	p. 4601-4609.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5851
DOI	10.1021/acs.est.7b06405
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment.

Theodore M Flynn / Dionysios A Antonopoulos / Kelly A Skinner / Jennifer M Brulc / Eric Johnston / Maxim I Boyanov / Man Jae Kwon / Kenneth M Kemner / Edward J O'Loughlin

PLoS ONE, Vol 16, Iss 5, p e

2021 Volume 0251883

Abstract: Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. ...

Abstract	Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of FeIII reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory FeIII-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly "sulfate-reducing" phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Reduction of Sb(V) by coupled biotic-abiotic processes under sulfidogenic conditions

Clayton R. Johnson / Dionysios A. Antonopoulos / Maxim I. Boyanov / Theodore M. Flynn / Jason C. Koval / Kenneth M. Kemner / Edward J. O'Loughlin

Heliyon, Vol 7, Iss 2, Pp e06275- (2021)

2021

Abstract: Increasing use and mining of antimony (Sb) has resulted in greater concern involving its fate and transport in the environment. Antimony(V) and (III) are the two most environmentally relevant oxidation states, but little is known about the redox ... ...

Abstract	Increasing use and mining of antimony (Sb) has resulted in greater concern involving its fate and transport in the environment. Antimony(V) and (III) are the two most environmentally relevant oxidation states, but little is known about the redox transitions between the two in natural systems. To better understand the behavior of antimony in anoxic environments, the redox transformations of Sb(V) were studied in biotic and abiotic reactors. The biotic reactors contained Sb(V) (2 mM as KSb(OH)6), ferrihydrite (50 mM Fe(III)), sulfate (10 mM), and lactate (10 mM), that were inoculated with sediment from a wetland. In the abiotic reactors, The interaction of Sb(V) with green rust, magnetite, siderite, vivianite or mackinawite was examined under abiotic conditions. Changes in the concentrations of Sb, Fe(II), sulfate, and lactate, as well as the microbial community composition were monitored over time. Lactate was rapidly fermented to acetate and propionate in the bioreactors, with the latter serving as the primary electron donor for dissimilatory sulfate reduction (DSR). The reduction of ferrihydrite was primarily abiotic, being driven by biogenic sulfide. Sb and Fe K-edge X-ray absorption near edge structure (XANES) analysis showed reduction of Sb(V) to Sb(III) within 4 weeks, concurrent with DSR and the formation of FeS. Sb K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy analysis indicated that the reduced phase was a mixture of S- and O-coordinated Sb(III). Reduction of Sb(V) was not observed in the presence of magnetite, siderite, or green rust, and limited reduction occurred with vivianite. However, reduction of Sb(V) to amorphous Sb(III) sulfide occurred with mackinawite. These results are consistent with abiotic reduction of Sb(V) by biogenic sulfide and reveal a substantial influence of Fe oxides on the speciation of Sb(III), which illustrates the tight coupling of Sb speciation with the biogeochemical cycling of S and Fe.
Keywords	Antimony ; Biogeochemistry ; Dissimilatory sulfate reduction ; Microbial reduction ; Iron sulfide ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	500
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Application of an in-situ soil sampler for assessing subsurface biogeochemical dynamics in a diesel-contaminated coastal site during soil flushing operations

Kwon, Man Jae / Baknoon Ham / Edward J. O'Loughlin / Moojoon Shim / Soonjae Lee / Yunho Hwang

Elsevier Ltd Journal of environmental management. 2018 Jan. 15, v. 206

2018

Abstract: Subsurface biogeochemistry and contaminant dynamics during the remediation of diesel-contamination by in-situ soil flushing were investigated at a site located in a coastal region. An in-situ sampler containing diesel-contaminated soils separated into ... ...

Abstract	Subsurface biogeochemistry and contaminant dynamics during the remediation of diesel-contamination by in-situ soil flushing were investigated at a site located in a coastal region. An in-situ sampler containing diesel-contaminated soils separated into two size fractions (<0.063- and <2-mm) was utilized in two monitoring wells: DH1 (located close to the injection and extraction wells for in-situ soil flushing) and DH2 (located beyond sheet piles placed to block the transport of leaked diesel). Total petroleum hydrocarbon (TPH) concentrations and biogeochemical properties were monitored both in soil and groundwater for six months. A shift occurred in the groundwater type from Ca-HCO3 to Na-Cl due to seawater intrusion during intense pumping, while the concentrations of Ni, Cu, Co, V, Cr, and Se increased substantially following surfactant (TWEEN 80) injection. The in-situ sampler with fine particles was more sensitive to variations in conditions during the remedial soil flushing process. In both wells, soil TPH concentrations in the <0.063-mm fraction were much higher than those in the <2-mm fraction. Increases in soil TPH in DH1 were consistent with the expected outcomes following well pumping and surfactant injection used to enhance TPH extraction. However, the number of diesel-degrading microorganisms decreased after surfactant injection. 16S-rRNA gene-based analysis also showed that the community composition and diversity depended on both particle size and diesel contamination. The multidisciplinary approach to the contaminated site assessments showed that soil flushing with surfactant enhanced diesel extraction, but negatively impacted in-situ diesel biodegradation as well as groundwater quality. The results also suggest that the in-situ sampler can be an effective monitoring tool for subsurface biogeochemistry as well as contaminant dynamics.
Keywords	biodegradation ; chromium ; coasts ; cobalt ; community structure ; copper ; groundwater ; microorganisms ; monitoring ; nickel ; particle size ; petroleum ; polluted soils ; polysorbates ; remediation ; saltwater intrusion ; soil flushing ; surfactants ; vanadium ; water quality ; wells
Language	English
Dates of publication	2018-0115
Size	p. 938-948.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	184882-3
ISSN	1095-8630 ; 0301-4797
ISSN (online)	1095-8630
ISSN	0301-4797
DOI	10.1016/j.jenvman.2017.11.053
Database	NAL-Catalogue (AGRICOLA)

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Article: Seasonal microbial variation accounts for arsenic dynamics in shallow alluvial aquifer systems

Zheng, Tianliang / Edward J. O’Loughlin / Hongchen Jiang / Teng Ma / Theodore M. Flynn / Yamin Deng / Yanxin Wang / Yiqun Gan

Journal of hazardous materials. 2019 Apr. 05, v. 367

2019

Abstract: Determining the temporal variation of microbial communities in groundwater systems is essential to improve our understanding of hydrochemical dynamics in aquifers, particularly as it relates to the fate of redox-sensitive contaminants like arsenic (As). ... ...

Abstract	Determining the temporal variation of microbial communities in groundwater systems is essential to improve our understanding of hydrochemical dynamics in aquifers, particularly as it relates to the fate of redox-sensitive contaminants like arsenic (As). Therefore, a high-resolution hydrobiogeochemical investigation was conducted in the As-affected alluvial aquifer systems of the Jianghan Plain. In two 25 m-deep monitoring wells, the seasonal variation in the composition of groundwater microbial communities was positively correlated with the change in groundwater level (R = 0.47 and 0.39 in NH03B and NH05B, respectively, P < 0.01), implying that the latter could be a primary driver of the seasonal microbial dynamics. In response to the fluctuating groundwater level, iron (Fe) reducers within the Desulfuromonadales were dominant (9.9 ± 4.7% among different sampling sites) in groundwater microbial communities during the monsoon season and associated with high concentrations of Fe(II) and As, while the predominance (16.7 ± 15.2% among different sampling sites) of iron-oxidizers the Gallionellaceae was accompanied by low Fe(II) and As in the non-monsoon season. These results suggest that microbially-mediated iron reduction/oxidation may have governed the seasonal mobilization/scavenging of As in groundwater. Our results provide new insights into mechanisms responsible for seasonal variations in groundwater As concentrations in similar aquifer systems.
Keywords	alluvial aquifer ; arsenic ; Gallionellaceae ; groundwater ; iron ; microbial communities ; monitoring ; monsoon season ; oxidation ; seasonal variation ; water table ; wells
Language	English
Dates of publication	2019-0405
Size	p. 109-119.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2018.12.087
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

Man Jae Kwon / Edward J O'Loughlin / Maxim I Boyanov / Jennifer M Brulc / Eric R Johnston / Kenneth M Kemner / Dionysios A Antonopoulos

PLoS ONE, Vol 11, Iss 1, p e

2016 Volume 0146689

Abstract: Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing ... ...

Abstract	Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Coastal inundation regime moderates the short-term effects of sediment and soil additions on seawater oxygen and greenhouse gas dynamics

Peter Regier / Nicholas D. Ward / Alex Izquierdo / Andrew H. Baldwin / Donnie Day / Julia McElhinny / Kaizad Patel / Rodrigo Vargas / Jianqiu Zheng / Exchange Consortium / Allison Myers-Pigg / Silver Alford / Michael P. Back / Vanessa Bailey / Jade Bolinger / Madison Bowe / Maxim I. Boyanov / Jacob A. Cianci-Gaskill / Nathan A. Conroy /

Matthew J. Cooper / Alex Demeo / Kyle Derby / Derek Detweiler / Suzanne Devres-Zimmerman / Erin Eberhard / Keryn Gedan / LeeAnn Haaf / Khadijah K. Homolka / Erin Johnson / Kenneth M. Kemner / Aliya Khan / Matthew Kirwan / Payton Kittaka / Erika Koontz / Adam Langley / Riley Leff / Scott Lerberg / Allison M. Lewis / Sairah Malkin / Amy M. Marcarelli / Steven E. McMurray / Tyler Messerschmidt / Taylor C. Michael / Holly A. Michael / Elizabeth C. Minor / Brian Moye / Thomas J. Mozdzer / Allison N. Myers-Pigg / Neubauer Scott / Cooper G. Norris / Edward J. O'Loughlin / Opal Otenburg / Andrea Pain / Kaizad F. Patel / Stephanie C. Pennington / Michael Philben / Evan Phillips / Dannielle Pratt / J. Alan Roebuck Jr. / Lauren Sage / Daniel Sandborn / Stacy Smith / Alex Smith / Samina Soin-Voshell / Bongkeun Song / Amanda Sprague-Getsy / Kari St Laurent / Lorie Staver / Alice Stearns / Lucie Stetten / Rebecca Swerida / Ethan J. Theuerkauf / Katherine Tully / Elizabeth Watson / Coreen Weilminster

Frontiers in Marine Science, Vol

a microcosm experiment

2023 Volume 10

Abstract: The frequency and persistence of tidal inundation varies along the coastal terrestrial-aquatic interface, from frequently inundated wetlands to rarely inundated upland forests. This inundation gradient controls soil and sediment biogeochemistry and ... ...

Abstract	The frequency and persistence of tidal inundation varies along the coastal terrestrial-aquatic interface, from frequently inundated wetlands to rarely inundated upland forests. This inundation gradient controls soil and sediment biogeochemistry and influence the exchange of soils and sediments from terrestrial to aquatic domains. Although a rich literature exist on studies of the influence of tidal waters on the biogeochemistry of coastal ecosystem soils, few studies have experimentally addressed the reverse question: How do soils (or sediments) from different coastal ecosystems influence the biogeochemistry of the tidal waters that inundate them? To better understand initial responses of coastal waters that flood coastal wetlands and uplands, we conducted short-term laboratory experiments where seawater was amended with sediments and soils collected across regional gradients of inundation exposure (i.e., frequently to rarely inundated) for 14 sites across the Mid-Atlantic, USA. Measured changes in dissolved oxygen and greenhouse gas concentrations were used to calculate gas consumption or production rates occurring during seawater exposure to terrestrial materials. We also measured soil and water physical and chemical properties to explore potential drivers. We observed higher oxygen consumption rates for seawater incubated with soils/sediments from frequently inundated locations and higher carbon dioxide production for seawater incubated with soils from rarely inundated transect locations. Incubations with soil from rarely inundated sites produced the highest global warming potential, primarily driven by carbon dioxide and secondarily by nitrous oxide. We also found environmental drivers of gas rates varied notably between transect locations. Our findings indicate that seawater responses to soil and sediment inputs across coastal terrestrial-aquatic interfaces exhibit some consistent patterns and high intra- and inter-site variability, suggesting potential biogeochemical feedback loops as inundation regimes ...
Keywords	greenhouse gases ; dissolved oxygen ; aquatic carbon cycle ; terrestrial-aquatic interface ; coastal inundation ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	550
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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