Natural Attenuation in Streambed Sediment Receiving Chlorinated

Mar 22, 2017 - Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks. Burcu Şimşir†‡∥⊥,...
0 downloads 0 Views 2MB Size
Subscriber access provided by UB + Fachbibliothek Chemie | (FU-Bibliothekssystem)

Article

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks Burcu Simsir, Jun Yan, Jeongdae Im, Duane Graves, and Frank E Löffler Environ. Sci. Technol., Just Accepted Manuscript • DOI: 10.1021/acs.est.6b05554 • Publication Date (Web): 22 Mar 2017 Downloaded from http://pubs.acs.org on March 29, 2017

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

Environmental Science & Technology is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 37

Environmental Science & Technology

TOC graphic 60x47mm (300 x 300 DPI)

ACS Paragon Plus Environment

Environmental Science & Technology

1

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from

2

Underlying Fracture Networks

Page 2 of 37

3 4

Burcu Şimşir1,2,3,4, Jun Yan2,3,4,5,6, Jeongdae Im7, Duane Graves8 and

5

Frank E. Löffler1,2,3,4,6*

6 7

1

8

TN 37996; 2Center for Environmental Biotechnology, University of Tennessee, Knoxville,

9

TN 37996, USA; 3Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN

Department of Civil and Environmental Engineering, University of Tennessee, Knoxville,

10

37831; 4Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory,

11

Oak Ridge, TN 37831; 5Key Laboratory of Pollution Ecology and Environmental

12

Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang,

13

Liaoning 110016, P.R.China; 6Department of Microbiology, University of Tennessee,

14

Knoxville, TN 37996; 7Department of Microbiology, University of Massachusetts,

15

Amherst, MA 01002; 8Geosyntec Consultants, Knoxville, TN 37919.

16 17

*

18

University of Tennessee

19

Department of Microbiology

20

M409 Walters Life Science Bldg.

21

Knoxville, TN 37996

22

Phone: (865) 974-4933

23

Fax:

24

E-mail: [email protected]

Corresponding author

(865) 974-4007

1 ACS Paragon Plus Environment

Page 3 of 37

25

Environmental Science & Technology

Abstract

26

Contaminant discharge from fractured bedrock formations remains a remediation

27

challenge. We applied an integrated approach to assess the natural attenuation potential of

28

sediment that forms the transition zone between upwelling groundwater from a chlorinated

29

solvent-contaminated fractured bedrock aquifer and the receiving surface water. In situ

30

measurements demonstrated that reductive dechlorination in the sediment attenuated

31

chlorinated compounds before reaching the water column. Microcosms established with

32

creek sediment or in situ incubated Bio-Sep beads degraded C1-C3 chlorinated solvents to

33

less chlorinated or innocuous products. Quantitative PCR and 16S rRNA gene amplicon

34

sequencing revealed the abundance and spatial distribution of known dechlorinator

35

biomarker genes within the creek sediment, and demonstrated that multiple dechlorinator

36

populations degrading chlorinated C1-C3 alkanes and alkenes coinhabit the sediment.

37

Phylogenetic classification of bacterial and archaeal sequences indicated a relatively

38

uniform distribution over spatial (300 meters horizontally) scale, but Dehalococcoides and

39

Dehalobacter were more abundant in deeper sediment, where 5.7 ± 0.4 × 105 and 5.4 ± 0.9

40

× 106 16S rRNA gene copies per gram of sediment, respectively, were measured. The

41

microbiological and hydrogeological characterization demonstrated that microbial

42

processes at the fractured bedrock-sediment interface were crucial for preventing

43

contaminants reaching the water column, emphasizing the relevance of this critical zone

44

environment for contaminant attenuation.

45 46

Key-words: Chlorinated solvents, natural attenuation, reductive dechlorination,

47

organohalide respiration, Dehalococcoides, Dehalobacter, fractured rock contaminant

48

discharge, critical zone 2 ACS Paragon Plus Environment

Environmental Science & Technology

49

Introduction

50

Chlorinated solvents have been widely used in a variety of industrial, military, and

51

household applications since the 1940s.1, 2 Their extensive use, improper handling and

52

disposal practices as well as accidental spills resulted in widespread subsurface and

53

groundwater contamination.1, 3 Common chlorinated solvents including tetrachloroethene

54

(PCE), trichloroethene (TCE), carbon tetrachloride (CT), and 1,1,1-trichloroethane

55

(TCA)3 tend to form dense non-aqueous phase liquids (DNAPLs), which move

56

gravitationally along interconnected fractures and form pools in low points in fractured

57

bedrock formations. A significant mass of chlorinated solvents in the fractured rock site

58

diffuse into low-permeability zones,4-6 and back diffusion into water-bearing fractures

59

serves as long-term source of groundwater contamination.5, 7, 8

60

Page 4 of 37

In the last two decades, various in situ remediation technologies, including

61

bioremediation, thermal and chemical treatments have been successfully applied to treat

62

chlorinated solvent contamination in porous medium aquifers;3, 9 however, the remediation

63

of fractured bedrock formations remains challenging due to difficulties in characterizing

64

complicated fracture networks, back diffusion of contaminant from low-permeability

65

zones, and the challenge of targeted delivery of remedial fluids.2, 4, 10-12 An alternate

66

remedial approach focuses on treatment at the fractured bedrock-sediment interface, where

67

contaminated groundwater discharges to surface waters. Recent studies have shown that

68

such hyporheic zones are “hotspots” of microbial activities playing relevant roles for

69

contaminant attenuation.13-16

70

Organohalide-respiring bacteria (OHRB) use chlorinated hydrocarbons as terminal

71

electron acceptors, and a number of species belonging to different genera (e.g., Geobacter,

72

Dehalobacter (Dhb), Desulfitobacterium, and Sulfurosprillum) have been demonstrated to 3 ACS Paragon Plus Environment

Page 5 of 37

Environmental Science & Technology

73

couple reductive dechlorination of PCE to TCE or cis-1,2-dichloroethene (cis-DCE) with

74

energy conservation.9 In contrast, complete reductive dechlorination to environmentally

75

benign ethene appears to be restricted to some strains of the species Dehalococcoides

76

mccartyi (Dhc).9 Dhb are involved in dechlorination of a range of chlorinated compounds

77

including chlorinated aromatics,17 chlorinated ethanes,18 chlorinated methanes,19, 20 as well

78

as PCE.21 Dehalogenimonas spp. have been implicated in dehalogenation of chlorinated

79

alkanes,22 and recently in reductive dechlorination of trans-1,2-dichloroethene (trans-

80

DCE) to VC.23 Studies demonstrated significant correlations between the abundance of

81

OHRB and observed in situ dehalogenation activities.9 Therefore, 16S rRNA genes and

82

reductive dehalogenase (RDase) genes from known OHRB serve as biomarkers to assess

83

in situ bioremediation activity and potential.9, 24

84

At a former metal manufacturing facility located adjacent to Third Creek, a

85

Tennessee River tributary in Knoxville, TN (Figure 1), chlorinated solvents, primarily

86

PCE, TCE, TCA, and CT were released and penetrated the underlying fractured bedrock

87

formation. Although no DNAPL source zones could be identified, dissolved phase

88

concentrations of total chlorinated volatile organic compounds (cVOCs) exceeded 10 mg

89

L-1 in bedrock monitoring wells indicative of free-phase chlorinated solvents (Table S1).

90

Spent solvents are the primary source of groundwater contamination and, as such, the

91

solvents would be co-contaminated with the oils and grease from the cleaning operation.

92

Additionally, machining and lubricating oils and mineral spirits were used throughout the

93

history of the facility but in much smaller quantities than the chlorinated solvents. These

94

limited, and often localized, sources of hydrocarbons were not quantified during site

95

assessments but are thought to have supported the modest and incomplete microbial

96

transformation of contaminants observed in the fractured bedrock (Table S1), indicating 4 ACS Paragon Plus Environment

Environmental Science & Technology

97

the need for alternative remedies at the Third Creek site. This study evaluated the role of

98

the streambed sediment as a natural barrier preventing contaminant discharge into Third

99

Creek surface water. Integrated efforts characterizing the hydrogeological (e.g., flow

100

paths) and microbiological site conditions at the Third Creek site demonstrated efficient

101

natural attenuation in the sediment.

Page 6 of 37

102 103

Material and Methods

104

Chemicals. Chlorinated compounds were of >99% purity. PCE and CT were purchased

105

from ACROS Organics (Morris Plains, NJ), TCE was obtained from Fisher Scientific

106

(Pittsburgh, PA), and cis-DCE, vinyl chloride (VC), ethene, TCA, dichloromethane

107

(DCM), chloroform (CF), chloromethane (CM), 1,2-dichloropropane, 1,1-dichloroethane

108

(DCA), and chloroethane (CA) were obtained from Sigma-Aldrich-Fluka (St. Louis, MO).

109

Site characterization. The manufacturing site is bounded by Third Creek on its west side

110

(Figure 1). The facility used chlorinated solvents as degreasers from the mid-1930s ending

111

in the late 1990s. During the course of manufacturing activities, chlorinated solvents,

112

primarily PCE, TCE, and, to a smaller extent, TCA and CT, were released resulting in

113

contamination of the underlying groundwater-bearing fractured bedrock (Figure S1-2).

114

Direct observation of soil and bedrock cores failed to locate DNAPL although

115

contaminant concentrations as high as 120 mg/L were measured in non-flowing fractures

116

(Figure S3). The presence of cis-DCE, VC, DCA and CF in several bedrock monitoring

117

wells indicated that some contaminant transformation occurred; however, high

118

concentrations of parent compounds and no ethene and ethane formation indicated limited

119

dechlorination capacity within the fracture network (Table S1). Groundwater seepage rates

120

were measured with leak-tested seepage meters.25 Horizontal and vertical bedrock 5 ACS Paragon Plus Environment

Page 7 of 37

Environmental Science & Technology

121

groundwater flow direction was evaluated using seasonal groundwater elevations from

122

monitoring wells screened at multiple depths and staff gauges in the creek. The SI

123

provides additional details about the site characterization efforts.

124

Sediment pore water diffusion sampling. To measure concentrations of cVOCs,

125

methane, ethene, and ethane, as well as geochemical parameters, sediment pore water

126

diffusion samples were collected with depth-discrete diffusion samplers loaded with 40-

127

mL glass vials.26 Before placement of the samplers into the sediment, the 40-mL glass

128

vials were filled with deionized water and covered with either polyethylene film for cVOC

129

sampling, or a porous, nonwoven fabric for measurement of geochemical parameters. The

130

samplers were installed in the same locations as the seepage meters 0-0.55 m (0-1.8 ft)

131

below the sediment surface, and left in the creek for 2 weeks to achieve equilibrium with

132

the pore water. After recovery of the samplers, the vials were immediately sealed and

133

shipped to analytical laboratories (SiREM, Guelph, Canada and Microbac, Maryville, TN)

134

for volatile fatty acids (VFAs), cVOC and anions measurements.

135

Sediment collection. Grab sediment samples and cores were collected from locations #1,

136

#2 and #3 (Figure 1). These locations were chosen based on the observed sediment cVOC

137

concentrations and the site’s hydrogeological characteristics. Top layer sediment samples

138

were collected using autoclaved, sealable glass containers (Mason jars). Deeper sediment

139

layers were obtained using direct push tools (AMS, Inc., American Falls, ID). The plastic

140

liners and caps were wiped with 70% ethanol before use. All other materials (spatulas,

141

containers, etc.) were autoclaved and aseptic techniques were applied to the extent feasible.

142

All core samples were immediately transferred to sterile Mason jars, filled completely

143

with creek water to exclude air, capped and placed in a cooler with ice packs.

6 ACS Paragon Plus Environment

Environmental Science & Technology

Page 8 of 37

144

Depth-resolved sediment collection. Depth-discrete diffusion samplers were employed to

145

collect sediment at multiple depths at Location #3. The diffusion sampler was loaded with

146

40-mL glass vials evenly spaced over a length of 99 cm (3.2 ft). The vial openings were

147

covered with plastic mosquito netting (1-mm mesh size) held in place with rubber bands.

148

The loaded sampler was pushed into the sediment to a depth of about 55 cm (1.8 ft). A

149

second sampler loaded with customized Bio-Trap samplers (about 200 Bio-Sep beads per

150

sampler, Microbial Insights, www.microbe.com) was placed in the sediment in the same

151

location. After a 1-month incubation period, the samplers were removed and the glass

152

vials with sediment material were immediately closed with sterile Teflon-lined rubber

153

septa. The vials and the Bio-Sep bead cartridges were placed individually in Ziploc bags,

154

immediately transferred to a cooler with ice and transported to the laboratory for

155

microcosm setup and DNA extraction.

156

Sample handling. Grab samples and sediment core samples from the same locations were

157

combined and mixed inside an anoxic glove box filled with H2/N2 (3/97%, vol/vol).

158

Approximately 100 g of sediment material from each of the three sampling locations was

159

transferred to sterile plastic tubes and stored at -80°C. The remaining sediment materials

160

were kept at 4°C and microcosms were established within 1 week of sample collection.

161

Sediment materials collected in the 40-mL glass vials from eight different depths were

162

individually transferred to sterile plastic tubes, homogenized and stored at -80°C for

163

molecular analyses. The Bio-Trap samplers collected from eight depths were opened

164

inside the glove box and about 200 Bio-Sep beads per depth sample were transferred to a

165

sterile plastic tube for DNA extraction and microcosm experiments. All procedures used

166

strictly aseptic techniques. To prevent cross contamination, sediment samples from

167

different locations were not handled simultaneously. 7 ACS Paragon Plus Environment

Page 9 of 37

Environmental Science & Technology

168

Microcosm setup. For sediment microcosm setup inside the anoxic glove box,

169

approximately 4 g (wet weight) of the sediment from locations #1, #2, or #3 were

170

transferred to sterile 60-mL glass serum bottles. Twenty-six mL of anoxic, bicarbonate-

171

buffered mineral salts medium27 amended with 5 mM lactate was added to each bottle

172

before the vessels were sealed with autoclaved butyl rubber stoppers (Geo-Microbial

173

Technologies, Inc., Ochelata, OK, USA). Neat PCE, TCE, cis-DCE, VC, TCA, DCA, 1,2-

174

dichloropropane, CT, CF, DCM, and CM were added to triplicate microcosms with 5 or

175

10 µL Hamilton glass syringes (Hamilton 85925 and 80370) to achieve initial aqueous

176

phase concentrations of approximately 0.2 mM (12.5-33.1 mg/L). One microcosm for

177

each treatment was autoclaved for 60 min at 121°C. An additional set of live control

178

microcosms received all amendments except the cVOC additions.

179

To obtain depth-resolved information about microbial reductive dechlorination

180

activity, additional microcosms were established with in situ incubated Bio-Sep beads

181

collected at Location #3. Inside the glove box, five beads were transferred to sterile 60-mL

182

glass serum bottles containing 30 mL of reduced mineral salts medium amended with 5

183

mM lactate. The bottles were closed with butyl rubber stoppers and PCE, TCE, cis-DCE,

184

VC, or TCA were added to reach aqueous phase concentrations of approximately 0.2 mM.

185

Initially, cVOCs could not be measured due to sorption to the Bio-Sep beads but

186

quantitative analysis was possible in transfer cultures. After a 2-month incubation period,

187

3% (vol/vol) culture suspension without beads was transferred to fresh medium amended

188

with 5 mM lactate and 0.2 mM of the respective cVOC. Enrichment cultures that showed

189

no reductive dechlorination received 6 mL of H2 to ensure that electron donor availability

190

was not a limitation. All microcosms and enrichment cultures were incubated statically at

191

room temperature in the dark and monitored over a 20-month incubation period. 8 ACS Paragon Plus Environment

Environmental Science & Technology

Page 10 of 37

192

DNA isolation, qPCR, and 16S rRNA gene amplicon sequencing. To assess the spatial

193

distribution of known dechlorinators in relation to the three different sampling locations

194

and sediment depth at Location #3, PCR, quantitative PCR (qPCR), and 16S rRNA gene

195

fragment amplicon sequencing were performed. DNA was extracted from 0.25 g of wet

196

sediment using the MoBio PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA). DNA

197

extraction from Bio-Sep beads (~160 beads/depth) was performed by Microbial Insights

198

using established procedures.28 Published primer sets and PCR conditions were used to

199

amplify total bacterial,29 Dhc,30 Dhb,31 Dehalogenimonas22 and Geobacter lovleyi strain

200

SZ32 16S rRNA genes and dcpA encoding a 1,2-dichloropropane-to-propene RDase.33 For

201

increased sensitivity of detection, a nested PCR approach was applied 34 (see SI for

202

details). qPCR to enumerate total bacterial, Dhc and Dhb 16S rRNA genes, as well as the

203

bvcA, vcrA, tceA, and cfrA RDase genes used published primers and probes and followed

204

established protocols (Table S2).

205

To compare the microbial communities at locations #1, #2 and #3, amplification of

206

the hypervariable V1-V3 and V3-V5 regions of the 16S rRNA gene and subsequent

207

pyrosequencing of the PCR amplicons was performed with barcoded-primers35-38 (Table

208

S2). Library preparation was performed as described38 with minor modifications (SI), and

209

pyrosequencing was performed on a 454 FLX Life Sciences Genome Sequencer (Roche

210

Diagnostics) according to manufacturer’s instructions. Sequence data analyses followed

211

established procedures (see SI).

212

Analytical Methods. cVOCs, ethene, ethane, propene and methane were monitored using

213

an Agilent 7890 gas chromatograph (GC) equipped with a flame ionization detector and a

214

DB-624 capillary column (60 m by 0.32 mm with a film thickness of 1.18 µm) as

9 ACS Paragon Plus Environment

Page 11 of 37

Environmental Science & Technology

215

described39. Details of the method for cVOCs measurements by SIREM Laboratory, are

216

given in SI.

217 218

Results.

219

Third Creek site hydrological features. Available hydrogeological data sets from 46

220

sampling locations on both sides of Third Creek consistently indicated that groundwater

221

has an upward gradient, a vertical gradient, and horizontal gradients sloping toward the

222

creek from both sides. The groundwater seepage meters placed in creek sediment

223

confirmed, as predicted by vertical (Figure 1) and horizontal gradients (not shown), that

224

the creek received groundwater with maximum, mean and median seepage rates of 3,380,

225

721 and 205 mL/m2 day, respectively, at Location #3. The broad range of measured

226

seepage rates were likely influenced by the creek stage, sampling location, and

227

groundwater elevation. The lowest mean and median seepage rates of 47 and 5.4 mL/m2

228

day, respectively, were measured near Location #1, and occasionally negative values (i.e.,

229

losing water) were observed. Assuming the highest rate of seepage (3,380 mL/m2day), a

230

sediment depth of 0.52 meters, a sediment porosity of 20 percent, and no retardation of

231

cVOC migration in the sediments, the shortest retention time for groundwater seeping

232

through the sediment into the creek was calculated to be approximately 30 days.

233

The seepage measurements and vertical and horizontal groundwater gradients

234

suggest that Third Creek receives groundwater from underlying fractures downstream of

235

Location #1 (Figure 1). The elevation data suggest that the creek transitions from a losing

236

to a gaining creek along the perimeter of the contaminated area near Location #1 (see SI

237

for details). Based on the average creek widths of 7.3 meters between locations #1 and #2

238

and 10.4 meters between locations #2 and #3, segment lengths of 226.5 meters between 10 ACS Paragon Plus Environment

Environmental Science & Technology

Page 12 of 37

239

locations #1 and #2 and 77.1 meters between locations #2 and #3, the yearly volume of

240

groundwater seeping into Third Creek between locations #1 and #3 was estimated at

241

42,000 to 170,000 L/year using median and mean seepage rates, respectively.

242

Third Creek site geochemical characteristics. At Location #3, sediment pore water

243

measurements detected cis-DCE, VC, ethene, ethane and methane in the deep sediment,

244

whereas significantly lower cVOC concentrations were measured near the sediment-

245

surface water interface. Concentrations varied with depth (Figure 2) and maximum ethene,

246

ethane and methane concentrations of 0.25, 0.08 and 5.2 mg/L, respectively, were

247

measured near the sediment-surface water interface. This observation suggests the

248

formation of ethene and ethane as reductive dechlorination products with their further

249

degradation occurring in shallower sediment layers. Using Location #3 ethene, ethane, and

250

cVOC data, the change in ethene and ethane concentration from 0.52 meters to 0.22

251

meters depth accounts for approximately 92 percent of the loss in cVOCs on a mole basis.

252

cVOC concentrations were lower near the sediment-surface water interface and the cis-

253

DCE and VC concentrations were less than the method quantification limit of < 0.01 mg/L.

254

Maximum cis-DCE and VC concentrations of 0.78 mg/L and 0.33 mg/L, respectively,

255

were observed in the deeper sediment at Location #3. The lack of cVOC detections at the

256

sediment/surface water interface could be the result of dilution with the creek water;

257

however, the upward flow of water into the creek, the lack of cVOC detections below the

258

sediment/water interface, and the presence of methane in the shallow sediment indicate

259

that the influence of surface water on pore water cVOC concentrations is inconsequential.

260

With the exception of cis-DCE (0.03 mg/L) in the deep sediment at Location #1, no

261

cVOCs were detected in sediment pore waters collected at locations #1 and #2 (Table S3).

262

TCE concentrations were generally below 0.01 mg/L in the deep sediment, but TCE was 11 ACS Paragon Plus Environment

Page 13 of 37

Environmental Science & Technology

263

occasionally detected near the sediment-surface water interface (Figure 2, Table S3). In

264

addition, concentration gradients of VFAs, sulfate, and chloride were observed in the

265

sediment pore water at Location #3. VFA concentrations of 374 mg/L in the deep

266

sediment pore water decreased to 4 mg/L in pore water collected near the sediment-

267

surface water interface, and sulfate concentrations increased from