Molecular and Kinetic Characterization of ... - ACS Publications

Jan 26, 2017 - and Kartik Chandran*,†. †. Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York,...
0 downloads 0 Views 1MB Size
Subscriber access provided by Fudan University

Article

Molecular and kinetic characterization of planktonic Nitrospira spp. selectively enriched from activated sludge Mee-Rye Park, Hongkeun Park, and Kartik Chandran Environ. Sci. Technol., Just Accepted Manuscript • DOI: 10.1021/acs.est.6b05184 • Publication Date (Web): 26 Jan 2017 Downloaded from http://pubs.acs.org on January 30, 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 32

1

Environmental Science & Technology

Title :

2

Molecular and kinetic characterization of planktonic Nitrospira spp. selectively enriched

3

from activated sludge

4 5 6

Authors : Mee-Rye Park1, Hongkeun Park1 and Kartik Chandran1,*

7 8 9 10

Affilation : 1

Department of Earth and Environmental Engineering, Columbia University, 500 West

120th Street, New York, New York 10027, USA.

11 12

Correspondent footnote :

13

Kartik Chandran, Department of Earth and Environmental Engineering, Columbia

14

University, 500 West 120th Street, New York, New York 10027. Phone : (212) 854 9027,

15

email : [email protected]

16 17 18

* To whom all correspondence should be addressed.

19

ACS Paragon Plus Environment

Environmental Science & Technology

20

Abstract

21

Nitrospira spp. are chemolithoautotrophic nitrite oxidizing bacteria (NOB), which are ubiquitous

22

in natural and engineered environments. However, there exist few independent biokinetic studies

23

on Nitrospira spp., likely because their isolation and selective enrichment from environmental

24

consortia such as activated sludge can be challenging. Herein, planktonic Nitrospira spp. cultures

25

closely related to Candidatus Nitrospira defluvii (Nitrospira lineage I) were successfully

26

enriched from activated sludge in a sequencing batch reactor by maintaining sustained limiting

27

extant nitrite and dissolved oxygen concentrations. Morphologically, the enrichment consisted

28

largely of planktonic cells with an average characteristic diameter of 1.3 ± 0.6 µm. Based on

29

respirometric assays, estimated maximum specific growth rate (µmax), nitrite half saturation

30

coefficient (KS), oxygen half saturation coefficient (KO) and biomass yield coefficient (Y) of the

31

enriched cultures were 0.69 ± 0.10 d-1, 0.52 ± 0.14 mg-N/L, 0.33 ± 0.14 mg-O2/L and 0.14 ±

32

0.02 mg-COD/mg-N, respectively. These parameters collectively reflect not just higher affinities

33

of this enrichment for nitrite and oxygen, respectively, but also a higher biomass yield and

34

energy transfer efficiency relative to Nitrobacter spp. Used in combination, these kinetic and

35

thermodynamic parameters can help towards the development and application of energy efficient

36

biological nutrient removal processes through effective Nitrospira out-selection.

37

Keywords: nitrite oxidizing bacteria; Nitrospira spp.; planktonic; kinetics; half saturation

38

coefficient; maximum specific growth rate; out-selection; anammox

39

ACS Paragon Plus Environment

Page 2 of 32

Page 3 of 32

Environmental Science & Technology

40

1. Introduction

41

Nitrite-oxidizing bacteria (NOB) play an important role in natural and engineered nitrogen

42

cycling systems including conventional biological nutrient removal (BNR) processes. In recent

43

years, alternatives to conventional BNR processes such as anaerobic ammonium oxidation

44

(anammox) and nitritation-denitritation have been more widely applied owing to the energy and

45

chemical savings that they offer

46

oxidation of ammonium partially to nitrite by ammonia-oxidizing bacteria (AOB), in parallel

47

with

48

chemoorganoheterotrophic nitrogen removal.

49

Among the different NOB found in wastewater treatment systems, Nitrospira spp. and

50

Nitrobacter spp. represent the most dominant NOB in terms of diversity and populations

51

Recently discovered Nitrotoga have been also regarded as important NOB in full-scale

52

wastewater treatment systems

53

detect only NOB. However, Nitrotoga were competitive with Nitrospira and Nitrobacter during

54

long-term cultivation at 5 and 10 °C, respectively 6, 9.

55

Specifically, those related to Nitrospira spp. are relatively more abundant in mainstream

56

processes (treating sewage streams) than the more conventionally studied NOB related to

57

Nitrobacter spp. and Nitrotoga proliferating at low temperature. Therefore, energy efficient

58

process alternatives to conventional mainstream BNR need to accomplish out-selection of

59

Nitrospira spp. rather than other NOB. Commonly used limiting factors (e.g. free ammonia and

60

free nitrous acid) applied for NOB out-selection10, 11 in sidestream reactors may not be relevant

61

to selectively suppress Nitrospira spp. in mainstream reactors because of the low extant free

62

ammonia concentrations therein as well as possibly distinct biokinetic characteristics and

NOB

out-selection,

1, 2

. Energy efficiency of these processes is engendered by the

followed

5-8

directly

by

either

chemolithoautotrophic

or

3, 4

.

, where they often coexist with Nitrospira but occasionally

ACS Paragon Plus Environment

Environmental Science & Technology

Page 4 of 32

63

sensitivities of Nitrospira spp. compared to Nitrobacter spp. Given such challenges, in

64

mainstream systems, the strategies for NOB out-selection and stable nitritation have necessitated

65

a combination of several factors such as intermittent aeration, and controlled COD input, coupled

66

with solids retention time (SRT) control

67

Accordingly, fundamental studies of Nitrospira spp. physiology and kinetics are essential to

68

inform NOB out-selection under mainstream wastewater treatment conditions. However, such

69

studies are exceedingly rare owing to the frequent proliferation of Nitrobacter spp. in engineered

70

NOB reactors or enrichments. Some previous laboratory studies have attempted to overcome

71

such challenges by enriching Nitrospira spp. through serial dilution with additional selective

72

pressure of amendment with antibiotics 14. However, such approaches are not entirely applicable

73

to engineered wastewater treatment processes either from a kinetic or physiological perspective.

74

Nitrospira spp. have been reported to be sensitive to the concentrations of their substrates, nitrite

75

and oxygen. The growth of Nitrospira spp. was inhibited at high nitrite concentrations (above 80

76

mg-N/L in bulk liquid), where Nitrobacter spp. were selected

77

and low dissolved oxygen (DO) below 0.5 mg-O2/L favored the competition of Nitrospira spp.

78

over Nitrobacter spp. 16

79

Here, we hypothesized that Nitrospira spp. can be enriched from a mixed environmental

80

microbial consortium such as activated sludge through long-term continuous reactor operation

81

under limiting extant nitrite and DO concentrations. If successful, such an enrichment would

82

provide more representative knowledge on the eco-physiology, metabolism and kinetics under

83

conditions similar to that in activated sludge processes. Accordingly, the objectives of this study

84

were to (1) selectively enrich Nitrospira spp. from activated sludge in a continuously operated

85

sequencing batch reactor (SBR) (2) characterize the microbial ecology of the SBR during the

2, 12, 13

.

1, 4, 15

ACS Paragon Plus Environment

. Both long SRT (40 days)

Page 5 of 32

Environmental Science & Technology

86

course of enrichment and (3) determine key kinetic parameters including the maximum specific

87

growth rate (µmax), oxygen half saturation coefficient (KO), nitrite half saturation coefficient (KS)

88

and thermodynamic parameters including the biomass yield coefficient (Y) and energy transfer

89

efficiency (ε), describing the Nitrospira spp. enrichment.

90 91

2. Materials and Methods

92

2.1. Reactor setup and operation

93

Planktonic Nitrospira spp. cultures were cultivated in a lab-scale SBR with a working volume of

94

6 L, hydraulic retention time (HRT) of 0.5 d and a target SRT of 15 d. The SBR was seeded with

95

activated sludge from the Blue Plains advanced wastewater treatment plant (Washington, D.C.)

96

and was operated at four 6 h cycles per day, each comprising 5 h continuous feed and react, 0.75

97

h settle, and 0.25 h decant phases. The SBR phases were automatically controlled via a digital

98

controller (Chrontrol Corp., San Diego, CA). SRT was controlled by manually withdrawing

99

biomass from the SBR at the end of the feed and react phase. The influent concentration of nitrite,

100

which served as the sole energy source during the period of operation, was increased

101

successively through four phases in the following sequence: 40 ± 1.20 mg-N/L (phase 1, days 0

102

to 23), 100 ± 1.73 mg-N/L (phase 2, days 24 to 57), 160 ± 2.38 mg-N/L (phase 3, days 58 to 99),

103

and finally 200 ± 1.81 mg-N/L (phase 4, days 100 to 222). The SBR was operated with cyclic

104

aeration (2 min air-on and 3 min off) to maintain extant reactor DO concentrations between 0.5 -

105

1 mg-O2/L during the feed and react phases by facilitating oxygen diffusion into the liquid by

106

gentle mixing with a magnetic stirrer. DO was monitored in real-time using online respirometry

107

using Clark-type electrodes (YSI 5331, Yellow Springs, OH), interfaced to an online DO meter

108

(YSI 5300A, Yellow Springs, OH) and to a personal computer. The SBR was operated at room

ACS Paragon Plus Environment

Environmental Science & Technology

Page 6 of 32

109

temperature (22 ± 1 °C). The feed medium contained the following constituents per liter of tap

110

water: 0.005 g (NH4)2SO4; 0.2 - 1 g NaNO2; 0.007 g CaCO3; 0.5 g NaCl; 0.05 g MgCl2 · 6H2O;

111

0.15 g KH2PO4; 33.8 µg MnSO4 · H2O; 49.4 µg H3BO3; 43.1 µg ZnSO4 · 7H2O; 37.1 µg (NH4)6

112

Mo7O24·4H2O; 25.0 µg CuSO4·5H2O; 973.0 µg FeSO4· 7H2O

113

controlled at 7.5 ± 0.1 with 1M NaHCO3. Reactor samples were collected right before the settle

114

phase of the SBR. 15 ml samples from the reactor and influent medium tank were collected in

115

duplicates and centrifuged at 8,000 x g for 10 min. The concentrations of nitrite (diazotization

116

colorimetry) and nitrate (ion selective electrode, Fisher, Waltham, MA) in the supernatant were

117

used to monitor the SBR performance. Ion Chromatography (Thermo Scientific Dionex ICS-

118

2100., Sunnyvale, CA) was also used to measure nitrite and nitrate concentrations during

119

intensive 6 h profiles obtained during individual SBR cycles. Total reactor biomass and effluent

120

biomass concentrations were approximated using total chemical oxygen demand (tCOD)

121

measurements (Hach Chemical Co., Loveland, CO) owing to the absence of organic carbon in

122

the SBR feed.

123

2.2. DNA extraction and quantification

124

DNA was extracted from biomass samples using a DNeasy Blood & Tissue kit (Qiagen, Inc.,

125

Germantown, MD). The concentrations of Nitrospira spp., Nitrobacter spp., and AOB were

126

quantified in triplicate via SYBR green chemistry quantitative polymerase chain reaction (qPCR),

127

specifically targeting Nitrospira and Nitrobacter 16S rRNA genes, and ammonia

128

monooxygenase subunit A (amoA) gene, respectively. Total bacterial concentrations were also

129

quantified using eubacterial 16S rRNA gene targeted primers (Table 1). Standard curves for

130

qPCR were generated via serial decimal dilutions of plasmid DNA containing specific target

ACS Paragon Plus Environment

17

. The pH was automatically

Page 7 of 32

Environmental Science & Technology

131

gene inserts. The absence of primer-dimer was confirmed via melt curve analysis on every qPCR

132

assay conducted (data not shown).

133 134

2.3. Next generation sequencing of amplicon library and sequence analysis

135

DNA extracts were purified using QIAquick DNA Cleanup kit with QIAcube (Qiagen, CA). The

136

quality and quantity of DNA were checked using NanoDrop Lite Spectrophotometer

137

(Thermofisher, MA). Barcoded fusion primers with sequencing adaptors and 1055F/1392R

138

universal primer set were applied in each sample for multiplex sequencing. Prior to template

139

preparation, library quantification was performed with KAPA Library Quantification kit for Ion

140

Torrent (KAPA biosystems, MA) to avoid polyclonality of Ion Sphere Particles (ISP). Template

141

preparation with DNA library followed by ISP enrichment was performed using the Ion

142

OneTouch2 system following the manufacturer’s instruction (Ion OT2 400 kit, Product No.

143

4479878). The enriched ISP was loaded onto an Ion Torrent 316 chip and run on an Ion Torrent

144

PGM™ according to manufacturer’s instructions (Ion PGM™ Sequencing 400 Kit, Product No.

145

4482002). Ion Torrent Suite software ver. 4.0.2 was used for base calling, signal processing and

146

quality filtering (> Phred score of 15) of the raw sequences. Mothur software was applied for

147

post-run bioinformatic analysis of the amplicon sequences 18. Relative microbial abundance was

148

mapped using heatmap modules in “R” software and phylogenetic affiliation among community

149

members was inferred using the neighbor-joining method on Molecular Evolutionary Genetics

150

Analysis 6.0 (MEGA 6.0) software

151

computational model. Operational taxonomy units (OTUs) were determined using Mothur and

152

reference sequences retrieved from the GeneBank database.

19

with 1000 bootstrap repetitions and Jukes-Cantor

153

ACS Paragon Plus Environment

Environmental Science & Technology

Page 8 of 32

154

2.4. Morphological characterization of enrichment cultures

155

Biomass samples from the SBR were collected and 5 µl aliquots were uniformly spread on a

156

glass microscope slide. Phase contrast microscopy was performed on a Nikon i80 microscope

157

(Nikon Instruments Inc., NY) at 40x * 10x with image acquisition using Nikon camera and

158

SPOT 4.6 Advanced software (Diagnostic Instruments Inc., MI). For obtaining representative

159

size distribution of the enriched cultures, 368 objects (cells or cell aggregates) were sized, as

160

recommended in a previous study

161

(Scion Corporation, MD) to measure a projected two-dimensional cross-sectional area of

162

visualized cells or cell aggregates. The projected area diameter (da), which corresponds to the

163

diameter of an equivalent circle with the projected cross-sectional area (A) of the cells or cell

164

aggregates, was calculated using Eqn. 1 21.

165

da =2ට π

166

where,

167

da: projected area diameter, µm

168

A: projected cross-sectional area, µm2.

169

2.5. Determination of biokinetic parameters

170

Biokinetic parameters describing the Nitrospira spp. enrichment were estimated using extant

171

respirometric assays as previously described

172

washed three times with nitrogen free feed-medium at pH 7.5. Extant respirometric assays were

173

performed in duplicate 100 mL jacketed glass vessels, which were filled with washed biomass

174

and sealed with a Clark-type polarographic DO electrode (YSI Model 5300A, Yellow Springs,

175

OH). Respirometric assays were initiated by injecting 8.7 µL of a 75 g N/L stock of NaNO2 into

176

the respirometric vessels to achieve an initial nitrite concentration of 4 mg-N/L. DO consumption

20

. Images were post-processed on Scion image software

A

(1)

22

. Briefly, biomass withdrawn from the SBR was

ACS Paragon Plus Environment

Page 9 of 32

Environmental Science & Technology

177

in response to NO2--N oxidation was continuously monitored at 1 Hz in LabVIEW (National

178

Instruments, Austin, TX) using custom-built virtual instruments. The maximum specific growth

179

rate (µmax) was obtained based on the maximum oxygen uptake rates measured during a given

180

batch respirometric assay (Eqn. S1, Supplementary Information). The oxygen half saturation

181

coefficient (KO) was estimated from four batch experiments (Table S1, Supplementary

182

Information) under non-limiting nitrite concentrations. Similarly, the nitrite half saturation

183

coefficient (KS) and biomass yield coefficient (Y) were estimated under non-limiting DO

184

concentrations (achieved using air or pure oxygen, Table S1, Supplementary Information).

185

Raw respirograms (DO profiles as a function of time) were transformed using the slope function

186

in MS ExcelTM to yield oxygen uptake rate (OUR) profiles over time. DO and OUR profiles

187

were processed as shown in Figure S1 and S2 and equations S1 - S4 (Supplementary

188

Information).

189

The thermodynamics and growth stoichiometry of the enriched Nitrospira were expressed in

190

terms of the fraction of electrons channeled for biosynthesis (fs) and energy transfer efficiency

191

(ߝ) 23, as shown in equations S5 - S7 (Supplementary Information).

192 193

3. Results and discussion

194

3.1. Reactor performance

195

Over the course of the study, the average maximal degree of nitrite removal at the end of each

196

phase of reactor operation was 99.8 ± 0.2 % (n = 4), 95.8 ± 2.9 % (n = 5), 93.0 ± 2.1 % (n = 2)

197

and 97.0 ± 3.7 % (n = 8), respectively (Fig. 1). The corresponding conversion of nitrite to nitrate

198

was 95.3 ± 2.2 %, 96.5 ± 10.1 %, 98.8 ± 2.2 % and 97.2 ± 3.9, respectively. Within each

199

operating phase, transient nitrite accumulation was observed in response to step increases in the

ACS Paragon Plus Environment

Environmental Science & Technology

Page 10 of 32

200

influent nitrite concentrations, followed systematically by near complete oxidation of nitrite to

201

nitrate. The purpose of gradual increase of influent nitrite concentrations was to increase the

202

amount of enriched Nitrospira spp. Indeed, as the average biomass concentrations in the reactor

203

gradually increased from 161.3 ± 14.6 mg/L (n = 3), 183.5 ± 7.5 mg/L (n = 3), 308.1 ± 7.4 mg/L

204

(n = 3) to 361.7 ± 37.3 mg/L (n = 8) in each phase, respectively, effluent nitrite concentrations

205

gradually decreased and the reactor achieved ultimate steady state.

206 207

3.2. Microbial community composition during selective enrichment of Nitrospira spp.

208

The initial SBR biomass samples harbored a broad diversity of microorganisms, which included

209

AOB, NOB and heterotrophic bacteria (Fig. 2). Methylotrophic bacteria were also detected

210

likely owing to the use of methanol as an electron and carbon source in the full-scale wastewater

211

plant, from which the SBR was inoculated. Among AOB and NOB, Nitrosomonas spp. and

212

Nitrobacter spp. were initially detected in the SBR biomass (Fig. 2). The concentrations of

213

Nitrospira spp., Nitrobacter spp., and AOB during SBR start-up were 7.0 × 107 ± 1.2 × 106, 3.0

214

× 107 ± 8.4 × 106 and 1.0 × 106 ± 2.6 × 104 gene copies/mL, respectively (Fig. 3). During the

215

course of enrichment, the concentrations of Nitrospira spp. increased to a terminal range of 7.7 ×

216

108 ± 7.5 × 107 gene copies/mL towards the end of phase 4, while the concentrations of

217

Nitrobacter spp. and AOB decreased to 1.7 × 106 ± 1.2 × 105 and 1.0 × 105 ± 1.7 × 104 gene

218

copies/mL, respectively (Fig. 3). The enriched Nitrospira spp. were closely related to Candidatus

219

Nitrospira defluvii (97% 16S rRNA sequence similarity), which is affiliated with Nitrospira

220

lineage I (Fig. 4). Based on qPCR, Nitrospira spp. contributed to 99.6 ± 0.1 % (n = 12) of the

221

total bacteria 16S rRNA gene copy number at the end of phase 4 of enrichment.

ACS Paragon Plus Environment

Page 11 of 32

Environmental Science & Technology

222

A possible explanation of the high enrichment of Nitrospira spp. could be their reported higher

223

affinity for nitrite and DO (KS = 0.1 – 1.1 mg-N/L; KO = 0.5 – 0.6 mg-O2/L) compared to

224

Nitrobacter spp. (KS = 0.3 – 7.6 mg-N/L; KO = 0.2 – 4.3 mg-O2/L) 24-29. Indeed, when the reactor

225

was under ultimate steady-state operation, in-situ SBR cycle profiles showed consistently non-

226

detectable nitrite concentrations (Fig. 5).

227

Previous studies have indeed shown that nitrite concentrations are the primary driver for the

228

competition between Nitrospira spp. and Nitrobacter spp., with higher nitrite concentrations (80

229

– 520 mg-N/L in the bulk liquid) favoring the growth of Nitrobacter spp. over Nitrospira spp.

230

and vice-versa

231

influence possible niche differentiation of Nitrospira strains from different phylogenetic lineages

232

33, 34

233

lineage II

234

concentrations observed each time the influentt nitrite concentrations were stepped up, might

235

have selected for Nitrospira of lineage I rather than lineage II in this study.

236

Beside nitrite concentrations, operational DO concentration was a critical parameter affecting

237

Nitrospira community composition in the nitrifying reactors. The SBR DO concentrations in this

238

study were in the range of 0.5 -1.1 mg-O2/L, which is close to previously reported KO values (0.5

239

– 0.6 mg-O2/L)

240

previously, long-term exposure to low DO concentrations below 0.5 mg-O2/L resulted in an

241

enrichment of Nitrospira spp. over Nitrobacter spp.16 Furthermore, within Nitrospira

242

themselves, limiting DO concentrations favored Nitrospira lineage I over lineage II 35. In other

243

studies, NOB exhibited a lag phase in nitrate production or nitrite consumption after anoxic

244

periods in continuous reactors resulting in transient nitrite accumulation 36, 37.

1, 4, 15, 30-32

. Furthermore, extant nitrite concentrations have been suggested to

. Nitrospira defluvii (lineage I) displayed higher nitrite tolerance compared to the member of 33, 34

. Based on these previous findings, the transiently non-limiting nitrite

25, 29

and thereby suggests some degree of DO limitation as well. As described

ACS Paragon Plus Environment

spp.

Environmental Science & Technology

Page 12 of 32

245

From a general perspective, the resulting ecology and kinetics of engineered biological processes

246

are a function of the operating configuration and influent characteristics. Alternative reactor

247

design and operating strategies could possibly result in different organisms and kinetics.

248

However, such differentiation was not the main focus of this study.

249

In this study, we demonstrate Nitrospira spp. proliferation at the expense of nearly all other

250

bacteria in a solely nitrite-fed SBR subjected to long-term dual DO and nitrite limitation.

251

Although growth of AOB has been shown at sustained limiting to non-detectable ammonia

252

concentrations

253

range 0.33 ± 0.05 % (n = 3), 0.03 ± 0.02 % (n = 3), 0.01 ± 0.01 % (n = 4), and 0.02 ± 0.003 % (n

254

= 4) of the total 16S rRNA gene copies, respectively, during the four phases of enrichment. The

255

possibility of ammonia oxidizing archaea (AOA) proliferation at limiting ammonia

256

concentrations as demonstrated previously 41 was not interrogated in the SBR, given the principal

257

focus on NOB herein. Heterotrophic bacteria (belonging to the genera Weeksella, Schlesneria,

258

Methylovorus and Propionivivibrio) were detected despite the absence of organic carbon in the

259

SBR influent, potentially supported by organic metabolic by-products released by the NOB

260

themselves 42.

261

The results of qPCR and 16S rRNA gene amplicon sequencing are expected to be somewhat

262

different. Our aim was to be completely transparent and thus we included both sets of results.

263

Specifically, the difference of Nitrospira spp abundance calculated using qPCR and 16S rRNA

264

gene amplicon sequencing can be attributed to specificities of primers between Nitrospira 16S

265

rRNA gene and universal 16S rRNA gene. For assay validation, specificities of Nitrospira and

266

total bacteria 16S rRNA primer sets were checked using Test-Prime by running in silico PCR on

267

the SILVA databases 43. The specificities for the Nitrospira and total bacteria suite of primers are

38-40

, relatively negligible fractions of AOB were measured in this study, in the

ACS Paragon Plus Environment

Page 13 of 32

Environmental Science & Technology

268

100% and 56%, respectively, with no mismatches. This means that Nitrospira 16S rRNA gene

269

primer set can cover Nitrospira spp more specifically than universal 16S rRNA gene primer set.

270

Also, qPCR results are expected to be more quantitative because the qPCR data was an absolute

271

quantification based on a standard curve using known concentrations of plasmid.

272

On the other hand, 16S rRNA gene amplicon sequencing is useful for identification and

273

classification of the bacterial community.

274 275

3.3. Morphology of enriched Nitrospira spp cultures.

276

The Nitrospira spp. enrichment was largely comprised of planktonic cells with an overall

277

average characteristic diameter of 1.3 ± 0.6 µm (Fig. 6). Cell aggregates were occasionally

278

observed and were in the size range 3 - 4 µm, significantly lower than those previously reported

279

in activated sludge in the range 73 - 593 µm,

280

nearly devoid of filamentous microorganisms, which contribute symptomatically towards

281

aggregation and floc formation in activated sludge 44, 45.

282

The observed planktonic morphology of the Nitrospira spp. enrichment cultures was distinct

283

than reported in previous studies, where Nitrospira spp., were present in cell aggregates either by

284

themselves or in conjunction with other AOB, NOB and heterotrophic bacteria

285

previously reported that Ca. Nitrospira defluvii secreted increasing degrees of extracellular

286

polymeric substances (EPS) when grown in batch culture with increasing initial nitrite

287

concentrations. The secreted EPS could potentially directly contribute to cell aggregation or

288

support the growth of flocculant heterotrophic biomass

289

Nitrospira defluvii appeared under conditions of long periods of starvation, increasing cell

25, 29

. Furthermore, SBR biomass samples were

34

3, 34, 46, 47

. It was

. In another study, planktonic cells of

ACS Paragon Plus Environment

Environmental Science & Technology

14

Page 14 of 32

290

density and nitrate accumulation

. However, the underlying basis for the planktonic

291

morphology enriched herein remains to be conclusively determined.

292

Nevertheless, the specific reason for the low degree of cellular aggregation in the Nitrospira spp.

293

biomass enriched herein is not exactly clear and needs further mechanistic investigation.

294 295

3.4. Kinetic characterization of planktonic Nitrospira spp.

296

The average µmax of the Nitrospira spp. enrichment was 0.69 ± 0.10 d-1 (Table 2), which

297

corresponded to an average doubling time (td) of 1 d. The estimated KS value of 0.52 ± 0.14 mg-

298

N/L in Nitrospira spp. (lineage I Ca. Nitrospira defluvii) was lower than the KS values of

299

Nitrobacter spp. reported in previous studies

300

hypothesis that Nitrospira in lineage II have higher affinity for nitrite than these organisms in

301

lineage I

302

Nitrospira lineage I (KS = 0.42 mg-N/L), which was lower than that of Nitrospira lineage II (KS

303

= 0.14 mg-N/L)33. Estimated KO values of 0.33 ± 0.04 mg-O2/L in Nitrospira spp. determined in

304

this study were also lower than those reported for Nitrobacter spp.

305

affinities for genus Nitrospira have been studied previously

306

Nitrospira lineage I (Ca. Nitrospira defluvii) was determined for the first time in this study.

307

Our results are in alignment with the widely held notion that Nitrospira spp. are K-strategists

308

possessing relatively higher affinity for nitrite and oxygen. Further, the low propensity for cell

309

aggregation observed in this study likely resulted in lower substrate mass-transfer limitation and

310

correspondingly lower estimates of the nitrite and oxygen affinity coefficients (KS and KO,

311

respectively), relative to previous studies with a higher degree of aggregation. Overall, such

312

theoretical expectations and experimental observations are also consistent with the relative

33, 49

27, 28, 48

. Moreover, previous studies suggested the

. Indeed, the KS value in this study was close to reported nitrite affinity of

7, 25

ACS Paragon Plus Environment

26, 29

While the oxygen

, the KO value of planktonic

Page 15 of 32

Environmental Science & Technology

313

enrichment of Nitrospira spp. in mixed culture biofilms, where they can be exposed to substrate

314

limitation in terms of nitrite, DO and even inorganic carbon 1, 31, 32.

315

From a fundamental perspective, Nitrospira spp. typically encode for periplasmic nitrite

316

oxidoreductase (NXR), which is involved in the oxidation of NO2--N to NO3--N 50. In contrast,

317

Nitrobacter spp. encode for a cytoplasmic NXR 51, 52, which requires the transport of NO2--N and

318

NO3--N in opposite directions across the inner membrane. Periplasmic oxidation of NO2--N by

319

Nitrospira spp. has multiple advantages, including the generation of a higher proton motive force

320

(for subsequent energy transduction) per unit NO2--N oxidized

321

needed trans-membrane NO2--N and NO3--N exchange. Together, these factors could potentially

322

contribute to the higher competitive advantage of Nitrospira spp. over other NOB under a wide

323

variety of nitrite limited environments including conventional engineered BNR processes.

324

Thermodynamics and stoichiometry of growth

325

Estimated values of the biomass yield coefficient (Y) of the Ca. Nitrospira defluvii enrichment

326

were 0.14 ± 0.02 mg biomass COD produced/mg-N oxidized, calculated as described previously

327

53

328

oxidized, using an oxygen-nitrite equivalence of 1.14 mg-O2/mg-N (Table 3) and assuming

329

preferential assimilation of NH3 and CO2 for biosynthesis

330

electron efficiency (ߝ) 23 for the Ca. Nitrospira defluvii enrichment herein was 0.7 (Table 3). The

331

estimated values of Y, fS and ε, were within the range computed based on values reported in

332

literature for Nitrospira spp. enrichments (Table 3). Furthermore, descriptors of the growth

333

stoichiometry (Y and fS) and thermodynamic efficiency (ε) for Nitrospira spp. were uniformly

334

higher than for Nitrobacter spp. (Table 3). These results are notable, given that most previous

335

studies focus on biokinetics while characterizing or comparing different types of NOB. In

50

and the lack of otherwise

. This corresponds to a fS value of 0.12 ± 0.02 mg biomass COD produced/mg NO2--NOD

22, 53

ACS Paragon Plus Environment

. The corresponding computed

Environmental Science & Technology

336

particular, this is the first study to estimate thermodynamic parameters including both biomass

337

yield coefficient and energy transfer efficiency for Nitrospira lineage I. Rather, the higher

338

electron capture efficiency and biomass yields of Nitrospira spp. also likely contribute to their

339

increased competitiveness in nitrite- (or even oxygen-) limited environments. Based on this

340

study, engineered strategies typically associated with shortcut biological nitrogen removal

341

(BNR) processes such as sustained low DO operation appear to be inappropriate to select against

342

Nitrospira spp. Rather, alternatives such as intermittently non-limiting DO concentrations (as

343

engendered by periodic aeration of sequential aerobic-anoxic zones) could be more appropriate.

344

The results of this study actually then provide the underlying basis for NOB out-selection

345

approaches such as the AOB versus NOB (AVN) control technology 2, 54.

Page 16 of 32

346 347

In sum, we report the selective enrichment of planktonic Nitrospira spp. cultures in a continuous

348

reactor process along with corresponding estimates of key biokinetic, stoichiometric and

349

thermodynamic coefficients. In general, our hypotheses regarding selective enrichment of

350

Nitrospira spp. under sustained NO2--N and DO limitation were largely supported by

351

experimental results. As the wastewater industry transitions to more energy efficient BNR

352

alternates that require NOB out-selection or washout, it becomes necessary to develop a rigorous

353

understanding of the eco-physiology, biokinetics, thermodynamics of both the desirable (in casu,

354

aerobic and anaerobic AOB) and undesirable (in casu, NOB) protagonists. Subsequently, this

355

understanding could potentially be used in conjunction with mechanistic models to develop

356

engineered bioprocess strategies to achieve both clean water as well as energy-efficiency

357

objectives.

358

ACS Paragon Plus Environment

Page 17 of 32

Environmental Science & Technology

359

Acknowledgements

360

This study was supported by Water Environment & Reuse Foundation and the Hampton Roads

361

Sanitation District.

362

Supporting Information Available This information is available free of charge via the Internet

363

at http://pubs.acs.org.

364

ACS Paragon Plus Environment

Environmental Science & Technology

365

Page 18 of 32

Table 1. Summary of primers information for qPCR. Target gene

Primer

Nucleotide Sequence (5'-3')

Universal

1055F

ATGGCTGTCGTCAGCT

16S rRNA

1392R

ACGGGCGGTGTGTAC

Nitrospira

NTSPAf

CGCAACCCCTGCTTTCAGT

16S rRNA

NTSPAr

CGTTATCCTGGGCAGTCCTT

Nitrobacter

Nitro-1198f

ACCCCTAGCAAATCTCAAAAAACCG

16S rRNA

Nitro-1423r

CTTCACCCCAGTCGCTGACC

amoA-1F

GGGGTTTCTACTGGTGGT

amoA-2R

CCCCTCKGSAAAGCCTTCTTC

amoA

Reference 55

56

57

366 367 368

ACS Paragon Plus Environment

58

Page 19 of 32

369

Environmental Science & Technology

Table 2. Summary of biokinetic parameters NOB

Nitrospira spp.

µmax

KS

KO

(1/day)

(mg-N/L)

(mg-O2/L)

0.69 ± 0.10

0.52 ± 0.14

0.33 ± 0.04

This studya

0.9 – 1.1

0.54

29a

0.11 – 0.50

0.47

25b

0.45 - 0.52

28c

0.13 – 0.39

59c

0.18

48b

0.3 – 1.7 1.2 – 1.3

Nitrobacter spp.

0.38 – 1.69

29a

0.17 – 4.32

26b

0.39 – 1.28

0.69 – 7.6

28c

0.48

1.49

27a

0.77 370

a

enriched culture

371

b

mixed culture

372

c

pure culture

Reference

373 374

ACS Paragon Plus Environment

60b

Environmental Science & Technology

Page 20 of 32

375

Table 3. Summary of calculated stoichiometric and thermodynamic coefficients describing

376

biomass growth

Culture type

fSb

Y (mg-COD/mg-N)

(mg-COD/mg-

ߝ

Reference

NOD)

enriched Nitrospira

0.14 ± 0.02

0.12 ± 0.02

0.7

This study

cultures

0.12 - 0.2a

0.11 - 0.18

0.64 - 0.86

29

enriched

0.08a

0.07

0.51

24

0.07 – 0.1a

0.06 - 0.09

0.51 - 0.58

27

0.1a

0.62

61

0.1

0.62

62

Nitrobacter cultures NOB in nitrifying enriched cultures NOB

0.12a

377

a

reported values in literature.

378

b

NO2--N has a nitrogenous oxygen demand of 1.14 mg-O2/mg-N.

379 380

ACS Paragon Plus Environment

Page 21 of 32

Environmental Science & Technology

381

382 383

Figure 1. Performance of the enrichment SBR. Error bars represent the standard deviation of

384

duplicate measurements.

385 386 387 388 389 390 391 392

ACS Paragon Plus Environment

Environmental Science & Technology

Page 22 of 32

393 394

Figure 2. Microbial community composition (at the genus level) during the course of enrichment

395

(phase 1, day 0 – 23; phase 2, day 24 – 57; phase 3, day 58 – 99; phase 4, day 100 – 222),

396

describing the the top sixteen most abundant genera.

397 398 399

ACS Paragon Plus Environment

Page 23 of 32

Environmental Science & Technology

400 401

Figure 3. Concentrations of total bacteria, Nitrospira spp., Nitrobacter spp., and AOB in the

402

enrichment SBR. Error bars represent the standard deviation of triplicate measurements.

403 404 405 406 407 408

ACS Paragon Plus Environment

Environmental Science & Technology

409 410

Figure 4.

Phylogenetic affiliation among sequences from fifty high-abundance operational

411

taxonomic units after final enrichment (Day 158 sample) based on next generation sequencing of

412

16S rRNA gene amplicons with references in the genus Nitrospira. The tree was constructed

413

using the neighbor-joining algorithm and nodes supported by bootstrap values are indicated.

414

Scale bar represents 1% sequence divergence.

415

ACS Paragon Plus Environment

Page 24 of 32

Page 25 of 32

Environmental Science & Technology

416 417

Figure 5. Profiles of SBR nitrite, nitrate and DO concentrations during a representative 6 h cycle

418

on day 222. Error bars represent the standard deviation of triplicate measurements.

419

ACS Paragon Plus Environment

Environmental Science & Technology

Page 26 of 32

420 421

Figure 6. Phase contrast microscope image of Nitrospira spp. cells (at 40X * 10X magnification).

422

Samples obtained on day 222 of SBR operation.

423 424

ACS Paragon Plus Environment

Page 27 of 32

Environmental Science & Technology

425

References

426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468

1. Park, H.; Rosenthal, A.; Ramalingam, K.; Fillos, J.; Chandran, K., Linking community profiles, gene expression and N-removal in anammox bioreactors treating municipal anaerobic digestion reject water. Environmental science & technology 2010, 44, (16), 6110-6116. 2. Regmi, P.; Miller, M. W.; Holgate, B.; Bunce, R.; Park, H.; Chandran, K.; Wett, B.; Murthy, S.; Bott, C. B., Control of aeration, aerobic SRT and COD input for mainstream nitritation/denitritation. Water research 2014, 57, 162-171. 3. Daims, H.; Nielsen, J. L.; Nielsen, P. H.; Schleifer, K.-H.; Wagner, M., In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Applied and Environmental Microbiology 2001, 67, (11), 5273-5284. 4. Nogueira, R. a. M., Luis F, Competition between Nitrospira spp. and Nitrobacter spp. in nitrite‐oxidizing bioreactors. Biotechnology and bioengineering 2006, 95, (1), 169-175. 5. Alawi, M.; Lipski, A.; Sanders, T.; Spieck, E., Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic. The ISME journal 2007, 1, (3), 256-264. 6. Alawi, M.; Off, S.; Kaya, M.; Spieck, E., Temperature influences the population structure of nitrite‐oxidizing bacteria in activated sludge. Environmental microbiology reports 2009, 1, (3), 184-190. 7. Saunders, A. M.; Albertsen, M.; Vollertsen, J.; Nielsen, P. H., The activated sludge ecosystem contains a core community of abundant organisms. The ISME journal 2016, 10, (1), 11-20. 8. Lücker, S.; Schwarz, J.; Gruber-Dorninger, C.; Spieck, E.; Wagner, M.; Daims, H., Nitrotoga-like bacteria are previously unrecognized key nitrite oxidizers in full-scale wastewater treatment plants. The ISME journal 2015, 9, (3), 708-720. 9. Karkman, A.; Mattila, K.; Tamminen, M.; Virta, M., Cold temperature decreases bacterial species richness in nitrogen‐removing bioreactors treating inorganic mine waters. Biotechnology and bioengineering 2011, 108, (12), 2876-2883. 10. Wang, Q.; Ye, L.; Jiang, G.; Hu, S.; Yuan, Z., Side-stream sludge treatment using free nitrous acid selectively eliminates nitrite oxidizing bacteria and achieves the nitrite pathway. water research 2014, 55, 245-255. 11. Courtens, E. N.; Spieck, E.; Vilchez-Vargas, R.; Bodé, S.; Boeckx, P.; Schouten, S.; Jauregui, R.; Pieper, D. H.; Vlaeminck, S. E.; Boon, N., A robust nitrifying community in a bioreactor at 50° C opens up the path for thermophilic nitrogen removal. The ISME journal 2016. 12. Yang, Q.; Peng, Y.; Liu, X.; Zeng, W.; Mino, T.; Satoh, H., Nitrogen removal via nitrite from municipal wastewater at low temperatures using real-time control to optimize nitrifying communities. Environmental science & technology 2007, 41, (23), 8159-8164. 13. Ge, S.; Peng, Y.; Qiu, S.; Zhu, A.; Ren, N., Complete nitrogen removal from municipal wastewater via partial nitrification by appropriately alternating anoxic/aerobic conditions in a continuous plug-flow step feed process. water research 2014, 55, 95-105. 14. Spieck, E.; Hartwig, C.; McCormack, I.; Maixner, F.; Wagner, M.; Lipski, A.; Daims, H., Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge. Environ Microbiol 2006, 8, (3), 405-15. 15. Wagner, M.; Loy, A.; Nogueira, R.; Purkhold, U.; Lee, N.; Daims, H., Microbial community composition and function in wastewater treatment plants. Antonie Van Leeuwenhoek 2002, 81, (1-4), 665-680.

ACS Paragon Plus Environment

Environmental Science & Technology

469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514

Page 28 of 32

16. Liu, G.; Wang, J., Long-term low DO enriches and shifts nitrifier community in activated sludge. Environmental science & technology 2013, 47, (10), 5109-5117. 17. Ehrich, S.; Behrens, D.; Lebedeva, E.; Ludwig, W.; Bock, E., A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Archives of Microbiology 1995, 164, (1), 16-23. 18. Schloss, P. D.; Westcott, S. L.; Ryabin, T.; Hall, J. R.; Hartmann, M.; Hollister, E. B.; Lesniewski, R. A.; Oakley, B. B.; Parks, D. H.; Robinson, C. J.; Sahl, J. W.; Stres, B.; Thallinger, G. G.; Van Horn, D. J.; Weber, C. F., Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75, (23), 7537-41. 19. Tamura, K.; Stecher, G.; Peterson, D.; Filipski, A.; Kumar, S., MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution 2013, 30, (12), 2725-2729. 20. Lines, R.; Harfield, J.; Griffiths, W.; Rood, A.; Alderliesten, M. In Standardisation in particle sizing, Analytical Proceedings, 1984; Royal Society of Chemistry: 1984; pp 159-172. 21. Allen, T., Particle size measurement. Springer: 2013. 22. Chandran, K.; Smets, B. F., Single‐step nitrification models erroneously describe batch ammonia oxidation profiles when nitrite oxidation becomes rate limiting. Biotechnology and bioengineering 2000, 68, (4), 396-406. 23. McCarty, P. L., Environmental biotechnology: principles and applications. Tata McGraw-Hill Education: 2012. 24. Blackburne, R.; Vadivelu, V. M.; Yuan, Z.; Keller, J., Determination of growth rate and yield of nitrifying bacteria by measuring carbon dioxide uptake rate. Water Environment Research 2007, 79, (12), 2437-2445. 25. Manser, R.; Gujer, W.; Siegrist, H., Consequences of mass transfer effects on the kinetics of nitrifiers. Water Research 2005, 39, (19), 4633-4642. 26. Laanbroek, H. J.; Bodelier, P. L.; Gerards, S., Oxygen consumption kinetics of Nitrosomonas europaea and Nitrobacter hamburgensis grown in mixed continuous cultures at different oxygen concentrations. Archives of microbiology 1994, 161, (2), 156-162. 27. Vadivelu, V. M.; Yuan, Z.; Fux, C.; Keller, J., Stoichiometric and kinetic characterisation of Nitrobacter in mixed culture by decoupling the growth and energy generation processes. Biotechnology and bioengineering 2006, 94, (6), 1176-1188. 28. Nowka, B.; Daims, H.; Spieck, E., Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation. Applied and environmental microbiology 2015, 81, (2), 745-753. 29. Blackburne, R.; Vadivelu, V. M.; Yuan, Z.; Keller, J., Kinetic characterisation of an enriched Nitrospira culture with comparison to Nitrobacter. Water Research 2007, 41, (14), 3033-3042. 30. Ahn, J. H.; Yu, R.; Chandran, K., Distinctive microbial ecology and biokinetics of autotrophic ammonia and nitrite oxidation in a partial nitrification bioreactor. Biotechnology and bioengineering 2008, 100, (6), 1078-1087. 31. Ma, Y.; Sundar, S.; Park, H.; Chandran, K., The effect of inorganic carbon on microbial interactions in a biofilm nitritation–anammox process. Water Res 2015, 70, 246-254. 32. Park, H.; Sundar, S.; Ma, Y.; Chandran, K., Differentiation in the microbial ecology and activity of suspended and attached bacteria in a nitritation‐anammox process. Biotechnology and bioengineering 2015, 112, (2), 272-279.

ACS Paragon Plus Environment

Page 29 of 32

515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560

Environmental Science & Technology

33. Maixner, F.; Noguera, D. R.; Anneser, B.; Stoecker, K.; Wegl, G.; Wagner, M.; Daims, H., Nitrite concentration influences the population structure of Nitrospira‐like bacteria. Environmental Microbiology 2006, 8, (8), 1487-1495. 34. Nowka, B.; Off, S.; Daims, H.; Spieck, E., Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages. FEMS microbiology ecology 2015, 91, (3), fiu031. 35. Park, H.-D.; Noguera, D. R., Nitrospira community composition in nitrifying reactors operated with two different dissolved oxygen levels. Journal of microbiology and biotechnology 2008, 18, (8), 1470-1474. 36. Gilbert, E. M.; Agrawal, S.; Brunner, F.; Schwartz, T.; Horn, H.; Lackner, S., Response of different Nitrospira species to anoxic periods depends on operational DO. Environmental science & technology 2014, 48, (5), 2934-2941. 37. Brotto, A. C.; Li, H.; Dumit, M.; Gabarró, J.; Colprim, J.; Murthy, S.; Chandran, K., Characterization and mitigation of nitrous oxide (N2O) emissions from partial and full‐ nitrification BNR processes based on post‐anoxic aeration control. Biotechnology and bioengineering 2015, 112, (11), 2241-2247. 38. Chandran, K.; Love, N. G., Physiological state, growth mode, and oxidative stress play a role in Cd(II)-mediated inhibition of Nitrosomonas europaea 19718. Appl. Environ. Microbiol. 2008, 74, (8), 2447-2453. 39. Bollmann, A.; Schmidt, I.; Saunders, A. M.; Nicolaisen, M. H., Influence of starvation on potential ammonia-oxidizing activity and amoA mRNA Levels of Nitrosospira briensis. Appl. Environ. Microbiol. 2005, 71, (3), 1276-1282. 40. Bollmann, A.; Bar-Gilissen, M.-J.; Laanbroek, H. J., Growth at Low Ammonium Concentrations and Starvation Response as Potential Factors Involved in Niche Differentiation among Ammonia-Oxidizing Bacteria. Appl. Environ. Microbiol. 2002, 68, (10), 4751-4757. 41. Prosser, J. I.; Nicol, G. W., Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 2012, 20, (11), 523-531. 42. Rittmann, B. E.; Regan, J. M.; Stahl, D. A., Nitrification as a source of soluble organic substrate in biological treatment. Water science and Technology 1994, 30, (6), 1-8. 43. Klindworth, A.; Pruesse, E.; Schweer, T.; Peplies, J.; Quast, C.; Horn, M.; Glöckner, F. O., Evaluation of general 16S ribosomal RNA gene PCR primers for classical and nextgeneration sequencing-based diversity studies. Nucleic acids research 2012, gks808. 44. Grady, C. P. L. J.; Daigger, G. T.; Lim, H. C., Biological Wastewater Treatment. 2 ed.; Marcel Dekker: New York, 1999. 45. Eikelboom, D., Filamentous organisms observed in activated sludge. Water Research 1975, 9, (4), 365-388. 46. Kindaichi, T.; Ito, T.; Okabe, S., Ecophysiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by microautoradiography-fluorescence in situ hybridization. Applied and Environmental Microbiology 2004, 70, (3), 1641-1650. 47. Juretschko, S.; Timmermann, G.; Schmid, M.; Schleifer, K.-H.; Pommerening-Röser, A.; Koops, H.-P.; Wagner, M., Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Applied and Environmental Microbiology 1998, 64, (8), 3042-3051. 48. Alleman, J., Elevated nitrite occurrence in biological wastewater treatment systems. Water science and technology 1985, 17, (2-3), 409-419.

ACS Paragon Plus Environment

Environmental Science & Technology

561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606

Page 30 of 32

49. Daims, H.; Maixner, F.; Lücker, S.; Stoecker, K.; Hace, K.; Wagner, M., Ecophysiology and niche differentiation of Nitrospira-like bacteria, the key nitrite oxidizers in wastewater treatment plants. Water science and technology 2006, 54, (1), 21-27. 50. Lücker, S.; Wagner, M.; Maixner, F.; Pelletier, E.; Koch, H.; Vacherie, B.; Rattei, T.; Damsté, J. S. S.; Spieck, E.; Le Paslier, D., A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proceedings of the National Academy of Sciences of the United States of America 2010, 107, (30), 13479-13484. 51. Starkenburg, S. R.; Chain, P. S.; Sayavedra-Soto, L. A.; Hauser, L.; Land, M. L.; Larimer, F. W.; Malfatti, S. A.; Klotz, M. G.; Bottomley, P. J.; Arp, D. J., Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied and Environmental Microbiology 2006, 72, (3), 2050-2063. 52. Starkenburg, S. R.; Larimer, F. W.; Stein, L. Y.; Klotz, M. G.; Chain, P. S.; SayavedraSoto, L. A.; Poret-Peterson, A. T.; Gentry, M. E.; Arp, D. J.; Ward, B., Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Applied and Environmental Microbiology 2008, 74, (9), 2852-2863. 53. Chandran, K.; Smets, B. F., Estimating biomass yield coefficients for autotrophic ammonia and nitrite oxidation from batch respirograms. Water research 2001, 35, (13), 31533156. 54. Miller, M. W.; Bunce, R.; Regmi, P.; Hingley, D. M.; Kinnear, D.; Murthy, S.; Wett, B.; Bott, C. B., A/B process pilot optimized for nitrite shunt: High rate carbon removal followed by BNR with ammonia-Based cyclic aeration control. Proceedings of the Water Environment Federation 2012, 2012, (10), 5808-5825. 55. Ferris, M.; Muyzer, G.; Ward, D., Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Applied and Environmental Microbiology 1996, 62, (2), 340-346. 56. Kindaichi, T.; Kawano, Y.; Ito, T.; Satoh, H.; Okabe, S., Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real‐time quantitative PCR. Biotechnology and bioengineering 2006, 94, (6), 1111-1121. 57. Graham, D. W.; Knapp, C. W.; Van Vleck, E. S.; Bloor, K.; Lane, T. B.; Graham, C. E., Experimental demonstration of chaotic instability in biological nitrification. The ISME journal 2007, 1, (5), 385-393. 58. Rotthauwe, J.-H.; Witzel, K.-P.; Liesack, W., The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology 1997, 63, (12), 4704-4712. 59. Watson, S. W.; Bock, E.; Valois, F. W.; Waterbury, J. B.; Schlosser, U., Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium. Archives of Microbiology 1986, 144, (1), 1-7. 60. Yoshioka, T.; Hisayoshi, T.; Saijo, Y., Growth kinetic studies of nitrifying bacteria by the immunofluorescent counting method. The Journal of General and Applied Microbiology 1982, 28, (2), 169-180. 61. Chandran, K.; Smets, B. F., Optimizing experimental design to estimate ammonia and nitrite oxidation biokinetic parameters from batch respirograms. Water Research 2005, 39, (20), 4969-4978. 62. McCarty, P. L., Thermodynamics of biological synthesis and growth. Air and water pollution 1965, 9, (10), 621.

ACS Paragon Plus Environment

Page 31 of 32

Environmental Science & Technology

607

ACS Paragon Plus Environment

Environmental Science & Technology

ACS Paragon Plus Environment

Page 32 of 32