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Letters in Applied Microbiology ISSN 0266-8254

ORIGINAL ARTICLE

Isolation and characterization of atrazine-degrading strain


Shewanella sp. YJY4 from cornfield soil
J.Y. Ye, J.B. Zhang, J.G. Gao, H.T. Li, D. Liang and R.M. Liu
College of Life Science, Northeast Agricultural University, Harbin, China

Significance and Impact of Study: A new isolated strain, YJY4 showed high atrazine-degrading ability,
being able to degrade 100 mg l1 atrazine completely in 36 h. Strain YJY4 was identified as Shewanella
sp. and contained atrazine-degrading atzA, atzB and atzC genes. This study examined the degradation
mechanism and metabolic ability of this strain and for the bioremediation of contaminated environ-
ments, provides more strain selection and determines the strain of atrazine bioremediation potential.

Keywords Abstract
atrazine, biodegradation, identify, metabolic
ability, Shewanella sp.. Atrazine has been used worldwide for over 50 years as a chemical herbicide. A
strain of bacteria, YJY4 which utilizes atrazine as its sole nitrogen source for
Correspondence growth was isolated from agricultural black soil in northeastern China. 16S
Rongmei Liu, College of Life Science, North- rDNA sequencing identified YJY4 as a Shewanella sp. PCR analysis and
east Agricultural University, Harbin 150030,
sequencing confirmed that YJY4 contained atrazine-degrading atzA, atzB and
China.
E-mail: lrm1975@sina.com
atzC genes. These genes revealed high similarity with those in Pseudomonas sp.
ADP and Arthrobacter sp. TC1. The strain YJY4 was observed to degrade
2015/2270: received 4 November 2015, atrazine (100 mg l1) to cyanuric acid completely after 36 h. To the best of
revised 10 May 2016 and accepted 10 May our knowledge, YJY4 was the first reported Shewanella sp. to grow in pure
2016 culture with atrazine serving as a sole source of nitrogen. Therefore, YJY4 may
help with atrazine biodegradation and may become an abundant resource of
doi:10.1111/lam.12584
atrazine degradation strains.

To reverse atrazine pollution, many physical and chem-


Introduction
ical removal methods have been proposed. However,
Atrazine (2-chloro-4-ethylamino-6-isopropyl-amino-s-triazine) these methods make toxic byproducts to spread easily
is a triazine herbicide principally used for controllingcer- and cause water pollution. A biodegradable, cost-effective
tain deep-rooted perennial herb that can kill annual and highly efficient method that causes no secondary pol-
broadleaf and grass weeds, perennial weeds also has a lution would be an ideal solution to the problem of atra-
certain extent, primarily in corn (Zea mays L.) field and zine contamination.
sorghum (Chinese sorghum) field (Solomon et al. 2013). Many bacteria that can partially degrade and even fully
Due to its long residual period and long-term heavy mineralize atrazine have been isolated. These strains
use, atrazine has caused serious pollution in soil, water include Pseudomonas sp. ADP (Siripattanakul et al. 2009),
and other natural environments and it has been detected Arthrobacter aurescens TC1 (Sajjaphan et al. 2004), Pseu-
in high amounts in environmental waters (Ralebits et al. daminobacter sp. C147 (Topp et al. 2000), Arthrobacter sp.
2002; Tsui and Roy 2008). Currently, atrazine has been AD1 (Cai et al. 2003), Rhodococcus sp. MB-P1 (Fazlurrah-
identified as an endocrine disrupting chemical (EDC; man et al. 2009), Bacillus subtilis HB-6 (Wang et al. 2014)
Safe 2005; Guerit et al. 2008). Studies have demonstrated and Pseudomonas aeruginosa (Fernandes et al. 2014).
that long-term exposure to low doses of atrazine inter- Although these strains are from more than 10 genera
fere with the endocrine system of an organism (Bianchi of Gram-positive and Gram-negative bacteria, their degra-
et al. 2006). dation genes are highly conserved with nucleotide

Letters in Applied Microbiology 63, 45--52 © 2016 The Society for Applied Microbiology 45
Bioremediation of atrazine Y. Jinyu et al.

sequence similarity between 97 and 100%. According to smooth colony, orange in colour, on LB agar plates after
the composition of the degrading genes, atrazine-degrad- 48 h of incubation. It was selected for further studies.
ing bacteria can be classified into two types. One type
contains the degradation genes atzA, atzB, atzC, atzD,
Identification and 16S rDNA analysis of strain YJY4
atzE and atzF, which can completely degrade atrazine.
Another type contains the degradation genes trzN/atzA, The 16S rDNA sequences of strain YJY4 was size of
atzB and atzC, which can transform atrazine into non- 1515 bp (GenBank accession number KP231202). The
toxic cyanuric acid. Atrazine-degrading genes atzA and BLAST calculation results showed that strain YJY4’s 16S
trzN, atzD and trzD have the same functionality (Meyer rDNA gene sequence has 99% similarity with the She-
et al. 2009). The genes trzN/atzA, atzB and atzC encode wanella sp. RB5-M4 (GenBank accession number
for three hydrolytic enzymes that catalyse the degradation JN019028). Subsequently, similar 16S rDNA phylogenetic
of atrazine to cyanuric acid. The genes trzD/atzD, atzE tree was constructed with neighbour-joining methods and
and atzF encode the necessary enzymes for ring cleavage the results showed that the strain YJY4 had a close
that catalyse the degradation of cyanuric acid to CO2 and relationship with many Shewanella sp. (Fig. 1). On the
NH3. To date, two of the most extensively studied atra- basis of its physiological characteristics and the
zine degradation strains are Pseudomonas sp. ADP, which constructed phylogenetic tree, strain YJY4 was identified
contains the gene atzABCDEF located on plasmid pADP- as Shewanella sp.
1, and A. aurescens TC1, which contains degrading genes Members of the phylogeny Shewanella sp. are metaboli-
trzN-atzBC located on plasmid pTC-1. cally versatile bacteria, and many Shewanella sp. strains
In recent years, Shewanella sp. are widely distributed in have been reported to degrade pollutants such as ben-
various environments (soil, rivers, oceans and sediments; zoapyrene, naphthylaminesulfonic azo dye amaranth, hex-
Hau and Gralnick 2007). They are capable of degrading ahydro- 1, 3, 5- trinitro- 1, 3, 5- triazine, as well as
including, nitroaromatics, azo dyes and polyhalogenated others (Zhao et al. 2005; Hong et al. 2007; Chang et al.
compounds (Wang et al. 2015). However, there has never 2014). Several reports have also found that Shewanella sp.
been a report of Shewanella sp. capable of degrading tri- strains can degrade acetaldehyde, phenol, malachite green
azine compounds. and methyl violet B (Chen et al. 2010; Liu et al. 2015).
In this study, a high-efficiency atrazine degrader, She- However, strain YJY4 was the first reported Shewanella
wanella sp. YJY4, was isolated from a cornfield where sp. found to grow in pure culture with atrazine as a sole
atrazine had been used for a long time, and the strain nitrogen source (de Souza et al. 1998a; Getenga et al.
was characterized. Strain YJY4 was the first reported She- 2009; Wang et al. 2014). All of these indicate that the
wanella sp. to grow in pure culture with triazine herbicide Shewanella sp. has great ecological diversity and possesses
atrazine serving as a sole source of nitrogen. The purpose potential capacity for bioremediation of organic
of this study was to explain the degradation mechanism pollution.
and metabolic ability of this strain and for the bioremedi-
ation of contaminated environments provide more strain
Detection of atrazine-degrading genes in strain YJY4
selection and indicate the Shewanella sp. YJY4 of organic
pollution bioremediation potential. Atrazine-degrading enzyme gene trzN, atzA, atzB, atzC,
atzD, atzE, atzF and trzD, using the primers listed in
Table 1. After amplification, we obtained 05 kb atzA,
Results and discussion
05 kb atzB and 06 kb atzC, and there were no other
products for other atrazine-degrading genes such as atzD,
Enrichment and isolation of strain YJY4
atzE, atzF, trzD and trzN (Fig. 2). We also attempted to
At the end of the enrichment cycles, the bacterial consor- amplify cyanuric acid genes that were unsuccessful, and
tium was plated on LB medium to isolate the organisms. the results were alike as those presented in Fig. 2. The
Five distinct members were isolated. The degradation nucleotide sequences of atzA from Shewanella sp. YJY4
experiments showed that these strains exhibited a poten- showed 98% sequence similarity with the Pseudomonas
tial ability to degrade atrazine in the AMSM medium sp. ADP (Genbank accession number U66917) and the
with the interval of 123–100% in 7 days. Strain YJY4 had nucleotide sequences of atzB and atzC from Shewanella
the highest degradability, which was at 100%. Physiologi- sp. YJY4 showed 99% sequence similarity with the
cal and morphological characteristics indicate YJY4 was a Arthrobacter sp. TC1 (Genbank accession number
Gram-negative bacterium, and can take advantage of atra- CP000475). This indicates that Shewanella sp. harbours
zine as its sole nitrogen source. Strain YJY4 formed a atzA, atzB and atzC genes.

46 Letters in Applied Microbiology 63, 45--52 © 2016 The Society for Applied Microbiology
Y. Jinyu et al. Bioremediation of atrazine

Shewanella sp. WW001 (AB111109)


79
59 Shewanella sp. THREE-12 (KF650764)

Shewanella sp. BC01 (JX119023)


81
Shewanella sp. 184 (AF387349)

55 Shewanella sp. PIM1 (GQ359960)


56
66 Shewanella sp. LHB20 (GQ850519)
80
Shewanella sp. Hac319 (DQ307732)

Shewanella sp. MK03 (AY690713)

Shewanella sp. PIC1 (GQ359955)


36
Shewanella sp. YJY4 (KP231202)
86
71 Shewanella sp. RB5-M4 (JN019028)

90 Shewanella sp. CN-32 (NR 074817)

Shewanella sp. SIC1 (AB039738)

Shewanella sp. ALL-2 (KC211018)

93 Shewanella sp. MS1 (KM522840)

0·001

Figure 1 Phylogenetic tree of the 16S rDNA sequences of Shewanella sp. YJY4. The calculations were performed according to a neighbour-join-
ing analysis (bootstrap number = 1000), and the bar indicates 0001 substitution per nucleotide position.

The atzA, atzB, atzC, atzD, atzE and atzF genes were nitrate and atrazine as its sole nitrogen source in the 24
found in atrazine-degrading strain ADP (de Souza et al. and 28 h, respectively, required to reach a stationary
1998b; Garcia-Gonzalez et al. 2005). The first three genes phase. The medium with ammonium nitrate as its sole
encode the enzymes required for the conversion of atra- nitrogen source had a lag phase of nearly 4 h, while med-
zine to cyanuric acid. The next three genes encode the ium with atrazine as its sole nitrogen source had a lag
enzymes required for removal of cyanuric acid to NH3 phase nearly 8 h. This indicates that strain YJY4 with
and CO2. The biochemical mechanism is the same, atrazine as its sole nitrogen source in the growth requires
despite different hydrolysing enzymes (AtzA vs. TrzN; certain adaptability. In addition, with the medium with
Meyer et al. 2009). Therefore, the genetic potential for cyanuric acid as the sole nitrogen source, strain YJY4 did
atrazine degradation seems to be close to that of strain not substantially grow. This indicated that strain YJY4
TC1. This also implies that the strain YJY4 cannot take cannot utilize nitrogen from cyanuric acid for growth.
advantage of cyanuric acid as its sole nitrogen source for
growth.
Atrazine biodegradation analysis
We also investigated the ability of Shewanella sp. YJY4 to
Atrazine and cyanuric acid utilization of Shewanella sp.
degrade atrazine (Fig. 3b). When the strain utilized atra-
YJY4
zine as its sole nitrogen source, over time, the concentra-
To determine the growth ability of Shewanella sp. YJY4 tion of atrazine decreased and at 12–16 h had been
and measure whether it can utilize atrazine or cyanuric degraded by half. After 36 h, atrazine could not be
acid as its sole nitrogen source, we measured the growth detected by HPLC. This indicates that 100% of atrazine
of strain YJY4 in medium where its sole nitrogen source (100 mg) was degraded after 36 h incubation with the
was ammonium nitrate, atrazine or cyanuric acid strain YJY4. In contrast, we also detected the concentra-
(Fig. 3a). Strain YJY4 was able to utilize ammonium tion of cyanuric acid by HPLC, where concentration was

Letters in Applied Microbiology 63, 45--52 © 2016 The Society for Applied Microbiology 47
Bioremediation of atrazine Y. Jinyu et al.

Table 1 PCR primers, annealing temperatures and expected product sizes in the amplification of atrazine-degrading genes

Gene Primer Sequence (50 ?30 ) Annealing (°C) Size (kb)

atzA atzA-1 CCA TGT GAA CCA GAT CCT 56 526


atzA-2 TGA AGC GTC CAC ATT ACC
atzB atzB-1 TCA CCG GGG ATG TCG CGG GC 54 500
atzB-2 CTC TCC CGC ATG GCA TCG GG
atzC atzC-1 GCT CAC ATG CAG GTA CTC CA 50 600
atzC-2 GTA CCA TAT CAC CGT TTG CCA
atzD atzD-1 GGA GAC ATC ATA TGT ATC ACA TCG ACG TTT TC 55 1100
atzD-2 CCA ATA AGC TTA GCG CGG GCA ATG ACT GCA
atzE atzE-1 TAC GCG GTA AAG AAT CTG TT 52 1000
atzE-2 GGA GAC CGG CTG AGT GAG A
atzF atzF-1 CGA TCG GAA AAA CGA ACC TC 53 900
atzF-2 CGA TCG CCC CAT CTT CGA AC
trzD trzD-1 CCT CGC GTT CAA GGT CTA CT 58 750
trzD-2 TCG AAG CGA TAA CTG CAT TG
trzN trzN-1 ATG ATC CTG ATC CGC GGA CTG A 50 1370
trzN-2 CTA CAA GTT CTT GGG AAT GAG TG

M 1 2 3 4 5 6 7 8 The pathway for atrazine degradation is well established


(Wackett et al. 2002; Zhang et al. 2012). Several atrazine-
degrading strains were isolated from agricultural soils in
France, USA, Canada, China and India. But Shewanella
sp. YJY4 was the first reported strain that utilizes atrazine
as its sole nitrogen source for growth. Because it can uti-
lize many kinds of organic pollutants, it may possess great
5000 bp potential as bioremediation for organic pollution.
3000 bp
2000 bp Materials and methods
1000 bp
750 bp Soils
500 bp
The bacteria described in this study were isolated from
250 bp the surface soil layer of a cornfield (Yichun City, Hei-
100 bp
longjiang Province, China) where the use of atrazine was
for long-term (0–15 cm). Soil samples were sieved (50-
mm mesh) to remove stones and plant debris and then
Figure 2 Agarose gel electrophoresis (1%) of atrazine-degrading stored at 4°C in plastic bag until use.
gene PCR product generated from strain YJY4. Lane M corresponds
to DM 2000 Plus DNA molecular weight marker. Lane 1 to lane 8 pre-
sents the PCR amplification products for trzN, atzA, atzB, atzC, trzD, Chemicals and media
atzD, atzE and atzF.
Atrazine standard sample (≥99% purity) was purchased
from Harbin Limin Technology Ltd (Harbin, China).
increased over time. The reduction of the amount of atra- Cyanuric acid standard sample (≥98% purity) was
zine was inversely proportional to the increase in the purchased from Sinopharm Chemical Reagent Co., Ltd.
amount of cyanuric acid. Due to these results, we specu- (Beijing, China). Other chemicals used in this paper were
late that strain YJY4 may only be able to degrading atra- analytical grade reagents, and those used for HPLC analy-
zine to cyanuric acid and cannot use cyanuric acid as its ses were of HPLC grade reagents.
nitrogen source for growth. Therefore, the final product The liquid enrichment media used was mineral salts
of strain YJY4 degrading atrazine might be the cyanuric medium (MSM). MSM contained 10 g l1 of KH2PO4,
acid. 60 g l1 of Na2HPO412H2O, 02 g l1 of MgSO47H2O,
Given this result, the proposed pathway for atrazine 05 g l1 of NaCl, 3 g l1 of glucose and 1 ml l1 of
degradation by Shewanella sp. YJY4 was shown in Fig. 4. trace element concentrate solution (pH 70). Trace

48 Letters in Applied Microbiology 63, 45--52 © 2016 The Society for Applied Microbiology
Y. Jinyu et al. Bioremediation of atrazine

(a) (b)
100
0·7
90
0·6
80
0·5 70
60
0·4
50
0·3 40
0·2 30
20
0·1
10
0 0
0 4 8 12 16 20 24 28 32 36 0 4 8 12 16 20 24 28 32 36

Figure 3 (a) Growth of strain Shewanella sp. YJY4 in MSM containing atrazine, cyanuric acid and ammonium nitrate (100 mg l1), respectively,
as the sole nitrogen source. Error bars represent the mean (SD) of three independent samples. (b) Metabolism of atrazine by Shewanella sp.
YJY4 in MSM containing atrazine (100 mg l1) as the sole nitrogen source. Error bars represent the mean (SD) of three independent samples.
(a) ( ) Ammonium nitrate, ( ) Atrazine, ( ) Cyanuric acid. (b) ( ) Atrazine, ( ) Cyanuric acid.

Cl OH OH OH

N N atzA N N atzB N N atzC N N

H7C3HN N NHC2H5 H7C3HN N NHC2H5 H7C3HN N OH HO N OH

Atrazine Hydroxyatrazine N-isopropylammelide Cyanuric acid

Figure 4 Proposed pathways of atrazine degradation by Shewanella sp. YJY4.

element concentrate solution contained 04 g l1 of plates (100 mg l1 of atrazine). Mature consortiums were
Na2B4O710H2O, 05 g l1 of Na2MoO42H2O, 08 g l1 repeatedly cross-vaccinated on AMSM plates to separate
of CuSO45H2O, 2 g l1 of FeSO47H2O, 2 g l1 of the pure culture. Among the selected isolates, a bacterium
MnSO4H2O, 10 g l1 of ZnSO47H2O and 5 g l1 of showed high atrazine-degrading activity. This strain was
EDTA. As required, atrazine (atrazine mineral salts med- named YJY4 and was selected for further experiments.
ium, AMSM) or cyanuric acid (cyanuric acid mineral salts
medium, CMSM) was added as the sole nitrogen source.
Identification of atrazine-degrading strain YJY4
Lysogeny broth (LB) medium contained 10 g l1 tryp-
tone, 5 g l1 yeast extract and 10 g l1 NaCl. Preparation Identification of strain YJY4 was based on 16S rDNA gene
of solid medium included the addition of 16 g l1 of sequence analysis. Extraction of total genomic strain YJY4
agar. The pH of media was regulated to 72 before steril- was the use of GenElute bacterial genome DNA extraction
ization. Sterilization conditions were 115°C for 30 min. kit (Sigma-Aldrich, Shanghai, China). PCR analysis for
bacterial was using 16S universal primers. Universal pri-
mers were used—27F (50 -AGAGTTTGATCCTGGCTCAG-
Enrichment and isolation
30 ) as the forward primer and 1492R (50 -TACGGC-
Five grams of the soil specimen was added to a 250-ml TACCTTGTTACGACT T-30 ) as the reverse primer (Frank
Erlenmeyer flask with 100 ml AMSM (50 mg l1 of atra- et al. 2008). The PCR conditions were as follows: at 94°C
zine). The specimen was incubated aerobically and shaken preheated 5 min, 30 cycles of three steps at 94°C denatu-
at 150 rev min1 at 30°C. Ten millilitres of enrichment ration 1 min, at 54°C annealed 1 min, and at 72°C exten-
culture was then inoculated into fresh AMSM for 7 days, sion 2 min, respectively, and at 72°C final extension
where the atrazine concentration was increased to 10 min. The products of PCR were divided on a 1% agar-
100 mg l1. This process was repeated eight times with the ose gel electrophoresis. The resulting DNA fragments were
exception of the final enrichment incubation, where the purified through AxyPrepTM DNA gel extraction kit
atrazine concentration was increased to 500 mg l1. The (Axygen, Hangzhou, China), and then cloned into a
eventually culture was diluted and coated on AMSM agar pMD18-T vector (TaKaRa, Dalian, China). The vector

Letters in Applied Microbiology 63, 45--52 © 2016 The Society for Applied Microbiology 49
Bioremediation of atrazine Y. Jinyu et al.

was transformed into Escherichia coli strain DH5a. resulting precipitate was resuspended in sterile water to
Sequenced gene fragments was completed by the Suzhou OD600 = 01. AMSM medium containing 100 mg l1
Genewiz Biotechnology Co., Ltd. (Suzhou, China). atrazine was inoculated using 1% concentration of the
The sequences were analysed using the GenBank resuspension. Aliquots were taken every 4 h, and atrazine/
nucleotide database. Sequence alignments and phyloge- cyanuric acid content was measured over a period of
netic analysis were performed using the CLUSTAL W and 36 h. All experiments were performed in triplicate.
MEGA ver. 5.0 (Philadelphia, PA). A phylogenetic bootstrap Atrazine concentration and cyanuric acid yield was
analysis using 1000 replicates for each sequence was used quantified by HPLC (Waters 600; Waters) equipped with a
with a 50% minimum for branch reliability. dual k absorbance detector (Waters 2487; Waters, Milford,
MA) and a reversed phase C18 column (Agilent Eclipse
XDB-C 18, 46 mm 9 150 mm; Agilent, Beijing, China).
PCR detection of atrazine-degrading genes
For the detection of atrazine (Kadian et al. 2008), the
Extraction of total genomic strain YJY4 was the use of flow rate was 10 ml min1 (acetonitrile : water =
GenElute (Shanghai, China) bacterial genome DNA 80 : 20, v : v), the column temperature was 25°C, and
extraction kit and it was used as a template to amplify the UV detector set at a wavelength of 221 nm. The
atzA, atzB, atzC, atzD, atzE, atzF, trzD and trzN genes, retention time of atrazine is 26 min. For detection of the
respectively. The primers have been previously described yield of cyanuric acid (Vaclavik et al. 2010), the flow rate
(Mulbry et al. 2002; Devers et al. 2004; Zhang et al. 2011). was 10 ml min1 (50 mM K2HPO4/methanol = 95 : 5,
The primer sequences, annealing temperature, products v : v), the column temperature was 35°C, and the UV
size and references are shown in the Table 1. The PCR detector set at a wavelength of 213 nm. The retention
conditions were as follows: at 94°C preheated 5 min, 30 time of atrazine is 15 min.
cycles of three steps at 94°C denaturation 1 min, at 54°C
annealed 1 min, at 72°C extension 45, 45, 45, 60, 60, 60,
Acknowledgements
60 and 90 s to atzA, atzB, atzC, atzD, atzE, atzF, trzD and
trzN genes, respectively, and at 72°C final extension This study was supported by the Heilongjiang Provincial
10 min (Table 1). Sequencing and sequence analysis were National Science Foundation (12521021), Dr Start-up
showed as described in Materials and methods 24. Fund in Northeast Agricultural University of China (No.
2010RCB54).
Growth capacity of strain YJY4
Conflict of Interest
Three 100 ml cultures of liquid medium containing
100 mg l1 atrazine (AMSM), 100 mg l1 cyanuric acid We declare that we have no financial and personal rela-
(CMSM), or 100 mg l1 ammonium nitrate (NH4NO3) tionships with other people or organizations that can
(MSM) were grown. AMSM and CMSM were used to inappropriately influence our work, there is no profes-
determine whether strain YJY4 could utilize atrazine and sional or other personal interest of any nature or kind in
cyanuric acid as its sole nitrogen source. In contrast, MSM any product, service and/or company that could be con-
was used to understand whether atrazine and cyanuric acid strued as influencing the position presented in, or the
inhibited the growth of the strain YJY4. Bacteria were cul- review of the manuscript entitled.
tured for 24 h and later centrifuged at 10 752 g. The result-
ing cell pellet was resuspended in sterile water and adjusted
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