Microbial Community and Atrazine-Degrading Genetic Potential in Deep Zones of a Hypersaline Lake-Aquifer System
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area
2.2. Groundwater Sampling
2.3. DNA Extraction
2.4. Cloning
2.5. Strain Isolation
2.6. Sequencing of the 16S rRNA Gene Fragment
2.7. PCR Assays of Atrazine-Degrading Genes
3. Results
3.1. Physico-Chemical Parameters of Deep Groundwater
3.2. Structure of the Groundwater Microbial Community
3.3. Isolation of Groundwater Bacteria Strain
3.4. Atrazine Degrading Genetic Potential of Groundwater Bacterial Isolates
4. Discussion
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Gene | Primer | Nucleotide Sequence (5’→3’) | Annealing Temperature (°C) | Reference |
---|---|---|---|---|
atzA | atzA_F | CCA TGT GAA CCA GAT CCT | 58 | [29] |
atzA_R | TGA AGC GTC CAC ATT ACC | |||
atzB | atzB_F | TCA CCG GGG ATG TCG CGG GC | 60 | [29] |
atzB_R | CTC TCC CGC ATG GCA TCG GG | |||
atzC | atzC_F | GCT CAC ATG CAG GTA CTC CA | 58 | [29] |
atzC_R | GTA CCA TAT CAC CGT TTG CCA | |||
atzD | atzD_F | TCC CAC CTG ACA TCA CAA AC | 60 | [30] |
atzD_R | GGG TCT CGA GGT TTG ATT G | |||
atzE | atzE_F | GAG CCT CTG TCC GTA GAT CG | 60 | [30] |
atzE_R | GAT GGC GTG TAC CGT TTA CC | |||
atzF | atzF_F | ACC AGC CCT TGA ATC ATC AG | 60 | [30] |
atzF_R | TAT TGT CCC GAT ACC CAA CG | |||
trzN | trzN_F | CAC CAG CAC CTG TAC GAA GG | 57 | [31] |
trzN_R | GAT TCG AAC CAT TCC AAA CG | |||
trzD | trzD_F | CCT CGC GTT CAA GGT CTA CT | 60 | [32] |
trzD_R | TCG AAG CGA TAA CTG CAT TG | |||
16S rRNA | 27F | AGA GTT TGA TCC TGG CTC AG | 53 | [33] |
1492R | CGG TTA CCT TGT TAC GAC TT |
Family | Closest Type Strain Associated | No. of Clones | RA 1 (%) |
---|---|---|---|
Pseudomonadaceae | Pseudomonas alcaligenes NEB 585 | 1 | 29.2 |
Pseudomonas alcaliphila AL15-21 | 1 | ||
Pseudomonas azotoformans NBRC 12693 | 2 | ||
Pseudomonas cedrina CFML 96-198 | 1 | ||
Pseudomonas chengduensis MBR | 1 | ||
Pseudomonas gessardii CIP 105469 | 5 | ||
Pseudomonas libanensis CIP 105460 | 1 | ||
Pseudomonas paralactis DSM 29164 | 10 | ||
Pseudomonas pseudoalcaligenes Stanier 63 | 2 | ||
Pseudomonas resinovorans ATCC 14235 | 1 | ||
Pseudomonas silesiensis A3 | 1 | ||
Comamonadaceae | Acidovorax facilis LMG 2193 | 1 | 29.2 |
Comamonas phosphate WYH 22-41 | 1 | ||
Hydrogenophaga atypica BSB 41.8 | 1 | ||
Hydrogenophaga taeniospiralis 2K1 | 21 | ||
Ramlibacter ginsenosidimutans BXN5-27 | 2 | ||
Sphingomonadaceae | Sphingomonas olei K-1-16 | 1 | 10.1 |
Sphingopyxis bauzanensis BZ30 | 7 | ||
Sphingopyxis fribergensis Kp5.2 | 1 | ||
Moraxellaceae | Acinetobacter johnsonii ATCC 17909 | 5 | 9.0 |
Acinetobacter seohaensis SW-100 | 3 | ||
Chromatiaceae | Pararheinheimera aquatica GR5 | 1 | 9.0 |
Pararheinheimera chironomi K19414 | 4 | ||
Pararheinheimera mesophila IITR-13 | 1 | ||
Pararheinheimera texasensis A62-14B | 2 | ||
Caulobacteraceae | Brevundimonas vesicularis Busing | 1 | 4.5 |
Phenylobacterium immobile E | 1 | ||
Phenylobacterium mobile GZ6 | 1 | ||
Phenylobacterium muchangponense A8 | 1 | ||
Xanthomonadaceae | Arenimonas maotaiensis YT8 | 1 | 2.2 |
Stenotrophomonas koreensis TR6-01 | 1 | ||
Rhodobacteraceae | Paracoccus carotinifaciens E-396 | 1 | 2.2 |
Rhodobacter sphaeroides 2.4.1 | 1 | ||
Rhizobiaceae | Rhizobium selenitireducens B1 | 2 | 2.2 |
Bacillaceae | Bacillus aquimaris TF-12 | 1 | 2.2 |
Brevibacterium frigoritolerans DSM 8801 | 1 |
Isolated Strain | Family | Closest Type Strain Associated | E Value | Identities | Gaps |
---|---|---|---|---|---|
GW38-1 | Microbacteriaceae | Microbacterium fluvii YSL3-15 | 0.0 | 98.6% | 0/830 (0%) |
GW38-2 | Microbacterium ginsengisoli Gsoil 259 | 0.0 | 98.3% | 1/526 (0%) | |
GW38-3 | Microbacterium hatanonis FCC-01 | 0.0 | 99.7% | 1/665 (0%) | |
GW38-4 | Microbacterium maritypicum DSM 12512 | 0.0 | 99.5% | 1/826 (0%) | |
GW38-5 | Labedella endophytica EGI 6500705 | 0.0 | 99.6% | 2/746 (0%) | |
GW38-6 | Micrococcaceae | Arthrobacter agilis DSM 20550 | 0.0 | 97.9% | 1/741 (0%) |
GW38-7 | Nesterenkonia halotolerans YIM70084 | 0.0 | 99.9% | 1/737 (0%) | |
GW38-8 | Kocuria palustris TAGA27 | 0.0 | 99.6% | 2/499 (0%) | |
GW38-9 | Dietziaceae | Dietzia maris DSM 43672 | 0.0 | 100% | 0/695 (0%) |
GW38-10 | Nocardioidaceae | Nocardioides nanhaiensis YIM M13091 | 0.0 | 97.8% | 0/547 (0%) |
GW38-11 | Intrasporangiaceae | Ornithinimicrobium kibberense. K22-20 | 0.0 | 96.6% | 2/832 (0%) |
GW38-12 | Bacillaceae | Bacillus safensis FO-36b | 0.0 | 100% | 0/597 (0%) |
GW38-13 | Enterococcaceae | Enterococcus durans JCM 8725 | 0.0 | 99.5% | 3/605 (0%) |
GW38-14 | Pseudomonadaceae | Pseudomonas paralactis DSM 29164 | 0.0 | 100% | 0/758 (0%) |
Strain | Closest Bacteria Associated | trzN | atzA | atzB | atzC | trzD | atzD | atzE | atzF |
---|---|---|---|---|---|---|---|---|---|
GW38-1 | Microbacterium fluvii | - | - | - | + | - | - | - | - |
GW38-3 | Microbacterium hatanonis | - | + | - | - | - | - | - | - |
GW38-4 | Microbacterium maritypicum | + | - | - | + | - | - | - | - |
GW38-5 | Labedella endophytica | - | - | - | - | + | - | - | - |
GW38-6 | Arthrobacter agilis | + | + | - | - | - | - | - | - |
GW38-7 | Nesterenkonia halotolerans | + | - | - | - | + | - | - | + |
GW38-10 | Nocardioides nanhaiensis | + | + | - | - | - | - | - | + |
GW38-14 | Pseudomonas paralactis | + | - | + | - | - | - | + | - |
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Espín, Y.; Aranzulla, G.; Álvarez-Ortí, M.; Gómez-Alday, J.J. Microbial Community and Atrazine-Degrading Genetic Potential in Deep Zones of a Hypersaline Lake-Aquifer System. Appl. Sci. 2020, 10, 7111. https://doi.org/10.3390/app10207111
Espín Y, Aranzulla G, Álvarez-Ortí M, Gómez-Alday JJ. Microbial Community and Atrazine-Degrading Genetic Potential in Deep Zones of a Hypersaline Lake-Aquifer System. Applied Sciences. 2020; 10(20):7111. https://doi.org/10.3390/app10207111
Chicago/Turabian StyleEspín, Yolanda, Giuliana Aranzulla, Manuel Álvarez-Ortí, and Juan José Gómez-Alday. 2020. "Microbial Community and Atrazine-Degrading Genetic Potential in Deep Zones of a Hypersaline Lake-Aquifer System" Applied Sciences 10, no. 20: 7111. https://doi.org/10.3390/app10207111