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| Status |
Public on Jun 11, 2018 |
| Title |
Dual bioaugmentation with Desulfitobacterium hafniense Y51 and redox-trained fermenting communities for decontamination of PCE polluted river sediment: a microcosm study |
| Platform organism |
Desulfitobacterium hafniense |
| Sample organism |
Desulfitobacterium hafniense Y51 |
| Experiment type |
Expression profiling by array
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| Summary |
The physiology of D. hafniense strain Y51 under close to natural conditions were examined: D. hafniense Y51 was subjected to a variety of limiting conditions (carbon or electron acceptor) or ammonium deprivation, in chemostat. Its physiology was assessed by transcriptomic and proteomic analyses and compared to that in batch culture. Electron donor/acceptor-limited growth conditions cause a switch to alternative metabolic pathways allowing the organism with a capacity to survive in polluted environments and with a readiness to use alternative electron acceptors such as PCE; (ii) nitrogen limitation induces nitrogen fixation implying a robustness vis-a-vis ammonia shortage; (iii) limiting conditions trigger a general stress response that should enable the organism to cope with even more environmental constraints.
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| Overall design |
A custom-designed array based on the complete genome sequences of D. hafniense DCB-2 and Y51 (NCBI Genbank accession numbers NC_007907 and NC_011830, respectively). The array contains 21905 distinct 45 to-60 oligonucleotides designed with PICKY (Chou et al., 2004; Chou et al., 2009), including two or three probes per target transcript, as well as sense and antisense probes targeting intergenic regions that were larger than 60 oligonucleotides. In total, 11652 probes targeting genes and intergenic regions shared by both genomes. Probes were printed in duplicate on the Agilent 8 x 60 K custom gene expression microarray platform, containing in addition 1319 Agilent control probes.
Expression profiling of: 1) batch culture with 10ml pure hexadecane and 2) river sediment.
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| Contributor(s) |
Tian Y, Vargas-López R |
| Citation missing |
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| |
| Submission date |
Jun 10, 2018 |
| Last update date |
Jun 13, 2018 |
| Contact name |
Ye Tian |
| E-mail(s) |
ye.tian@wur.nl
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| Phone |
+31317480046
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| Organization name |
Wageningen University
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| Department |
AFSG
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| Lab |
The Laboratory of Microbiology
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| Street address |
Stippeneng 4
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| City |
Wageningen |
| ZIP/Postal code |
6708 WE |
| Country |
Netherlands |
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| Platforms (1) |
| GPL24288 |
Agilent-031125 Desulfitobacterium hafniense oligonucleotide microarray 8x60k |
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| Samples (4)
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| GSM3181845 |
batch culture with 10ml pure hexadecane, replicate 1 |
| GSM3181846 |
batch culture with 10ml pure hexadecane, replicate 2 |
| GSM3181847 |
batch culture with 10ml pure hexadecane, replicate 3 |
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| Relations |
| BioProject |
PRJNA475420 |
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