Citation:

fiz006

Name: Nitrogen and sulfur-cycling genes in sediments from a fish farming area in Bolinao, Philippines, 2017-06-10 and 2017-06-11
Published: 2019-04-26
License: https://creativecommons.org/licenses/by/4.0/
Keywords: marine aquaculture; nutrient loading; Philippines

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Abstract:

Physicochemical parameters and relative abundance of selected nutrient cycling genes were measured in sediment and pore water samples taken from a fish farming area (Site S3 16◦23.097 N, 119◦55.551 E, depth 12.6m) and a control site (Site S1 16◦22.960 N, 119◦54.723 E, depth 15m) not influenced by fish farming. From each site, five pairs of cores representing five biological replicates were collected. One core from each pair was used for physicochemical analysis while the other cores were used for microbial community analysis. Samples from S1 were collected on 2017-06-10 and samples from S3 were collected the following day.

Nitrogen (bacterial ammonia monooxygenase/ amoA and nitrite reductase/ nirK) and sulfur (dissimilatory sulfate reductase/ dsrA and sulfur oxidation/ soxB) cycling genes were quantified and normalized against the abundance of the 16S rRNA gene.

Keyword(s):

marine aquaculture; nutrient loading; Philippines

Project(s):

Aquaculture practice in tropical coastal ecosystems - understanding ecological and socio-economic consequences (ACUTE)

Funding:

Leibniz Association (Leibniz Association), grant/award no. SAW-2015-ZMT-4 : Aquaculture practice in tropical coastal ecosystems - understanding ecological and socio-economic consequences

Coverage:

Median Latitude: 16.383810 * Median Longitude: 119.918925 * South-bound Latitude: 16.382670 * West-bound Longitude: 119.912000 * North-bound Latitude: 16.384950 * East-bound Longitude: 119.925850

Date/Time Start: 2017-06-10T00:00:00 * Date/Time End: 2017-06-11T00:00:00

Minimum Elevation: -15.0 m * Maximum Elevation: -12.6 m

Event(s):

Guiguiwanen_channel_S1 (OC; off cage site) * Latitude: 16.382670 * Longitude: 119.912000 * Date/Time Start: 2017-06-10T00:00:00 * Date/Time End: 2017-06-11T00:00:00 * Elevation: -15.0 m * Location: Philippines * Method/Device: Diver-held corer (DHC) * Comment: Five pairs of cores representing five biological replicates were collected in a 5 × 5 m square pattern with four pairs of cores at the corners and one pair in the middle

Guiguiwanen_channel_S3 (FC; fish cage) * Latitude: 16.384950 * Longitude: 119.925850 * Date/Time Start: 2017-06-10T00:00:00 * Date/Time End: 2017-06-11T00:00:00 * Elevation: -12.6 m * Location: Philippines * Method/Device: Diver-held corer (DHC) * Comment: Five pairs of cores representing five biological replicates were collected in a 5 × 5 m square pattern with four pairs of cores at the corners and one pair in the middle

Comment:

Note: in the publication, S1 is referred to as the off cage site or site OC, while S3 is referred to as the fish cage site or site FC

Parameter(s):

#	Name	Short Name	Principal Investigator	Method/Device	Comment
1	Event label	Event	Moncada, Chyrene
2	Site	Site	Moncada, Chyrene
3	Core	Core	Moncada, Chyrene
4	Nitrite reductase, nirK gene, relative abundance	nirK	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Interface
5	Nitrite reductase, nirK gene, relative abundance	nirK	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Sediment
6	Nitrite reductase, nirK gene, relative abundance	nirK	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Porewater
7	Ammonia monooxygenase, amoA gene, relative abundance	amoA	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Interface
8	Ammonia monooxygenase, amoA gene, relative abundance	amoA	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Sediment
9	Ammonia monooxygenase, amoA gene, relative abundance	amoA	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Porewater
10	Dissimilatory sulfate reductase, dsrA gene, relative abundance	dsrA	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Interface
11	Dissimilatory sulfate reductase, dsrA gene, relative abundance	dsrA	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Sediment
12	Dissimilatory sulfate reductase, dsrA gene, relative abundance	dsrA	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Porewater
13	Sulfur oxidizing multi-enzyme, gene soxB, relative abundance	soxB	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Interface
14	Sulfur oxidizing multi-enzyme, gene soxB, relative abundance	soxB	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Sediment
15	Sulfur oxidizing multi-enzyme, gene soxB, relative abundance	soxB	Moncada, Chyrene	Extraction: Mobio DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, USA); Analysis: Shimadzu Biospec Nano microvolume spectrophotometer	Porewater

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Size:

140 data points

Data

Download dataset as tab-delimited text — use the following character encoding:

1 Event	2 Site	3 Core	4 nirK (Interface)	5 nirK (Sediment)	6 nirK (Porewater)	7 amoA (Interface)	8 amoA (Sediment)	9 amoA (Porewater)	10 dsrA (Interface)	11 dsrA (Sediment)	12 dsrA (Porewater)	13 soxB (Interface)	14 soxB (Sediment)	15 soxB (Porewater)
Guiguiwanen_channel_S1	S1	6	0.011220271	0.013193771	0.004959145	0.000598618	0.000887834	0.000880683	0.005797325	0.011144468	0.008776738	0.008057863	0.007736499	0.007964849
Guiguiwanen_channel_S1	S1	7	0.008012753	0.008517296	0.004404991	0.000594764	0.000986953	0.000587370	0.008611479	0.012245645	0.008623363	0.009482551	0.011817542	0.006906235
Guiguiwanen_channel_S1	S1	8	0.008562976	0.006367440	0.004161880	0.000422763	0.001009910	0.000732030	0.005260845	0.011360197	0.011234584	0.003785111	0.006201937	0.008155057
Guiguiwanen_channel_S1	S1	9	0.012418685	0.006878717	0.004354154	0.000833214	0.000903540	0.000691030	0.011802199	0.012306505	0.009654934	0.007619298	0.005723740	0.004223884
Guiguiwanen_channel_S1	S1	10	0.005517277	0.004063382	0.004539045	0.000925124	0.000922834	0.000735815	0.010135935	0.012298231	0.012467019	0.004983569	0.004161771	0.005847510
Guiguiwanen_channel_S3	S3	6	0.003893916	0.003347555	0.002872585	0.000723625	0.000744116	0.000502116	0.008762941	0.009746095	0.006218616	0.004805891	0.003252855	0.000979530
Guiguiwanen_channel_S3	S3	7	0.004027949	0.003371250	0.002872585	0.000832455	0.000847948	0.000788435	0.009885239	0.009633216	0.010468295	0.001498555	0.002998422	0.003207518
Guiguiwanen_channel_S3	S3	8	0.005222012	0.003371250	0.002439962	0.000665079	0.000706298	0.000595575	0.009731658	0.008911740	0.009818801	0.002024742	0.005309253	0.008217142
Guiguiwanen_channel_S3	S3	9	0.005048327	0.003390131	0.002836009	0.000754128	0.000766687	0.000833024	0.007873994	0.009465788	0.012422896	0.007688936	0.006824496	0.005408074
Guiguiwanen_channel_S3	S3	10	0.004972457	0.003817971	0.002256732	0.000778981	0.000857109	0.000633840	0.009202923	0.008146136	0.007657297	0.006180781	0.003744560	0.001096025