Dataset: Winam Gulf Metagenomic Time Series

Name: Metagenomic Time Series of Winam Gulf, Lake Victoria from 2022-2023 (ASI Lake Victoria project)
Published: 2024-07-09
Keywords: water quality, Great Lakes, harmful algal blooms, Cyanobacteria, phytoplankton, African Great Lakes, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.931936.1

Spatial Extent: N:-0.0623 E:36.425 S:-0.7586 W:34.03812

Winam Gulf, Lake Victoria

Temporal Extent: 2022-06-24 - 2023-06-03

Project:

IRES Track II: Advanced studies institute on water quality and harmful algal blooms in Lake Victoria (ASI Lake Victoria)

Principal Investigator:

George S. Bullerjahn (Bowling Green State University, BGSU)

Co-Principal Investigator:

Robert Michael McKay (University of Windsor)

Student:

Lauren Hart (University of Michigan)

Brittany N. Zepernick (University of Tennessee Knoxville, UTK)

Contact:

Brittany N. Zepernick (University of Tennessee Knoxville, UTK)

BCO-DMO Data Manager:

Sawyer Newman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-07-09

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Metagenomic Time Series of Winam Gulf, Lake Victoria from 2022-2023 (ASI Lake Victoria project)

Abstract:

Compared to the other "Great Lakes" (Laurentian Great Lakes of North America and Lake Baikal of Russia) the African Great Lakes have remained widely unstudied. This serves as a substantial research gap within the limnological literature given the African Great Lakes contribute approximately 25% of all global, accessible freshwater. Lake Victoria of the African Great Lakes is notable for its large size - serving as the second largest freshwater lake in the world by surface area. Yet, Lake Victoria is also known for the prolific year-long cyanobacterial blooms that occur throughout her waters such as the Winam Gulf. These blooms are fueled by intense agricultural and anthropogenic development much like other freshwater harmful algal blooms. However, unlike other freshwater blooms such as those occurring in Lake Erie and Lake Taihhu - these cyanobacterial blooms have remained widely uncharacterized (especially using molecular techniques). The central study area is the Winam Gulf of Lake Victoria, Kenya. This is a relatively shallow, hypereutrophic system that has various rivers serving as nutrient loading sources (such as the Sondu River). This dataset also contains opportunistic samples collected from a variety of riverine systems and Lakes Simbi and Naivasha. Here, we present the biological, chemical and physical data corresponding to a two year metagenomic time series of the Winam Gulf, Lake Victoria. We further present the physiochemical data of eight outgroup samples including adjacent riverine systems and Lakes Simbi and Naivasha.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2024-07-09	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.931936.1	2024-07-18

Methods & Sampling

Water samples were collected from Lake Victoria were depth discrete (1.0 meters) collections performed using a Van Dorn sampler. Samples were collected on 0.22 micron sterivex filters for subsequent DNA extraction and stored at room temperature in DNA/RNA Shield (Zymo). Concurrently, a multiparameter sonde was deployed to record temperature, pH, dissolved oxygen, conductivity, turbidity etc. In addition, sterivex filtrate was collected and stored at -20 degrees Celsius for subsequent dissolved nutrient analysis at the Ohio State Stone Laboratory.

In turn, samples were collected for chlorophyll a and processed using a 24 hour 90% acetone extraction performed at -20 degrees Celsius followed by quantification using a fluorometer. Samples for toxin analysis (microcystin) were collected and stored at -20C until processing using standard ELISA kits.

In situ analysis was performed with a field Algae Torch (bbe Moldaenke) fluorometer, which was equipped with chlorophyll a and phycocyanin probes. We collected data in the form of cells per liter by lowering the fluorometer into the water column at the same depths where water samples were collected. We then converted the data to percentages to determine the relative abundance of cyanobacteria in the context of the full phytoplankton community (Brown, et al. 2024).

The toxin data was collected and processed as follows: whole water samples were collected at the designated sample depth (refer to the “Sampling_depth” column within the primary data file of this dataset) and lysed using three freeze / thaw cycles. The lysate was investigated for the presence of the cyanobacterial toxin / secondary metabolite “microcystin” using the Microcystins/Nodularins (ADDA) ELISA kit (Gold Standard Diagnostics, Warminster, PA) (Brown, et al. 2024). Absorbance was read at 450 nm on a Multiskan FC Microplate Photometer (Thermo Fisher Scientific Inc).

Problems/Issues

Due to logistical limitations - not all the measurements performed in 2022 could be repeated in 2023. Hence, there exists some discontinuity/gaps in the time series.

Data Processing Description

In the data file, "NA" values are not applicable because that type of data was not collected for that site. The same equipment was not readily available at each site or each year.

If the analysis was run for a sample but no "data" could be detected (meaning it read "too low to detect" or some on-numerical output indicating a negative result), this is indicated by "ND" values in the primary data file (meaning not detected).

BCO-DMO Processing

- Changed date format from %M/%D/%Y to %Y-%M-%D
- Removed units from parameter names
- Replaced special characters in parameter names with underscores ("_") (e.g. "TN:TP" renamed "TN_TP_ratio"; "Algal_Torch_%_cells_cyano" renamed "Algal_Torch_percentage_cells_cyano"

Data Files

File
931936_v1_Winam_Gulf_metagenomic_time_series.csv (Comma Separated Values (.csv), 19.07 KB) MD5:dfafe96a96b20b1b561ba3814c5f1a4d Primary data file for dataset ID 931936, version 1

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Office of International Science and Engineering	IRES-1953468

Deployments

None available yet

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Library_ID	Label the raw sequence library is listed as on the NCBI Sequence Read Archive.	unitless	sequence
Site_Name	The site number and name assigned to the sample site by the captain during that survey.	unitless	site
Replicate_id	The biological replication ID.	unitless	replicate
SampleID	Raw sequence sample ID assigned by sequencing core.	unitless	sample
StudyID	Raw study ID assigned by the sequencing core.	unitless	SRA_study
Sample_type	Type of bioinformatic analysis sample was sequenced for.	unitless	sample_type
Lake_or_river	The name of the lake or river the sample was collected from.	unitless	site
Lat	Latitude coordinates of sample site in decimal degrees; a positive value indicates a Northern coordinate.	decimal degrees	lat
Lon	Longitude coordinates of sample site in decimal degrees; a negative value indicates a Western coordinate.	decimal degrees	lon
Collection_date	The date the sample was collected. Format: %Y-%m-%d	unitless	date
Env_broad_scale	Environment sample corresponds to broadly and corresponding ID.	unitless	sample_descrip
Site_depth	The maximum depth of the water column.	meters (m)	depth_bottom
Sampling_depth	The depth at which the sample was collected in the water column.	meters (m)	depth
Preservation	Type of preservation sample was subjected to for later DNA extraction.	unitless	treatment
Filter_size	The size of the sterivex filter that was used to collect the water sample.	um	filter_size
pH	The pH (in negative log of hydrogen ions).	unitless	pH
Temp	Temperature of the water column.	degrees C	temp
Nitrate	Dissolved nitrate concentration in water sample.	ug / L	NO3
Diss_oxygen	Dissolved oxygen concentration in the water column.	mg / L	O2
Conductivity	Conductivity of the water column.	uS / cm	cond
Secchi	Measure of water transparency.	meters	depth_secchi
Turbidity	Measure of water transparency / cloudiness.	NTU	turbidity
Microcystin	Concentration of cyanobacterial toxin - particulate microcystin - in water column.	ug / L	no_bcodmo_term
TN_TP_ratio	Ratio of total particulate nitrogen to total particulate phosphorus in the water column .	unitless	N_to_P
Chlorophyll_a	Measurement of total chlorophyll a concentration in the water column (greater than 0.22 __m size).	ug / L	chl_a
Total_phosphorus	Total particulate phosphorus concentration in the water column.	ug / L	P
Dissolved_phosphorus	Dissolved phosphorus concentration in the water column.	ug / L	DOP
Soluble_reactive_phosphorus	Dissolved soluble reactive phosphorus concentration in the water column.	ug / L	P
Ammonia	Dissolved ammonia concentration in the water column.	ug / L	NH3
Nitrate_Nitrite	Dissolved nitrate + nitrite concentration in the water column.	umol / L	NO3_NO2
Nitrite	Dissolved nitrite concentration in the water column.	umol / L	NO3
Silicate	Dissolved silicate concentration in the water column.	umol / L	Silicate
Total_nitrogen	Total particulate nitrogen concentration in the water column.	umol / L	N
Total_dissolved_nitrogen	Total dissolved nitrogen concentration in the water column.	ug / L	N
Weather	Weather observations during sample collection.	unitless	weather
Wave_height	Wave height in body of water.	meters	wave_height
Wind_speed	Wind speed at time of sample colelction.	knots	no_bcodmo_term
Salinity	Salinity of the water column.	g / kg	sal
Atmospheric_temperature	Temperature of the air.	degrees C	temp_air
Particulate_cylindrospermopsin	Concentration of cyanobacterial toxin - particulate cylindrospermopsin - in water column.	ng / mL	no_bcodmo_term
ORP	Oxidation-Reduction Potential of water column.	mV	Ox_Red
Algal_Torch_cyano_sonde	Concentration of cyanobacterial cells (those possessing phycocyanin pigment) in the water column.	cells / L	no_bcodmo_term
Algal_Torch_sonde_total_cells	Concentration of all photosynthetic cells (those possessing chlorophyll a) in the water column.	cells / L	chl_a
Algal_Torch_percentage_cells_cyano	Percentage of cyanobacteria cells compared to the entire photosynthetic community.	unitless	no_bcodmo_term
Site_Description	Additional sample site descriptors that have regional or ecological context.	unitless	site_descrip
Station_observations	Additional sample site descriptors that have regional or ecological context.	unitless	site_descrip
Site_Classification	Additional sample site descriptors that have regional or ecological context.	unitless	site_descrip
Notes	Further observations made that correspond to data interpretation or would be of use to researchers (including those who collaborated on this project).	unitless	comment