LIMNO_TLICE English utf8 dataset McMurdo Dry Valleys LTER Information Manager im@mcmlter.org pointOfContact 2020-04-20 ISO 19115-2 Geographic Information - North American Profile Metadata - Data with Biological Extensions ISO 19115-2:2009(E) Transplant Lake Integrated Connectivity Experiment (tLICE) in Taylor Valley, Antarctica, January 2018 2020-04-20 publication Rachael Morgan-Kiss Miami University http://miamioh.edu/ morganr2@miamioh.edu https://photopsychrophile.weebly.com pointOfContact documentDigital The purpose of this experiment, performed as part of the McMurdo Dry Valleys Long Term Ecological Research (MCM LTER) program, was to investigate the impact of lake level rise and moat expansion on microbial community diversity and function in the East Lobe of Lake Bonney, located in Taylor Valley, Antarctica. The “tLICE” experiment tested the following MCM5 Hypotheses: H3-Disturbance increases connectivity and accelerates shifts towards homogeneity, and H4-Decreased heterogeneity reduces community resistance and resilience. Lake water from the East Lobe of Lake Bonney was collected at depths representing maximum phytoplankton productivity (5 m, 17 m, 23 m), and transferred to dialysis bags. The bags were then attached to PVC frames and transplanted to new locations within the lake in two experiments: 1) a moat transplant, in which 5 m communities were transplanted to the open water moat; and 2) shallow to deep transplant, in which communities from all three sampling depths were moved 3 m down the water column to mimic approximately one decade of lake level rise. Transplanted samples were incubated under these conditions for two weeks, and then frames were recovered and samples were processed for a number of measurements. This data package includes the following measurements: nutrient concentration, chlorophyll-a content, chlorophyll fluorescence, cell density, amplicon gene sequences (16S and 18S rRNA genes), and physical parameters. Name: Shasten Sherwell Role: associated researcher Name: Kathleen A. Welch Role: lab technician Name: Renée F. Brown Role: data manager completed McMurdo Dry Valleys LTER Information Manager im@mcmlter.org pointOfContact disturbance inorganic nutrients population dynamics theme LTER Core Areas English Lake Bonney is a saline lake with permanent ice cover at the western end of Taylor Valley in the McMurdo Dry Valleys of Victoria Land, Antarctica. It is 7 kilometres or 4.3 mi long and up to 900 metres or 3,000 ft wide. A narrow channel only 50 metres or 160 ft wide. Lake Bonney at Narrows separates the lake into East Lake Bonney 3.32 square kilometres or 1.28 sq mi and West Lake Bonney, 0.99 square kilometres or 0.38 sq mi. The west lobe is flanked by Taylor glacier. Valley: Taylor Distance to Sea : 25 Maximum Length (km): 4.8 Maximum Width (km): 0.9 Maximum Depth (m): 37 Surface Area (km^2): 3.32 Ice Thickness Average Surface (m): 3 - 4.5 Volume (m^3 * 10^6): 54.7 162.536209106445 162.353210449219 -77.724441528320 -77.697700500488 ground condition 2018-01-13 2018-01-28 https://mcm.lternet.edu/sites/default/files/data/LIMNO_TLICE_0.csv LIMNO_TLICE eng; US McMurdo Dry Valleys LTER LIMNO_TLICE Data Source Definition : tLICE measurements Number of Header Lines : 1 Orientation : Column Quote Character : &quot;Field Delimiter : , false DATASET_CODE Internal code COLLECTION_DATE Date sample was collected for analyses. Date Time Format: MM/DD/YYYY LOCATION Lake where sample was collected. SAMPLE_TYPE Was the sample from the water column or the moat? TREATMENT Was the sample a control or transplant? REPLICATE Sample replicate - either A, B, or C. TIMEPOINT T0 = timepoint 0, or the beginning of the experiment for the respective sample. T1 = timepoint 1, or the end of the experiment for the respective sample. DEPTH_M Depth in the water column. SRP_MM Phosphate molar concentration. NO2_MM Nitrite molar concentration. NO3_MM Nitrate molar concentration. NH4_MM Ammonium molar concentration. CHLA_UG_L Chlorophyll-a concentration, as averaged from two replicates. CHLA_BL_UG_L Chlorophyll-a fluorescence of the blue-green algae. CHLA_GR_UG_L Chlorophyll-a fluorescence of the green algae. CHLA_BR_UG_L Chlorophyll-a fluorescence of the brown algae. CHLA_PE_UG_L Chlorophyll-a fluorescence of the phycoerythrin algae. CHLA_TOTAL_UG_L Total chlorophyll-a fluorescence. FV_FM_BL Photochemical efficiency (Fv/Fm) of the blue-green algae. FV_FM_GR Photochemical efficiency (Fv/Fm) of the green algae. FV_FM_BR Photochemical efficiency (Fv/Fm) of the brown algae. FV_FM_PE Photochemical efficiency (Fv/Fm) of the phycoerythrin algae. YII_BL Photosystem II photochemical yield of the blue-green algae. YII_GR Photosystem II photochemical yield of the green algae. YII_BR Photosystem II photochemical yield of the brown algae. YII_PE Photosystem II photochemical yield of the phycoerythrin algae. NPQ_BL Non-photochemical quenching coefficient for the blue-green algae. NPQ_GR Non-photochemical quenching coefficient for the green algae. NPQ_BR Non-photochemical quenching coefficient for the brown algae. NPQ_PE Non-photochemical quenching coefficient for the phycoerythrin algae. NO_BL Non-regulated photochemical quenching coefficient for the blue-green algae. NO_GR Non-regulated photochemical quenching coefficient for the green algae. NO_BR Non-regulated photochemical quenching coefficient for the brown algae. NO_PE Non-regulated photochemical quenching coefficient for the phycoerythrin algae. PHOTOTROPHS_CELLS_ML Phototroph cell density. HETEROTROPHS_LARGE_CELLS_ML Heterotroph cell density, where cell size >1 um. HETEROTROPHS_SMALL_CELLS_ML Heterotroph cell density, where cell size <1 um. ACCN_16S NCBI accession number for associated 16S rRNA gene raw sequence reads. ACCN_18S NCBI accession number for associated 18S rRNA gene raw sequence reads. COMMENTS Comments. DBF https://mcm.lternet.edu/sites/default/files/data/LIMNO_TLICE_0.csv https://mcm.lternet.edu/sites/default/files/data/LIMNO_TLICE_CTP.csv LIMNO_TLICE_CTP eng; US McMurdo Dry Valleys LTER LIMNO_TLICE_CTP Data Source Definition : Physical parameters (i.e., conductivity, temperature, PAR) Number of Header Lines : 1 Orientation : Column Quote Character : &quot;Field Delimiter : , false DATASET_CODE Internal code. Collection Date Date sample was collected. Date Time Format: MM/DD/YYYY LOCATION Lake where sample was collected. SAMPLE_TYPE Was the sample from the water column or the moat? DEPTH_M Depth in the water column. CONDUCTIVITY_MS_CM Conductivity TEMPERATURE_C Water temperature PAR_UMOL_M2_S Photosynthetically active radiation COMMENTS Comments DBF https://mcm.lternet.edu/sites/default/files/data/LIMNO_TLICE_CTP.csv dataset Nutrient concentration Lake water samples were collected at specific depths with a five-liter Niskin bottle. One 100 mL sub-sample was filtered through a combusted (475 degree centigrades for 4 hours) and acidified (the acidification step began with the 2008-2009 season) Whatman 25 mm GF/F using a bell jar apparatus. The filtrate was collected in a 125 mL acid washed Nalgene bottle and stored at -20 degrees centigrades until analysis  at the Crary Analytical Lab. Nutrient assays are performed with a Lachat Quickchem AE Autoanalyzer using standard methods. Ammonia was analyzed using the phenol hypochlorite method. Nitrite was determined by diazotization with sulfanilamide and NED. Nitrate was determined by reducing nitrate to nitrite by passing a sample through a copperized cadmium column and analyzing for nitrite, which yields nitrate + nitrite (N+N) concentration. The nitrate concentration was determined by subtracting the nitrite concentration from the N+N concentration. Soluble Reactive Phosphorus was determined using ammonium molybdate methods. Chlorophyll-a content Lake water samples were collected at specific depths with a five-liter Niskin bottle. Two-100 mL were filtered through a combusted (475 C for 4 hours) Whatman 25 mm GF/F using a bell jar apparatus. The filter was folded in half (organic material inside), placed in a glassine envelope, covered with aluminum foil, and frozen immediately for later analysis at McMurdo Station. All of the following laboratory methods were performed in a darkened environment. At McMurdo Station, a chlorophyll-a stock concentrate was prepared by dissolving 1 mg of chlorophyll-a standard (Sigma, Anacystic nidulans) in a 100 ml volumetric flask and diluting it to mark with 90% acetone (~10,000 micrograms per liter chlorophyll-a). A Beckman DU-640 UV/vis spectrophotometer was used to determine the actual chlorophyll-a concentration of the stock concentrate and the concentration of the stock dilutions. The absorbance of the stock concentrate was measured at 665 nm and 750 nm (non-acidified readings are denoted by a subscript "o"). The stock concentrate was acidified in the cuvette using 2-4 drops of 3 N HCl. The absorbance after acidification was measured at 665 nm and 750 nm (acidified readings are denoted by a subscript "a"). Chlorophyll-a content was determined using the following equation (Strickland and Parsons 1972; Parsons et al. 1984): Chl-a (micrograms per liter)= [26.7*((ABS665o - ABS665a) - (ABS750o - ABS 750a))*1000]/l where: ABS665o = ABS at 665 nm with no acid ABS665a = ABS at 665 nm plus acid ABS750o = ABS at 750 nm with no acid ABS750a = ABS at 750 nm with acid l = cuvette path length (1 cm) The stock solution was used to prepare six to ten standard dilutions of chlorophyll-a ranging from ~1.5 micrograms per liter to 500 micrograms per liter, plus a blank of 90% acetone. 90% acetone was used to dilute the standards. Fo and Fa were obtained for each standard by collecting initial fluorescence data on the Turner 10-AU fluorometer, and then acidifying the standard in the cuvette with 4 drops of 3 N HCl. The cuvette was briefly vortexed before determining Fa. The actual concentrations of the working standards were computed from the spectrophotometrically determined concentration of the stocks. A standard curve of chlorophyll-a concentration vs Fo-Fa was prepared. Each filter was placed into a 20 ml scintillation vial and extracted with 10 ml of 90% acetone. The extract was incubated for ~12 hours under cold (&lt;0C), dark conditions. After incubation, the extract was briefly vortexed and 4 ml dispensed into the cuvette; the cuvette was inserted into the Turner 10-AU fluorometer. After Fo was determined, the sample was acidified with 4 drops of 3 N HCl, vortexed, and Fa was determined. The cuvette was rinsed three times with DI water and three times with 90% acetone to ensure there was no cross contamination of sample or acid between samples. The cuvette exterior was wiped with Kimwipes. The Fo-Fa was determined for each sample and chlorophyll-a concentration (microgram per liter) was calculated by comparison with the standard curve as below: Chlorophyll-a (micrograms per liter) = (((Fo-Fa) - y-intercept)/slope) * (ml extracted/ml filtered), where: Fo-Fa = measured sample fluorescence minus acidified fluorescence y-intercept = fluorescence when Chl-a concentration is zero slope = fluorescence/Chl-a (micrograms per liter) ml extracted = ml of 90% acetone used to extract the Chl-a on the filters ml filtered = ml of actual sample filtered in the field Chlorophyll fluorescence Samples were collected from various depths with a 5-L niskin bottle or dialysis bags. Chlorophyll fluorescence measurements were also conducted using the PHYTO-PAM II phytoplankton analyzer (Heinz Walz, Effeltrich, Germany). Prior to deployment in the field, algal references were constructed in the laboratory using pure cultures of Lake Bonney algae, Chlamydomonas sp. ICE-MDV (chlorophytes), Isochrysis sp. MDV (mixed/brown group), and an Antarctic cryptophyte, Gemigera cryophila. These references were then used to deconvolute the algal classes and estimate Chlorophyll-a/L. In addition, the following PSII photochemical parameters were measured for each algal class: i) FV/FM – maximum PSII photochemical efficiency, ii) Y(PSII) – effective quantum yield of PSII, iii) Y(NPQ) – non photochemical quenching, iv) Y(NO) – non-regulated nonphotochemical quenching. Cell density Lake water was collected with a 5-L niskin bottle. 4.5 mL of lake water was transferred to a 5 mL cryovial and 500 μL of TE glycerol buffer (5% glycerol + 1XTE buffer) was added. Samples were flash frozen in liquid nitrogen and shipped back to the US on dry ice. Flow cytometry was performed on a BD Acurri flow cytometer. Samples were passed through a 40 μm filter, various stains were applied, and measurements were taken for a minimum of 30,000 events. Analysis of the events consisted of first gating for singlet cells by graphing FSC-H vs FSC-A. SYBR® Green I was used to count bacteria by adding 10 μl of working stock (1:100 dilution in DMSO) to 500 μl of sample in black tubes, inverting 10 times, and incubating on ice for 10 minutes before measuring on FL1. Chlorophyll autofluorescence (~430/670) was monitored on unstained samples on channel FL3 (488/&gt;670). Amplicon gene sequences Samples collected from the water column (500 mL) or dialysis bags (200-300 mL) were gently vacuum filtered (0.3 mBar) onto 47 mm Pall Supor® 450 polyethersulfone membranes (Pall Corporation, NY). Filters were immediately cryopreserved in liquid nitrogen and stored at -80 until nucleic acid extraction. DNA from filters was extracted with the MP FastDNATM SPIN DNA kit (MP Biomedicals, CA) following the manufacturer’s instructions. The V4 of the 16S rRNA gene and the V9 of the 18S rRNA gene were amplified using the primer sets which encode F515/R806 for bacteria and F1391/R1501 for eukaryotes. Both PCR and MiSeq sequencing reactions were performed following protocols provided by the Earth Microbiome Project. We sequenced samples in-house using a 300-cycle MiSeq Reagent Kit v2 (Illumina, CA) on a MiSeq platform with a 2 X 150 bp paired-end run in the presence of 25 % PhiX sequencing control DNA. Sequences are embedded in a single fastq file (one each for 16S and 18S) which pools together all the raw sequences from the project.  Physical parameters A LI-COR LI-193SA spherical quantum sensor and a LI-190SA flat sensor were attached to a LI-COR datalogger to record instantaneous under-ice PAR and PAR incident on the surface of the lake ice. Data were recorded in an outside incubation hole covered by an opaque tarp, unless otherwise noted. The upper 3-6 meters of each profile, depending upon ice thickness for each lake, represents conditions within the ice melt hole and is not representative of actual lake water.  Metadata Access Constraints: none Metadata Use Constraints: none annually McMurdo Dry Valleys LTER http://mcmlter.org/ pointOfContact