Rachael M. Morgan-Kiss 2020-04-20 tabular digitial data McMurdo Dry Valleys LTER McMurdo Dry Valleys LTER 10.6073/pasta/00cbcc20ab63feb5bb69a9109f35b697 https://mcm.lternet.edu/content/transplant-lake-integrated-connectivity-experiment-tlice-taylor-valley-antarctica-january 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. 2018-01-13 2018-01-28 ground condition As needed 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 -77.697700500488 -77.724441528320 57m 57m meter LTER Core Areas disturbance inorganic nutrients population dynamics None <cntperp> <cntper>McMurdo Dry Valleys LTER Information Manager</cntper> </cntperp> <cntemail>im@mcmlter.org</cntemail> Name: Shasten Sherwell Role: associated researcher Name: Kathleen A. Welch Role: lab technician Name: Renée F. Brown Role: data manager Not Applicable Not Applicable Field and/or Lab Methods 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.  Nutrient concentrationLake 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 contentLake 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 acidABS665a = ABS at 665 nm plus acidABS750o = ABS at 750 nm with no acidABS750a = ABS at 750 nm with acidl = 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 (<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 fluorescencey-intercept = fluorescence when Chl-a concentration is zeroslope = fluorescence/Chl-a (micrograms per liter)ml extracted = ml of 90% acetone used to extract the Chl-a on the filtersml filtered = ml of actual sample filtered in the fieldChlorophyll fluorescenceSamples 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 densityLake 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/>670).Amplicon gene sequencesSamples 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 parametersA 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.  unknown LIMNO_TLICE tLICE measurements Dataset code Internal code The data provider Internal code Sample collection date. Date sample was collected for analyses. The data provider calendar date/time MM/DD/YYYY gregorian calendar Location Lake where sample was collected. The data provider Lake where sample was collected. Sample type Was the sample from the water column or the moat? The data provider Was the sample from the water column or the moat? Treatment Was the sample a control or transplant? The data provider Was the sample a control or transplant? Sample replicate Sample replicate - either A, B, or C. The data provider 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. The data provider 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 Depth in the water column. The data provider meter Soluble reactive phosphorus Phosphate molar concentration. The data provider milliM Nitrite concentration Nitrite molar concentration. The data provider milliM Nitrate concentration Nitrate molar concentration. The data provider milliM Ammonium concentration Ammonium molar concentration. The data provider milliM Chlorophyll-a concentration. Chlorophyll-a concentration, as averaged from two replicates. The data provider microgramsPerLiter Chlorophyll-a fluorescence (blue-green algae) Chlorophyll-a fluorescence of the blue-green algae. The data provider microgramsPerLiter Chlorophyll-a fluorescence (green algae) Chlorophyll-a fluorescence of the green algae. The data provider microgramsPerLiter Chlorophyll-a fluorescence (brown algae) Chlorophyll-a fluorescence of the brown algae. The data provider microgramsPerLiter Chlorophyll-a fluorescence (phycoerythrin algae) Chlorophyll-a fluorescence of the phycoerythrin algae. The data provider microgramsPerLiter Total chlorophyll-a fluorescence. Total chlorophyll-a fluorescence. The data provider microgramsPerLiter Photochemical efficiency (blue-green algae) Photochemical efficiency (Fv/Fm) of the blue-green algae. The data provider Photochemical efficiency (Fv/Fm) of the blue-green algae. Photochemical efficiency (green algae) Photochemical efficiency (Fv/Fm) of the green algae. The data provider Photochemical efficiency (Fv/Fm) of the green algae. Photochemical efficiency (brown algae) Photochemical efficiency (Fv/Fm) of the brown algae. The data provider Photochemical efficiency (Fv/Fm) of the brown algae. Photochemical efficiency (phycoerythrin algae) Photochemical efficiency (Fv/Fm) of the phycoerythrin algae. The data provider Photochemical efficiency (Fv/Fm) of the phycoerythrin algae. Photosystem II photochemical yield (blue-green algae) Photosystem II photochemical yield of the blue-green algae. The data provider Photosystem II photochemical yield of the blue-green algae. Photosystem II photochemical yield (green algae) Photosystem II photochemical yield of the green algae. The data provider Photosystem II photochemical yield of the green algae. Photosystem II photochemical yield (brown algae) Photosystem II photochemical yield of the brown algae. The data provider Photosystem II photochemical yield of the brown algae. Photosystem II photochemical yield (phycoerythrin algae) Photosystem II photochemical yield of the phycoerythrin algae. The data provider Photosystem II photochemical yield of the phycoerythrin algae. Non-photochemical quenching coefficient (blue-green algae) Non-photochemical quenching coefficient for the blue-green algae. The data provider Non-photochemical quenching coefficient for the blue-green algae. Non-photochemical quenching coefficient (green algae) Non-photochemical quenching coefficient for the green algae. The data provider Non-photochemical quenching coefficient for the green algae. Non-photochemical quenching coefficient (brown algae) Non-photochemical quenching coefficient for the brown algae. The data provider Non-photochemical quenching coefficient for the brown algae. Non-photochemical quenching coefficient (phycoerythrin algae) Non-photochemical quenching coefficient for the phycoerythrin algae. The data provider Non-photochemical quenching coefficient for the phycoerythrin algae. Non-regulated photochemical quenching coefficient (blue-green algae) Non-regulated photochemical quenching coefficient for the blue-green algae. The data provider Non-regulated photochemical quenching coefficient for the blue-green algae. Non-regulated photochemical quenching coefficient (green algae) Non-regulated photochemical quenching coefficient for the green algae. The data provider Non-regulated photochemical quenching coefficient for the green algae. Non-regulated photochemical quenching coefficient (brown algae) Non-regulated photochemical quenching coefficient for the brown algae. The data provider Non-regulated photochemical quenching coefficient for the brown algae. Non-regulated photochemical quenching coefficient (phycoerythrin algae) Non-regulated photochemical quenching coefficient for the phycoerythrin algae. The data provider Non-regulated photochemical quenching coefficient for the phycoerythrin algae. Phototroph cell density Phototroph cell density. The data provider cellsPerMilliliter Heterotroph cell density, where cell size >1 um Heterotroph cell density, where cell size >1 um. The data provider cellsPerMilliliter Heterotroph cell density, where cell size <1 um Heterotroph cell density, where cell size <1 um. The data provider cellsPerMilliliter Accession number (16S rRNA genes) NCBI accession number for associated 16S rRNA gene raw sequence reads. The data provider NCBI accession number for associated 16S rRNA gene raw sequence reads. Accession number (18S rRNA genes) NCBI accession number for associated 18S rRNA gene raw sequence reads. The data provider NCBI accession number for associated 18S rRNA gene raw sequence reads. Comments Comments. The data provider Comments. McMurdo Dry Valleys LTER The data distributor shall not be liable for innacuracies in the content http 1 0 1 column , https://mcm.lternet.edu/sites/default/files/data/LIMNO_TLICE_0.csv None LIMNO_TLICE_CTP Physical parameters (i.e., conductivity, temperature, PAR) Dataset code Internal code. The data provider Internal code. Sample collection date. Date sample was collected. The data provider calendar date/time MM/DD/YYYY gregorian calendar Location Lake where sample was collected. The data provider Lake where sample was collected. Sample type Was the sample from the water column or the moat? The data provider Was the sample from the water column or the moat? Depth Depth in the water column. The data provider meter Conductivity Conductivity The data provider millisiemensPerCentimeter Temperature Water temperature The data provider celsius PAR Photosynthetically active radiation The data provider micromolePerMeterSquaredPerSecond Comments Comments The data provider Comments McMurdo Dry Valleys LTER The data distributor shall not be liable for innacuracies in the content http 1 0 1 column , https://mcm.lternet.edu/sites/default/files/data/LIMNO_TLICE_CTP.csv None 2020-04-20 2020-04-20 McMurdo Dry Valleys LTER http://mcmlter.org/ Biological Data Profile of the Content Standards for Digital Geospatial Metadata devised by the Federal Geographic Data Committee. Drupal Ecological information Management Systems, version D7, Biological Data Profile module