uid=MCM,o=EDI,dc=edirepository,dc=org all public read limno_bacteria Cristina Takacs-Vesbach cvesbach@unm.edu http://www.wildmicrobiome.org https://orcid.org/0000-0002-5535-2201 John Priscu jpriscu@montana.edu https://orcid.org/0000-0001-5807-6364 McMurdo Dry Valleys LTER http://mcmlter.org/ Jade Lawrence jlawrence1@unm.edu https://orcid.org/0009-0005-2603-342X field technician Kathleen Welch kathleen.welch@colorado.edu https://orcid.org/0000-0003-1028-3086 lab technician Renée Brown rfbrown@unm.edu https://orcid.org/0000-0002-4986-7663 data manager Amy Chiuchiolo

LRES, 334 Leon Johnson Hall Bozeman MT 59717 US

(406) 994-2360 (406) 994-5863 achiuchiolo@montana.edu former field crew Inigo San Gil

Department of Biology, MSC03 2020 University of New Mexico Albuquerque NM 87131 US

(505) 277-2625 (505) 277-2541 isangil@lternet.edu former data manager 2025-02-19 English

An important part of the McMurdo Long Term Ecological Research (LTER) is monitoring of spatial and temporal patterns, and processes that control bacterial production in perennial ice-covered lakes. This data set quantifies thymidine (TdR) uptake by bacteria, which can be used to estimate bacterial production.

bacteria bacterial production limnology LTER Controlled Vocabulary Antarctica bacteria lake limnology production thymidine Station Keywords population dynamics LTER Core Areas The energy of activation was experimentally derived for Lake Bonney (Priscu, unpublished). If the average of the kill treatment uptake exceeds live treatment uptake, uptake is reported as zero.

This data package is released under the Creative Commons Attribution 4.0 International License (CC BY 4.0; http://creativecommons.org/licenses/by/4.0/), which allows consumers (hereinafter referred to as “Data Users”) to freely reuse, redistribute, transform, or build on this work (even commercially) so long as appropriate credit is provided. Accordingly, Data Users are required to properly cite this data package in any publications or in the metadata of any derived products that result from its use (in whole or in part). A recommended citation is provided on the summary metadata page associated with this data package in the McMurdo Dry Valleys LTER Data Catalog (https://mcmlter.org/data), and a generic citation may be found on the summary metadata page in the repository where this data package was obtained. When these data contribute significantly to the contents of a publication, Data Users must also acknowledge that data were provided by the NSF-supported McMurdo Dry Valleys Long Term Ecological Research program (OPP-2224760). This data package has been released in the spirit of open scientific collaboration. Hence, Data Users are strongly encouraged to consider consultation, collaboration, and/or co-authorship (as appropriate) with the data package creator(s). Data Users should be aware these data may be actively used by others for ongoing research; thus, coordination may be necessary to prevent duplicate publication. Data Users should also recognize that misinterpretation of data may occur if they are used outside the context of the original study. Hence, Data Users are urged to contact the data package creator(s) if they have any questions regarding methodology or results. While substantial efforts are made to ensure the accuracy of this data package (with all its components), complete accuracy cannot be guaranteed. Periodic updates to this data package may occur, and it is the responsibility of Data Users to check for new versions. This data package is made available “as is” and comes with no warranty of accuracy or fitness for use. The creator(s) of this data package and the repository where these data were obtained shall not be liable for any damages resulting from misinterpretation, use, or misuse of these data. Finally, as a professional courtesy, we kindly request Data Users notify the primary contact referenced in the metadata when these data are used in the production of any derivative work or publication. Notification should include an explanation of how the data were used, along with a digital copy of the derived product(s). Thank you.

https://mcm.lternet.edu/content/thymidine-uptake-rates-estimating-bacterial-production-lakes-mcmurdo-dry-valleys-antarctica 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): 54.7 162.353210449219 162.536209106445 -77.697700500488 -77.724441528320 57 57 meter 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. Valley: Taylor Distance to Sea : 28 Maximum Length (km): 2.6 Maximum Width (km): 0.9 Maximum Depth (m): 40 Surface Area (km^2): 0.99 Ice Thickness Average Surface (m): 2.8-4.5 Volume (m^3 * 10^6): 10.1 162.269104003906 162.354934692383 -77.714805603027 -77.727287292480 57 57 meter The Lake Fryxell basin is formed by a moraine depression in a wider portion of the Taylor Valley. It has a number of moraine islands and shallower areas, as well as several relatively well developed deltas. The lake is fed by at least 10 meltwater streams with a total drainage catchment of 230 km2. The lake is dammed to the southwest by the Canada Glacier and is topographically closed. It is perennially ice covered; during summer months, an ice-free moat generally forms around much of the lake margin. Lake levels have risen ~2 m between 1971 and 1996. There are no surface outflows; the only known water loss is through ice ablation (evaporation, sublimation and physical scouring). Valley: Taylor Distance to Sea : 9 Maximum Length (km): 5.8 Maximum Width (km): 2.1 Maximum Depth (m): 20 Surface Area (km^2): 7.08 Ice Thickness Average Surface (m): 3.3 - 4.5 Volume (m^3 * 10^6): 25.2 163.048782348633 163.259582519531 -77.597076416016 -77.622711181641 18 18 meter Lake Hoare occupies a narrower portion of the Taylor Valley, dammed by the Canada Glacier. It would drain almost completely without this dam. There are a number of islands which may be related to an old terminal of Canada Glacier. The lake is fed primarily from direct runoff from the glacier, as well as meltwater streams. (Lake level rose ~1.5 m between 1972 and 1996). There are no surface outflows; the only known water loss is through ice ablation (evaporation, sublimation and physical scouring). Valley: Taylor Distance to Sea : 15 Maximum Length (km): 4.2 Maximum Width (km): 1 Maximum Depth (m): 34 Surface Area (km^2): 1.94 Ice Thickness Average Surface (m): 3.1 - 5.5 Volume (m^3 * 10^6): 17.5 162.784423828125 162.935836791992 -77.623085021973 -77.639259338379 73 73 meter Lake Joyce lies in the Pearse Valley against the Taylor Glacier. Valley: Pearse Distance to Sea : 44 Maximum Length (km): 1 Maximum Width (km): 1 Maximum Depth (m): 35 Surface Area (km^2): 0.83 Ice Thickness Average Surface (m): 3.9 - 5.6 Volume (m^3 * 10^6): 4.9 161.608886718750 161.662445068359 -77.715972900391 -77.726486206055 301 301 meter Lake Miers lies in the Miers Valley. Valley: Miers Distance to Sea : 20 Maximum Length (km): 1.5 Maximum Width (km): 0.7 Maximum Depth (m): 21 Surface Area (km^2): 1.3 Ice Thickness Average Surface (m): 3.4 - 6 Volume (m^3 * 10^6): 2.9 163.812332153320 163.886840820313 -78.094047546387 -78.101478576660 240 240 meter Lake Vanda is located in the Wright Valley, adjacent to the Taylor Valley. It is fed primarily by the Onyx River, which has its origin at Lake Brownworth, and ultimately at the Lower Wright Glacier located ~27 km east of the lake. The lake has no outflow. Valley: Wright Distance to Sea : 47 Maximum Length (km): 8 Maximum Width (km): 2 Maximum Depth (m): 75 Surface Area (km^2): 5.2 Ice Thickness Average Surface (m): 2.8 - 4.2 Volume (m^3 * 10^6): 160 161.391906738281 161.691970825195 -77.518882751465 -77.542304992676 143 143 meter 1993-10-27 2023-11-21 Data from this table was submitted to INSTAAR by John Priscu's team at Montana State University. The raw data files listed  under 'file name' are the names of the original files submitted. The 1993/94 and 1994/95 datasets are Microsoft Excel version 6.0 files, and  the 1995/96, 1996/97 and 1997/98 datasets are ascii text files. Upon arrival at INSTAAR, the data manager fine-tuned the location codes and  limno runs to match those provided in the "locations, dates, codes for lake chemistry, biology samples" file. The file was imported into Microsoft Access on INSTAAR's Unix system, and can currently be found there. The file was then exported in ascii, comma delimited text and MS-DOS text (table layout) on the MCM LTER web site. Both of these files are linked to this web page above. Information for the metadata was  obtained from the Metatdr9697.rtf file. The file was called up using  Microsoft Word version 6.0. Text from this file was used to create this page in html format.   In 2006, this metadata was standardized by Chris Gardner and Inigo San Gil using the EML format.     In 2014, this metadata was enhanced using the Drupal Ecological Information Management System (Inigo San Gil)   Per A. Chiuchiolo and J. Priscu suggestion, 4 columns were added to the data table to reflect new methodologies: Starting season 06/07, we included Leucine measurements in our bacterial production assay, and we also started a new method and did comparisons with the old method. McMurdo Dry Valleys LTER Information Manager im@mcmlter.org McMurdo Dry Valleys LTER http://mcmlter.org/ McMurdo Dry Valleys LTER

Lake water samples were collected at specific depths with a five-liter Niskin bottle during normal LTER limnological sampling. Sub-samples were decanted into three 1-L Nalgene bottles (2-light and 1-amber), two-500 mL amber Nalgene bottles, three-150 mL borosilicate glass bottles, two-20 mL scintillation vials, and one-30 mL serum vial. Five-20 mL scintillation vials (3-live treatments, 2-kill treatments) were prepared at each depth for TDR analysis. TDR samples (10 mL) were taken from the one-liter amber Nalgene bottle and placed in each scintillation vial. 0.5 mL filtered formalin (0.2 micro m) was pipetted into each killed treatment vial. 3H Thymidine was pipetted into each vial (final concentration of 20 nM thymidine), first the live treatments and then the kill treatments. Samples were incubated in the dark at 1-4 degC for 20 hours (thymidine incorporation has been shown to be linear for 20 hours under these conditions, Priscu unpublished). At the end of the incubation period 10 mL of ice cold 10 percent TCA was added to stop thymidine uptake and precipitate nucleotides. Vials were stored at 4 degC until filtered. Each sample was filtered through a 0.2 micro m Nucleopore polycarbonate membrane filter. Both the scintillation vial and filter tower were rinsed three times with 5 percent TCA. Each filter was placed into a new scintillation vial and 15 mL of Cytoscint cocktail was added. Samples were counted with a pre-calibrated (3H) liquid scintillation counter. Thymidine uptake rate (TDR nM d-1) was calculated using the following equation: nM TDR/day = (DPML - DPMK) * a /(alpha * t)  where DPML is the average dpm for the live treatment, DPMK is the average dpm for the kill treatment, a is the final concentration of thymidine in each vial (20nM), alpha is the total dpm added to each vial, and t is the incubation period. The thymidine uptake rate was adjusted to the ambient lake temperature using the Arrhenius equation: TDRadj = TDR * e^(Ea (( 1 / (CI + 273 K)) - ( 1 / (CA + 273K))) / R )   where Ea is the energy of activation (12,600 cal mol-1, Q10 = 2.2),degCI is the incubation temperature (degC),degCA is the ambient lake water temperature at specific depth,and R is a gas constant (1.987 cal mol-1 K-1). During the 0607 season, the Priscu group did a comparison of the "filtration method" used in previous seasons (see above and also Appendix 6.11 "Previously used Methods" of the Limnological Methods Manual; Takacs, C.T. and J.C. Priscu. 1998. Bacterioplankton dynamics in the McMurdo Dry Valley lakes: Production and biomass loss over four seasons. Microbial Ecology 36:239-250), with the "centrifugation method" used by the Palmer (PAL) LTER (Fuhrman, J. A. and F. Azam. 1982. Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: evaluation and field results. Marine Biology 66:109-120). Results showed no significant difference between the two methods (ELB 0-20 m: mean and standard deviation of nM TDR/d determined via filtration method, 0.0114 and 0.0097, respectively; mean and standard deviation of nM TDR/d determined via centrifugation method, 0.0129 and 0.0131, respectively; paired t-test T value, -1.063; P value, 0.328). We therefore continued measurement of bacterial production in seasons following the 0607 season using the centrifugation method. We also complemented our thymidine data with 3H-leucine incorporation data, as is done in the PAL LTER, for selected seasons for comparative purposes. The new method via centrifugation is as follows: Lake water samples were collected at specific depths with a five-liter Niskin bottle during normal LTER limnological sampling. Sub-samples were decanted into two 1-L Nalgene bottles (amber). Five-2 mL microcentrifuge tubes (3-live treatments, 2-kill treatments) were prepared at each depth for TDR or Leu analysis. 3H Thymidine or Leucine was pipetted into each live treatment tube (final concentration of 20 nM). Samples (1.5 mL) were taken from a one-liter amber Nalgene bottle and placed in each tube (both live and kill treatments). Live tubes were capped, inverted several times, and incubated in the dark at 1-4 deg C for 20 hours (thymidine incorporation has been shown to be linear for 20 hours under these conditions, Priscu unpublished). 100 micro L of ice cold 100 percent TCA was added to each kill treatment tube. Tubes were capped, inverted several times, and placed on ice for 15 minutes. 3H Thymidine or Leucine was pipetted into each kill treatment tube (final concentration of 20 nM). Tubes were capped and incubated in the dark at 1-4 deg C for 20 hours. At the end of the incubation period, 100 micro L of ice cold 100 percent TCA was added to the live treatment tubes to stop thymidine or leucine uptake and precipitate nucleotides. Samples were inverted and placed on ice for 15-30 minutes. All tubes were stored at 4 deg C until processing. Each sample was centrifuged at 14,000 (~15,000 x g) for 15 minutes. Supernatant was poured out and tube was tapped to get the last drops out of the tube. 1 ml of cold 5 percent TCA was added to each tube. Tubes were re-spun for 5 minutes, supernatant poured out, and tube tapped to get the last drops out. 1 ml of cold 80 percent ethanol was added to each tube. Tubes were re-spun for 5 minutes, supernatant poured out, and tube tapped to get the last drops out. Tubes were dried overnight in fume hood with caps off. 1 ml of Cytoscint ES scintillation cocktail was added to each tube, tubes were vortexed, and samples were counted with a pre-calibrated (3H) liquid scintillation counter. Thymidine or Leucine uptake rate (TDR or Leu nM d-1) was calculated using the following equation: nM TDR or Leu day -1 = ((DPML - DPMK) * a) / (alpha * t) where DPML is the average dpm for the live treatment,DPMK is the average dpm for the kill treatment,a is the final concentration of thymidine in each vial (20nM),alpha is the total dpm added to each vial, and t is the incubation period. The thymidine or leucine uptake rate was adjusted to the ambient lake temperature using the Arrhenius equation: TDR or LEU adj = TDR or Leu * e^(Ea (( 1 / (CI + 273 K)) - ( 1 / (CA + 273 K))) / R ) where Ea is the energy of activation (12,600 cal mol-1, Q10 = 2.2),degCI is the incubation temperature (degC),degCA is the ambient lake water temperature (degC) at specific depth,and R is a gas constant (1.987 cal mol-1 K-1).

LIMNO_BACT_PROD mcmlter-lake-bacterial_production-20250218.csv 392654 1 1 \n column , " https://mcm.lternet.edu/sites/default/files/data/mcmlter-lake-bacterial_production-20250218.csv DATASET_CODE DATASET_CODE Code to ID the data table string Code to ID the data table LIMNO_RUN Limno Run Code for lake's sampling location and date string Code for lake's sampling location and date LOCATION NAME LOCATION NAME Name of lake where measurement was made string Name of lake where measurement was made LOCATION CODE LOCATION CODE Code for site where measurement was made string Code for site where measurement was made DATE_TIME DATE_TIME Date on which sample was gathered date mm/dd/yyyy DEPTH (m) DEPTH (m) Distance below ice from which sample was drawn meter 1 real 1 25 Required entry None given TDR (nM TDR/day) TDR (nM TDR/d) Thymidine uptake rate using tritiated thymidine and the filtration method. nMTDR/day 0.001 real 0 1 Null None given TDR COMMENTS TDR COMMENTS Helpful hints about the sample string Helpful hints about the sample FILE NAME FILE NAME Name of file in which data was submitted string Name of file in which data was submitted DEPTH MASL DEPTH MASL Depth referred to the Sea level. Distance below Mean Average Sea water level reference from which sample was drawn meter 1 real TDR CENT (nM TDR/day) TDR CENT (nM TDR/day) Thymidine uptake rate using tritiated thymidine and the centrifugation method. nMTDR/day 0.001 real 0 1 Null None given TDR CENT COMMENTS TDR CENT COMMENTS Helpful hints about the sample string Helpful hints about the sample LEU CENT (nM Leu/day) LEU CENT (nM Leu/day) Leucine uptake rate using tritiated leucine and the centrifugation method nM Leu/day 0.001 real 0 1 Null None given LEU CENT COMMENTS LEU CENT COMMENTS Helpful hints about the sample string Helpful hints about the sample