News

20
April
2019

Postdoc position on Nitrogenase biogeochmistry

We have an opening for a postdoc at the Princeton Environmental Institute as part of a NASA funded project to the Zhang and Kopf labs to study microbial biogeochemistry of the nitrogen cycle. The link to the position is https://www.princeton.edu/acad-positions/position/11441

7
April
2019

3rd Rocky Mountain Geobiology Symposium

The annual Rocky Mountain Geobiology Symposium took place at CU Boulder this year for the first time. A huge thanks to the grad student organizing team and everyone for joining us and making it such a fantastic day of fun science

20
March
2019

Kick-off for the Center for Microbial Exploration (CME) at CU Boulder

Fantastic kick-off event for CU’s new Center for Microbial Exploration connecting faculty and students interested in microbial research across the campus. Check out upcoming events on the CME website.

15
January
2019

Shaelyn's first paper out in print!

Silverman SN, Kopf SH, Bebout BM, Gordon R, Som SM. Morphological and isotopic changes of heterocystous cyanobacteria in response to N2 partial pressure. Geobiology. 2019;17:60–75. Congratulations to Shae, first student-lead paper from the lab! All data and analysis available on GitHub. Explore them interactively on Binder Binder.

5
January
2019

Launch of the isoverse

Isoverse is a suite of platform-independent (Windows, Mac, Linux), open-source data tools for the efficient and reproducible processing of stable isotope data. Although written primarily in R, it can be used in both RMarkdown as well as Jupyter data processing notebooks. Due to the design based on the popular tidyverse style of R programming, all isoverse packages are easily extendable and work great with tidyverse packages such as tidyr, dplyr and ggplot. It includes isoreader to read IRMS data files, isoprocessor to perform common calculations on IRMS data, and isoviewer to process files interactively... read more
7
December
2018

New labware: balch tube tower

The Tube Tower is a flexible 3D printer layout for small foot print vertical incubation of anaerobic (i.e. stoppered & crimp-sealed) balch culture tubes. Gas exchange between media and headspace is maximized due to the horizontal position of the tubes. Tubes are secured in place with a 6” (15.2cm) wide 1/8” (3.2mm) thick standard acryl panel that slides in from... read more
1
December
2018

Two new papers on lipid-SIP

Two new papers out in the Journal of Bacteriology and Rapid Communications in Mass Spectrometry, respectively, by Caltech collaborator Caj Neubauer on refinements of heavy water lipid-SIP and its application in cystic fibrosis research: Refining the Application of Microbial Lipids as Tracers of Staphylococcus aureus Growth Rates in Cystic Fibrosis Sputum and Towards measuring growth rates of pathogens during infections by D2O-labeling lipidomics. Congrats Caj! See publications for full references and this link for a great commentary on this work by Tara Gallagher, Joann Phan and Katrine Whiteson.

12
November
2018

Princeton-Boulder Exchange: Ciara visiting the Sigman Lab

Grad. student Ciara Asamoto continues the Princeton-Boulder exchange with a visit to the Sigman Lab.

1
October
2018

New paper on nitrogen isotopes under iron limitation

New paper out in Geochimica et Cosmochimica Acta by Princeton collaborator Darcy McRose on the Effect of iron limitation on the isotopic composition of cellular and released fixed nitrogen in Azotobacter vinelandii. Congrats Darcy! See publications for full reference.

15
September
2018

New paper on carbon isotopes in methanogenesis

New paper out in Geochimica et Cosmochimica Acta by Templeton Lab student Hannah Miller on Large carbon isotope variability during methanogenesis under alkaline conditions. Congrats Hannah! See publications for full reference.

22
August
2018

New general interest science class: Our Microbial Planet

Microbes are everywhere! They are the unseen force that rules our planet – present, past and future. Ingenious tiny master chemists too small to see by naked eye yet so powerful and resilient they can survive even the most extreme places on our planet – boiling hot, freezing cold, bone-dissolving acid, the vacuum of space! We invite you to join... read more
1
August
2018

Princeton-Boulder Exchange: Zhang lab members visit CU Boulder

Zhang Lab members Eunah Han and Dr. Ashley Maloney visit the Geomicrobial Physiology Lab for the summer. Welcome Eunah and Ashley!

26
July
2018

Geobio summer celebration

The Geobio crew celebrates at the Rayback Collective and says good-bye and thank you to Nabil and our visitor from Israel Ari Meilijson

2
June
2018

New labware: headplate holder

The headplate holder makes upright assembly of chemostat head plates easy without the risk of damaging head plate attachments or needing to work on the glass vessel itself. The holders can be stacked for headplates with attachments that are too long for a single holder (see example on the right). read more
8
April
2018

2nd Rocky Mountain Geobiology Symposium

The second Rocky Mountain Geobiology Symposium (RMGS) once again took place at the Colorado School of Mines in Golden, CO. Enormous thanks to John Spear, Emily Kraus, Blake Stamps and everyone at Mines for organizing the second symposium and a fantastic day of science with participants from all over the Rocky Mountain states.

14
December
2017

New paper on virus-host interactions

New paper out in Environmental Microbiology from work spear-headed by collaborator Ally Pasulka, Interrogating marine virus‐host interactions and elemental transfer with BONCAT and nanoSIMS‐based methods. Congrats Ally! See publications for full reference. Supplementary materials available on GitHub.

4
December
2017
21
August
2017

New upper level class: Introduction to Geomicrobiology

Welcome to our microbial world! Microbes are everywhere - including the human body where they outnumber your own cells by ~10 to 1. They have co-evolved with the Earth’s environment for billions of years and are the most ingenious chemists on the planet. What role did they play over the course of Earth’s history and how do they shape Earth... read more
12
August
2017

Goldschmidt 2017

Sebastian is giving a talk in session 11d: Nitrogen isotopes in biogeochemical cycles and food webs and co-organizing session 15f: Novel tools and approach for investigating biogeochemical cycling and organic signatures of microbial activity at the 2017 Goldschmidt conference in Paris. Come join us for these exciting sessions!

4
May
2017

New R package on CRAN: lans2r

The [email protected] (short LANS) Matlab module written by Lubos Polerecky (Polerecky L., Adam B., Milucka J., Musat N., Vagner T. and Kuypers M. M. M. (2012). Environ. Microbiol. 14, 1009–1023.) makes it easy to process NanoSIMS data and draw regions of interest (ROIs). The lans2r package provides a convenient interface to import ion maps and ROI data generated by LANS... read more
25
April
2017

AbSciCon 2017

Shaelyn Silverman is presenting her first talk at an international scientific conference at the Astrobiology Science Conference in Mesa, AZ on her senior thesis. Congrats Shae! S. N. Silverman, S. Kopf, R. Gordon, B. Bebout, S. Som. Measuring Ancient N2 Pressure Using Fossilized Cyanobacteria. Abstract #3242.

8
April
2017

1st Rocky Mountain Geobiology Symposium

The first Rocky Mountain Geobiology Symposium (RMGS) took place at the Colorado School of Mines in Golden, CO with participants from all over the Rocky Mountain states and beyond enjoying a fantastic day of science, new connections, sunny Colorado spring weather and a memorable end-of-day at Golden’s New Terrain Brewing. Big thanks to John Spear, Emily Kraus, Blake Stamps and everyone at Mines for all the hard work fundraising and organizing an amazing day to kick off the RMGS tradition.

4
April
2017

Shaelyn's thesis defense

Shaelyn Silverman successfully defended her senior thesis on the Morphological and Isotopic Changes of Anabaena cylindrica PCC 7122 in Response to N2 Partial Pressure. After a year of hard work first with Sanjoy Som at NASA Ames over the summer after her junior year, followed by research in the Geomicrobial Physiology Lab at CU Boulder during her senior year, Shae presented a fantastic written thesis and presentation and received the much deserved highest honors recommendation. Congratulations to Shaelyn for an outstanding senior thesis!

3
March
2017

First lab visitor: Matt Salie

The lab welcomes its first visitor. Matt Salie from the Williamson Lab at the Scripps Research Institute is visiting us this week to gain experience with continuous culturing techniques and gather preliminary data for his postdoctoral work on proteome dynamics. Welcome Matt!

19
January
2017

Geomicrobial Physiology Lab ready

Our culturing lab finished construction!

After several months of renovations, the construction on the Geomicrobial Physiology culturing lab in the Benson Earth Sciences building wrapped up earlier this week and we officially moved in today. Several pieces of equipment are already set up and ready to go and the first set of experiments is under way - it’s going to be an exciting Spring!

Getting ready to rock



The evolution of the new lab

18
December
2016

Hiring a research assistant

The Isotope Geomicrobiology Group is seeking a highly qualified research technician and laboratory manager starting in February 2017. The Isotope Geomicrobiology Group comprises the Kopf and Wing labs located in the Benson Earth Sciences building and is focused on studying the physiology and geologic signatures (isotope effects and lipid biomarkers) of diverse geochemically relevant microorganisms (phototrophic, heterotrophic and chemolithotrophic aerobes and anaerobes across all domains of life). We regularly combine aspects of aerobic and anaerobic laboratory culture, continuous culture, molecular biology, fluorescence microscopy, aqueous chemistry, isotopic analysis, and experimental design (3D-printing, microcontroller & circuit setup), and are looking for a highly motivated individual with excellent technical, communicational and organizational skills who is looking to apply and expand their existing skillset in a friendly and highly collaborate research environment. For additional details and the CU Boulder application portal, please consult the official job posting.

10
December
2016

Shaelyn and Allison presenting at AGU

Shaelyn Silverman is presenting a poster on Measuring Ancient Air Pressure Using Fossilized Cyanobacteria (Abstract ID 121646) on work that is part of her Senior Thesis at CU Boulder together with Sanjoy Som (NASA Ames). Allison Lee is presenting a poster on how Iron availability influences 15N-isotope fractionation during nitrogen fixation by aerobic chemoheterotroph Azotobacter vinelandii (Abstract ID 184186) on work that is part of her undergraduate research in Xinning Zhang’s new lab at Princeton University. First time at AGU, congratulations to both and have a great time at the conference!

29
November
2016

GC-IMRS installation

The installation of our GC-IRMS is under way!

Our new gas-chromatograph (GC) isotope ratio mass spectrometer (IRMS) is getting installed and we are looking forward to getting everything up an running. This is one of the instruments housed in the Organic Geochemistry Laboratory (OGL) in the new Sustainability, Energy and Environment Complex (SEEC). The OGL is a shared space with Julio Sepúlveda and Gifford Miller that provides a fantastic environment for all types of organic geochemistry research. The new GC-IRMS will complement the existing instrumentation and analytical tools acquired by Julio (an LC-Orbitrap and GC-triple quadrupole) and will allow us to determine the isotopic composition of specific organic compounds buy coupling the separating power of a gas chromatograph via a combustion/pyrolysis interface to the precision of an isotope ratio mass spectrometer.

20
August
2016

New graduate class on Stable Isotope Fractionation

Where do isotope effects in biogeochemical transformations come from? How are they expressed and preserved in the environment? What can (and can’t) they tell us about the processes, environments and organisms producing them? This graduate-level course will investigate the origins of stable isotope fractionation in geochemical systems with special emphasis on the role of biological catalysts as key drivers of... read more
15
August
2016

Lab renovations have begun

Our culturing lab is under construction!

The Geomicrobial Physiology culturing lab in the Benson Earth Sciences building is officially under construction with renovations scheduled to finish at the end of the year. We look forward to moving in and getting everything up and running early in the new year.