What we're reading:
Each week we are reading and discussing texts, both science and non-science, first-authored by BIPOC and LGBTQ+ individuals. We discuss these readings during lab meeting, and then write a brief summary highlighting what we've learned. If you have suggestions for what we should read next please email Wally: [email protected].
2021.05
Leprich, Dalton J., Flood, B.E., Schroedl, P.R., Ricci, E., Marlow, J.J., Girguis, P.R., Bailey, J.V. “Sulfur Bacteria Promote Dissolution of Authigenic Carbonates at Marine Methane Seeps.” The ISME Journal, 2021, doi:10.1038/s41396-021-00903-3.
Researchers at the University of Minneapolis Twin-Cities tested the hypothesis that sulfur oxidation by chemotrophic bacterial mats were influencing the dissolution of carbonate rocks at the Del Mar methane seep off the coast of San Diego. They ran scanning electron microscopy and biofilm reactor experiments with the bacteria Celeribacter baekdonensis. They found that the oxidation of hydrogen sulfide and thiosulfate by the bacteria was causing dissolution of carbonate boulders at the seep because of the created acidic microenvironments. Their results suggest the potential for sulfur oxidizing bacteria to influence the carbon flux from sediments to the ocean, however further research will be required to accurately understand the impacts of the bacterial mats at known and unknown cold seeps.
Dalton J. Leprich, Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities. @DaltonLeprich
Remi Work and Ryan Shipley chose this paper and wrote this description.
Leprich, Dalton J., Flood, B.E., Schroedl, P.R., Ricci, E., Marlow, J.J., Girguis, P.R., Bailey, J.V. “Sulfur Bacteria Promote Dissolution of Authigenic Carbonates at Marine Methane Seeps.” The ISME Journal, 2021, doi:10.1038/s41396-021-00903-3.
Researchers at the University of Minneapolis Twin-Cities tested the hypothesis that sulfur oxidation by chemotrophic bacterial mats were influencing the dissolution of carbonate rocks at the Del Mar methane seep off the coast of San Diego. They ran scanning electron microscopy and biofilm reactor experiments with the bacteria Celeribacter baekdonensis. They found that the oxidation of hydrogen sulfide and thiosulfate by the bacteria was causing dissolution of carbonate boulders at the seep because of the created acidic microenvironments. Their results suggest the potential for sulfur oxidizing bacteria to influence the carbon flux from sediments to the ocean, however further research will be required to accurately understand the impacts of the bacterial mats at known and unknown cold seeps.
Dalton J. Leprich, Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities. @DaltonLeprich
Remi Work and Ryan Shipley chose this paper and wrote this description.
2020.10.27
Kranzler, C.F., Krause, J.W., Brzezinski, M.A., Edwards, B.R., Biggs, W.P., Maniscalso, M., McCrow, J.P., Van Mooy, B.A.S., Bidle, K.D., Allen, A.E., and Thamatrakoln, K. Silicon limitation facilitates virus infection and mortality of marine diatoms. Nat Microbiol 4, 1790–1797 (2019). https://doi.org/10.1038/s41564-019-0502-x
Viruses are considered key players in ocean biogeochemical cycles estimating to turn over more than 25% of photosynthetically fixed carbon. Research also suggests viruses may stimulate aggregation, sinking and export of organic carbon. Diatoms are among the largest and most globally distributed organisms contributing up to 40% of total marine primary production. By converting dissolved silicon into biogenic silica, diatoms provide a mechanism for coupling silicon and carbon cycles. Kranzler et al (2019) used metatranscriptomic analysis, the study of real time function and whole gene expression in nature, of cell-associated diatom viruses to explore the link between Si stress and viral infections in the coastal waters of California. Their key findings suggest faster infection and mortality in Si-limited populations strengthen the ‘viral shunt’ – weakening the biological pump in Si-limited oceanic systems. Kranzler et al (2020) suggest viral infections represent a type of mechanistic control over diatom-mediated biogeochemical cycling (in Si-limited systems) that has not previous been recognized.
Dr. Chana Kranzler is a postdoctoral fellow at the Department of Marine and Coastal Sciences, Rutgers University
Melissa Hagy chose this paper and wrote this description.
Kranzler, C.F., Krause, J.W., Brzezinski, M.A., Edwards, B.R., Biggs, W.P., Maniscalso, M., McCrow, J.P., Van Mooy, B.A.S., Bidle, K.D., Allen, A.E., and Thamatrakoln, K. Silicon limitation facilitates virus infection and mortality of marine diatoms. Nat Microbiol 4, 1790–1797 (2019). https://doi.org/10.1038/s41564-019-0502-x
Viruses are considered key players in ocean biogeochemical cycles estimating to turn over more than 25% of photosynthetically fixed carbon. Research also suggests viruses may stimulate aggregation, sinking and export of organic carbon. Diatoms are among the largest and most globally distributed organisms contributing up to 40% of total marine primary production. By converting dissolved silicon into biogenic silica, diatoms provide a mechanism for coupling silicon and carbon cycles. Kranzler et al (2019) used metatranscriptomic analysis, the study of real time function and whole gene expression in nature, of cell-associated diatom viruses to explore the link between Si stress and viral infections in the coastal waters of California. Their key findings suggest faster infection and mortality in Si-limited populations strengthen the ‘viral shunt’ – weakening the biological pump in Si-limited oceanic systems. Kranzler et al (2020) suggest viral infections represent a type of mechanistic control over diatom-mediated biogeochemical cycling (in Si-limited systems) that has not previous been recognized.
Dr. Chana Kranzler is a postdoctoral fellow at the Department of Marine and Coastal Sciences, Rutgers University
Melissa Hagy chose this paper and wrote this description.
2020.10.20
Ramírez-Castañeda, V. (2020). Disadvantages in preparing and publishing scientific papers caused by the dominance of the English language in science: The case of Colombian researchers in biological sciences. PLOS ONE, 15(9), e0238372. https://doi.org/10.1371/journal.pone.0238372
In science, success is often measured by the number scientific papers published in high impact factor journals. Many of these high impact factor journals are published in English leaving researchers from English as a Foreign Language (EFL) countries at a disadvantage. Ramírez-Castañeda (2020) explores these disadvantages through the lens of Colombian doctoral students. The author used a survey to determine the impact publishing in English has on the students. They found that the students incur significant financial and productivity costs to publish in English. They found that almost half of the students had an article rejected or revisions requested due to their English grammar and that students spend about almost 100 more hours writing articles in English than they do in Spanish, their native language. Greater than 90% of students ask others for editing favors and almost 60% have paid to get their articles edited. This cost can range anywhere from 25% to greater than 50% of their monthly salary. This article highlights the inequities in scientific publishing and highlights the need for equity-based changes in the scientific publishing process.
Valeria Ramírez Castañeda is a graduate student at the University of California, Berkeley.
Alia Al-Haj chose this paper and wrote this description.
Ramírez-Castañeda, V. (2020). Disadvantages in preparing and publishing scientific papers caused by the dominance of the English language in science: The case of Colombian researchers in biological sciences. PLOS ONE, 15(9), e0238372. https://doi.org/10.1371/journal.pone.0238372
In science, success is often measured by the number scientific papers published in high impact factor journals. Many of these high impact factor journals are published in English leaving researchers from English as a Foreign Language (EFL) countries at a disadvantage. Ramírez-Castañeda (2020) explores these disadvantages through the lens of Colombian doctoral students. The author used a survey to determine the impact publishing in English has on the students. They found that the students incur significant financial and productivity costs to publish in English. They found that almost half of the students had an article rejected or revisions requested due to their English grammar and that students spend about almost 100 more hours writing articles in English than they do in Spanish, their native language. Greater than 90% of students ask others for editing favors and almost 60% have paid to get their articles edited. This cost can range anywhere from 25% to greater than 50% of their monthly salary. This article highlights the inequities in scientific publishing and highlights the need for equity-based changes in the scientific publishing process.
Valeria Ramírez Castañeda is a graduate student at the University of California, Berkeley.
Alia Al-Haj chose this paper and wrote this description.
2020.09.15
Halsey, S.J., Strickland, L.R., Scott-Richardson, M., Perrin-Stowe, T. and Massenburg, L., (2020). Elevate, don’t assimilate, to revolutionize the experience of scientists who are Black, Indigenous and people of colour. Nature Ecology & Evolution, pp.1-3.
Wally Fulweiler chose this paper and still needs to write this description.
Halsey, S.J., Strickland, L.R., Scott-Richardson, M., Perrin-Stowe, T. and Massenburg, L., (2020). Elevate, don’t assimilate, to revolutionize the experience of scientists who are Black, Indigenous and people of colour. Nature Ecology & Evolution, pp.1-3.
Wally Fulweiler chose this paper and still needs to write this description.
2020.08.17
Chaudhary, B. and Berhe, A.A., (2020). Ten simple rules for building an anti-racist lab.
STEM fields still lack diversity and some fields have shown little improvement over the last 40 years. The authors explain that under-representation of minority groups especially Black, Indigenous, and people of color (BIPOC) can in part be attributed to bias, discrimination, and harassment. Chaudhary and Berhe comment that in order to change the system that allows for this continued mistreatment we must take anti-racist actions as individuals and collectively as a lab to effect change and support underrepresented minorities in our labs, depts., and institutions. In this paper, the authors provide ten simple rules that labs can adopt to “promote racial and ethnic diversity, equity, and inclusion in science.”
Dr. Bala Chaudhary (@BalaChaudhary) is an Assistant Professor in the Department of Environmental Science and Studies at DePaul University. Her lab focused on plant-soil-microbe interactions. Dr. Asmeret Berhe (@aaberhe) is a Professor of Soil Biogeochemistry and Falasco Chair in Earth Sciences, University of California, Merced. Her lab focuses on the effect of erosion, fire, and climate change on soil organic matter.
Nia Bartolucci chose this paper and wrote the description.
Chaudhary, B. and Berhe, A.A., (2020). Ten simple rules for building an anti-racist lab.
STEM fields still lack diversity and some fields have shown little improvement over the last 40 years. The authors explain that under-representation of minority groups especially Black, Indigenous, and people of color (BIPOC) can in part be attributed to bias, discrimination, and harassment. Chaudhary and Berhe comment that in order to change the system that allows for this continued mistreatment we must take anti-racist actions as individuals and collectively as a lab to effect change and support underrepresented minorities in our labs, depts., and institutions. In this paper, the authors provide ten simple rules that labs can adopt to “promote racial and ethnic diversity, equity, and inclusion in science.”
Dr. Bala Chaudhary (@BalaChaudhary) is an Assistant Professor in the Department of Environmental Science and Studies at DePaul University. Her lab focused on plant-soil-microbe interactions. Dr. Asmeret Berhe (@aaberhe) is a Professor of Soil Biogeochemistry and Falasco Chair in Earth Sciences, University of California, Merced. Her lab focuses on the effect of erosion, fire, and climate change on soil organic matter.
Nia Bartolucci chose this paper and wrote the description.
2020.08.10
Marín-Spiotta, E., Barnes, R. T., Berhe, A. A., Hastings, M. G., Mattheis, A., Schneider, B., & Williams, B. M. (2020). Hostile climates are barriers to diversifying the geosciences. Advances in Geosciences, 53, 117–127. https://doi.org/10.5194/adgeo-53-117-2020
The geosciences influence every single person on this planet and help solve some of societies’ most critical issues (e.g., energy, water quality, natural hazards, climate change). Despite being relevant to our livelihoods, the geosciences are the least diverse disciplines in the United States. In fact, 90 % of US citizen graduate students in the geosciences are white (Wilson et al., 2018) and only 30% of women make up the STEM workforce (Wilson, 2017, 2019). This lack of diversity is largely due to hostile climates in the geosciences consisting of biases, discrimination, and harassment. Furthermore, these behaviors are built upon a history of exclusion, predispositions of what scientists should look like and marginalization of those from underrepresented groups. In this paper, Marín-Spiotta et al., (2020) highlights the reasons why the geosciences lack diversity, discusses recent initiatives to diversify science and ultimately calls for the reexamination of these barriers to make geoscience equitable for all.
Dr. Erika Marín-Spiotta is a Professor of Geography at the University of Wisconsin-Madison and an advocate for underrepresented groups in STEM. Be sure to follow her on Twitter (@emsaurios) to learn more about her work.
Claudia Mazur chose this paper and wrote the description.
Marín-Spiotta, E., Barnes, R. T., Berhe, A. A., Hastings, M. G., Mattheis, A., Schneider, B., & Williams, B. M. (2020). Hostile climates are barriers to diversifying the geosciences. Advances in Geosciences, 53, 117–127. https://doi.org/10.5194/adgeo-53-117-2020
The geosciences influence every single person on this planet and help solve some of societies’ most critical issues (e.g., energy, water quality, natural hazards, climate change). Despite being relevant to our livelihoods, the geosciences are the least diverse disciplines in the United States. In fact, 90 % of US citizen graduate students in the geosciences are white (Wilson et al., 2018) and only 30% of women make up the STEM workforce (Wilson, 2017, 2019). This lack of diversity is largely due to hostile climates in the geosciences consisting of biases, discrimination, and harassment. Furthermore, these behaviors are built upon a history of exclusion, predispositions of what scientists should look like and marginalization of those from underrepresented groups. In this paper, Marín-Spiotta et al., (2020) highlights the reasons why the geosciences lack diversity, discusses recent initiatives to diversify science and ultimately calls for the reexamination of these barriers to make geoscience equitable for all.
Dr. Erika Marín-Spiotta is a Professor of Geography at the University of Wisconsin-Madison and an advocate for underrepresented groups in STEM. Be sure to follow her on Twitter (@emsaurios) to learn more about her work.
Claudia Mazur chose this paper and wrote the description.
2020.08.03
Katija, K., Troni, G., Daniels, J. et al. Revealing enigmatic mucus structures in the deep sea using DeepPIV. Nature 583, 78–82 (2020). https://doi.org/10.1038/s41586-020-2345-2
Giant larvaceans in the deep sea reside in “snot palaces” that protect them from predators and help them filter food from the surrounding seawater. These tadpole-like creatures are important in marine carbon cycling, and their complex snot houses could provide inspiration for NASA engineers looking to build structures on the moon. Despite their ecological importance, giant larvaceans have remained enigmatic for decades, as collecting their delicate, gelatinous houses for study in the lab is no easy feat. To circumvent this problem, a team of scientists and engineers led by Kakani Katija designed a novel laser-scanning underwater instrument and used it to observe giant larvaceans in their natural habitat. In a series of dive missions, Katija’s team obtained images of the houses, and then used software to create 3-D reconstructions of them. These models provide glimpses into the inner-workings of larvaceans’ houses, which had only seen from the outside before, and provide insights into how these mysterious creatures function. Such work is only the beginning—the team plans to use their laser scan technology to study other deep sea animals, to better understand how much carbon they remove from the surface ocean.
Kakani Katija is a Principal Engineer at the Monterey Bay Research Institute and leads the Bioinspiration Lab.
Emily Chua chose this paper and wrote the description.
Katija, K., Troni, G., Daniels, J. et al. Revealing enigmatic mucus structures in the deep sea using DeepPIV. Nature 583, 78–82 (2020). https://doi.org/10.1038/s41586-020-2345-2
Giant larvaceans in the deep sea reside in “snot palaces” that protect them from predators and help them filter food from the surrounding seawater. These tadpole-like creatures are important in marine carbon cycling, and their complex snot houses could provide inspiration for NASA engineers looking to build structures on the moon. Despite their ecological importance, giant larvaceans have remained enigmatic for decades, as collecting their delicate, gelatinous houses for study in the lab is no easy feat. To circumvent this problem, a team of scientists and engineers led by Kakani Katija designed a novel laser-scanning underwater instrument and used it to observe giant larvaceans in their natural habitat. In a series of dive missions, Katija’s team obtained images of the houses, and then used software to create 3-D reconstructions of them. These models provide glimpses into the inner-workings of larvaceans’ houses, which had only seen from the outside before, and provide insights into how these mysterious creatures function. Such work is only the beginning—the team plans to use their laser scan technology to study other deep sea animals, to better understand how much carbon they remove from the surface ocean.
Kakani Katija is a Principal Engineer at the Monterey Bay Research Institute and leads the Bioinspiration Lab.
Emily Chua chose this paper and wrote the description.
2020.07.14
Wanelik, K.M., Griffin, J.S., Head, M.L., Ingleby, F.C. and Lewis, Z., Breaking barriers? Ethnicity and socioeconomic background impact on early career progression in the fields of ecology and evolution. Ecology and Evolution.
Like other STEM (Science, Technology, Engineering, and Mathematics) fields, ecology, evolutionary biology, and behavior (EEB) suffer from a lack of diversity. Wanelik et al. (2020) surveyed 188 early career scientists in EEB to examine the impact of ethnicity, age, sexual orientation, sex, socioeconomic background, and disability on career progression. They found that ethnic minorities reported having fewer non-first author publications and those from lower socio-economic backgrounds were more likely to be in teaching and research positions as opposed to research-only positions with research-only positions perceived as more prestigious by the UK-based authors. About half of the respondents that answered questions concerning overcoming barriers in academia had left academia due to these barriers while those that remain in academia broadly mentioned “people” and “opportunities” as ways of overcoming barriers. Although this study contains a limited dataset, it provides insight into areas to focus on to increase equity across ethnicities and socio-economic backgrounds in early career progression.
Dr. Wanelik is a Postdoctoral Research Associate in Evolution, Ecology, and Behaviour at The University of Liverpool and Joanne Griffin is a PhD student in Evolution, Ecology, and Behaviour at The University of Liverpool.
Tseng, M., El-Sabaawi, R.W., Kantar, M.B., Pantel, J.H., Srivastava, D.S. and Ware, J.L., 2020. Strategies and support for Black, Indigenous, and people of colour in ecology and evolutionary biology. Nature Ecology & Evolution, pp.1-3.
Black, Indigenous, and people of color (BIPOC) face many barriers and discrimination in every part of their academic journey. Tseng et al. (2020) provide strategies for BIPOC working in Ecology and Evolutionary Biology (EEB) to break through these barriers. These strategies include taking care of your mental health, being realistic with what lies ahead, speaking up strategically, choosing your battles and pacing yourself, asking questions, knowing that you can inspire and effect change, recognizing your own privilege, and trusting yourself. This is a very uplifting article containing many pieces of sound advice for academics at any level. Pieces of advice I found particularly useful are remembering that “the EEB world is not representative of the world at large” and to tailor battles for your career stage. In our discussion of privilege, Nia Bartolucci mentioned a lesson she drew from this paper was to recognize the struggles of the people that came before us in academia and how they have changed things to make our lives a little easier and that, moving forward, we should strive to do the same for those that come after us.
Dr. Tseng is an Assistant Professor in the Department of Botany at The University of British Columbia.
Alia Al-Haj chose these papers and wrote the descriptions.
Wanelik, K.M., Griffin, J.S., Head, M.L., Ingleby, F.C. and Lewis, Z., Breaking barriers? Ethnicity and socioeconomic background impact on early career progression in the fields of ecology and evolution. Ecology and Evolution.
Like other STEM (Science, Technology, Engineering, and Mathematics) fields, ecology, evolutionary biology, and behavior (EEB) suffer from a lack of diversity. Wanelik et al. (2020) surveyed 188 early career scientists in EEB to examine the impact of ethnicity, age, sexual orientation, sex, socioeconomic background, and disability on career progression. They found that ethnic minorities reported having fewer non-first author publications and those from lower socio-economic backgrounds were more likely to be in teaching and research positions as opposed to research-only positions with research-only positions perceived as more prestigious by the UK-based authors. About half of the respondents that answered questions concerning overcoming barriers in academia had left academia due to these barriers while those that remain in academia broadly mentioned “people” and “opportunities” as ways of overcoming barriers. Although this study contains a limited dataset, it provides insight into areas to focus on to increase equity across ethnicities and socio-economic backgrounds in early career progression.
Dr. Wanelik is a Postdoctoral Research Associate in Evolution, Ecology, and Behaviour at The University of Liverpool and Joanne Griffin is a PhD student in Evolution, Ecology, and Behaviour at The University of Liverpool.
Tseng, M., El-Sabaawi, R.W., Kantar, M.B., Pantel, J.H., Srivastava, D.S. and Ware, J.L., 2020. Strategies and support for Black, Indigenous, and people of colour in ecology and evolutionary biology. Nature Ecology & Evolution, pp.1-3.
Black, Indigenous, and people of color (BIPOC) face many barriers and discrimination in every part of their academic journey. Tseng et al. (2020) provide strategies for BIPOC working in Ecology and Evolutionary Biology (EEB) to break through these barriers. These strategies include taking care of your mental health, being realistic with what lies ahead, speaking up strategically, choosing your battles and pacing yourself, asking questions, knowing that you can inspire and effect change, recognizing your own privilege, and trusting yourself. This is a very uplifting article containing many pieces of sound advice for academics at any level. Pieces of advice I found particularly useful are remembering that “the EEB world is not representative of the world at large” and to tailor battles for your career stage. In our discussion of privilege, Nia Bartolucci mentioned a lesson she drew from this paper was to recognize the struggles of the people that came before us in academia and how they have changed things to make our lives a little easier and that, moving forward, we should strive to do the same for those that come after us.
Dr. Tseng is an Assistant Professor in the Department of Botany at The University of British Columbia.
Alia Al-Haj chose these papers and wrote the descriptions.
2020.07.07
Bulseco AN, Vineis J, Spivak A, Giblin AE, Murphy AE, Bowen JL (2020) Metagenomics coupled with biogeochemical rate measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments. Limnology & Oceanography. DOI: 10.1002/lno.11326
Salt marshes are highly valued for the many ecosystem services they provide. One ecosystem function of particular interest is the capacity of these systems to sequester and store carbon. However, one aspect of this function that remains less clear is the microbial mechanisms that drive carbon cycling and how this function is being impacted by global change and other anthropogenic stressors such as nutrient addition. Using a metagenomic approach, Bulseco et al (2020) set up a controlled flow-through reactor experiment to determine how nitrogen addition affects organic matter decomposition across a depth gradient in salt marsh sediment cores. Metagenomic and organic matter analyses revealed that genes associated with respiration were found in higher abundance in shallow sediments where organic matter was more available and that genes associated with resource limitation were found in higher abundance in deeper sediment where organic matter was less available. Additionally, the authors found that nitrogen enrichment significantly increased rates of respiration and that these increased rates were correlated with genes that code for enzymes involved in microbial respiration pathways. Overall this study provides novel insights into the linking of biogeochemical processes and the genes that underlie them and strengthens our understanding of microbial dynamics in salt marsh ecosystems.
Dr. Bulseco is starting as an Assistant Professor in Marine Chemistry at Eckerd College in the Fall. Follow her on Twitter (@MarshMicrobe) to keep up with all the exciting work she does!
Nia Bartolucci chose this paper and wrote this description.
Bulseco AN, Vineis J, Spivak A, Giblin AE, Murphy AE, Bowen JL (2020) Metagenomics coupled with biogeochemical rate measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments. Limnology & Oceanography. DOI: 10.1002/lno.11326
Salt marshes are highly valued for the many ecosystem services they provide. One ecosystem function of particular interest is the capacity of these systems to sequester and store carbon. However, one aspect of this function that remains less clear is the microbial mechanisms that drive carbon cycling and how this function is being impacted by global change and other anthropogenic stressors such as nutrient addition. Using a metagenomic approach, Bulseco et al (2020) set up a controlled flow-through reactor experiment to determine how nitrogen addition affects organic matter decomposition across a depth gradient in salt marsh sediment cores. Metagenomic and organic matter analyses revealed that genes associated with respiration were found in higher abundance in shallow sediments where organic matter was more available and that genes associated with resource limitation were found in higher abundance in deeper sediment where organic matter was less available. Additionally, the authors found that nitrogen enrichment significantly increased rates of respiration and that these increased rates were correlated with genes that code for enzymes involved in microbial respiration pathways. Overall this study provides novel insights into the linking of biogeochemical processes and the genes that underlie them and strengthens our understanding of microbial dynamics in salt marsh ecosystems.
Dr. Bulseco is starting as an Assistant Professor in Marine Chemistry at Eckerd College in the Fall. Follow her on Twitter (@MarshMicrobe) to keep up with all the exciting work she does!
Nia Bartolucci chose this paper and wrote this description.