New genome announcement from the Perron Lab
Several new genome sequences of Bacillus subtilis and Bacillus velezensis strains were published by the Perron lab. These beneficial bacteria are used in making of many traditional fermented foods, and these strains in particular were isolated from samples of Kimchee cabbage.
Two Perron lab alums, Tejaswee Neupane and Rachael Mendoza, are coauthors on this paper, as most of the work was done by them as a part of their senior projects!
Full text: https://mra.asm.org/content/ga/9/23/e00085-20.full.pdf
Citation: Perron, G. G., Neupane, T., & Mendoza, R. A. (2020). Draft Genome Sequences of Bacillus subtilis Strains TNC1 (2019), TNC3 (2019), and TNW1 (2019), as well as Bacillus velezensis Strains TNC2 (2019) and TNW2 (2019), Isolated from Cabbage Kimchee. Microbiology Resource Announcements, 9(23).
Two Perron lab alums, Tejaswee Neupane and Rachael Mendoza, are coauthors on this paper, as most of the work was done by them as a part of their senior projects!
Full text: https://mra.asm.org/content/ga/9/23/e00085-20.full.pdf
Citation: Perron, G. G., Neupane, T., & Mendoza, R. A. (2020). Draft Genome Sequences of Bacillus subtilis Strains TNC1 (2019), TNC3 (2019), and TNW1 (2019), as well as Bacillus velezensis Strains TNC2 (2019) and TNW2 (2019), Isolated from Cabbage Kimchee. Microbiology Resource Announcements, 9(23).
Robertson Lab: Migratory birds and bird/building collisions
Migratory birds facing a number of hazards during their journeys. Collisions with buildings have become a major conservation problem for them, but the exact reason why so many birds collide with buildings is unclear. Several studies suggest that birds are attracted to nighttime building lighting. Bruce Robertson helped discover a new kind of light pollution, polarized light pollution, that could also be responsible. The light that reflects from glass buildings gets polarized, which may cause it to look like a water body at a distance, instead of a large dangerous object approaching fast. This collaboration between Bruce Robertson at Bard College and Sirena Lao and Scott Loss at the University of Oklahoma asked whether polarized, or unpolarized light pollution was more strongly associated with bird collisions with buildings in downtown Minneapolis. We found that birds were most likely to collide with individual windows that were lit at night, but that there was little evidence that polarized light pollution was attracting birds. This suggests that turning out the lights in each room of office buildings can help migratory birds avoid collisions.
Lao, S., Robertson, B.A., Anderson, A.W., Blair, R.B., Eckles, J.W., Turner, R.J. and Loss, S.R., 2020. The influence of artificial night at night and polarized light on bird-building collisions. Biological Conservation, 241, p.108358.
Lao, S., Robertson, B.A., Anderson, A.W., Blair, R.B., Eckles, J.W., Turner, R.J. and Loss, S.R., 2020. The influence of artificial night at night and polarized light on bird-building collisions. Biological Conservation, 241, p.108358.
Collins Lab: Soil microbes and seed germination
New paper by a recent Bard graduate Liz Miller ’18, in collaboration between labs of Dr. Collins and Dr. Perron:
Miller, E. C., Perron, G. G., & Collins, C. D. (2019). Plant‐driven changes in soil microbial communities influence seed germination through negative feedbacks. Ecology and evolution, 9(16), 9298-9311.
As plants grow, fungal pathogens accumulate around the roots of plants. Negative plant-soil feedbacks occur when these pathogens reduce the success of individual plants belonging to the same species. As a consequence, pathogens regulate the density of their specific plant hosts, and plants tend to grow best when their neighbor is a different plant species.
While seedlings and adult plants are known to suffer from these negative feedbacks, much less is known about the effect of species-specific pathogens on seeds. We tested whether seeds of seven different species experienced higher mortality in soils “conditioned” by plants of their own species (soils where pathogens were allowed to accumulate over time around the plant roots), versus soils conditioned by a different species. We also used metagenomics tools to identify potential pathogens driving the feedbacks.
We discovered that seeds of several grassland plant species experience negative feedbacks, i.e., the die more in their own soil than in soil of neighboring species. We also found that the putative pathogens driving these feedbacks differed depending on which species conditioned the soil a seed was buried in. Our results suggest that negative feedbacks at the seed stage may play a role in population persistence and plant diversity, and that the role of particular pathogens for driving feedbacks may depend on which plant species are in the neighborhood.
Miller, E. C., Perron, G. G., & Collins, C. D. (2019). Plant‐driven changes in soil microbial communities influence seed germination through negative feedbacks. Ecology and evolution, 9(16), 9298-9311.
As plants grow, fungal pathogens accumulate around the roots of plants. Negative plant-soil feedbacks occur when these pathogens reduce the success of individual plants belonging to the same species. As a consequence, pathogens regulate the density of their specific plant hosts, and plants tend to grow best when their neighbor is a different plant species.
While seedlings and adult plants are known to suffer from these negative feedbacks, much less is known about the effect of species-specific pathogens on seeds. We tested whether seeds of seven different species experienced higher mortality in soils “conditioned” by plants of their own species (soils where pathogens were allowed to accumulate over time around the plant roots), versus soils conditioned by a different species. We also used metagenomics tools to identify potential pathogens driving the feedbacks.
We discovered that seeds of several grassland plant species experience negative feedbacks, i.e., the die more in their own soil than in soil of neighboring species. We also found that the putative pathogens driving these feedbacks differed depending on which species conditioned the soil a seed was buried in. Our results suggest that negative feedbacks at the seed stage may play a role in population persistence and plant diversity, and that the role of particular pathogens for driving feedbacks may depend on which plant species are in the neighborhood.
Keesing Lab: Modeling livestock-wildlife coexistence
Biology professor Felicia Keesing and her colleagues published a paper in Scientific Reports that describes a mathematical model that can be used to manage livestock on grazing lands around the world. While previous models to manage livestock grazing exist, they require a lot of data and those data are hard to collect, making the models less useful. Keesing’s team developed a model that requires very little data yet makes sophisticated predictions, including estimating how much grass would be left over to support wild grazers. The model successfully predicted grass abundance at the team’s field sites in Kenya.
Jude Lab: Middle school kids help to find violacein-producing microbes
In this paper, co-authored with biologists from NY public schools, and several Bard students, Professor Brooke Jude describes how middle schoolers can be productively involved in real microbiological research.
See the full paper here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798820/
See the full paper here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798820/
News from the Keesing lab
There was lots of exciting news from the Keesing Lab in 2020. Felicia Keesing coauthored a suite of papers, including “Species that can make us ill thrive in human habitats” that was published in Nature; “Spatial and temporal patterns of the emerging tick-borne pathogen Borrelia miyamotoi in blacklegged ticks (Ixodes scapularis) in New York” in the journal Parasites & Vectors, and “A new genetic approach to distinguish strains of Anaplasma phagocytophilum that appear not to cause human disease,” in the journal Ticks and Tick-borne Diseases.
In September 2020 professor Keesing was also a featured scientist on the BBC One documentary “Extinction: The Facts with David Attenborough”. Her statements as an expert were included in articles published in The Guardian, The Scientist, Smithsonian Magazine, Canada’s National Observer, and Inside Higher Ed.
In September 2020 professor Keesing was also a featured scientist on the BBC One documentary “Extinction: The Facts with David Attenborough”. Her statements as an expert were included in articles published in The Guardian, The Scientist, Smithsonian Magazine, Canada’s National Observer, and Inside Higher Ed.
From the Dueker Lab
The urban environment is complex and often highly contaminated. This paper from prof. Eli Dueker’s lab takes a close look at how this contamination influences bacteria in urban air. The bacteria present in urban waterways were compared with the bacteria present in urban air, showing that there are many sources for atmospheric bacteria in an urban environment, including sewage contaminated waterways and polluted terrestrial areas. We also observed a ubiquitous distribution of sewage-associated bacteria, in water and air at several urban sites, highlighting the prevalence of of sewage contamination in crowded urban centers and underscoring the complexity of managing this form of pollution in water and air. Surprisingly, we also found that, despite the absence of obvious ecological structures, the air harbored a much more diverse bacterial community than that found in urban waterways. This provides evidence for the possibility of an atmospheric “ecology” and is a step towards understanding the role of megacities in determining the quality of urban air.
Citation: Dueker, M. E., French, S., & O’Mullan, G. D. (2018). Comparison of Bacterial Diversity in Air and Water of a Major Urban Center. Frontiers in Microbiology, 9.
Link: https://www.frontiersin.org/articles/10.3389/fmicb.2018.02868/full
Citation: Dueker, M. E., French, S., & O’Mullan, G. D. (2018). Comparison of Bacterial Diversity in Air and Water of a Major Urban Center. Frontiers in Microbiology, 9.
Link: https://www.frontiersin.org/articles/10.3389/fmicb.2018.02868/full
Collins Lab: The ecology of sacred groves
For centuries followers of the Ethiopian Orthodox Church have conserved patches of native trees around church buildings as sacred sanctuaries for church communities. Today there are as many as 20 000 church forests in northern Ethiopia’s Amhara Peoples National Regional State – these unique social-ecological systems offer an opportunity to study multiple natural forest patches across a large multipurpose landscape, including in many places where little or no other natural forest remains. This image is a satellite photo of Robit Bata church, located 15 km north of the city of Bahir Dar, and three km upstream of Lake Tana (the largest lake in Ethiopia). The natural forest at Robit Bata church hosts some of the only mature indigenous trees in the local landscape. In her recent paper, Bard professor Cathy Collins and colleagues illustrate how understanding patterns in the tree species composition of church forests requires consideration of the complex interplay between ecological gradients and anthropogenic influences over time. This publication also made a cover page of the January issue of “Ecography” journal.
Citation: Reynolds, T. W., Collins, C. D., Wassie, A., Liang, J., Briggs, W., Lowman, M., … & Adamu, E. (2017). Sacred natural sites as mensurative fragmentation experiments in long‐inhabited multifunctional landscapes. Ecography, 40(1), 144-157.
Citation: Reynolds, T. W., Collins, C. D., Wassie, A., Liang, J., Briggs, W., Lowman, M., … & Adamu, E. (2017). Sacred natural sites as mensurative fragmentation experiments in long‐inhabited multifunctional landscapes. Ecography, 40(1), 144-157.
Robertson and students publish lab research
Animals caught in ‘ecological traps’ prefer the worst available habitats. This happens when environmental change makes habitats look superficially attractive when they are actually dangerous. Ecological traps are increasingly common, but it remains unclear how susceptible animals are to them. Aquatic flies, for example, can be highly attracted to asphalt because it reflects polarized light the same way that natural water bodies do.
In this study, Bard professor Bruce Robertson and his Bard students exposed seven ecologically similar species of aquatic flies to different levels of polarized light, including abnormally strong polarized light associated with man-made habitats that are dangerous to them. They found that, in every species tested, animals actually preferred levels of polarized light typical of asphalt where their eggs perish, over levels typical of natural ponds. We also found that the degree of their preference depended on whether the cue was closer or more distant from a natural river.
Citation: Robertson, B. A., Keddy-Hector, I. A., Shrestha, S. D., Silverberg, L. Y., Woolner, C. E., Hetterich, I., & Horváth, G. (2018). Susceptibility to ecological traps is similar among closely related taxa but sensitive to spatial isolation. Animal Behaviour, 135, 77-84.
In this study, Bard professor Bruce Robertson and his Bard students exposed seven ecologically similar species of aquatic flies to different levels of polarized light, including abnormally strong polarized light associated with man-made habitats that are dangerous to them. They found that, in every species tested, animals actually preferred levels of polarized light typical of asphalt where their eggs perish, over levels typical of natural ponds. We also found that the degree of their preference depended on whether the cue was closer or more distant from a natural river.
Citation: Robertson, B. A., Keddy-Hector, I. A., Shrestha, S. D., Silverberg, L. Y., Woolner, C. E., Hetterich, I., & Horváth, G. (2018). Susceptibility to ecological traps is similar among closely related taxa but sensitive to spatial isolation. Animal Behaviour, 135, 77-84.
Blood meal effects on the tick microbiome
Ticks are parasites that ingest blood from their hosts. During their blood meals, they can also ingest microbes, such as bacteria, from their host’s blood, which could influence the microbial community, or “microbiome”, of the tick itself. Using high-throughput sequencing, Felicia Keesing and her colleagues sampled the microbiomes of ticks that had fed on individuals of five different host species — raccoons, Virginia opossums, striped skunks, red squirrels, and gray squirrels. They found that ticks that had fed on different host species had significantly different microbiomes. This is important because some of the microbes that ticks can acquire during their blood meals are pathogens of humans, including the bacterium that causes Lyme disease.
Publication link: https://www.sciencedirect.com/science/article/abs/pii/S1877959X18303297
Full citation: Landesman, W. J., Mulder, K., Allan, B. F., Bashor, L. A., Keesing, F., LoGiudice, K., & Ostfeld, R. S. (2019). Potential effects of blood meal host on bacterial community composition in Ixodes scapularis nymphs. Ticks and tick-borne diseases.
Publication link: https://www.sciencedirect.com/science/article/abs/pii/S1877959X18303297
Full citation: Landesman, W. J., Mulder, K., Allan, B. F., Bashor, L. A., Keesing, F., LoGiudice, K., & Ostfeld, R. S. (2019). Potential effects of blood meal host on bacterial community composition in Ixodes scapularis nymphs. Ticks and tick-borne diseases.
Tickbusters in the New Yorker
We are excited to learn that the Tick Project, led by Bard professor Felicia Keesing, is now featured by The New Yorker magazine!
https://www.newyorker.com/magazine/2019/07/29/tickbusters-on-the-lookout-for-lyme
Check out this beautiful story by Micah Hauser:
…
Keesing said, “I don’t like ticks any more than the next person, but I do admire them. They are survivors. Those things live for two years and eat three times. They can survive ninety-five-degree, humid, horrible summers and twenty-below winters. If you are going to root for the little guy—”…
“And their saliva!” Ostfeld interrupted. “They have a pharmacopoeia in their saliva. How do you stay attached to an animal without being detected, shrugged off, squished, or broken in half, for up to a week or so?
…
Read more on the New Yorker website!
https://www.newyorker.com/magazine/2019/07/29/tickbusters-on-the-lookout-for-lyme
Check out this beautiful story by Micah Hauser:
…
Keesing said, “I don’t like ticks any more than the next person, but I do admire them. They are survivors. Those things live for two years and eat three times. They can survive ninety-five-degree, humid, horrible summers and twenty-below winters. If you are going to root for the little guy—”…
“And their saliva!” Ostfeld interrupted. “They have a pharmacopoeia in their saliva. How do you stay attached to an animal without being detected, shrugged off, squished, or broken in half, for up to a week or so?
…
Read more on the New Yorker website!
Dueker Lab: Onshore wind speed and microbial aerosols at urban waterfronts
In this new paper, Bard professor Elias Dueker and collaborators study microbes that fly in the air, after small droplets of water get lifted from the ocean surface by the coastal wind. They found that depending on the wind speed, different amounts of microbes were picked up, and they were transported different distances into the city. They also described which types of microbes are more likely to get airborne, compared to those found below the water surface.
Citation: Dueker, M. E., O’Mullan, G. D., Martínez, J. M., Juhl, A. R., & Weathers, K. C. (2017). Onshore Wind Speed Modulates Microbial Aerosols along an Urban Waterfront. Atmosphere, 8(11), 215.
Citation: Dueker, M. E., O’Mullan, G. D., Martínez, J. M., Juhl, A. R., & Weathers, K. C. (2017). Onshore Wind Speed Modulates Microbial Aerosols along an Urban Waterfront. Atmosphere, 8(11), 215.
Nine genome announcements from Brooke Jude's lab
The lab of Professor Brooke Jude published nine draft genomes of bacteria endemic to the Hudson Valley watershed. This work is a result of several senior projects performed in the Biology program, and three biology graduates (Alexandra Bettina, Georgia Doing, and Kelsey O’Brien) are now first authors on three publications!
Bettina, A. M., Doing, G., O’Brien, K., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed. Genome announcements, 6(3), e01426-17.
Doing, G., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed. Genome announcements, 6(1), e01428-17.
O’Brien, K., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed. Genome announcements, 6(1), e01429-17.
Bettina, A. M., Doing, G., O’Brien, K., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed. Genome announcements, 6(3), e01426-17.
Doing, G., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed. Genome announcements, 6(1), e01428-17.
O’Brien, K., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed. Genome announcements, 6(1), e01429-17.
Biology of fog in Maine, and in Namib desert
The lab of professor Eli Dueker published a new study on the microbial composition of fog in Maine and in the Namib Desert. Dr. Dueker and collaborators found that fog particles lift microorganisms off the surface of water, and deposit them inland, increasing the microbial diversity.
The study has made quite a splash in the press; look at these substantive and interesting reviews, one in The Atlantic, and this one on the Atlas Obscura website.
Professor Dueker was also invited for a radio interview at WAMC: you can listen to it here.
Full citation: Dueker, M. E. and S. Evans, R. Logan, and K. C. Weathers (2018). The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition. Science of the Total Environment 647: 1547-1556.
The study has made quite a splash in the press; look at these substantive and interesting reviews, one in The Atlantic, and this one on the Atlas Obscura website.
Professor Dueker was also invited for a radio interview at WAMC: you can listen to it here.
Full citation: Dueker, M. E. and S. Evans, R. Logan, and K. C. Weathers (2018). The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition. Science of the Total Environment 647: 1547-1556.
Robertson Lab: Solar panels and aquatic insects
Professor Bruce Robertson had two new publications in the fall 2016: one review on the theory of evolutionary traps, and an experimental study, in which he and his colleagues from Hungary looked at the polarizing properties of solar panels, and the effects this light polarization may have on the life cycle of aquatic insects. This line work was since continued by Bard students, and will undoubtedly bring more senior projects next year.
Citations:
Száz, D., Mihályi, D., Farkas, A., Egri, Á., Barta, A., Kriska, G., … & Horváth, G. (2016). Polarized light pollution of matte solar panels: anti-reflective photovoltaics reduce polarized light pollution but benefit only some aquatic insects. Journal of Insect Conservation, 20(4), 663-675.
Robertson, B. A., & Chalfoun, A. D. (2016). Evolutionary traps as keys to understanding behavioral maladapation. Current Opinion in Behavioral Sciences, 12, 12-17.
Citations:
Száz, D., Mihályi, D., Farkas, A., Egri, Á., Barta, A., Kriska, G., … & Horváth, G. (2016). Polarized light pollution of matte solar panels: anti-reflective photovoltaics reduce polarized light pollution but benefit only some aquatic insects. Journal of Insect Conservation, 20(4), 663-675.
Robertson, B. A., & Chalfoun, A. D. (2016). Evolutionary traps as keys to understanding behavioral maladapation. Current Opinion in Behavioral Sciences, 12, 12-17.
No effect of transformation on the evolution of phage resistance
In this paper, Professor Gabriel Perron and the team tested a particular hypothesis about the mechanisms of bacterial evolution, and found that the data did not support this hypothesis. It is a really nice example of a publication that faithfully presents important negative results, when an attractive, logical, and perfectly plausible hypothesis has to be rejected based on experimental evidence.
Citation: McLeman, A., Sierocinski, P., Hesse, E., Buckling, A., Perron, G., Hülter, N., … & Vos, M. (2016). No effect of natural transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system. Scientific Reports, 6.
Link to full text: http://www.nature.com/articles/srep37144
Citation: McLeman, A., Sierocinski, P., Hesse, E., Buckling, A., Perron, G., Hülter, N., … & Vos, M. (2016). No effect of natural transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system. Scientific Reports, 6.
Link to full text: http://www.nature.com/articles/srep37144
Microbial fuel cells in the classroom
A publication by Brooke and Craig Jude in JMBE is focused on building microbial fuel cells (bacterially powered batteries) in college and local school classrooms! These microbial fuel cells serve as lab projects in Brooke Jude’s Environmental Microbiology course and are also constructed when local 8th grade classes visit Bard through events sponsored by the Center For Civic Engagement -- events led by Bard students!
Citation and full-text link: Jude CD, Jude BA. Powerful Soil: Utilizing Microbial Fuel Cell Construction and Design in an Introductory Biology Course. J Microbiol Biol Educ. 2015 Dec 1;16(2):286-8. doi: 10.1128/jmbe.v16i2.934. eCollection 2015 Dec.
Citation and full-text link: Jude CD, Jude BA. Powerful Soil: Utilizing Microbial Fuel Cell Construction and Design in an Introductory Biology Course. J Microbiol Biol Educ. 2015 Dec 1;16(2):286-8. doi: 10.1128/jmbe.v16i2.934. eCollection 2015 Dec.
Antibiotic resistance in ancient permafrost soil
The rise of antibiotic resistance found in microbial pathogens was driven by the use and misuse of antibiotics in modern medicine and agriculture. However, the extent to which antibiotic pollution impacted microbial communities found in soil and remote environments is unclear. Using a metagenomic approach to investigate microbes found in the Canadian high Arctic, Dr. Perron and colleagues found common microbial pathogens resistant to multiple antibiotics among these remote Arctic microbial communities. Dr. Perron’s team also showed that although antibiotic-resistant bacteria were also found in 5,000 years old permafrost soils, these bacteria did not show resistance profiles normally associated with infection.
Citation: Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, & Desai MM. (2015). Functional characterization of bacteria isolated from ancient Arctic soil exposes diverse resistance mechanisms to modern antibiotics. PLoS ONE. 10: e0069533
Citation: Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, & Desai MM. (2015). Functional characterization of bacteria isolated from ancient Arctic soil exposes diverse resistance mechanisms to modern antibiotics. PLoS ONE. 10: e0069533
Dueker Lab: Microbial exchange among water, sediment, and air
A paper, recently published by Eli Dueker and co-authors, analyzes migration and exchange of bacteria between sewage, sediment, water, and air. The papers discusses possible implications of this often overlooked exchange of small particles on public health, and on strategies of waste disposal.
Citation: O’Mullan, G. D., Dueker, M. E., & Juhl, A. R. (2017). Challenges to Managing Microbial Fecal Pollution in Coastal Environments: Extra-Enteric Ecology and Microbial Exchange Among Water, Sediment, and Air. Current Pollution Reports, 3(1), 1-16.
Citation: O’Mullan, G. D., Dueker, M. E., & Juhl, A. R. (2017). Challenges to Managing Microbial Fecal Pollution in Coastal Environments: Extra-Enteric Ecology and Microbial Exchange Among Water, Sediment, and Air. Current Pollution Reports, 3(1), 1-16.