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Building competence and tools for tracing the trajectories of long distance dissemination of microorganisms via the atmosphere – from source to sink

2019/10/10

Participants of the workshop on

“Linking sources and sinks in the long distance aerial dissemination of microorganisms”

that took place from 3-6 Sept 2019 near Reykholt, Iceland

 

How far can microorganisms travel via the atmosphere? Can we determine how regions and continents are linked in the flight paths of microorganisms: what are the sources of microorganisms that fall with rain, for example, and the most common pathways of movement? These are some of the challenging questions in epidemiology that need to be addressed to understand the potential for spread of diseases that affect plants, humans and domestic and wild animals. Likewise, for microorganisms that can influence atmospheric processes, such as those that can function as ice nucleating particles (INPs), it is useful to know where are the upwind sources of the INPs that might influence rainfall downwind. The answers to these questions could reveal the connectivity between different land covers – via the microorganisms they emit and receive – and they could therefore open doors to innovations that would either uncouple or enhance this connectivity.

Long distance (LD) movement of particles in the atmosphere is directly visible only in certain cases of massive release such as when a volcano erupts, when large swathes of forests burn or when a storm mobilizes tons of topsoil or desert dust.  Otherwise, the probable pathways of LD movement of particles in the atmosphere are revealed by compiling corroborating evidence. Such epidemiological detective work has shown the likely LD airborne dissemination – across hundreds of kilometers – for the viruses causing avian influenza in Iowa [Zhao et al. 2019] and porcine foot and mouth disease in Israel [Klausner et al. 2015], and for virus-carrying insect vectors of malaria, of bovine ephemeral fever and of bovine lumpy skin disease leading to various outbreaks in Israel [Klausner et al. 2018]. For plant pathogens, the likely pathways of LD airborne dissemination across oceans and continents have been described for spores of the fungi causing rust diseases of wheat, coffee, soybean and sugar cane [Brown & Hovmøller, 2002; Isnard et al. 2005], the fungi causing phoma leaf spotting and stem canker of oilseed rape [Grinn-Gofroń et al. 201] and for spores of the oomycete that causes blue mold of tobacco [Blanco-Meneses et al. 2018].

The successful detective work to elucidate the LD aerial dissemination trajectories of microorganisms has been facilitated by two features common to most of the cases indicated above, viz. there are few candidate sources (because the microorganism has a limited number of habitats or hosts) and there are well identified aerial trajectories linking sinks to the putative sources. But how can we identify sources and the trajectories that link them to sinks when these conditions are not met? With its broad host range and aptitude to colonize a diverse range of habitats, the ubiquitous ice nucleation active and potentially plant pathogenic bacterium Pseudomonas syringae is a very good example [Morris et al. 2013]. When we observed genetically diverse lines of this bacterium fall out with a single precipitation event on a snow-covered Jungfraujoch at 3580 m altitude in Switzerland [Stopelli et al. 2017] we were intrigued about their possible source. Backwards trajectories of the air masses that brought this precipitation, provided by the Jungfraujoch observatory staff, indicated several sites where the air masses had the greatest residence time to accumulate microbial passengers. Northern regions of Iceland were among them. To search Iceland for possible sources of the strains of P. syringae that were disseminated with snowfall to Jungfraujoch, I obtained funding from the Campus France Jules Verne exchange program, in collaboration with Oddur Vilhelmsson and Auður Sigurbjörnsdóttir from the University of Akureyri, for a project entitled “Icelandic landscapes as sources of bioaerosols that facilitate precipitation on the European continent”.

The first exchange between our teams resulted in the discovery of very abundant and diverse populations of P. syringae on most of the annual and perennial plants that we sampled. These populations of P. syringae included strains that were candidates in our search for clones or near clones of P. syringae migrating to various sites on the European continent, including Jungfraujoch, that we had in our vast collection of this bacterium (work in progress). Nevertheless, we were uncertain how best to establish convincing evidence to link the sinks with the putative sources. Therefore, we decided that, for the second year of our exchange program, we would organize a workshop of scientists who are actively exploring this question and building tools relative to various environmental microorganisms.

This led to a freelance workshop on “Linking sources and sinks in the long distance aerial dissemination of microorganisms” that took place from 3 to 6 September 2019 at the cozy Nes farm near Reykholt, Iceland. I refer to the workshop as “freelance” because it was not funded by any particular foundation or project, but rather it was the fruit of all participants making the effort to find their own means to attend.

The goal of the workshop was to brainstorm to develop strategies to assess and validate trajectories of long distance dissemination of ubiquitous microorganisms and to identify their sources. The expected outcome of the workshop that I anticipated included:

  • Methods to create hypotheses about likely LD trajectories of microorganisms
  • Statistical tools to compare sinks with potential sources
  • Approaches to exploiting land use data bases to identify optimal study sites
  • Indicators of “microbiological volcanoes” (i.e. site-specific markers of microbial biogeographical diversity)

 

I organized the workshop based on lessons I learned from the MILAF meetings about what makes for dynamic, engaging and productive workshops:

  • Limit the number of participants to about 20 while assuring a balance of scientific disciplines and gender.
  • Involve participants in organizing the workshop content.
  • Assure that everyone knows each other and their respective areas of competence at the start of the meeting.
  • Hold sessions for learning about key concepts. (These sessions are not necessarily meant to focus on the research of the participants, but sometimes the work of participants are among examples that illustrate certain concepts well).
  • Motivate discussion and debate about these concepts and about the general subject of the workshop.
  • From the debate and discussion, identify a couple of exciting questions that could be developed into research project proposals.
  • Break out into working groups to build project proposals.
  • Hold restitutions and debate about the proposals.
  • Discuss possible follow-up on the ideas developed in the workshop.

Several participants opened the door to some exciting additional activities by proposing that, in addition to presentations and discussions, we could set up some real-time experiments to illustrate critical questions about sampling and comparing populations from sinks and putative sources. So, here is a brief summary of the specific workshop contents illustrated with photos.

 

3 Sept: After brief introductory presentations by all of the participants, the group started a run of a high-flow-rate impinger. These inexpensive and versatile impingers, calibrated by Tina Šantl-Temkiv and colleagues [Šantl-Temkiv et al 2017] were brought to the workshop site by participants Pauline Vannier and Aurélien Daussin, collaborators of Tina from Matis in Reykjavik, Iceland. We ran the sampler in hopes of collecting enough microbial mass to attempt sequencing the air metagenome on site.

In the afternoon we heard and debated different points of view on ways to estimate and validate putative aerial trajectories of microorganisms. Debates were nourished by the presentations of Samuel Soubeyrand on the statistical and mathematical tools to estimate probable trajectories (see post on Twitter) and of Leda Kobziar on pyroaerobiology [Kobziar et al. 2018] (see Twitter post). One of the most surprising discoveries for the workshop participants was the apparent capacity of certain bacteria and fungi to survive the intense heat of burning, making us wonder if forest fires could be veritable microbial volcanoes.  Federico Carotenuto and Tina led the discussion about the implications of the range of available tools and markers of trajectories.

Aurélien, Pauline and Tina setting up the air sampler at the workshop site (photo: C. Lacroix)

 

Discussing how long to run the sampler and we expect to collect (photo C. Lacroix)

 

Tina and Federico lead the discussion about tools available for elucidating aerial trajectories (photo O. Berge)

 

4 Sept was dedicated to presentations and discussion about potentially unique sources of microorganisms and how to describe them. Christopher Carr and Noelle Bryan led us through all of the details – both theoretical and hands-on – of sequencing the DNA collected in environmental samples with nanopore technology, and in particular with a MinION personal sequencer that they brought with them. The details of their presentations brought us face-to-face with the important – and often limiting – quantitative aspects of air sampling. The need for a high-volume air sampler became very apparent. They also brought all of the materials needed to prepare samples for sequencing and Noelle conducted the preps during the discussions. This allowed participants to get a very real sense of what is involved in describing the genetic diversity of field samples – knowledge that needed updating for some of us biologists and was new to most of the participants from math and physical sciences.

In the afternoon we discussed several examples of studies of various habitats that could leverage research on linking sources and sinks of aerially disseminated microorganisms. Oddur illustrated how the melting Arctic, including the retreating glaciers in Iceland and the cryoconite habitats they foster, could be both source and sink of novel microorganisms that need to be traced. Pauline presented on-going research about the fate of microorganisms deposited from the air on newly formed volcanic islands and in particular the island of Surtsey that was formed between 1963 and 1967 following an underwater basaltic eruption on the southeast Icelandic rift zone. Brent Christner presented the approach that his team used to characterize the microorganisms associated with relatively low altitude nimbostratus clouds typical of subtropical regions such as Louisiana and to develop hypotheses about their origins [Joyce et al. 2019]. To conclude the afternoon, Christelle Lacroix and Auður presented a synthetic overview of a rational approach to assessing and validating trajectories of ubiquitous microorganisms and to identify their sources. This set the stage for how the breakout groups would approach the construction of their project proposals.

 

Chris explaining tons of important technical details about nanopore sequencing

 

Chris showing some of the equipment for personal nanopore sequencing

 

Noelle worked diligently all day during presentations and discussions to prepare samples for sequencing (photo C. Lacroix)


Mathematician Davide Martinetti (left) inquiring about the nature of the information provided by nanopore sequencing showing on Chris Carr’s (right) screen (photo C. Lacroix)

 

The group anticipating results from the sequencing of the air sample collected the previous day (photo C. Lacroix)

 

Oddur pointing out glaciers near the University of Akureyri (photo O. Berge)

 

Brent explaining how the source of microorganisms deposited on snow during a major dust event in Europe was determined [Weil et al. 2017]

 

5 Sept. The morning was dedicated to presentations and discussions about how to compare putative source and sink populations of microorganisms, how much similarity to expect, how to assess their similarity and how to corroborate their link. Two approaches were discussed: the search for clones in sink and putative source populations and the statistical comparison of the genetic structure of metapopulations. I presented the results to date about how we screened for the similarity and define clones within strains of P. syringae from vegetation in Iceland (collected in 2018), strains detected in air on Jungfraujoch and inhabiting various habitats in France. This led to a general discussion about the meaning of “clones”, for which we found no final consensus. Davide Martinetti  then presented a synthetic overview of the various approaches for testing hypotheses about similarity of microbial populations.

Just before lunch we split into working groups.  Over the course of the previous days, there were subjects that came to the forefront for which I felt the participants would be motivated. So rather than spending time on struggling for a group consensus on themes for the working groups, I exclaimed my usual “Hey everybody, I have some ideas!” – and the ideas were accepted quite well.  From there, the participants broke up into 3 groups with the objective of building a proposal to address a specific question about long distance aerial dissemination of microorganisms and preparing a restitution for the next day where they would:

  • State the specific objectives of the project.
  • Indicate the background knowledge on which the project is founded (i.e. what we think that we know).
  • Describe the experimental approach to attain the objectives and indicate an approximate time frame.
  • Indicate the research perspectives that the results would create.

 

Whatever the subject – this time it’s about the hunt for clones of P. syringae in sink and putative source populations – Cindy always talks with her hands (phptp C. Lacroix)

 

Davide is also adept in manual gestures to explain how to test hypotheses about the similarity of diverse microbial populations.

 

At every pause participants mulled around in discussion or to discover details about the sequencing materials (photo C. Lacroix)

Working groups buzzed all afternoon at different nooks at the Nes farm

 

After a long day of cogitation, the group went for dinner at the restaurant of a near-by hot springs

 

6 Sept. After Christopher and Noelle summarized the results of the sequencing attempt and what we learned about the DNA collection and recovery procedure, we listened to the restitutions of the project proposals. Here I will present brief overviews of the projects without giving away too many details, because it seems that the projects are being considered for further elaboration and execution by the teams that developed them. That, in itself, indicates the value of such a workshop and demonstrates the high level of investment by the participants.

 

Group 1 consisted of Brent, Davide, Aurélien, Christelle and Claudia Mignani to foster synergy between microbiology, statistics, ecology, and Earth sciences. They presented a project where they propose to extrapolate the insight gained from Brent’s work on identifying the sources of microorganisms recovered from precipitation that formed in nimbostratus clouds in Louisiana [Joyce et al. 2019] to a greater range of geographic situations across North America. The project would be based on setting up sampling in an existing network of habitat observatories. The contrasting land uses but similar origins of air masses at different sampling sites could help disentangle local from distant origins of microorganisms.

Group 2 consisted of Tina, Pauline, Samuel, Chris and Odile Berge to foster synergy between aerobiology, microbiology, Earth sciences, ecology of extreme environments, and statistical analysis of air mass movement. The aim was to develop a project proposal addressing the probable sources of the microorganisms arriving to Surtsey island and how to account for them in elucidating the colonization history of the island. To demonstrate the tools that can help address this aim, Samuel very efficiently conducted a trajectory analysis of the air masses arriving to Surtsey and overlaid them with available data on the land covers and habitats of Iceland. From these results, they estimated the main habitats that would be most likely to contribute to aerially disseminated microbes arriving to Surtsey and how they would proceed with testing that these habitats were indeed the real sources. The work on this project proposal led Pauline to realize the importance of setting up a collaboration with Samuel to pursue more thorough calculations of air mass patterns and to learn from my team’s work on P. syringae as a probable emigrant from the Icelandic mainland vegetation. We have now submitted a project proposal to the Jules Verne program to initiate this collaboration.

Group 3 consisted of Leda, Noelle, Federico, Moshe Rhodes and Fabio Gonçalves to foster synergy between aerobiology, atmospheric physics, meteorology, microbiology and forestry. This group based their proposal on available models for trajectories of smoke plumes from vegetation fires and observations about viable microorganisms associated with these plumes. They proposed to elucidate the specific conditions in which microorganisms can survive vegetation fires and to discriminate between the microorganisms in the plume that originate from the vegetation from those that are entrained from the atmosphere by the smoke plume as it moves. As they developed this project, the members of this group came to realize its significance for the dissemination of plant diseases between forests and other habitats where burning is part of normal management practices. The conventional wisdom is that burning is a means of cleaning because microorganism are believed to be eliminated in the process. Hopefully, members of this group will be able to secure funding and contribute to a paradigm change in plant disease epidemiology.

Here is a video of an simulated smoke plume to give you an idea of the capacity for prediction.

 

 

The road back to home

At the closure of the meeting on the afternoon of 6 September, Odile, Christelle and I drove back to Reykjavik. We had already enjoyed our adventure of discovering Iceland’s beauty the weekend before the workshop. We needed to collect a few more samples of prairie grasses in hopes of finding more strains of P. syringae that could be sisters of those blown away to where we were soon heading. The leisurely drive was an opportunity for me to think about the past few days of intense and fun cogitation and the incredible productivity of the workshop. I was also so pleased to be able to continue working closely with numerous young scientists from the MILAF meetings and to observe them blossom, mature and maintaining a keen interest in microbes at the interface of land-atmosphere feedbacks.

As the clouds menace, Odile and I are elated to have collected the last of our samples for this trip.

 

Christelle (center), Odile (right) and I will have great memories of the incredible beauty of Iceland (here we are in Snæfellsjökull National Park on the west coast) that will carry us along to our next visit in 2020 for the 10th International Symposium on Pseudomonas syringae in Akureyri.

 

References

Postdoctoral Fellowship: Characterizing and tracing biological aerosols in Southern Brazil to improve climate models

2019/04/06

A postdoctoral research position for scientists with a PhD in environmental sciences and experience in microbiology,  atmospheric sciences (physics and/or chemistry) and collaborative field campaigns (see description below).

The position is for 2 years, renewable, starting as soon as possible, at the University of Sao Paulo – IAG/USP

For further information, contact

Dr. Fabio Gonçalves:  fabio.goncalves -a- iag.usp.br      or

Dr. Cindy E. Morris:  cindy.morris -a- inra.fr

= = = = = = = = = = = = = = = =

The 500 km long Serra da Mantiqueira range in south-eastern Brazil creates very favorable conditions for the formation of massive cumulonimbus clouds that produce rainstorms, hail and lightning. These phenomena can have serious effects on the main agricultural productions of this region such as coffee, citrus and bio-fuel sugarcane. Aerosols emitted from land-cover can catalyze or limit these atmospheric phenomena depending on their characteristics (ice nuclei and cloud condensation nuclei) and abundance. In many cases, these aerosols are microbial cells or debris (bacteria and fungi) that can also have impacts on plant health. The FAPESP-funded project on “Primary Biological Aerosol Particles: Sampling and modeling in Southern Brazil to improve climate models” led by Dr. Fabio Gonçalves of the Institute of Astronomy, Geophysics and Atmospheric Sciences at the University of Sao Paulo seeks to assess the emission rates of these bio-aerosols from agricultural land-cover in Minas Gerais and Sao Paulo States to improve model predictions of cloud behavior.

We have funding for a postdoctoral researcher – with a PhD in environmental sciences and experience in microbiology, atmospheric physics and/or chemistry and with collaborative field campaigns involving team work  – to characterize the emissions of bio-aerosols and in particular biological ice nucleating particles (INPs) at experimental sites in Minas Gerais and Sao Paulo States in relation to land cover and agricultural practices. The data will be used for improving cloud modeling (including cloud microphysics´ schemes) in another part of the project.

The main objective of the postdoctoral researcher will be to evaluate the strength of major land cover (coffee, Brachiaria spp., Eucalyptus and indigenous restoration forest trees) as sources of biological INPs and the effect of season and various agricultural practices on their abundance. This work will involve measuring flux of biological INPs as influenced by coffee harvest mechanization and by different forest restoration practices in particular. Flux measurements will be conducted in coffee plantations on platforms that are under construction and with flux towers in forested regions in collaboration with the Laboratory of Tropical Sylviculture and the WeForest foundation. Passenger balloon flights will also be used in order to obtain data on aerosol dispersion.

This interdisciplinary project will be conducted in collaboration with a team of scientists from 5 research institutes and universities in Brazil, from INRA, France; the University of Lund, Sweden; CNR of Italy and Aarhus University, Denmark representing expertise in atmospheric physics, meteorology, microbiology, molecular biology, astrobiology, environmental engineering, and cloud modeling.

Mapping the after-effect of rain to determine where and when bio-aerosols influence rainfall

2018/03/19

This blog post summarizes how and why I have pursued making maps of the after-effect of rainfall across continental US (3000 sites) and Western Europe and the Mediterranean basin (500 sites). As described in the posting below, I believe that maps of the intensity of rainfall feedback are a useful tool to clarify the contexts under which aerosols markedly influence the outcome of atmospheric processes that lead to rainfall.  The maps, and the tools to make and analyze the maps, are freely available: http://w3.avignon.inra.fr/rainfallfeedback/

 

 

Aerosols play a vital role in the formation and amount of precipitation because they can influence the number and rate at which eventual rain drops form. In other words, there are conditions under which, without certain types of aerosols, rainfall might not occur. However, because aerosols are ever-present in the atmosphere and their effects cannot be easily separated from those of the synoptic conditions, it is a challenge to determine how important they are in the outcome of events leading to rainfall. Furthermore, there are many different sources of aerosols, and their types and abundances vary over space and time. This lack of uniformity further complicates quests to understand their significance in atmospheric processes and to generalize results from field studies.

Decades ago, the atmospheric physicist Keith Bigg started to suspect that he could capitalize on the temporal variability of aerosols to assess how they influence rainfall. Early in his career he observed that the atmospheric concentration of INPs (ice nucleating particles) increased right after rainfall and continued to accumulate for up to about 3 weeks (Bigg, 1958). He reasoned that marked changes in the rare aerosols – under relatively constant synoptic conditions – could reveal how these aerosols influence rainfall. Compared to the very abundant cloud condensation nuclei, INPs are relatively rare. So, perhaps the shifts in their abundance after rainfall could provide insight into the extent to which INPs influence the outcome of processes leading to rainfall. Keith started to explore rainfall data from weather stations across Australia to search for patterns that would be consistent with a lingering increase in INPs.  But, he was nevertheless perplexed about the mechanism that brought about this increase. He couldn’t think of any physical process that could sustain INP production over weeks. And furthermore, he had the impression that the curves of INP increase that he plotted looked like classic growth curves of organisms.

The discovery that certain microorganisms can catalyze the freezing of super-cooled water came about 20 years later – in the late 1970’s (as summarized by Chris Upper and Gabor Vali, 1995). This discovery sparked new research questions among physicists about the behavior of microorganisms as atmospheric INPs and among plant pathologists about their role in frost damage to the plants on which they lived. It took yet another 30 years for physicists and biologists to start consistently working together on questions of how the growing list of biological INPs can influence atmospheric processes (see Decade of Interdisciplinarity). All the while, Keith was ingesting this new perspective on ice nuclei and he was cogitating.

Since the early 1980’s, when I was a graduate student at the University of Wisconsin (in the lab where one of the two independent discoveries of biological ice nucleation activity was made), I had heard about a couple of eclectic scientists who had novel ideas about the role of microorganisms in rainfall. One of these was David Sands, a plant pathologist from Montana State University with whom I eventually linked up to initiate the research network described above. The other was Keith Bigg, an Australian atmospheric physicist who had some precise ideas about the interaction of microorganisms with rain and who was trying to do some experiments to gain support for them. The opportunity to meet Keith came in 2011 when Uli Pöschl (Max Planck Institute, Mainz, Germany) asked me to help him organize a session on bio-aerosols at the annual meeting of the IUGG (International Union of Geodesy and Geophysics) in Melbourne, Australia. By 2011 Keith had long retired from his official association with a research institute, but I managed to contact him at his home in Sydney and asked if he would be willing to come to Melbourne to attend the session. On the day of the session, I sat in one of the available seats near the front of the room for the talks just before our bio-aerosol session. When the gentleman seated next to me asked a particularly insightful question to the speaker, I was convinced that this was Keith. And indeed it was.

This was the beginning of a long intellectual journey. Keith described to me the methods he developed to find a feedback signal in historical rainfall data from Australia. He mapped the signals of rainfall feedback across Australia in search of how land use might influence the signal because land use can affect aerosol sources. To a microbiologist and epidemiologist such as myself, the notions of variability of aerosol types and of their abundance over space and time sounded very much like population dynamics and genetic diversity of microorganisms. These are basic staples for research in disease epidemiology.  But I was not sure that I understood the mathematics that he used. It seemed like a sort of time series analysis. And I wanted to see the confidence intervals associated with the signal that he measured. Keith agreed that I could engage some additional help.

At the research center where I work (INRA’s research center in Avignon, France) there is a strong program in spatial statistics and a team of scientists who have learned the pedagogic tools for communicating with biologists (INRA’s BioSP research unit). I knocked on the door of Samuel Soubeyrand who, still early in his career, had a reputation for excellent pedagogic and communication skills and lots of patience. I put him to the test with my approximate explanations of Keith’s ideas. Eventually, after 3 years of a very technical discussion between Samuel and Keith via email – with me in the middle asking lots of dumb questions in hopes of catching up in my understanding – we produced a tool to calculate an index that represents the rainfall feedback signal and to calculate its confidence intervals (Soubeyrand et al, 2014), and we mapped the index based on 100-year daily rainfall data across about 100 sites in Australia (Bigg et al, 2015).

The discovery of the ice nucleation activity of microorganisms that live on plants allowed Keith to suspect that the lingering after-effect of rainfall on subsequent rainfall is due to changes in amounts of bio-aerosols from rain-induced growth. This growth could transform negligible amounts of INPs into critical quantities that could influence atmospheric processes. As such, the Rainfall Feedback Index (RFI) indicates the extent to which atmospheric processes are sensitive to aerosols. Therein lies a key to capitalizing on the variability of aerosols over time to reveal their importance for rainfall.  Mapping RFI across continents would, in turn, provide the means to capitalize on spatial variability to uncover its influence on rainfall.

When I finally understood that the primary importance of the RFI is as a proxy for the dynamics of biological aerosols (and not for the amount of rain generated by feedback), I became somewhat obsessive about mapping this phenomenon. This obsession has its roots in my training in plant pathology where I learned about the importance of pathogen dynamics for epidemiology and disease management. But you might wonder how the management of plant health is related to the physics of rainfall formation.  It is related to the ideas that have been sparked about the practical applications of the microorganism-rainfall interaction.

There is more and more discussion about how microorganisms could be leveraged to “make rain” as scientists and the public learn about a possible role for microorganisms in rainfall. While that is a noble goal that should be considered, we cannot lose sight of the fact that some of the most active and wide spread bio-INPs can also cause disease to crops. The losses caused by these microorganisms can be of considerable importance economically and for food security. These dual-role microorganisms include the rust fungi such as Puccinia spp. (Morris et al, 2013), various strains of the bacterium Pseudomonas syringae (Berge et al, 2014) and several species of the fungus Fusarium including F. avenaceum and more that will likely be revealed soon. Questions about “making rainfall” are part of the battle to combat the consequences of climate change. Fortunately, this battle rallies a strong force. But it can also be blind to other efforts to protect the environment. This was illustrated clearly at the 2011 IUGG meeting I attended in Melbourne where a plenary speaker highly recommended that production of wheat and other large scale annual crops be intensified with heavy fertilizer inputs to assure that the plants sequester sufficient carbon. I sprung up during the question session to ask if he was aware that most of the major agricultural research institutes, especially those in Europe, were now mandated to work on de-intensifying the inputs of synthetic fertilizers into agriculture out of concern for deleterious effects on the environment. Clearly, the disciplines of Earth Sciences and of Agronomy had had little communication up to that date. Any effort to tweak plant-associated microorganisms to influence rainfall will need to assure that trade-offs between dual roles of microorganisms have been considered. By mapping the RFI, I felt that I could contribute to 1) clarifying where and when microbial INPs are beneficial for rainfall, 2) identifying specifically which microorganisms are implicated and 3) how they are related to crops. If there is corroborative evidence from field observations that potential plant pathogens are strong suspects as decisive actors in the formation of rainfall, then we will need to assess a critical epidemiological question about the quantities of the pathogen that are involved: Do these quantities pose significant threats to crop health or are they in a range where plant health can be managed by inherent resistance of the plant and/or agronomic practices?

In October 2014 I started to download daily rainfall data from the website of NOAA’s National Centers for Environmental Information. I was looking for sites in the US with roughly 100 years of daily data like Keith had used for his study of Australia. At first I was timid about downloading because I was not sure if the data were open access. But little by little I understood that this was an open service. Being quite content with the 1250 sites I found in the western US, I convinced Samuel that mapping the RFI for these sites would lead to fascinating results. After I manually formatted the data to fit to the R programing code that he developed to calculate the RFI, he kindly complied with my request.  I also convinced him that it would be great to have a website where everyone can see the maps, access the RFI results and learn how to make their own maps (see the previous blog post on Rainfall Feedback maps). With the help of Keith, David Sands and Jessie Creamean, an early career atmospheric chemist who participated in the MILAF mentoring workshops that David and I had organized (see The MILAF meetings), this effort also led to a publication in BAMS last year that describes the tools and the trends across the western US (Morris et al, 2017). The acceptance of our work for publication in a highly respected meteorological journal was reassuring that our tool had potential to give novel insight into the role of aerosols in rainfall formation.

Although I was encouraged to continue mapping the RFI, I was hoping that other scientists would get excited and want to make maps to ease my work. I also felt that I had made many demands on Samuel’s time and that maybe I should cool down for a while. But then the results of the 2016 US presidential election changed everything. By early December 2016 there was a strong concern in the community of Earth Systems scientists that the new US government would close or limit access to data bases related to climate change research. And so, on 15 December 2016, I started a marathon of screening the NOAA website for the data needed to calculate the RFI across the rest of the continental US and in Western Europe and the Mediterranean basin – all while keeping in mind that I needed to “run this marathon” in my spare time such as evenings and weekends. Six months later I had data from 1700 additional weather stations in the US and 500 across Europe, northern Africa and the Middle East and had formatted some of them.  I also had developed very painful carpal tunnel syndrome in my right hand (that I managed to eventually overcome without an operation). To help ease my hand and the amount of data manipulation it was doing, one of the scientists in my team, Christelle Lacroix, wrote a program with R software to automate the data formatting and the extraction of the metadata concerning the location of the weather stations and the range of dates of the data at each site. Christelle also helped me de-bug the R package that Samuel installed on a computer in my office so that I could make the calculations of RFI myself. And eventually, I didn’t bother anyone about the maps until early July 2017 when I finished the calculations for Europe and again last week (early March 2018) when I finished the calculations for the 1700 sites in the eastern half of the US.

I pursued the making of the maps posted at http://w3.avignon.inra.fr/rainfallfeedback/ for several years. But Keith has been working on the foundation of these maps for the whole duration of my life, i.e. for 60 years. That is an incredible achievement as a scientist. After meeting Keith in 2011, I traveled back to Australia twice to visit him again and to learn as much as I could about his insights on rainfall feedback and to imbibe in his historical perspective. It is a rare opportunity when knowledge can be directly transmitted across multiple generations, and it gave me a great sense of responsibility to receive such a gift. I hope that I have done justice to what I have learned. And I hope that the next generation is listening and interested.

 

References

Berge O., Monteil C.L., Bartoli C., Chandeysson C., Guilbaud C., Sands D.C., Morris C.E.   2014. A user’s guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. PLoS One 9(9): e105547. doi:10.1371/journal.pone.010554

 

Bigg EK. 1958. A long period fluctuation in freezing nucleus concentrations. J. Meteorology 15: 561-562.

 

Bigg E.K., Soubeyrand S., Morris C.E. 2015. Persistent after-effects of heavy rain on concentrations of ice nuclei and rainfall suggest a biological cause.  Atmos. Chem. Phys. 15: 2313-2326

 

Morris C.E., Sands D.C., Glaux C., Samsatly J., Asaad S., Moukahel A.R., Gonçalves F.L.T., Bigg E.K. 2013. Urediospores of rust fungi are ice nucleation active at > −10 °C and harbor ice nucleation active bacteria.  Atmos. Phys. Chem. 13:4223-4233.

 

Morris C.E., Soubeyrand S., Bigg E.K., Creamean J.M., Sands D.C. 2017. Mapping rainfall feedback to reveal the potential sensitivity of precipitation to biological aerosols. Bull. Amer. Meteorol. Soc. doi.org/10.1175/BAMS-D-15-00293.1  (June 2017:1109-1118)

 

Soubeyrand S., Morris C.E., Bigg E. K. 2014. Analysis of fragmented time directionality in time series to elucidate feedbacks in climate data. Environmental Modeling and Software 61:78-86

 

Upper C.D., Vali G. 1995. The discovery of bacterial ice nucleation and its role in the injury of plants by frost. In Biological Ice Nucleation and its Applications, edited by R. E. Lee, Jr., G. J. Warren and L. V. Gusta. St. Paul: APS Press.

A voice for flying bacteria

2017/08/31

Narratives and storytelling are useful tools for communicating science to non-expert audiences but they often have negative connotations when used among scientists (Dahlstrom, 2014). However, allegories, metaphors and other tools of storytelling can be extremely useful even for communication among scientists across disparate disciplines when scientists from one discipline effectively constitute non-experts relative to scientists from other disciplines. Furthermore, to integrate information from wide ranging sources into an understanding of complex systems that largely surpass the scales of time and space in which we readily comprehend our existence, we might have to tell ourselves stories to put all of the pieces together. Surely that is how my brain works to build an understanding of the emission of bacteria into the atmosphere, their flight, their interaction with clouds, their subsequent trajectory, their genetic diversification and their overall life history.

Once upon a time this summer when I was listening to an alluring version of Dust in the Wind by Korean guitar virtuoso Sungha Jung (https://goo.gl/vvFg8t), a story about flying ice nucleation active bacteria literally popped into my head. It is perhaps one of the stories that I have been telling myself without really being conscious of this mental construction. The story took on a life of its own and led me into an obsessive attempt to tell it the best I could, as a song with illustrations.

As for my previous  song “Clouds: When Physics meets Biology “, this new song illustrates how scientific discoveries can inspire poetry. It also illustrates that the process of rational reasoning associated with science is one aspect of the complex workings of the brain that can inspire the subtleties and nuances of art.  Together they help us to understand.

« We are more than dust in the wind »  is a video available on You Tube. The video presents the song and then presents the scientific information on which the lyrics were founded. I encourage you to use it in your teaching or in communicating with your friends, family and colleagues if you think that it could be helpful. Please note that unlike my previous song, I did not have any professional help in putting this together. Hopefully the amateurism will not distract too much from the message.

= = = = =

Dahlstrom MF. 2014. Using narratives and storytelling to communicate science with nonexpert audiences. PNAS. 111 :13614-13620. doi/10.1073/pnas.1320645111

MILAF – 2017: Biophysical atmospheric processes, 1 – 3 November 2017

2017/07/31

Workshop announcement

MILAF – 2017: Biophysical atmospheric processes

1 – 3 November 2017

Sven Lovén Center for Marine Infrastructure, University of Gothenburg, Sweden

Background

For the past decade there has been a growing effort to bring together scientists in the Life Sciences, Earth Sciences, Chemistry, Physics and Mathematics to explore the interaction of biological aerosol particles with cloud processes leading to rain and snowfall. This effort has been motivated by the discovery of the highly efficient power of certain microorganisms and various other biological particles to catalyze the freezing of water. The ubiquitous distribution of these biological particles in nature enables them to play analogous roles to other non-biological aerosol particles (dust, soot etc.), in facilitating the heterogeneous nucleation of condensed water that leads to precipitation in the form of rain, ice and snow. The fact that biological particles have been shown to catalyze ice formation at much warmer temperatures than non-biological particles underpins fundamental questions about how precipitation and biological systems are linked.  The answers to such questions have important implications for understanding climate forcing and feedbacks, including the interplay between aerobiology, species dispersal and the planetary energy budget.

As part of this effort, a series of MILAF (Microbes at the Interface of Land-Atmosphere Feedbacks) workshops have been dedicated to mentoring early career scientists who can contribute to the future of this evolving and exciting interdisciplinary research theme (this link includes details about the objectives, organization and content of previous meetings: https://bioice.wordpress.com/2016/12/26/the-milaf-meetings/). These workshops are aimed at creating collegial interactions among the diverse participants to optimize the synergy of disciplines, which often lack a common language. Thus the goal is to enhance the passion of the participants and revisit subjects where there exists consensus on the state of knowledge, while identifying the major challenges and opportunities wherein collaboration may fill distinct scientific knowledge gaps. The workshops have spurred numerous collaborations.

Objectives and venue

To continue in the spirit of the earlier MILAF workshops, the next workshop on biophysical atmospheric processes will be held from 1 – 3 November 2017 at the Kristineberg location of the Sven Lovén Center for Marine Infrastructure (http://loven.gu.se/english) of the University of Gothenburg, Sweden.

The workshop will focus on bridging knowledge gaps and building and growing interdisciplinary collaborations on two specific themes:

1) Non-classical approaches to nucleation in the atmosphere and

2) The significance of biologically catalyzed nucleation and precipitation for long distance dissemination of microorganisms and eventual species dispersal and co-evolution with the climate.

These themes were chosen because aerosol forcing remains the single most uncertain feedback in Earth system modeling.  A key lack of fundamental understanding stems from deficient representations of how ice in clouds forms and metamorphoses — and what promotes and/or inhibits ice crystal growth.  Observations demonstrate that only a minor fraction of the atmospheric particles stimulate ice formation and growth in clouds, with important implications for precipitation and cloud-radiative feedbacks. However, there is a growing consensus that biological materials catalyze ice nucleation more efficiently than other substances.  Therein lies a host of interesting implications for biological, physical, and chemical sciences. For example, atmospheric dispersal of microorganisms, is a potential pathway for ancient and contemporary colonization and exchange of genetic material and thus has posed selective pressure on microbes for over 3 billion years. Microbes that have traits enabling them to actively interact with global water and element cycles may acquire benefits relative to others without such traits.  Adaptations like those that would initiate atmospheric water phase transitions to trigger deposition, could promote survival and successful dispersal for such biogenic materials.  That said, both the biological and fundamental molecular-level physical understanding of nucleation in the atmosphere is lacking.

Organization

The workshop will be organized to facilitate rich interactions among participants and to limit, as much as possible, the costs for the participants. The activities of the workshop will balance the time dedicated to formal presentations with time for group discussion and prospection. The specific organization will be set up by the scientific committee depending on proposals from the participants. There will be no registration fees. The organizers have obtained sufficient funding to accommodate costs for about 30 participants. This funding will cover housing for the nights of 1, 2 and 3 November at the Sven Lovén Center (double occupancy in most cases), and all meals on these dates except the evening meal on 3 November.  Participants will be expected to pay for their travel, and for the evening meal at the end of the workshop if they want to participate in this meal. Participants should plan to arrive on the night of 31 Oct (at or nearby the workshop site) and to depart on 4 Nov.

How to participate

All participants will be expected to play active roles in the workshop. To participate, please submit two documents:

1) A short description of the topic that you would like to discuss at the meeting. This topic could be a subject for a formal presentation or for orchestrated group debate to assess the consensus or diversity of viewpoints.

2) A short statement (less than 1 page) about why you would like to participate in this meeting.

In the event that the number of applications exceeds the current budget allocation, the scientific committee will either select participants among the candidates (to assure that a diversity of scientific competences are represented) or they will invite all applicants to participate but ask them to pay a registration fee so that funds for housing and meals can be distributed to all participants.  Please submit your requests as soon as possible to Cindy Morris (cindy.morris-at-inra.fr) (replace “-at-” by “@” before sending message). We will finalize the list of participants by 1 October to give participants time to organize their travel.

 

Scientific Committee

-Erik Thomson, Assistant Professor for Research, Dept. of Chemistry and Molecular Biology, Univ. of Gothenburg, SE. Local Organizer

-Cindy E. Morris, Research Director, Plant Pathology Research Unit, INRA, Avignon, FR

-Tina Santl-Temkiv, Assistant Professor, Department of Physics and Astronomy, Aarhus University, DK.

-Brent Christner, Professor, Dept. of Microbiology and Cell Science, Univ. of Florida, USA.

-Vaughan Phillips, Senior Lecturer, Dept. Physical Geography and Ecosystem Science, Lund University, SE.

Taming microbial ice nucleators, Part II : a short video

2017/04/18

In the blog entry of 4 Jan 2016 I summarized activities dedicated to informing policy makers and the public about the role of vegetation in Earth’s climate beyond being sinks for CO2 . The follow-up of these activities led to the publication of a paper illustrating the various ways that vegetation (trees and forests in particular) contribute to the water cycle and to climate cooling (see Trees, forests and water: Cool insights for a hot world  ) and to a webinar.

For the webinar I pre-recorded my presentation on “Biological Rainfall Triggers”. Given that this presentation was meant to succinctly introduce the basic concepts for non-specialists, it might be a useful teaching tool.  Therefore, here is the link to the mp4 version of the file.

When physics meets biology there is poetry and music

2017/02/01

Most of us working in the area of biological ice nucleation are intensely fascinated by and in love with this subject. Fascination drives research. And love for this subject does what love does: it can inspire art. Throughout the past decade of interacting with the various disciplines and persepctives about biological ice nucleation and how it could impact clouds, I have listened to expressions and explanations about mechanisms and processes in clouds that have sent me dreaming. This dreaming led to lyrics that emerged spontaneously in my mind as I was riding my bike to work in the countryside near my lab trying to avoid stray dogs and an occasional wild boar and her piglets. The lyrics were set to the melody from Joni Mitchell’s Both Sides Now, a song that begins with her impressions of clouds. After receiving positive feedback about the lyrics and encouragement to record it and share it online, I succumbed to this advice – as an experiment and as an opportunity to witness all of the “materials and methods” involved.  I suppose that this is ultimate interdisciplinarity.

You can read the lyrics are at the end of this posting, below. I was encouraged to copyright them, so I did. Likewise, a professional musician recommended that I obtain permission to publish what is known as a “cover”, i.e. my version of an existing song. This can be done via an agency that centralizes such requests and obtains permissions from the original author/artist. This is important if one intends to charge listeners for downloading – which is not my case. But I wanted the full experience of producing a cover, so I sought out the permission.

 

You can listen to the song Clouds: When Physics meets Biology via streaming on the Sound Cloud website (the name of this website is a nice coincidence).

This song could be a sort of educational tool, especially if it were accompanied by a video. I was afraid of only being able to conceive something full of cloud clichés that did not have the same artistic quality as the music and lyrics – so I did not even attempt to make a video.  If anyone has ideas for an artistic and informative video to accompany the song, please let me know.

 

Here is how the audio file of the song was produced:

The recording consists of 16 audio tracks managed with Logic Pro X software. Fifteen of the tracks were audio files (drums, organ, bass, guitars and voice) and one track was the “cloud impulse” program from a synthesizer pad. The main accompaniments were played on a 1991 Martin D41 acoustic guitar, a 1960 Fender Jazz master electric guitar, a handmade (“Elvis Presley Graceland” model) bass and a Hammond B3 organ. The guitar solo interlude between the second and third verses was played on a handmade (“License Plate” model) electric guitar. Guitars, bass and organ were played by Danny Mangold, a guitarist, guitar-maker and producer from Seattle, Washington, who also crafted the handmade guitars. The drum accompaniment was a track produced by looping a drum sample from a recording of Aaron Comess, drummer for the Spin Doctors band. Lyrics were sung by Cindy Morris and recorded with an ADK Hamburg microphone. Production of the audio file required 2 hours for production of an original demonstration version of the bed tracks and 5 hours of recording of the voice tracks and mixing. Lyrics were copyrighted by C.E. Morris on 30 Jan 2017 and permission for publication of a cover version of the original Both Sides Now song by Joni Mitchel was obtained on 28 Jan 2017 from the Harry Fox Agency before the .mp3 version of the audio file was uploaded to Sound Cloud. The .wav version was saved for use where listeners are likely to use excellent speakers beyond what their cell phones, computers and tablets permit. This file can be obtained from Cindy Morris.

guitars

 

The lyrics

Clouds: When Physics meets Biology

[cover version of Both Sides Now, Joni Mitchell]

Lyrics (except for first 4 lines of the first verse) by Cindy Morris, copyright 2017.

 

[Verse 1]

Rows and flows of angel hair

And ice cream castles in the air

And feather canyons everywhere,

We’ve looked at clouds that way.

 

But are they blankets or albedo shields?

Or lakes of rain for crops in fields?

Impressions in the painter’s dream

Meet a science theme.

 

[Chorus]

We’ve looked at clouds that come and go

That surge or fade, or rain or snow

How can we hold them in our hands,

In hopes to one day understand?

 

[Verse 2]

Particles and drops so small

That billow in the clouds so tall.

Nucleate and aggregate

Will make the great rains fall.

 

They say that microbes are at the core

When crystals splinter and thunder roars.

When physics meets biology

Imagination soars.

 

[Chorus]

We’ve looked at clouds superficially

But now we want to really see

The complex web of processes

Do we really know clouds at all?

 

[Verse 3]

Proteins in the dance of ice

Hold water bonds that they’ve enticed.

With such appeal, their fate is sealed

Encased in falling rime.

 

Leaf blades spring as drops rebound

And trickle deep into the ground.

To be absorbed and launched again

For yet another round.

 

[Chorus]

Aerosols in masquerade

Take fleeting shapes in a white parade

Where Gibb’s free energy is king

We really shall know clouds someday.