I am back from Panama. Living and working in California. This month I have to do a a lot of bioinformatics. Several datasets are waiting to be analyzed. I am now actively using R Markdown and Jupyter notebooks to make my work more transparent and reproducible. Stephanie organized a workshop for the Carlson, Power, Ruhi and Grantham group at UC Berkeley on data management plans. I found myself in all categories: the planning stage of a project, fieldwork, wet lab, data analysis, statistics, bioinformatics, preparing a paper, and post-publication. This is postdoctoral life. And it is beautiful.
Last week I read this blog several times. It gives me goosebumps because it describes my life in very beautiful words. It touches me right in the middle. What is a postdoc?
This blog post is by Jeremy Yoder, now professor Jeremy Yoder. He is a member in the committee of The Molecular Ecologist. They offered me to write blog posts for their website. I am extremely happy to fulfill this job. The journal Molecular Ecology is one of my favorites and I find it important to make its publications accessible to everybody. Writing for this website is one step in the right direction. I am planning to explain exciting Molecular Ecology articles to the general public and discuss trends in this field of research. Additionally, I am also looking forward to contributing articles about the challenges and strategies of researchers (mostly postdocs) who are trying to juggle work and family. I envision this website as a platform to assist academia in becoming a more inclusive environment. I know that the other bloggers are on the same page and I am extremely thankful that they offered me to become a part of their writing team.
I have been half sick as of yesterday and today. However, as a parent you cannot just lie in bed and wait until you recover. Sorry world for spreading my bugs. Yesterday afternoon, we went to Stinson beach to remember at what a beautiful place we are allowed to life. Today we joined the Chinese New Year party at the UC village. Such parties make this place unique. It feels so special to walk 300m to a community center and meet fellow researcher families from all over the world on a boring Sunday to celebrate the year of the dog. We met people who spoke Mandarin, Bangla, Japanese and English. We used too much glitter, ate good free food and took silly photos. I am enjoying every second of being affiliated with the best public university in this country.
Today David Coil and I are flying to Panama for a our first official sample collection. I feel like I am fully prepared, including all necessary vaccinations, a travel laptop from Jonathan that I just set up fresh, an extra phone with a Panamanian SIM card and local number, money in small bills, having informed my bank about my credit card, lots of different kinds of collection tubes, DNA extraction kits, petri dishes, culturing media for bacteria, anaerobic incubation chambers, diving equipment, Linnea’s dissection scope, insect repellent, treated clothes against mosquitoes and ticks, instant coffee, and most importantly, photo equipment.
Honestly, I did not sleep much the last couple of nights. However, the collection schedule is penciled down, my future research plans have taken some shape and in theory, I am fully prepared.
What you must know before reading this blog is that here at Berkeley most talks are great. You could go to a seminar every single day and learn new things and hear brilliant people talking. This also applies to graduate students‘ exit talks. The last one I went to was by Tristan Nunez. See here.
Today it is Keith Bouma-Gregson. He did a PhD in Mary Power’s lab in Integrative Biology at UC Berkeley. He will be moving on to work with Jill Banfield now. Check her out. She is awesome. http://nanogeoscience.berkeley.edu/
Mary Power’s introduction:
Keith worked on a variety of projects on food web ecology, aquatic ecology, cyanobacterial genomics (mostly Phormidium: a toxic cyanobacterium), public health and citizen science. He also worked a lot on the Eel river restoration project. http://www.eelriverrecovery.org. Keith involved local people so that they would learn what the problems are with cyanobacteria and the toxins that they produce.
There is a funny, dark, little story. Somebody found a human skull in a river in Humboldt County. The police wanted to use their sniffing dogs to find the rest of the body but they did not know whether they could let their dogs into the water because of the toxic cyanobacteria. So Keith went there and checked it for them. He could confirm that the waters were safe. So whenever these detectives will have similar problems they know now who they have to contact…
Full hearts, clear eyes on the eel can’t lose. FULL HEARTS, CLEAR EYES ON THE EEL CAN’T LOSE. (you have to scream it out loud).
OK. Now Keith will start his talk:
Background: Water systems in California have been affected heavily by human alterations like pollution, damming, or the addition of fertilizers. The climate in California is mediterranean, the highest water levels occur at the wrong time for agriculture. Hence, humans built dams and reservoirs for saving it. Consequently, there is not enough water for the ecosystem when it needs it for its highest productivity. Due to the huge anthropogenic impacts on Californian waters, cyanobacterial blooms have increased. These bacteria will bloom and become the most common taxa in the environment. Legrand et al. showed in the journal Toxins in 2017 that cyanobacterial blooms are increasing recently (shown in Lake Zurich, Switzerland). Cyanobacteria produce toxins that are harmful to the mammalian liver and nerves. Not all strains contain the genes to produce these toxins.
Keith’s thesis: was based on the Eel River system. UC Berkeley has a field station in the middle of this system, the Angelo Coast Range Reserve. By the way, I did a large part of my fieldwork on O. mykiss in this reserve. Keith monitored the Eel River for cyanobacteria. He wanted to find out where, when and who is there. Together with Professor Kudela at UC Santa Cruz, Keith built Solid Phase Absporption Toxin Trackers (SPATTs) to measure toxins in the water. The toxin Anatoxin-a showed very high levels throughout the watershed. The highest levels were measured in August when the river temperatures were highest. At this point, Keith did not know which taxa were producing these toxins.
Keith went ahead and identified all cyanobacteria he could find in the system. He described mostly Anabaena spp. (Nostocales) and Phormidium spp. (Oscillatoriales). To do this, Keith collected green mats in the field, brought them to the lab and measured their toxin concentrations. He could find Anatoxin-a and Microcystin toxins in all mats. The levels were so high that they would kill a dog and maybe even be toxic to a cow. Moreover, Anabaena spp. were associated with low flowing water. It builds clumps and they get stuck in eddies and pools of the river. This could be a health risk for humans swimming in the river. Keith performed an experiment to investigate when cyanobacteria float and when they sink to the ground in the natural river. He found that they remain buoyant for days in a natural light regime (Bouma-Gregson et al. in Harmful Algae 2017).
He learned the following:
Cyanotoxins are produced by benthic Anabaena and Phormidium.
Anatoxin-a is frequent and shows high concentrations.
Cyanobacteria float at high concentrations in the river during summer and could represent a potential health risk.
As a next step, Keith performed genome resolved metagenomics. He collected cyanobacteria at 22 different sites across the Eel River system, extracted their DNA and assembled them into contigs to get a draft metagenome. Then he binned out individual genomes into draft genomes. With these samples he would first describe the bacterial composition and then look for the Anatoxin-a synthesis operon. He could find this operon in 7 samples. Then he linked the presence/absence of this operon to bacterial community composition. He found that samples with this operon clustered together. This was mostly driven by the presence of Burkholderiales.
Keith also identified the main energy pathways in his microbial mats. Most bacteria in his samples had genes for carbon oxidation. He did not find any bacteria that use methane, hydrogen or sulfate to gain energy. However, he found a few bacteria that metabolize Urease. Many of his bacteria contained a gene that codes for a transporter that can transport phosphate inside their bodies. Moreover, they also have a pathway where they excrete an enzyme into their environment that binds inorganic phosphorus and transforms it to phosphate which they then can import back into their cells. It seems that these bacteria are super effective at scavenging phosphorus, even if its concentrations are low. This could be an explanation why Phormidium dominates in the Eel river system that has high organic nitrogen levels and low phosphorus levels.
Keith ended his talk with the following statement: Cyanobacteria have been around in our environment ‚forever‘ so the goal should not be to eradicate them but to learn more about them and how to deal with them.
This is Keith. He is also active on twitter as @K_BoumaGregson
The feelings of a parent are intensive. I love research and I adore my kids. If I can combine family time with doing research it makes me complete. Happy. Satisfied.
at the coast
On a much more negative emotion, have you heard that the kelp forests in Northern California are all dying? It all started in 2013 when a disease killed most sea star populations along the Pacific Coast of North America. These starfish are the main predators of purple sea urchins. Sea urchins have since then been thriving. Their main food is kelp! Another problem is the rising of the ocean water temperature. Kelp needs cold temperatures. In 2014 the Pacific waters in California have been exceptionally warm due to global warming on the long term but also El Niño on the short term. Global warming alone is often not the sole cause for extinctions but it makes a system more vulnerable. If other factors like disease outbreaks or natural disasters are added to the equation, their combined effects will cause species to become extinct. Today, more than 90% of the kelp forests are gone. However, kelp forests play a key role in marine ecology. They provide shelter and food for many creatures, including young fish that hide in their stalks and abalone. Abalone are sea snails that apparently taste deliciously. They have very pretty houses that shine like a rainbow. If you go diving down there right now you would see a desert full of purple sea urchins (Strongylocentrotus purpuratus) who are starving but not dying. Interestingly, they keep alive and reproduce. Besides these urchins you would find thousands if not millions of empty abalone shells. What can you do? It is not pretty. Divers are trying now to remove the sea urchins to give the kelp a chance to regrow next spring. Check out this video: removing sea urchins
The shiny inside of an abalone shell
Two abalone trying to find some food.
I went to a pretty site between Fort Ross and Jenner which is in the middle of this devastating phenomenon for a different purpose. I am planning to work with porcelain crabs in the future. Mostly in Panama. However, I am based in California and sometimes it would be easier to do projects right here. Now I need to find healthy porcelain crab populations to work with.
blue P. manimaculis
Spontaneously, as usual, we went to celebrate Jacoby’s second birthday at a beautiful beach with numerous tide pools. Linnea and I investigated the biodiversity, while the guys were enjoying a gorgeous winter sunset.
Wie versprochen habe ich mich Mitte Oktober in ein Flugzeug gesetzt und bin rund um die Welt geflogen um den Valser Forellen zu helfen. Ich habe mich bei Mami eingenistet, wenig, aber schöne Zeit mit meiner Familie und Freunden verbracht und alles für den letzten Tag vorbereitet. Denn an diesem Tag ging es den Valser Forellen an den Kragen.
Wir haben so viele Forellen im Laichgebiet gesammelt wie möglich und die dann nach Trun in die Fischzucht gebracht. Dort haben wir sie gemessen, markiert, Fotos gemacht, und für jeden Fisch haben wir auch Gewebeproben und Hautschleim gesammelt. Das Wichtigste war aber, dass wir untersucht haben, ob die Fische laichreif sind oder nicht. Knapp die Hälfte der Weibchen, die da im Laichgebiet herumhängen sind nämlich nicht zum Laichen da. Für die Laichreife habe ich mich vor allem auf Roland verlassen. Er hat jeden einzelnen Fisch angeschaut und bewertet.
Jetzt schwimmen sie alle wieder im Schongebiet. Hoffentlich überleben sie das Jahr. Und ich sitze wieder hier in Kalifornien…
Ich war für diesen Trip ganz alleine unterwegs und ich hätte es nicht geschafft ohne die Hilfe meiner Familie und Freunde. Ein ganz grosses und dickes Dankeschön an meine Lieben aus dem Nachthimmel über San Francisco.
Mit Ennio auf dem Mittenberg
Der Valser Rhein
Zurück in der Fischzucht werden die Fische betäubt.
I have this personal feeling about Humboldt County. I seem to love it. I don’t know if I could live there. I don’t like the meth heads. However, I always love to visit. I also met the nicest people there. Tommy Williams made it possible that I could go sample fish close to Arcata. An opportunity I had already given up on. He wrote to me on Friday. And on Sunday we were already in Arcata.
I sampled young of the year from Prairie Creek the first day. Prairie Creek is super pretty. On the way there we saw lots of elk hanging out in the water. We had beautiful fall weather and sampled in the middle of a redwood forest. I joined John’s crew, including Chris and Reed. The day was phantastic! These guys are super nice and showed me how to use a seine – a kind of net to catch juveniles. At Prairie Creek there are almost only Coho salmon (Oncorhynchus kisutch) research projects. Yet, I am only interested in O. mykiss. Here comes the special challenge: at this life stage you cannot discern O. mykiss from cutthroat trout (Oncorhynchus clarki), which are also very common in this creek. Three very similar species in one little creek. I just doubled my sample size and I will use genetic markers later to find out who ist what. I was a one-woman-show and processed all my fish alone. I got a bit tired but then I met Jesse and Jolyon, two other fish researchers in the same creek. Jolyon offered me some smoked Chinook salmon that he had caught and smoked the day before. It was delicious and gave me a lot of energy to finish this field day!
Is this an O. mykiss or an O. clarki???
Looks like an O. mykiss…
little Coho YOY
Big cutthroat trout!
I spent the evening with my family. We had good food and beer. Arcata is a little jewel.
The second day I spent with Colin and Eric at Freshwater Creek. They are stars in seining. They caught whatever they wanted with their net. Two AmeriCorps had their first day in the field. AmeriCorps are volunteers who work for about a year in conservation projects at many different locations all across the state of California. Colin taught them a lot about monitoring Coho salmon and estimating their survival during the winter season. I tagged along and learned a lot.
While I was working, Donny enjoyed the area with the kids and met his old College friend Mike and his family. We heard about wildfires further down south and during the second day the sky got grey and full of smoke. The wind brought the smoke up to us. Our phones did not work anymore because some fibre cables were burnt. Luckily, we found each other again. We met at Freshwater Creek and Linnea helped me finish processing the fish.
The same night I drove the whole family back down to Albany. It was dark but we could see the wildfires between Willits and Ukiah! Right next to the highway. Huge fires. I have never seen something like that before.
I had a short night because I had to get up early the next morning to sample fish in Marin County at Walker Creek with Greg and his crew. He also had a helper from the AmeriCorps! For this sampling day Laura joined me to help. She is a great helper and very pleasant to hang out with! On the way home we went to taste some French cheese at a farm close to Point Reyes. The sky was orange and full of ashes. The particles in the air made the sun redder than usual. Totally surreal.
Sticklebacks! Very stickly!
Roach on its head
The last couple of days I had several meetings to organize lab work, work on the frog project, and teach researchers about health care. I hurried from meeting to meeting. Everything seemed pretty surreal in the constant smoke and strange sunlight. Even breathing was getting harder and harder. The Bay Area is a smoke hole!
Today, my dear neighbor and guinea pig sitter Tristan gave a talk at our Wildlife and Conservation Seminar at ESPM. I took notes and I am posting them here.
A finishing talk: That is how we mark the end in the graduate program at ESPM. Let’s honor Tristan!!!
Animals: move biomass and seeds around, alter nutrient cycles, pollinate. With warming they have to move away to find their niches (e.g., colder places).
How do animals ‚cross roads‘ of climate change and of alterations in landscape. —> Human alterations of the environment. ???
I. Animal movements shape environments:
Example: Hippos graze at night on land. During the day they hang out in the water to stay cool and poop (Pennisi 2015 in Science). They connect land and water ecosystems. Webcam at mpalalive.org. They tagged hippos and studied where they are grazing, resting and moving around in space. GPS. Grazing, Resting, Transit. Taking that map, they modeled biomass transfer. Hippos remove biomass during grazing but add it again during pooping. Use GPS technology to measure how poop is moved around. Could be applied to cows and grazing in California landscapes. Places of resting and pooping are hotspots of biomass decomposition (i.e., nitrogen rich).
II. With changing environment animals move to more suitable habitats:
International agencies (banks and private) encourage Africa to do more land use and use irrigation system to produce food (crops). Species distribution models often ignore hydrology. Tristan addressed the following questions: Would the inclusion of hydrology improve distribution models? Does it change how we model species distributions? What are the effects of the conversion from rain-fed system to irrigated system?
Models including hydrology performed better than atmospheric models. What is an atmospheric model? I don’t know. Key finding: If you include hydrology into the model there are much fewer suitable areas! If you model how Africa is going to look like in 2070, including hydrology in the model, you almost don’t see any change in suitability of habitats for hippos. However, if you now also account for irrigation change due to an increase in agriculture, there is an 68% loss of suitable habitats. Take home messages: Including hydrology improves distribution models, projections differ between atmospheric and hydrological model, and land use will affect suitable habitat for animals. Don’t ignore hydrology when modeling species distributions even if you are working on terrestrial animals.
III. How do climate niches move through time:
40% of mammals are unable to keep pace with climate change. Temperature has been increasing during the last 100 years, however, there is a lot of variation in the rate of increase. For the last part of his dissertation, Tristan compared different biomes and how they move through time.
Here he showed a R simulation that shows how deserts moved through time in the western USA. Now animals need to be able to follow their niches. I think Tristan is not yet finished with this chapter.
How do animals shape the environment. Link movement metrics and human footprint. Help land managers by predicting which climate changes and landscape alterations are coming in the near future. Be able to react to it!
If you want to read more about hippos and their ecoystems check this out!
Well, on Friday, almost two weeks ago, we decided to fly to Panama. It just made sense to join our STRI collaborators during their field trip and to take Linnea out of school while her regular teacher was still sick. When we arrived at San Francisco airport very early in the morning of Saturday, the lady at the check-in told us that we could not fly to Panama because Linnea’s passport will expire on December 1st and to fly to Panama you would need your passport to be valid for 3 full months. This is where our Panama trip ended.
We went back home to Albany and slept for an hour. Then I had the brilliant idea of calling the Swiss embassy and asking them for an emergency passport. Unfortunately, they were closed on a Saturday. Donny spent some time on google and found out that today (!) there was the yearly passport day in San Francisco where people, especially families, can get passports. So, we drove to Berkeley, made passport photos, copied birth certificates, called grandma, and rushed to San Francisco. At the passport office, we got called up immediately and ordered Linnea’s passport. However, the friendly lady told us that it would take 4-6 weeks to mail the passport to us. If we wanted if faster it would cost extra and still take 2 weeks. Then, Donny started crying. He explained the lady that this trip to Panama could change our lives. He told them about me and my research and that he wanted to see the country before moving there with the kids. The lady left, talked to her supervisor and came back. She told us that Linnea’s passport will be ready in 2h.
Seven hours later we sat on the plane to Miami, 15 hours later we arrived in Panama City.
We arrived on a Sunday. The first evening we went for a 2h walk with the stroller and both kids to check out downtown Panama City. It was interesting, safe, but not very exciting. After a trip to ‘Price Smart’, the brother of ‘Sams’ we had gotten enough snacks for the rest of the days and enough of downtown City. On Monday, I went on a field trip with Jarrod and Harilaos. Jarod picked me up from my hotel and I helped him prepare tubes and stuff in the lab on the island of Naos for our dissections later that day. The lab is very impressive. They have every kind of equipment, from gel electrophoresis to fume hood and MiSeq sequencer. Better than most of the Swiss labs I have seen.
Then Harilaos invited me for coffee at his house. An old colonial house with lots of Coatimundis begging for toast.
I liked the experienced greek and his strong, Italian coffee. He drove us across the country to the Carribean site, to Galeta, where we sampled urchins. We drove through a rainforest, the autopista and in the end a beautiful mangrove forest. There were several checkpoints where they asked us for identification and collection permits. At Galeta we met Haris’ technician Axel, his postdoc Carlos, and his intern Tanner. Here is a link to Carlos‘ personal blog!
We collected four different species of urchins (Diadema sp., Eucidaris sp., Echinometra lucintra, and Echinometra viridis).
Diadema in their natural habitat:
Three different species of Sea urchins in their natural habitat:
Then, we drove back to the laboratory and dissected them to identify the microbes living on and inside them. Harilaos, Jarrod and I dissected. We split the work up so that each of us would dissect at least 3 individuals of each species and we kept track of who did what. We collected their fecal pellets first. Then, we poked them with a syringe and sucked out their coelomic fluid. Then, we collected a few spines. After cutting the poor animal open, we also took a piece of their intestines and a piece of gonad.
Late at night I made it back to the hotel and passed out pretty soon. The next day I went back to Naos and had more time to talk to Harilaos. He showed me all their facilities and how to keep urchins and crabs in tanks. Later that day he introduced me to Alexandra Hiller, a collaborator who works on Porcellanidae. We talked for several hours and she told me some fascinating stories. I got lots of ideas.
That night we went to see Dumas, a Panamanian friend who was in my PhD cohort at Lausanne University. He and his wife Emilie (jurasienne) have a nice little house in Paraiso. We stayed until late and talked. Linnea fell in love with Emilie. We played with their two dogs (Chocolate and Dubois – or something similar) and hung out in their hammock.
The next morning, we got picked up early and drove to the jungle of Gamboa. Our guide Carl (the owner of the Jungle Land Panama Ecolodge) drove us on a boat along the Panama Canal. He enjoys talking. We took several side rivers and met monkeys. Capuchin monkeys, Spider monkeys, Howler monkeys, and Cotton-top tamarin monkeys. Carl goes and feeds them every day, so they recognize him and jump on the boat when he shows up. Not sure what I should think about it. The French-Canadian tourists with flip flops and beers on our boat definitely enjoyed it.
The canal is pretty impressive. They are constantly dredging and making it wider and bigger. Some of their cranes are from Germany from post-war times.
On the canal:
2000 containers of toys, cars, crap from Asia to Europe…
Then we arrived at the lodge. It is a wild and fantastic place!!!
After a rich lunch, Linnea and I went kayaking while Donny and Jacoby took a little nap. Linnea is a great companion! She told me everything she knows about the jungle. We left the kayaks and took a little hike to a waterfall. I jumped down and Linnea was a bit jealous. I promised we could come back when she is a bit older and can jump too. She was sitting in the water and waiting for me until the little minnows started nibbling on her.
We stayed overnight at the lodge. I went swimming with Jacoby and we enjoyed all the night creatures. Linnea sat on the balcony at dark and looked at the bats. There were lots of them. During the day, we saw a lot of birds. However, I do not know them all by name. I am not a passionate birder. I recognized the Brown pelican, Snail Kites, Purple Marten, some swifts, hummingbirds,
On Thursday, we traveled back to the big city of Panama. On the way, we saw a sloth. People here like to take them down from the trees so that tourists can take pictures of them. That is pretty sad. It costs them a lot of energy to climb back up the trees. Their diet is not very nutrient rich and they need to save their energy!
I don’t even want to start writing about the sad Boa constrictor that is living with Carl. She does not live a very happy life.
On my last day I saw Alexandra one more time and we talked crabs.
Panama is beautiful. There is such a rich life here. Most people I met were very nice. However, it is also very complicated. Last night I went to a bar alone. I ordered a beer and a sandwich. The bartender told me that I was absolutely crazy to walk alone into a bar without speaking Spanish and being a white lady. It confuses me that I do not know the rules here in Panama. Three people pointed out that I am white during my trip. I do not fully understand what is going on. I am motivated to learn Spanish and I think it will help. However, as blond as I am, I think I will never be taken seriously in Panama. I find this pretty racist. I am feeding a family of four with a postdoc salary. My computer was stolen two weeks ago. I have almost no money left and still I got charged ten times more than locals. A weird feeling. Tomorrow we are flying to Florida for the weekend before returning back to California.
We saw alligators in the Everglades and I found a dead Porcellanid during snorkeling at Bill Baggs State Park in Key Biscayne while Donny took care of the last Baseball moves on my phone. This is called convenience.
We are reaching out to hear from others what tools they are using to assign and visualize gene functions in environmental samples of microbial communities.
Our dataset is simple. We did a metagenomic analysis of two pools (samples/sites). First, we co-assembled the whole metagenome for each pool. Then, we used anvi’o to bin individual bacterial and archaeal genomes within the pools. These genomes (bins) were then fed into RAST. This online software gives you a table of known genes for each bin. At the moment we have an array of tables with known microbial genes for each pool that we would like to visualize/summarize in an aesthetically pleasing way. We tried to use summary statistics in MG-RAST, but the upload failed eight times in a row (including several attempts of uploading individual bins as fasta files, co-assembled metagenomes as fasta files, and sequence reads before assembly as fastq files). The upload failures were identified as cashing problems or internal errors.
We went back to using anvi’o using NCBI COG assignments, following their infant gut pangenome tutorial (http://merenlab.org/tutorials/infant-gut/) which in the end gives you a similar output to RAST in tabular format.
What software are people using out there to compare, assign and visualize gene functions across samples and across bins? Can these tabular outputs be used as inputs for any software producing visually pleasing figures?