Department of destruction

Five weeks ago, we landed in Zürich. Back home in Switzerland. Since then I went through many emotions and memories. Constantly inhaling everything around me. Privilege. Mostly privilege. Swiss people don’t know how privileged they are. I have been breathing cristal clean air and drinking the most pure and tasty water since months. I have talked to researchers being funded by millions of Swiss taxpayer dollars (Franken, actually). I have looked at sparsely populated paradise valleys. I have touched the most happy and friendly cows in the world.

Lots of fieldwork on brown trout in Graubünden with Roland Tomaschett, graduate student Victor Ammann and many invaluable helpers from my family

Giachen explores his home

Trip to Vienna with my mom to meet Jillian Petersen

Ennio growing up

Family time with Mayra and Miguel

Gelateria di Berna Nostalgia

Ennio creating mosaics with the kids at Lake Geneva during my collaboration with the Engel lab at UNIL

Quality family time at my brother Emanuel’s farm

Linnea playing in front of EAWAG, The Swiss Federal Institute of Aquatic Science and Technology where I met professors Jakob Brodersen and Ole Seehausen

Now I am back in California. We were looking forward to returning to heaven. Instead, we realized that the apocalypse is here. Right now.

Today: Smoke in the city

Fires in July: The County Fire west towards Lake Berryessa has burned over 22,000 acres without containment on Sunday, July 1, 2018 in Napa County.

Donny and I made a list. I accomplished 40 important tasks in Switzerland. I worked without a break. Now I am looking out of the window and wonder about life. Davis is covered in smoke. Inside. Outside. Everywhere. Climate change is here. Right now. We are all in it. Privileged people and less privileged people as well. Everybody. It is absolutely surreal for me to see people walking through the smoke with face masks. In the most beautiful state in the world. It is burning down.

UC Davis closed two days ago. Jonathan Eisen, my sponsor and mentor at UC Davis fought for it. The health risks are simply too big. Public schools were open until today. Mostly because so many parents work and can’t afford to keep their kids at home. However, the air quality became so bad today that all schools are closed now. We are not sure if we will stay in Davis over the weekend.

It seems like we are all working for the department of destruction. By the way, did you know that there is a Department of Destruction? We learned about it after we forgot our passports in the airplane from Paris to Zürich. We had been flying from San Francisco to Paris. The kids were super nice, but Jacoby decided not to sleep. So, we stayed up with him. Doing things. After immigration and transfer in Paris, we fell asleep on the plane to Switzerland. All four of us. Like a coma. We actually fell asleep before the plane departed from Paris. Somebody had to wake us up in Zürich. When we rushed out of the plane, we forgot the passports on the plane. When I called later and asked at Air France, the cleaning personnel, the airport police; we were told that our passport were found. Somebody brought them to the airport police. The Swiss one was destroyed immediately according to Swiss law. The Americans were sent to the embassy and were going to be destroyed within 21 days. At the Department of Destruction. This is us.

Family dinners

We started this new tradition of having dinner together. This was just not our thing. However, it is wonderful if it is just Donny, Linnea, Jacoby and I.

The rules are: Everybody has to say something about their day. Everybody has to listen to the others talk. In the end everybody has to ask a question about the world.

Linnea hit off the first couple of nights by asking:

  • Are all stars suns?
  • How many days since you were five years old?
  • How old is God?
  • Would you have enough time to count to one hundred trillions before you die if you spoke it out loud?
  • Why are you sometimes angry at me and sometimes you feel sorry for the same thing?

Internship and Master thesis project of David Zeugin

This post is written by David Zeugin, University of Lausanne

My project with Laetitia was about the decline of a European grayling (Thymallus thymallus) population in Lake Thun, Switzerland. We looked at the effects of inbreeding on offspring survival. To manage this population, juveniles are bred each year in a hatchery from a stock of captive fish and released into the wild. However, breeding fish in a hatchery leads inevitably to inbreeding. We investigated the effects of this inbreeding by comparing reproduction success of wild fish and captive ones simultaneously in a climate chamber at the university. During the course of their development, we measured embryo survival, time until hatching and sizes of larvae. Additionally, we tried to develop a gynogenesis protocol.

Getting the fish (grayling) in Kandersteg, BE.

Gynogenesis allows the creation of artificial diploid homozygote offspring from the haploid genetic material in the eggs of the mother. Eggs are fertilized with inactivated sperm and then exposed to heat shock or radiation to trigger cell division. Eggs and sperm from wild fish and hatchery stock were used for this protocol. The effects of inbreeding at different levels; i.e., crossing wild individuals vs. crossing hatchery stock fish vs. crossing a female with itself was measured by stressing the resulting embryos with three fish pathogens, Pseudomonas fluorescens, Aeromonas salmonicida and Aeromonas sobria.

Inactivating the sperm.

Inside the UV box.

We had a very low success rate of gynogenesis. The number of viable diploid offspring for each female was so low that we could not statistically compare their performance to the other grayling embryos and larvae. The number of viable embryos was relatively high but they all died before hatching. However, grayling embryos coming from parents that had been produced and raised in hatcheries reacted with a higher mortality and earlier hatching compared to the offspring of wild fish when presented to both A. salmoncida and A. sobria

fertilized eggs

Most of the gynogens are dying.

Head and eyes become visible.

The supervision of Laetitia in this project helped me to take initiatives, to be rigorous in my experimental design and conduct, and to develop my communication skills. I directly profited from her large knowledge on the subject and appreciated that Laetitia was supervising my work and at the same time giving me the opportunity to develop my own hypothesis on the project.

I am now a Ph.D. candidate in the Ionta lab and work on neuroscience. I am studying the neural basis of visuo-motor control and how they interact in the human brain.  https://iontalab.org

In the climate chamber

lots of data

freshly hatched

Living with Wolves in California

Wildlife seminar by Kent Laudon

Es ist wieder einmal an der Zeit einen Blog auf Deutsch zu erfassen. Es geht um Wölfe. Kent Laudon arbeitet für die Behörden. Er ist sozusagen ein Amtsbiologe. Er hat sich auf Wölfe spezialisiert.

Der Raum ist voll. Ich habe ihn noch nie so vollgestopft gesehen. Absolut soziopolitisch. Kalifornien hat seit ein paar Jahren ein Wolfsrudel. Genau wie Graubünden.

Im Vergleich zu Graubünden ist die Geschichte hier etwas anders verlaufen. Die Europäer haben Nutztiere mitgebracht und alle natürlichen Raubtiere ausgerottet. Die Wölfe in Kalifornien wurden ganz ausgerottet, Bären nur teilweise. Seit 1996 (etwa 100 Jahre später) wandern Wölfe wieder ein aus Kanada.

Im Vortrag geht es vor allem und Sichtungen von Wölfen. Alle Wölfe hier tragen Halsbänder mit Sendern. Das Amt hier weiss genau wo die Wölfe sind. Laudon fährt mit seinem riesigen Pick-up truck durch den Wald, sein Mountain Bike im Kofferraum und sucht Signale seiner Wölfe. Amt für Jagd und Fischerei auf Amerikanisch. Wenn die Wölfe sich in die Wildnis zurückziehen steigen die Biologen auf Pferde um. Freiwillige Mitarbeiter hat es genug. Sogar ehemalige Förster und aktive Jäger.

Ich nehme nicht viel mit vom Vortrag ausser ein paar schönen Erinnerungen, Fotos und Videos. Was mich erstaunt ist wie weit die Wölfe wandern jeden Tag. Die Karte zeigt Idaho, Oregon und Kalifornien und der Wolf läuft darin herum wie auf einem Fussballfeld. Schnell einmal 100km at Tag.

Auch sehr spannend sind die Videoaufnahmen im Juli 2015 wo am gleichen Tag Wölfe und Bären zu sehen sind.

Wölfe laufen gerne auf Strassen und Wanderwegen. Hier in Kalifornien benutzen sie auch Flüsse, die im Sommer austrocknen als Korridore.

Die Mehrheit der Bevölkerung in Kalifornien lebt immer noch im 1924 als die Wölfe erfolgreich ausgerottet wurden. Kent sieht seinen Job vor allem darin, mit Leuten zu reden und aufzuklären. Was fehlt im grossen Teil der Bevölkerung sind Grundkenntnisse der Ökologie ihrer eigenen Umwelt. Als Beispiel dazu zeigt Kent wie sich die Populationsdichte der Wölfe an die der Hirsche anpasst. Wenn es viele Hirsche hat, dann vermehren sich die Wölfe. Dann essen sie viele Hirsche und deren Population bricht zusammen. Ein Jahr später bricht die Wolfpopulation ein und die Hirsche können sich wieder erholen (Daten aus Wisconsin).

Für die mit Grundkenntnissen auf Englisch habe ich hier noch ein paar sehr spannende Unterlagen. Und das hier. Adrian Treves konnte sehr schön aufzeigen und quantiativ bestätigen, dass der kontrollierte Abschuss von Wölfen durch die Regierung dem Ruf des Wolfes schadet. Wenn die Bevölkerung sieht dass die Regierung eine geschützte Art abschiesst, dann empfinden sie den Wolf nicht mehr als schützenswert. In einigen Gebieten hat das sogar dazu geführt, dass Jagdfrevel zugenommen hat.

Als ich Kent darauf angesprochen habe, hat er ganz aggressiv reagiert. Wie immer. Wölfe = Emotionen. Er meinte, es sei die Aufgabe der Regierung, die Wolfspopulation zu kontrollieren und regulieren. Er sagt das, nachdem er gerade das Raubtier-Beutetiere Schema gezeigt hat.

Ich habe mich hier reingesetzt für eine Pause von einem langen Tag im Büro. Es war erfrischend. Ich habe viel an unsere Calanda Wölfe gedacht. Vor ein paar Tagen habe ich nach langer Zeit wieder einmal eine Nachricht von einem Freund aus Graubünden erhalten. Das hat mich riesig gefreut. Es haben mich also noch nicht alle vergessen daheim. Passt gut auf eure Wölfe auf! Gell Ueli! Liebe Grüsse.

Einmal um die Sonne mit den Calanda Wölfen

Getting ready for my second Panama Trip

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.

David and I will keep you entertained with our traveling blog at: https://istmobiome.net/

Keith Bouma-Gregson’s exit talk

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

 

 

Fieldwork, research and a happy birthday

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

Abalone snail

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.

Petrolisthes cinctipes

Petrolisthes manimaculis

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.

Creatures in the tide pools:

young dungeness crab

Cancer antennarius – rock crab

giant sea star

solitary anemone

My most precious assistant

Done.

Ein Familienunternehmen

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

Daheim

Vals

Der Valser Rhein

Im Laichgebiet

Zurück in der Fischzucht werden die Fische betäubt.

markiert..

fotographiert….

beprobt…

Gewebeproben

Und für alle Ewigkeit aufbewahrt.