2019

2019 was actually a pretty intense year for me. I tried to publish. And to survive. I made a collection of the happiest moments on photo. Now we are taking off. Driving south.

Pura Vida
a luci(ni)d bounty
Soul mate support system
My first faculty job interview
My California love
Iron Kittens
Mami
World Dance
The girl who lives in the forest
Riding into the sunset
My proudest moment of the year
Skate like a girl
A big dog at heart
what if…
just peace
The caterpillar
blue eyes
How is Khris Davis feeling?
Ex Luna
My family, strong.

My proudest career moment

A few weeks ago, I was asked what my proudest career moment was. Here you go:

I am having a hard time to be proud of myself. But my husband just reminded me that I had 3 first-author manuscripts accepted about a month ago – all on the same day! One was about frog demographies. We modeled abundances of individual frogs at different life stages for that paper. (We even accounted for their detection probabilities!) It all started as a side-project when I was still in Stephanie Carlson’s lab at UC Berkeley. Sébastien Nusslé had started analyzing this dataset but he left because he founded a company with his very successful wife Semira Gonseth. GenKnowMe. Hence, I adopted another orphan project. Kathleen Matthews, a friend and mentor of Stephanie’s had collected data on frog demographies in Kings Canyon National Park. She hiked out to Dusy Basin every summer for 18 years to count Rana sierrae. The Sierra Nevada Mountain Yellow-legged Frog. Kathleen and her team counted frogs at different life stages throughout the summer. From when the ice melted at this high elevation habitat in spring, until winter came back in early fall. I convinced Zack Steel, a graduate student at UC Davis (now postdoc at UC Berkeley) with great experience in population modeling, to help me analyze this dataset after Sébastien had left. We investigated which biotic and environmental factors affected frog demographies before this local population went extinct in 2013.

Find the paper here, it is all open access.

Abstract: The Sierra Nevada yellow-legged frog (Rana sierrae) was once an abundant and widely distributed amphibian in California’s alpine ranges. Rana sierrae is adapted to high-elevation, fishless habitats. Its adaptions are reflected in a unique life cycle that involves a flexible, extended juvenile phase due to the short growing season typical of its alpine habitat. However, today this species is critically endangered, and most populations have been extirpated from their native range. Here, we present an 18-yr-long demographic study of a R. sierrae population in 15 lakes at Dusy Basin in Kings Canyon National Park. We focused on the period leading up to the arrival of the pathogenic chytrid fungus, Batrachochytrium dendrobatidis (Bd), and the subsequent local extinction of R. sierrae. We used N-mixture abundance modeling, which accounts for detection probabilities, to quantify factors affecting frog abundance at different life stages. The abundance of subadult and adult frogs was negatively associated with the presence of introduced trout (Oncorhynchus mykiss and O. aquabonita). Frog abundance in all life stages was positively associated with lake surface area. The propensity of lakes drying correlated negatively with abundance of eggs, subadults, and adults in the following year. Moreover, drought years, characterized by longer summers and less winter snowpack, led to higher rates of lakes drying. Finally, our results suggest that the frequency of such droughts in the region has increased since 1937. Increased frequency or severity of droughts is expected to decrease the value of shallow lakes for Sierra Nevada yellow-legged frogs because these habitats are prone to drying. We discuss our results in terms of future restoration strategies, including reintroduction and probiotic treatment, in this changed and changing ecosystem.

The second paper that was published on my lucky day was an invited perspective about the implications of host hybridization for microbial symbioses. I wrote this paper on my own but I got support from Cassie Ettinger and Jonathan Eisen. I really enjoyed writing this piece because it let me muse about my greatest interests including speciation, hybridization, evolution of microbial symbioses, and clams. Lots of clams. I also want to mention Shana Goffredi at Occidental College, Perrine Cruaud at Laval University in Québec, and people at the Monterey Bay Aquarium Research Institute (MBARI) who all provided nice images to me to create a nice figure.

Also open access!

Check it out here: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15262

Abstract: Evolutionary adaptation is the adjustment of species to a new or changing environment. Engaging in mutualistic microbial symbioses has been put forward as a key trait that promotes the differential, evolutionary success of many animal and plant lineages (McFall-Ngai 2008). Microbial mutualists allow these organisms to occupy new ecological niches where they could not have persisted on their own or would have been constrained by competitors. Vertical transmission of beneficial microbial symbionts from parents to the offspring is expected to link the adaptive association between a given host and microbe, and it can lead to coevolution and sometimes even co-speciation (Fisher et al. 2017). Vertical transmission also causes bottlenecks that strongly reduce the effective population size and genetic diversity of the symbiont population. Moreover, vertically transmitted symbionts are assumed to have fewer opportunities to exchange genes with relatives in the environment. ‘In a From the Cover article in this issue of Molecular Ecology, Breusing et al. (2019) investigated whether hybridization among different host species could lead to inter-species exchange of otherwise strictly vertically transmitted symbionts. Hybridization of divergent lineages can potentially cause intrinsic and extrinsic incompatibilities, swamp rare alleles, and lead to population extinctions. In some cases, however, it might also create novel trait combinations that lead to evolutionary innovation (Marques et al. 2019). Breusing et al. (2019) linked the concept of hybridization to symbiont transmission, and their findings have significant implications for the study of evolution of vertically transmitted symbionts and their hosts.

Figure 1: Chemosynthetic bacterial symbionts of vesicomyid clams.

A.1) Phreagena soyoae gills; photo generously provided by Professor Shana Goffredi (ORCID: 0000-0002-9110-9591), Occidental College, Los Angeles, CA, USA. A.2) Transverse section of gill fixed for fluorescent in situ hybridization (FISH). A.3) Symbionts hybridized with bacterial probe in orange and DAPI-stained frontal ciliated host cells in blue. A.4) Same specimen and coloring, at higher magnification. Each host cell (bacteriocyte; grey highlighting) contains hundreds; i.e., a population of bacterial symbiont cells. Images A.2, A.3, and A.4 were kindly provided by Dr. Perrine Cruaud (ORCID: 0000-0001-8628-3600) at the Laboratory of Microbiology of the Extreme Environments (LMEE), Ifremer, Brest, France. B) Breusing et al. (2019) constructed haplotype networks for host genes (mitochondrial: mtCOI; nuclear: ANT, H3), as well as symbiont genes (16S rRNA gene: sym16S) of two host species (light green = P. soyoae, dark green = Archivesica gigas). Each circle represents a haplotype with circle size showing its frequency in the dataset. Mixed haplotypes are shown as pie charts of light and dark green. C.1, C.2) Deep sea hydrocarbon seep collection site at Pescadero Basin in the Gulf of California, Mexico from the expedition in 2015 when Breusing et al. (2019)’s samples were collected in their natural habitat. An image-use agreement was provided by the Monterey Bay Aquarium Research Institute (MBARI).

And the third one was a whitepaper that resulted from a workshop I organized together with Matt Leray and Jarrod Scott a year ago. That one is my personal gem because it was just such a unique experience to organize a workshop, meet new people and make new friends, and then write a paper with everybody. Here we discuss how host-associated microbiomes contribute to ecosystem structure and function in marine systems. We highlight the rise of the Isthmus of Panama as a great (if not the greatest) natural experiment to study the ecology and evolution of marine microbial symbioses and host-associated microbiomes.

Of course open access as well: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000533

Abstract: The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host–microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.

First day of first grade

Today was Linnea’s first day of first grade at school. As it turns out, she is in her favorite classroom with her favorite teacher. Miss Eagle!

When this summer break started, I was concerned. Not sure how that would play out with my husband watching the kids the whole summer without a break for him. I traveled a lot. I had to let go. Let him do his own thing. Let him feed them what he thinks is right. Let him decide how much screen time they would get and how much play time.

It worked very well. Linnea had a super creative summer. The most creative girl I know. I am proud of my husband. He supports her dance. He lets her create.

I am not too concerned about Buddha. The two of them are living in a symbiosis where both partners benefit.

I know that she ate too many popsicles and slept with the dog when she missed me at night. But that is OK.

There might be a bit of a bias towards marine creatures. But that is OK, too.

Business owls. They watch what you are doing.
This helmet keeps your thoughts secret. Not even business owls can read them.
Polarizing light
Working on a kelp forest.
3D animals floating around her room!
cat meow
Dropping-in with Papa
Spraying
The squid before the Megalodon
An anglerfish waving in the wind.

Paper out!

Today, Cassie’s and my article on metagenome-assembled genomes in two hot springs of Kamchatka, Russia was published in Scientific Reports. Cassie and I only analyzed the data. The whole story is much older and involves many more people, including Elizabeth Burgess who originally collected the samples as a graduate student in Jürgen Wiegel’s lab. Or Russell Neches, who went to Kamchatka himself and had played with this dataset before us. And Ray Keren who encouraged and distracted me with his fascination for arsenic biochemical pathways.

Laura Hug led the way in the beginning and Chris Brown provided the tools when we got stuck.

We are all working really hard and sometimes don’t even find the time to celebrate or to be proud. I had a hard time today to enjoy. Now it is sinking in slowly. I am incredibly proud of Cassie. Working on this project with Cassie cheered me up, it motivated me to do things right, and it gave me a strong feeling of peace.

We learned a lot and we tried to do it right. In every aspect. Guillaume showed us many tricks. And Jonathan believed in us.

And A. Murat Eren was very important too. A bright star on the horizon. And the Banfield lab. We got a lot of inspiration. Obscure archaea are awesome.

At some point, when we are all a bit less busy, Jonathan might write a blog post about the background and history of our article…

The article itself can be found here: https://www.nature.com/articles/s41598-019-39576-6

Poster of our research at #LAMG2018

Two weeks ago, we presented at poster about our current fish research at the Lake Arrowhead Microbial Genomics Meeting #LAMG2018.

Abstract:

In most species with an external breeding system and no parental care it is generally assumed that males only provide genes to the next generation. Recent studies however demonstrated that offspring can also inherit non-genetic traits, such as epigenetic effects or bacteria. Here we characterized symbiont bacterial communities in milt of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) and tested whether bacteria are transferred from the father vertically to the next generation. We used a full-factorial breeding design and in vitro fertilizations in order to separate genetic and environmental effects on offspring performance. For the fertilizations we either washed milt with antimicrobial compounds or we left it untreated. We found a high diversity of bacteria in the milt of different sires and we monitored bacterial communities on developing embryos until one day after hatching. Offspring that originated from washed milt hatched later and were smaller than their natural fullsiblings. This difference in size persisted until ten days after hatching (the end of our experiment). Our results are discussed in the light of anthropogenic influences (i.e., micropollutants in freshwater systems) and the coevolution of hosts and their microbiomes.

PIT tagging

Während meinen Untersuchungen im Winter 2016 und 2017 in Zusammenarbeit mit Claus Wedekind von der Uni Lausanne, dem Kanton Graubünden (Marcel Michel, Amt für Jagd und Fischerei AJF) und Roland Tomaschett, dem Fischereiaufseher in Trun haben wir bereits einiges über die Bachforellen in Vals gelernt.

Etwa 40% der Weibchen laichen während der Laichzeit nicht. Sie sehen normal und gesund aus. Genetisch stellen sie keine Untergruppe dar. Es gibt keine Anzeichen von Inzucht. Ihr genetisches Geschlecht stimmt mit dem Phänotypen überein. Sie haben kein Y-Chromosom und besitzen normale Ovarien. Wir wissen immer noch nicht warum sie nicht laichen. Diesen Winter möchten wir sie markieren um herauszufinden, ob sie ein Jahr später laichen werden. Vielleicht laichen sie nur jedes zweite Jahr um Ressourcen zu sparen.

Im Rahmen des jährlichen Laichfischfangs in Trun (geplant für den 17. Oktober 2018) schlagen wir vor, eine Stichprobe von laichreifen Rognern, sowie auch eine Stichprobe von unreifen Laichtieren nach Trun in die Fischzucht zu bringen (analog zu den Versuchen in 2017).  In der Fischzucht in Trun werden diese Fische dann nach Laichreife sortiert und sachgemäss betäubt. Die betäubten Fische werden vermessen und mit einem Transponder markiert. Gemessen werden Fischlänge, Gewicht und Fettanteil (ich werde mein persönliches Messgerät mitbringen, das wir erfolgreich für Regenbogenforellen in Kalifornien eingesetzt haben).  Als Transponder werden PIT tags (Passive Integrative Transponders) vorgeschlagen da sie (i) inaktiv sind (senden keine Radiowellen aus und brauchen keine Batterien), (ii) einen individuellen Barcode enthalten und so jedes einzelne Tier wiedererkannt werden kann, (iii) wasserdicht, steril und für das Tier störungsfrei sind.  Die Fische werden nach dem Experiment wieder am natürlichen Laichplatz ausgesetzt.

Beim Laichfischfang ein Jahr später können die Fische individuell wiedererkannt werden und es wird bestimmt werden, welche Fische nun laichen oder nicht. Weiter können dank den individuellen Transpondern auch wertvolle demographische Daten über Laichreife, Fruchtbarkeit und Überlebensraten gesammelt werden. Falls das Aussetzen von Laichen keine natürliche Überlebensstrategie darstellt sondern ein Problem müssen wir herausfinden, was mit den Valser Forellen nicht stimmt. Vielleicht hat es Mikroverunreinigungen im Wasser? Der Steinbruch oder Verhütungshormone könnten da eine Rolle spielen.

Als Vorbereitung für dieses Markierungsprojekt habe ich vor zwei Wochen einen Kurs im Markieren von Fischen in der Warm Springs Hatchery in Geyserville, Kalifornien besucht. Mein Lehrer war Ben White, der lokale Fischereiaufseher.

Linnea durfte seine Fische füttern!

Normalerweise werden die Transponder einfach in die Bauchhöhle eingeführt. Da unsere Fische in Vals aber kurz vor dem Laichen stehen ist das keine gute Idee. Die Wahrscheinlichkeit ist gross, dass die Transponder während dem Laichen verloren gehen. Sie können mit den Eiern abgelaicht werden. Deshalb musste ich lernen, wie ich die Fische im Rücken in den dorsalen Muskel markieren kann ohne sie dabei zu verletzen.

Zuerst habe ich mit ein paar toten Silberlachsen (Oncorhynchus kisutch) geübt. Die sind am gleichen Morgen gestorben und ich durfte sie zum Üben brauchen.

Das hat gleich gut geklappt. Als Test habe ich dann meinen Tag wieder gesucht…

Am Nachmittag haben wir zehn junge Regenbogenforellen markiert (2 Jahre alt). Diese Fische hat Ben nach der Markierung eine Woche lang überwacht. Alle haben die Prozedur überlebt und schon nach zwei Tagen war keine Wunde mehr erkennbar.

Da Geyserville nicht gerade auf dem Weg liegt haben wir gleich das Wochenende in der Gegend verbracht und im Zelt an ein paar spektakulären Orten übernachtet.

Hier schlagen wir das Nachtlager auf!

Geyserville heisst nicht umsonst Geyserville. Hier gibt es viele heisse Quellen und Geysire. Wir haben einen verässlichen Geyser besucht. Er hat mich sehr beeindruckt. Und auch motiviert. Während den letzten zwei Wochen habe ich drum mit Cassie unser Paper über Mikroorganismen in heissen Quellen auf der Kamchatka Halbinsel in Russland fertig geschrieben.

Old faithful in Geyserville

Embracing advocacy in science

Freshwater systems are endangered. Habitat degradation, chemical pollution, altered hydrology, species invasions, overexploitation and climate change are threatening these habitats, here and now. The American Fisheries Society is trying to raise awareness about the importance of freshwater ecosystems. These systems can be considered biodiversity hotspots and they provide ecosystem services. However, it is really hard to lobby for them because the human use of freshwater for agriculture, energy and other economic developments (T)trumps conservation concerns in the society. We are responsible – I feel responsible, for making the public aware of their freshwater systems. We need to go out and communicate with the people.

Two weeks ago, I was invited by Suzanne Kelson, a PhD student in Stephanie’s lab to go talk to high school students from Moraga, a small town in the neighborhood of Berkeley. We went out to a little creek and discussed this freshwater habitat in the field with students. We measured stream flow, invertebrate biodiversity, hydrology and explained how a watershed is built up. I talked about fish migration, reproduction and the interaction with bacteria in salmonids, mostly steelheads. Each little station that was led by Suzanne, Hana Moidu, Jordan Wingenroth, and Brian Kastl gave the students insight into a different study area of freshwater biology. Together we provided each puzzle piece to give the students a greater picture. I felt like they walked away with more awareness for their surrounding environment. They were surprised to see so much in their little neighborhood creek. I am convinced they will experience their party/stroll/car- or bike ride at the river differently next time.

Back at home I read an essay in the Fisheries Magazine April 2018 by Marcy Cockrell, Kate Dubickas, Megan Hepner, and Matthew McCarthy (Fisheries, Vol 43, No. 4). They are reaching out to scientists and encourage them to advocate for policy issues. The believe that all citizens have a responsibility to engage in the political process, especially scientists. Advocating for science-related issues should not be a conflict of interest but a necessary step towards a more holistic scientific method and a more informed society.

They list the following nine guidelines how scientists could advocate:

  1. Gain experience working with a variety of activities and organizations.
  2. Join a professional society that already plays a role in advocacy, for example AAAS (the American Association for the Advancement of Science).
  3. Become involved with local or national chapters of conservation-minded NGOs, trade organizations, or general membership groups.
  4. Be proactive in communicating science.
  5. Engage in dialogue with decision makers.
  6. Gauge interest among colleagues.
  7. Build and use your network.
  8. Apply to formal opportunities for communication training and professional development.
  9. Vote!

Thank you Suzanne for inviting me to your outreach activity. I think we took care of points 4, 6 and 7. I also would like to thank Stephanie for being a great role model how to actively pursue all numbers 1-9, advocating for freshwater sciences and building a great community of freshwater scientists (for example Mary Power, Ted Grantham and Albert Ruhi), a new hotspot at UC Berkeley!

Brian Kastl explains to the students how to calculate water flows in the creek.

Die East Bay noch einmal voll auskosten

Gestern sind Linnea und ich mit dem Velo ans Meer gefahren. Dort haben wir auf Donny und Jacoby gewartet, die uns mit dem SAAB und der Camping Couch gefolgt sind.

Es windet so stark dass beide ihre Hüte festhalten müssen. Das ist normal hier in Albany. Schwedische Sommerbrise.

Meine Familie und die Skyline von San Francisco. Ganz klein irgendwo da draussen wohnt Gino.

Zum Znacht Bananenblüten mit Nudeln und Chnobli aus der Berkeley Bowl.