Just a quick post here – there is a new PeerJ preprint I just found out about via automated Google Scholar alerts that seems like it may be of interest: Distinct root-associated bacterial communities on three wild plant species growing in a common field from Kristin Aleklett, Jonathan W Leff, Noah Fierer, and Miranda Hart.
Monthly Archives: October 2014
What’s that in my Seagrass?
This past weekend we took Bethany Dixon (@MsBethDixon)’s class of AP Bio students out to Bodega Marine Laboratory to make winogradsky columns from seagrass sediments. For more information about what we were doing, why we did it and what the heck a winogradsky column is see Jenna’s previous posts, AP Bio Winogradskies and AP Bio Winogradskies Pt 2. As part of the experience, the students had to opportunity to wade out into a seagrass meadow to collect samples and thus the mysteries begin! Follow along on twitter with #APBioGradsky!
UNSOLVED MYSTERIES:
What is that I see in my seagrass roots? What is that is that sticky white stuff? Fungi? Underwater spiderweb?
When placed underwater this strange organism looks like a wiggly worm brain – what the heck is it?? Zombie slug?
AP Bio Winogradsky Recipes
This past weekend we took Bethany Dixon’s class of AP Bio students from Western Sierra Collegiate Academy out to Bodega Marine Laboratory to make winogradsky columns from seagrass sediments. For more information about what we were doing, why we did it and what the heck a winogradsky column is see Jenna’s previous posts, AP Bio Winogradskies and AP Bio Winogradskies Pt 2. For more winogradsky goodness see: Adventures with Winogradskies, Further Adventures with Winogradskies, Even More Adventures with Winogradskies and On the Road Again: Adventures with Winogradskies. Keep up to date with these columns by following along on twitter with #APBioGradsky!
How to Make a Winogradsky: We gave the AP Bio class a standard winogradsky recipe and then five “experimental” recipes. These recipes are described below.
Standard (10x Recipe)
cellulose 1 g
sodium sulfate 1 g
ammonium chloride 0.1 g
calcium carbonate 0.1 g
potassium phosphate 0.1 g
diatomaceous earth 300g
This is the standard recipe which we are using for our “control” columns.
Potassium Nitrate (10x Recipe)
cellulose 1 g
sodium sulfate 1 g
ammonium chloride 0.1 g
calcium carbonate 0.1 g
potassium phosphate 0.1 g
diatomaceous earth 300g
potassium nitrate 0.1 g
This recipe adds potassium nitrate to the standard recipe. By adding potassium nitrate, we hope to encourage denitrification (the process by which microbes take in nitrate and produce N2). By encouraging denitrification, we hope to enrich for microbes potentially involved in the nitrogen cycle.
Ammonium Acetate (10x Recipe)
cellulose 1 g
sodium sulfate 1 g
ammonium chloride 0.1 g
calcium carbonate 0.1 g
potassium phosphate 0.1 g
diatomaceous earth 300g
ammonium acetate 0.1 g
This recipe adds ammonium acetate to the standard recipe. By adding ammonium acetate, we hope to encourage nitrification (the process by which microbes take in ammonia and produce nitrite). By encouraging nitrification, we hope to enrich for microbes potentially involved in the nitrogen cycle. Also ammonium acetate provides an additional carbon source for the microbes and should help encourage microbial growth.
Iron(III) Phosphate (dihydrate) (10x Recipe)
cellulose 1 g
sodium sulfate 1 g
Iron(III) Phosphate (dihydrate) 0.1 g
calcium carbonate 0.1 g
potassium phosphate 0.1 g
diatomaceous earth 300g
This recipe replaces ammonium chloride from the standard recipe with Iron(III) phosphate (dihydrate). Iron is a necessary co-factor for nitrogen fixation and both iron and phosphorus have been posited to co-limit nitrogen fixation in the ocean. By adding iron(III) phosphate, we hope to encourage nitrogen fixation (the process by which microbes take in N2 and produce ammonia). By encouraging nitrogen fixation, we hope to enrich for microbes potentially involved in the nitrogen cycle.
Seagrass Roots (10x Recipe)
Seagrass roots 1g
sodium sulfate 1 g
ammonium chloride 0.1 g
calcium carbonate 0.1 g
potassium phosphate 0.1 g
diatomaceous earth 300g
This recipe replaces cellulose from the standard recipe with seagrass roots. Since we are trying to culture seagrass associated microbes, we thought that it would be interesting to use seagrass roots as the carbon source for the winogradsky columns. We hope that this will result in an enrichment of microbes that from symbiotic relations with seagrass roots.
Elemental Sulfur (10x Recipe)
cellulose 1 g
sodium sulfate 1 g
ammonium chloride 0.1 g
calcium carbonate 0.1 g
potassium phosphate 0.1 g
diatomaceous earth 300g
elemental sulfur 0.1g
This recipe adds elemental sulfur to the standard recipe. By adding elemental sulfur, we hope to enrich for microbes involved in the sulfur cycle.
Collecting seagrass and sediment!
Inoculation: We had the students prepare their recipes on their first day and then inoculate them on their second day. We inoculated them with seagrass sediment and water collected from Bodega Bay by the AP Bio class. We mixed the sediment and water collected vigorously and let the sediment settle. The water was then used to inoculate the columns.
Inoculating our winogradskies!
The finished columns! #APBioGradsky
AP Bio Winogradskies (Pt. 2)
Even with a few days distance from the (hopefully) inaugural field trip with the AP Bio class from Rocklin Collegiate Academy, I’m still shocked by how smoothly everything went. On Friday, we set up the Winogradsky columns (see post here.) On Saturday morning, were were so fortunate to be at the Bodega Marine Lab on the day when UC Davis Biological Sciences freshman are bussed out to the BML for a tour and some proselytizing for marine biology as a field of study. Because there was already staff on hand for the freshman tours, we were offered the opportunity to have our class go on the same tour. After the tour and an inspirational overview, given by Dr. Eric Sanford, of ongoing research at BML, we had lunch and then killed time at the dorms while waiting for the tide to go down.
I’d borrowed 3 pairs of waders for the students who were adventurous enough to get into the chilly water to collect seagrass plants and sediment. However, after polling the students, I realized that almost everyone was pretty excited about putting on the waders, so I grabbed a bunch more. At 2:30, low tide, we went to Westside Park to hunt for seagrass beds. From the shore, it was pretty easy to spot the dark patches in the water that I assumed were them. So, we walked across the mudflat for about 100 yards and then just a few feet into the water, they were right in the thick of them!
We gave them spades and buckets and they dug right in. The buckets were filled up about halfway with sediment and plants, and topped off with seawater. After about an hour, we had to drag them away, they loved looking at all of the crazy marine invertebrates and eggs that were attached to the leaves. Back at the lab, we stirred the buckets, let the sediment settle a little, and then loaded up the columns. They’re now in the hands of WSCA’s AP Bio class, and we’re really looking forward to watching them develop!
AP Bio Winogradskies
For the Seagrass Microbiome project, one thing we’d like to do is to build a culture/reference genome collection for microbes found in association with seagrasses. For now, we are just working on this for Zostera marina, both because it is our primary experimental model organism and because we have easy year-round access to it at Bodega Bay.
However, while we hope to do more of it in the future, the Eisen lab isn’t currently set up to isolate the types of organisms that we think are likely to play an important role in seagrass adaptation to marine sediments, e.g., sulfur-oxidizing microbes (which require anaerobic conditions to grow). So, for now, we are using an enrichment tool known as a Winogradsky column to grow lots of sulfur oxidizers (and other things, but we’ll focus on sulfur oxidation here.)
In Winogradsky columns, sulfur and oxygen gradients cause microbes to stratify themselves according to their ability to utilize the available electron donors and acceptors. These microbial layers are visible to the eye, making Winogradsky columns a great classroom tool for teaching students about microbial physiology, biogeochemistry, ecological niches, succession, and much more.
Bethany Dixon is an AP Biology teacher at Western Sierra Collegiate Academy, a charter school in Rocklin, California. She has been building Winogradsky columns in her classroom for a couple of years now. We have teamed up to have her students build Winogradsky columns that have been inoculated with seagrass bed sediment. One thing we know is that we will be able to enrich for seagrass-associated microbes with a variety of metabolic capabilities. But, we don’t know much more than that. For example, how many different species will be oxidizing sulfur in these columns? Will the same microbial species perform sulfur oxidation in every column that’s made from the same sediment? What will happen if we add a bunch of elemental sulfur to the column? Will that change the makeup of the sulfur oxidizing community in the columns? Will it affect the shape of the sulfur gradient? Will it affect how quickly the layers form in the columns? Will it kill the column?
So, we arranged for Bethany’s AP Bio class to come to UC Davis’ Bodega Marine Lab (BML) to collect some sediment and inoculate some Winogradsky columns. Typically, Winogradsky columns are built by mixing sediment with a carbon source (like newspaper) and a sulfur source (like egg yolk), topping it off with water, and then sealing it. I got the idea of using diatomaceous earth as a physical matrix and laboratory chemicals for the carbon source (cellulose) and sulfur source (sodium sulfate) from Tom Benoit at McMurry University. We just make a slurry of the sediment and water, let the big particles settle, and then add the water to the columns.
This is really cool because we can control and systematically vary the chemical composition of each column. So, with the AP Bio class, we have defined 5 experimental “recipes” and each student is making two columns, with one experimental and one standard recipe. We’ll discuss the five experimental recipes in a follow-up post.
Today, the students arrived at the BML. We spent the afternoon weighing out and mixing chemicals, and loading our 50ml conical tube columns. Tomorrow, at low tide, we’ll head over to a seagrass bed, load up a bucket with sediment, and haul it back to the lab to inoculate the columns!
You can follow our progress here, or in real-time on Twitter with the hashtag #APBioGradksy
One of the experimental recipes involves substituting macerated seagrass roots for cellulose. Everyone visited the experimental tanks to grab some seagrass roots for those. They would have spent hours here, checking out the different tanks, watching the sea stars, urchins, and sea hares.
Lake Arrowhead: Posters, Comics and Doodles Galore!
Two weeks or so ago, Hannah and I presented posters on our respective seagrass microbiome work at the Lake Arrowhead Microbial Genomics meeting. Attending the meeting was a wonderful experience for both of us and the talks and people were just phenomenal! For a brief overview of each day and the accompanying storify see: Day 1, Day 2 and Day 3. Some of the talks and posters were uploaded to F1000.
On the left you can see me dutifully standing in front of my poster. On the right you can see Hannah explaining her poster to a fellow LAMG-er! Hannah’s poster is one of the ones uploaded to F1000 and can be found here.
My poster can be seen below – I took inspiration from comic books when coming up with the design.
Of course, taking inspiration from comic books then meant I was obligated to produce a comic version of my poster which you can see below!
And to conclude some of my favorite doodles from my Lake Arrowhead notes:
From Nancy Moran’s talk:
From Nicole Perna’s talk:
From Jenna Morgan Lang’s talk:
From Jeffrey Foster’s talk:
From Jennifer Gardy’s talk: (inspired by the “cat break”)
Seagrasses and Other SAVs at Chesapeake Bay
I recently went to Chesapeake Bay to collect submerged aquatic vegetation (SAV) for the Seagrass Microbiome Project. I found a lot of aquatic plants that were related to seagrass, which will be useful for comparing the SAV microbiome between species, not just within seagrass (Zostera marina). The plan was to embark on a five-day trip down the Potomac and James Rivers, hitting 12 sites and a 13’th out in the Bay. The rivers provide a near-replicate salinity gradient, allowing us to observe microbiome changes across varying salinities as well as species. Unfortunately, the amount of sampling we planned to get done was a bit too ambitious. We got through 11 sites, only 3 of which had SAVs, all on the Potomac. So goes field sampling, I guess.
Here is a selection of pictures of what was found at some of the sites with tentative identifications:
Ceratophyllum demersum, found at the most freshwater site on the Potomac
Really dead Vallisneria americana, tons of which was found at the most freshwater site on the Potomac
Myriophyllum spicatum, found in a very muddy and sedimented wetlands area, surrounded by Spartina.
Vallisneria again? Wasn’t sure at first since it had those oddly curly leaves, but it seems Vallisneria has a lot of leaf morphologies and this is one of them. Found at the second most freshwater sight, happily growing on a rocky coast.
Sadly, a lot of the sites were boating areas or were otherwise heavily impacted by human activities. Almost all the sites had water with boating oil floating atop it. Most of the coasts were filled with terrestrial and semi-aquatic plants, but no aquatic vegetation whatsoever. Just bare, sandy coasts and water filled with oil. It really solidified how important seagrasses and SAVs are to ecosystems. They thrived in areas of the Potomac with higher biodiversity and less anthropogenic influence. And having waded through tangles of SAVs, I can assure everyone that they really do a great job filtering trash that flows outward from land.
The Seagrass Microbiome Project is hiring a postdoc!
Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon Green (http://pages.uoregon.edu/green/) is currently seeking a postdoctoral researcher to explore fundamental questions in microbial ecology and evolution. Applicants should have a PhD in a biological, computational, mathematical, or statistical field with extensive training using theory and/or modeling to understand the ecology and evolution of complex biological communities, and strong writing skills. Experience developing and applying quantitative phylogenetic ecological methods is highly desirable, but not explicitly required for candidates who have otherwise demonstrated strong quantitative skills.
The successful candidate will play a key role in the Seagrass Microbiome Project (http://seagrassmicrobiome.org) in collaboration among Jonathan Eisen http://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) at the University of California, Davis. The Seagrass Microbiome Project aims to integrate the long interest in seagrass ecology and ecosystem science with more recent work on microbiomes to produce a deeper, more mechanistic understanding of the ecology and evolution of seagrasses and the ecosystems on which they depend. Our studies of the community of microorganisms that live in and on seagrasses – the seagrass “microbiome” – will contribute to a broader understanding of host-microbe systems biology, and will benefit from ongoing University of Oregon research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).
The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Please email questions regarding the position to Jessica Green (jlgreen@uoregon.edu).
To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references
Submit materials to ie2jobs@uoregon.edu. Subject: Posting 14431
To ensure consideration, please submit applications by November 1, 2014, but the position will remain open until filled.
Women and minorities encouraged to apply. We invite applications from qualified candidates who share our commitment to diversity.
The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status
On the Road Again: Adventures with Winogradskies
On the Road Again: The Long Arduous Journey of Waiting for Our Microbes to Grow
Have you been waiting to hear about Winogradskies? Well, wait no more! We are here with your Winogradsky update! If you’ve forgotten what a Winogradsky column is and our goals for them I urge you to visit: Adventures with Winogradskies, Further Adventures with Winogradskies and Even More Adventures with Winogradskies to refresh your memory.
**Note all photographs in this post were taken approx. 2 weeks ago and thus the winogradskies herein described are reflective of that time point.
After 10 weeks:
These columns haven’t experienced much change except for a small increase in biomass towards the top of the layers. These three vials all still look relatively visually identical, which is reassuring as they were inoculated from the same water source and *should* be replicates of each other.
Microbial succession in action???? The two large columns that get full light (left and middle columns) were solid pink/black at 7 weeks, but now we are seeing some snow-white colored microbes intruding in. I wonder what these snow-white microbes are and what the earlier coal-black and pretty-in-pink microbes were doing metabolically that allowed the white microbes to now flourish in the columns. Alternatively, there could be no white microbes – perhaps the white is just the diatomaceous earth which is now visible again as the pink and black microbes recede into the past.
Overall, there is not a lot to report on the 5 mL tubes that were inoculated with water from different sampling locations. Except in the one above where we see a tiny band of purple!! This is the first 5 mL tube to show the presence of any pink and/or purple microbes!
Experimental Tubes (where we added either Potassium Nitrate or Ammonium Acetate) – After 9 weeks:
Overall, these tubes also look fairly similar to their 7 week incarnation. However, one of the Ammonium Acetate added vials has less black microbes at the bottom of the tube than it had previously (appearance of white microbes?). The Potassium Nitrate added vials appear to have a slight increase in the thickness of the layers.
Left to Right: Nothing Added, Ammonium Acetate Added, Ammonium Acetate Added (Kept in Dark) – Nothing Added, Potassium Nitrate Added, Potassium Nitrate Added (Kept in Dark)
The most noticeable difference is that the Ammonium Acetate added dark vial’s liquid portion has a green hue which it didn’t have before. Additionally the pinkish hue in the liquid in the Ammonium Acetate added light vial is much darker than it was before. The Potassium Nitrate vials are similar to their 7 week counterparts; they just have more biomass and/or bubbles.
Update over. Hopefully, you’ll hear from us again fairly soon with a new update on our lovable wino’s!
The Seagrass Microbiome Project 