Polynucleobacter spp.

If you were to try thinking of a model ‘lake’ bacterium you may consider using a Polynucleobacter spp.

Some taxonomy (if you are into that type of thing):

Phylum – Proteobacteria
Class- Betaproteobacteria
Order – Burkholderiales
Family – Burkholderiaceae
Genus – Polynucleobacter

Members of the genus Polynucleobacter are considered ‘cosmopolitan’, at least in freshwater ecosystems. Common species in this genus are P. necessarius and P. cosmopolitanu. These organisms are globally widely distributed and chances are that next time you jump into your favorite lake or wade across your local stream you will cross paths with a member of this group. Along with their distribution, these organisms are also temporally variable and one study showed that their relative abundance can fluctuate from 4 – >50% of the total microbial community (Hahn et al., 2005 AEM). However, in some Michigan lakes the abundance of this group is <1% showing that there is large spatial variability too (unpublished). Despite this, none would disagree that this group of organisms is fascinating.

In my opinion, the species P. necessariusmay be one of the more interesting in this group (see image below from Bergey’s Manual® of Systematic Bacteriology: Volume Two The Proteobacteria Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria). For some time we have known that P. necessarius is an endosymbiont of ciliates (specifically Euplotes spp.). In addition, this interaction is known to be an obligate symbiosis and ciliates that are cleared of their endosymbiont die soon there after. Furthermore, P. necessarius has been implicated as the agent responsible for mate killing among these ciliates. Why does this interaction exist? How did it come to be? If you weren’t captivated by the spatial and temporally variability, I bet you are now.

Feel free to share your thoughts or do a little research of your own (via the web of course).

Bergey’s Manual® of Systematic Bacteriology Volume Two The Proteobacteria Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria

Crap

Well I had a really good post for the first week, but it was lost during publishing. 😦 Maybe I need to move my hosting.

New Weekly Posts

Ok. Starting next week I am going to make weekly posts about aquatic microbes. My idea is that each week I can highlight an organism commonly found in either freshwater or marine ecosystems. This should be fun.

Post Field Season Day-to-day

So my field season is now over. I am all done on lakes for this summer and I find myself thinking about what I should do next summer. There must be a way to top my adventure this summer. I will just have to start planning earlier. As I sit here now listening to the rain sprinkling down outside of my office window I find myself reflecting on the summers activities and what my post field season day-to-day will be like. I have spent the recent weeks mostly in the lab; trying to not think much about the piles of data accumulating on my desk and on my hard drive. Some of my lab activities have been fruitful, yet others have been disappointing and thus have taken a strong toll on my motivation. I have a few more days of working in the lab prior to my trek back to campus for the fall and spring. I need to wrap up a few things and prepare my mind for the challenges it will encounter in the next few weeks.

Between classes and teaching I will mostly be working with R. I can see insightful graphs and hours of frustration in my near future. How will I depict my data and what coding errors will I run into? At the moment all I have is the environmental data. The goal will be to apply this data to the biological data, but when will I have said data. Well I have no idea. I have yet to extract any bit of nucleic acid and without that I am left empty handed. I can see long weekends and couch surfing at KBS in my future. I will have to carefully plan my activities so that I will be able to do extractions, purifications, amplifications, purifications, quantifications, and submissions in short one to two day spurts interrupted by long weeks of classes and teachings. This should be fun to say the least.

Aside from my lab activities, I have so many other research activities staring me down. This is like an academic staring contest between me and my work. There is the review sitting on the desk in front of me. That is due by Monday so I have some motivation. Then there is the papers to read and the things to write. How about a draft of this and a outline of that. It all makes sense in my head but when I sit down to actually work there are so many ideas that it is hard to focus, but I try to conquer it one step at a time. A good cup of coffee helps and maybe even a doughnut.

Well the rain is letting up and I see a hint of blue in the sky. Time to make progress on this review and enjoy the rest of the weekend. The post field season day-to-day may not be as exciting as the field work and amazing summer activities that I thoroughly enjoy, but it isn’t the worst thing in the world. I am just going to battle it day by day and hope that I win the staring contest.

Back!!!!

I’m back at KBS!!! And now that I have internet again I can post what happened on the ‘lost days’. But first sleep.

Sonde Day!!!!

I am up early as usual. Brew the coffee and get to work. I start by trying to check my email which hasn’t worked since I’ve been here. I was able to check one account, but not the University Mail account. Hopefully nothing is important. Today is Sonde Day so I get them all ready for deployment. After breakfast we head out the Ives Lake (right in front of our house). Only forgot one thing, but at least now we know what we will need later in the day. Deployment was a success!!!! (Finally something worked). After a short meeting with Wayne I am ready for the day. I have a map and GPS and I know where I am going to deploy the sondes. It takes a little planning, but I figure out how to manage the locked and unlocked boats thing. Only being able to check out one key at a time makes for an interesting task.

We start off by making out way to this mysterious Huron Mountain Club proper. We cross the first bridge slightly weary of what is to come. Finally we start to see some small cabins off the road. As we make the last turn on the path we come to a cabin city. These are log cabins and not the type that just have log siding, these are real log cabins. They are probably from local logs (from in the reserve), and seem to be very old. This looks like something out of a movie. We pull into an area to park so that we can walk around to find what we need to find, an office with boat keys. Immediately when we stop someone asks up if they can “help up”. I have learned that this is code for: “What are you doing here?!?!”. We explain that we are with the ‘Foundation’ and are looking for the person with the boat keys. We are directed to the correct location. On the way we meet some cool people: the person who runs the store, maintenance guy, security officers, fire safety officer, and Sarah the person with the boat keys. All of these people turn out to be very helpful.

We get our first key and head to the first lake, Howe Lake, and start out to find it. “In these woods the only things I would expect to find are Big Foot and Robin Hood” – Mario. We park and find the boat house. Wow, these are some really nice boats: handmade wood row boats (Very Nice!!!!). Not only are these boats nice, but the row like a charm. We are now off to start some science. It doesn’t take us long to finish Howe lake and then we are off the Rush Lake (we don’t need a key for these boats). I hear that Rush Lake is 300 feet deep. We row out and start deploying our sonde. Lowering the weight we realize that indeed this lake is really, really deep. I hope we have enough line (it uses about half of the 450’ of mason’s line that I brought; don’t worry the sonde is only a meter down). I can’t wait to take the depth sounder on this lake.

We finish in time for lunch, so we row over to a spot that was recommended, Devil’s Kitchen. We finally find it (an exposed rock face with a large rock over hang and a fire pit. Lunch is great. After lunch it is time to find Pony Lake which is hidden south of Rush. We row around on Rush until we are at the closest point to Pony. We then tie up the boat and gather our gear. The plan is the wade into Pony. We start bushwhacking until we find Pony. The mosquitoes are horrible. We find it and wade in, this is mucky!!!! Once we are done we quickly get out of there, but wait: look at this fungus! (Insert picture). We practically run back to the boat, get everything in and row away as fast as possible hoping that the mosquitoes don’t follow. Finally clear. We row back to the boat house and pack up.

Now it is back to get the next key: Lake Ann. Lake Ann is not easily accessible. We either have to row across Mountain Lake and try to find the hidden boat landing and then hike in to Lake Ann, or hike from the Mountain Lake boat house to Lake Ann. We choose to hike the entire way. This requires us to hike across two mountains, but we aren’t scared. These are more like glorified hills. The hike takes about an hour. We have all of our gear tied to our backs. The hike was amazing. We frolic through the woods and to the Lake Ann boat house. By this time we are getting tired and it is 5:45 PM so we quickly row out and do what we have come to accomplish. We then start our trek back. We are supposed to be back at 7, so we pick up the pace. We make it in about 45 min and we were still alive (maybe not run a 5K alive but alive none the less). We first have to return the key to the office and then return to Lake Ives. What a day!

After a quick chat with Wayne about my day and about what I plan on doing tomorrow I relax a bit. Pasta for dinner sounds great. I have a few more things to finish up, but there is live music (Cynthia and her band practicing for the Red House Opening: Banjo, Fiddle, Stand-up Bass, and Guitar). I guess I will have a little whiskey and wind-down. As the sun goes down I am sitting on the porch listening to the fish jump. These are some good size fish. There is a large bass chasing flies not 20 yards from where I am sitting. All I can think of is how much it sucks that I can’t fish this lake. Stupid Club rules!

 

Where did we go today?

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First day at the Hurons

Well I am about to call it a night. We arrived in Big Bay, MI around 4 PM. Turns out that my Garmin thinks that Big Bay is actually the gate to the Huron Mountain Club. The good thing is that I was trying to get to this exact location. When I arrived I was surprised to see that there was a professional guard at the gate. I didn’t know that this was such a serious place. After I check in we are on our way to find the stone house, and only made one wrong turn. The stone house is amazing (pictures to follow). It is right on Lake Ives and surrounded by ‘mountains’ (large hills really). We got everything checked in and learned the ‘law of the land’. Apparently I still don’t have permission to access lakes. What a time to find out. It is not clear to me how you can fund a project but not support it when time comes.

While waiting to hear if we are allowed on lakes or not I just unpack and get settled. A hot shower is amazing after a weekend of driving and camping. Finally the mysterious Wayne shows up to tell me about lake access. This then becomes more complicated. The ‘club’ has boats at most of the lakes I am going to sample. I am required to use those boats, but some of which are locked and I must get a key. I can get the key from the club house but I can only get one key at a time and it must be returned that day. Oh my, this is going to be interesting. Also, Wayne tells me that it may not be the best idea to deploy my sondes. What!!!! No, you can’t take that away from me.

What to do now? First I set up the weather station. Then I sat down with my notes to figure out what exactly I am going to do. Number one; deploy sonde at 7 AM on Lake Ives.

 

Well I am off to bed. Night!

Time to go to the Hurons

We wake up post storm, but still dry. We have a lot to get done so we make a quick meal and pack up to leave. We only have 3/16th of a tank of gas, but let’s first stop at Miners Castle to see what that is about. It is easy to find and another really cool place (insert picture). While there we meet the clerk at the souvenir shop. We chat a bit and she tells us that we should go to the ranger station and talk to them about Chapel. So we are off, but first let’s get some fuel. At the ranger station Megan stays in vehicle while I go in to find a ranger. Almost to the door, I hear a ‘oops’ from Megan. ‘Hungry Megan’ got out of the van and accidentally pressed lock instead of unlock in order to get into our cooler of food. Not noticing this, she gets out and shuts her door; locking the keys in the van (insert picture). Crap!!!! So, I go into the ranger station to ask for assistance and they give me the sheriff’s number. Great. Megan waits outside while I ask about Chapel Lake. The lady at the station gives me the contact information for the aquatic ecologist that works with the parks service. I’ve got a lead. I’ll give that person a call ASAP. I return to the van to wait for local sheriff to help us but when he arrives he can’t help us so we have to call a tow truck. 40 bucks later we are on the road again. Off to the Huron Mountains. We stop in Marquette for some lunch. We ate at this really great restaurant (V something). The food (white fish) was amazing. Once our bellies were full we departed for the Hurons (first stopping for a little food and 60 lbs of ice)

Canyon Lake Sampling Day

Bright and early after night one of camping: time to eat, clean up and organize supplies for a day of sampling. The goal is to sample Chapel Lake. We have a good bit of gear to take infield measurements and collect water for chemical and biological samples. We write out exactly what we are going to do and everything is ready to go: boat (check), field gear (check), sample containers (check), packed lunch (check). I think we are ready. We drive to the lake and start off the find somewhere to put in a canoe. The website says that we can portage a canoe, but it is not marked on the maps. So we first go to the right: nothing. Then we go to the left: nothing. WTF!!!!

We head back to the van to get a few things before setting out the really scout this lake. We set out on the east side of the lake. It is quite obvious that there are steep inclines on both the east and the west sides. This is going to be an adventure. I wonder if we are allowed off the path. We hike north along the east side until we see some areas that look like paths (it looks like a path to me). We then hiked down the hill (probably 80 feet down) and found that there is a second hill that we need to get down (another 60-70 feet). We finally make it down and work our way to the lake. This is a gorgeous lake with cliffs on all sides. The water is as calm as can be. And what is this, the water is not clear. There may be some elevated DOC here too!!!! Awesome!!! Now I really want to sample this lake, but I will never get a boat down that hill. So we go back up and hike along to see if there is another entrance. We find another possibility, but will not be able to get a canoe down it either. So we keep going. Next we find the famed waterfall. Amazing!!!! Now we have a super awesome lake, but still now way to sample.

We keep going all to way to Lake Superior (past the north side of Chapel). Chapel rock is quite the site. There we find the creek that comes from Chapel and flows towards Superior. Now what? Let’s trek up the creek!!!!! It is only a kilometer. The creek is shallow and we only encounter a few beaver damns. It is a long walk, but it wasn’t bad. We walked all the way to the lake. Once there we decided to find the easiest way back to the trail on the west side of the lake. So we made a b-line through the woods. Hahaha. Bushwhacking is fun!!!! What a great adventure. We finally show up on the path and continue southwards to see if there is an entrance to the lake. Nothing: not even steep inclines, there are full fledge cliffs!!!! We are not going to get into the lake today! BUST!!!!!! Looks like you can’t just walk into any lake in the UP. Well at least we spend the entire day scouting the lake. I have hiked around this entire lake and now I am determined to sample it. Maybe not this week, but I will conquer it!!!!!!

We call it a day and head back to camp: food and prepping some stuff for the Hurons. The sky is clouding over and we hear the thunder approach from the distance. Let’s hurry up and get things put away so we can take shelter in the tent. The storm rolls in with a loud bang. We kill time by playing card in the tent until we decide to call it a night. The rain and thunder are calming after a long day in the field.

On the road again

So after a good two hours of packing the van, and then unpacking to reorganize so that everything fits we were ready to leave. But first a twenty minute search for my coffee!!!!!

Finally pulling out of KBS on our journey to the Upper Peninsula