Bacteria in the atmosphere - another extreme environment?

A group out of Denmark recently did biochemical and bacteriological analysis of hailstones. A quick glance at some neat things in here: 

• bacteria found at a density of ~2000 cells/ml. That's not very high compared to soil at ~10,000,000 cells/g, but hey, this is in a hailstone! 
• Single cloud droplets however are not individually very poluation. The researchers estimate that 1 in 1,000,000 storm cloud droplets have a a bacterial cell in them. 
• this paper also touches on the carbon sources and how that may relate to the bacteria

Realize that there are a lot of bacteria hanging out in the atmosphere. There's been a lot of work on this recently, and some of it suggests that these bacteria are metabolically active while up there. There is also research that suggests that these bacteria can act as nucleation points for condensation. I like another statement that is made in this paper that considers the atmosphere as yet another one of our "extreme environments"  - another model for life on other planets perhaps? 


Šantl-Temkiv et al. 2013 Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud. PLOS 



http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053550

Life in subglacial Antarctic lake

Over the past year or so a number of research teams have been drilling deep into glacial ice to get at pockets of water deep below that have been in theory isolated for a very long time from the outside environment. They want to see what exactly can live in those conditions and see if these are some new life forms that we just haven't seen before. What is this environment like? Well, no sunlight penetrating down there, so no light energy driving energy production down there. Very cold too, and the pressure must be reasonably high.

One of the challenges that comes with these studies is that they have to drill a long ways down, and they have to be able to support that any life they find was from the water pocket and not contamination from above carried down by the drill.

There is a nice New York Times article about this that can be found at this link (Feb 6, 2012, Science section). They also have a great photo that shows the first view into one particular lake that I have linked into here. Looks different from what you might expect, yes? There are microbes down there and they are doing things. Keep in mind that this particular subglacial lake is 23 square miles big and ..... 5 feet deep.

We've had a number of students recently who are interested in Astrobiology. Astrobiologists are very interested in microbial life in extreme environments because it helps us understand what kinds of features of life on other planets we might expect to see if we were to find something.

On that note, I noticed that just the other day the Mars rover did a very nice drilling into the surface - will have to read more on this to see if there are plans to check for evidence of life. If so, you can bet that DNA-based approaches will be involved.

Living in sub-zero brine

Murray et al. 2012. Microbial life at −13 °C in the brine of an ice-sealed Antarctic lake. PNAS

Lake Vida is in the Antartic, how's this for a place to live:

• sits at -13 deg C
• salt concentrations 6 times that of sea water
• sits under 50-100 ft of ice
• aphotic (little or no light penetrates)
• anoxic (no oxygen)

(taken from Nature journal's website here)

As always though, microbes abound - albeit ~10-fold lower concentrations than lakes, and a lot more tiny cells that normal. Now that doesn't mean the diversity is high - in the survey they found ~32 species in 8 different phyla - but c'mon, give any microbes credit for living down there!

The researchers cored deep, viewed the cells via fluorescent staining and microscopy, and coupled that with rRNA gene sequence analysis.

Link to the original article: http://www.pnas.org/content/early/2012/11/21/1208607109

Link to more general article: http://www.nature.com/news/life-abounds-in-antarctic-lake-sealed-under-ice-1.11884

Earth Microbiome project (EMP)

there are a group of scientists that are trying to use 16s and metagenomic analysis across all of Earth's ecosystems. The goal is an incredible number of environmental samples (10K-200K depending on the source of the info) expected to generate 15 trillion base pairs of DNA sequence information.

http://www.earthmicrobiome.org/

This is an incredible project that should yield some pretty fantastic insights into microbial life on this planet

For current students: The importance of this project relates back to the fact that so many (an estimated 99%) of the bacteria out there are not easily cultured by our standard techniques, therefore we seldom detect that they are there and in many instance, we have never detected them. By analyzing the DNA we can detect their presence and estimate their diversity by comparing the DNA to microbes that we have already worked with. Expect this project to reveal many new lineages of bacterial life!

trying to understand a microbe that can't be cultivated

BioTechniques - Seawater Microbe’s DNA Demystified

A theme that I put out there all the time in my class relates to how we have been discovering over the years how we often don't even know that the microbes that are most dominant in a system exist, much less what they're doing. In this article, the authors run a metagenomic study - sequencing all the DNA that's in a sample of water they take from some surface seawater. They knew that something noncultivatible dominates that but did not have it in culture. From the metagenomic DNA they were able to sew together all the sequences that presumably came from that dominant organism thereby giving them the genomic data that they could analyze. With that data they could analyze what capabilities that microbe has - metabolic pathways, motility, ability to deal with light, etc. Very fascinating. This kind of approach will become increasing important in the next years

did I mention that the group they studied make up 50% of the microbes in the ocean? And can't be cultivated? That's wild that it could be that important in the system yet we can't cultivate it. It would be like trying to talk about the trees on Elon's campus but not being able to see the oaks....

Here's the link to the original article

http://www.sciencemag.org/content/335/6068/587.abstract

Ancient genomics sheds light on past plagues

This caught my eye as I had just talked a bit about Yersinia pestis in class about 1-2 weeks ago. This species is generally assigned as the causative agent of the plague that wiped out 1/3 of Europe in the mid1300's. Researchers obtained DNA from Black Plague victims from the 1300's and were able to pull out and sequence the genome of the bacterium that caused it. Their initial questions were 1) was Y. pestis actually the cause and 2) if so, how did this strain relate to today's strains?

When they compared the genome to modern Y. pestis, they found that 1) it was indeed Y. pestis, and 2) there is little change between the ancient strain and the current strain suggesting that it wasn't necessarily a abnormally virulent strain.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10549.html

A few posts ago I noted the use of genomics to track modern epidemics. This study adds a unique component by analyzing ancient genomes. Took a peek at the methods - they had to enrich the DNA by using modern Y. pestis fragments to pull out the ancient bacterial DNA, otherwise it's a needle in a haystack! 

Megavirus chilensis takes current award for biggest virus

From Oct 10, 2011 issue of PNAS

http://www.pnas.org/content/early/2011/10/04/1110889108.abstract

isolated from the sea near Chile, somewhat related to the prior record-holder Mimivirus, contains 1120 protein-coding genes, 1.26 Mbp of DNA, and size of ~0.2-0.3 uM

(image from geekosystem.com)

next generation sequencing strikes again

A while back I noted a "proof-of-concept" study where researchers took a problematic strain of E. coli from an outbreak, pumped out the genomic sequence and analysis in a few days and were able to make great strides in understanding the nature of why this particular strain was a problem.

The same research group have now applied that to Klebsiella pneumoniae Oxa-48 - a bacterial strain responsible for hospital infections in the Netherlands. This really seems to support the importance of DNA technology advances and how genomic level information will be used in the future.

Changing role of clinical work in Microbiology

http://www.microbeworld.org/index.php?option=com_jlibrary&view=article&id=7429&utm_source=twitterfeed&utm_medium=twitter&utm_campaign=twitter

Highlights:

• advances in molecular biology are what's changing things (Microbial Renaissance #2, right?)
• cost and accessibility of these tools is still somewhat of an issue, limiting widespread use

New tech sequences bacterial genome in 2 hrs

http://www.iontorrent.com/technology-how-does-it-work-more/

How it works (if you're into this kind of thing): 

many miniwells, each with strand of DNA (stands that you want to sequence) anchored. Wash specific nucleotide (ex. dATP) over the slide. If that specific nucleotide gets incorporated, sensors detect the release of H+ ions from the reaction which lets you know "yep, that was an A". Generates 100 bp length reads - of course it's 1.4 million of them. They sequenced bacterial genomes (5x-10x coverage) in 2 hours with just 6 hours of prep time for each sample. 

Interestingly enough, they also sequenced Gordon Moore's genome as a test. He's the guy who developed Moore's Law which describes how technology doubles. His genome coast $50K to do but they think that this technology will advance quickly to get close to that target $1000 genome that everyone talks about. Not sure how much the bacterial genomes cost each

Link to the Nature summary

whole genome sequencing of E.coli in outbreak

Article in Genome Technology this month: (click to see it)

stresses the power of the genomics age. Check out this timeline:
- received sample on May 30
- completed genome sequencings on June 1
- Genomes assembled and submitted to NCBI by June 2

Findings
- that E. coli was a new strain
- that E. coli had many antibiotic resistance genes

concept of "Genomic epidemiology"discussed

Another part of this article looks at MRSA and genomic sequencing of 63 isolates - identifying 6700 SNP (single nucleotide polymorphisms) that accounted for the variability seen and related to the microevolutionary changes being seen.

E. coli outbreak resources from NY Times

http://topics.nytimes.com/topics/reference/timestopics/subjects/e/e_coli_bacteria/index.html