I’m happy to say that the first half of 2019 has been fairly productive from a publishing standpoint, with five papers out so far. Both Celeste and Jordan have first-author Genome Announcements in MRA:
And I published a short commentary proposing that we conduct risk assessment using expected value calculations when designing and evaluating studies aimed at cultivating new microorganisms from nature:
Finally, a third Dead Zone paper with Olivia Mason’s lab (Lauren Campbell’s second first authorship paper on the topic), in collaboration with Nancy Rabalais, is out now as well:
Campbell, Lauren G., J. Cameron Thrash, Nancy N. Rabalais, and Olivia U. Mason. 2019. Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure. PLoS ONE 14(4): e0209055.
Our paper on the cultivation and genomics of the freshwater SAR11 strain LSUCC0530 has been published online in the ISME Journal (Here). The SAR11 LD12 lineage evolved to colonize freshwater ecosystems, and, like its marine cousins, occurs as one of the most abundant freshwater bacterioplankton worldwide. Strain LSUCC0530 represents the first cultivated representative of the LD12 clade and presented the Thrash lab with an unprecedented opportunity to provide new insights into the important evolutionary processes behind marine-freshwater transitions. Specifically, we demonstrated the capacity of strain LSUCC0530 to grow in salinities up to 5, provided evidence for LD12 ecotype differentiation based on temperature, and developed a hypothesis on how the loss of key genetic functions enabled the SAR11 clade to transition into fresh water. This work is only the beginning of our exploration into the SAR11 LD12 clade and its marine-freshwater transition, so be on the look out for more data soon!
If you have any questions or want to know more about LSUCC0530, please feel free to contact us! We are more than willing to answer any questions you may have.
It is with great excitement that I get to post that our manuscript on cultivating members of the microbial majority using an artificial seawater medium is finally out! This manuscript represents the hard work of not just myself, but Dr. Thrash, our undergraduates (past and present), and Austen Webber. Over the last two years, I have traveled to sites along the Gulf of Mexico collecting water for cultivation experiments (> 2000 miles traveled, > 4500 well inoculated). From the sites along the coasts of Louisiana, we have cultivated organisms from the Gulf of Mexico representing many important marine clades: SAR11, SAR116, OM43, OM252, Roseobacter, and many more. While isolating these organisms is important, it is also important to isolate organisms that represent abundant taxa within your source water. We compared OTUs from community sequencing of the source water to our isolate sequences to demonstrate that our method frequently captured some of the most abundant organisms in the system.
This work also represents the first instance where many of these clades were isolated from the Gulf of Mexico, and importantly, on an artificial seawater medium. While high throughput, dilution-to-extinction culturing using natural seawater has been highly successful, we hope that this new approach using artificial seawater media will help more researchers cultivate important microorganisms without the hassle of collecting large volumes of natural seawater and needing a boat.
If you have any questions, please feel free to contact us! We are more than willing to answer any questions you may have. You can check out our list of organisms isolated so far HERE!
On March 23rd, research on the microbial variation across a 5500 km transect of Antarctic surface sediment that Dr. Thrash and I had worked on with Dr. Deric Learman from Central Michigan University was finally published in Frontiers in Microbiology under the special topic: Microbiology of the rapidly changing polar environments. Since then, the article has had >1200 views from around the globe and was one of the top ten articles in Frontiers in Microbiology for the month of March. The research began when I was a Masters student in Dr. Learman’s lab. When I came here to LSU, Dr. Thrash was added to the project. This research would of never happened without the help of Dr. Andrew Mahon (CMU), Dr. Scott Santos (Auburn), Dr. Kenneth Halanych (Auburn), and Dr. Pamala Brannock (Auburn). Each one helped collect our sediment samples while they were out to sea doing their own research. I’d also like to thank Dr. Ben Temperton (University of Exeter) who helped with our analyzes. We are excited to finally have it published!
Here is a quick blurb on it:
Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that harbors under explored levels of biodiversity. Our work focuses on the seemingly “invisible” inhabitants of the ocean floor that boarder the western and peninsula portion of the Antarctic continent. While microorganisms are the smallest forms of life on Earth, they are abundant (typically more than 10 million cells per gram of sediment) and influence the cycling of important nutrient such as carbon and nitrogen. They also represent the foundation of the food chain that supports larger and more complex forms of life. To study this environment, ocean sediment samples from the continental shelf of western Antarctica were collected over a 5,500 km transect from the Ross Sea to the Weddell Sea. By using 16S and 18S rRNA amplicon sequencing, this work has shown these sediments to be incredibly diverse and were distinguished by their correlations to organic matter and stable isotope fractions (TN, δ13C, etc.). Our work further demonstrates the versatility of marine microbial life and its ability to persist at near zero temperatures as well as greatly increases the available information for this region.
There are some exciting developments in the world of SAR11 microbiology, and I’d like to take a moment to summarize recent research I’ve been involved in. All three papers have come out this year in The ISME Journal.
The single-cell genomes from Thrash et al., 2014, aligned linearly according to scaffold size, showing (outside-in) GC content, scaffold boundaries, coding regions according to pan-genome status, and shared elements unique to the subclade Ic with orange lines
The final main project of my postdoc with Steve Giovannoni was a characterization of a deep-water subclade of the larger SAR11 group using single-cell genomics and metagenomics. This was a collaboration between our lab and that of Ramunas Stepanauskas and Ed DeLong, and although it began at Oregon State, the work carried over (like many projects do) into my appointment at LSU. The main findings of the paper were that this “subclade Ic” dominated deep-water metagenomic reads compared to extant surface-originated genomes, and that a few gene-content specific variations could be identified that may distinguish these organisms from the surface strains, but that, on the whole, the main observable differences were in global genomic footprints such as expected average genome size, average coding region size, intergenic spacer size, and preferential amino acid substitutions. The deep water ecotype, subclade Ic, has obviously been evolving separately from the surface subclades for some time based on these accumulated variations and phylogenomic branch lengths, however, it also appears these organisms share a similar metabolic niche with the surface strains: they are predicted to be obligate aerobic organisms with a particular appetite for common metabolic intermediates found in the cellular milieu of most organisms: simple carboxylic and amino acids and C1 and methylated compounds.
Steve was also invited to write a Winogradski Review article in coordination with him recently being given the prestigious Jim Tiedge Award from ISME. Ben Temperton, who is also a former postdoc of Steve’s, and who worked closely with me on the subclade Ic study, above, was a co-author. Steve took the opportunity to review many of the observed variations between streamlining selection on free-living, small genomes like SAR11 and Prochlorococcus, and the small genomes of obligate intracellular symbionts like Rickettsia. Importantly, the review also pointed out that examples of streamlining selection are becoming more prevalent as data from single-cell genomics and assembled metagenomes continues to pour in. Indeed, the odd nutrient requirements that are sometimes a result of streamlining selection may be at the heart of the difficulty in cultivating many of these organisms in the lab.
Dovetailing nicely with the theoretical concepts brought up in Steve’s review was a third piece from our lab, a detailed study on an unusual vitamin requirement in SAR11 that was discovered by Paul Carini, currently postdoc-ing with Alyson Santoro. This work identified that members of many SAR11 subclades are unable to make the vitamin thiamine by typical synthetic means, because they lack a single gene in an otherwise complete pathway, thiC. As a result, they are unable to synthesize 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), a direct precursor to thiamine. However, Paul also discovered that SAR11 has the capacity to use free HMP in media to relieve thiamine limitation, and identified a putative transporter for HMP in several SAR11 genomes. Additionally, HMP measurements from the Sargasso Sea and cultivation experiments pointed to a possible natural source of HMP from cyanobacteria, thus providing an explanation for how SAR11 can remain successful without the key thiC gene.
Two of the scientists that I just went on the shelf hypoxia cruise with, Nancy Rabalais (who was also the Chief Scientist) and Gene Turner, and their colleagues have published an aggregate report of 26 years of shelf hypoxia research in ES&T (see link above). They also develop a statistical model based on the data, which even takes into account things like variations in sampling methodology over the years. The model is part of how the estimates for future hypoxia are made.
