The
inability to culture marine bacteria has acted as a major obstacle in the study
of marine microbiology. In recent years the development of cost-effective
molecular techniques, such as high-throughput genome sequencing (HTS), has
taken great strides to mitigate against the constraints of culture-dependency. However,
it is arguable that HTS is insufficient in gaining a holistic understanding of
any one organism’s biology. Masashi Yamaguchi of Chiba University, Japan uses 3D
reconstructions of electron micrographs to study the ultrastructure of
microbes, where culture is often not yet possible. In 2006, he coined the word
‘structome’, defined as ‘quantitative and three-dimensional structural
information of a whole cell at the electron microscopic level’. Structomic analysis
has the potential to reveal mysteries about cellular function and phenotypes hidden
to HTS and takes an alternate approach to over-coming culture difficulties by
bringing marine microbes to life in the in
silico laboratory.
Previously,
Yamaguchi has fully reconstructed the model yeast Saccharomyces cerevisiae (2011), the human pathogen Mycobacterium tuberculosis (2015) and
the esoteric ‘Myojin parakaryote’ (Parakaryon
myojinensis) (2012), which displays an intermediate bacterial-eukaryote
microanatomy. In this study, Yamaguchi and colleagues describe the structome of
an unusual spiral bacterium they name ‘Myojin spiral bacteria’ (MSB). Using a
dual approach of serial ultrathin sectioning and high-voltage electron
microscopy (HVEM) tomography, they reconstruct nine MSB cells discovered in an
environmental sample from a deep-sea hydrothermal vent. Structomic analysis
showed that the cells were ~1.8μm in length, aflagellate and possessed a unique
fibrous layer. Spirality was observed to be both clockwise and anti-clockwise,
suggesting that these samples either represent two distinct species or that this
species is capable of morphological heterogeneity.
The
ultrastructure of this bacterium is intriguing. The fibrous layer is unique and
thought to play a role in maintaining the integrity of the spiral morphology,
although its composition is unknown. The spiral morphology is also in itself a
mystery. Being aflagellate, it lacks the endoflagellum between the inner and
outer membrane of spirochaetes, such as that observed in the syphilis bacterium
Treponema pallidum. The function of
the spiral shape is therefore too unknown. Strikingly, the ribosomal density of
the cytoplasm is only 1.2% that of E.
coli, which the authors hypothesise may be a result of the slow growth rate
typically associated with deep-sea organisms. The reconstruction of the
microanatomy in this species has therefore revealed insights, even if
preliminary, that would not be found using more conventional ‘-omics’.
Overall,
this study offers a fascinating new addition to Yamaguchi’s three-dimensional,
microbial menagerie. As a method for marine microbiology, 3D analysis is
greatly underexploited, yet has the potential to complement the findings of HTS
genomic studies greatly. Automation of high-throughput 3D reconstruction lags behind that of genomic technologies, and so structomic analysis is desperately
lacking an analogous revolution. While the author’s proposal of using ribosomal
density to approximate growth rates is somewhat contentious (there is no
comprehensive understanding of how this differs between clades), structomics is
a nascent method in marine microbiology, which could yield great benefits if
further developed.
While the
advances made by HTS are momentous, we have become somewhat detached, amidst
the swathes of multiomic data, with the living organisms from whence these
biomolecules came. Structomics has the potential to bring at least some focus
back to the cell.
Reviewed
Paper: Yamaguchi, M., Yamada, H., Higuchi, K., Yamamoto, Y., Arai,
S., Murata, K., ... & Chibana, H. (2016). High-voltage electron microscopy
tomography and structome analysis of unique spiral bacteria from the deep sea. Microscopy, dfw016. http://jmicro.oxfordjournals.org/content/early/2016/05/25/jmicro.dfw016.abstract
ReplyDeleteHi Davis,
interesting topic! Do the authors give any other reason why this particular organism was chosen, apart from it being interesting? Has this bacterium been studied before?
Thanks,
Johanna
Hi Johanna,
ReplyDeleteThis bacterium is not yet cultured and therefore was not 'chosen' as such, but rather described by chance from an environmental sample. Due to the LPSN description of species by culture and genetics, structomics is insufficient alone to describe a new species and thus this one has no name (perhaps it actually has been sequenced before, its genome lost in a metadatabase somewhere!). However, insights can be gained even without culture. If you are interested, I think the best example of this is the structural description of the parakaryote and the possible ramifications that it may have for eukaryogenesis:
Yamaguchi, M., Mori, Y., Kozuka, Y., Okada, H., Uematsu, K., Tame, A., ... & Yokoyama, K. (2012). Prokaryote or eukaryote? A unique microorganism from the deep sea. Journal of electron microscopy, dfs062. http://jmicro.oxfordjournals.org/content/early/2012/09/28/jmicro.dfs062.short
Thanks,
Davis
Hi Davis,
ReplyDeleteI am very interested in your thoughts on these methods and how they can move forward, do you think that 3D reconstruction of microbes has the ability to be widely used as HTS, can the technology move forward in terms of speed and cost to make it widely available. I see that you fully appreciate that multiple methods are required to fully understand how these marine microbes that cannot be cultured work. Do you think by using 3D reconstructions along with HTS can allow us to determine the metabolic capacity and will then allow to culture these organisms, which is currently critical in officially taxanomically identify marine microbes.
Thanks
Natasha
This comment has been removed by the author.
ReplyDeleteHi Natasha,
ReplyDeleteThank you for your interest. It is difficult to predict the future impact of 3D reconstruction on marine microbiology. I think it has the potential to compliment data from HTS and to marry the genetic and structural components of a particular uncultured microbe (particularly eukaryotes, whose organelle structure can be quite telling). The automation of 3D reconstruction by TEM tomography and other techniques is well developed - and MRI/CAT scans in human biomedicine are already there - but such automation is not possible on such a scale in marine microbes, and 3D reconstructions. Serial ultrathin sectioning is often used, which is laborious on a large scale. It may one day be possible, to scan an environmental sample and bin the 3D morphology of the components into clusters, much as is already done with HTS metabarcoding. However, for now, I think structomics is a great tool for investigating the idiosyncrasies of unusual/model taxa. For a comprehensive review on 3D techniques (a bit dated now), I recommend this book chapter:
Müller-Reichert, T., Mancuso, J., Lich, B., & McDonald, K. (2010). Three-dimensional reconstruction methods for Caenorhabditis elegans ultrastructure. Methods in cell biology, 96, 331-361. http://www.sciencedirect.com/science/article/pii/S0091679X10960159
Its about nematodes but the principles are the same. As for the role in culturing, you raise a very intriguing possibility - studying HTS + structomics could approximate the conditions needed for cultured, but the downside is cells are killed to gain this data so if the sample is rare there may be some problems with this! The details will probably, like a lot of micro/molecular biology, come down to trial and countless, countless error.
Thanks a lot,
Davis
Hi Davis,
ReplyDeletethanks for the reference i found it very interesting and i does help understanding this topic. I feel that this is a very intriguing topic and an area of marine microbiology that could possibly be a pivotal point in this area if the time and effort are put in by people in this subject.
Thanks
Natasha