Appreciation towards culture collections

Posted on July 10, 2024   by Dr Hiroyuki Imachi and Dr Masaru K. Nobu

Dr Hiroyuki Imachi and Dr Masaru K. Nobu take us behind the scenes of their latest publication 'Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.' published in International Journal of Systematic and Evolutionary Microbiology. 

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We are researchers working at the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Japan, focusing on microbial ecology and evolution. In this study, we present a taxonomic description and propose a new taxonomic name for strain MK-D1, which was isolated from deep-sea sediment. Strain MK-D1 has attracted attention as the first cultured representative of Asgard archaea, an archaeal group thought to be related to the origin of eukaryotes. Isolation and characterization of the strain took a long time (12 years and 3 years, respectively) due to its extremely slow growth rate, low cell density, and the requirement to grow only under anaerobic conditions with syntrophic partners. Our next goal was to support new directions of research on this archaeal group by improving the efficiency of cultivation as much as possible, making the strain available through culture collections, and assigning the strain a name validated by the International Code of Nomenclature of Prokaryotes (ICNP).

There are about 100 public culture collections worldwide, but only a few can handle fastidious anaerobic microorganisms. Over the past three years, we have approached four major cultural collections capable of handling anaerobic microorganisms, providing a detailed cultivation protocol, given how slow-growing and fastidious the strain is. Much to our surprise, one culture collection declined our request to deposit the strain due to the slow growth and low cell density. For the other three, two unfortunately could not preserve the strain and only one culture collection succeeded – Japan Collection of Microorganisms (JCM), Japan. We believe one of the key reasons for the success was support from Dr Takashi Itoh and Dr Shingo Kato at JCM, who each have excellent expertise in handling anaerobic archaea (30+ years) and fastidious microorganisms (10+ years). Regardless, we are extremely grateful for these culture collections that considered and/or attempted cultivation of this fastidious strain.

Upon checking the ICNP rules and consultation with the International Committee on Systematics of Prokaryotes (ICSP), we understood that validation of a strain typically requires that the strain be available from at least two culture collections in different countries. Exceptions have been made for strains with clear challenges in maintenance (e.g., Pyrococcus yayanosii strain CH1, an archaeon required cultivation under high-pressure conditions). After a review process and a gathering of the ICSP chair, ICSP judicial commission chairman, and IJSEM editor-in-chief, our strain was granted an exception because of its exceptionally low cell yield and the need to confirm growth by qPCR. This led to the acceptance of our manuscript and validation of the new taxonomic nomenclature of strain MK-D1 from the species- to kingdom-level.

Over the past years, many asked us how we would name the phylum strain MK-D1 belongs to. At the time of isolation, we proposed the genus and species name Candidatus Prometheoarchaeum syntrophicum for strain MK-D1 belonging to a candidate phylum “Lokiarchaeota” of the superphylum-level group “Asgard” archaea (Imachi et al Nature 2020). After this, two major changes in nomenclature and taxonomy took place. First, in 2021, prokaryotic phylum names were validly published for the first time and, associated with this, new rules were set, indicating that all validated phylum names should be based on the type genus (e.g., Proteobacteria [whose type genus is Pseudomonas] was changed to Pseudomonadota; Oren and Garrity, IJSEM 2021). Second, the group “Asgard” archaea was gradually shifted to be considered a phylum-level rather than a superphylum-level lineage and tentatively given the name “Asgardarchaeota” in the Genome Taxonomy Database (Rinke et al., Nature Microbiology 2021). Following the genus name we had proposed prior to these changes, the ICNP rules, the scientific community’s agreement that “Asgard” archaea represent a phylum-level lineage, the validation of the genus and species name of strain MK-D1 naturally led to the phylum name Promethearchaeota (and the associated kingdom Promethearchaeati). 

Many researchers had also asked whether we would propose taxonomic nomenclature via the “Code of Nomenclature of Prokaryotes Described from DNA Sequence Data” (SeqCode), using the genomic sequence of strain MK-D1 as the type material. We opted not to do so as we believed that, for science, the following three need to be accomplished together: (i) standardization of the cultivation and preservation protocol, (ii) sharing of the strain with the scientific community via culture collections, and (iii) validation/organization of taxonomy and nomenclature. Live strains are crucial resources in promoting scientific and industrial advancements, not just in experiment/cultivation-based microbiology research but also substantiation of hypotheses derived from genome-based research. This is to say, both culture collections and the rules set by the ICSP are essential for sustaining the field of microbiology and, thus, we believed that proposing taxonomic nomenclature via SeqCode would not benefit the field.

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© H. Imachi, M.K. Nobu, and JAMSTEC Scanning electron microscopy image of Promethearchaeum syntrophicum strain MK-D1

Moreover, while the SeqCode (as it stands now) attempts to help organize the taxonomy of uncultured prokaryotes, it is viewed as potentially harmful to the field of microbiology (see discussion here). To quote a letter from Dr Markus Göker to curators at culture collections:

“Acceptance of the SeqCode by the ICSP would … devalue the work of culture collections. Although often advertised otherwise, the SeqCode does not define itself as a code for the uncultivated, but as a code that uses genome sequences as nomenclatural types, thereby making the deposition of type strains superfluous, even if they are available. The SeqCode also removes any incentive to deposit a culture of a taxon with an already ‘validly published’ name once it becomes available.

As ECCO wrote in 2020: If the proposal is accepted, it will no longer be strictly necessary to deposit any material in public collections, be it type-strains, DNA-extracts or environmental samples. This of course does not mean that we think that efforts to isolate and study new species in culture would be completely discarded nor that all scientists who have regularly been depositing strains will suddenly stop to do so, but overall the motivation to do all that is needed for depositing type-strains in a public collection will decrease. … This should be a major concern to all stakeholders, especially in the light of climate change and the accelerated loss of biodiversity."

Our hopes is that the nomenclatural conflict regarding ‘Asgard’ archaea between our study proposing Promethearchaeota by ICNP rules (Imachi et al., IJSEM 2024) and ‘Asgardarchaeota’ proposed by Tamarit et al. through the SeqCode (Systematic and Applied Microbiology, 2024) will stimulate further discussion towards reaching an agreement on nomenclatural rules best suited for protecting and promoting the field of microbiology and culture collections.