International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020

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. Novel taxa described since the last meeting of the Subcommittee The names indicated in inverted commas have been proposed in effective publications, but have not yet been validated by publication in the IJSEM (do not figure in a validation list).

Species and nomenclatural type strain
Origin T-strain Genome NCBI assembly (RefSeq) accession

MINUTE 6. NEW SPECIES, SINCE THE LAST MEETING
We commented that proposed names should attempt to best reflect the biology of the new taxa. For instance, we have doubts if, in the case of newly described genera, the suffix 'rhizobium' should be used as the root of the name when the bacterium is not present in the soil environment or is simply nonsymbiotic, like the recently proposed genus names Georhizobium [4] and Pseudorhizobium [5,6]. Similarly, the species name Agrobacterium fabacearum was proposed for Agrobacterium genomic species G1 (5), as it has, by chance, been isolated as an endophyte in bean root nodules, but not specifically as a symbiont. In the past, Agrobacterium G1 strains were isolated from several plant types [7] and detected in soils associated with Poaceae rhizospheres [8]. The plant specificity suggested for the genomic species G1 by the name fabacearum is somehow misleading. As a matter of fact and at the same time, Velázquez et al. [9] published evidence that A. tumefaciens is the correct name for the Agrobacterium genomic species G1, solving the long-standing problem

Species and nomenclatural type strain
Origin  [5,11]. The transfer of Sinorhizobium to Ensifer, proposed 20 years ago [12], was never accepted by the wider scientific community, as witnessed by the tenfold higher number of recent publications using the name Sinorhizobium.
Resurrection of the distinction would make biological sense, as it would now separate symbiotic and non-symbiotic clades.

7.2.
We discussed the report of Weisberg et al. [3], which mainly focuses on oncogenic plasmids of agrobacteria, including a large set of strains, introducing several interesting new methods of analysis, defining nine distinct plasmid groups, and having potential impacts on taxonomy of these bacteria. Advances in Ti/Ri plasmid analysis are significant, but the classification of the bacteria carrying these plasmids remains unclear. The polyphyletic group agrobacteria (tumorigenic and rhizogenic Rhizobiaceae species) is somehow considered as a taxonomic entity, without considering current evidence that biovar 2 belongs to the genus Rhizobium and biovar 3 to the genus Allorhizobium. It is clear that Ti plasmids are transmissible among several genera in the family Rhizobiaceae, even though transmission events remain rare. Known biovars of agrobacteria remain the main hosts of oncogenic plasmids, with evidence of correlation and stable coexistence between chromosomal backgrounds and Ti plasmids, likely explained by their co-evolution. In this respect it was also recently reported that Ti plasmids can be maintained in Neorhizobium species in nature [13]. In addition, Weisberg et al. [3] suggested that there is a new group of pathogenic agrobacteria that is apparently a sister species of biovar 2. It might be similar to the species Rhizobium tumorigenes, which should be checked when sequences are available.

7.3.
Following Ormeño-Orrillo et al. [14], González et al. [15] reported a robust Rhizobium phylogenomic study using ribosomal protein genes that are recommended as phylomarkers. This serves as a framework to analyse the variation profile of the Rhizobium accessory genome and provides evidence on the lateral transfer of symbiotic plasmids, as shown before for the tropici group [16]. This report confirms the misclassification of a number of strains in the NCBI previously reported by several authors.

7.4.
Hördt et al. [11] reported an extensive genome-based taxonomic revision of the Alphaproteobacteria, including rhizobia and agrobacteria and extending the family Rhizobiaceae, with relevant proposals at several levels (species, genus, family, order) that will presumably be soon submitted to the International Journal of Systematic and Evolutionary Microbiology (IJSEM) for validation.

7.5.
Rhizobium ruizarguesonis [17,18] is within genospecies C of the R. leguminosarum species complex, so this is now the formal name for genospecies C. There are now five named species within the R. leguminosarum species complex (R. leguminosarum, R. laguerreae, R. sophorae, R. ruizarguesonis and 'R. indicum') and a recent study indicates that there are more that could be named in future [19].

MINUTE 8. ADJOURNMENT
The meeting was adjourned at 13.17 UTC on 6 July 2020. As usual, it was decided to continue the meeting online until 18 December 2020.

MINUTE 9. IMPACT OF THE NAGOYA PROTOCOL ON TAXONOMY
To propose a valid description of a new species name, the type strain needs to be made available freely to the scientific community. Rule 30 [20] of the International Code of Nomenclature of Prokaryotes requires that a viable culture of that strain must be deposited in at least two publicly accessible culture collections in two different countries from which subcultures must be available with no access restriction. Changing these rules has been regularly discussed among scientists in recent years, especially regarding the acceptance of genome sequence availability in replacement of the deposition of a live bacterial culture, referring to the description of taxa not based on isolates, e.g. based on metagenome-derived sequences, which are at the moment restricted to the Candidatus status. At the origin of this requirement of type strain availability for species description is the principle that taxonomy exists to inform biology. Microbiologists should have access to described bacterial cultures, and not only to their genome sequences, to study their biological properties towards increasing knowledge in fundamental research and devising applications of these organisms. Yet, the difficulty remains for a number of authors to describe new species due to genetic resources access regulations in their respective countries, where, in some cases, even the genome sequence cannot be published. Public international culture collections follow the rules of the Nagoya Protocol and acknowledge the sovereign rights and legislation of the country of origin. They can only accept deposits which are obtained in respect of the laws and regulation of the country of origin. Thus, the certificate of deposit can only be issued if type strains are available without restriction, at least for research purposes. In Brazil, for instance, the law allows deposit of strains in collections abroad. However, the law requires foreign researchers to always have an official partnership with a Brazilian institution and Brazilian scientists to perform research on genetic materials from Brazil. In practice, this national regulation requires foreign researchers to sign material transfer agreements (MTAs) or other contracts with Brazilian institutions, which is already considered as a restriction on the distribution of type strains by the ICSP. In several countries, such as Algeria, strains cannot be deposited without restrictions on their distribution, which prevents any new species description in this country. This, of course, is an issue relevant to the taxonomy of all microorganisms, not specifically to those bacteria within the scope of this Subcommittee. The Subcommittee agreed that a solution to the problem needs to be worked out at the level of the national authorities whose rules and regulations are creating problems for their own researchers. It is the responsibility of the latter to explain the rules better to their national authorities and give them a better insight into the situation. If the authorities prohibit deposit of a type strain, then they should be made aware that no new bacteria from their country can be described. This is a loss for the local scientists as well as for science worldwide. If biodiversity is not described and made available beyond national borders, it will not be used and cannot lead to local benefits from use by international partners. All the documentation that public culture collections require from their customers in the framework of the Nagoya Protocol is precisely to ensure that the country of origin is acknowledged and any benefits can be equitably shared. Although in some particular situations some species can indeed be endemic to a single country, most bacterial taxa are likely to be found more widely if efforts are made to look for them. It must be emphasized that the endemic character of a species can be validated and further reinforced for the country of origin only by allowing its comparison (through its type strain) with future descriptions internationally. In the time course of this discussion, the Subcommittee became aware of a working group at the ICSP Executive Board level on type strain accessibility and MTAs attached to type strains. Soon an Editorial should be published in the IJSEM to remind readers what the purpose of a type strain is, and to make updated recommendations (ICSP Executive Board, 29 October 2020, minute 8; www. the-icsp. org/ reports).

MINUTE 10. CLOSING
The online phase of this meeting was closed on 18 December 2020.
Funding information