International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021

Minutes of the closed meeting of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference, 5 July 2021, followed by online discussion until 31 December 2021, and list of recent species.


Minute 5. Following up the progress in resolutions (minutes 5.1 and 5.2) of the previous (2020) meeting
As decided in our two past meetings, some members edited information on rhizobia and agrobacteria on Wikipedia pages.Wikipedia is an open resource, which is accessible to everybody.It seems that the taxonomic information on many of the Wikipedia pages have been updated in connection with the List of Prokaryotic names with Standing in Nomenclature (LPSN; www.bacterio.net/).Thus, the members were encouraged to improve and add more biological information on Wikipedia pages (rather than only the taxonomic changes, which are updated by the LPSN regularly).The Subcommittee blog (https://taxonomyagrorhizo.blogspot.com/) does not necessarily reflect the official decisions made by our Subcommittee.Therefore, the members are encouraged to use the blog as an unofficial public outlet to write their opinions and comments, and to increase interactions and visibility of our recommendations.

Minute 6. New species and genera, since the last meeting
The LPSN provides valuable and up to dated taxonomic information; however, it seems that the LPSN is not necessarily linked to genomic sequences for all taxa.We thus, decided to carry on maintaining the list of new species and genera that were published since our last meeting (Table 1).

Minute 7. Nagoya protocol
The Brazilian member (Jerri Zilli) mentioned that they had promising meetings and negotiations with authorities of the ministry of environment of Brazil.Since last year, the Ministry of Environment has improved the rules for accessibility of bacterial strains regarding the Nagoya Protocol.In the case of India, the strains isolated from India are not sufficiently accessible to describe a new species.However, some researchers are in discussion with the government in India about making the rules acceptable, which might enable researchers to validate names of new species isolated from India in future.

Minute 8. Recent information on LTP database
The new version of All-Species Living Tree Project (LTP) has been recently released [2] (https://imedea.uib-csic.es/mmg/ltp/).The LTP database contains the 16S rRNA gene sequences of all type strains with validly published names until December 2020, as well as all sequences of new species not yet listed in the notification lists of the International Journal of Systematic and Evolutionary Microbiology, but published in this journal.The new release has three major features: (i) an improved alignment; (ii) new reconstructions of the global phylogeny of the classified species; and (iii) a list of taxa that need to be evaluated.The LTP aims to regularly update the validly published nomenclatural classification changes and new taxa proposals.The LTP is a very useful database since it can show the phylogenetic position of all validated rhizobial and agrobacterial species names, although we note that related species do not always have distinct 16S rRNA gene sequences [3][4][5] Minute 9. Recent relevant publications in taxonomy 9.1.We discussed the recent paper by Velázquez et al. [6], in which the authors pointed out that strain ATCC 4720 T is the authentic type strain of Agrobacterium tumefaciens.The authors noted that the strains NCIB 9042 T and ATCC 4720 T were recorded as the original type strains of Agrobacterium radiobacter and A. tumefaciens, respectively.Nevertheless, in the list of the valid names of bacteria complied by Skerman et al. [7], the strains ATCC 19358 T and ATCC 23308 T were reported as the types strain of A. radiobacter and A. tumefaciens, respectively.In the case of A. radiobacter, this did not create a problem, since both cultures represented the same strain, just from different culture collections.However, this misnaming caused serious taxonomic problems for A. tumefaciens since the strain ATCC 23308 T showed 87 % DNA-DNA relatedness with A. radiobacter IAM 12048 T in a study by Sawada et al. [8].Based on this result, Sawada et al. [8] proposed the rejection of the name A. tumefaciens since A. radiobacter has priority according to Rule 38 of the Bacteriological Code.During the last decades, several researchers used the 'wrong' strain ATCC 23308 T (B6 T =CFBP 2413 T =HAMBI 1811 T =ICMP 5856 T =LMG 187 T =NCPPB 2437 T ) as the type strain of A. tumefaciens [9,10].For instance, Mousavi et al. [10] proposed that A. tumefaciens was placed in a monophyletic clade with A. radiobacter.Therefore, they proposed that A. tumefaciens is no longer a valid species name since it was described after A. radiobacter.Based on the results of the average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) performed by Velázquez et al. [6], the ANIb and dDDH values between A. tumefaciens ATCC 4720 T and A. radiobacter NCIB 9042 T were 86.5 and 31.3 %, respectively.This clearly shows that strain ATCC 4720 T belongs to a different species rather than A. radiobacter.Therefore, the authors requested the Judicial Commission to issue an opinion correcting the type strain of A. tumefaciens from ATCC 23308 T to ATCC 4720 T , and have been waiting for the decision of the Judicial Commission.We discussed this issue, and members were in favour of the proposal of retaining A. tumefaciens as a valid species name, with ATCC 4720 T as the type strain.

9.2.
The main results of a recent manuscript [11] were presented by two members of our Subcommittee (Nemanja Kuzmanović and Florent Lassalle).In this study, the authors performed a phylogenomic study of 94 strains of the family Rhizobiaceae.Based on the results of a phylogeny based on 170 nonrecombinant loci (using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86%), the genus name Sinorhizobium should be retained as a valid genus name that encompasses 17 species.Moreover, the authors proposed delineation of a new genus name Xaviernesmea gen.nov.for the former species Rhizobium Table 1.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 International Journal of Systematic and Evolutionary Microbiology (have not been included in a validation list).

Origin
Type strain genome NCBI assembly accession

Paraburkholderia
Paraburkholderia acidicola G-6302 T (=ATCC 31363 T =BCRC 13035 T ) Soil, Japan GCF_002362315.1 [53] Paraburkholderia acidiphila 7Q-K02 T (=KCTC 62472 T =LMG 29209 T ) Forest soil, PR China GCF_009789655.1 [25] Paraburkholderia acidisoli DHF22 T (=GDMCC 1.1448 T =LMG 30262 T ) Forest soil, PR China GCF_009789675.1 [25] Table 1.Continued Continued oryzae, which had an uncertain phylogenetic position in previous studies [10,12].The authors created 14 new species combination in the family Rhizobiaceae, and proposed delineation of two new genera for some of the current members of the genera Neorhizobium and Rhizobium.Interestingly, the authors of this work also proposed that a threshold of cpAAI >86 % could be used to separate the genera of the family Rhizobiaceae.The delineation of a new subgenus instead of a new genus was discussed in our meeting.Even though subgenus is an acceptable and official taxonomic level in classification of prokaryotes, most of the members thought that using subgenus might cause unnecessary complexities in the taxonomy of agrobacteria and rhizobia.However, we cannot forbid researchers to propose a subgenus.

Minute 10. Adjournment of videoconference
The meeting by videoconference was adjourned at 12 : 53 UTC on 5 July 2021.As usual, it was decided to continue the meeting and discussion online until 31 December 2021.

ONLINE CONTINUATION OF MEETING Minute 11. New members
Three scientists were later contacted by the Subcommittee secretary.George Colin diCenzi (Queen's University, Canada) and Praveen Rahi (National Centre for Cell Science, India) were further elected as regular members, and contributed in the online discussion to prepare the present minutes.

Minute 12. Reclassification of Ochrobactrum Lupini as Brucella Anthropi
In 2005, Ochrobactrum lupini was described based on a polyphasic study including phenotypic, chemotaxonomic, and molecular features (16S and 23S rRNA) of the strains isolated from Lupinus albus [13].However, a new study based on multiple genome ANI approaches, dDDH and phylogenetic analysis by Volpiano et al. [14] showed that similarity between the type strains Ochrobactrum anthropi ATCC 49188 A recent paper [16] presented genomic distance metrics among a large number of type strains in the Rhizobiales.Particularly relevant to our remit are their proposals that R. fabae [17] should be considered as a later heterotypic synonym of R. pisi [18], and that R. azibense [19] should be considered as a later heterotypic synonym of R. gallicum [20].We support both these proposals.

Minute 14. Proposal for revising the ICNP rules
Recently, Rahi [21] published an opinion on the vexed subject of the Nagoya Protocol and access to type strain cultures.In this paper, he proposed "the problems imposed by policies designed to increase accessibility to genetic resources could be resolved by revising the ICNP rules to accommodate the many researchers working in countries that are signatories of the Convention on Biological Diversity and the Nagoya Protocol.This could be achieved by redefining 'restriction-free access' in Rule 30 [4] of the Code and by keeping regulated access to cultures under international legislation, like the Convention on Biological Diversity, the Nagoya Protocol and quarantine laws, free from restriction".The Subcommittee has not yet discussed this publication, although the issue is one that it has considered previously.

Minute 15. Resignation and thanks
Dr. Philippe de Lajudie, Prof. Kristina Lindström and Prof. Xavier Nesme announced their resignation from the Subcommittee because of retirement.The Subcommittee expressed their warm thanks to Philippe de Lajudie for taking his commitment as Secretary seriously as well as his long and active years of membership with appreciated contributions.The Subcommittee expressed their sincere appreciations to Prof. Kristina Lindström for her excellent professional contributions to the Subcommittee for such a long time, and particularly during all the years when she was Secretary and worked hard to keep the Subcommittee members active.The Subcommittee extended sincere gratitude to Prof. Xavier Nesme for his contributions and thoughtful ideas while a member of the Subcommittee.The Subcommittee also remembers with gratitude Prof. Wenxin Chen (1926-2021, China Agricultural University), who was a member of the Subcommittee until 2015, and of course she and her laboratory have made huge contributions to taxonomy of rhizobia over very many years, describing a large number of new species.

Minute 16. Membership status
Article 6 of the Statutes of the ICSP details rules on the organization and missions of subcommittees and specifies membership rules [22].The members of our Subcommittee are listed as below:

13. Rhizobium fabae is a synonym of Rhizobium pisi and Rhizobium azibense is a synonym of Rhizobium gallicum
[14].lupiniLUP21T (97.55 % ANIb, 98.25 % ANIm, 97.99 % gANI, 97.94 % OrthoANI and 83.9 % dDDH) exceeds the usual species delineation threshold.Thus, the authors proposed that O. lupini should be considered a later heterotypic synonym of O. anthropi.More recently, Hördt et al.[15]have proposed the amalgamation of the entire genus Ochrobactrum into Brucella.They described both Brucella anthropi and B. lupini, but we consider that B. lupini is a later heterotypic synonym of B. anthropi in light of the evidence provided by Volpiano et al.[14].