The family Rhizobiaceae of the class Alphaproteobacteria is highly diverse and currently consists of at least 276 validly published or proposed species across 38 genera. Despite several recent studies proposing revisions to the family Rhizobiaceae , anomalies and inconsistencies in the taxonomy of this family remain. Here, we revisit the taxonomy of the family Rhizobiaceae with a focus on the genus Rhizobium . First, we generated whole-genome sequences for 12 Rhizobium type strains that previously lacked publicly available genome sequences. We then applied an established phylogenomic framework to reappraise the taxonomic classification of 242 Rhizobiaceae type strains. Our data suggest that Rhizobium aegyptiacum is a later heterotypic synonym of Rhizobium aethiopicum , and they contradict a recent suggestion that Rhizobium azibense and Rhizobium gallicum are synonymous. In addition, we propose the formation of 8 new genera ( Allohoeflea gen. nov., Arminella gen. nov., Gillisella gen. nov., Limnomicrobium gen. nov., Martinezella gen. nov., Neohoeflea gen. nov., Parahoeflea gen. nov. and Velazquezella gen. nov.) and 32 novel combinations to fix paraphyletic genera or account for monophyletic type strains that are clearly distinguishable based on core-proteome average amino acid identity comparisons. Lastly, our data suggest that the type strain of Rhizobium arsenicireducens may have been lost and that a neotype should be designated.

Arbuscular mycorrhizal (AM) fungi are often considered host generalists. Although the host-mediated assembly of AM fungal communities is well documented, its functional significance remains poorly understood, particularly in organic and low-input agroecosystems, where crop–weed interactions may influence the soil AM fungal reservoir. We investigated plant and AM fungal functional traits, mycorrhizal dependency (MD), and root AM communities in three legume crops and five weed species grown in pots with the same indigenous AM fungal inoculum. AM fungal communities were characterized using SSU rRNA gene clone libraries, sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analysis. Of 825 examined clones, 792 were assigned to AM fungi, representing 23 RFLP types. Plant species significantly affected the plant traits, root colonization, spore density, extraradical mycelium density, and MD. PERMANOVA revealed that plant species explained 97.3% of the variation in the AM fungal community structure, although this result should be interpreted cautiously because within-species dispersion may have contributed to the explained variance. RELATE analysis showed a significant association between the AM fungal community structure and plant–AM fungal functional traits. The specific root length, shoot and root N concentrations, AM fungal colonization, and spore abundance best explained community patterns. Legume crops supported greater AM fungal development and positive growth responses, whereas several weeds hosted diverse AM communities without showing biomass benefits. These findings highlight that weed management could indirectly influence AM fungal persistence through host-mediated community assembly, although field validation is required.

Opinion 131 addresses a Request for an Opinion asking the Judicial Commission to conserve the genus name Proteus Hauser 1885 (Approved Lists 1980) over its earlier homonym, the protozoan genus name Proteus Müller 1786. The Judicial Commission agrees that the later homonym is illegitimate and that the replacement of the prokaryotic name Proteus would be undesirable. It is also concluded that Proteus Müller 1786 is an objectively invalid name under the International Code of Zoological Nomenclature. Judicial Opinions 9, 12 and 130 serve as precedents for the conservation of Proteus Hauser 1885 (Approved Lists 1980) over Proteus Müller 1786. This action is taken here and makes the prokaryotic name Proteus legitimate.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

The family Rhizobiaceae of the class Alphaproteobacteria is highly diverse and currently consists of at least 276 validly published or proposed species across 38 genera. Despite several recent studies proposing revisions to the family Rhizobiaceae , anomalies and inconsistencies in the taxonomy of this family remain. Here, we revisit the taxonomy of the family Rhizobiaceae with a focus on the genus Rhizobium . First, we generated whole genome sequences for 12 Rhizobium type strains that previously lacked publicly available genome sequences. We then applied an established phylogenomic framework to reappraise the taxonomic classification of 242 Rhizobiaceae type strains. Our data suggest that Rhizobium aegyptiacum is a later heterotypic synonym of Rhizobium aethiopicum , and they contradict a recent suggestion that Rhizobium azibense and Rhizobium gallicum are synonymous. In addition, we propose the formation of ten new genera ( Allohoeflea gen. nov., Arminia gen. nov., Fluviimicrobium gen. nov., Gillisella gen. nov., Limnomicrobium gen. nov., Martinezia gen. nov., Neohoeflea gen. nov., Parahoeflea gen. nov., Velazquezia gen. nov., and Yannia gen. nov.) and 35 novel combinations to fix paraphyletic genera or account for monophyletic type strains that are clearly distinguishable based on core-proteome average amino acid identity (cpAAI) comparisons. Lastly, our data suggest that the type strain of Rhizobium arsenicireducens may have been lost, and that either a neotype should be designated or the taxonomic status of this species should be revised. ### Competing Interest Statement The authors have declared no competing interest. Natural Sciences and Engineering Research Council, https://ror.org/01h531d29, ALLRP-597321-24 Spanish Ministry of Science and Innovation, PID2022-138373NA-I00 Genome Canada, https://ror.org/029s29983, CSAFS-ICT 19308

ABSTRACT Neotropical Beta-rhizobia have a particular affinity to the large legume ( Fabaceae ) genus Mimosa and some of its relatives in the tribe Mimosae of the Caesalpinioideae subfamily. However, little is still known about the ecology of this interaction, especially the relationship between the rhizobia of “widespread” pan-tropical Mimosa species like M. pudica and the rhizobia that nodulate endemic Mimosa species that are very restricted in their habitats. The objective of this study was to examine the microsymbionts of Mimosa spp. and some other mimosoids in climates ranging from tropical to subtropical, humid to semi-arid, with varied soil characteristics and altitudes, with the aim of testing the hypothesis that widespread species have more cosmopolitan symbiont preferences than endemic ones. Nodules were sampled from more than 40 Mimosa spp. and related taxa in eleven Brazilian states, many endemics or biome-restricted, but particular attention was paid to sample nodules from the widespread species M. pudica at all locations. The Mimosa symbionts comprised 19 potential 16S rRNA and recA groups at the species level, with 16 belonging to the genus Paraburkholderia , including six lineages that may represent new species. The remaining genotypes consisted of 14 strains in two lineages of Cupriavidus that were mainly isolated from M. pudica growing at low altitudes, plus a single lineage of Rhizobium also from M. pudica . It is concluded that a high diversity of Paraburkholderia strains dominate as symbionts of Mimosa in the acidic soils of its main center of radiation in Central Brazil but that Cupriavidus and Rhizobium comprise a significant minority of symbionts of widespread Mimosa spp., especially M. pudica , in lowland or disturbed areas with less acidic soils. Mimosa symbiont diversity is thus driven either by edapho-climatic characteristics for widespread species and/or by co-evolution of the symbiotic partners for endemic species.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

Rhizobia are bacteria that form nitrogen-fixing nodules in legume plants. The sets of genes responsible for both nodulation and nitrogen fixation are carried in plasmids or genomic islands that are often mobile. Different strains within a species sometimes have different host specificities, while very similar symbiosis genes may be found in strains of different species. These specificity variants are known as symbiovars, and many of them have been given names, but there are no established guidelines for defining or naming them. Here, we discuss the requirements for guidelines to describe symbiovars, propose a set of guidelines, provide a list of all symbiovars for which descriptions have been published so far, and offer a mechanism to maintain a list in the future.

Backgroud The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. Results The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. Conclusion The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

The species Rhizobium indigoferae and Sinorhizobium kummerowiae were isolated from legume nodules and the 16S rRNA sequences of their respective type strains, CCBAU 71042T T and CCBAU 71714T, T , were highly divergent from those of the other species of the genera Rhizobium and Sinorhizobium, , respectively. However, the 16S rRNA gene sequences obtained for strains CCBAU 71042T T and CCBAU 71714T T several years after description, were different from the original ones, showing 100 % similarity to the type strains of Rhizobium leguminosarum and Sinorhizobium meliloti, , respectively. Phylogenetic analyses of two housekeeping genes, recA and atpD, , confirmed the high phylogenetic closeness of strains CCBAU 71042T T and CCBAU 71714T T to the respective type strains of R. leguminosarum and S. meliloti. . In the present work, we compared the genomes of the type strains of R. indigoferae and S. kummerowiae available in several culture collections with those of the respective type strains of R. leguminosarum and S. meliloti, , some of them obtained in this study. The calculated average nucleotide identity-BLAST and digital DNA-DNA hybridization values in both cases were higher than those recommended for species differentiation, supporting the proposal for the reclassification of the type strains of R. indigoferae and S. kummerowiae into the species R. leguminosarum and S. meliloti, , respectively.

Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

The alphaproteobacterial order Hyphomicrobiales consists of 38 families comprising at least 152 validly published genera as of January 2024. The order Hyphomicrobiales was first described in 1957 and underwent important revisions in 2020. However, we show that several inconsistencies in the taxonomy of this order remain and we argue that there is a need for a consistent framework for defining families within the order. We propose a common genome-based framework for defining families within the order Hyphomicrobiales, suggesting that families represent monophyletic groups in core-genome phylogenies that share pairwise average amino acid identity values above ~75 % when calculated from a core set of 59 proteins. Applying this framework, we propose the formation of four new families and to reassign the genera Salaquimonas, Rhodoblastus, and Rhodoligotrophos into Salaquimonadaceae fam. nov., Rhodoblastaceae fam. nov., and Rhodoligotrophaceae fam. nov., respectively, and the genera Albibacter, Chenggangzhangella, Hansschlegelia, and Methylopila into Methylopilaceae fam. nov. We further propose to unify the families Bartonellaceae, Brucellaceae, Phyllobacteriaceae, and Notoacmeibacteraceae as Bartonellaceae; the families Segnochrobactraceae and Pseudoxanthobacteraceae as Segnochrobactraceae; the families Lichenihabitantaceae and Lichenibacteriaceae as Lichenihabitantaceae; and the families Breoghaniaceae and Stappiaceae as Stappiaceae. Lastly, we propose to reassign several genera to existing families. Specifically, we propose to reassign the genus Pseudohoeflea to the family Rhizobiaceae; the genera Oricola, Roseitalea, and Oceaniradius to the family Ahrensiaceae; the genus Limoniibacter to the emended family Bartonellaceae; the genus Faunimonas to the family Afifellaceae; and the genus Pseudochelatococcus to the family Chelatococcaceae. Our data also support the recent proposal to reassign the genus Prosthecomicrobium to the family Kaistiaceae.

Neotropical Beta-rhizobia have a particular affinity to the large legume (Fabaceae) genus Mimosa and some of its relatives in the tribe Mimosae of the Caesalpinioideae subfamily. However, little is still known about the ecology of this interaction, especially the relationship between the rhizobia of “widespread” pan-tropical Mimosa species like M. pudica and the rhizobia that nodulate endemic Mimosa species that are very restricted in their habitats. The objective of this study was to examine the microsymbionts of Mimosa spp. and other mimosoids in climates ranging from tropical to subtropical, humid to semi-arid, with varied soil characteristics and altitudes, with the aim of testing the hypothesis that widespread species have more cosmopolitan symbiont preferences than endemic ones. Nodules were sampled from >30 Mimosa spp. and related taxa in 13 Brazilian states covering all five national regions; many of the species were endemics or biome-restricted, but particular attention was also paid to sample nodules from the widespread species M. pudica at all locations. The Mimosa symbionts comprised 21 potential 16S rRNA and recA groups at the species level, with 17 belonging to the genus Paraburkholderia, including four lineages that may represent new species. The remaining genotypes consisted of 14 strains in two lineages of Cupriavidus that were mainly isolated from M. pudica growing at low altitudes, and a single lineage of Rhizobium also from M. pudica. In addition, a strain of Trinickia symbiotica was isolated from M. misera. It is concluded that diverse genotypes of Paraburkholderia dominate as symbionts of Mimosa in the acidic soils of its main center of radiation in Central Brazil but that Cupriavidus and Rhizobium comprise a significant minority of symbionts of widespread Mimosa spp., especially M. pudica, in lowland or disturbed areas with less acidic soils. Mimosa symbiont selection is thus driven either by edapho-climatic characteristics for widespread species and/or by co-evolution of the symbiotic partners for endemic species.

Opinion 130 deals with a Request for an Opinion asking the Judicial Commission to clarify whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate. The Request is approved and an answer is given. The name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate because it is a later homonym of the validly published cyanobacterial name Rhodococcus Hansgirg 1884. The Judicial Commission also clarifies that it has the means to resolve such cases by conserving a name over an earlier homonym. It is concluded that the name Rhodococcus Zopf 1891 (Approved Lists 1980) is significantly more important than the name Rhodococcus Hansgirg 1884 and therefore the former is conserved over the latter. This makes the name Rhodococcus Zopf 1891 (Approved Lists 1980) legitimate.

Genomic evidence indicates that the Rhizobium leguminosarum species complex comprises multiple distinct species, perhaps 18 or more. Of the five earliest genospecies (gs) to be described, only two have formal names: R. leguminosarum sensu stricto (gsE) and Rhizobium ruizarguesonis (gsC). Here, we provide formal descriptions and names for the other three genospecies, based on the publicly available genome sequences for multiple strains of each species: Rhizobium brockwellii sp. nov. (gsA, 37 strains, type strain CC275e T =LMG 6122 T = ICMP 2163 T =NZP 561 T = PDDCC 2163 T =HAMBI 13 T ), Rhizobium johnstonii sp. nov. (gsB, 54 strains, type strain 3841 T = LMG 32736 T =DSM 114642 T ) and Rhizobium beringeri sp. nov. (gsD, 8 strains, type strain SM51 T = LMG 32895 T = DSM 115206 T ). Each species forms a well-supported clade in a phylogeny based on 120 concatenated core genes. All strains have average nucleotide identity (ANI) above 96 % with the relevant type strain and below 96 % with all other type strains. Each species is characterised by a number of genes that are absent or rare in other species.

While shaping of plant microbiome composition through ‘host filtering’ is well documented in legume–rhizobium symbioses, it is less clear to what extent different varieties and genotypes of the same plant species differentially influence symbiont community diversity and composition. Here, we compared how clover host varieties and genotypes affect the structure of Rhizobium populations in root nodules under conventional field and controlled greenhouse conditions. We first grew four Trifolium repens (white clover) F 2 crosses and one variety in a conventional field trial and compared differences in root nodule Rhizobium leguminosarum symbiovar trifolii (Rlt) genotype diversity using high‐throughput amplicon sequencing of chromosomal housekeeping ( rpoB and recA ) genes and auxiliary plasmid‐borne symbiosis genes ( nodA and nodD ). We found that Rlt nodule diversities significantly differed between clover crosses, potentially due to host filtering. However, variance in Rlt diversity largely overlapped between crosses and was also explained by the spatial distribution of plants in the field, indicative of the role of local environmental conditions for nodule diversity. To test the effect of host filtering, we conducted a controlled greenhouse trial with a diverse Rlt inoculum and several host genotypes. We found that different clover varieties and genotypes of the same variety selected for significantly different Rlt nodule communities and that the strength of host filtering (deviation from the initial Rhizobium inoculant composition) was positively correlated with the efficiency of symbiosis (rate of plant greenness colouration). Together, our results suggest that selection by host genotype and local growth conditions jointly influence white clover Rlt nodule diversity and community composition.

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(1) To assess the biological N fixation (BNF) potential of varieties of faba bean (Vicia faba L.) cropped with or without compost in an experimental field-scale rotation with no recent history of legumes, (2) to enumerate soil populations of Rhizobium leguminosarum sv. viciae (Rlv), and to genetically characterize the nodulating Rlv strains, (3) compare BNF with other sites in Britain. BNF was evaluated from 2012 to 2015 using 15 N natural abundance. Treatments were either PK fertilizer or compost. Soil rhizobial populations were determined using qPCR, the symbiotic rhizobia genotyped (16 S rRNA, nodA and nodD genes), and their BNF capacity assessed ex situ. The reliance of legumes on BNF at other British sites was estimated in a single season, and their nodulating symbionts examined. Faba bean obtained most of its N through BNF (>80%) regardless of variety or year. N-accumulation by cvs Babylon and Boxer increased with compost treatment in 2014/2015. Rhizobial populations were c. 105-106 Rlv cells g−1 soil regardless of field or treatment. 157 Rlv microsymbionts grouped into two large nodAD clades; one mainly from V. faba, and the other from various legumes. All isolates nodulated, and some performed better than commercial inoculant strains. Faba bean can provide most of its nitrogen through BNF and leave economically valuable residual N for subsequent crops. Recent legume cropping in northern Europe is not essential for effective nodulation: rhizobia may persist in a range of farmland locations. Nevertheless, there is the potential to apply elite rhizobial strains as inoculants in some soils.

A Biolog (sole carbon source utilisation) user database of tropical and temperature rhizobial strains was created and used in conjunction with the partial 16S rRNA sequencing method to characterise 12 rhizobial isolates from African acacias and other tropical woody legumes. There was close agreement between the two methods but also some significant discrepancies. A high degree of diversity was shown in the relatively small sample of isolates, with 4 out of 5 of the currently proposed rhizobial genera represented. This is the first time Biolog has shown congruence with genotypic fingerprinting using a wide selection of rhizobial reference and test strains.