Bradyrhizobia are abundant soil bacteria, which can form nitrogen-fixing symbioses with leguminous plants, including important crops such as soybean, cowpea and peanut. Many bradyrhizobia can denitrify, but studies have hitherto focused on a few model organisms. We screened 39 diverse Bradyrhizobium strains, isolated from legume nodules. Half of them were unable to reduce N 2 O, making them sources of this greenhouse gas. Most others could denitrify NO 3 − to N 2. Timeresolved gas kinetics and transcription analyses during transition to anaerobic respiration revealed a common regulation of nirK, norCB and nosZ (encoding NO 2 − , NO and N 2 O reductases), and differing regulation of napAB (encoding periplasmic NO 3 − reductase). A prominent feature in all N 2-producing strains was a virtually complete hampering of NO 3 − reduction in the presence of N 2 O. In-depth analyses suggest that this was due to a competition between electron transport pathways, strongly favouring N 2 O over NO 3 − reduction. In a natural context, bacteria with this feature would preferentially reduce available N 2 O, produced by themselves or other soil bacteria, making them powerful sinks for this greenhouse gas. One way to augment such populations in agricultural soils is to develop inoculants for legume crops with dual capabilities of efficient N 2-fixation and efficient N 2 O reduction.
HighlightsOn MPN assessment, native rhizobium population size on the study site was less than 10 cfu g−1 of soil.On a wide range of on-farm trials, inoculation (I) increased chickpea grain yields for 99% of target farmers.I and P fertilizer in combination, resulted on average, in a 38% yield increase over the control plots.Variation in response to rhizobium inoculation was mostly independent of agro-ecology and soil type.Rhizobial inoculation offers a cheap and highly effective means for the sustainable intensification of smallholder agriculture.
Forty-two chickpea-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations of Ethiopia and were characterized on the basis of 76 phenotypic traits. Furthermore, 18 representative strains were selected and characterized using multilocus sequence analyses of core and symbiotic gene loci. Numerical analysis of the phenotypic characteristics grouped the 42 strains into 4 distinct clusters. The analysis of the 16S rRNA gene of the 18 strains showed that they belong to the Mesorhizobium genus. On the basis of the phylogenetic tree constructed from the combined genes sequences (recA, atpD, glnII, and gyrB), the test strains were distributed into 4 genospecies (designated as genospecies I-IV). Genospecies I, II, and III could be classified with Mesorhizobium ciceri, Mesorhizobium abyssinicae, and Mesorhizobium shonense, respectively, while genospecies IV might represent an unnamed Mesorhizobium genospecies. Phylogenetic reconstruction based on the symbiosis-related (nifH and nodA) genes supported a single cluster together with a previously described symbiont of chickpea (M. ciceri and Mesorhizobium mediterraneum). Overall, our results corroborate earlier findings that Ethiopian soils harbor phylogenetically diverse Mesorhizobium species, justifying further explorative studies. The observed differences in symbiotic effectiveness indicated the potential to select effective strains for use as inoculants and to improve the productivity of chickpea in the country.
A total of 18 strains, representing members of the genus
Mesorhizobium
, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours
Mesorhizobium plurifarium
,
Mesorhizobium amorphae
,
Mesorhizobium septentrionale
and
Mesorhizobium huakuii
was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus
Mesorhizobium
. The DNA–DNA relatedness between the representative strains of genospecies I–III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39aT ( = LMG 26966T = HAMBI 3295T), AC99bT ( = LMG 26968T = HAMBI 3301T) and AC98cT ( = LMG 26967T = HAMBI 3306T) are proposed as type strains for the respective novel species.
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