Sofie De Meyer

Arsenic (As) in soil, such as mining waste, is a concern for communities with legacy contamination. While the chronic health effects of As exposure through drinking water are well documented, the association between As in soil and population-wide health impacts is complex, involving factors like soil accessibility, soil properties, and exposure modes. This review summarizes evidence of associations between As in soil and human health, as well as biomarker and bioaccessibility evidence of exposure pathways. Fourteen studies were included in the final analysis. Reviewed studies reported associations between As in soil and birth outcomes, neurological effects, DNA damage, and cancer. Some of these health outcomes are not known to be linked to As in drinking water and were reported over a range of soil concentrations, indicating inconsistencies. Higher soil As concentrations are associated with higher As in human biospecimens, suggesting direct and indirect soil ingestion as primary exposure pathways. The subpopulations more likely to be exposed include younger children and those involved in soil-based activities. Future research should focus on standardized epidemiological studies, longitudinal studies, soil exposure and mitigating factors, combined exposure biomarker studies, the behavior of the different As species, soil dose related to bioavailability/bioaccessibility, and effects with other elements.

Pasture legumes must be adequately and effectively nodulated in order to reach nitrogen-fixation targets. Of 225 pasture paddocks sampled across the Central Tablelands, Central West, Monaro and Riverina regions of New South Wales, 93% had inadequate legume nodulation. Legume content was significantly higher in the mixed faming zone (>50%, Central West and Riverina) than the permanent pasture zone (26%, Central Tablelands; 28% Monaro). Available phosphorus (P) was below critical levels in 40% of paddocks sampled and sulfur (S) in 73% of paddocks; >35% of all paddocks had soil pHCa <5.0. Deficiency of P was more prevalent in the Central Tablelands (63% of paddocks), whereas S deficiency occurred more frequently in the Central West (95% of paddocks). Legume nodule scores were associated with host legume species, soil pH, available P and/or S, and cation exchange capacity, which collectively accounted for 73% of variation. For Trifolium spp., at soil pHCa >5.55, nodulation was predicted to be near adequate (score 3.95, where adequate = 4). At pHCa <5.55, higher available S resulted in a higher nodulation score (2.42) than in paddocks where S was deficient (score 0–1.97). These results suggest that improving the capacity of legumes to supply nitrogen should focus on addressing soil acidity and plant nutrition, specifically P and S.

Five strains of Gram-stain-negative, rod-shaped bacteria were isolated from Carmichaelia and Montigena root nodules. Based on 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium , and to be most closely related to Mesorhizobium jarvisii ATCC 33669T (100–99.6 % sequence similarity), Mesorhizobium huakuii IAM 14158T (99.9–99.6 %), Mesorhizobium japonicum MAFF303099T (99.8–99.6 %) and Mesorhizobium erdmanii USDA 3471T (99.8–99.5 %). Additionally, the strains formed distinct groups based on housekeeping gene analysis and were most closely related to M. jarvisii ATCC 33669T (89.6–89.5 and 97.6–97.3 % sequence similarity for glnII and recA, respectively), M. erdmanii USDA 3471T (94.3–94.0 and 94.9–94.1 %), M. japonicum MAFF303099T (90.0–89.9 and 96.7–96.2 %) and M. huakuii IAM 14158T (89.9–90.0 and 95.4–94.9 %). Chemotaxonomic data supported the assignment of the strains to the genus Mesorhizobium and DNA–DNA hybridizations, average nucleotide identity analysis, matrix-assisted laser desorption ionization time-of-flight MS analysis, physiological and biochemical tests differentiated them genotypically and phenotypically from their nearest neighbouring species. Therefore, these strains are considered to represent a novel species, for which the name Mesorhizobium carmichaelinearum sp. nov. is proposed. The type strain is ICMP 18942T (=MonP1N1T=LMG 28414T).

Given that phosphate supplies may diminish and become uneconomic to mine after 2020, there is a compelling need to develop alternative industries to support the population on Christmas Island. Former mine sites could be turned into productive agricultural land, however, large-scale commercial agriculture has never been attempted, and, given the uniqueness of the island, the diversity of rhizobia prior to introducing legumes needed evaluation. Therefore, 84 rhizobia isolates were obtained from nine different hosts, both crop and introduced legumes, located at seven sites across the island. Based on 16S rRNA and recA gene sequence analysis, the isolates grouped into 13 clades clustering within the genus Bradyrhizobium, Ensifer, Cupriavidus and Rhizobium. According to the sequences of their symbiosis genes nodC and nifH, the isolates were classified into 12 and 11 clades, respectively, and clustered closest to tropical or crop legume isolates. Moreover, the symbiosis gene phylogeny and Multi Locus Sequence Analysis gene phylogeny suggested vertical transmission in the alpha-rhizobia but horizontal transmission within the beta-rhizobia. Furthermore, this study provides evidence of a large diversity of endemic rhizobia associated with both crop and introduced legumes, and highlights the necessity of inoculation for common bean, chickpea and soybean on the Island.

Phaseolus vulgaris (common bean) was introduced to Kenya several centuries ago but the rhizobia that nodulate it in the country remain poorly characterised. To address this gap in knowledge, 178 isolates recovered from the root nodules of P. vulgaris cultivated in Kenya were genotyped stepwise by the analysis of genomic DNA fingerprints, PCR-RFLP and 16S rRNA, atpD, recA and nodC gene sequences. Results indicated that P. vulgaris in Kenya is nodulated by at least six Rhizobium genospecies, with most of the isolates belonging to R. phaseoli and a possibly novel Rhizobium species. Infrequently, isolates belonged to R. paranaense, R. leucaenae, R. sophoriradicis and R. aegyptiacum. Despite considerable core-gene heterogeneity among the isolates, only four nodC gene alleles were observed indicating conservation within this gene. Testing of the capacity of the isolates to fix nitrogen (N2) in symbiosis with P. vulgaris revealed wide variations in effectiveness, with ten isolates comparable to R. tropici CIAT 899, a commercial inoculant strain for P. vulgaris. In addition to unveiling effective native rhizobial strains with potential as inoculants in Kenya, this study demonstrated that Kenyan soils harbour diverse P. vulgaris-nodulating rhizobia, some of which formed phylogenetic clusters distinct from known lineages. The native rhizobia differed by site, suggesting that field inoculation of P. vulgaris may need to be locally optimised.

Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume–rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.

Nine Gram-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules. All strains were able to nodulate and fix nitrogen with Lebeckia ambigua apart from WSM4178T, WSM4181 and WSM4182. Based on the 16S rRNA gene phylogeny, all strains were closely related to Paraburkholderia species (98.4–99.9 %), belonging to the Betaproteobacteria class and Burkholderiaceae family. According to 16S rRNA gene phylogeny the closest relative for WSM4174–WSM4177 and WSM4179–WSM4180 was Paraburkholderia tuberum (99.80–99.86 %), for WSM4178T was Paraburkholderia caledonica (98.42 %) and for WSM4181–WSM4182 was Paraburkholderia graminis (99.79 %). Analysis of the gyrB and recA housekeeping genes supported the assignment of WSM4181–WSM4182 to P. graminis and the other investigated strains could be assigned to the genus Paraburkholderia . The results of DNA–DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of WSM4178T from the closest validly published Paraburkholderia species. However, WSM4174–WSM4177 and WSM4179–WSM4180 could not reliably be distinguished from its closest neighbour and therefore complete genome comparison was performed between WSM4176 and P. tuberum STM678T which gave ANI values of 96–97 %. Chemotaxonomic data, including fatty acid profiles and quinone data supported the assignment of the strains to the genus Paraburkholderia . On the basis of genotypic and phenotypic data one novel species, Paraburkholderia fynbosensis sp. nov. (WSM4178T=LMG 27177T=HAMBI 3356T), is proposed and the isolation of P. tuberum and P. graminis from root nodules of Lebeckia ambigua is reported.