Diversity of endemic rhizobia on Christmas Island: Implications for agriculture following phosphate mining

Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018

Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424^T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.

Phosphate mining activities affect crop rhizosphere fungal communities

Phosphate mining releases heavy metals into the surrounding environment. In this study, the effects of phosphate mining on rhizosphere soil fungi in surrounding crops, including Lactuca sativa var. angustata, Glycine max (L.) Merr., and Triticum aestivum L., were assessed. Phosphate mining significantly reduced the crop rhizosphere fungal diversity (P < 0.05). The relative abundances of Fusarium and Epicoccum increased in mining rhizosphere soil compared with the baseline. Beta diversity analysis indicated that phosphate mining led to the differentiation of fungal community structure in plant rhizospheres. Guild analysis indicated that different plant rhizosphere fungi developed various guilds in response to phosphate mining stress. Nine fungi were isolated from soil samples, with solubilization index values ranging from 1.1 to 2.5. Two efficient phosphate solubilizers, Epicoccum nigrum and Fusarium verticillioides, were enriched in phosphate mining rhizosphere soil samples. The dissolution kinetics of inorganic phosphorus and alkaline phosphatase activity assay showed strong phosphorus dissolution ability of the isolated fungi. Penicillium aculeatum, Trichoderma harzianum, Chaetomium globosum, and F. verticillioides showed strong tolerance to multiple heavy metals. This study furthers our understanding of how rhizosphere fungal ecology is affected by phosphate mining and provides important resources for the remediation of phosphate mining soil pollution.

Cupriavidus agavae sp. nov., a species isolated from Agave L. rhizosphere in northeast Mexico

During the isolation of bacteria from the Agave L. rhizosphere in northeast Mexico, four strains with similar BOX-PCR patterns were collected. The 16S rRNA gene sequences of all four strains were very similar to each other and that of the type strains of Cupriavidus metallidurans CH34T (98.49 % sequence similarity) and Cupriavidus necator N-1T (98.35 %). The genome of strain ASC-9842T was sequenced and compared to those of other Cupriavidus species. ANIb and ANIm values with the most closely related species were lower than 95%, while the in silico DNA–DNA hybridization values were also much lower than 70 %, consistent with the proposal that they represent a novel species. This conclusion was supported by additional phenotypic and chemotaxonomic analyses. Therefore, the name Cupriavidus agavae sp. nov. is proposed with the type strain ASC-9842T (=LMG 26414T=CIP 110327T).