Revealing the Draft Genome Sequence of Bradyrhizobium sp. Strain USDA 3458, an Effective Symbiotic Diazotroph Isolated from Cowpea (Vigna unguiculata) Genotype IT82E-16.

Pairing plants with plant growth-promoting bacteria is critical to the future of agriculture. Bradyrhizobium sp. strain USDA 3458 isolated from Vigna unguiculata (cowpea) paired with cowpea genotype IT82E-16 represents a novel combination in arid regions. Here, we report the draft genome sequence of strain USDA 3458.

Elucidation of the Genome of Bradyrhizobium sp. Strain USDA 3456, a Historic Agricultural Diazotroph from Cowpea (Vigna unguiculata).

Bradyrhizobium sp. strain USDA 3456 is a historic strain from the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) National Rhizobium Germplasm Collection isolated from Vigna unguiculata (cowpea) in 1966. Strain USDA 3456 has been utilized in global agricultural applications, including improving soil nitrogen fertility. The draft genome sequence here provides a genetic reference of a novel diazotroph.

Rubrobacter spartanus sp. nov., a moderately thermophilic oligotrophic bacterium isolated from volcanic soil.

Bacterial strain HPK2-2T was isolated from soil adjacent to the caldera of Kilauea Volcano in Hawaii Volcanoes National Park. HPK2-2T is a chemoorganoheterotroph that shows optimal growth at 50 °C (range 45-55 °C) and pH 8.0 (range 5.0-10.0). Sequence analysis of the 16S subunit of the rRNA gene showed that HPK2-2T is most closely related to the type strain of Rubrobactertaiwanensis (ATCC BAA-406T), with which it shared 94.5 % sequence identity. The major fatty acids detected in HPK2-2T were C18 : 0 14-methyl and C16 : 0 12-methyl; internally branched fatty acids such as these are characteristic of the genus Rubrobacter. The only respiratory quinone detected was MK-8, which is the major respiratory quinone for all members of the family Rubrobacteraceae examined thus far. We propose that HPK2-2T represents a novel species of the genus Rubrobacter, for which we propose the name Rubrobacterspartanus (type strain HPK2-2T; DSM 102139T; LMG 29988T).

Complex N acquisition by soil diazotrophs: how the ability to release exoenzymes affects N fixation by terrestrial free-living diazotrophs.

Terrestrial systems support a variety of free-living soil diazotrophs, which can fix nitrogen (N) outside of plant associations. However, owing to the metabolic costs associated with N fixation, free-living soil diazotrophs likely rely on soil N to satisfy the majority of cellular N demand and only fix atmospheric N under certain conditions. Culture-based studies and genomic data show that many free-living soil diazotrophs can access high-molecular weight organic soil N by releasing N-acquiring enzymes such as proteases and chitinases into the extracellular environment. Here, we formally propose a N acquisition strategy used by free-living diazotrophs that accounts for high-molecular weight N acquisition through exoenzyme release by these organisms. We call this the 'LAH N-acquisition strategy' for the preferred order of N pools used once inorganic soil N is limiting: (1) low-molecular weight organic N, (2) atmospheric N and (3) high-molecular weight organic N. In this framework, free-living diazotrophs primarily use biological N fixation (BNF) as a short-term N acquisition strategy to offset the cellular N lost in exoenzyme excretion as low-molecular weight N becomes limiting. By accounting for exoenzyme release by free-living diazotrophs within a cost-benefit framework, investigation of the LAH N acquisition strategy will contribute to a process-level understanding of BNF in soil environments.

Streptomyces thermoautotrophicus does not fix nitrogen.

Streptomyces thermoautotrophicus UBT1 has been described as a moderately thermophilic chemolithoautotroph with a novel nitrogenase enzyme that is oxygen-insensitive. We have cultured the UBT1 strain, and have isolated two new strains (H1 and P1-2) of very similar phenotypic and genetic characters. These strains show minimal growth on ammonium-free media, and fail to incorporate isotopically labeled N2 gas into biomass in multiple independent assays. The sdn genes previously published as the putative nitrogenase of S. thermoautotrophicus have little similarity to anything found in draft genome sequences, published here, for strains H1 and UBT1, but share >99% nucleotide identity with genes from Hydrogenibacillus schlegelii, a draft genome for which is also presented here. H. schlegelii similarly lacks nitrogenase genes and is a non-diazotroph. We propose reclassification of the species containing strains UBT1, H1, and P1-2 as a non-Streptomycete, non-diazotrophic, facultative chemolithoautotroph and conclude that the existence of the previously proposed oxygen-tolerant nitrogenase is extremely unlikely.