Genomic insights into a free-living, nitrogen-fixing but non nodulating novel species of Bradyrhizobium sediminis from freshwater sediment: Three isolates with the smallest genome within the genus Bradyrhizobium

Jin, Chun-Zhi; Wu, Xuewen; Zhuo, Ya; Yang, Yizi; Li, Taihua; Jin, Feng-Jie; Lee, Hyung-Gwan; Jin, Long

doi:10.1016/j.syapm.2022.126353

Cited by 15 publications

(6 citation statements)

References 56 publications

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“…Each strain contained carbon fixation genes ranging from 45 to 67 ( Figure 3 ). Previous studies have shown that not all Bradyrhizobium are capable of photosynthesis, 30 and in our study, the genes for photosynthetic carbon fixation, such as ACAT , FBA , GAPDH , glpX-SEBP , maeB , mdh , pgk , rpiA , tktA , and TPI , were present in all strains, suggesting that despite the presence of carbon fixation genes many strains do not possess photosynthetic ability. The strain B. elkanii USDA61 has been noted to be non-photosynthetic, 31 but carbon fixation genes were present.…”

Section: Resultssupporting

confidence: 48%

Comparative genomics analysis reveals genetic characteristics and nitrogen fixation profile of Bradyrhizobium

Zhong,

Hu,

et al. 2024

iScience

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Section: Resultssupporting

confidence: 48%

Comparative genomics analysis reveals genetic characteristics and nitrogen fixation profile of Bradyrhizobium

Zhong,

Hu,

et al. 2024

iScience

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“…We successfully amplified the nifH gene in all isolated strains and the tree generated with their sequences also grouped the nine T. magnatum bradyrhizobial strains in a separate clade with high bootstrap support. The nifH genes of T. magnatum bradyrhizobia appear to be evolutionarily closer to that of the free‐living, nitrogen‐fixing and non‐nodulating B. sediminis isolated from freshwater sediment (Jin et al, 2022 ) rather than the nifH sequences of the root symbiotic and nodulating species.…”

Section: Discussionmentioning

confidence: 89%

In vitro interactions between Bradyrhizobium spp. and Tuber magnatum mycelium

Graziosi,

Puliga,

Iotti

et al. 2024

Environ Microbiol Rep

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Tuber magnatum is the most expensive truffle, but its large‐scale cultivation is still a challenge compared to other valuable Tuber species. T. magnatum mycelium has never been grown profitably until now, which has led to difficulties to studying it in vitro. This study describes beneficial interactions between T. magnatum mycelium and never before described bradyrhizobia, which allows the in vitro growth of T. magnatum mycelium. Three T. magnatum strains were co‐isolated on modified Woody Plant Medium (mWPM) with aerobic bacteria and characterised through microscopic observations. The difficulties of growing alone both partners, bacteria and T. magnatum mycelium, on mWPM demonstrated the reciprocal dependency. Three bacterial isolates for each T. magnatum strain were obtained and molecularly characterised by sequencing the 16S rRNA, glnII, recA and nifH genes. Phylogenetic analyses showed that all nine bacterial strains were distributed among five subclades included in a new monophyletic lineage belonging to the Bradyrhizobium genus within the Bradyrhizobium jicamae supergroup. The nifH genes were detected in all bacterial isolates, suggesting nitrogen‐fixing capacities. This is the first report of consistent T. magnatum mycelium growth in vitro conditions. It has important implications for the development of new technologies in white truffle cultivation and for further studies on T. magnatum biology and genetics.

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“…SJA-15 was reported to be an anaerobic bacterium capable of fermenting carbohydrates ( Speirs et al, 2019 ). Gemmatimonadaceae can decompose cellulose ( Frossard et al, 2021 ), and Bradyrhizobium primarily fixes nitrogen ( Jin et al, 2022 ). The relative abundance of SC-I-84 in DH5 was greater than that of DCK and DH2, and related studies have shown that SC-I-84 is related to the content of elemental N in the soil ( Yang et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

The effects of adding exogenous lignocellulose degrading bacteria during straw incorporation in cold regions on degradation characteristics and soil indigenous bacteria communities

et al. 2023

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Low temperature is one of the bottleneck factors that limits the degradation of straw during rice straw incorporation. Determining strategies to promote the efficient degradation of straw in cold regions has become a highly active research area. This study was to investigate the effect of rice straw incorporation by adding exogenous lignocellulose decomposition microbial consortiums at different soil depths in cold regions. The results showed that the lignocellulose was degraded the most efficiently during straw incorporation, which was in deep soil with the full addition of a high-temperature bacterial system. The composite bacterial systems changed the indigenous soil microbial community structure and diminished the effect of straw incorporation on soil pH, it also significantly increased rice yield and effectively enhanced the functional abundance of soil microorganisms. The predominant bacteria SJA-15, Gemmatimonadaceae, and Bradyrhizobium promoted straw degradation. The concentration of bacterial system and the depth of soil had significantly positive correlations on lignocellulose degradation. These results provide new insights and a theoretical basis for the changes in the soil microbial community and the application of lignocellulose-degrading composite microbial systems with straw incorporation in cold regions.

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Genomic insights into a free-living, nitrogen-fixing but non nodulating novel species of Bradyrhizobium sediminis from freshwater sediment: Three isolates with the smallest genome within the genus Bradyrhizobium

Cited by 15 publications

References 56 publications

Comparative genomics analysis reveals genetic characteristics and nitrogen fixation profile of Bradyrhizobium

Comparative genomics analysis reveals genetic characteristics and nitrogen fixation profile of Bradyrhizobium

In vitro interactions between Bradyrhizobium spp. and Tuber magnatum mycelium

The effects of adding exogenous lignocellulose degrading bacteria during straw incorporation in cold regions on degradation characteristics and soil indigenous bacteria communities

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