A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria

Abstract. Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China), located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon–Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs) of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g−1 soil and 0.97 × 106 to 12.78 × 106 g−1 soil, respectively. Redundancy analysis (RDA) revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial communities beneath Potentilla were different from those beneath Carex.

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Endophytic nitrogen fixation – a possible ‘hidden’ source of nitrogen for lodgepole pine trees growing at unreclaimed gravel mining sites

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz172 ◽

2019 ◽

Vol 95 (11) ◽

Cited By ~ 8

Author(s):

Kiran Preet Padda ◽

Akshit Puri ◽

Chris Chanway

Keyword(s):

Nitrogen Fixation ◽

Lodgepole Pine ◽

Nifh Gene ◽

Control Treatment ◽

Nitrogen Fixing ◽

Nitrogen Fixing Bacteria ◽

Mining Sites ◽

Greenhouse Study ◽

Gravel Mining ◽

Pine Trees

ABSTRACT Lodgepole pine (Pinus contorta var. latifolia) trees have been thriving on unreclaimed gravel mining sites in British Columbia, Canada, with tissue nitrogen-content and growth-rate unaffected by extremely low soil nitrogen-levels. This indicates that pine trees could be accessing a hidden nitrogen source to fulfill their nitrogen requirements – possibly via endophytic nitrogen-fixation. Endophytic bacteria originally isolated from native pine trees growing at gravel sites were selected (n = 14) for in vitro nitrogen-fixation assays and a year long greenhouse study to test the overall hypothesis that naturally occurring endophytic nitrogen-fixing bacteria sustain pine tree growth under nitrogen-limited conditions. Each of the 14 bacteria colonized the internal tissues of pine trees in the greenhouse study and fixed significant amounts of nitrogen from atmosphere (23%–53%) after one year as estimated through 15N isotope dilution assay. Bacterial inoculation also significantly enhanced the length (31%–64%) and biomass (100%–311%) of pine seedlings as compared to the non-inoculated control treatment. In addition, presence of the nifH gene was confirmed in all 14 bacteria. Our results support the possibility that pine trees associate with nitrogen-fixing bacteria, capable of endophytic colonization, to survive at unreclaimed gravel mining pits and this association could potentially be utilized for effective reclamation of highly disturbed sites in a sustainable manner.

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Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens

Molecules ◽

10.3390/molecules23123077 ◽

2018 ◽

Vol 23 (12) ◽

pp. 3077 ◽

Cited By ~ 5

Author(s):

Katerin Almendras ◽

Jaime García ◽

Margarita Carú ◽

Julieta Orlando

Keyword(s):

Bacterial Communities ◽

Fragment Length Polymorphism ◽

Multivariate Analyses ◽

Nifh Gene ◽

Shannon Index ◽

Nitrogen Fixing ◽

Nitrogen Fixing Bacteria ◽

Symbiotic Interaction ◽

Different Types ◽

Terricolous Lichens

Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.

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Phylogenetic diversity of nitrogen-fixing bacteria and thenifHgene from mangrove rhizosphere soil

Canadian Journal of Microbiology ◽

10.1139/w2012-016 ◽

2012 ◽

Vol 58 (4) ◽

pp. 531-539 ◽

Cited By ~ 16

Author(s):

Jianyin Liu ◽

Mengjun Peng ◽

Youguo Li

Keyword(s):

Phylogenetic Trees ◽

Rhizosphere Soil ◽

Nifh Gene ◽

Soil Samples ◽

Community Diversity ◽

Nitrogen Fixing ◽

Pcr Cloning ◽

Nitrogen Fixing Bacteria ◽

Soil Dna ◽

Mangrove Ecosystems

Nine types of nitrogen-fixing bacterial strains were isolated from 3 rhizosphere soil samples taken from mangrove plants in the Dongzhaigang National Mangrove Nature Reserve of China. Most isolates belonged to Gammaproteobacteria Pseudomonas , showing that these environments constituted favorable niches for such abundant nitrogen-fixing bacteria. New members of the diazotrophs were also found. Using a soil DNA extraction and PCR-cloning-sequencing approach, 135 clones were analyzed by restriction fragment length polymorphism (RFLP) analysis, and 27 unique nifH sequence phylotypes were identified, most of which were closely related to sequences from uncultured bacteria. The diversity of nitrogen-fixing bacteria was assessed by constructing nifH phylogenetic trees from sequences of all isolates and clones in this work, together with related nifH sequences from other mangrove ecosystems in GenBank. The nifH diversity varied among soil samples, with distinct biogeochemical properties within a mangrove ecosystem. When comparing different mangrove ecosystems, the nifH gene sequences from a specific site tended to cluster as individual groups. The results provided interesting data and novel information on our understanding of diazotroph community diversity in the mangrove ecosystems.

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Effects of Cellulolytic Bacteria on Nitrogen-Fixing Bacteria, 16S rRNA, nifH Gene Abundance, and Chemical Properties of Water Hyacinth Compost

Journal of soil science and plant nutrition ◽

10.1007/s42729-020-00399-4 ◽

2021 ◽

Author(s):

Sirinapa Chungopast ◽

Preecha Yodying ◽

Mika Nomura

Keyword(s):

16S Rrna ◽

Water Hyacinth ◽

Nifh Gene ◽

Chemical Properties ◽

Nitrogen Fixing ◽

Cellulolytic Bacteria ◽

Nitrogen Fixing Bacteria ◽

Gene Abundance ◽

And Chemical Properties

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Evaluation of the diversity of nitrogen-fixing bacteria in soybean rhizosphere by nifH gene analysis

Microbiology ◽

10.1134/s0026261712050116 ◽

2012 ◽

Vol 81 (5) ◽

pp. 621-629 ◽

Cited By ~ 9

Author(s):

A. K. Kizilova ◽

L. V. Titova ◽

I. K. Kravchenko ◽

G. A. Iutinskaya

Keyword(s):

Nifh Gene ◽

Gene Analysis ◽

Nitrogen Fixing ◽

Nitrogen Fixing Bacteria

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High diversity of nitrogen-fixing bacteria in upper reaches of Heihe River, Northwestern China

Biogeosciences Discussions ◽

10.5194/bgd-10-5015-2013 ◽

2013 ◽

Vol 10 (3) ◽

pp. 5015-5039 ◽

Cited By ~ 1

Author(s):

X. S. Tai ◽

W. L. Mao ◽

G. X. Liu ◽

T. Chen ◽

W. Zhang ◽

...

Keyword(s):

Water Conservation ◽

Gene Diversity ◽

Nifh Gene ◽

Wiener Index ◽

Qilian Mountains ◽

Northwestern China ◽

Heihe River ◽

Meadow Soil ◽

Nitrogen Fixing ◽

Nitrogen Fixing Bacteria

Abstract. Vegetation plays a key role to water conservation in southern Qilian Mountains (Northwestern China), the upper reaches of Heihe River. Nitrogen-fixing bacteria are crucial for vegetation protection because they can supply plants with nitrogen source. Nevertheless, little is known about nitrogen-fixing bacteria in this region. In present study, nifH gene clone libraries were established for detecting the difference of nitrogen-fixing bacterial communities between Potentilla parvifolia shrub and Carex alrofusca meadow in the southern Qilian Mountains. All the identified nitrogen-fixing bacterial clones belonged to Proteobacteria. At the genus level, the Azospirillum sp. was only detected in shrub soil while Thiocapsa sp., Derxiasp., Ectothiorhodospira sp., Mesorhizobium sp., Klebsiella sp., Ensifer sp., Methylocella sp. and Peseudomonas sp. were just detected in meadow soil. Shannon–Wiener index of nifH gene ranged from 1.5 to 2.8 and was higher in meadow soil than shrub soil. Contrarily, the nifH gene copies and CFUs of cultured nitrogen-fixing bacteria ranged from 0.4 × 107 to 6.9 × 107 copies g−1 soil and 0.97 × 106 to 12.78 × 106 g−1 soil, respectively. Furthermore, both of them were lower in meadow soil than shrub soil. Statistical analysis revealed that diversity and copies of nifH gene mostly correlated with aboveground biomass in shrub soil. In meadow soil, nifH gene diversity was principally affected by altitude while copies did by soil available K.

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The Flora Compositions of Nitrogen-Fixing Bacteria and the Differential Expression of nifH Gene in Pennisetum giganteum z.x.lin Roots

BioMed Research International ◽

10.1155/2021/5568845 ◽

2021 ◽

Vol 2021 ◽

pp. 1-10

Author(s):

Biaosheng Lin ◽

Jiamin Liu ◽

Xue Zhang ◽

Changren Weng ◽

Zhanxi Lin

Keyword(s):

Copy Number ◽

Nifh Gene ◽

Seedling Stage ◽

Growth Stages ◽

Nitrogen Fixing ◽

Nitrogen Fixing Bacteria ◽

Relative Expression ◽

Ct Value ◽

Jointing Stage ◽

Different Growth Stages

The flora compositions of nitrogen-fixing bacteria in roots of Pennisetum giganteum z.x.lin at different growth stages and the expression and copy number of nitrogen-fixing gene nifH were studied by Illumina Miseq second-generation sequencing technology and qRT-PCR. The results showed that there were more than 40,000~50,000 effective sequences in 5 samples from the roots of P. giganteum, with Proteobacteria and Cyanobacteria as the dominant nitrogen-fixing bacteria based on the OTU species annotations for each sample and Bradyrhizobium as the core bacterial genera. The relative expression and quantitative change of nifH gene in roots of P. giganteum at different growth stages were consistent with the changes in the flora compositions of nitrogen-fixing microbia. Both revealed a changing trend with an initial increase and a sequential decrease, as well as changing order as jointing stage>maturation stage>tillering stage>seedling stage>dying stage. The relative expression and copy number of nifH gene were different in different growth stages, and the difference among groups basically reached a significant level ( p < 0.05 ). The relative expression and copy number of nifH gene at the jointing stage were the highest, and the 2-△△CT value was 4.43 folds higher than that at the seedling stage, with a copy number of 1.32 × 10 7 /g. While at the dying stage, it was the lowest, and the 2-△△CT value was 0.67 folds, with a copy number of 0.31 × 10 7 /g.

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