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

2012 ◽  
Vol 58 (4) ◽  
pp. 531-539 ◽  
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.

scholarly journals First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

2019 ◽  
Vol 7 (12) ◽  
pp. 585 ◽  
Author(s):  
Witoon Purahong ◽  
Dolaya Sadubsarn ◽  
Benjawan Tanunchai ◽  
Sara Fareed Mohamed Wahdan ◽  
Chakriya Sansupa ◽  
...  
Keyword(s):  
Community Composition ◽  
Rhizosphere Soil ◽  
Plant Root ◽  
Nifh Gene ◽  
Nitrogen Fixing ◽  
Ecological Functions ◽  
Rhizophora Stylosa ◽  
Bacterial Phyla ◽  
Mangrove Tree ◽  
Mangrove Ecosystems

Mangrove forest trees play important ecological functions at the interface between terrestrial and marine ecosystems. However, despite playing crucial roles in plant health and productivity, there is little information on microbiomes of the tree species in mangrove ecosystems. Thus, in this study we aimed to characterize the microbiome in soil (rhizosphere) and plant (root, stem, and leaf endosphere) compartments of the widely distributed mangrove tree Rhizophora stylosa. Surprisingly, bacterial operational taxonomic units (OTUs) were only confidently detected in rhizosphere soil, while fungal OTUs were detected in all soil and plant compartments. The major detected bacterial phyla were affiliated to Proteobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Several nitrogen-fixing bacterial OTUs were detected, and the presence of nitrogen-fixing bacteria was confirmed by nifH gene based-PCR in all rhizosphere soil samples, indicating their involvement in N acquisition in the focal mangrove ecosystem. We detected taxonomically (54 families, 83 genera) and functionally diverse fungi in the R. stylosa mycobiome. Ascomycota (mainly Dothideomycetes, Eurotiomycetes, Sordariomycetes) were most diverse in the mycobiome, accounting for 86% of total detected fungal OTUs. We found significant differences in fungal taxonomic and functional community composition among the soil and plant compartments. We also detected significant differences in fungal OTU richness (p < 0.002) and community composition (p < 0.001) among plant compartments. The results provide the first information on the microbiome of rhizosphere soil to leaf compartments of mangrove trees and associated indications of ecological functions in mangrove ecosystems.

A Survey of Asymbiotic Nitrogen Fixation in the Rhizosphere of Weeds

Weed Science ◽  
1978 ◽  
Vol 26 (2) ◽  
pp. 148-150 ◽  
Author(s):  
A. R. Conklin ◽  
P. K. Biswas
Keyword(s):  
Thin Film ◽  
Nitrogen Fixation ◽  
Acetylene Reduction ◽  
Rhizosphere Soil ◽  
Soil Samples ◽  
Reduction Technique ◽  
Nitrogen Fixing ◽  
Weed Species ◽  
Nitrogen Fixing Bacteria ◽  
Asymbiotic Nitrogen Fixation

The occurrence of asymbiotic nitrogen fixing bacteria in the rhizosphere of twenty weed species has been investigated. Using the roll tube method root-rhizosphere soil samples were diluted and added to test tubes containing low N media. Tubes were flushed with nitrogen, stoppered, and rolled to form a thin film of media on the inner wall. After 7 days incubation the nitrogen fixation rates were estimated using the acetylene reduction technique. Rates ranged from 38 to 783 nmoles acetylene reduced per hour. Of twenty species tested, three showed high rhizosphere populations of asymbiotic nitrogen fixing bacteria.

scholarly journals High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

2013 ◽  
Vol 10 (8) ◽  
pp. 5589-5600 ◽  
Author(s):  
X. S. Tai ◽  
W. L. Mao ◽  
G. X. Liu ◽  
T. Chen ◽  
W. Zhang ◽  
...  
Keyword(s):  
Water Conservation ◽  
Bacterial Communities ◽  
Nifh Gene ◽  
Qilian Mountains ◽  
Northwestern China ◽  
Heihe River ◽  
Meadow Soil ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Gene Copies

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.

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

2019 ◽  
Vol 95 (11) ◽  
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.

Molecular identification of diazotroph microbial consortia in mountain soil

2010 ◽  
Vol 5 (5) ◽  
pp. 664-673 ◽  
Author(s):  
Rahela Carpa ◽  
Anca Butiuc-Keul ◽  
Cristina Dobrotă ◽  
Vasile Muntean
Keyword(s):  
Gene Diversity ◽  
Nifh Gene ◽  
Flood Plain ◽  
Soil Samples ◽  
Microbial Consortia ◽  
Nitrogen Fixing ◽  
Vegetation Zone ◽  
Vegetation Zones ◽  
Primer Sets ◽  
Nifh Genes

AbstractNitrogen fixing microbial consortia from soil samples taken from five altitudinal vegetation zones (alpine, subalpine, coniferous, beech, Maleia flood plain) of Parâng Massif, Romania, were isolated and identified. Molecular characterisation of nitrogen fixing consortia was carried out by PCR and nested PCR with 7 primer sets specific to nifH genes. All nifH genes are specific to nitrogen fixation and are found within phylogenetically related organisms which have the nitrogenase enzyme complex. These molecular studies allowed the assessment of nifH gene diversity within these nitrogen fixing microbial consortia from different type of soils. At high altitude, a consortium of nitrogen fixing bacteria dominated by Azotobacter chroococcum and Azospirillum brasilense was found. Clostridium, Rhizobiales, Herbaspirillum, Frankia species were also found in different rations depending on the altitudinal vegetation zone.

scholarly journals Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3077 ◽  
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.

Research on Improvement of Nitrogenase Activity of Free-Living Nitrogen-Fixing Bacteria Using DBD Plasma

2013 ◽  
Vol 671-674 ◽  
pp. 2674-2678 ◽  
Author(s):  
Yan Yun Zhu ◽  
Xiao Li Zhu ◽  
Fang She Yang
Keyword(s):  
Rhizosphere Soil ◽  
Barrier Discharge ◽  
Nitrogenase Activity ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Dbd Plasma ◽  
Nitrogen Fixing Bacteria ◽  
Free Living ◽  
Reduction Assay ◽  
Rrna Sequencing

Nitrogen-fixing bacteria were screened from the rhizosphere soil of plants in Shaanxi in China. 36 free-living nitrogen-fixing bacterial strains were isolated and their nitrogenase activity were determined by acetylene reduction assay (ARA), two strains named FLNB03 and FLNB09 with higher nitrogenase activity were isolated and identified by 16S rRNA sequencing. The datum showed that FLNB03 was similar to Acinetobacter and their similarity reached 99%, FLNB09 was similar to Agrobacterium sp. and their similarity reached 99%. Then both of them were treated using Dielectric Barrier Discharge (DBD) plasma for mutation and their mutants called FLNB03-2 and FLNB09-3 were obtained. The nitrogenase activity of FLNB03-2 was 0.61±0.10 nmol•107cfu-1•h-1, and that of FLNB09-3 was 0.40±0.05 nmol•107cfu-1•h-1, their nitrogenase activity increased by 22.00% and 14.29% than their original bacteria respectively. FLNB03-2 and FLNB09-3 might be used as microbial fertilizer.

scholarly journals Distribution and Abundance of Azotobacter in Wheat Fields of Bangladesh

1970 ◽  
Vol 24 (2) ◽  
pp. 151-153
Author(s):  
Muhammad Ali Akond ◽  
Sanzida Mubassara ◽  
M Motiur Rahman
Keyword(s):  
Nitrogen Fixation ◽  
Laboratory Condition ◽  
Rhizosphere Soil ◽  
Heterotrophic Bacteria ◽  
Soil Samples ◽  
Nitrogen Fixing ◽  
Positive Correlation ◽  
Wheat Field

The distribution and abundance of Azotobacter as well as heterotrophic bacteria in root, rhizosphere soil and non-rhizosphere soil samples from various wheat fields of four different areas under three districts were investigated in this study. The potential for nitrogen-fixation of five Azotobacter isolates was also detected. All samples tested were positive in their capacity to harbouring Azotobacter with a range of 26-100%. The population of heterotrophic bacteria ranged from 2.1 x 107 to 1.2 x 108 cfu/g sample. Ranges of total number of Azotobacter in different samples were 5.2 x 104 to 7.2 x 104 cfu/g, 17.2 x 104 to 25.5 x 104 cfu/g, and 12.4 x 104 to 16.7 x 104 cfu/g respectively for root, rhizosphere soil and non-rhizosphere soil. A positive correlation was found in Azotobacter colonization between root and rhizosphere, but it was negative in case of the population between heterotrophic bacteria and Azotobacter in rhizosphere. The highest amount of N was found to be fixed by the isolate M1 and the lowest by the isolate M4 and it was respectively 9.26 and 5.45 mg N/g substrate. In terms of the capacity to fix nitrogen in laboratory condition the five isolates of Azotobacter could be arranged as M1> M3 > M5 > M4 > M2. Keywords: Azotobacter, Wheat field, Nitrogen fixing potentialDOI: http://dx.doi.org/10.3329/bjm.v24i2.1262

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