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.

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.

scholarly journals Changes in Nitrogen-Fixing and Ammonia-Oxidizing Bacterial Communities in Soil of a Mixed Conifer Forest after Wildfire

2005 ◽  
Vol 71 (5) ◽  
pp. 2713-2722 ◽  
Author(s):  
Chris M. Yeager ◽  
Diana E. Northup ◽  
Christy C. Grow ◽  
Susan M. Barns ◽  
Cheryl R. Kuske
Keyword(s):  
Bacterial Communities ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Fixing ◽  
Conifer Forest ◽  
Mixed Conifer ◽  
Mixed Conifer Forest ◽  
In Fire ◽  
Sequence Types

ABSTRACT This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH3-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.

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.

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 Nitrogen Fixing and Phosphate Mineralizing Bacterial Communities in Sweet Potato Rhizosphere Show a Genotype-Dependent Distribution

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 231 ◽  
Author(s):  
Joana Montezano Marques ◽  
Jackeline Rossetti Mateus ◽  
Thais Freitas da Silva ◽  
Camila Rattes de Almeida Couto ◽  
Arie Fitzgerald Blank ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Bacterial Community ◽  
Sweet Potato ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Permutation Test ◽  
Nifh Gene ◽  
Gene Copy ◽  
Nitrogen Fixing ◽  
Phosphate Mineralization

We hypothesize that sweet potato genotypes can influence the bacterial communities related to phosphate mineralization and nitrogen fixation in the rhizosphere. Tuberous roots of field-grown sweet potato from genotypes IPB-149, IPB-052, and IPB-137 were sampled three and six months after planting. The total community DNA was extracted from the rhizosphere and analyzed by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR), based on the alkaline phosphatase coding gene (alp gene) and on the nitrogenase coding gene (nifH gene). The cluster analysis based on DGGE showed that plant age slightly influenced the bacterial community related to phosphate mineralization in the rhizosphere of IPB-137, although it did not affect the bacterial community related to nitrogen fixation. The statistical analysis of DGGE fingerprints (Permutation test, p ≤ 0.05) showed that nitrogen-fixing bacterial community of IPB-052 statistically differed from genotypes IPB-149 and IPB-137 after six months of planting. The bacterial community of IPB-137 rhizosphere analyzed by alp gene also showed significant differences when compared to IPB-149 in both sampling times (p ≤ 0.05). In addition, alp gene copy numbers significantly increased in abundance in the rhizosphere of IPB-137 after six months of planting. Therefore, plant genotype should be considered in the biofertilization of sweet potato.

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

Microbiology ◽  
2012 ◽  
Vol 81 (5) ◽  
pp. 621-629 ◽  
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

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

2013 ◽  
Vol 10 (3) ◽  
pp. 5015-5039 ◽  
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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