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

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, <i>nifH</i> gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the <i>Potentilla parvifolia</i> shrubland and the <i>Carex alrofusca</i> meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, <i>Azospirillum</i> was only detected in the shrubland soil, while <i>Thiocapsa</i>, <i>Derxia</i>, <i>Ectothiorhodospira</i>, <i>Mesorhizobium</i>, <i>Klebsiella</i>, <i>Ensifer</i>, <i>Methylocella</i> and <i>Pseudomonas</i> were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained <i>nifH</i> sequences obtained from the meadow soils, while lineage IV was mainly composed of <i>nifH</i> sequences obtained from the shrubland soils. The Shannon–Wiener index of the <i>nifH</i> 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 <i>nifH</i> 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 <i>nifH</i> gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, <i>nifH</i> 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 <i>Potentilla</i> were different from those beneath <i>Carex</i>

Linkages of Soil Nutrients and Diazotrophic Microbiome under Sugarcane-Legume Intercropping

“…The predominance of nifH OTUs related to proteobacteria and the nonappearance of nifH gene sequence related to Cyanobacteria, Firmicutes and Archaea has been also described from some previous studies [25,31,33,60,68]. Unexpectedly, there was no evidence of Gamma-proteobacterial nifH…”

“…It is a convenient marker in culture-independent studies, to provide evidence for significant N fixation in diverse environments [25,27]. To date, culture-independent methods have investigated N fixation in different habitats, including soils [16,[28][29][30][31], plant parts [30,31] and water resources [32,33]. By focusing on the sequences of the nifH genes, large numbers of sequence data have been also obtained by independent culture methods [34,35].…”

“…Moreover, plant biomass, chemical composition of the litter and root exudates may be playing the role as an intermediate for the composition of diazotrophic bacteria. Soil physicochemical factors, like pH and water holding capacity, microbial biomass carbon and nitrogen, total nitrogen, potassium, phosphorus and available phosphorus, electrical conductivity and soil nutrient availability, have also been identified as drivers of nifH gene diversity and abundance in different environments [28,[31][32][33].…”

Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes

“…By comparison, the pH values of other global soils stated that those from Antarctica region had alkaline pH (8.5–9.9) and the dominant phylum was Cyanobacteria and Proteobacteria with Geobacter as predominant genus [53]. Soils with pH close to neutral (6.7) from the Arctic tundra and scrubland soils were dominated by Rhodopseudomonas genus [54, 55], whereas those with pH higher than 7 by Methylocella [56] and Bradyrhizobium [25] for Tibetan prairie soil and Quilian meadows, respectively.…”

“…[19], Azospirillum spp. [22], Herbaspirillum lustianum [23], Cupriavidus taiwanensis —recently known as Ralstonia taiwanensis [19], Burkholderia tuberum , Burkholderia phymatum and Burkholderia cepacia [3, 22, 24], several strains of γ- Proteobacteria [25] and δ-Proteobacteria [3]. …”