Analysis of nifH gene diversity in red soil amended with manure in Jiangxi, south China

Teng, Qihui; Sun, Bo; Fu, Xinrui; Li, Shunpeng; Cui, Zhongli; Cao, Hui

doi:10.1007/s12275-008-0184-1

Cited by 24 publications

(18 citation statements)

References 37 publications

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“…However, this type of top 10 phylum variety in the bacterial community was not affected by straw returning and manure treatments (Figure 3), indicating that soil bacterial environment is a continuous process, and different fertilization measurements will have a similar effect (Mazzola and Strauss, 2013). The distribution of each phylum varied (Figure 3), which was consistent with Teng et al (2009) who suggested that adding organic manure to soil can stimulate certain bacteria species and render them the dominant species. Planctomycetes is a kind of anaerobic ammonium oxidizing bacteria, which can be used to participate in the soil carbon and nitrogen cycle (Koji and Kamagata, 2014).…”

Section: Discussionsupporting

confidence: 75%

Changes in bacterial community of soil induced by long-term straw returning

Chen

Liu

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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Straw returning is an effective way to improve soil quality. Whether the bacterial community development has been changed by long-term straw returning in non-calcareous fluroacquic soil is not clear. In this study, the following five treatments were administered: soil without fertilizer (CK); wheat and corn straw returning (WC); wheat straw returning with 276 kg N ha −1 yr −1 (WN); manure, 60,000 kg ha −1 pig manure compost (M) and wheat and corn straw returning with 276 kg N ha −1 yr −1 (WCN). The high-throughput 16S rRNA sequencing technology was used to evaluate the bacterial communities. The results showed that the community was composed mostly of two dominant groups (Proteobacteria and Acidobacteria). Bacterial diversity increased after the application of straw and manure. Principal component analyses revealed that the soil bacterial community differed significantly between treatments. The WCN treatment showed relatively higher total soil N, available P, available K, and organic carbon and invertase, urease, cellulase activities and yield than the WC treatment. Our results suggested that application of N fertilizer to straw returning soil had significantly higher soil fertility and enzyme activity than straw returning alone, which resulted in a different bacterial community composition, Stenotrophomonas, Pseudoxanthomonas, and Acinetobacter which were the dominant genera in the WC treatment while Candidatus, Koribacter and Granulicella were the dominant genera in the WCN treatment. To summarize, wheat and maize straw returning with N fertilizer would be the optimum proposal for improving soil quality and yield in the future in non-calcareous fluro-acquicwheat and maize cultivated soils in the North China Plain in China.

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Section: Discussionsupporting

confidence: 75%

Changes in bacterial community of soil induced by long-term straw returning

Chen

Liu

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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“…Thus, high-throughput deep sequencing approaches are essential to improve our knowledge of the diversity of these functional genes. In the present study, using barcoded 454-pyrosequencing approach, we found high diversity (ranging from ∼3100 to ∼11200 unique nucleotide sequences) of nifH , archaeal amoA , bacterial amoA and nosZ genes in the soil ecosystem, which far surpasses the diversity of the N-cycling genes observed in previous studies [54], [55], [56], [57], [58], [59], [60], [61]. The rarefaction curves of these genes were close to saturation after sequencing ∼1000 for each sample, indicating that such a sequencing effort is sufficient to elucidate the diversity and structure of the complex soil N-cycling communities.…”

Section: Discussioncontrasting

confidence: 57%

Changes in N-Transforming Archaea and Bacteria in Soil during the Establishment of Bioenergy Crops

2011

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Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.

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“…Niederberger et al (2012) demonstrated that temperature, which is closely correlated to altitude, may be a driving factor in the composition of the nitrogen-fixing bacterial community in Antarctic soil. Soil K concentration has also been identified as a driver of the nifH gene in several environments (Teng et al, 2009;Hayden et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

“…Plant-specific differences in the nitrogen-fixing bacterial community may be related to plant species, biomass, the chemical composition of litter and root exudates (Shaffer et al, 2000;Bürgmann et al, 2005;Hsu and Buckley, 2009;Knelman et al, 2012). Soil physicochemical factors, such as pH and water content (Zhan and Sun, 2011), microbial biomass carbon and microbial biomass nitrogen (Hayden et al, 2010), total nitrogen and total potassium (Teng et al, 2009;Hayden et al, 2010), total phosphorus and reactive phosphorus (Reed et al, 2010;Zou et al, 2011;Romero et al, 2012), electrical conductivity (Hayden et al, 2010;Hamilton et al, 2011) and nutrient level (Jasrotia and Ogram, 2008;Zhan and Sun, 2012), have also been identified as drivers of nifH gene diversity and abundance in many environments.…”

Section: S Tai Et Al: High Diversity Of Nitrogen-fixing Bacteriamentioning

confidence: 99%

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

et al. 2013

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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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Analysis of nifH gene diversity in red soil amended with manure in Jiangxi, south China

Cited by 24 publications

References 37 publications

Changes in bacterial community of soil induced by long-term straw returning

Changes in bacterial community of soil induced by long-term straw returning

Changes in N-Transforming Archaea and Bacteria in Soil during the Establishment of Bioenergy Crops

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

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