Evidence for the functional significance of diazotroph community structure in soil

Hsu, Shi-Fang; Buckley, Daniel H.

doi:10.1038/ismej.2008.82

Cited by 223 publications

(161 citation statements)

References 67 publications

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“…In the southern Qilian Mountains, the Shannon diversity index of the nitrogen-fixing bacteria in the shrubland soil was lower than that of the bacteria in the meadow soils. Hsu and Buckley (2009) have found that higher levels of vegetation biomass reduce nitrogen-fixing bacterial diversity, and a higher vegetation biomass was observed in the shrubland soil than in the meadow soil (Table 1).…”

Section: Discussionmentioning

confidence: 99%

“…Hamelin et al (2002) indicated that certain plants mediate favourable niches for nitrogen-fixing bacteria. 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%

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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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Section: Discussionmentioning

confidence: 99%

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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“…For example, our data showed a reduction of 24.6% and 40.7% in the signal intensities of various genes involved in nitrification and denitrification, respectively. Changes in the community structure have been shown to have functional significance for processes mediated by a narrow spectrum of organisms, such as nitrogen fixation and nitrification (Hsu and Buckley, 2009). Shifts in the microbial community of these specialists' bacteria can have strong impact on ecosystem functionality.…”

Section: Discussionmentioning

confidence: 99%

Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

et al. 2011

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The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how ‘Candidatus Liberibacter asiaticus’ (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that ‘Ca. L. asiaticus’ infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in ‘Ca. L. asiaticus’-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of ‘Ca. L. asiaticus’ infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the ‘Ca. L. asiaticus’-infected citrus rhizosphere. Our results showed that the microbial community of the ‘Ca. L. asiaticus’-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by ‘Ca. L. asiaticus’ infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability of citrus-producing agro-ecosystems.

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“…The structure of microbial communities can in turn have important implications for the rates of soil processes. For example, variation in microbial community structure in soils has been observed to influence rates of denitrification, nitrification, and nitrogen fixation [15][16][17][18][19][20]. This suggests that long-term organic management will shift microbial community composition and diversity relative to conventionally managed soils and that these changes will have qualitative and quantitative impacts on soil processes [7,9,21,22].…”

Section: Introductionmentioning

confidence: 99%

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

2013

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We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ( 13 C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 − as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.2

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Evidence for the functional significance of diazotroph community structure in soil

Cited by 223 publications

References 67 publications

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

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

Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

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