The abundance of nitrogen cycle genes amoA and nifH depends on land-uses and soil types in South-Eastern Australia

Hayden, Helen L.; Drake, Judy; Imhof, Mark; Oxley, Alan; Norng, S.; Mele, Pauline M.

doi:10.1016/j.soilbio.2010.06.015

Cited by 136 publications

(73 citation statements)

References 35 publications

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“…This is supported by the results of Yeager et al ( 2005 ), which showed few significant differences between nitrogenfixing and ammoniaoxidizing bacterial profiles from moderately and severelyburned mixed conifer forest soils. We did note significant correlations between pH and C:N ratio and Nfixing communities, which was consistent with previous reports that changes in C:N ratio (Deslippe et al 2005; Coelho et al 2008 ) and pH (Hayden et al 2010 ) can influence soil nifH profiles.…”

Section: Discussionsupporting

confidence: 93%

Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests

et al. 2014

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Following a pine beetle epidemic in British Columbia, Canada, we investigated the effect of fire severity on rhizosphere soil chemistry and ectomycorrhizal fungi (ECM) and associated denitrifying and nitrogen (N)fixing bacteria in the root systems of regenerating lodgepole pine seedlings at two site types (wet and dry) and three fire severities (low, moderate, and high). The site type was found to have a much larger impact on all measurements than fire severity. Wet and dry sites differed significantly for almost all soil properties measured, with higher values identified from wet types, except for pH and percent sand that were greater on dry sites. Fire severity caused few changes in soil chemical status. Generally, bacterial communities differed little, whereas ECM morphotype analysis revealed ectomycorrhizal diversity was lower on dry sites, with a corresponding division in community structure between wet and dry sites. Molecular profiling of the fungal ITS region confirmed these results, with a clear difference in community structure seen between wet and dry sites. The ability of ECM fungi to colonize seedlings growing in both wet and dry soils may positively contribute to subsequent regeneration. We conclude that despite consecutive landscape disturbances (mountain pine beetle infestation followed by wildfire), the "signature" of moisture on chemistry and ECM community structure remained pronounced. Electronic supplementary materialThe online version of this article

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Section: Discussionsupporting

confidence: 93%

Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests

et al. 2014

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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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“…Differences between sites may be associated with variations in geomorphic zones as shown by Hayden et al, (2010) who demonstrated that differences in abundance of amoA were more related to soil chemistry and microbial biomass carbon.…”

Section: Discussionmentioning

confidence: 99%

“…Surface waters containing high amounts of nitrate can become eutrophicated and suffer a significant loss in biodiversity (Singh and Verma 2007). In Australian agricultural soils, the abundance of genes associated with nitrogen fixation and ammonium oxidation have been estimated before through realtime polymerase chain reaction (PCR) according to land-use and soil type (Bissett, et al 2014, Cavagnaro, et al 2008, Hayden, et al 2010. Previous studies have suggested that the nitrogen cycle can be affected by tillage due to soil aeration and a subsequent quick response of microbial communities to this disturbance (Cavagnaro, et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Effect of strategic tillage in soil microbial communities in Vertisols from Queensland, Australia

Florez¹,

Andrea²

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In the last decades, tendency amongst growers in Australia has been towards practising minimum disturbance for soil preparation and complete stubble retention.Consequently, farmers have reduced labour, energy and machinery costs, and improved soil quality and crop profitability. However, there is scepticism around such practices given the build-up of herbicide resistant weeds, stubble-borne diseases and nutrient stratification. To address these issues, occasional tillage (or strategic tillage, ST) has been applied to fields under long-term no-tillage (NT). ST aims to overcome constraints arisen by no-tillage and takes into account soil water content, tools for deployment and timing of application. Soil microbial communities play an important role in soil function and are often used as early indicators of soil disturbance due to their prompt response to environmental changes. I compared biological indicators of soil health including microbial biomass, microbial enzymatic activity, metabolic diversity, genetic structure; diversity of bacterial, archaeal and fungal communities, and abundances of nitrogen cycle genes to assess the impact of ST on long-term NT. In Hermitage, ST was applied to soils under NT and conventional tillage (CT), in which stubble was retained. Soil samples were collected 3.5 and 13 months after ST operations. While it is clear that there would be immediate effects on soil biology, I chose these time points to allow a reasonable amount of time to evaluate whether microbial communities can restore and provide the ecosystem function needed for crop performance. I observed differences between NT and CT in enzymatic activity after 3.5 months, possibly attributed to physico-chemical properties and land management. However, one year after tillage deployment there were no changes in the biological indicators, microbial structure and diversity that were measured after ST.High throughput 16S rRNA gene amplicon sequencing targeting bacteria and archaea revealed 69 operational taxonomic units (OTU's) at relative abundances higher than 1%. The most abundant phyla were Crenarchaeota (25%) and Acidobacteria (28.1%).Fungal communities profiled by internal transcribed region (ITS) amplicon high throughput sequencing showed no significant differences between treatments. The 3 most abundant phylum was Ascomycota (60%) with a relative abundance higher than Nevertheless, assessment of abundance of nitrogen cycle genes for the three sites showed a significant impact of ST management. In Hermitage and Jimbour, nitrogen fixers tended to be enriched after ST application probably due to organic residue incorporation, previously shown to influence the abundance of these organisms. In contrast, the abundance of nitrogen fixing communities tended to decrease on surface soils in Biloela. The decrease may be related to inorganic forms of N affecting the nitrogenase activity in diazotrophic communities. Ammonia oxidizing bacteria (AOB) had an increase in abundance after ST application in Hermitage for soils under NT...

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The abundance of nitrogen cycle genes amoA and nifH depends on land-uses and soil types in South-Eastern Australia

Cited by 136 publications

References 35 publications

Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests

Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests

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

Effect of strategic tillage in soil microbial communities in Vertisols from Queensland, Australia

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