pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing

Hu, Hang‐Wei; Zhang, Limei; Dai, Yu; Di, Hongjie

doi:10.1007/s11368-013-0726-y

Cited by 211 publications

(126 citation statements)

References 53 publications

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“…3). On the other hand, numerous studies indicated that AOA plays a more dominant role in mediating nitrification in acid soils, with comprehensive evidence provided by the 13 CO 2 -DNA-SIP and 454 bar-coded pyrosequencing techniques (Zhang et al 2012;Hu et al 2013). In this study, a higher abundance of AOA than AOB was only found in W-FL 2 soil with the lowest pH of 5.49 among the investigated soils.…”

Section: Discussion Dmpp Inhibits Nitrification Through Impairing Thementioning

confidence: 45%

“…Thirdly, the possibility of heterotrophic growth has been suggested for AOA (Tourna et al 2011), such as group I.1c, well known as a major lineage of AOA (Lehtovirta et al 2009). The potential of heterotrophic nitrification was further suggested by Hu et al (2013), who found that the group I.1c abundance had a significant positive correlation with soil organic C. Therefore, DMPP could inhibit nitrification by inhibiting AOB growth, and the inefficiency of DMPP on AOA-mediated nitrification could be caused by the different enzyme systems and the mixotrophic growth of AOA.…”

Section: Discussion Dmpp Inhibits Nitrification Through Impairing Thementioning

confidence: 95%

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Effects of 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and the abundance and community composition of soil ammonia oxidizers in three land uses

Shi

et al. 2016

Biol Fertil Soils

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The application of the nitrification inhibitor, 3,4-dimethylpyrazole-phosphate (DMPP), is considered as an effective strategy to mitigate agricultural nitrogen loss. However, the inhibitory effect of DMPP on nitrification is variable and the importance of the soil microbial community composition to the variability is poorly understood. In this study, nine soils were collected across three land uses to investigate the impact of DMPP on nitrification and associated dynamics of ammonia oxidizers in a 28-day microcosm incubation. The results showed that the efficacy of DMPP at inhibiting net nitrification rates varied highly from no effect to 63.6 % during the first week of incubation. The abundance of ammonia-oxidizing bacteria (AOB), rather than ammoniaoxidizing archaea (AOA), was significantly correlated with nitrate concentrations across three land uses and significantly inhibited by DMPP addition. DMPP had higher efficacy in neutral and alkaline wheat and vegetable soils, compared with pasture soils. Canonical correspondence analysis suggested that soil pH was the most influential factor explaining the community composition of AOB and AOA in the collected soils. However, neither ammonium nitrate nor DMPP addition had a significant effect on the community composition of AOB or AOA during the incubation indicated by non-metric multidimensional scaling ordination. Taken together, our findings indicated that DMPP slowed nitrification by inhibiting the growth of AOB, and DMPP application affected the abundance of AOB more than the ammonia oxidizer community composition.

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Section: Discussion Dmpp Inhibits Nitrification Through Impairing Thementioning

confidence: 45%

Section: Discussion Dmpp Inhibits Nitrification Through Impairing Thementioning

confidence: 95%

Effects of 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and the abundance and community composition of soil ammonia oxidizers in three land uses

Shi

et al. 2016

Biol Fertil Soils

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“…As the most important feature of soil, pH affected soil microbes not only by conditioning enzymes activity but also by constraining the availability of nutrients through determining the ionization equilibrium in soil. For instance, pH determined the community composition and biogeography of ammonia oxidizers by affecting ionization equilibrium of nitrate and ammonia in soils [17]. And pH-driven diversity patterns were observed horizontally [6] as well as along the elevational gradient [38].…”

Section: Altitudinal Distribution Patterns Of Soil Microorganisms Onmentioning

confidence: 99%

“…In fact, both bacteria and archaea have been found to be remarkably abundant and functionally important in terrestrial ecosystems, and could contribute differently to ecosystem functioning and biogeochemical cycling [17]. Archaea and bacteria highly differ in their metabolic characteristics and genetic features [18], indicating that these two prokaryotic taxa may respond differently to environmental factors.…”

Section: Introductionmentioning

confidence: 99%

Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau

et al. 2014

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Unraveling the distribution patterns of plants and animals along the elevational gradients has been attracting growing scientific interests of ecologists, whether the microbial communities exhibit similar elevational patterns, however, remains largely less documented. Here, we investigate the biogeographic distribution of soil archaeal and bacterial communities across three vertical climate zones (3,106-4,479 m.a.s.l.) in Mt. Shegyla on the Tibetan Plateau, by combining quantitative PCR and high-throughput barcoded pyrosequencing approaches. Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation. Acidobacteria dominated in the bacterial communities, Marine benthic group A dominated in the archaeal communities, and the relative abundance of both taxa changed significantly with elevation. At the taxonomic levels of domain, phylum, and class, more bacterial taxa than archaeal exhibited declining trend in diversity along the increasing elevational gradient, as revealed by Shannon and Faith's phylogenetic diversity indices. Unweighted UniFrac distance clustering showed that the bacterial communities from the mountainous temperate zone clustered together, whereas those from the subalpine cool temperate zone clustered together. However, the partitioning effect of elevational zones on the archaeal community was much weaker compared to that on bacteria. Redundancy analysis revealed that soil geochemical factors explained 58.3 % of the bacterial community variance and 75.4 % of the archaeal community variance. Taken together, we provide evidence that soil bacteria exhibited more apparent elevational zonation feature and decreased diversity pattern than archaea with increasing elevation, and distribution patterns of soil microbes are strongly regulated by soil properties along elevational gradient in this plateau montane ecosystem.

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“…Advances in sequencing technology are expanding our view of the microbial communities in unprecedented ways. New highthroughput pyrosequencing methods are increasing dramatically the number of sequences, allowing deeper coverage and improving our statistical power as well (Wang et al 2012;Hu et al 2013). A combination of more advanced methods may provide a comprehensive and complementary view in understanding of the marine sediment bacteria community.…”

Section: Bacterial Taxonomic Diversity In Jiaozhou Bay Sedimentsmentioning

confidence: 99%

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Liu

et al. 2014

J Soils Sediments

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Purpose Although coastal marine sediments harbor diverse bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking in typical environments along the China coast. We studied the diversity and composition of bacterial community in the sediment of Jiaozhou Bay and characterized their spatiotemporal patterns, aiming to analyze the effects of geographic heterogeneity, seasonal difference, anthropogenic activity, and eutrophication gradient on the bacterial ecology. Materials and methods Sixteen full-length bacterial 16S rRNA gene clone libraries were constructed from the sediment bacteria at four stations (A5, B2, D1, and D7) of Jiaozhou Bay over four seasons (February, May, August, and November). The bacterial diversity and community structure variation were analyzed. Results and discussion A total of 1088 16S rRNA gene sequences and 746 distinct operational taxonomic units (OTUs) (at 97 % sequence similarity level) were retrieved from the 16 clone libraries. Libraries of each sample revealed a high diversity, and a total of 17 bacterial phyla were identified.Bacteria lineages Proteobacteria (mostly γ-Proteobacteria and δ-Proteobacteria), Actinobacteria, Bacteroidetes, and Planctomycetes, which are commonly found in marine sediments, were the dominant divisions in our samples. Meanwhile, some uncommon phyla, such as Deinococcus-Thermus and Lentisphaerae, were also detected. Distinct spatial patterns and noticeable seasonal variations of bacteria community were observed, indicating that environmental heterogeneity in spatial variation other than in temporal variation may be more important in determining the bacterial communities. Most of the abundant OTUs were related to sequences retrieved from the heavy-metal-polluted environments, indicating that the Jiaozhou Bay might be influenced by pollution. Conclusions The bacterial communities in Jiaozhou Bay sediments are highly diverse. The four typical stations that we chose might experience different anthropogenic effects and eutrophication gradients, which shaped their bacterial community composition. The environment of Jiaozhou Bay may be under pressure exerted by multi-dimension anthropogenic activities. This study provided a novel insight into the bacterial community variations in Jiaozhou Bay, enriching knowledge about ecological bioindicators and mechanisms that maintain bacterial diversity and shape bacterial community composition.

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pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing

Cited by 211 publications

References 53 publications

Effects of 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and the abundance and community composition of soil ammonia oxidizers in three land uses

Effects of 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and the abundance and community composition of soil ammonia oxidizers in three land uses

Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

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