Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

Wessén, Ella; Söderström, Mats; Stenberg, Maria; Bru, David; Hellman, Maria; Welsh, Allana; Thomsen, Frida; Klemedtson, L.; Philippot, Laurent; Hallin, Sara

doi:10.1038/ismej.2010.206

Cited by 132 publications

(117 citation statements)

References 60 publications

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“…The ratio of AOA to AOB was larger than 1 at about 75% of the sites, and the greatest value of this ratio was primarily observed in the Hengshui and Xingtai reaches. In the natural environment, AOA are generally more abundant than AOB (Wessén et al, 2011;Leininger et al, 2006;Wu et al, 2010), and the abundance of AOA (Mincer et al, 2007) and AOB (Stehr et al, 1995) in the water column is commonly in the range of 10 2 to 10 5 gene copies/mL, which is consistent with the results of the present study.…”

Section: Physicochemical Characteristicssupporting

confidence: 92%

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Chao

Shan

Zhang

et al. 2014

Journal of Environmental Sciences

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a b s t r a c tThe Haihe River is characterized by high ammonia pollution. Therefore, it is necessary to determine how environmental factors, such as heavy metals in the river limit the spatial distribution of ammonia-oxidizing microorganisms. In this study, the relationships between five heavy metals and ammonia-oxidizing microorganisms were studied. The results showed that under high ammonia, low oxygen and high concentrations of suspended particles, ammonia-oxidizing bacteria (AOB) ranged from 10 1.3 to 10 4.8 gene copies/mL and ammonia-oxidizing archaea (AOA) ranged from 10 2.7 to 10 4.9 gene copies/mL. The average metal concentrations in water were 23.57 (Cr), 21.58 (Ni), 65.09 (Cu), 622.03 (Zn) and 10.16 (As) μg/L, with those of Zn, Cu and Cr being higher than the US EPA criteria. Scatter plots of microbial abundance and metals indicated that both AOA and AOB were limited by heavy metals, but in different ways. As had an inhibitory effect on AOB, while Ni and Zn promoted AOA, and the other metals investigated showed no significant correlation with microbial abundance. Overall, our results indicated that the effects of heavy metals on ammonia-oxidizing microorganisms in water are complex, and that the final effect is determined by the physiological role of each element in the microorganisms, as well as environmental conditions such as complexation of organic matter, not simply the total metal concentration.

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Section: Physicochemical Characteristicssupporting

confidence: 92%

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Chao

Shan

Zhang

et al. 2014

Journal of Environmental Sciences

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“…Subsequently, the spatial variation of pollutants and other soil chemical parameters may regulate the spatial patterns of microbial communities (Tö rneman et al, 2008;Bengtsson et al, 2010). Association between spatial patterns of environmental factors and the distribution of microbial taxa as well as their activities can be elucidated via geostatistical modelling (Philippot et al, 2009;Bru et al, 2010;Enwall et al, 2010;Wessén et al, 2011). Furthermore, the choice of taxonomic level to address the microbial community responses is a crucial issue.…”

Section: Introductionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

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“…Additionally, the distribution patterns of AOB and AOA as a function of soil pH have been demonstrated at different land scales using molecular methods and bioinformatics analysis (Nicol et al 2008;Gubry-Rangin et al 2011;He et al 2012;Hu et al 2013). However, the effects of other factors, such as soil structure, on the dynamics of AOB and AOA as well as their nitrification activity are little understood (Wessen et al 2011;Yao et al 2013). Girvan et al mentioned that soil type was the primary determinant of the composition of the total and active bacterial communities in arable soils (Girvan et al 2003).…”

Section: Introductionmentioning

confidence: 99%

“…Among these factors, soil type was identified as the key driver shaping ammonia oxidizer community structure and abundance in soils and sediments (Chen et al 2010;Shen et al 2014). Soil texture varying in clay or sand content could be one of the reasons explaining the fluctuation in the size and structure of AOB and AOA, as well as their function, measured in different soil types (Wessen et al 2011;Silva et al 2012). Comparative analysis for nitrification capacity of different agricultural soils is therefore both useful and necessary for assessing N use efficiency and by extension, N management practices.…”

Section: Introductionmentioning

confidence: 99%

Contrasting response of nitrification capacity in three agricultural soils to N addition during short-term incubation

Shen

Zhang

2014

J Soils Sediments

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Purpose Human disturbance is a major culprit driving imbalances in the biological transformation of nitrogen from the nonreactive to the reactive pool and is therefore one of the greatest concerns for nitrogen (N) cycling. The objective of this study was to compare potential nitrification rates and the abundance of ammonia oxidizers responsible for nitrification, with the amendment of external N in different agricultural soils. The abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) at the end of incubation in the soil microcosms was determined using the real-time PCR.Results and discussion There was a significant decrease in ammonium concentration in the QY soil from the highest to the lowest N-loading treatments, while no significant difference in ammonium concentrations was detected among the different N-loading treatments for the SY and FQ soils. A significantly higher potential nitrification rate (PNR) was observed in the FQ soil while lowest PNR was found in the QY soil. Quantitative PCR analysis of AOB amoA genes demonstrated that AOB abundance was significantly higher in the high N-loading treatments than in the control for the QY soil only, while no significant difference among treatments in the SY and FQ soils. A significant positive correlation between PNR and AOB amoA abundance, however, was found for the SY and FQ soils, but not for the QY soil. Little difference in AOA amoA abundance between different Nloading treatments was observed for all the soils. Conclusions This study suggested that ammonia oxidation capacity in the FQ and SY soils was higher than those in the QY soil with the addition of ammonium fertilizer for a shortterm. These findings indicated that understanding the differential responses of biological nitrification to varying input levels of ammonium fertilizer is important for maximizing N use efficiency and thereby improving agricultural fertilization management.

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Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

Cited by 132 publications

References 60 publications

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Contrasting response of nitrification capacity in three agricultural soils to N addition during short-term incubation

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