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Ecosystem-specific selection of microbial ammonia oxidizers in an acid soil  [PDF]
M. Saiful Alam,G. Ren,L. Lu,Y. Zheng
Biogeosciences Discussions , 2013, DOI: 10.5194/bgd-10-1717-2013
Abstract: The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the availability of ammonia substrate and the supply of oxygen. The interactions and evolutions of AOA and AOB communities along ecological gradients of substrate availability in complex environment have been much debated, but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB in response to long-term field fertilization and flooding management in an acid soil. Real-time quantitative PCR of amoA genes demonstrated that the abundance of AOA was significantly stimulated after conversion of upland to paddy soils, while slight decline of AOB populations was observed. DGGE fingerprints of amoA genes further revealed remarkable changes in community compositions of AOA in paddy soil when compared to upland soil. Sequencing analysis revealed that upland soil was dominated by AOA within the soil group 1.1b lineage, while the marine group 1.1a lineage predominated AOA communities in paddy soils. Irrespective of upland and paddy soils, long-term field fertilizations led to higher abundance of amoA genes of AOA and AOB than control treatment that received no fertilization, whereas archaeal amoA gene abundances outnumbered their bacterial counterpart in all samples. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster 3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization treatments. The results of this study suggest that the marine group 1.1a AOA could be better adapted to low-oxygen environment than AOA ecotypes of the soil group 1.1b lineage, and implicate that long-term flooding as the dominant selective force driving the community diversification of AOA populations in the acid soil tested.
Spatial distribution of archaeal and bacterial ammonia oxidizers in the littoral buffer zone of a nitrogen-rich lake
Yu Wang,Guibing Zhu,Lei Ye,Xiaojuan Feng,Huub J M Op den Camp,Chengqing Yin,
Yu Wang
,Guibing Zhu,Lei Ye,Xiaojuan Feng,Huub J. M. Op den Camp,Chengqing Yin

环境科学学报(英文版) , 2012,
Abstract: The spatial distribution and diversity of archaeal and bacterial ammonia oxidizers (AOA and AOB) were evaluated targeting amoA genes in the gradient of a littoral buffer zone which has been identified as a hot spot for N cycling. Here we found high spatial heterogeneity in the nitrification rate and abundance of ammonia oxidizers in the five sampling sites. The bacterial amoA gene was numerically dominant in most of the surface soil but decreased dramatically in deep layers. Higher nitrification potentials were detected in two sites near the land/water interface at 4.4-6.1 μg NO2--N/(g dry weight soil·hr), while only 1.0-1.7 μg NO2--N/(g dry weight soil·hr) was measured at other sites. The potential nitrification rates were proportional to the amoA gene abundance for AOB, but with no significant correlation with AOA. The NH4 + concentration was the most determinative parameter for the abundance of AOB and potential nitrification rates in this study. Higher richness in the surface layer was found in the analysis of biodiversity. Phylogenetic analysis revealed that most of the bacterial amoA sequences in surface soil were affiliated with the genus of Nitrosopira while the archaeal sequences were almost equally affiliated with Candidatus ‘Nitrososphaera gargensis’ and Candidatus ‘Nitrosocaldus yellowstonii’. The spatial distribution of AOA and AOB indicated that bacteria may play a more important role in nitrification in the littoral buffer zone of a N-rich lake.
Habitat-Associated Phylogenetic Community Patterns of Microbial Ammonia Oxidizers  [PDF]
Antoni Fernàndez-Guerra, Emilio O. Casamayor
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047330
Abstract: Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo) is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene). In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic) for most of the habitats indicated γAOA > γAOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing microorganisms. The emerged picture of AOB and AOA distribution in different habitats provides a new view to understand the ecophysiology of ammonia oxidizers on Earth.
Different Land Use Intensities in Grassland Ecosystems Drive Ecology of Microbial Communities Involved in Nitrogen Turnover in Soil  [PDF]
Annabel Meyer, Andreas Focks, Viviane Radl, Daniel Keil, Gerhard Welzl, Ingo Sch?ning, Steffen Boch, Sven Marhan, Ellen Kandeler, Michael Schloter
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073536
Abstract: Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.
Priming of Soil Carbon Decomposition in Two Inner Mongolia Grassland Soils following Sheep Dung Addition: A Study Using 13C Natural Abundance Approach  [PDF]
Xiuzhi Ma, Per Ambus, Shiping Wang, Yanfen Wang, Chengjie Wang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0078578
Abstract: To investigate the effect of sheep dung on soil carbon (C) sequestration, a 152 days incubation experiment was conducted with soils from two different Inner Mongolian grasslands, i.e. a Leymus chinensis dominated grassland representing the climax community (2.1% organic matter content) and a heavily degraded Artemisia frigida dominated community (1.3% organic matter content). Dung was collected from sheep either fed on L. chinensis (C3 plant with δ13C = ?26.8‰; dung δ13C = ?26.2‰) or Cleistogenes squarrosa (C4 plant with δ13C = ?14.6‰; dung δ13C = ?15.7‰). Fresh C3 and C4 sheep dung was mixed with the two grassland soils and incubated under controlled conditions for analysis of 13C-CO2 emissions. Soil samples were taken at days 17, 43, 86, 127 and 152 after sheep dung addition to detect the δ13C signal in soil and dung components. Analysis revealed that 16.9% and 16.6% of the sheep dung C had decomposed, of which 3.5% and 2.8% was sequestrated in the soils of L. chinensis and A. frigida grasslands, respectively, while the remaining decomposed sheep dung was emitted as CO2. The cumulative amounts of C respired from dung treated soils during 152 days were 7–8 times higher than in the un-amended controls. In both grassland soils, ca. 60% of the evolved CO2 originated from the decomposing sheep dung and 40% from the native soil C. Priming effects of soil C decomposition were observed in both soils, i.e. 1.4 g and 1.6 g additional soil C kg?1 dry soil had been emitted as CO2 for the L. chinensis and A. frigida soils, respectively. Hence, the net C losses from L. chinensis and A. frigida soils were 0.6 g and 0.9 g C kg?1 soil, which was 2.6% and 7.0% of the total C in L. chinensis and A. frigida grasslands soils, respectively. Our results suggest that grazing of degraded Inner Mongolian pastures may cause a net soil C loss due to the positive priming effect, thereby accelerating soil deterioration.
Effects of mineral fertilizer addition on leaf functional traits and photosynthetic characteristics of Leymus chinensis from a temperate grassland in Inner Mongolia in China

XIAO Shengsheng,DONG Yunshe,QI Yuchun,PENG Qin,HE Yating,LIU Xinchao,

环境科学学报 , 2010,
Abstract: This study explored the responses of leaf functional traits and photosynthetic characteristics of Leymus chinensis to different nitrogen (N) addition rates (0,5,10 and 20 g·m-2·a-1) in the Xilin River Basin in Inner Mongolia. In addition, the potential carbon sequestration of grassland plants exposed to increased N supply was estimated. The results showed that N addition (N-10 treatments) significantly increased the leaf area, relative chlorophyll content, leaf N concentration and net photosynthetic rates of L. chinensis. The N addition also extended the peak period of photosynthesis. With the increase of N addition rates, the transpiration rate, internal CO2 concentration gradually decreased, but instantaneous water-use efficiency and stomatal conductance increased gradually. The results indicated moderate N input would enhance CO2 sequestration through photosynthesis in semiarid temperate grassland.
Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters  [PDF]
Laura A. Sauder, Katja Engel, Jennifer C. Stearns, Andre P. Masella, Richard Pawliszyn, Josh D. Neufeld
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023281
Abstract: Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology.
Productivity responses of different functional groups to litter addition in typical grassland of Inner Mongolia

WANG Jing,ZHAO Meng-Li,Walter WILLMS,WANG Zhong-Wu,HAN Guo-Dong,
,赵萌莉,Walter WILLMS,王忠武,韩国栋

植物生态学报 , 2010,
Abstract: Aims Much research has been done on litter in forest ecosystems,but little has been done in grassland ecosys-tems,although litter plays an important role in grasslands. Our objectives were to determine how litter affects aboveground biomass and productivity of different functional groups and whether litter addition has a positive or negative effect in typical grassland. Methods We added litter to typical grassland after frost in October 2002. Then we sampled peak standing crop in August from 2003 to 2007. W...
Impacts of Future Grassland Changes on Surface Climate in Mongolia  [PDF]
Fan Zhang,Xing Li,Weimin Wang,Xinli Ke,Qingling Shi
Advances in Meteorology , 2013, DOI: 10.1155/2013/263746
Abstract: Climate change caused by land use/cover change (LUCC) is becoming a hot topic in current global change, especially the changes caused by the grassland degradation. In this paper, based on the baseline underlying surface data of 1993, the predicted underlying surface data which can be derived through overlaying the grassland degradation information to the map of baseline underlying surface, and the atmospheric forcing data of RCP 6.0 from CMIP5, climatological changes caused by future grassland changes for the years 2010–2020 and 2040–2050 with the Weather Research Forecast model (WRF) are simulated. The model-based analysis shows that future grassland degradation will significantly result in regional climate change. The grassland degradation in future could lead to an increasing trend of temperature in most areas and corresponding change range of the annual average temperature of ?0.1°C–0.4°C, and it will cause a decreasing trend of precipitation and corresponding change range of the annual average precipitation of 10?mm–50?mm. This study identifies lines of evidence for effects of future grassland degradation on regional climate in Mongolia which provides meaningful decision-making information for the development and strategy plan making in Mongolia. 1. Introduction During the last millennium, human beings have changed natural ecosystems, such as converting forest lands and grasslands into croplands, pastures, and bare soil [1]. The land use and cover changes (LUCC), in which the human activities play a dominant role, interact with the environment and have significant effects on the ecosystems at the local, regional, and global scales and consequently directly or indirectly exert great influence on the global climate changes [2–5]. Anthropogenic climate changes gradually attracted worldwide concerns in recent years. The interaction mechanisms between land surface processes and climatic conditions have been increasingly investigated and modeled. These LUCC will continue to exert impacts on the climate in the future. The conversion from one land use/cover type to another is more often than an impermanent change. Thus any impact on the climate due to this change would not be short lived; rather it would be a long term effect having lasting effects on the climate [6]. Significant global warming occurred in the twentieth century and especially in the most recent decades. Global mean surface air temperature increased with a rate of 0.07°C per decade from 1906 to 2005 [7]. It seems that the magnitude of importance of LUCC on future climate can only be
Ammonia sources and sinks in an intensively managed grassland canopy
M. David, B. Loubet, P. Cellier, M. Mattsson, J. K. Schjoerring, E. Nemitz, R. Roche, M. Riedo,M. A. Sutton
Biogeosciences (BG) & Discussions (BGD) , 2009,
Abstract: Grasslands represent canopies with a complex structure where sources and sinks of ammonia (NH3) may coexist at the plant level. Moreover, management practices such as mowing, hay production and grazing may change the composition of the sward and hence the source-sink relationship at the canopy level as well as the interaction with the atmosphere. There is therefore a need to understand the exchange of ammonia between grasslands and the atmosphere better, especially regarding the location and magnitude of sources and sinks. Fluxes of atmospheric NH3 within a grassland canopy were assessed in the field and under controlled conditions using a dynamic chamber technique (cuvette). These cuvette measurements were combined with extraction techniques to estimate the ammonium (NH4+) concentration and the pH of a given part of the plant or soil, leading to an estimated ammonia compensation point (Cp). The combination of the cuvette and the extraction techniques was used to identify the potential sources and sinks of NH3 within the different compartments of the grassland: the soil, the litter or senescent "litter leaves", and the functioning "green leaves". A set of six field experiments and six laboratory experiments were performed in which the different compartments were either added or removed from the cuvettes. The results show that the cuvette measurements agree with the extraction technique in ranking the strength of compartment sources. It suggests that in the studied grassland the green leaves were mostly a sink for NH3 with a compensation point around 0.1–0.4 μg m 3 and an NH3 flux of 6 to 7 ng m 2 s 1. Cutting of the grass did not increase the NH3 fluxes of the green leaves. The litter was found to be the largest source of NH3 in the canopy, with a Cp of up to 1000 μg m 3 NH3 and an NH3 flux up to 90 ng m 2 s 1. The litter was found to be a much smaller NH3 source when dried (Cp=160 μg m 3 and FNH3=35 ng m 2 s 1 NH3). Moreover emissions from the litter were found to vary with the relative humidity of the air. The soil was a strong source of NH3 in the period immediately after cutting (Cp=320 μg m 3 and FNH3=60 ng m 2 s 1), which was nevertheless always smaller than the litter source. The soil NH3 emissions lasted, however, for less than one day, and were not observed with sieved soil. They could not be solely explained by xylem sap flow extruding NH4+. These results indicate that future research on grassland-ammonia relationships should focus on the post-mowing period and the role of litter in interaction with meteorological conditions.
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