Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [ 13 C]bicarbonate assimilation assay showed stoichiometric incorporation of 13 C into Archaeaspecific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to "Candidatus Nitrosopumilus maritimus" revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N 2 O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated "Candidatus Nitrosoarchaeum koreensis."
This paper presents an efficient technique for performing a spatially inhomogeneous edge-preserving image smoothing, called fast global smoother. Focusing on sparse Laplacian matrices consisting of a data term and a prior term (typically defined using four or eight neighbors for 2D image), our approach efficiently solves such global objective functions. In particular, we approximate the solution of the memory-and computation-intensive large linear system, defined over a d-dimensional spatial domain, by solving a sequence of 1D subsystems. Our separable implementation enables applying a linear-time tridiagonal matrix algorithm to solve d three-point Laplacian matrices iteratively. Our approach combines the best of two paradigms, i.e., efficient edge-preserving filters and optimization-based smoothing. Our method has a comparable runtime to the fast edge-preserving filters, but its global optimization formulation overcomes many limitations of the local filtering approaches. Our method also achieves high-quality results as the state-of-the-art optimization-based techniques, but runs ∼10-30 times faster. Besides, considering the flexibility in defining an objective function, we further propose generalized fast algorithms that perform Lγ norm smoothing (0 < γ < 2) and support an aggregated (robust) data term for handling imprecise data constraints. We demonstrate the effectiveness and efficiency of our techniques in a range of image processing and computer graphics applications.
We present a descriptor, called fully convolutional selfsimilarity (FCSS), for dense semantic correspondence. To robustly match points among different instances within the same object class, we formulate FCSS using local selfsimilarity (LSS) within a fully convolutional network. In contrast to existing CNN-based descriptors, FCSS is inherently insensitive to intra-class appearance variations because of its LSS-based structure, while maintaining the precise localization ability of deep neural networks. The sampling patterns of local structure and the self-similarity measure are jointly learned within the proposed network in an end-to-end and multi-scale manner. As training data for semantic correspondence is rather limited, we propose to leverage object candidate priors provided in existing image datasets and also correspondence consistency between object pairs to enable weakly-supervised learning. Experiments demonstrate that FCSS outperforms conventional handcrafted descriptors and CNN-based descriptors on various benchmarks.
Nitrification of excess ammonia in soil causes eutrophication of water resources and emission of atmospheric N(2) O gas. The first step of nitrification, ammonia oxidation, is mediated by Archaea as well as Bacteria. The physiological reactions mediated by ammonia-oxidizing archaea (AOA) and their contribution to soil nitrification are still unclear. Results of non-culture-based studies have shown the thaumarchaeotal group I.1b lineage of AOA to be dominant over both AOA of group I.1a and ammonia-oxidizing bacteria in various soils. We obtained from an agricultural soil a highly enriched ammonia-oxidizing culture dominated by a single archaeal population [c. 90% of total cells, as determined microscopically (by fluorescence in situ hybridization) and by quantitative PCR of its 16S rRNA gene]. The archaeon (termed 'strain JG1') fell within thaumarchaeotal group I.1b and was related to the moderately thermophilic archaeon, Candidatus Nitrososphaera gargensis, and the mesophilic archaeon, Ca. Nitrososphaera viennensis with 97.0% and 99.1% 16S rRNA gene sequence similarity respectively. Strain JG1 was neutrophilic (growth range pH 6.0-8.0) and mesophilic (growth range temperature 25-40°C). The optimum temperature of strain JG1 (35-40°C) is > 10°C higher than that of ammonia-oxidizing bacteria (AOB). Membrane analysis showed that strain JG1 contained a glycerol dialkyl glycerol tetraether, GDGT-4, and its regioisomer as major core lipids; this crenarchaeol regioisomer was previously detected in similar abundance in the thermophile, Ca. N. gargensis and has been frequently observed in tropical soils. Substrate uptake assays showed that the affinity of strain JG1 for ammonia and oxygen was much higher than those of AOB. These traits may give a competitive advantage to AOA related to strain JG1 in oligotrophic environments. (13) C-bicarbonate incorporation into archaeal lipids of strain JG1 established its ability to grow autotrophically. Strain JG1 produced a significant amount of N(2) O gas - implicating AOA as a possible source of N(2) O emission from soils. Sequences of archaeal amoA and 16S rRNA genes closely related to those of strain JG1 have been retrieved from various terrestrial environments in which lineage of strain JG1 is likely engaged in autotrophic nitrification.
N 2 O gas is involved in global warming and ozone depletion. The major sources of N 2 O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N 2 O produced by soil AOA and associated N 2 O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N 2 O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), d 15 N bulk and d 18 O -N 2 O of soil AOA strains were 13-30%, À 13 to À 35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A 15 N-NH 4 þ -labeling experiment indicated that N 2 O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N 2 O from AOA may be attributable to the relative contributions of these two processes. The highest N 2 O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N 2 O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N 2 O emissions from soil nitrification may be attributable to AOA.
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