Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments

The family Gallionellaceae

\ua9 2014 Springer-Verlag Berlin Heidelberg. All rights reserved. The family Gallionellaceae comprises the genus Gallionella with one established type species, Gallionella ferruginea. The phylogenetic position of Gallionellaceae, as determined by 16S-rDNA sequence comparisons, is among the β-proteobacteria. Its phylogenetic neighbors are Methylophilaceae, Nitrosomonadaceae, and Spirillaceae. The family contains gram-negative, chemolithoautotrophic, neutrophilic, and aerobic ferrous iron-oxidizing bacteria with the ability to secrete an extracellular twisted stalk composed of numerous fibers. Gallionellaceae can be found where anaerobic groundwater containing ferrous iron reaches an environment that contains oxygen. Large amounts of stalk material are usually produced; this material attracts iron hydroxides and many trace metals, giving it a brown, macroscopic appearance. The stalk and iron hydroxide masses formed may eventually cause severe clogging of ditches, drinking-water wells, and any other facilities utilizing iron-bearing, anaerobic groundwater. The family is relevant to biotechnological processes, as it can be used to remove ferrous iron when producing drinking water from groundwater

An outline of indirect holographic methods for antenna measurements and microwave imaging

Indirect microwave holographic techniques offer a simple, low cost technique for a range of microwave measurements including the determination of antenna characteristics and the ability to provide good quality images of passive objects. This work provides a brief outline of the basic theory of indirect microwave holography and how it can be used for the reconstruction of scattered complex fields at the measurement plane and how these results can be back propagated to provide the scattered fields at any preselected observation plane. It provides an outline of the different techniques required for antenna measurement and the imaging of passive objects. It demonstrates how indirect holography can be used to determine the far field radiation pattern of a high gain antenna and reconstruct the complex antenna aperture fields. This work also demonstrates the use of indirect holography for the imaging of passive objects. The techniques described have been validated by experimental results on a range of objects including buried objects

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments