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Bacteria and archaea are essential for the formation and sustainability of soil. They form a significant proportion of the soil biomass, and modern molecular techniques have shown their communities to be extremely diverse. This phylogenetic diversity is linked to physiological diversity, and the vast array of metabolic processes performed by these organisms ensures their central and essential role in soil biogeochemical cycles and ecosystem functions. This chapter presents the fundamental characteristics of bacteria and archaea, and highlights recent advancements in our understanding of their diversity, physiology, and interactions with their physico-chemical and biological environments. It places these advancements within the context of the soil ecosystem to demonstrate their contribution to fundamental soil processes across a wide range of scales, but also in the more applied areas of biodegradation and antibiotic production.

Ecological studies of soil microorganisms require reliable techniques for assessment of microbial community composition, abundance, growth, and activity. Soil structure and physicochemical properties seriously limit the applicability and value of methods involving direct observation, and ecological studies have focused on communities and populations, rather than single cells or microcolonies. Although ammonia-oxidizing archaea were discovered 5 years ago, there are still no cultured representatives from soil and there remains a lack of knowledge regarding their genomic composition, physiology, or functional diversity. Despite these limitations, however, significant insights into their distribution, growth characteristics, and metabolism have been made through the use of a range of molecular methodologies. As well as the analysis of taxonomic markers such as 16S rRNA genes, the development of PCR primers based on a limited number of (mostly marine) sequences has enabled the analysis of homologues encoding proteins involved in energy and carbon metabolism. This chapter will highlight the range of molecular methodologies available for examining the diversity, growth, and activity of ammonia-oxidizing archaea in the soil environment.

Publisher Summary This chapter begins with a description of the microbial groups carrying out nitrification and their distribution in major habitats. This is followed by a discussion of the influence of nitrifier physiology, physiological diversity, and environmental factors on their community structure, environmental distribution, activities, and ecosystem function. N2 oxidation in most environments is considered to be dominated by Gram-negative autotrophic N2 oxidizers. Environmental clone sequences suggest the existence of two novel clusters, Nitrosospira cluster 1 and Nitrosomonas cluster 5, which are not currently represented in laboratory cultures. NH3-oxidizing archaea are traditionally associated with extreme environments but the analysis of 16S rRNA environmental clones has demonstrated their abundance in a wide range of ‘non-extreme’,” mesophilic environments. NO2-oxidizers have been studied less frequently and biochemical and physiological studies have focused on Nitrobacter. The chapter deals with the community structure of nitrifiers in natural environments. Molecular techniques represent a major advance on cultivation-based methods and it is now possible to study NH3 oxidizer diversity and community composition. Factors influencing the ecology of nitrifying bacteria outlines the enrichment and isolation of the pure cultures of nitrifying bacteria, measurement of nitrification activity, maximum specific growth rate of nitrifiers, affinity of nitrifying bacteria for ammonia and nitrite, inhibition of nitrifiers by high substrate concentration, transformation of carbon compounds by nitrifying bacteria, nitrification at low-oxygen concentrations, starvation mechanisms and biofilm formation, formation of cell aggregates by nitrifying bacteria, influence of salt concentration on nitrifiers, and influence of pH on nitrifier growth and activity.

Publisher Summary This chapter provides an overview of the taxonomy and characteristics of soil prokaryotes and shows their importance for prokaryote growth and activity and soil function. Prokaryotes are distinguished from eukaryotes by the absence of a unit membrane-bound nucleus and, usually, the lack of other cell organelles. Ribosomes in prokaryotes are smaller (70S) than in eukaryotes (80S) and no eukaryote is able to fix atmospheric N2. Despite the apparent, relative simplicity of prokaryotic cells, as a group they have the greater taxonomic and functional diversity. Globally, organic carbon in prokaryotes is equivalent to that in plants, and they contain 10-fold more nitrogen. They also possess the most efficient dispersal and survival mechanisms. Consequently, prokaryotes are of enormous importance in the creation, maintenance, and functioning of the soil. The focus in this chapter is on phylogeny and general features of prokaryotes such as cell structure, metabolism, physiology, and biodegradation capacity. Basic concepts related to differentiation, secondary metabolism, and antibiotic productions are explained.

Publisher Summary This chapter highlights the physiology of autotrophic ammonia- and nitrite-oxidizing bacteria. Several aspects of the physiology of nitrifiers of relevance to their growth and activity in natural environments are considered. The chapter describes the basic features of the biochemistry of ammonia and nitrite oxidation and discusses the growth limiting factors and activity of these organisms. The influence of oxygen concentration, pH value, and inhibitors on their physiology is also described. Nitrification plays a central role in the nitrogen cycle of terrestrial and aquatic ecosystems, converting the most reduced form of nitrogen, NH3, to the most oxidized form, NO3. Nitrifying bacteria occupy niches in many ecosystems and compete successfully with faster and more efficiently growing organisms for oxygen, ammonia, and carbon dioxide. Nitrifiers are capable of reversing the nitrification process, carrying out denitrification and producing nitrite, ammonia, nitrous and nitric oxides, and gaseous nitrogen. Ammonia oxidizers can metabolize urea and can assimilate carbon from methane while nitrite oxidizers can grow anaerobically in the presence of organic compounds and nitrate.