Abstract
We examine and discuss literature targeted at identifying “active” subpopulations of soil microbial communities with regard to the factors that affect the balance between mineralization and immobilization/assimilation of N. Whereas a large fraction (≥50%) of soil microbial biomass can immediately respire exogenous substrates, it remains unclear what percentage of both bacterial and fungal populations are capable of expressing their growth potential. The factors controlling the relative amounts of respiratorily responsive biomass versus growth-active biomass will impact the balance between N mineralization and N immobilization. Stable isotope probing of de novo DNA synthesis, and pyrosequence analyses of rRNA:rDNA ratios in soils have identified both numerically dominant and rare microbial taxa showing greatest growth potential. The relative growth responses of numerically dominant or rare members of a soil community could influence the amount of N immobilized into biomass during a “growth” event. Recent studies have used selective antibiotics targeted at protein synthesis to measure the relative contributions of fungi and bacteria to ammonification and consumption, and of NH3-oxidizing archaea (AOA) and bacteria (AOB) to NH3 oxidation. Evidence was obtained for bacteria to dominate assimilation and for fungi to be involved in both consumption of dissolved organic nitrogen (DON) and its ammonification. Soil conditions, phase of cropping system, availability, and soil pH influence the relative contributions of AOA and AOB to soil nitrification. A recent discovery that AOA can ammonify organic N sources and oxidize it to serves to illustrate roles for AOA in both the production and consumption of . Clearly, much remains to be learned about the factors influencing the relative contributions of bacteria, archaea, and fungi to processing organic and inorganic N, and their impact on the balance between mineralization and immobilization of N.
Highlights
The soil N cycle consists of several N pools and inter-connected transformations (Figure 1)
The placement of soil microbial diversity and dynamics into context with biological functions associated with the N cycle still remains a grand challenge (Myrold and Bottomley, 2008; Strickland et al, 2009; McGuire and Treseder, 2010)
Evidence has been obtained recently for both the marine AOA “Candidatus Nitrosopumilus maritimus” strain SCM1 and a soil AOA “Candidatus Nitrosotalea devanaterra” having high. These findings have provided the impetus to identify the soil factors that affect the relative contributions of AOA and AOB to soil nitrification
Summary
The soil N cycle consists of several N pools and inter-connected transformations (Figure 1). Conservation of soil N depends on the maintenance of a balance between the rate of depolymerization of organic N, the portion of it that is mineralized to NH+4 , and the rate of NH+4 consumption by three different sinks: (a) plant growth, (b) heterotrophic microbial assimilation, and (c) NH3-oxidizing bacteria (AOB) and archaea (AOA). Speaking, when sink (c) is larger than (a) plus (b), NO−3 accumulates and becomes vulnerable to leaching and/or denitrification from the ecosystem. Gross rates of microbial NH+4 and NO−3 assimilation are positively and linearly related to gross N mineralization rates. The fact that heterotrophic NH+4 assimilation (Nassim) can be a sink of substantial magnitude in the same soil volume where NH+4 is being produced by mineralization (Nmin) has prompted a variety of explanations over the years. It has been proposed that Nmin and Nassim processes are carried out concurrently by physically separated microbial populations growing on different C sources of different C:N ratios
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