Ecology of denitrifying microorganisms: Communities and their functioning

Denitrification and denitrifier diversity

Denitrifier communities in the environment are either explored via classical cultivation-dependent approaches to isolate denitrifying microorganisms or via cultivation-independent approaches based on the detection of functional marker genes. While the isolation of denitrifiers allows insights into the phylogeny and physiology of the organisms, the latter approach allows insight into the diversity, structure and abundance of denitrifier communities. We use both to isolate and characterize denitrifiers with denitrification genes that are closely related to those of uncultured organisms and evaluate their importance for nitrogen cycling in soils by using cultivation-independent methods.

Soil denitrifier communities and their functioning in selected environments

Up to 30% of the loss of nitrogen gas from terrestrial ecosystems was estimated to originate from arid soil ecosystems at least in part due to the vast area they occupy. However, severe water limitation limits microbial activity, e.g. very low or even undetectable denitrification activity over extended time spans. We found that denitrifier abundance and diversity in soils from arid regions (Chile, sclerophyllous matorral/Atacama Desert; Namibia, Okavango region) are generally low but enhanced microbial activity as a consequence of occasional precipitation events seem to account for most of the nitrogen turnover.

Another particular soil ecosystem is Amazonian dark earth (Terra preta de Indio) which is presumably of anthropogenic origin with high fertility and resilience to soil management. Due to its unique properties it has gained considerable attention and an implementation of replica materials with similar properties in future agricultural practice is discussed. The effects on nitrogen cycling and N2O emissions from soils, however, are not understood and we for the first time evaluate microbial communities involved in nitrogen cycling and their function in these and adjacent managed soils.

Relationships between denitrifier structure and function

It is a long-standing question in microbial ecology whether the structure of a community determines its function and structure-function relationships were hypothesized particularly for functional groups with a narrow physiology such as denitrifiers. Ex situ denitrification assays gave evidence that three soils from distant locations which differed in cultivation history and pedoclimatic origin harbor communities with profoundly different abilities to conduct efficient and balanced denitrification. Although the interactions were complex our results indicate that the contrasting performance of the communities is attributable to different regulation of denitrification by the dominating species within the three communities. Moreover, it seems that diversity, structure and abundance are relevant for the functioning of the communities and hence for the propensity of soils to emit N2O.