Soil aggregates as massively concurrent evolutionary incubators

Soil aggregation, a key component of soil structure, has mostly been examined from the perspective of soil management and the mediation of ecosystem processes such as soil carbon storage. However, soil aggregation is also a major factor to consider in terms of the fine-scale organization of the soil microbiome. For example, the physico-chemical conditions inside of aggregates usually differ from the conditions prevalent in the bulk soil and aggregates therefore increase the spatial heterogeneity of the soil. In addition, aggregates can provide a refuge for microbes against predation since their interior is not accessible to many predators. Soil aggregates are thus clearly important for microbial community ecology in soils (for example, Vos et al., 2013; Rillig et al., 2016) and for microbially driven biogeochemistry, and soil microbial ecologists are increasingly appreciating these aspects of soil aggregation. Soil aggregates have, however, so far been neglected when it comes to evolutionary considerations (Crawford et al., 2005) and we here propose that the process of soil aggregation should be considered as an important driver of evolution in the soil microbial community

Nitrogen loss from soil through anaerobic ammonium oxidation coupled to iron reduction

The oxidation of ammonium is a key step in the nitrogen cycle, regulating the production of nitrate, nitrous oxide and dinitrogen. In marine and freshwater ecosystems, anaerobic ammonium oxidation coupled to nitrite reduction, termed anammox, accounts for up to 67% of dinitrogen production. Dinitrogen production through anaerobic ammonium oxidation has not been observed in terrestrial ecosystems, but the anaerobic oxidation of ammonium to nitrite has been observed in wetland soils under iron-reducing conditions. Here, we incubate tropical upland soil slurries with isotopically labelled ammonium and iron(iii) to assess the potential for anaerobic ammonium oxidation coupled to iron(iii) reduction, otherwise known as Feammox, in these soils. We show that Feammox can produce dinitrogen, nitrite or nitrate in tropical upland soils. Direct dinitrogen production was the dominant Feammox pathway, short-circuiting the nitrogen cycle and resulting in ecosystem nitrogen losses. Rates were comparable to aerobic nitrification and to denitrification, the latter being the only other process known to produce dinitrogen in terrestrial ecosystems. We suggest that Feammox could fuel nitrogen losses in ecosystems rich in poorly crystalline iron minerals, with low or fluctuating redox conditions. Includes Supplementary Information

Environmental modification and niche construction: developing O2 gradients drive the evolution of the Wrinkly Spreader

The evolutionary success of the novel Wrinkly Spreader (WS) genotypes in diversifying Pseudomonas fluorescens SBW25 populations in static liquid microcosms has been attributed to the greater availability of O2 at the air–liquid (A–L) interface where the WS produces a physically cohesive-class biofilm. However, the importance of O2 gradients in SBW25 adaptation has never been examined. We have explicitly tested the role of O2 in evolving populations using microsensor profiling and experiments conducted under high and low O2 conditions. Initial colonists of static microcosms were found to establish O2 gradients before significant population growth had occurred, converting a previously homogenous environment into one containing a resource continuum with high and low O2 regions. These gradients were found to persist for long periods by which time significant numbers of WS had appeared colonising the high O2 niches. Growth was O2 limited in static microcosms, but high O2 conditions like those found near the A–L interface supported greater growth and favoured the emergence of WS-like genotypes. A fitness advantage to biofilm formation was seen under high but not low O2 conditions, suggesting that the cost of biofilm production could only be offset when O2 levels above the A–L interface were high. Profiling of mature WS biofilms showed that they also contained high and low O2 regions. Niches within these may support further diversification and succession of the developing biofilm population. O2 availability has been found to be a major factor underlying the evolutionary success of the WS genotype in static microcosms and illustrates the importance of this resource continuum in microbial diversification and adaptation

Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks

Spatial organisation of bacteria could contribute to the persistence of anoxic hotspots in soils, however such processes are difficult to observe directly. Here, the authors develop an experimental platform mimicking resource gradients postulated in soil aggregates to assess bacterial spatial organisation