Christopher M. Jones

Microbial communities are potentially useful indicators of the status of soil functioning in response to anthropogenic disturbances. However, the effect of compounded disturbances, particularly of different disturbance types, is of increasing interest given the multiple threats to soils. We hypothesized that microbial communities under continuous exposure to soil contaminants (’press’ disturbance) will be more affected by a second stressor, exemplified by drought (’pulse’ disturbance), than those in uncontaminated soil. To test this, we performed a two-phase experiment in which we first established outdoor soil mesocosms to assess the impact of separate copper (Cu) and polycyclic aromatic hydrocarbon (PAH) contamination gradients on total prokaryotic and ammonia oxidizing archaea (AOA) and bacterial (AOB) communities in two soils with contrasting properties over a 16-month period. We then subjected contaminated and uncontaminated soils to drought conditions in laboratory microcosms to test whether contamination legacy altered microbial resistance to drying and rewetting stress and if they could recover. We show that Cu and PAH contamination decreased the diversity and altered the composition of all communities as well as decreased AOA abundance and nitrification activity in both soils. Ammonia oxidizing archaeal and bacterial communities responded differently to drought stress across both soil and contamination types, though a consistent negative effect of Cu legacy was observed for nitrification activity. However, the composition and diversity of total microbial communities in contaminated soils were overall less resilient to drought stress, with stronger legacy effects of Cu contamination. These results underscore increased vulnerability of microbial communities in contaminated soils to climate change, with implications for soil functioning.

Microorganisms are essential for the functioning of agricultural soils but face increasing stress due to pollution and climate change. However, direct and legacy effects of agrochemicals on non-target microorganisms are poorly considered in environmental risk assessment. Here, we set up a two-phase microcosm experiment to assess the effect of the herbicides clopyralid, metribuzin and tembotrione (phase 1) on the abundance and activity of ammonia and nitrite oxidizing microorganisms involved in nitrification, a key step in soil N cycling, and how it influences their response to subsequent drying and rewetting stress (phase 2). Pesticide exposure in phase 1 did not affect the nitrifying guilds and nitrification activity. By contrast, drying-rewetting affected the abundance of the different guilds, with ammonia-oxidizing archaea and Nitrospira-type nitrite oxidizers showing low resistance to rewetting, but with minor differences between herbicide-treated and no-herbicide treated soils. Legacy effects of herbicide exposure were instead captured by the soil nitrate pools, where differences between droughted and control soils appeared larger in the no-herbicide than in the herbicide-treated soils, potentially indicating differences in drought-coping strategies depending on prior stress exposure. Our results highlight that multiple stressor scenarios can reveal effects not captured by end-point measurements in risk assessment procedures.

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of nitrate ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screened more than 1 million genomes for nrfA , encoding the nitrite reductase in nitrate ammonification. Nearly 50% of the nitrate ammonifier assemblies carry at least one denitrification gene and, contrary to the current paradigm, have higher potential for nitrous oxide production than reduction. We then used a phylogeny-based approach to recruit nrfA and denitrification nitrite reductase gene fragments in 1,861 metagenomes covering the major terrestrial biomes. Denitrification genes dominated, except in tundra, and random forest modelling teased apart the influence of the soil C/N on nitrate ammonifier vs denitrifier abundances, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and the factors ultimately controlling the fate of nitrate in soil.

The rhizosphere is a hotspot for denitrification. The nitrous oxide (N₂O) reductase among denitrifiers and nondenitrifying N₂O reducers is the only known N₂O sink in the biosphere. We hypothesized that the composition of root-associated N₂O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N₂O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N₂O availability, determined as potential N₂O production rates, but for sunflower no N₂O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N₂O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N₂O.

During the last decades, atmospheric nitrogen loading in mountain ranges of the Northern Hemisphere has increased substantially, resulting in high nitrate concentrations in many lakes. Yet, how increased nitrogen has affected denitrification, a key process for nitrogen removal, is poorly understood. We measured actual and potential (nitrate and carbon amended) denitrification rates in sediments of several lake types and habitats in the Pyrenees during the ice-free season. Actual denitrification rates ranged from 0 to 9 μmol N₂O m⁻² h⁻¹ (mean, 1.5 ± 1.6 SD), whereas potential rates were about 10-times higher. The highest actual rates occurred in warmer sediments with more nitrate available in the overlying water. Consequently, littoral habitats showed, on average, 3-fold higher rates than the deep zone. The highest denitrification potentials were found in more productive lakes located at relatively low altitude and small catchments, with warmer sediments, high relative abundance of denitrification nitrite reductase genes, and sulphate-rich waters. We conclude that increased nitrogen deposition has resulted in elevated denitrification rates, but not sufficiently to compensate for the atmospheric nitrogen loading in most of the highly oligotrophic lakes. However, there is potential for high rates, especially in the more productive lakes and landscape features largely govern this.