Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.How arable farming affects soil fungal biogeography is poorly understood. Here, the authors find that prevalent fungal groups become more abundant, whereas rare groups become fewer or absent in arable lands across Europe, suggesting a biotic homogenization due to arable farming

Diversity and ecology of NrfA-dependent ammonifying microorganisms

Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements

Catchment controls of denitrification and nitrous oxide production rates in headwater remediated agricultural streams

Heavily modified headwater streams and open ditches carry high nitrogen loads from agricultural soils that sustain eutrophication and poor water quality in downstream aquatic ecosystems. To remediate agricultural streams and reduce the export of nitrate (NO3-), phosphorus and suspended sediments, two-stage ditches with constructed floodplains can be implemented as countermeasures. By extending hydrological connectivity between the stream channel and riparian corridor within constructed floodplains, these remediated ditches enhance the removal of NO3- via the microbial denitrification process. Ten remediated ditches were paired with upstream trapezoidal ditches in Sweden across different soils and land uses to measure the capacity for denitrification and nitrous oxide (N2O) production and yields under denitrifying conditions in stream and floodplain sediments. To examine the controls for denitrification, water quality was monitored monthly and flow discharge continuously along reaches. Floodplain sediments accounted for 33% of total denitrification capacity of remediated ditches, primarily controlled by inundation and stream NO3- concentrations. Despite reductions in flow-weighted NO3- concentrations along reaches, NW removal in remediated ditches via denitrification can be masked by inputs of NW-rich groundwaters, typical of intensively managed agricultural landscapes. Although N2O production rates were 50 % lower in floodplains compared to the stream, remediated ditches emitted more N2O than conventional trapezoidal ditches. Higher denitrification rates and reductions of N2O proportions were predicted by catchments with loamy soils, higher proportions of agricultural land use and lower floodplain elevations. For realizing enhanced NO3- removal from floodplains and avoiding increased N2O emissions, soil type, land use and the design of floodplains need to be considered when implementing remediated streams. Further, we stress the need for assessing the impact of stream remediation in the context of broader catchment processes, to determine the overall potential for improving water quality

Loss in soil microbial diversity constrains microbiome selection and alters the abundance of N-cycling guilds in barley rhizosphere

Plant roots are shaping microbial communities that are distinct from the surrounding soil. These root-associated microbial communities can have both positive and negative effects on the host nutrient acquisition and thereby growth, yet how loss of soil microbial diversity will constrain the plant microbiome selection is relatively unknown. In this study, we manipulated the soil microbial community using a removal-by-dilution approach to examine how microbial diversity modulates microbiome selection in barley, including microbial guilds involved in nitrogen (N) cycling processes causing N loss, and its consequences for plant performance. We found that microbial diversity loss reduced the barley's ability to recruit specific microorganisms from the soil and only members of the Alphaproteobacteria and Bacteroidetes were enriched in both rhizosphere and root-associated compartments irrespective of dilution level. Loss in soil microbial diversity and the presence of plants affected the N-cycling communities, with the abundance of nitrous oxide reducers being 2-4 times higher in both barley compartments in the lower diversity soils. In these soils, the low abundance of bacterial ammonia oxidizers (close or below detection level in the barley compartments) was concomitant with an increase in leaf greenness (ca. 12%), an indicator of the plant N status. The reduction in soil microbial diversity was thus coupled to a change in functional traits of rhizosphere and root-associated communities, with consequences for plant performance. This work contributes to our understanding of plant-microbe interactions, which is needed to steer the crop microbiome towards increased N-use efficiency while minimizing negative environmental impact

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance

Trade-offs between nitrogen and phosphorus removal with floodplain remediation in agricultural streams

To improve water quality and reduce instream erosion, floodplain remediation along agricultural streams can provide multiple ecosystem services through biogeochemical and fluvial processes. During floodplain inundation, longer water residence time and periodic anoxic conditions can lead to increased nitrogen (N) removal through denitrification but also mobilization of phosphorus (P), impeding overall water quality improvements. To investigate the capacity for N and P processing in remediated streams, we measured potential denitrification and nitrous oxide production and yields together with potential P desorption and P fractions in floodplain and stream sediments in ten catchments in Sweden. Sediment P desorption was measured as equilibrium P concentration, using P isotherm incubations. Denitrification rates were measured with the acetylene inhibition method. Sediment nutrient process rates were combined with hydrochemical monitoring along remediated streams and their paired upstream control reaches of trapezoidal shape to determine the impact of floodplains on water quality. The correlation between floodplain denitrification rates and P desorption (r = 0.53, p = 0.02) revealed a trade-off between soluble reactive P (SRP) and nitrate removal, driven by stream water connectivity to floodplains. Nitrous oxide production was not affected by differences in P processing, but nitrous oxide yields decreased with higher denitrification and P desorption. The release of SRP from floodplains (0.03 ± 0.41 mg P kg−1 day−1) was significantly lower than from trapezoidal stream banks (0.38 ± 0.37 mg P kg−1 day−1), predicted by long-term SRP concentrations in stream water and floodplain inundation frequency. The overall impact of SRP release from floodplains on stream SRP concentrations in remediated reaches was limited. However, the remediated reaches showing increased stream SRP concentrations were also frequently inundated and had higher labile P content and coarse soil texture in floodplain sediments. To fully realize the potential for water quality improvements with constructed floodplains in agricultural streams, the promotion of denitrification through increased inundation should be balanced against the risk of P release from sediments, particularly in streams with high SRP inputs

Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.Nitrate ammonifiers are poorly known despite their importance for soil nitrogen retention. This study shows that they are phylogenetically diverse and globally distributed across terrestrial biomes and that the outcome of the competition with denitrifiers is controlled by soil nitrate

Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions

Agricultural soils are a main source of nitrous oxide (N2O), a potent greenhouse gas and the dominant ozone -depleting substance emitted to the atmosphere. The only known sink of N2O in soil is the microbial reduction of N2O to N2. Carbon (C) availability is a key factor in determining microbial community composition in soil. However, its role in shaping the structure of N2O reducing communities in soil is unexplored. In this study, a microcosm experiment was set up in which two arable soils with contrasting edaphic properties were incubated anaerobically for 83 days with four different C substrates: glucose, acetate, hydroxyethylcellulose (HEC) and mixture of the three. We show that the effect of C addition on the abundance and diversity of clade I and clade II nosZ genes, encoding different variants of the N2O reductase, varies across the different C substrates differently in contrasting soil types, yet still plays an important role in selecting specific taxa of N2O reducers under deni-trifying conditions. We observed an increase of betaproteobacterial clade I and II N2O reducing species with addition of HEC, whereas alphaproteobacterial clade I species and clade II species within other Proteobacteria and Bacteriodetes were associated with glucose and acetate. These results show that specific C-substrates select for certain lineages of nitrous oxide reducers and influence patterns of niche partitioning within clades of N2O reducers, whereas other soil factors drive differences between clade I and II nosZ communities