Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils

Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale

The impact of agricultural management on soil aggregation and carbon storage is regulated by climatic thresholds across a 3000 km European gradient

Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (-56%) and SOC stocks (-35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration

Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts

Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope 33P from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring 33P and transferred 64% more 33P to plants compared with AMF in cropland soils. Fungicide application best explained hyphal 33P transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced 33P uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.The Digging Deeper project was funded through the 2015–2016 BiodivERsA COFUND call for research proposals, with the national funders Swiss National Science Foundation (grant 31BD30-172466), Deutsche Forschungsgemeinschaft (317895346), Swedish Research Council Formas (contract 2016-0194), Ministerio de Economía y Competitividad (Digging_Deeper, Ref. PCIN-2016-028) and Agence Nationale de la Recherche (ANR, France; grant ANR-16-EBI3-0004-01).Peer reviewe

Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts

We thank all the farmers and farm managers for allowing us to sample their fields and for completing our detailed questionnaires. We also thank A. Bonvicini, L. Schönholzer, M. Macsai, F. Tamburini, H. Gamper, S. Müller, D. Bürge, M. Zuber, S. Zhao, V. Somerville, A. Brugger, O. Scholz, D. Bugmann, R. Heiz, B. Seitz and M. Roser for help with field work, the design and execution of the greenhouse experiment and lab analyses. We also thank J. Helfenstein and the anonymous reviewers for valuable feedback on the manuscript. The Digging Deeper project was funded through the 2015–2016 BiodivERsA COFUND call for research proposals, with the national funders Swiss National Science Foundation (grant 31BD30-172466), Deutsche Forschungsgemeinschaft (317895346), Swedish Research Council Formas (contract 2016-0194), Ministerio de Economía y Competitividad (Digging_Deeper, Ref. PCIN-2016-028) and Agence Nationale de la Recherche (ANR, France; grant ANR-16-EBI3-0004-01).Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope 33P from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring 33P and transferred 64% more 33P to plants compared with AMF in cropland soils. Fungicide application best explained hyphal 33P transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced 33P uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.BiodivERsA COFUNDSwiss National Science FoundationDeutsche ForschungsgemeinschaftSwedish Research Council FormasMinisterio de Economía y CompetitividadAgence Nationale de la RechercheDepto. de Farmacología, Farmacognosia y BotánicaFac. de FarmaciaTRUEpu

Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils

Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale

Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts

Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope 33P from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring 33P and transferred 64% more 33P to plants compared with AMF in cropland soils. Fungicide application best explained hyphal 33P transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced 33P uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems

Complete Characterization of Stratified Ecosystems of the Salar de Llamara (Atacama Desert)

Salar de Llamara is situated in the north of the Atacama Desert, which is the driest desert and one of the most irradiated places on Earth. Besides, its subterranean hypersaline waters contain a high content of arsenic, among other compounds such as heavy metals that are poisonous to life in the concentrations present. Despite these extreme conditions, diverse microbial communities flourish in gypsum stratified ecosystems (microbial mats and evaporitic domes).Here, we reviewed all the analysis carried out in these communities, involving taxonomic and functional studies by culture-independent techniques, analysis of the physicochemical parameters of the water and its relation with the microbial ecosystems, together with pigments, mineralogy, and the microscopic view.Regarding taxonomy, the major points analyzed were: (1) the taxonomic trends at phylum level showed that Proteobacteria and Bacteroidetes were the major components of these communities. (2) A low proportion of sequences associated with the phylum Cyanobacteria were detected in all the studied samples. (3) The increased proportion of sequences that could not be affiliated with any taxonomic group that is deposited in the databases. (4) The large amount of rare phyla represented by candidate phyla, such as OD1, OP1, OD8, Hyd24-12, and NKB19.The functional analysis, carried out in these gypsum evaporite systems, revealed that there was only a minor presence of oxygenic photosynthesizers in the community, and anoxygenic photosynthesis appears as an alternative for primary production. Since the Calvin?Benson cycle was scant, the low abundance of oxygenic photosynthesizers was also related to unusual carbon fixation pathways.Regarding physicochemical parameters of the water, the most interesting results were: (1) a huge amount of arsenic; (2) high salinity; (3) low nutrients and high levels of some ions, such as sodium, sulfate, and calcium. The low dissolved oxygen in most of the set points was low, which was consistent with the low proportion of oxygenic photosynthesizers in all the samples studied.Regarding the mineralogy, gypsum mainly compounded all the evaporitic domes, and the microbial mats present halite as the main mineral component.Fil: Rasuk, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Contreras Leiva, Manuel. Centro de Ecología Aplicada; ChileFil: Kurth, Daniel German. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; Argentin

Methanogens and Methanogenesis in Hypersaline Environments

Methanogenesis is controlled by redox potential and permanency of anaerobic conditions; and in hypersaline environments, the high concentration of terminal electron acceptors, particularly sulfate, is an important controlling factor. This is because sulfate-reducing microbes, compared with methanogens, have a greater affinity for, and energy yield from, competitive substrates like hydrogen and acetate. However, hypersalinity is not an obstacle to methylotrophic methanogenesis; in many cases hypersaline environments have high concentrations of noncompetitive substrates like methylamines, which derive from compatible solutes such as glycine betaine that is synthesized by many microbes inhabiting hypersaline environments. Also, depletion of sulfate, as may occur in deeper sediments, allows increased methanogenesis. On the other hand, increasing salinity requires methanogens to synthesize or take up more compatible solutes at a significant energetic cost. Acetoclastic and hydrogenotrophic methanogens, with their lower energetic yields, are therefore more susceptible than methylotrophic methanogens, which further explains the predominance of methylotrophic methanogens like Methanohalophilus and Methanohalobium spp. in hypersaline environments. There are often deviations from the picture outlined above, which are sometimes difficult to explain. Identifying the role of uncultivated Euryarchaeota in hypersaline environments, elucidating the effects of different ions (which have differential stress effects and potential as electron acceptors), and understanding the effects of salinity on all microbes involved in methane cycling will help us to understand and predict methane production in hypersaline environments. A good demonstration of this is a recent discovery of extremely haloalkaliphilic methanogens living in hypersaline lakes, which utilize the methyl-reducing pathway and form a novel class “Methanonatronarchaeia” in the Euryarchaeota