{"type": "FeatureCollection", "features": [{"id": "10.1016/j.apsoil.2017.09.041", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:15:13Z", "type": "Journal Article", "created": "2017-11-20", "title": "Ammonia-Oxidizing Archaea Are More Sensitive Than Ammonia-Oxidizing Bacteria To Long-Term Application Of Green Manure In Red Paddy Soil", "description": "Abstract Growing winter green manure is an effective method for improving nitrogen (N) management in paddy fields to enhance rice production. Ammonia oxidization is a key process in N cycling in these soils, but effects of green manuring on ammonia oxidizers have not been fully addressed for red paddy soils. The objective of this study was to investigate long-term impacts of winter green manure on abundance and diversity of ammonia oxidizers in rice paddy soils of Southern China. The field experiment established in 1982 included four treatments: rice-rice-winter fallow (RRF), rice-rice-ryegrass (RRG), rice\u2013rice\u2013rape (RRP) and rice\u2013rice\u2013milk vetch (RRV). The abundance and diversity of amoA genes from ammonia-oxidizing archaea (AOA) and bacteria (AOB) were quantified using quantitative PCR and 454 pyrosequencing, respectively. The AOA were more abundant than AOB in red paddy soils, with ratios of AOA to AOB from 36 to 1686. Long-term application of milk vetch increased the abundance of both AOA and AOB after green manures were incorporated. Some of the relative abundances of most abundant operational taxonomic units (OTUs) of AOA increased and others decreased after application of green manures, while most abundant OTUs of AOB remained unaffected. Redundancy analysis (RDA) found a clear separation between milk vetch and winter fallow, indicating that the community structure of AOA was influenced by application of milk vetch. Phylogenetic analysis showed that the most dominant OTUs of AOA and AOB were affiliated with Nitrososphaera and Nitrosospira, respectively. In conclusion, in red paddy soil, long-term application of milk vetch increased the abundances of AOA and AOB after incorporated. Moreover, long-term application of green manures had more profound influences on AOA community than on AOB in red paddy soils.", "keywords": ["Ammonia-oxidizing bacteria", "0301 basic medicine", "2. Zero hunger", "03 medical and health sciences", "Paddy soil", "Green manure", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Ammonia-oxidizing archaea"], "contacts": [{"organization": "Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China ( host institution ), Gao, Songjuan ( author ), Cao, Weidong ( author ), Zou, Chunqin ( author ), Gao, Jusheng ( author ), Huang, Jing ( author ), Bai, Jinshun ( author ), Zeng, Naohua ( author ), Shimizu, Katsu-yoshi ( author ), Wright, Alan ( UF author ), Dou, Fugen ( author ),", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2017.09.041"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2017.09.041", "name": "item", "description": "10.1016/j.apsoil.2017.09.041", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2017.09.041"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-03-01T00:00:00Z"}}, {"id": "10.1038/s41396-019-0465-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:16:45Z", "type": "Journal Article", "created": "2019-06-27", "title": "Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands", "description": "Abstract

Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale. Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea , growing under oxygen-limited conditions. Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale. Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea , growing under oxygen-limited conditions. Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.