{"type": "FeatureCollection", "features": [{"id": "10.1007/s11104-016-3073-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:15:36Z", "type": "Journal Article", "created": "2016-10-10", "title": "Response Of Soil Microbial Community To Afforestation With Pure And Mixed Species", "description": "\u00a9 2016, Springer International Publishing Switzerland.Objectives: Afforestation changes soil chemical properties over several decades. In contrast, microbial community structure can be shifted within the first decade and so, the direct effects of tree species can be revealed. The aim of this study was to determine the alteration of soil microbial community composition 10\u00a0years after afforestation by trees with contrasting functional traits. Methods: The study was conducted at the BangorDIVERSE temperate forest experiment. Soil samples were collected under single, two and three species mixtures of alder and birch, beech and oak - early and secondary successional species, respectively, and contiguous agricultural field. Soil was analysed for total carbon (C) and nitrogen (N) contents, and microbial community structure (phospholipid fatty acids (PLFAs) analysis). Results and conclusions: The total PLFAs content (370\u2013640\u00a0nmol\u00a0g\u22121soil) in forest plots increased for 30 to 110\u00a0% compared to the agricultural soil (290\u00a0nmol\u00a0g\u22121soil). In contrast, soil C, N and C/N ratios were altered over 10\u00a0years much less - increased only up to 20\u00a0% or even decreased (for beech forest). Afforestation increased bacterial PLFAs by 20\u2013120\u00a0%, whereas it had stronger impact on the development of fungal communities (increased by 50\u2013200\u00a0%). These effects were proved for all forests, but were more pronounced under the monocultures compared to mixtures. This indicates that species identity has a stronger effect than species diversity. Principal component analysis of PLFAs revealed that under mono and three species mixtures similar microbial communities were formed. In contrast, gram-positive PLFAs and actinomycete PLFAs contributed mainly to differentiation of two species mixtures from other forests. Thus, at the early afforestation stage: i) soil biological properties are altered more than chemical, and ii) tree species identity affects more than species amount on both processes.", "keywords": ["2. Zero hunger", "570", "Microbial biomarkers", "Plant microbial interactions", "Soil solution", "Tree identity", "0401 agriculture", " forestry", " and fisheries", "Woodland", "04 agricultural and veterinary sciences", "15. Life on land", "Land use change", "Ammonium and nitrate", "Forest composition"]}, "links": [{"href": "https://doi.org/10.1007/s11104-016-3073-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-016-3073-0", "name": "item", "description": "10.1007/s11104-016-3073-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-016-3073-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-10-10T00:00:00Z"}}, {"id": "10.1007/s11104-018-3810-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:15:36Z", "type": "Journal Article", "created": "2018-10-27", "title": "Hidden miners \u2013 the roles of cover crops and soil microorganisms in phosphorus cycling through agroecosystems", "description": "Phosphorus (P) is a limiting nutrient in many agroecosystems and costly fertilizer inputs can cause negative environmental impacts. Cover crops constitute a promising management option for sustainable intensification of agriculture. However, their interactions with the soil microbial community, which is a key driver of P cycling, and their effects on the following crop, have not yet been systematically assessed. We conducted a meta-analysis of published field studies on cover crops and P cycling, focusing on plant-microbe interactions. We describe several distinct, simultaneous mechanisms of P benefits for the main crop. Decomposition dynamics, governed by P concentration, are critical for the transfer of P from cover crop residues to the main crop. Cover crops may enhance the soil microbial community by providing a legacy of increased mycorrhizal abundance, microbial biomass P, and phosphatase activity. Cover crops are generally most effective in systems low in available P, and may access \u2018unavailable\u2019 P pools. However, their effects on P availability are difficult to detect by standard soil P tests, except for increases after the use of Lupinus sp. Agricultural management (i.e. cover crop species selection, tillage, fertilization) can improve cover crop effects. In summary, cover cropping has the potential to tighten nutrient cycling in agricultural systems under different conditions, increasing crop P nutrition and yield.", "keywords": ["2. Zero hunger", "Conservation agriculture", "Mobilisation Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.

3.Graphical Abstract

A step-by-step method for creating a tailored 3D culture medium for study of soil microbes.

The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion\uffe2\uff84\uffa2 resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion\uffe2\uff84\uffa2 particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.

In California, aflatoxin contamination of almond, fig, and pistachio has become a serious problem in recent years due to long periods of drought and probably other climatic changes. The atoxigenic biocontrol product Aspergillus flavus AF36 has been registered for use to limit aflatoxin contamination of pistachio since 2012 and for use in almond and fig since 2017. New biocontrol technologies employ multiple atoxigenic genotypes because those provide greater benefits than using a single genotype. Almond, fig, and pistachio industries would benefit from a multi-strain biocontrol technology for use in these three crops. Several A. flavus vegetative compatibility groups (VCGs) associated with almond, fig, and pistachio composed exclusively of atoxigenic isolates, including the VCG to which AF36 belongs to, YV36, were previously characterized in California. Here, we report additional VCGs associated with either two or all three crops. Representative isolates of 12 atoxigenic VCGs significantly (P < 0.001) reduced (>80%) aflatoxin accumulation in almond and pistachio when challenged with highly toxigenic isolates of A. flavus and A. parasiticus under laboratory conditions. Isolates of the evaluated VCGs, including AF36, constitute valuable endemic, well-adapted, and efficient germplasm to design a multi-crop, multi-strain biocontrol strategy for use in tree crops in California. Availability of such a strategy would favor long-term atoxigenic A. flavus communities across the affected areas of California, and this would result in securing domestic and export markets for the nut crop and fig farmer industries and, most importantly, health benefits to consumers.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "aflatoxins", "0303 health sciences", "almonds", "Food Contamination", "15. Life on land", "Ficus", "Prunus dulcis", "6. Clean water", "California", "03 medical and health sciences", "aspergillus flavus", "Aflatoxins", "13. Climate action", "Pistacia", "pistachios", "Microbial Interactions", "figs", "california", "Aspergillus flavus"]}, "links": [{"href": "https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-08-18-1333-RE"}, {"href": "https://doi.org/10.1094/pdis-08-18-1333-re"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Disease", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1094/pdis-08-18-1333-re", "name": "item", "description": "10.1094/pdis-08-18-1333-re", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1094/pdis-08-18-1333-re"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-01T00:00:00Z"}}, {"id": "10.3389/fams.2019.00018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:21:28Z", "type": "Journal Article", "created": "2019-04-12", "title": "Metabolic Games", "description": "Metabolic networks have been used to successfully predict phenotypes based on optimization principles. However, a general framework that would extend to situations not governed by simple optimization, such as multispecies communities, is still lacking. Concepts from evolutionary game theory have been proposed to amend the situation. Alternative metabolic states can be seen as strategies in a \u201cmetabolic game,\u201d and phenotypes can be predicted based on the equilibria of this game. In this survey, we review the literature on applying game theory to the study of metabolism, present the general idea of a metabolic game, and discuss open questions and future challenges.", "keywords": ["T57-57.97", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Applied mathematics. Quantitative methods", "flux balance analysis", "microbial interactions", "01 natural sciences", "QA273-280", "metabolic modeling", "0103 physical sciences", "metabolic networks", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "evolutionary game theory", "Probabilities. Mathematical statistics", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://doi.org/10.3389/fams.2019.00018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Applied%20Mathematics%20and%20Statistics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fams.2019.00018", "name": "item", "description": "10.3389/fams.2019.00018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fams.2019.00018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-12T00:00:00Z"}}, {"id": "10.6084/m9.figshare.19169609", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:25:19Z", "type": "Dataset", "created": "2022-05-16", "title": "Data and code from Semchenko et al. (2022) New Phytologist 10.1111/nph.18118", "description": "Open AccessData and code used in Semchenko M, Barry KE, de Vries FT, Mommer L, Maci\u00e1-Vicente JG (2022) Deciphering the role of specialist and generalist plant\u2013microbial interactions as drivers of plant\u2013soil feedback. New Phytologist, 10.1111/nph.18118 for the analysis of host ranges across plant-associated fungal and oomycete guilds.
", "keywords": ["2. Zero hunger", "host specifity", "Ecology", "plant-soil feedback", "FOS: Biological sciences", "mycorrhizas", "15. Life on land", "ecology", "microbial interactions", "plant pathogens", "saprotrophs"], "contacts": [{"organization": "Semchenko, Marina, Barry, Kathryn E., de Vries, Franciska T., Mommer, Liesje, Moora, Mari, Maci\u00e1-Vicente, Jose G.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.6084/m9.figshare.19169609"}, {"rel": "self", "type": "application/geo+json", "title": "10.6084/m9.figshare.19169609", "name": "item", "description": "10.6084/m9.figshare.19169609", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.6084/m9.figshare.19169609"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.6084/m9.figshare.19169609.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:25:19Z", "type": "Dataset", "created": "2022-05-16", "title": "Data and code from Semchenko et al. (2022) New Phytologist 10.1111/nph.18118", "description": "Open AccessData and code used in Semchenko M, Barry KE, de Vries FT, Mommer L, Maci\u00e1-Vicente JG (2022) Deciphering the role of specialist and generalist plant\u2013microbial interactions as drivers of plant\u2013soil feedback. New Phytologist, 10.1111/nph.18118 for the analysis of host ranges across plant-associated fungal and oomycete guilds.
", "keywords": ["2. Zero hunger", "host specifity", "Ecology", "plant-soil feedback", "FOS: Biological sciences", "mycorrhizas", "15. Life on land", "ecology", "microbial interactions", "plant pathogens", "saprotrophs"], "contacts": [{"organization": "Semchenko, Marina, Barry, Kathryn E., de Vries, Franciska T., Mommer, Liesje, Moora, Mari, Maci\u00e1-Vicente, Jose G.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.6084/m9.figshare.19169609.v1"}, {"rel": "self", "type": "application/geo+json", "title": "10.6084/m9.figshare.19169609.v1", "name": "item", "description": "10.6084/m9.figshare.19169609.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.6084/m9.figshare.19169609.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10568/100306", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:25:51Z", "type": "Journal Article", "created": "2019-02-25", "title": "AtoxigenicAspergillus flavusIsolates Endemic to Almond, Fig, and Pistachio Orchards in California with Potential to Reduce Aflatoxin Contamination in these Crops", "description": "

In California, aflatoxin contamination of almond, fig, and pistachio has become a serious problem in recent years due to long periods of drought and probably other climatic changes. The atoxigenic biocontrol product Aspergillus flavus AF36 has been registered for use to limit aflatoxin contamination of pistachio since 2012 and for use in almond and fig since 2017. New biocontrol technologies employ multiple atoxigenic genotypes because those provide greater benefits than using a single genotype. Almond, fig, and pistachio industries would benefit from a multi-strain biocontrol technology for use in these three crops. Several A. flavus vegetative compatibility groups (VCGs) associated with almond, fig, and pistachio composed exclusively of atoxigenic isolates, including the VCG to which AF36 belongs to, YV36, were previously characterized in California. Here, we report additional VCGs associated with either two or all three crops. Representative isolates of 12 atoxigenic VCGs significantly (P < 0.001) reduced (>80%) aflatoxin accumulation in almond and pistachio when challenged with highly toxigenic isolates of A. flavus and A. parasiticus under laboratory conditions. Isolates of the evaluated VCGs, including AF36, constitute valuable endemic, well-adapted, and efficient germplasm to design a multi-crop, multi-strain biocontrol strategy for use in tree crops in California. Availability of such a strategy would favor long-term atoxigenic A. flavus communities across the affected areas of California, and this would result in securing domestic and export markets for the nut crop and fig farmer industries and, most importantly, health benefits to consumers.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "aflatoxins", "0303 health sciences", "almonds", "Food Contamination", "15. Life on land", "Ficus", "Prunus dulcis", "6. Clean water", "California", "03 medical and health sciences", "aspergillus flavus", "Aflatoxins", "13. Climate action", "Pistacia", "pistachios", "Microbial Interactions", "figs", "california", "Aspergillus flavus"]}, "links": [{"href": "https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-08-18-1333-RE"}, {"href": "https://doi.org/10568/100306"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Disease", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10568/100306", "name": "item", "description": "10568/100306", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10568/100306"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-01T00:00:00Z"}}, {"id": "2898547471", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:26:58Z", "type": "Journal Article", "created": "2018-10-27", "title": "Hidden miners \u2013 the roles of cover crops and soil microorganisms in phosphorus cycling through agroecosystems", "description": "Phosphorus (P) is a limiting nutrient in many agroecosystems and costly fertilizer inputs can cause negative environmental impacts. Cover crops constitute a promising management option for sustainable intensification of agriculture. However, their interactions with the soil microbial community, which is a key driver of P cycling, and their effects on the following crop, have not yet been systematically assessed. We conducted a meta-analysis of published field studies on cover crops and P cycling, focusing on plant-microbe interactions. We describe several distinct, simultaneous mechanisms of P benefits for the main crop. Decomposition dynamics, governed by P concentration, are critical for the transfer of P from cover crop residues to the main crop. Cover crops may enhance the soil microbial community by providing a legacy of increased mycorrhizal abundance, microbial biomass P, and phosphatase activity. Cover crops are generally most effective in systems low in available P, and may access \u2018unavailable\u2019 P pools. However, their effects on P availability are difficult to detect by standard soil P tests, except for increases after the use of Lupinus sp. Agricultural management (i.e. cover crop species selection, tillage, fertilization) can improve cover crop effects. In summary, cover cropping has the potential to tighten nutrient cycling in agricultural systems under different conditions, increasing crop P nutrition and yield.", "keywords": ["2. Zero hunger", "Conservation agriculture", "Mobilisation We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.

3.Graphical Abstract

A step-by-step method for creating a tailored 3D culture medium for study of soil microbes.

The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion\uffe2\uff84\uffa2 resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion\uffe2\uff84\uffa2 particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.