Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.Isoprene (2-methyl-1,3-butadiene), the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, is highly reactive and can have diverse and often detrimental atmospheric effects, which impact on climate and health. Most isoprene is produced by terrestrial plants, but (micro)algal production is important in aquatic environments, and the relative bacterial contribution remains unknown. Soils are a sink for isoprene, and bacteria that can use isoprene as a carbon and energy source have been cultivated and also identified using cultivation-independent methods from soils, leaves and coastal/marine environments. Bacteria belonging to the Actinobacteria are most frequently isolated and identified, and Proteobacteria have also been shown to degrade isoprene. In the freshwater-sediment isolate, Rhodococcus strain AD45, initial oxidation of isoprene to 1,2-epoxy-isoprene is catalyzed by a multicomponent isoprene monooxygenase encoded by the genes isoABCDEF. The resultant epoxide is converted to a glutathione conjugate by a glutathione S-transferase encoded by isoI, and further degraded by enzymes encoded by isoGHJ. Genome sequence analysis of actinobacterial isolates belonging to the genera Rhodococcus, Mycobacterium and Gordonia has revealed that isoABCDEF and isoGHIJ are linked in an operon, either on a plasmid or the chromosome. In Rhodococcus strain AD45 both isoprene and epoxy-isoprene induce a high level of transcription of 22 contiguous genes, including isoABCDEF and isoGHIJ. Sequence analysis of the isoA gene, encoding the large subunit of the oxygenase component of isoprene monooxygenase, from isolates has facilitated the development of PCR primers that are proving valuable in investigating the ecology of uncultivated isoprene-degrading bacteria.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "550", "QH301 Biology", "Review Article", "Plants", "15. Life on land", "6. Clean water", "Mixed Function Oxygenases", "Actinobacteria", "Soil", "03 medical and health sciences", "Hemiterpenes", "13. Climate action", "Pentanes", "11. Sustainability", "Butadienes", "Microalgae", "Rhodococcus"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/66436/1/Published_manuscript.pdf"}, {"href": "http://www.nature.com/articles/s41396-018-0072-6.pdf"}, {"href": "https://repository.essex.ac.uk/21526/1/s41396-018-0072-6.pdf"}, {"href": "https://doi.org/10.1038/s41396-018-0072-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41396-018-0072-6", "name": "item", "description": "10.1038/s41396-018-0072-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41396-018-0072-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-20T00:00:00Z"}}, {"id": "10.1038/s41396-023-01467-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:20:12Z", "type": "Journal Article", "created": "2023-07-14", "title": "Nitrification and beyond: metabolic versatility of ammonia oxidising archaea", "description": "AbstractAmmonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "human microbiome", "Review Article", "Gastrointestinal Microbiome", "3. Good health", "lactic acid bacteria", "03 medical and health sciences", "probiotics", "Health", "Lactobacillales", "food microbiome; human microbiome; lactic acid bacteria; probiotics", "food microbiome", "Food Microbiology", "Humans"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/811718/2/FEMSMicroRev%2c2020_LABfoodgut.pdf"}, {"href": "http://academic.oup.com/femsre/article-pdf/44/4/454/37084083/fuaa015.pdf"}, {"href": "https://doi.org/10.1093/femsre/fuaa015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Reviews", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsre/fuaa015", "name": "item", "description": "10.1093/femsre/fuaa015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsre/fuaa015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-18T00:00:00Z"}}, {"id": "10.1098/rspa.2019.0098", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:21:22Z", "type": "Journal Article", "created": "2019-08-14", "title": "Silicon isotopes in Arctic and sub-Arctic glacial meltwaters: the role of subglacial weathering in the silicon cycle", "description": "Glacial environments play an important role in high-latitude marine nutrient cycling, potentially contributing significant fluxes of silicon (Si) to the polar oceans, either as dissolved silicon (DSi) or as dissolvable amorphous silica (ASi). Silicon is a key nutrient in promoting marine primary productivity, contributing to atmospheric CO 2 removal. We present the current understanding of Si cycling in glacial systems, focusing on the Si isotope (\uffce\uffb4 30 Si) composition of glacial meltwaters. We combine existing glacial \uffce\uffb4 30 Si data with new measurements from 20 sub-Arctic glaciers, showing that glacial meltwaters consistently export isotopically light DSi compared with non-glacial rivers (+0.16\uffe2\uff80\uffb0 versus +1.38\uffe2\uff80\uffb0). Glacial \uffce\uffb4 30 Si ASi composition ranges from \uffe2\uff88\uff920.05\uffe2\uff80\uffb0 to \uffe2\uff88\uff920.86\uffe2\uff80\uffb0 but exhibits low seasonal variability. Silicon fluxes and \uffce\uffb4 30 Si composition from glacial systems are not commonly included in global Si budgets and isotopic mass balance calculations at present. We discuss outstanding questions, including the formation mechanism of ASi and the export of glacial nutrients from fjords. Finally, we provide a contextual framework for the recent advances in our understanding of subglacial Si cycling and highlight critical research avenues for assessing potential future changes in these environments. Glacial environments play an important role in high-latitude marine nutrient cycling, potentially contributing significant fluxes of silicon (Si) to the polar oceans, either as dissolved silicon (DSi) or as dissolvable amorphous silica (ASi). Silicon is a key nutrient in promoting marine primary productivity, contributing to atmospheric CO 2 removal. We present the current understanding of Si cycling in glacial systems, focusing on the Si isotope (\uffce\uffb4 30 Si) composition of glacial meltwaters. We combine existing glacial \uffce\uffb4 30 Si data with new measurements from 20 sub-Arctic glaciers, showing that glacial meltwaters consistently export isotopically light DSi compared with non-glacial rivers (+0.16\uffe2\uff80\uffb0 versus +1.38\uffe2\uff80\uffb0). Glacial \uffce\uffb4 30 Si ASi composition ranges from \uffe2\uff88\uff920.05\uffe2\uff80\uffb0 to \uffe2\uff88\uff920.86\uffe2\uff80\uffb0 but exhibits low seasonal variability. Silicon fluxes and \uffce\uffb4 30 Si composition from glacial systems are not commonly included in global Si budgets and isotopic mass balance calculations at present. We discuss outstanding questions, including the formation mechanism of ASi and the export of glacial nutrients from fjords. Finally, we provide a contextual framework for the recent advances in our understanding of subglacial Si cycling and highlight critical research avenues for assessing potential future changes in these environments. Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.