{"type": "FeatureCollection", "features": [{"id": "10.1046/j.1365-3040.2002.00831.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:35Z", "type": "Journal Article", "created": "2003-03-12", "title": "N-2 Fixation By Acacia Species Increases Under Elevated Atmospheric Co2", "description": "Abstract<p>In the present study the effect of elevated CO2 on growth and nitrogen fixation of seven Australian Acacia species was investigated. Two species from semi\uffe2\uff80\uff90arid environments in central Australia (Acacia aneura and A. tetragonophylla) and five species from temperate south\uffe2\uff80\uff90eastern Australia (Acacia irrorata, A. mearnsii, A. dealbata, A. implexa and A. melanoxylon) were grown for up to 148\uffe2\uff80\uff83d in controlled greenhouse conditions at either ambient (350\uffe2\uff80\uff83\uffc2\uffb5mol\uffe2\uff80\uff83mol\uffe2\uff88\uff921) or elevated (700\uffe2\uff80\uff83\uffc2\uffb5mol\uffe2\uff80\uff83mol\uffe2\uff88\uff921) CO2 concentrations. After establishment of nodules, the plants were completely dependent on symbiotic nitrogen fixation. Six out of seven species had greater relative growth rates and lower whole plant nitrogen concentrations under elevated versus normal CO2. Enhanced growth resulted in an increase in the amount of nitrogen fixed symbiotically for five of the species. In general, this was the consequence of lower whole\uffe2\uff80\uff90plant nitrogen concentrations, which equate to a larger plant and greater nodule mass for a given amount of nitrogen. Since the average amount of nitrogen fixed per unit nodule mass was unaltered by atmospheric CO2, more nitrogen could be fixed for a given amount of plant nitrogen. For three of the species, elevated CO2 increased the rate of nitrogen fixation per unit nodule mass and time, but this was completely offset by a reduction in nodule mass per unit plant mass.</p>", "keywords": ["0106 biological sciences", "0301 basic medicine", "2. Zero hunger", "Acacia mearnsii", "Elevated atmospheric CO2", "Aneura Acacia", "Acacia", "growth response", "15. Life on land", "01 natural sciences", "Acacia dealbata", "Relative growth rate", "03 medical and health sciences", "nitrogen fixation", "Acacia aneura", "Nitrogenase", "Keywords: carbon dioxide enrichment", "Acacia melanoxylon"]}, "links": [{"href": "https://doi.org/10.1046/j.1365-3040.2002.00831.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1046/j.1365-3040.2002.00831.x", "name": "item", "description": "10.1046/j.1365-3040.2002.00831.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1046/j.1365-3040.2002.00831.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2002-03-21T00:00:00Z"}}, {"id": "10.1093/jxb/erq249", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:05Z", "type": "Journal Article", "created": "2010-08-27", "title": "Plant Physiology And Proteomics Reveals The Leaf Response To Drought In Alfalfa (Medicago Sativa L.)", "description": "Despite its relevance, protein regulation, metabolic adjustment, and the physiological status of plants under drought is not well understood in relation to the role of nitrogen fixation in nodules. In this study, nodulated alfalfa plants were exposed to drought conditions. The study determined the physiological, metabolic, and proteomic processes involved in photosynthetic inhibition in relation to the decrease in nitrogenase (N(ase)) activity. The deleterious effect of drought on alfalfa performance was targeted towards photosynthesis and N(ase) activity. At the leaf level, photosynthetic inhibition was mainly caused by the inhibition of Rubisco. The proteomic profile and physiological measurements revealed that the reduced carboxylation capacity of droughted plants was related to limitations in Rubisco protein content, activation state, and RuBP regeneration. Drought also decreased amino acid content such as asparagine, and glutamic acid, and Rubisco protein content indicating that N availability limitations were caused by N(ase) activity inhibition. In this context, drought induced the decrease in Rubisco binding protein content at the leaf level and proteases were up-regulated so as to degrade Rubisco protein. This degradation enabled the reallocation of the Rubisco-derived N to the synthesis of amino acids with osmoregulant capacity. Rubisco degradation under drought conditions was induced so as to remobilize Rubisco-derived N to compensate for the decrease in N associated with N(ase) inhibition. Metabolic analyses showed that droughted plants increased amino acid (proline, a major compound involved in osmotic regulation) and soluble sugar (D-pinitol) levels to contribute towards the decrease in osmotic potential (\u03a8(s)). At the nodule level, drought had an inhibitory effect on N(ase) activity. This decrease in N(ase) activity was not induced by substrate shortage, as reflected by an increase in total soluble sugars (TSS) in the nodules. Proline accumulation in the nodule could also be associated with an osmoregulatory response to drought and might function as a protective agent against ROS. In droughted nodules, the decrease in N(2) fixation was caused by an increase in oxygen resistance that was induced in the nodule. This was a mechanism to avoid oxidative damage associated with reduced respiration activity and the consequent increase in oxygen content. This study highlighted that even though drought had a direct effect on leaves, the deleterious effects of drought on nodules also conditioned leaf responsiveness.", "keywords": ["Proteomics", "0301 basic medicine", "570", "Rubisco", "Proteome", "[SDV]Life Sciences [q-bio]", "proteome", "N-2 FIXATION RESPONSE", "drought", "N2 fixation", "03 medical and health sciences", "XANTHOPHYLL CYCLE", "N-2 fixation", "2-CYSTEINE PEROXIREDOXIN", "Nitrogenase", "oxidative stress", "AMINO-ACIDS", "Photosynthesis", "climate", "agriculture", "Plant Proteins", "580", "N remobilization", "2. Zero hunger", "0303 health sciences", "photosynthesis", "PINITOL ACCUMULATION", "Drought", "RIBULOSE-1", "5-BISPHOSPHATE CARBOXYLASE-OXYGENASE", "Water", "BRASSICA-NAPUS", "N(O)-TERT-BUTYLDIMETHYLSILYL DERIVATIVES", "15. Life on land", "Research Papers", "6. Clean water", "Droughts", "[SDV] Life Sciences [q-bio]", "Plant Leaves", "nitrogen fixation", "Oxidative stress", "rubisco", "NITROGEN-FIXATION", "WATER-WATER CYCLE", "Medicago sativa"]}, "links": [{"href": "https://doi.org/10.1093/jxb/erq249"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/jxb/erq249", "name": "item", "description": "10.1093/jxb/erq249", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/jxb/erq249"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-08-25T00:00:00Z"}}, {"id": "10.3389/fmicb.2018.00703", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:36Z", "type": "Journal Article", "created": "2018-04-30", "title": "Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP \u2013 A Bioinformatics Pipeline for Analyzing nifH Amplicon Data", "description": "Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ('NifH MiSeq Illumina Amplicon Analysis Pipeline'), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.", "keywords": ["0301 basic medicine", "DIVERSITY", "nifH gene", "Microbiology", "03 medical and health sciences", "NifMAP", "Nitrogen fixation", "PARTICULATE METHANE MONOOXYGENASE", "MOLYBDENUM-NITROGENASE", "Primer evaluation", "MICROORGANISMS", "NifH gene", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "SEQUENCES", "GROUP-IV NITROGENASE", "AMPLIFICATION", "PERFORMANCE", "16. Peace & justice", "QR1-502", "primer evaluation", "nitrogen fixation", "106022 Microbiology", "COMMUNITIES", "N-2 FIXATION", "Illumina amplicon sequencing"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2018.00703"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2018.00703", "name": "item", "description": "10.3389/fmicb.2018.00703", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2018.00703"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-30T00:00:00Z"}}, {"id": "11353/10.1033274", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:26:12Z", "type": "Journal Article", "created": "2018-04-30", "title": "Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP \u2013 A Bioinformatics Pipeline for Analyzing nifH Amplicon Data", "description": "Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ('NifH MiSeq Illumina Amplicon Analysis Pipeline'), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.", "keywords": ["0301 basic medicine", "DIVERSITY", "nifH gene", "Microbiology", "03 medical and health sciences", "NifMAP", "Nitrogen fixation", "PARTICULATE METHANE MONOOXYGENASE", "MOLYBDENUM-NITROGENASE", "Primer evaluation", "MICROORGANISMS", "NifH gene", "2. Zero hunger", "106022 Mikrobiologie", "0303 health sciences", "SEQUENCES", "GROUP-IV NITROGENASE", "AMPLIFICATION", "PERFORMANCE", "16. Peace & justice", "QR1-502", "primer evaluation", "nitrogen fixation", "106022 Microbiology", "COMMUNITIES", "N-2 FIXATION", "Illumina amplicon sequencing"]}, "links": [{"href": "https://doi.org/11353/10.1033274"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11353/10.1033274", "name": "item", "description": "11353/10.1033274", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11353/10.1033274"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-30T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Nitrogenase&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Nitrogenase&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Nitrogenase&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Nitrogenase&offset=4", "hreflang": "en-US"}], "numberMatched": 4, "numberReturned": 4, "distributedFeatures": [], "timeStamp": "2026-07-27T18:04:37.668463Z"}