{"type": "FeatureCollection", "features": [{"id": "10.1007/s00436-025-08483-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:14:48Z", "type": "Journal Article", "created": "2025-04-08", "title": "Implementation of real-time PCR assays for diagnosing intestinal protozoa infections", "description": "Abstract

Intestinal protozoa infections present a major public health challenge, particularly in areas with poor sanitation and limited access to clean water. Effective diagnostic methods are critical, yet traditional microscopy, though widely used for its simplicity, lacks the sensitivity and specificity of modern techniques like real-time Polymerase Chain Reaction (qPCR), making the latter a more effective tool for monitoring and assessing the burden of intestinal protozoa diseases. In this study, we implemented two duplex qPCR assays to detect Entamoeba dispar\uffe2\uff80\uff89+\uffe2\uff80\uff89Entamoeba histolytica and Cryptosporidium spp.\uffe2\uff80\uff89+\uffe2\uff80\uff89Chilomastix mesnili, along with singleplex assays for Giardia duodenalis and Blastocystis spp., using a 10 \uffc2\uffb5L reaction volume. This marks the first molecular detection of Chilomastix mesnili by qPCR, enhancing diagnostic precision. Using these, we analyzed stool samples from 70 patients on Pemba Island, Tanzania, before and 54 samples after treatment with 20, 25, or 30\uffc2\uffa0mg of emodepside or placebo, aiming to assess protozoa prevalence for this region and emodepside\uffe2\uff80\uff99s potential antiprotozoal effects. Our qPCR reliably detected protozoa in 74.4% of samples, with Entamoeba histolytica and Entamoeba dispar in 31.4% of cases. Notably, one-third of these infections were caused by Entamoeba histolytica. No significant reduction in protozoa was observed after emodepside treatment compared to placebo. The study highlights the utility of qPCR in providing species-level differentiation and improving the speed and cost-effectiveness of testing. The high prevalence of protozoa in this region underscores the need for continued monitoring and control efforts, though emodepside was not effective against protozoa infections. Studies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla\uffe2\uff80\uff94the Proteobacteria, Bacteroidetes, and Firmicutes\uffe2\uff80\uff94accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Geologic Sediments", "Salinity", "0303 health sciences", "Bacteria", "Genes", " rRNA", "Sequence Analysis", " DNA", "15. Life on land", "Archaea", "Polymerase Chain Reaction", "Texas", "6. Clean water", "Soil", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Water Microbiology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2010.3"}, {"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/ismej.2010.3", "name": "item", "description": "10.1038/ismej.2010.3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2010.3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-04T00:00:00Z"}}, {"id": "10.1093/jambio/lxac048", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:19:05Z", "type": "Journal Article", "created": "2023-03-17", "title": "Two species-specific TaqMan-based quantitative polymerase chain reaction assays for the detection in soil ofPaenibacillus polymyxainocula", "description": "AbstractAims

The increasingly widespread use of beneficial microbial inocula in agriculture gives rise to two primary needs: i) the assessment of the environmental risk, i.e. their impact on local soil microbiome and soil properties; ii) being able to track them and monitor their persistence and fate to both optimize their formulation and application method. In previous years, PCR-based methods have detected bacterial or fungal bioinoculant at the species or strain level. However, the selective detection, quantification, and monitoring of target microbial species in a complex ecosystem such as soil require that the tests possess high specificity and sensitivity.

Methods and results

The work proposes a quantitative real-time PCR detection method using TaqMan chemistry, showing high specificity and sensitivity for the Paenibacillus polymyxa K16 strain. The primer and probe sets were designed using the polymyxin gene cluster targeting pmxC and pmxE sequences. Validation tests showed that these assays allowed a discriminant and specific detection of P. polymyxa K16 in soil.

Conclusion

The TaqMan-assay developed could thus ensure the necessary level of discrimination required by commercial and regulatory purposes to detect and monitor the bioinoculant in soil.The trophic interactions between viruses, bacteria and protists play a crucial role in structuring microbial communities and regulating nutrient and organic matter flux. Here, we show that the impact on viral density by heterotrophic flagellates is related to their feeding behaviour (feeding on sedimented particles \uffe2\uff80\uff93 Thaumatomonas coloniensis, filter feeding of suspended particles \uffe2\uff80\uff93 Salpingoeca sp., and actively searching raptorial feeding \uffe2\uff80\uff93 Goniomonas truncata). Phage MS2 was co\uffe2\uff80\uff90incubated with flagellates and the natural bacterial and viral community originating from the same groundwater habitats where the flagellates were isolated. Three complementary assays, i.e. flow cytometry, qPCR and plaque assay, were used for enumeration of total viruses, total MS2 phages, and free and infectious MS2, respectively, to provide insights into the grazing mechanisms of the flagellates on viruses. Phage MS2 was actively removed by the suspension feeders T.\uffe2\uff80\uff89coloniensis and Salpingoeca sp. in contrast with the actively raptoriale grazer G.\uffe2\uff80\uff89truncata. The decline of viral titre was demonstrated to be caused by ingestion rather than random absorption by both qPCR and locating protein fluorescently labelled MS2 inside the flagellates. Further, we indicate that phages can be used as a minor carbon source for flagellates. Collectively, these data demonstrate that eliminating viruses can be an important function of protists in microbial food webs, carbon cycling and potentially water quality control.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Viral Plaque Assay", "Viral Load", "Flow Cytometry", "Real-Time Polymerase Chain Reaction", "7. Clean energy", "Carbon", "6. Clean water", "03 medical and health sciences", "Cercozoa", "Cryptophyta", "Choanoflagellata", "Levivirus"]}, "links": [{"href": "https://doi.org/10.1111/1758-2229.12119"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1758-2229.12119", "name": "item", "description": "10.1111/1758-2229.12119", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1758-2229.12119"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-19T00:00:00Z"}}, {"id": "10.1111/j.1365-3040.2008.01822.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:39Z", "type": "Journal Article", "created": "2008-04-22", "title": "Elevated Co2 Increases Photosynthesis, Biomass And Productivity, And Modifies Gene Expression In Sugarcane", "description": "ABSTRACT

Because of the economical relevance of sugarcane and its high potential as a source of biofuel, it is important to understand how this crop will respond to the foreseen increase in atmospheric [CO2]. The effects of increased [CO2] on photosynthesis, development and carbohydrate metabolism were studied in sugarcane (Saccharum ssp.). Plants were grown at ambient (\uffe2\uff88\uffbc370\uffe2\uff80\uff83ppm) and elevated (\uffe2\uff88\uffbc720\uffe2\uff80\uff83ppm) [CO2] during 50 weeks in open\uffe2\uff80\uff90top chambers. The plants grown under elevated CO2 showed, at the end of such period, an increase of about 30% in photosynthesis and 17% in height, and accumulated 40% more biomass in comparison with the plants grown at ambient [CO2]. These plants also had lower stomatal conductance and transpiration rates (\uffe2\uff88\uff9237 and \uffe2\uff88\uff9232%, respectively), and higher water\uffe2\uff80\uff90use efficiency (c.a. 62%). cDNA microarray analyses revealed a differential expression of 35 genes on the leaves (14 repressed and 22 induced) by elevated CO2. The latter are mainly related to photosynthesis and development. Industrial productivity analysis showed an increase of about 29% in sucrose content. These data suggest that sugarcane crops increase productivity in higher [CO2], and that this might be related, as previously observed for maize and sorghum, to transient drought stress.

", "keywords": ["2. Zero hunger", "0106 biological sciences", "Sucrose", "Light", "Reverse Transcriptase Polymerase Chain Reaction", "Temperature", "Humidity", "Carbon Dioxide", "15. Life on land", "Lignin", "01 natural sciences", "Saccharum", "Plant Leaves", "Gene Expression Regulation", " Plant", "Plant Stomata", "Biomass", "Gases", "Photosynthesis", "Cellulose"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-3040.2008.01822.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": "10.1111/j.1365-3040.2008.01822.x", "name": "item", "description": "10.1111/j.1365-3040.2008.01822.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-3040.2008.01822.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-07-09T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2006.00235.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:44Z", "type": "Journal Article", "created": "2006-11-21", "title": "The Effects Of Stubble Retention And Nitrogen Application On Soil Microbial Community Structure And Functional Gene Abundance Under Irrigated Maize", "description": "The effects of agronomic management practices on the soil microbial community were investigated in a maize production system in New South Wales, Australia. The site has been intensively studied to measure the impact of stubble management and N-fertilizer application on greenhouse gas emissions (CO(2) and N(2)O), N-cycling, pathology, soil structure and yield. As all of these endpoints can be regulated by microbial processes, the microbiology of the system was examined. Soil samples were taken after a winter fallow period and the diversity of the bacterial and fungal communities was measured using PCR-denaturing gradient gel electrophoresis. Stubble and N shifted the structure of bacterial and fungal communities with the primary driver being stubble addition on the fungal community structure (P<0.05 for all effects). Changes in C, N (total and NO(3)), K and Na, were correlated (P<0.05) with variation in the microbial community structure. Quantitative PCR showed that nifH (nitrogen fixation) and napA (denitrification) gene abundance increased upon stubble retention, whereas amoA gene numbers were increased by N addition. These results showed that the management of both stubble and N have significant and long-term impacts on the size and structure of the soil microbial community at phylogenetic and functional levels.", "keywords": ["Electrophoresis", "0301 basic medicine", "Nitrogen", "Genes", " Fungal", "Polymerase Chain Reaction", "Zea mays", "630", "Soil", "03 medical and health sciences", "Nitrogen Fixation", "Cluster Analysis", "Electrophoresis", " Gel", " Two-Dimensional", "Fertilizers", "Soil Microbiology", "2. Zero hunger", "Gel", "0303 health sciences", "Bacteria", "Bacterial", "Australia", "Fungi", "Agriculture", "15. Life on land", "6. Clean water", "Fungal", "Genes", "Genes", " Bacterial", "13. Climate action", "Two-Dimensional"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2006.00235.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2006.00235.x", "name": "item", "description": "10.1111/j.1574-6941.2006.00235.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2006.00235.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-03-01T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2007.00394.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:44Z", "type": "Journal Article", "created": "2007-10-19", "title": "Quantitation And Diversity Analysis Of Ruminal Methanogenic Populations In Response To The Antimethanogenic Compound Bromochloromethane", "description": "Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.", "keywords": ["Male", "0301 basic medicine", "Rumen", "Bromochloromethane", "Methanogens", "Molecular Sequence Data", "Euryarchaeota", "Methanobrevibacter", "Polymerase Chain Reaction", "630", "03 medical and health sciences", "2402 Applied Microbiology and Biotechnology", "Animals", "Methyl coenzyme-M reductase", "Phylogeny", "Gene Library", "2. Zero hunger", "0303 health sciences", "Hydrocarbons", " Halogenated", "2404 Microbiology", "Sequence Analysis", " DNA", "mcrA", "qPCR", "DNA", " Archaeal", "Cattle", "Oxidoreductases", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2007.00394.x", "name": "item", "description": "10.1111/j.1574-6941.2007.00394.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2011.01192.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:44Z", "type": "Journal Article", "created": "2011-09-01", "title": "Soil Characteristics More Strongly Influence Soil Bacterial Communities Than Land-Use Type", "description": "To gain insight into the factors driving the structure of bacterial communities in soil, we applied real-time PCR, PCR-denaturing gradient gel electrophoreses, and phylogenetic microarray approaches targeting the 16S rRNA gene across a range of different land usages in the Netherlands. We observed that the main differences in the bacterial communities were not related to land-use type, but rather to soil factors. An exception was the bacterial community of pine forest soils (PFS), which was clearly different from all other sites. PFS had lowest bacterial abundance, lowest numbers of operational taxonomic units (OTUs), lowest soil pH, and highest C : N ratios. C : N ratio strongly influenced bacterial community structure and was the main factor separating PFS from other fields. For the sites other than PFS, phosphate was the most important factor explaining the differences in bacterial communities across fields. Firmicutes were the most dominant group in almost all fields, except in PFS and deciduous forest soils (DFS). In PFS, Alphaproteobacteria was most represented, while in DFS, Firmicutes and Gammaproteobacteria were both highly represented. Interestingly, Bacillii and Clostridium OTUs correlated with pH and phosphate, which might explain their high abundance across many of the Dutch soils. Numerous bacterial groups were highly correlated with specific soil factors, suggesting that they might be useful as indicators of soil status.", "keywords": ["land use change", "DNA", " Bacterial", "0301 basic medicine", "RNA 16S", "polymerase chain reaction", "soil nitrogen", "DNA sequence", "soil microorganism", "electrokinesis", "chemistry", "phylogeny", "Real-Time Polymerase Chain Reaction", "soil", "Soil", "03 medical and health sciences", "NIOO", "RNA", " Ribosomal", " 16S", "genetics", "soil carbon", "Phylogeny", "Soil Microbiology", "phosphate", "biodiversity", "Alphaproteobacteria", "Netherlands", "growth", " development and aging", "2. Zero hunger", "abundance", "0303 health sciences", "real time", "Bacteria", "pH", "Denaturing Gradient Gel Electrophoresis", "microbiology", "denaturing gradient gel electrophoresis", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "bacterium", "bacterial DNA", "phylogenetics", "classification", "real time polymerase chain reaction", "microbial community", "Gammaproteobacteria"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2011.01192.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2011.01192.x", "name": "item", "description": "10.1111/j.1574-6941.2011.01192.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2011.01192.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-09-19T00:00:00Z"}}, {"id": "10.1371/journal.pntd.0012872", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:20:11Z", "type": "Journal Article", "created": "2025-02-18", "title": "Performance of real-time polymerase chain reaction and Kato-Katz for diagnosing soil-transmitted helminth infections and evaluating treatment efficacy of emodepside in randomized controlled trials", "description": "Background

The World Health Organization recommends the use of the microscopy-based Kato-Katz thick smear for diagnosing soil-transmitted helminth (STH) infections. Despite its simplicity and cost-effectiveness, the Kato-Katz method faces challenges, including reader subjectivity and reduced sensitivity. Real-time polymerase chain reaction (qPCR) technology offers standardized readouts and higher sensitivity, making it suitable for STH diagnosis and monitoring the treatment efficacy of emodepside within the framework of randomized controlled trials.

Methodology/Principal findings

We evaluated the performance of Kato-Katz versus qPCR for assessing treatment efficacy in terms of cure rates, of single doses of 5, 10, 15, 20, 25 and 30\uffe2\uff80\uff89mg of emodepside compared to 400\uffe2\uff80\uff89mg albendazole. Spearman\uffe2\uff80\uff99s rank correlation coefficient examined the correlation between STH eggs per gram in stool samples and qPCR Ct values. Diagnostic sensitivity of qPCR was calculated using a Bayesian latent class modelling approach with data from Ascaris lumbricoides infections. Agreement between Kato-Katz and qPCR at baseline was 93.57% for Trichuris trichiura, and 73.49% for both hookworm and A. lumbricoides. For the latter helminth qPCR demonstrated higher sensitivity (85.00% vs. 47.70%) and slightly lower specificity (93.40% vs. 99.40%) compared to Kato-Katz. We observed a fair to moderate agreement with negative correlation between Ct values and Kato-Katz egg counts. Treatment efficacy, as assessed by qPCR, was lower for all doses of emodepside and albendazole compared to Kato-Katz. Nonetheless, emodepside demonstrated higher cure rates against T. trichiura and A. lumbricoides infections compared to albendazole.

Conclusion/ Significance

Our study confirmed that qPCR is a sensitive diagnostic method for diagnosing STH infections compared to Kato-Katz and serves as a valuable tool for determining treatment efficacy in clinical trials. Furthermore, qPCR confirmed the better treatment efficacy of emodepside compared to albendazole, despite indicating lower cure rates than Kato-Katz.Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.

", "keywords": ["Polymerase Chain Reaction", "geography", "630", "1000 Technology", "Soil", "soil type", "RNA", " Ribosomal", " 16S", "C500 - Microbiology", "genetic polymorphism", "soil analysis", "Bacteria (microorganisms)", "Soil Microbiology", "2. Zero hunger", "article", "Agriculture", "Fabaceae", "Biodiversity", "legume", "04 agricultural and veterinary sciences", "Bacterial Typing Techniques", "microbial community", "Polymorphism", " Restriction Fragment Length", "0605 Microbiology", "Electrophoresis", "16S", "570", "Conservation of Natural Resources", "productivity", "RNA 16S", "soil microorganism", "0600 Biological Sciences", "DNA", " Ribosomal", "0700 Agricultural And Veterinary Sciences", "controlled study", "community composition", "Polymorphism", "Pisum sativum", "Ecosystem", "Ribosomal", "nonhuman", "Bacteria", "bacterial flora", "land use", "DNA", "15. Life on land", "bacterial disease", "Restriction Fragment Length", "C180 - Ecology", "physiology", "RNA", "Soils", "0401 agriculture", " forestry", " and fisheries", "bioavailability"]}, "links": [{"href": "https://doi.org/10.1128/aem.69.3.1800-1809.2003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.69.3.1800-1809.2003", "name": "item", "description": "10.1128/aem.69.3.1800-1809.2003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.69.3.1800-1809.2003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-03-01T00:00:00Z"}}, {"id": "10.1128/aem.71.5.2713-2722.2005", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:54Z", "type": "Journal Article", "created": "2005-05-03", "title": "Changes In Nitrogen-Fixing And Ammonia-Oxidizing Bacterial Communities In Soil Of A Mixed Conifer Forest After Wildfire", "description": "ABSTRACT

This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH 3 -N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Base Sequence", "Molecular Sequence Data", "15. Life on land", "Polymerase Chain Reaction", "Fires", "Trees", "Soil", "03 medical and health sciences", "Ammonia", "Nitrogen Fixation", "Oxidoreductases", "Oxidation-Reduction", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Chris M. Yeager, Diana E. Northup, Susan M. Barns, Cheryl R. Kuske, Christy C. Grow,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1128/aem.71.5.2713-2722.2005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.71.5.2713-2722.2005", "name": "item", "description": "10.1128/aem.71.5.2713-2722.2005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.71.5.2713-2722.2005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-05-01T00:00:00Z"}}, {"id": "10.1371/journal.pone.0200979", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:15Z", "type": "Journal Article", "created": "2019-04-11", "title": "Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR", "description": "Abstract

Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition.

To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer\uffc2\uffae, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers between 1.00 and 2.20 m below ground level.

Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition.

Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier.

These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Science", "Microbial Consortia", "DIVERSITY", "SOFTWARE", "Real-Time Polymerase Chain Reaction", "BACILLUS-SUBTILIS", "BIOMASS", "03 medical and health sciences", "BIOAUGMENTATION", "DNA", " Bacterial/chemistry", "MICROBIAL COMMUNITIES", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "16S RIBOSOMAL-RNA", "Q", "R", "PROFILES", "ACIDS", "TRANSFORMATION", "6. Clean water", "Microbial Consortia/genetics", "Enhancer Elements", " Genetic", "13. Climate action", "Medicine", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/365395v1.full.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0200979"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0200979", "name": "item", "description": "10.1371/journal.pone.0200979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0200979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-09T00:00:00Z"}}, {"id": "10.1266/ggs.88.93", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:20:06Z", "type": "Journal Article", "created": "2015-03-03", "title": "Soil Bacterial Community Structure In Five Tropical Forests In Malaysia And One Temperate Forest In Japan Revealed By Pyrosequencing Analyses Of 16s Rrna Gene Sequence Variation", "description": "Bacterial community structure was investigated in five tropical rainforests in Sarawak, Malaysia and one temperate forest in Kyoto, Japan. A hierarchical sampling approach was employed, in which soil samples were collected from five sampling-sites within each forest. Pyrosequencing was performed to analyze a total of 493,790 16S rRNA amplicons. Despite differences in aboveground conditions, the composition of bacterial groups was similar across all sampling-sites and forests, with Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes accounting for 90% of all Phyla detected. At higher taxonomic levels, the same taxa were predominant, although there was significant heterogeneity in relative abundance of specific taxa across sampling-sites within one forest or across different forests. In all forests, the level of bacterial diversity, estimated using the Chao1 index, was on the order of 1,000, suggesting that tropical rainforests did not necessarily have a large soil bacterial diversity. The average number of reads per species (OTUs) per sampling-site was 8.0, and more than 40-50% of species were singletons, indicating that most bacterial species occurred infrequently and that few bacterial species achieved high predominance. Approximately 30% of species were specific to one sampling-site within a forest, and 40-60% of species were uniquely detected in one of the six forests studied here. Only 0.2% of species were detected in all forests, while on average 32.1% of species were detected in all sampling-sites within a forest. The results suggested that bacterial communities adapted to specific micro- and macro-environments, but macro-environmental diversity made a larger contribution to total bacterial diversity in forest soil.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Bacteria", "Malaysia", "Genetic Variation", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "Polymerase Chain Reaction", "Trees", "03 medical and health sciences", "Japan", "RNA", " Ribosomal", " 16S", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1266/ggs.88.93"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes%20%26amp%3B%20Genetic%20Systems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1266/ggs.88.93", "name": "item", "description": "10.1266/ggs.88.93", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1266/ggs.88.93"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-01T00:00:00Z"}}, {"id": "10.1371/journal.pone.0038858", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:12Z", "type": "Journal Article", "created": "2012-06-11", "title": "Decline In Topsoil Microbial Quotient, Fungal Abundance And C Utilization Efficiency Of Rice Paddies Under Heavy Metal Pollution Across South China", "description": "Open AccessLos suelos agr\u00edcolas han estado cada vez m\u00e1s sujetos a la contaminaci\u00f3n por metales pesados en todo el mundo. Sin embargo, los impactos en la estructura y actividad de la comunidad microbiana del suelo de los suelos de campo a\u00fan no se han caracterizado bien. En 2009 se recolectaron muestras de tierra vegetal de campos de arroz contaminados con metales pesados (PS) y sus campos de fondo (BGS) en cuatro sitios del sur de China. Los cambios con la contaminaci\u00f3n met\u00e1lica en relaci\u00f3n con el BGS en el tama\u00f1o y la estructura de la comunidad de los microorganismos del suelo se examinaron con m\u00faltiples ensayos microbiol\u00f3gicos de medici\u00f3n de carbono de biomasa (MBC) y nitr\u00f3geno (MBN), recuento en placa de colonias cultivables y an\u00e1lisis de \u00e1cidos grasos fosfol\u00edpidos (PLFA) junto con el perfil de electroforesis en gel de gradiente desnaturalizante (DGGE) del gen de ARNr 16S y ARNr 18S y ensayo de PCR en tiempo real. Adem\u00e1s, se llev\u00f3 a cabo una incubaci\u00f3n de laboratorio de 7 d\u00edas a una temperatura constante de 25 \u00b0C para realizar un seguimiento adicional de los cambios en la actividad metab\u00f3lica. Si bien la disminuci\u00f3n de la contaminaci\u00f3n por metales en MBC y MBN, as\u00ed como en el tama\u00f1o de la poblaci\u00f3n cultivable, el contenido total de PLFA y el n\u00famero de bandas DGGE de bacterias no se observaron de manera significativa y consistente, de hecho se observ\u00f3 una reducci\u00f3n significativa de la contaminaci\u00f3n por metales en el cociente microbiano, en el tama\u00f1o de la poblaci\u00f3n f\u00fangica cultivable y en la proporci\u00f3n de PLFA f\u00fangicos a bacterianos de manera consistente en todos los sitios en una medida que var\u00eda de 6% a 74%. Adem\u00e1s, se observ\u00f3 un aumento consistentemente significativo en el cociente metab\u00f3lico de hasta un 68% bajo contaminaci\u00f3n en todos los sitios. Estas observaciones apoyaron un cambio de la comunidad microbiana con disminuci\u00f3n en su abundancia, disminuci\u00f3n en la proporci\u00f3n de hongos y, por lo tanto, en la eficiencia de utilizaci\u00f3n de C bajo contaminaci\u00f3n en los suelos. Adem\u00e1s, las proporciones de cociente microbiano, de hongos a bacterias y qCO2 son mejores indicativas de los impactos de los metales pesados en la estructura y actividad de la comunidad microbiana. Los efectos potenciales de estos cambios en el ciclo del carbono y la producci\u00f3n de CO2 en los arrozales contaminados merecen m\u00e1s estudios de campo.", "keywords": ["Microbial population biology", "Colony Count", " Microbial", "Agricultural and Biological Sciences", "Sociology", "Soil water", "Soil Pollutants", "Soil Microbiology", "2. Zero hunger", "Principal Component Analysis", "Temperature gradient gel electrophoresis", "Ecology", "Q", "Fatty Acids", "R", "Life Sciences", "Agriculture", "04 agricultural and veterinary sciences", "Biota", "Pollution", "6. Clean water", "FOS: Sociology", "Chemistry", "Physical Sciences", "Environmental chemistry", "Medicine", "Research Article", "Environmental Monitoring", "16S ribosomal RNA", "China", "Microorganism", "Environmental Impact of Heavy Metal Contamination", "Nitrogen", "Science", "Population", "Soil Science", "Real-Time Polymerase Chain Reaction", "Environmental science", "Microbial Ecology", "12. Responsible consumption", "Metals", " Heavy", "Genetics", "Biology", "Demography", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "Marine Microbial Diversity and Biogeography", "Oryza", "15. Life on land", "Topsoil", "Carbon", "Agronomy", "RNA", " Ribosomal", "13. Climate action", "FOS: Biological sciences", "Environmental Science", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0038858"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0038858", "name": "item", "description": "10.1371/journal.pone.0038858", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0038858"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-11T00:00:00Z"}}, {"id": "10.1371/journal.pone.0076447", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:13Z", "type": "Journal Article", "created": "2013-09-26", "title": "The Arbuscular Mycorrhizal Fungal Community Response To Warming And Grazing Differs Between Soil And Roots On The Qinghai-Tibetan Plateau", "description": "Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most plant species in terrestrial ecosystems, and are affected by environmental variations. To reveal the impact of disturbance on an AM fungal community under future global warming, we examined the abundance and community composition of AM fungi in both soil and mixed roots in an alpine meadow on the Qinghai-Tibetan Plateau, China. Warming and grazing had no significant effect on AM root colonization, spore density and extraradical hyphal density. A total of 65 operational taxonomic units (OTUs) of AM fungi were identified from soil and roots using molecular techniques. AM fungal OTU richness was higher in soil (54 OTUs) than in roots (34 OTUs), and some AM fungi that differed between soil and roots, showed significantly biased occurrence to warming or grazing. Warming and grazing did not significantly affect AM fungal OTU richness in soil, but warming with grazing significantly increased AM fungal OTU richness in roots compared to the grazing-only treatment. Non-metric multidimensional scaling analysis showed that the AM fungal community composition was significantly different between soil and roots, and was significantly affected by grazing in roots, whereas in soil it was significantly affected by warming and plant species richness. The results suggest that the AM fungal community responds differently to warming and grazing in soil compared with roots. This study provides insights into the role of AM fungi under global environmental change scenarios in alpine meadows of the Qinghai-Tibetan Plateau.", "keywords": ["0106 biological sciences", "Hot Temperature", "Science", "Molecular Sequence Data", "Population Dynamics", "Global Warming", "Plant Roots", "Polymerase Chain Reaction", "01 natural sciences", "Species Specificity", "Mycorrhizae", "Herbivory", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Analysis of Variance", "Base Sequence", "Models", " Genetic", "Altitude", "Q", "R", "Bayes Theorem", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Spores", " Fungal", "15. Life on land", "Biota", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Polymorphism", " Restriction Fragment Length", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0076447"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0076447", "name": "item", "description": "10.1371/journal.pone.0076447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0076447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-09-26T00:00:00Z"}}, {"id": "10.1371/journal.pone.0159680", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:15Z", "type": "Journal Article", "created": "2016-07-28", "title": "Impacts Of Grazing Intensity And Plant Community Composition On Soil Bacterial Community Diversity In A Steppe Grassland", "description": "Soil bacteria play a key role in the ecological and evolutionary responses of agricultural ecosystems. Domestic herbivore grazing is known to influence soil bacterial community. However, the effects of grazing and its major driving factors on soil bacterial community remain unknown for different plant community compositions under increasing grazing intensity. Thus, to investigate soil bacterial community diversity under five plant community compositions (Grass; Leymus chinensis; Forb; L. chinensis & Forb; and Legume), we performed a four-year field experiment with different grazing intensity treatments (no grazing; light grazing, 4 sheep\u00b7ha-1; and heavy grazing, 6 sheep\u00b7ha-1) in a grassland in China. Total DNA was obtained from soil samples collected from the plots in August, and polymerase chain reaction (PCR) analysis and denaturing gradient gel electrophoresis (DGGE) fingerprinting were used to investigate soil bacterial community. The results showed that light grazing significantly increased indices of soil bacterial community diversity for the Forb and Legume groups but not the Grass and L. chinensis groups. Heavy grazing significantly reduced these soil bacterial diversity indices, except for the Pielou evenness index in the Legume group. Further analyses revealed that the soil N/P ratio, electrical conductivity (EC), total nitrogen (TN) and pH were the major environmental factors affecting the soil bacterial community. Our study suggests that the soil bacterial community diversity was influenced by grazing intensity and plant community composition in a meadow steppe. The present study provides a baseline assessment of the soil bacterial community diversity in a temperate meadow steppe.", "keywords": ["2. Zero hunger", "Sheep", "Denaturing Gradient Gel Electrophoresis", "Science", "Q", "R", "Biodiversity", "04 agricultural and veterinary sciences", "15. Life on land", "Poaceae", "Polymerase Chain Reaction", "7. Clean energy", "3. Good health", "Medicine", "Animals", "0401 agriculture", " forestry", " and fisheries", "Ecosystem", "Soil Microbiology", "Research Article"], "contacts": [{"organization": "Deli Wang, Wei-chao Du, Dong-bo Liu, Tong-bao Qu, Tong-bao Qu, Li-Jun Yu, Zhiming Yang, Xia Yuan,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0159680"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0159680", "name": "item", "description": "10.1371/journal.pone.0159680", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0159680"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-07-28T00:00:00Z"}}, {"id": "10.2527/jas.2009-1786", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:21:26Z", "type": "Journal Article", "created": "2009-06-20", "title": "Effect Of Sward Dry Matter Digestibility On Methane Production, Ruminal Fermentation, And Microbial Populations Of Zero-Grazed Beef Cattle", "description": "Increasing the digestibility of pasture for grazing ruminants has been proposed as a low-cost practical means of reducing ruminant CH(4) emissions. At high feed intake levels, the proportion of energy lost as CH(4) decreases as the digestibility of the diet increases. Therefore, improving forage digestibility may improve productivity as DM and energy intake are increased. A zero-grazing experiment was conducted to determine the effect of sward DM digestibility (DMD) on DMI, CH(4) emissions, and indices of rumen fermentation of beef animals. Twelve Charolais-cross heifers were assigned to 1 of 2 treatments, with 6 heifers per dietary treatment. Additionally, 4 cannulated Aberdeen Angus-cross steers were randomly allocated to each of these 2 treatments in a crossover design. Dietary treatments consisted of swards managed to produce (i) high digestibility pasture (high DMD) or (ii) pasture with less digestibility (low DMD), both offered for ad libitum intake. All animals were zero-grazed and offered freshly cut herbage twice daily. In vitro DMD values for the high and low DMD swards were 816 and 706 g/kg of DM. Heifers offered the high DMD grass had greater (P < 0.001) daily DMI of 7.66 kg compared with 5.38 kg for those offered the low DMD grass. Heifers offered the high DMD grass had greater (P = 0.003) daily CH(4) production (193 g of CH(4)/d) than those offered the low DMD grass (138 g of CH(4)/d). However, when corrected for DMI, digestible DMI, or ingested gross energy, there was no difference (P > 0.05) in CH(4) production between dietary treatments. For cannulated steers, intake tended (P = 0.06) to be greater for the high DMD grass (5.56 vs. 4.27 kg of DM/d), but rumen protozoa (4.95 x 10(4)/mL; P = 0.62); rumen ammonia (34 mg of N/L; P = 0.24); rumen total VFA (103 mM; P = 0.58), and rumen pH (6.8; P = 0.43) did not differ between treatments. There was no difference in total bacteria numbers, relative expression of the mcrA gene, and numbers of cycles to threshold for fungi when determined using quantitative PCR between dietary treatments with mean values of 73.0 ng/microL, 0.958, and 21.75 C(T), respectively. Results of this study demonstrate that there was no difference in CH(4) production when corrected for intake or rumen fermentation variables of beef cattle offered a high or low digestibility sward.", "keywords": ["DNA", " Bacterial", "Male", "2. Zero hunger", "Rumen", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "Fatty Acids", " Volatile", "Polymerase Chain Reaction", "Random Allocation", "Ammonia", "RNA", " Ribosomal", " 16S", "Lolium", "Animals", "Cattle", "Digestion", "Female", "Least-Squares Analysis", "Methane"]}, "links": [{"href": "https://doi.org/10.2527/jas.2009-1786"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Animal%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2527/jas.2009-1786", "name": "item", "description": "10.2527/jas.2009-1786", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2527/jas.2009-1786"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-06-19T00:00:00Z"}}, {"id": "1959.7/uws:47852", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:26:33Z", "type": "Journal Article", "created": "2018-06-21", "title": "Identity of plant, lichen and moss species connects with microbial abundance and soil functioning in maritime Antarctica", "description": "We lack studies evaluating how the identity of plant, lichen and moss species relates to microbial abundance and soil functioning on Antarctica. If species identity is associated with soil functioning, distributional changes of key species, linked to climate change, could significantly affect Antarctic soil functioning.We evaluated how the identity of six Antarctic plant, lichen and moss species relates to a range of soil attributes (C, N and P cycling), microbial abundance and structure in Livingston Island, Maritime Antarctica. We used an effect size metric to predict the association between species (vs. bare soil) and the measured soil attributes.We observed species-specific effects of the plant and biocrust species on soil attributes and microbial abundance. Phenols, phosphatase and \u03b2-D-cellobiosidase activities were the most important attributes characterizing the observed patterns. We found that the evaluated species positively correlated with soil nutrient availability and microbial abundance vs. bare soil.We provide evidence, from a comparative study, that plant and biocrust identity is associated with different levels of soil functioning and microbial abundance in Maritime Antarctica. Our results suggest that changes in the spatial distribution of these species linked to climate change could potentially entail changes in the functioning of Antarctic terrestrial ecosystems.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "plants", "soil enzymology", "13. Climate action", "polymerase chain reaction", "XXXXXX - Unknown", "soil fungi", "14. Life underwater", "15. Life on land", "bacteria"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11104-018-3721-7.pdf"}, {"href": "https://doi.org/1959.7/uws:47852"}, {"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": "1959.7/uws:47852", "name": "item", "description": "1959.7/uws:47852", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:47852"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-21T00:00:00Z"}}, {"id": "20.500.14243/453423", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:26:49Z", "type": "Journal Article", "created": "2023-03-17", "title": "Two species-specific TaqMan-based quantitative polymerase chain reaction assays for the detection in soil ofPaenibacillus polymyxainocula", "description": "AbstractAims

The increasingly widespread use of beneficial microbial inocula in agriculture gives rise to two primary needs: i) the assessment of the environmental risk, i.e. their impact on local soil microbiome and soil properties; ii) being able to track them and monitor their persistence and fate to both optimize their formulation and application method. In previous years, PCR-based methods have detected bacterial or fungal bioinoculant at the species or strain level. However, the selective detection, quantification, and monitoring of target microbial species in a complex ecosystem such as soil require that the tests possess high specificity and sensitivity.

Methods and results

The work proposes a quantitative real-time PCR detection method using TaqMan chemistry, showing high specificity and sensitivity for the Paenibacillus polymyxa K16 strain. The primer and probe sets were designed using the polymyxin gene cluster targeting pmxC and pmxE sequences. Validation tests showed that these assays allowed a discriminant and specific detection of P. polymyxa K16 in soil.

Conclusion

The TaqMan-assay developed could thus ensure the necessary level of discrimination required by commercial and regulatory purposes to detect and monitor the bioinoculant in soil.Intestinal protozoa infections present a major public health challenge, particularly in areas with poor sanitation and limited access to clean water. Effective diagnostic methods are critical, yet traditional microscopy, though widely used for its simplicity, lacks the sensitivity and specificity of modern techniques like real-time Polymerase Chain Reaction (qPCR), making the latter a more effective tool for monitoring and assessing the burden of intestinal protozoa diseases. In this study, we implemented two duplex qPCR assays to detect Entamoeba dispar\uffe2\uff80\uff89+\uffe2\uff80\uff89Entamoeba histolytica and Cryptosporidium spp.\uffe2\uff80\uff89+\uffe2\uff80\uff89Chilomastix mesnili, along with singleplex assays for Giardia duodenalis and Blastocystis spp., using a 10 \uffc2\uffb5L reaction volume. This marks the first molecular detection of Chilomastix mesnili by qPCR, enhancing diagnostic precision. Using these, we analyzed stool samples from 70 patients on Pemba Island, Tanzania, before and 54 samples after treatment with 20, 25, or 30\uffc2\uffa0mg of emodepside or placebo, aiming to assess protozoa prevalence for this region and emodepside\uffe2\uff80\uff99s potential antiprotozoal effects. Our qPCR reliably detected protozoa in 74.4% of samples, with Entamoeba histolytica and Entamoeba dispar in 31.4% of cases. Notably, one-third of these infections were caused by Entamoeba histolytica. No significant reduction in protozoa was observed after emodepside treatment compared to placebo. The study highlights the utility of qPCR in providing species-level differentiation and improving the speed and cost-effectiveness of testing. The high prevalence of protozoa in this region underscores the need for continued monitoring and control efforts, though emodepside was not effective against protozoa infections. The World Health Organization recommends the use of the microscopy-based Kato-Katz thick smear for diagnosing soil-transmitted helminth (STH) infections. Despite its simplicity and cost-effectiveness, the Kato-Katz method faces challenges, including reader subjectivity and reduced sensitivity. Real-time polymerase chain reaction (qPCR) technology offers standardized readouts and higher sensitivity, making it suitable for STH diagnosis and monitoring the treatment efficacy of emodepside within the framework of randomized controlled trials.

Methodology/Principal findings

We evaluated the performance of Kato-Katz versus qPCR for assessing treatment efficacy in terms of cure rates, of single doses of 5, 10, 15, 20, 25 and 30\uffe2\uff80\uff89mg of emodepside compared to 400\uffe2\uff80\uff89mg albendazole. Spearman\uffe2\uff80\uff99s rank correlation coefficient examined the correlation between STH eggs per gram in stool samples and qPCR Ct values. Diagnostic sensitivity of qPCR was calculated using a Bayesian latent class modelling approach with data from Ascaris lumbricoides infections. Agreement between Kato-Katz and qPCR at baseline was 93.57% for Trichuris trichiura, and 73.49% for both hookworm and A. lumbricoides. For the latter helminth qPCR demonstrated higher sensitivity (85.00% vs. 47.70%) and slightly lower specificity (93.40% vs. 99.40%) compared to Kato-Katz. We observed a fair to moderate agreement with negative correlation between Ct values and Kato-Katz egg counts. Treatment efficacy, as assessed by qPCR, was lower for all doses of emodepside and albendazole compared to Kato-Katz. Nonetheless, emodepside demonstrated higher cure rates against T. trichiura and A. lumbricoides infections compared to albendazole.

Conclusion/ Significance

Our study confirmed that qPCR is a sensitive diagnostic method for diagnosing STH infections compared to Kato-Katz and serves as a valuable tool for determining treatment efficacy in clinical trials. Furthermore, qPCR confirmed the better treatment efficacy of emodepside compared to albendazole, despite indicating lower cure rates than Kato-Katz.Intestinal protozoa infections present a major public health challenge, particularly in areas with poor sanitation and limited access to clean water. Effective diagnostic methods are critical, yet traditional microscopy, though widely used for its simplicity, lacks the sensitivity and specificity of modern techniques like real-time Polymerase Chain Reaction (qPCR), making the latter a more effective tool for monitoring and assessing the burden of intestinal protozoa diseases. In this study, we implemented two duplex qPCR assays to detect Entamoeba dispar\uffe2\uff80\uff89+\uffe2\uff80\uff89Entamoeba histolytica and Cryptosporidium spp.\uffe2\uff80\uff89+\uffe2\uff80\uff89Chilomastix mesnili, along with singleplex assays for Giardia duodenalis and Blastocystis spp., using a 10 \uffc2\uffb5L reaction volume. This marks the first molecular detection of Chilomastix mesnili by qPCR, enhancing diagnostic precision. Using these, we analyzed stool samples from 70 patients on Pemba Island, Tanzania, before and 54 samples after treatment with 20, 25, or 30\uffc2\uffa0mg of emodepside or placebo, aiming to assess protozoa prevalence for this region and emodepside\uffe2\uff80\uff99s potential antiprotozoal effects. Our qPCR reliably detected protozoa in 74.4% of samples, with Entamoeba histolytica and Entamoeba dispar in 31.4% of cases. Notably, one-third of these infections were caused by Entamoeba histolytica. No significant reduction in protozoa was observed after emodepside treatment compared to placebo. The study highlights the utility of qPCR in providing species-level differentiation and improving the speed and cost-effectiveness of testing. The high prevalence of protozoa in this region underscores the need for continued monitoring and control efforts, though emodepside was not effective against protozoa infections. Cytokinins play crucial roles in diverse aspects of plant growth and development. Spatiotemporal distribution of bioactive cytokinins is finely regulated by metabolic enzymes. LONELY GUY (LOG) was previously identified as a cytokinin-activating enzyme that works in the direct activation pathway in rice (Oryza sativa) shoot meristems. In this work, nine Arabidopsis thaliana LOG genes (At LOG1 to LOG9) were predicted as homologs of rice LOG. Seven At LOGs, which are localized in the cytosol and nuclei, had enzymatic activities equivalent to that of rice LOG. Conditional overexpression of At LOGs in transgenic Arabidopsis reduced the content of N6-(\uffce\uff942-isopentenyl)adenine (iP) riboside 5\uffe2\uff80\uffb2-phosphates and increased the levels of iP and the glucosides. Multiple mutants of At LOGs showed a lower sensitivity to iP riboside in terms of lateral root formation and altered root and shoot morphology. Analyses of At LOG promoter:\uffce\uffb2-glucuronidase fusion genes revealed differential expression of LOGs in various tissues during plant development. Ectopic overexpression showed pleiotropic phenotypes, such as promotion of cell division in embryos and leaf vascular tissues, reduced apical dominance, and a delay of leaf senescence. Our results strongly suggest that the direct activation pathway via LOGs plays a pivotal role in regulating cytokinin activity during normal growth and development in Arabidopsis.