{"type": "FeatureCollection", "features": [{"id": "10.1007/s11356-017-0378-3", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-07-28T16:15:29Z", "type": "Journal Article", "created": "2017-10-09", "title": "Intra- and inter-specific variations in chitin in lichens along a N-deposition gradient", "description": "The mechanisms of nitrogen (N) tolerance in lichens are not yet fully understood. Here, we investigated how the increase of chitin content is related with N excess at inter- and intra-specific levels, by using species with differing ecological N tolerances (the tolerant Xanthoria parietina and Parmotrema hypoleucinum and the sensitive Evernia prunastri and Usnea sp.) and thalli of X. parietina and P. hypoleucinum from sites with different availabilities of N of agricultural origin (livestock), as confirmed by lichen N content and \u03b415N. Nitrogen, chitin (N-containing compound), and ergosterol contents were measured in lichen thalli. Nitrogen and chitin contents were higher in tolerant species than those in sensitive ones (inter-specific level) and in thalli collected from the N-polluted site than in thalli from the clean site (intra-specific level). We suggest that chitin contributes to N stress tolerance in lichens, and that excess N can be partially stored as chitin (non-toxic form) in the cell walls of tolerant species.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Ascomycota", "Biological Variation", " Population", "Lichens", "Nitrogen", "Ergosterol", "Chitin", "15. Life on land"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11356-017-0378-3.pdf"}, {"href": "https://doi.org/10.1007/s11356-017-0378-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20and%20Pollution%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11356-017-0378-3", "name": "item", "description": "10.1007/s11356-017-0378-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11356-017-0378-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-10-09T00:00:00Z"}}, {"id": "10.1101/2023.10.03.560709", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:18:27Z", "type": "Journal Article", "created": "2023-10-04", "title": "Bacteria face trade-offs in the decomposition of complex biopolymers", "description": "Abstract

Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system\uffe2\uff80\uff99s complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low- or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.

Author summary

The decomposition of polysaccharides by microbes is a key process in the global carbon cycle. It requires the joint action of a variety of microbially-produced extracellular enzymes. They can be broadly classified into endo-enzymes, that act in the middle of polymers, and exo-enzymes, that cleave units from polymer ends. Little is known about the benefits for microbes producing a certain enzyme type and the interplay between enzyme producing strategies in mixed communities. This hampers our comprehensive understanding of decomposition in terrestrial and marine ecosystems and thus limits the prediction of decomposition processes, for example in a changing climate.

Based on theoretical modelling, we revealed a fundamental trade-off in the action of these enzymes. While exo-enzymes are more efficient at high substrate conditions, endo-enzymes perform better when substrate is low. Generalists producing both enzymes expand their ecological niche of substrate availability compared to specialists only producing one of the two types. Complementary specialists only co-exist in oligotrophic conditions. We conclude that producing enzymes for specific steps within polymer degradation represents relevant ecological strategies for microbes in decomposer communities.Soil microbes are highly diverse and control most soil biogeochemical reactions. We examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying land use change. We examined paired native grasslands and adjacentEucalyptusplantations (previously grassland) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, we analyzed functional genes using the GeoChip 2.0 microarray, which simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grassland differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Most grassland profiles were similar, but plantation profiles generally differed from those of grasslands due to differences in functional gene abundance across diverse taxa. Eucalypts decreased ammonification and N fixation functional genes by 11% and 7.9% (P< 0.01), which correlated with decreased microbial biomass N and more NH4+in plantation soils. Chitinase abundance decreased 7.8% in plantations compared to levels in grassland (P= 0.017), and C polymer-degrading genes decreased by 1.5% overall (P< 0.05), which likely contributed to 54% (P< 0.05) more C in undecomposed extractable soil pools and 27% less microbial C (P< 0.01) in plantation soils. In general, afforestation altered the abundance of many microbial functional genes, corresponding with changes in soil biogeochemistry, in part through altered abundance of overall functional gene types rather than simply through changes in specific taxa. Such changes in microbial functional genes correspond with altered C and N storage and have implications for long-term productivity in these soils.

", "keywords": ["Nitrogen", "Argentina", "Sequence Homology", "soil science", "Microbiology", "333", "Trees", "Soil", "afforestation", "Cluster Analysis", "Biology", "Soil Microbiology", "Oligonucleotide Array Sequence Analysis", "2. Zero hunger", "Environmental Microbiology and Microbial Ecology", "Bacteria", "Chitinases", "Biodiversity", "DNA", "Gene Pool", "04 agricultural and veterinary sciences", "South America", "15. Life on land", "Microarray Analysis", "Carbon", "Uruguay", "0401 agriculture", " forestry", " and fisheries", "Eucalyptus plantation"]}, "links": [{"href": "https://doi.org/10.1128/aem.01126-09"}, {"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.01126-09", "name": "item", "description": "10.1128/aem.01126-09", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01126-09"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-10-01T00:00:00Z"}}, {"id": "10.3390/insects12020127", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:20:42Z", "type": "Journal Article", "created": "2021-02-02", "title": "Biocontrol of Melolontha spp. Grubs in Organic Strawberry Plantations by Entomopathogenic Fungi as Affected by Environmental and Metabolic Factors and the Interaction with Soil Microbial Biodiversity", "description": "

The efficacy of two strains of two Beauveria species (B. bassiana and B. brongniartii), individually or as co-inoculants, to control Melolontha sp. grubs was assessed in two organic strawberry plantations in relation to the environmental conditions, their abundance after soil inoculation, and their in vitro chitinolytic activity, thereby also verifying their impact on soil microbial communities. A reduction of the grubs\u2019 damage to strawberry plants was observed when compared to the untreated control in one plantation, irrespective of the strain used and whether they were applied as single or as co-inoculum. The metabolic pattern expressed by the two fungi in vitro was different: B. bassiana showed a higher metabolic versatility in the use of different carbon sources than B. brongniartii, whose profile was partly overlapped in the co-inoculum. Similar differences in the chitinolytic activity of each of the fungi and the co-inoculum were also pointed out. A higher abundance of B. bassiana in the soils receiving this species in comparison to those receiving B. brongniartii, together with its in vitro metabolic activity, could account for the observed diverse efficacy of pest damage control of the two species. However, environmental and climatic factors also affected the overall efficacy of the two bioinocula. According to the monitoring of the two species in soil, B. bassiana could be considered as a common native species in the studied locations in contrast to B. brongniartii, which seemed to be a non-endemic species. Nevertheless, the inoculation with both species or the co-inoculum did not consistently affect the soil microbial (fungi and bacteria) biodiversity, as expressed by the operational taxonomic unit (OTU) number and Shannon\u2013Wiener diversity index based on terminal restriction fragment length polymorphism (TRFLP) data. A small transient increase of the share of the inoculated species to the total fungal community was noted by the analysis of genes copy numbers only for B. brongniartii at the end of the third growing season.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Beauveria brongniartii", "Organic farming", "Science", "Q", "Beauveria brongniartii", "15. Life on land", "Chitinolytic activity", "Article", "chitinolytic activity", "03 medical and health sciences", "organic farming", "Beauveria bassiana", "European cockchafer", "Beauveria bassiana"]}, "links": [{"href": "http://www.mdpi.com/2075-4450/12/2/127/pdf"}, {"href": "https://iris.cnr.it/bitstream/20.500.14243/396830/1/insects-12-00127.pdf"}, {"href": "https://doi.org/10.3390/insects12020127"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Insects", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/insects12020127", "name": "item", "description": "10.3390/insects12020127", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/insects12020127"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-02T00:00:00Z"}}, {"id": "11353/10.2115948", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:24:04Z", "type": "Journal Article", "created": "2023-10-04", "title": "Bacteria face trade-offs in the decomposition of complex biopolymers", "description": "Abstract

Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system\uffe2\uff80\uff99s complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low- or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.

Author summary

The decomposition of polysaccharides by microbes is a key process in the global carbon cycle. It requires the joint action of a variety of microbially-produced extracellular enzymes. They can be broadly classified into endo-enzymes, that act in the middle of polymers, and exo-enzymes, that cleave units from polymer ends. Little is known about the benefits for microbes producing a certain enzyme type and the interplay between enzyme producing strategies in mixed communities. This hampers our comprehensive understanding of decomposition in terrestrial and marine ecosystems and thus limits the prediction of decomposition processes, for example in a changing climate.

Based on theoretical modelling, we revealed a fundamental trade-off in the action of these enzymes. While exo-enzymes are more efficient at high substrate conditions, endo-enzymes perform better when substrate is low. Generalists producing both enzymes expand their ecological niche of substrate availability compared to specialists only producing one of the two types. Complementary specialists only co-exist in oligotrophic conditions. We conclude that producing enzymes for specific steps within polymer degradation represents relevant ecological strategies for microbes in decomposer communities.

The efficacy of two strains of two Beauveria species (B. bassiana and B. brongniartii), individually or as co-inoculants, to control Melolontha sp. grubs was assessed in two organic strawberry plantations in relation to the environmental conditions, their abundance after soil inoculation, and their in vitro chitinolytic activity, thereby also verifying their impact on soil microbial communities. A reduction of the grubs\u2019 damage to strawberry plants was observed when compared to the untreated control in one plantation, irrespective of the strain used and whether they were applied as single or as co-inoculum. The metabolic pattern expressed by the two fungi in vitro was different: B. bassiana showed a higher metabolic versatility in the use of different carbon sources than B. brongniartii, whose profile was partly overlapped in the co-inoculum. Similar differences in the chitinolytic activity of each of the fungi and the co-inoculum were also pointed out. A higher abundance of B. bassiana in the soils receiving this species in comparison to those receiving B. brongniartii, together with its in vitro metabolic activity, could account for the observed diverse efficacy of pest damage control of the two species. However, environmental and climatic factors also affected the overall efficacy of the two bioinocula. According to the monitoring of the two species in soil, B. bassiana could be considered as a common native species in the studied locations in contrast to B. brongniartii, which seemed to be a non-endemic species. Nevertheless, the inoculation with both species or the co-inoculum did not consistently affect the soil microbial (fungi and bacteria) biodiversity, as expressed by the operational taxonomic unit (OTU) number and Shannon\u2013Wiener diversity index based on terminal restriction fragment length polymorphism (TRFLP) data. A small transient increase of the share of the inoculated species to the total fungal community was noted by the analysis of genes copy numbers only for B. brongniartii at the end of the third growing season.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Beauveria brongniartii", "Organic farming", "Science", "Q", "Beauveria brongniartii", "15. Life on land", "Chitinolytic activity", "Article", "chitinolytic activity", "03 medical and health sciences", "organic farming", "Beauveria bassiana", "European cockchafer", "Beauveria bassiana"]}, "links": [{"href": "http://www.mdpi.com/2075-4450/12/2/127/pdf"}, {"href": "https://iris.cnr.it/bitstream/20.500.14243/396830/1/insects-12-00127.pdf"}, {"href": "https://www.mdpi.com/2075-4450/12/2/127/pdf"}, {"href": "https://doi.org/20.500.14243/396830"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Insects", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.14243/396830", "name": "item", "description": "20.500.14243/396830", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.14243/396830"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-02T00:00:00Z"}}, {"id": "2763769552", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-07-28T16:24:47Z", "type": "Journal Article", "created": "2017-10-09", "title": "Intra- and inter-specific variations in chitin in lichens along a N-deposition gradient", "description": "The mechanisms of nitrogen (N) tolerance in lichens are not yet fully understood. Here, we investigated how the increase of chitin content is related with N excess at inter- and intra-specific levels, by using species with differing ecological N tolerances (the tolerant Xanthoria parietina and Parmotrema hypoleucinum and the sensitive Evernia prunastri and Usnea sp.) and thalli of X. parietina and P. hypoleucinum from sites with different availabilities of N of agricultural origin (livestock), as confirmed by lichen N content and \u03b415N. Nitrogen, chitin (N-containing compound), and ergosterol contents were measured in lichen thalli. Nitrogen and chitin contents were higher in tolerant species than those in sensitive ones (inter-specific level) and in thalli collected from the N-polluted site than in thalli from the clean site (intra-specific level). We suggest that chitin contributes to N stress tolerance in lichens, and that excess N can be partially stored as chitin (non-toxic form) in the cell walls of tolerant species.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Ascomycota", "Biological Variation", " Population", "Lichens", "Nitrogen", "Ergosterol", "Chitin", "15. Life on land"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11356-017-0378-3.pdf"}, {"href": "https://doi.org/2763769552"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20and%20Pollution%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2763769552", "name": "item", "description": "2763769552", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2763769552"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-10-09T00:00:00Z"}}, {"id": "28994014", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-07-28T16:24:51Z", "type": "Journal Article", "created": "2017-10-09", "title": "Intra- and inter-specific variations in chitin in lichens along a N-deposition gradient", "description": "The mechanisms of nitrogen (N) tolerance in lichens are not yet fully understood. Here, we investigated how the increase of chitin content is related with N excess at inter- and intra-specific levels, by using species with differing ecological N tolerances (the tolerant Xanthoria parietina and Parmotrema hypoleucinum and the sensitive Evernia prunastri and Usnea sp.) and thalli of X. parietina and P. hypoleucinum from sites with different availabilities of N of agricultural origin (livestock), as confirmed by lichen N content and \u03b415N. Nitrogen, chitin (N-containing compound), and ergosterol contents were measured in lichen thalli. Nitrogen and chitin contents were higher in tolerant species than those in sensitive ones (inter-specific level) and in thalli collected from the N-polluted site than in thalli from the clean site (intra-specific level). We suggest that chitin contributes to N stress tolerance in lichens, and that excess N can be partially stored as chitin (non-toxic form) in the cell walls of tolerant species.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Ascomycota", "Biological Variation", " Population", "Lichens", "Nitrogen", "Ergosterol", "Chitin", "15. 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