Dataset Information

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches.

ABSTRACT: Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.

SUBMITTER: Pascual J

PROVIDER: S-EPMC4711807 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches.

Pascual Javier J Blanco Silvia S García-López Marina M García-Salamanca Adela A Bursakov Sergey A SA Genilloud Olga O Bills Gerald F GF Ramos Juan L JL van Dillewijn Pieter P

PloS one 20160107 1

Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadet ...[more]

PMID: 26741495

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Project description:This dataset was obtained over repeated field-trips to the Sierra Nevada Massif and contains the physical parameters of its recognised water-bodies. It therefore defines the general cartography of the area, with data on individual features regarding the geographical coordinates (x, y, z), dimensions (length, width, depth), flooded surface area, stored water volume, shoreline length, as well as the area of associated green fringes and the length of their borders. These data were basically obtained using straightforward techniques, such as GPS, tape measurements and photographic interpretation. The data were then previously used to define the role of these water-bodies in the hydrology of the massif: relationships between number of water-bodies and water volumes between 2700 and 3200 m a.s.l. regarding watersheds (Mediterranean, Atlantic and total massif), relationships with green fringes, moment of maximum snowmelt discharge and the estimation of different components of water volumes discharged during the main period of thaw. The formation patterns of each water-body were also identified in their situational context, and the role played by each formation process on the stored water volume: the water-bodies close to the peak line (2918 m mean altitude) are highly dependant on the glacial processes that created the hollows in which they are located. Slope instability created water-bodies mainly located at lower altitudes and are more fragile due intense slope dynamics. In any case, these hydrological data show a paradoxical behaviour because despite its higher xericity, the Mediterranean watershed generally has higher water contents than the Atlantic. The cause of this hydrological imbalance between watersheds seems to be unrelated to the formation processes of the existing water-bodies. Sierra Nevada is considered to be clearly representative of a high mountain Mediterranean environment, where the data collected are a starting point to define the different habitats or for investigation of the hydrological processes of the massif and their evolution. Lack of such data is often a problem that in the present case is solved with this contribution.

Project description:Forest ecosystems can act as sinks of carbon and thus mitigate anthropogenic carbon emissions. When forests are actively managed, treatments can alter forests carbon dynamics, reducing their sink strength and switching them from sinks to sources of carbon. These effects are generally characterized by fast temporal dynamics. Hence this study monitored for over a decade the impacts of management practices commonly used to reduce fire hazards on the carbon dynamics of mixed-conifer forests in the Sierra Nevada, California, USA. Soil CO2 efflux, carbon pools (i.e. soil carbon, litter, fine roots, tree biomass), and radial tree growth were compared among un-manipulated controls, prescribed fire, thinning, thinning followed by fire, and two clear-cut harvested sites. Soil CO2 efflux was reduced by both fire and harvesting (ca. 15%). Soil carbon content (upper 15 cm) was not significantly changed by harvest or fire treatments. Fine root biomass was reduced by clear-cut harvest (60-70%) but not by fire, and the litter layer was reduced 80% by clear-cut harvest and 40% by fire. Thinning effects on tree growth and biomass were concentrated in the first year after treatments, whereas fire effects persisted over the seven-year post-treatment period. Over this period, tree radial growth was increased (25%) by thinning and reduced (12%) by fire. After seven years, tree biomass returned to pre-treatment levels in both fire and thinning treatments; however, biomass and productivity decreased 30%-40% compared to controls when thinning was combined with fire. The clear-cut treatment had the strongest impact, reducing ecosystem carbon stocks and delaying the capacity for carbon uptake. We conclude that post-treatment carbon dynamics and ecosystem recovery time varied with intensity and type of treatments. Consequently, management practices can be selected to minimize ecosystem carbon losses while increasing future carbon uptake, resilience to high severity fire, and climate related stresses.

Dataset Information

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches.

Publications

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches.

Similar Datasets

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