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Microbiomes are vital in promoting nutrient cycling and plant growth in soil ecosystems. However, microbiomes face adverse effects from multiple persistent pollutants, including per- and poly-fluoroalkyl substances (PFASs). PFASs threaten the fertility and health of soil ecosystems, yet the response of microbial community stability and trophic transfer efficiencies to PFASs is still poorly understood. This study explored the spatial patterns of PFASs in topsoil environments from the West Taihu Lake Basin of China and links their presence to soil microbial community stability at compositional and functional levels. Our results revealed that PFBA (13.87%), PFTrDA (11.63%), PFDoA (11.02%), PFOA (10.99%), and PFOS (10.39%) contributed the most to the spatial occurrence of PFASs. Soil properties, including salinity (14.47%), uniformity (9.68%), dissolved inorganic carbon (8.62%), and clay content (8.18%), affected PFASs distribution the most. In soil microbiomes, eukaryotic taxa had wider niche breadths and stronger community stability than prokaryotes when exposed to PFASs (p < 0.05). The presence of PFBA and PFHpA inhibited the functional stability of archaeal and bacterial communities (p < 0.05). PFBA and PFPeA reduced the structural stability of heterotrophic bacteria and Myxobacteria, respectively (p < 0.05). Based on null modeling, PFPeA significantly regulated the assembly processes of most microbial sub-communities (p < 0.01). The trophic transferring efficiencies of autotrophic bacteria to metazoan organisms were directly stimulated by PFASs (p < 0.05), and the potential trophic transferring efficiencies of methanogenic archaea to protozoa were inhibited by PFASs (p < 0.05). This study highlighted the potential contributions of PFASs to soil microbial community stability and food webs during ecological soil management.
Pubmed ID: 35750225 RIS Download
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Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions!
View all literature mentionsDatabase of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.
View all literature mentionsA collection of tools and class interfaces for the assembly of DNA reads.
View all literature mentionsSoftware for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases.
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