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 PMID:29682416  

Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing.

Luhua Yao | Dangjun Wang | Lin Kang | Dengke Wang | Yong Zhang | Xiangyang Hou | Yanjun Guo
PeerJ | 2018

Fertilization as one of the measures in restoring degraded soil qualities has been introduced on arid steppes in recent decades. However, the fertilization use efficiency on arid steppes varies greatly between steppe types and years, enhancing uncertainties and risks in introducing fertilizations on such natural system to restore degraded steppes.

Pubmed ID: 29682416

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This is a list of tools and resources that we have found mentioned in this publication.


UPARSE (tool)

RRID:SCR_005020

An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.

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Ribosomal Database Project (tool)

RRID:SCR_006633

A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow.

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UNITE (tool)

RRID:SCR_006518

A fungal rDNA internal transcribed spacer (ITS) sequence database (although additional genes and genetic markers are also welcome) to facilitate identification of environmental samples of fungal DNA. Additional important features include user annotation of INSD sequences to add metadata on, e.g., locality, habitat, soil, climate, and interacting taxa. The user can furthermore annotate INSD sequences with additional species identifications that will appear in the results of any analyses done. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. In addition, it also holds all fungal ITS sequences in the International Nucleotide Sequence Databases (INSD: NCBI, EMBL, DDBJ). Both sets of sequences may be used in any analyses carried out. UNITE is accompanied by a project management system called PlutoF, where users can store field data, document the sequencing lab procedures, manage sequences, and make analyses. PlutoF intends to make it possible for taxonomists, ecologists, and biogeographers to use a common platform for data storage, handling, and analyses, with the intent of facilitating an integration of these disciplines. A user can have an unlimited number of projects but still make analyses across any project data available to him.

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UCHIME (tool)

RRID:SCR_008057

An algorithm for detecting chimeric sequences.

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