Literature DB >> 35484416

DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic.

Paulo E A S Câmara1,2, Fábio Leal Viana Bones3, Fabyano Alvares Cardoso Lopes4, Fabio S Oliveira5, Cristine Chaves Barreto6, Diego Knop Henriques7, Larissa Paraguassu Campos8, Micheline Carvalho-Silva7, Peter Convey9,10, Luiz Henrique Rosa11.   

Abstract

Located 1140 km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.
© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Conservation; Environmental DNA; Soil; South Atlantic islands

Year:  2022        PMID: 35484416     DOI: 10.1007/s00248-022-02018-4

Source DB:  PubMed          Journal:  Microb Ecol        ISSN: 0095-3628            Impact factor:   4.552


  27 in total

1.  Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea.

Authors:  Daniel Pr Herlemann; Matthias Labrenz; Klaus Jürgens; Stefan Bertilsson; Joanna J Waniek; Anders F Andersson
Journal:  ISME J       Date:  2011-04-07       Impact factor: 10.302

2.  Diversity and Ecology of Chlorophyta (Viridiplantae) Assemblages in Protected and Non-protected Sites in Deception Island (Antarctica, South Shetland Islands) Assessed Using an NGS Approach.

Authors:  Paulo Eduardo Aguiar Saraiva Câmara; Micheline Carvalho-Silva; Otávio H B Pinto; Eduardo T Amorim; Diego Knop Henriques; Thamar Holanda da Silva; Franciane Pellizzari; Peter Convey; Luiz Henrique Rosa
Journal:  Microb Ecol       Date:  2020-08-28       Impact factor: 4.552

3.  Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:  Evan Bolyen; Jai Ram Rideout; Matthew R Dillon; Nicholas A Bokulich; Christian C Abnet; Gabriel A Al-Ghalith; Harriet Alexander; Eric J Alm; Manimozhiyan Arumugam; Francesco Asnicar; Yang Bai; Jordan E Bisanz; Kyle Bittinger; Asker Brejnrod; Colin J Brislawn; C Titus Brown; Benjamin J Callahan; Andrés Mauricio Caraballo-Rodríguez; John Chase; Emily K Cope; Ricardo Da Silva; Christian Diener; Pieter C Dorrestein; Gavin M Douglas; Daniel M Durall; Claire Duvallet; Christian F Edwardson; Madeleine Ernst; Mehrbod Estaki; Jennifer Fouquier; Julia M Gauglitz; Sean M Gibbons; Deanna L Gibson; Antonio Gonzalez; Kestrel Gorlick; Jiarong Guo; Benjamin Hillmann; Susan Holmes; Hannes Holste; Curtis Huttenhower; Gavin A Huttley; Stefan Janssen; Alan K Jarmusch; Lingjing Jiang; Benjamin D Kaehler; Kyo Bin Kang; Christopher R Keefe; Paul Keim; Scott T Kelley; Dan Knights; Irina Koester; Tomasz Kosciolek; Jorden Kreps; Morgan G I Langille; Joslynn Lee; Ruth Ley; Yong-Xin Liu; Erikka Loftfield; Catherine Lozupone; Massoud Maher; Clarisse Marotz; Bryan D Martin; Daniel McDonald; Lauren J McIver; Alexey V Melnik; Jessica L Metcalf; Sydney C Morgan; Jamie T Morton; Ahmad Turan Naimey; Jose A Navas-Molina; Louis Felix Nothias; Stephanie B Orchanian; Talima Pearson; Samuel L Peoples; Daniel Petras; Mary Lai Preuss; Elmar Pruesse; Lasse Buur Rasmussen; Adam Rivers; Michael S Robeson; Patrick Rosenthal; Nicola Segata; Michael Shaffer; Arron Shiffer; Rashmi Sinha; Se Jin Song; John R Spear; Austin D Swafford; Luke R Thompson; Pedro J Torres; Pauline Trinh; Anupriya Tripathi; Peter J Turnbaugh; Sabah Ul-Hasan; Justin J J van der Hooft; Fernando Vargas; Yoshiki Vázquez-Baeza; Emily Vogtmann; Max von Hippel; William Walters; Yunhu Wan; Mingxun Wang; Jonathan Warren; Kyle C Weber; Charles H D Williamson; Amy D Willis; Zhenjiang Zech Xu; Jesse R Zaneveld; Yilong Zhang; Qiyun Zhu; Rob Knight; J Gregory Caporaso
Journal:  Nat Biotechnol       Date:  2019-08       Impact factor: 54.908

Review 4.  A revised six-kingdom system of life.

Authors:  T Cavalier-Smith
Journal:  Biol Rev Camb Philos Soc       Date:  1998-08

5.  DADA2: High-resolution sample inference from Illumina amplicon data.

Authors:  Benjamin J Callahan; Paul J McMurdie; Michael J Rosen; Andrew W Han; Amy Jo A Johnson; Susan P Holmes
Journal:  Nat Methods       Date:  2016-05-23       Impact factor: 28.547

6.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.

Authors:  Anna Klindworth; Elmar Pruesse; Timmy Schweer; Jörg Peplies; Christian Quast; Matthias Horn; Frank Oliver Glöckner
Journal:  Nucleic Acids Res       Date:  2012-08-28       Impact factor: 16.971

7.  Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

Authors:  Leho Tedersoo; Kessy Abarenkov; R Henrik Nilsson; Arthur Schüssler; Gwen-Aëlle Grelet; Petr Kohout; Jane Oja; Gregory M Bonito; Vilmar Veldre; Teele Jairus; Martin Ryberg; Karl-Henrik Larsson; Urmas Kõljalg
Journal:  PLoS One       Date:  2011-09-15       Impact factor: 3.240

8.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.

Authors:  Daniel H Huson; Sina Beier; Isabell Flade; Anna Górska; Mohamed El-Hadidi; Suparna Mitra; Hans-Joachim Ruscheweyh; Rewati Tappu
Journal:  PLoS Comput Biol       Date:  2016-06-21       Impact factor: 4.475

9.  DNA metabarcoding uncovers fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica.

Authors:  Luiz Henrique Rosa; Thamar Holanda da Silva; Mayara Baptistucci Ogaki; Otávio Henrique Bezerra Pinto; Michael Stech; Peter Convey; Micheline Carvalho-Silva; Carlos Augusto Rosa; Paulo E A S Câmara
Journal:  Sci Rep       Date:  2020-12-15       Impact factor: 4.379

10.  Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.

Authors:  Shilin Chen; Hui Yao; Jianping Han; Chang Liu; Jingyuan Song; Linchun Shi; Yingjie Zhu; Xinye Ma; Ting Gao; Xiaohui Pang; Kun Luo; Ying Li; Xiwen Li; Xiaocheng Jia; Yulin Lin; Christine Leon
Journal:  PLoS One       Date:  2010-01-07       Impact factor: 3.240

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