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      Mangrove-Associated Fungal Communities Are Differentiated by Geographic Location and Host Structure

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          Abstract

          Marine fungi on the whole remain understudied, especially in the highly diverse Southeast Asian region. We investigated the fungal communities associated with the mangrove tree Avicennia alba throughout Singapore and Peninsular Malaysia. At each sampling location, we examined ten individual trees, collecting leaves, fruits, pneumatophores, and an adjacent sediment sample from each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analyses reveal significant differences in fungal communities collected from different locations and host structures. Mantel tests and multiple regression on distance matrices show a significant pattern of distance decay with samples collected close to one another having more similar fungal communities than those farther away. Submergence appears to drive part of the variation as host structures that are never submerged (leaves and fruits) have more similar fungal communities relative to those that are covered by water during high tide (pneumatophores and sediment). We suggest that fungi of terrestrial origins dominate structures that are not inundated by tidal regimes, while marine fungi dominate mangrove parts and sediments that are submerged by the incoming tide. Given the critical functions fungi play in all plants, and the important role they can have in determining the success of restoration schemes, we advocate that fungal community composition should be a key consideration in any mangrove restoration or rehabilitation project.

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          Most cited references 54

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          AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

           T.J White,  T. Bruns,  S. Lee (1990)
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            VARIATION IN PLANT RESPONSE TO NATIVE AND EXOTIC ARBUSCULAR MYCORRHIZAL FUNGI

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              Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

              Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation sequencing (NGS) can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity – which we define as dissimilarity between re-sequenced replicates of the same sample – decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                30 October 2019
                2019
                : 10
                Affiliations
                1Department of Biological Sciences, National University of Singapore , Singapore, Singapore
                2Tropical Marine Science Institute, National University of Singapore , Singapore, Singapore
                3School of Marine and Environmental Sciences, Universiti Malaysia Terengganu , Kuala Nerus, Malaysia
                Author notes

                Edited by: Mohamed Hijri, Université de Montréal, Canada

                Reviewed by: Christopher Smyth, Lock Haven University, United States; Huzefa A. Raja, University of North Carolina at Greensboro, United States

                *Correspondence: Benjamin J. Wainwright, dbsbjw@ 123456nus.edu.sg

                This article was submitted to Fungi and Their Interactions, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2019.02456
                6831645
                Copyright © 2019 Lee, Huang, Quek, Lee and Wainwright.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 4, Tables: 1, Equations: 0, References: 81, Pages: 9, Words: 0
                Categories
                Microbiology
                Original Research

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