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      Bacterial Communities Show Algal Host ( Fucus spp.)/Zone Differentiation Across the Stress Gradient of the Intertidal Zone

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          Abstract

          The intertidal zone often has varying levels of environmental stresses (desiccation, temperature, light) that result in highly stress-tolerant macrobiota occupying the upper zone while less tolerant species occupy the lower zone, but little comparative information is available for intertidal bacteria. Here we describe natural (unmanipulated) bacterial communities of three Fucus congeners ( F. spiralis, high zone; F. vesiculosus, mid zone; F. distichus, low zone) as well as those of F. vesiculosus transplanted to the high zone (Dry and Watered treatments) and to the mid zone (Procedural Control) during summer in Maine (United States). We predicted that bacterial communities would be different among the differently zoned natural congeners, and that higher levels of desiccation stress in the high zone would cause bacterial communities of Dry transplants to become similar to F. spiralis, whereas relieving desiccation stress on Watered transplants would maintain the mid-zone F. vesiculosus bacterial community. Bacteria were identified as amplicon sequence variants (ASVs) after sequencing the V4 hypervariable region of the 16S rRNA gene. Microbiome composition and structure were significantly different between the differently zoned congeners at each tissue type (holdfasts, receptacles, vegetative tips). ASVs significantly associated with the mid-zone congener were frequently also present on the high-zone or low-zone congener, whereas overlap in ASVs between the high-zone and low-zone congeners was rare. Only 7 of 6,320 total ASVs were shared among tissues over all congeners and transplant treatments. Holdfast bacterial community composition of Dry transplants was not significantly different from that of F. spiralis, but Watered holdfast communities were significantly different from those of F. spiralis and not significantly different from those of procedural controls. Additional stressor(s) appeared important, because bacterial communities of Dry and Watered transplants were only marginally different from each other ( p = 0.059). The relative abundance of Rhodobacteraceae associated with holdfasts generally correlated with environmental stress with highest abundance associated with F. spiralis and the two high-zone transplant treatments. These findings suggest that the abiotic stressors that shape distributional patterns of host species also affect their bacterial communities.

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          Pvclust: an R package for assessing the uncertainty in hierarchical clustering.

          Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option.
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            Bacterial community dynamics are linked to patterns of coral heat tolerance

            Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked.
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              Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait.

              Although drought is an increasing problem in agriculture, the contribution of the root-associated bacterial microbiome to plant adaptation to water stress is poorly studied. We investigated if the culturable bacterial microbiome associated with five grapevine rootstocks and the grapevine cultivar Barbera may enhance plant growth under drought stress. Eight isolates, over 510 strains, were tested in vivo for their capacity to support grapevine growth under water stress. The selected strains exhibited a vast array of plant growth promoting (PGP) traits, and confocal microscopy observation of gfp-labelled Acinetobacter and Pseudomonas isolates showed their ability to adhere and colonize both the Arabidopsis and grapevine rhizoplane. Tests on pepper plants fertilized with the selected strains, under both optimal irrigation and drought conditions, showed that PGP activity was a stress-dependent and not a per se feature of the strains. The isolates were capable of increasing shoot and leaf biomass, shoot length, and photosynthetic activity of drought-challenged grapevines, with an enhanced effect in drought-sensitive rootstock. Three isolates were further assayed for PGP capacity under outdoor conditions, exhibiting the ability to increase grapevine root biomass. Overall, the results indicate that PGP bacteria contribute to improve plant adaptation to drought through a water stress-induced promotion ability. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.
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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
                24 September 2020
                2020
                : 11
                : 563118
                Affiliations
                [1] 1School of Marine Sciences, University of Maine , Orono, ME, United States
                [2] 2Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory , Woods Hole, MA, United States
                [3] 3Département de Biologie, Université Laval , Québec, QC, Canada
                [4] 4Center for Data Science, Nell Hodgson Woodruff School of Nursing, Emory University , Atlanta, GA, United States
                Author notes

                Edited by: Jackie L. Collier, Stony Brook University, United States

                Reviewed by: Florian Weinberger, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany; Mahasweta Saha, Plymouth Marine Laboratory, United Kingdom

                *Correspondence: Susan H. Brawley, brawley@ 123456maine.edu

                Present address: Charlotte T. C. Quigley, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States; Kyle A. Capistrant-Fossa, Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, United States

                These authors share first authorship

                This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2020.563118
                7541829
                15274cc1-8802-4d9f-b0c5-74dc0194ddef
                Copyright © 2020 Quigley, Capistrant-Fossa, Morrison, Johnson, Morozov, Hertzberg and Brawley.

                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.

                History
                : 18 May 2020
                : 24 August 2020
                Page count
                Figures: 10, Tables: 3, Equations: 0, References: 119, Pages: 19, Words: 0
                Funding
                Funded by: National Science Foundation 10.13039/100000001
                Funded by: National Science Foundation 10.13039/100000001
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                desiccation,granulosicoccus,microbiome,octadecabacter,peptide nucleic acid clamps (pnas),rhodobacteraceae,transplant,zonation

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