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      Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

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          Abstract

          Saharan dust input and seasonal upwelling along North–West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2–3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.

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          Swarm: robust and fast clustering method for amplicon-based studies

          Frédéric Mahé, Torbjørn Rognes, Christopher Quince … (2014)
          Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.
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            Migrations and dynamics of the intertropical convergence zone.

            Tapio Schneider, Tobias Bischoff, Gerald Haug (2014)
            Rainfall on Earth is most intense in the intertropical convergence zone (ITCZ), a narrow belt of clouds centred on average around six degrees north of the Equator. The mean position of the ITCZ north of the Equator arises primarily because the Atlantic Ocean transports energy northward across the Equator, rendering the Northern Hemisphere warmer than the Southern Hemisphere. On seasonal and longer timescales, the ITCZ migrates, typically towards a warming hemisphere but with exceptions, such as during El Niño events. An emerging framework links the ITCZ to the atmospheric energy balance and may account for ITCZ variations on timescales from years to geological epochs.
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              The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives.

              T Ohno, Colleen Cavanaugh, A Tomitani … (2006)
              Cyanobacteria have played a significant role in Earth history as primary producers and the ultimate source of atmospheric oxygen. To date, however, how and when the group diversified has remained unclear. Here, we combine molecular phylogenetic and paleontological studies to elucidate the pattern and timing of early cyanobacterial diversification. 16S rRNA, rbcL, and hetR genes were sequenced from 20 cyanobacterial strains distributed among 16 genera, with particular care taken to represent the known diversity of filamentous taxa. Unlike most other bacteria, some filamentous cyanobacteria evolved a degree of cell differentiation, producing both specialized cells for nitrogen fixation (heterocysts) and resting cells able to endure environmental stress (akinetes). Phylogenetic analyses support the hypothesis that cyanobacteria capable of cell differentiation are monophyletic, and the geological record provides both upper and lower bounds on the origin of this clade. Fossil akinetes have been identified in 1,650- to 1,400-mega-annum (Ma) cherts from Siberia, China, and Australia, and what may be the earliest known akinetes are preserved in approximately 2,100-Ma chert from West Africa. Geochemical evidence suggests that oxygen first reached levels that would compromise nitrogen fixation (and hence select for heterocyst differentiation) 2,450-2,320 Ma. Integrating phylogenetic analyses and geological data, we suggest that the clade of cyanobacteria marked by cell differentiation diverged once between 2,450 and 2,100 Ma, providing an internal bacterial calibration point for studies of molecular evolution in early organisms.
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                Author and article information

                Contributors
                Journal
                Journal ID (nlm-ta): Front Microbiol
                Journal ID (iso-abbrev): Front Microbiol
                Journal ID (publisher-id): Front. Microbiol.
                Title: Frontiers in Microbiology
                Publisher: Frontiers Media S.A.
                ISSN (Electronic): 1664-302X
                Publication date (Electronic): 23 November 2018
                Publication date Collection: 2018
                Volume: 9
                Electronic Location Identifier: 2836
                Affiliations
                [1] 1Leibniz Centre for Tropical Marine Research (ZMT) , Bremen, Germany
                [2] 2Faculty of Biology and Chemistry (FB2), University of Bremen , Bremen, Germany
                [3] 3Max Plank Institute for Marine Microbiology , Bremen, Germany
                [4] 4Helmholtz Young Investigator Group SEAPUMP, Alfred Wegener Institute for Polar and Marine Research , Bremerhaven, Germany
                [5] 5Center for Marine Environmental Sciences (MARUM), University of Bremen , Bremen, Germany
                [6] 6Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) , Berlin, Germany
                [7] 7Institute of Biochemistry and Biology, University of Potsdam , Potsdam, Germany
                Author notes

                Edited by: Chuanlun Zhang, Southern University of Science and Technology, China

                Reviewed by: Stefan M. Sievert, Woods Hole Oceanographic Institution, United States; Eyal Rahav, Israel Oceanographic and Limnological Research, Israel

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

                Article
                DOI: 10.3389/fmicb.2018.02836
                PMC ID: 6265507
                PubMed ID: 30532746
                SO-VID: eb362f54-d21b-4766-be37-2d9ecc9dbdde
                Copyright © Copyright © 2018 Bachmann, Heimbach, Hassenrück, Kopprio, Iversen, Grossart and Gärdes.
                License:

                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
                Date received : 01 August 2018
                Date accepted : 05 November 2018
                Page count
                Figures: 5, Tables: 0, Equations: 0, References: 65, Pages: 13, Words: 0
                Categories
                Subject: Microbiology
                Subject: Original Research

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: prokaryotes,biodiversity,microbial ecology,alpha diversity,bray curtis dissimilarity,temperature,salinity,16s rrna illumina amplicon sequencing
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: prokaryotes, biodiversity, microbial ecology, alpha diversity, bray curtis dissimilarity, temperature, salinity, 16s rrna illumina amplicon sequencing

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