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      Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments

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          Abstract

          Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO 2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime ( p = 0.002), but not by variation in CO 2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH 4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.

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          Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

          The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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            Ocean acidification: the other CO2 problem.

            Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion, reduces ocean pH and causes wholesale shifts in seawater carbonate chemistry. The process of ocean acidification is well documented in field data, and the rate will accelerate over this century unless future CO2 emissions are curbed dramatically. Acidification alters seawater chemical speciation and biogeochemical cycles of many elements and compounds. One well-known effect is the lowering of calcium carbonate saturation states, which impacts shell-forming marine organisms from plankton to benthic molluscs, echinoderms, and corals. Many calcifying species exhibit reduced calcification and growth rates in laboratory experiments under high-CO2 conditions. Ocean acidification also causes an increase in carbon fixation rates in some photosynthetic organisms (both calcifying and noncalcifying). The potential for marine organisms to adapt to increasing CO2 and broader implications for ocean ecosystems are not well known; both are high priorities for future research. Although ocean pH has varied in the geological past, paleo-events may be only imperfect analogs to current conditions.
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              Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming

              Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature.
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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
                22 August 2018
                2018
                : 9
                : 1730
                Affiliations
                [1] 1The Scottish Association for Marine Science, Scottish Marine Institute , Oban, United Kingdom
                [2] 2Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool , Liverpool, United Kingdom
                [3] 3Sediment Ecology Research Group, School of Biology, Scottish Oceans Institute, University of St Andrews , Fife, United Kingdom
                [4] 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Glasgow, United Kingdom
                Author notes

                Edited by: Martin G. Klotz, Washington State University Tri-Cities, United States

                Reviewed by: Erwan G. Roussel, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), France; Karen Tait, Plymouth Marine Laboratory, United Kingdom

                *Correspondence: Katherine R. Duncan katherine.duncan@ 123456strath.ac.uk

                This article was submitted to Microbiological Chemistry and Geomicrobiology, a section of the journal Frontiers in Microbiology

                †These authors share first authorship

                Article
                10.3389/fmicb.2018.01730
                6115492
                30190707
                850497b8-2876-4220-b949-cd6818ebbb3b
                Copyright © 2018 Hicks, Liu, Gregory, Kenny, Lucaci, Lenzi, Paterson and Duncan.

                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
                : 22 March 2017
                : 11 July 2018
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 100, Pages: 15, Words: 10671
                Funding
                Funded by: Natural Environment Research Council 10.13039/501100000270
                Award ID: NE/E006795/1
                Funded by: NERC Environmental Bioinformatics Centre 10.13039/100008668
                Award ID: NBAF908 NBAF-L
                Funded by: Scottish Funding Council 10.13039/501100000360
                Award ID: HR09011
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                benthic biogeochemistry,microbial communities,biogeochemical cycles,environmental change,benthic microbial ecology,marine sediments

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