| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Brodie, Juliet, et al.
(författare)
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The future of the northeast Atlantic benthic flora in a high CO2 world
- 2014
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 4:13, s. 2787-2798
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Tidskriftsartikel (refereegranskat)abstract
- Seaweed and seagrass communities in the northeast Atlantic have been profoundly impacted by humans, and the rate of change is accelerating rapidly due to runaway CO2 emissions and mounting pressures on coastlines associated with human population growth and increased consumption of finite resources. Here, we predict how rapid warming and acidification are likely to affect benthic flora and coastal ecosystems of the northeast Atlantic in this century, based on global evidence from the literature as interpreted by the collective knowledge of the authorship. We predict that warming will kill off kelp forests in the south and that ocean acidification will remove maerl habitat in the north. Seagrasses will proliferate, and associated epiphytes switch from calcified algae to diatoms and filamentous species. Invasive species will thrive in niches liberated by loss of native species and spread via exponential development of artificial marine structures. Combined impacts of seawater warming, ocean acidification, and increased storminess may replace structurally diverse seaweed canopies, with associated calcified and noncalcified flora, with simple habitats dominated by noncalcified, turf-forming seaweeds.
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| 3. |
- Hurd, Catriona L., et al.
(författare)
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Ocean acidification as a multiple driver: how interactions between changing seawater carbonate parameters affect marine life
- 2019
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Ingår i: Marine and Freshwater Research. - : CSIRO Publishing. - 1323-1650 .- 1448-6059. ; 71:3, s. 263-274
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Tidskriftsartikel (refereegranskat)abstract
- ‘Multiple drivers’ (also termed ‘multiple stressors’) is the term used to describe the cumulative effects of multiple environmental factors on organisms or ecosystems. Here, we consider ocean acidification as a multiple driver because many inorganic carbon parameters are changing simultaneously, including total dissolved inorganic carbon, CO2, HCO3–, CO32–, H+ and CaCO3 saturation state. With the rapid expansion of ocean acidification research has come a greater understanding of the complexity and intricacies of how these simultaneous changes to the seawater carbonate system are affecting marine life. We start by clarifying key terms used by chemists and biologists to describe the changing seawater inorganic carbon system. Then, using key groups of non-calcifying (fish, seaweeds, diatoms) and calcifying (coralline algae, coccolithophores, corals, molluscs) organisms, we consider how various physiological processes are affected by different components of the carbonate system.
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| 4. |
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| 5. |
- Flynn, Kevin J, et al.
(författare)
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Misuse of the phytoplankton-zooplankton dichotomy : the need to assign organisms as mixotrophs within plankton functional types
- 2013
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Ingår i: Journal of Plankton Research. - : Oxford University Press (OUP). - 0142-7873 .- 1464-3774. ; 35:1, s. 3-11
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Tidskriftsartikel (refereegranskat)abstract
- The classic portrayal of plankton is dominated by phytoplanktonic primary producersand zooplanktonic secondary producers. In reality, many if not most planktontraditionally labelled as phytoplankton or microzooplankton should be identifiedas mixotrophs, contributing to both primary and secondary production. Mixotrophicprotists (i.e. single-celled eukaryotes that perform photosynthesis and grazeon particles) do not represent a minor component of the plankton, as some formof inferior representatives of the past evolution of protists; they represent a majorcomponent of the extant protist plankton, and one which could become moredominant with climate change. The implications for this mistaken identification, ofthe incorrect labelling of mixotrophs as “phytoplankton” or “microzooplankton”,are great. It extends from the (mis)use of photopigments as indicators of primaryproduction performed by strict photoautotrophs rather than also (co)locating mixotrophicactivity, through to the inadequacy of plankton functional type descriptionsin models (noting that mixotrophic production in the individual organism is not asimple sum of phototrophy and heterotrophy). We propose that mixotrophy shouldbe recognized as a major contributor to plankton dynamics, with due effortexpended in field and laboratory studies, and should no longer be side-lined inconceptual food webs or in mathematical models.
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| 6. |
- Mitra, Aditee, et al.
(författare)
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Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition : Incorporation of Diverse Mixotrophic Strategies
- 2016
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Ingår i: Protist. - : Elsevier BV. - 1434-4610 .- 1618-0941. ; 167:2, s. 106-120
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Tidskriftsartikel (refereegranskat)abstract
- Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic "phytoplankton" and phagotrophic "microzooplankton". However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an ecophysiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks. (C) 2016 The Authors. Published by Elsevier GmbH.
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| 7. |
- Mitra, Aditee, et al.
(författare)
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The role of mixotrophic protists in the biological carbon pump
- 2014
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 11, s. 995-1005
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Tidskriftsartikel (refereegranskat)abstract
- The traditional view of the planktonic foodweb describes consumption of inorganic nutrientsby photo-autotrophic phytoplankton, which in turn supports zooplankton and ultimately higher trophic levels. Pathways centred on bacteria provide mechanisms for nutrient recycling. This structure lies at the foundation of most models used to explore biogeochemical cycling, functioning of the biological pump, and the impact of climate change on these processes. We suggest an alternative paradigm, which sees the bulk of the base of this foodweb supported by protist plankton (phytoplankton and microzooplankton) communities that are mixotrophic – combining phototrophy and phagotrophy within a single cell. The photoautotrophic eukaryotic plankton and their heterotrophic microzooplankton grazers dominate only within immature environments (e.g., spring bloom in temperate systems). With their flexible nutrition, mixotrophic protists dominate in more mature systems (e.g., temperate summer, established eutrophic systems and oligotrophic systems); the more stable water columns suggested under climate change may also be expected to favour these mixotrophs. We explore how such a predominantlymixotrophic structure affects microbial trophic dynamics and the biological pump. The mixotroph dominated structure differs fundamentally in its flow of energy and nutrients, with a shortened and potentially more efficient chain from nutrient regeneration to primary production. Furthermore, mixotrophy enables a direct conduit for the support of primary production from bacterial production. We show how the exclusion of an explicit mixotrophic component in studies of the pelagic microbial communities leads to a failure to capture the true dynamics of the carbon flow. In order to prevent a misinterpretation of the full implications of climate change upon biogeochemical cyclingand the functioning of the biological pump, we recommend inclusion of multi-nutrient mixotroph models within ecosystem studies.
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| 8. |
- Raven, J A, et al.
(författare)
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Genomics and chloroplast evolution: what did cyanobacteria do for plants?
- 2003
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Ingår i: GenomeBiology. - : Springer Science and Business Media LLC. - 1465-6906. ; 4:3, s. 1-209
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Forskningsöversikt (refereegranskat)abstract
- The complete genome sequences of cyanobacteria and of the higher plant Arabidopsis thaliana leave no doubt that the plant chloroplast originated, through endosymbiosis, from a cyanobacterium. But the genomic legacy of cyanobacterial ancestry extends far beyond the chloroplast itself, and persists in organisms that have lost chloroplasts completely.
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| 9. |
- Renberg, Linda, et al.
(författare)
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A metabolomic approach to study major metabolite changes during acclimation to limiting CO2 in chlamydomonas reinhardtii
- 2010
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 154:1, s. 187-196
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Tidskriftsartikel (refereegranskat)abstract
- Using a gas chromatography-mass spectrometry-time of flight technique, we determined major metabolite changes during induction of the carbon-concentrating mechanism in the unicellular green alga Chlamydomonas reinhardtii. In total, 128 metabolites with significant differences between high-and low-CO2-grown cells were detected, of which 82 were wholly or partially identified, including amino acids, lipids, and carbohydrates. In a 24-h time course experiment, we show that the amino acids serine and phenylalanine increase transiently while aspartate and glutamate decrease after transfer to low CO2. The biggest differences were typically observed 3 h after transfer to low-CO2 conditions. Therefore, we made a careful metabolomic examination at the 3-h time point, comparing low-CO2 treatment to high-CO2 control. Five metabolites involved in photorespiration, 11 amino acids, and one lipid were increased, while six amino acids and, interestingly, 21 lipids were significantly lower. Our conclusion is that the metabolic pattern during early induction of the carbon-concentrating mechanism fit a model where photorespiration is increasing.
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| 10. |
- Uscher, Kayley M, et al.
(författare)
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Exploring Cyanobacterial Mutualisms
- 2007
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Ingår i: Annual Review of Ecology, Evolution, and Systematics. - : Annual Reviews. - 1543-592X .- 1545-2069. ; 38, s. 255-273
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- Cyanobacterial symbioses with eukaryotes are ancient associations that are widely distributed in aquatic and terrestrial environments. Cyanobacteria are a significant driving force in the evolution of their hosts, providing a range of services including photosynthesis, nitrogen fixation, UV protection, and defensive toxins. Although widespread, cyanobacteria occur in a limited range of hosts. Terrestrial symbioses are typically restricted to lichens and early evolved plants, and aquatic symbioses to sessile or slow-moving organisms. This review examines the underlying evolutionary processes that may have lead to these patterns. It also examines the facts that the degree of integration between symbiont and host, and the mode of transmission of the symbiont, do not appear to be an indication of how old the symbiosis is or how important it is to host well-being. Biparental transmission of symbionts may prolong the survival of gametes that persist in the environment, increasing chances of fertilization.AcronymsTerms
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