Contributions of anoxygenic and oxygenic phototrophy and chemolithotrophy to carbon and oxygen fluxes in aquatic environments

Raven, JA

doi:10.3354/ab01315

Cited by 50 publications

(68 citation statements)

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“…The anammox process is inhibited by oxygen, yet organisms quickly resume their activity once anaerobic conditions are restored (Strous et al 1999). Genomic and enzymatic studies of anammox bacteria provided initial evidence for usage of the WL-pathway for carbon fixation (Schouten et al 2004, Strous et al 2006, making this pathway potentially of wider significance in the pelagic realm, with a potential contribution of up to 3.5 Tg C y −1 (Raven 2009). Interestingly, CO dehydrogenase, the key enzyme of the WL-pathway, is very oxygen sensitive and, so far, the WL-pathway is only known to operate in anaerobic organisms growing under highly reducing conditions (Berg et al 2010a), unlike conditions prevailing in OMZs.…”

Section: Wwwannualreviewsorg • Beyond the Calvin Cyclementioning

confidence: 98%

“…Although other so-called alternative carbon fixation pathways have been known to exist for a long time, recognition of their relative contribution to local organic matter production and an appreciation of the ecological role of the organisms using these pathways have occurred only this past decade (Raven 2009). Presently, five CO 2 fixation pathways are known in addition to the CBB cycle: the reductive tricarboxylic acid (rTCA) cycle; the reductive acetyl-CoA, or Wood-Ljungdahl (WL) pathway; and the 3-hydroxypropionate (3-HP) bicycle; as well as the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) and dicarboxylate/4-hydroxybutyrate (DC/4-HB) cycles (Ljungdahl 1986, Buchanan & Arnon 1990, Berg et al 2007, Huber et al 2008, Zarzycki et al 2009).…”

Section: Introductionmentioning

confidence: 99%

“…Although the standing stock of primary producers is much smaller in the ocean compared with the land, approximately half of the global primary production occurs in the ocean due to a much higher turnover of biomass (Field et al 1998). In the ocean, most primary production occurs in the photic zone by cyanobacteria (e.g., Prochlorococcus, Synechococcus) and eukaryotic algae (e.g., diatoms and coccolithophorids), using the Calvin-Benson-Bassham (CBB) cycle for carbon fixation and oxygenic photosynthesis to conserve energy (Raven 2009, Scanlan et al 2009, Bowler et al 2010. This makes the CBB cycle the most significant carbon fixation pathway on today's Earth, and numerous reviews have summarized our understanding of this cycle and the importance of oxygenic photosynthesis for primary production on our planet (Shively et al 1998, Tabita 2004, Tabita et al 2007, Falkowski et al 2008, Raven 2009).…”

Section: Introductionmentioning

confidence: 99%

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Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

Hügler

Sievert

2011

Annu. Rev. Mar. Sci.

543

486

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Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out over the last decade have not only elucidated new pathways but also shown that autotrophic carbon fixation via pathways other than the CBB cycle can be significant. This has ramifications for our understanding of the carbon cycle and energy flow in the ocean. Here, we review the recent discoveries in the field of autotrophic carbon fixation, including the biochemistry and evolution of the different pathways, as well as their ecological relevance in various oceanic ecosystems.

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Section: Wwwannualreviewsorg • Beyond the Calvin Cyclementioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

Hügler

Sievert

2011

Annu. Rev. Mar. Sci.

543

486

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“…3), Calvin cycle, reverse TCA cycle, reductive acetyl CoA pathway, and dicarboxylatehydroxybutyrate cycle. This prediction becomes relevant in light of the described importance of the Calvin cycle in primary productivity estimations, [44][45][46][47][48][49][50] but the other CO 2¯x ation pathways remain understudied. [51][52][53][54] The EFM analysis is constrained by stoichiometry and does not violate the conservation of mass law, therefore it becomes useful to estimate the potential role of relevant metabolic pathways, including the alternative CO 2¯x ation pathways, coupling metagenomic datasets, and ecophysiological rates to limit the solution°ux space of the EFMs and make predictions for the rates of CO 2¯x ation pathways involved.…”

Section: Efm Analysis Of Metabolic Networkmentioning

confidence: 97%

Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources

Cerqueda-García

Falcón

2016

J. Bioinform. Comput. Biol.

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Microbialites and microbial mats are complex communities with high phylogenetic diversity. These communities are mostly composed of bacteria and archaea, which are the earliest living forms on Earth and relevant to biogeochemical evolution. In this study, we identified the shared metabolic pathways for uptake of inorganic C and N in microbial mats and microbialites based on metagenomic data sets. An in silico analysis for autotrophic pathways was used to trace the paths of C and N to the system, following an elementary flux modes (EFM) approach, resulting in a stoichiometric model. The fragility was analyzed by the minimal cut sets method. We found four relevant pathways for the incorporation of CO2 (Calvin cycle, reverse tricarboxylic acid cycle, reductive acetyl-CoA pathway, and dicarboxylate/4-hydroxybutyrate cycle), some of them present only in archaea, while nitrogen fixation was the most important source of N to the system. The metabolic potential to incorporate nitrate to biomass was also relevant. The fragility of the network was low, suggesting a high redundancy of the autotrophic pathways due to their broad metabolic diversity, and highlighting the relevance of reducing power source. This analysis suggests that microbial mats and microbialites are "metabolic pumps" for the incorporation of inorganic gases and formation of organic matter.

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“…The CBB cycle is also used by chemolithoautotrophic bacteria to fix carbon in the dark ocean (Badger and Bek, 2007;Walsh et al, 2009). Thus, the CBB cycle, being one of the six carbon fixation pathways described to date (Berg, 2011;Hügler and Sievert, 2011), is the main carbon fixation mechanism utilized by extant autotrophic organisms (Raven, 2009;Berg, 2011).…”

Section: Introductionmentioning

confidence: 99%

Diversity and Transcriptional Levels of RuBisCO Form II of Sulfur-Oxidizing γ-Proteobacteria in Coastal-Upwelling Waters with Seasonal Anoxia

et al. 2017

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Seasonal wind-driven upwelling, high primary production in surface waters, and oxygen deficiency in subsurface waters characterize the coastal ecosystem of the subtropical eastern South Pacific (ESP), and shape the nature and dynamics of the microbial community structure and function. We investigated the diversity, abundance, and transcriptional levels of the gene encoding the large subunit form II of the RuBisCO enzyme (cbbM) in the pelagic microbial community at a continental-shelf site off central Chile over 2 years. We focused on cbbM genes affiliated with the sulfur-oxidizing γ-proteobacteria cluster, whose members are known to dominate in oxygen-deficient marine environments and are highly abundant in the study area. Phylogenetic analysis of cbbM sequences suggests the presence of a novel group of chemolithoautotrophs, closely related to the SUP05/ARCTIC96BD-19 clade. Through (RT)-qPCR, we studied the cbbM gene abundance and transcript dynamics over an annual cycle, finding a significantly higher number of cbbM copies per unit volume in months of active upwelling and at depths in which oxygen was scarce or absent. The same temporal pattern was observed at the transcriptional level. We also analyzed the relative expression of key genes for carbon, nitrogen and sulfur cycling in six metatranscriptomic datasets, for two characteristic periods within the annual cycle: the anoxic upwelling and the suboxic downwelling. Our results indicate that coastal waters of the subtropical ESP contain transcriptionally active populations of carbon fixing pelagic bacteria, whose dynamics is controlled, in large part, by fluctuations in oxygen levels. They also suggest that chemolithoautotrophic processes coupled to the sulfur and nitrogen cycles become increasingly important for the carbon economy of marine coastal waters as oxygen concentrations decline.

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Contributions of anoxygenic and oxygenic phototrophy and chemolithotrophy to carbon and oxygen fluxes in aquatic environments

Cited by 50 publications

References 0 publications

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources

Diversity and Transcriptional Levels of RuBisCO Form II of Sulfur-Oxidizing γ-Proteobacteria in Coastal-Upwelling Waters with Seasonal Anoxia

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