Periodic Reporting for period 5 - APPELS (A Probe of the Periodic Elements for Life in the Sea)
Reporting period: 2021-12-01 to 2022-11-30
Metals are a fundamental component of life. Biological processing of oxygen, nitrogen, sulphur and carbon all rely on metalloproteins. But less than half of all metalloproteins are characterised. APPELS aims to unveil, via cutting-edge techniques, a comprehensive view of the essential elements to life in the ocean, at the heart of the carbon cycle and global change.
The objective of APPELS was to probe the expanse of the periodic table to provide a comprehensive definition of the elements required by the modern marine phytoplankton (the metallome) and the marine metalloproteome. APPELS will revolutionise our understanding of metal-binding by proteins and the required elements that control the efficacy of biological pumping of carbon to depth in the ocean.
We have defined the metallome for marine life, ultimately the ancient ancestor of life on land and human beings. APPELS has delivered an expansive definition of the metallome for different forms of marine life and the range of elemental concentrations that allow maximum growth of diverse phytoplankton chemotypes. It will pinpoint limiting and toxic thresholds for photosynthesisers, key to the chemical controls on the biological pump of atmospheric pCO2, and with implications for marine productivity in a future perturbed ocean and how elements will enter the marine foodchain.
APPELS has added entirely new dimensions to the interactions between the biological pump and the stoichiometry of ocean chemistry. These new dimentions include changing trace metals and major nutrients (Matsumoto et al., 2021), eludicating their role for different funcational groups of phytoplankton, and the microbes that replenish major nutrients (Shafiee et al., 2021) in the past, modern and future ocean (Zhang et al., 2022). Although APPELS reinforces the importance of Fe, we have shown that diatoms are also Mn limited in ~20% and dinoflagellates Zn limited in over 60% of the ocean. We highlight a previously overlooked role of Cu in limiting the growth of phytoplankton and suggest that trace metal supply may have a greater impact on the distribution of diatoms and dinoflagellates than on coccolithophores. Using projections of how trace metal concentrations may evolve with climate change, we show that the future oceans may promote widespread Zn limitation, shifting phytoplankton communities to groups that drive a weaker biological pump (Zhang et al., 2023).
The objective of APPELS was to probe the expanse of the periodic table to provide a comprehensive definition of the elements required by the modern marine phytoplankton (the metallome) and the marine metalloproteome. APPELS will revolutionise our understanding of metal-binding by proteins and the required elements that control the efficacy of biological pumping of carbon to depth in the ocean.
We have defined the metallome for marine life, ultimately the ancient ancestor of life on land and human beings. APPELS has delivered an expansive definition of the metallome for different forms of marine life and the range of elemental concentrations that allow maximum growth of diverse phytoplankton chemotypes. It will pinpoint limiting and toxic thresholds for photosynthesisers, key to the chemical controls on the biological pump of atmospheric pCO2, and with implications for marine productivity in a future perturbed ocean and how elements will enter the marine foodchain.
APPELS has added entirely new dimensions to the interactions between the biological pump and the stoichiometry of ocean chemistry. These new dimentions include changing trace metals and major nutrients (Matsumoto et al., 2021), eludicating their role for different funcational groups of phytoplankton, and the microbes that replenish major nutrients (Shafiee et al., 2021) in the past, modern and future ocean (Zhang et al., 2022). Although APPELS reinforces the importance of Fe, we have shown that diatoms are also Mn limited in ~20% and dinoflagellates Zn limited in over 60% of the ocean. We highlight a previously overlooked role of Cu in limiting the growth of phytoplankton and suggest that trace metal supply may have a greater impact on the distribution of diatoms and dinoflagellates than on coccolithophores. Using projections of how trace metal concentrations may evolve with climate change, we show that the future oceans may promote widespread Zn limitation, shifting phytoplankton communities to groups that drive a weaker biological pump (Zhang et al., 2023).
APPELS has allowed an expansive investigation of phytoplankton interactions with novel trace metals to understand both use of metals, and contrasting metal needs and management amongst different phytoplankton and microbe groups.
1) We have developed and optimised a novel method for direct analysis of 32 elements simultaneously in small volume of cell lysate in buffers with a high salt matrix (800µL, up to 30% TDS) (Zhang et al., 2018)
2) Our comparative genomic analysis of 26 complete proteomes and metal domain analysis of additional 608 partially complete sequences of phytoplankton reveal that groups with different evolutionary history have distinct metal-binding proteins and contrasting metal acquisition strategies, adapted to differing availability of trace metals. The secondary-endosymbiont-bearing lineages are better adapted to well-oxygenated, nutrient-poor environments. Such different metal requirements across these lineages suggest a drastic decline in open-ocean trace metal concentrations at the inception of the Mesozoic, contributing to the shifts in phytoplankton communities that drove major changes in ocean chemical buffering (Zhang et al., 2022).
3) We have demonstrated an interaction between the nutrient status of a cell, and its susceptibility to metal toxicity (Snow et al., 2020; Tostevin et al., 2022)
4) We have found that Cr (Zhang et al., in review for New Phyto.), U, Ni (Wang et al., 2023 in review for Nat. Geo.) and Tl (Zhang and Rickaby, 2020) can promote growth of some microorganisms when added beyond current environmental concentrations.
1) We have developed and optimised a novel method for direct analysis of 32 elements simultaneously in small volume of cell lysate in buffers with a high salt matrix (800µL, up to 30% TDS) (Zhang et al., 2018)
2) Our comparative genomic analysis of 26 complete proteomes and metal domain analysis of additional 608 partially complete sequences of phytoplankton reveal that groups with different evolutionary history have distinct metal-binding proteins and contrasting metal acquisition strategies, adapted to differing availability of trace metals. The secondary-endosymbiont-bearing lineages are better adapted to well-oxygenated, nutrient-poor environments. Such different metal requirements across these lineages suggest a drastic decline in open-ocean trace metal concentrations at the inception of the Mesozoic, contributing to the shifts in phytoplankton communities that drove major changes in ocean chemical buffering (Zhang et al., 2022).
3) We have demonstrated an interaction between the nutrient status of a cell, and its susceptibility to metal toxicity (Snow et al., 2020; Tostevin et al., 2022)
4) We have found that Cr (Zhang et al., in review for New Phyto.), U, Ni (Wang et al., 2023 in review for Nat. Geo.) and Tl (Zhang and Rickaby, 2020) can promote growth of some microorganisms when added beyond current environmental concentrations.
Within APPELS, we have been able to elucidate a role for trace metals in controlling the growth and distribution of different microbes that mediate the supply of nitrogen for the biological pump:
1) We have investigated the Fe requirements and Fe uptake strategies of the Nitrosopumilus maritimus strain SCM1, a strain representative of globally abundant marine AOA. N. maritimus growth may be Fe limited due to its highest iron requirement of all marine microbes (Shafiee et al., 2019). Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu). We propose the testable hypothesis that ammonia oxidation is limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time (Shafiee et al., 2021).
The differential response of algae to limiting and toxic levels of metals reveals contrasting metal management systems which explain both their global distribution and the phytoplankton succession during the geological past:
2) The different responses to Cr exposure reveal contrasting strategies for metal uptake and homeostasis in algal lineages. At high Cr(VI) concentrations, red lineages experience growth inhibition through reduced photosynthetic capability, while green lineages are completely unaffected. Green algae have higher specificity transporters to prevent Cr(VI) from entering the cell, and more specific intracellular stores of Cr within the membrane fraction than the red algae, which accumulate more Cr mistakenly in the cytosol fraction via lower affinity transport mechanisms (Wilson et al., 2019). Green algal approaches require greater nutrient investments in the more numerous transport proteins required and management of specific metals, a strategy better adapted to the resource-rich coastal waters. By contrast the red algae are nutrient efficient with fewer and less discriminate metal transporters which can be fast and better adapted in the oligotrophic, oxygenated open ocean which has prevailed since the deepening of the oxygen minimum zones at the start of the Mesozoic (Zhang et al., 2022).
The Ni isotopic fractionation by phytoplankton shows a totally new conceptual understanding of biological metal isotopic fractionation:
3) We have shown that, in contrast to biological isotopic fractionation for other elements, three cosmopolitan phytoplankton species preferentially take up isotopically heavy Ni from the culture media, with species-dependent magnitudes of fractionation, under varying Ni availability. This fractionation towards heavy Ni isotopes can be explained, in our experiments, by the strong Ni-binding of cellular metal acquisition systems, relative to weaker binding by ligands in the culture media, with a secondary influence of cellular relocation and/or efflux. In the open ocean, an inferred stronger binding of Ni to ligands present in seawater, relative to that of the phytoplankton, yields the inverse fractionation (towards light isotopes in the biomass) and limits the bioavailability of metals in the surface ocean. We demonstrate that Ni is limited for marine phytoplankton in the mid-latitude surface ocean with low Ni concentration and heavy Ni isotope composition (Wang et al., in review Nature Geoscience).
1) We have investigated the Fe requirements and Fe uptake strategies of the Nitrosopumilus maritimus strain SCM1, a strain representative of globally abundant marine AOA. N. maritimus growth may be Fe limited due to its highest iron requirement of all marine microbes (Shafiee et al., 2019). Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu). We propose the testable hypothesis that ammonia oxidation is limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time (Shafiee et al., 2021).
The differential response of algae to limiting and toxic levels of metals reveals contrasting metal management systems which explain both their global distribution and the phytoplankton succession during the geological past:
2) The different responses to Cr exposure reveal contrasting strategies for metal uptake and homeostasis in algal lineages. At high Cr(VI) concentrations, red lineages experience growth inhibition through reduced photosynthetic capability, while green lineages are completely unaffected. Green algae have higher specificity transporters to prevent Cr(VI) from entering the cell, and more specific intracellular stores of Cr within the membrane fraction than the red algae, which accumulate more Cr mistakenly in the cytosol fraction via lower affinity transport mechanisms (Wilson et al., 2019). Green algal approaches require greater nutrient investments in the more numerous transport proteins required and management of specific metals, a strategy better adapted to the resource-rich coastal waters. By contrast the red algae are nutrient efficient with fewer and less discriminate metal transporters which can be fast and better adapted in the oligotrophic, oxygenated open ocean which has prevailed since the deepening of the oxygen minimum zones at the start of the Mesozoic (Zhang et al., 2022).
The Ni isotopic fractionation by phytoplankton shows a totally new conceptual understanding of biological metal isotopic fractionation:
3) We have shown that, in contrast to biological isotopic fractionation for other elements, three cosmopolitan phytoplankton species preferentially take up isotopically heavy Ni from the culture media, with species-dependent magnitudes of fractionation, under varying Ni availability. This fractionation towards heavy Ni isotopes can be explained, in our experiments, by the strong Ni-binding of cellular metal acquisition systems, relative to weaker binding by ligands in the culture media, with a secondary influence of cellular relocation and/or efflux. In the open ocean, an inferred stronger binding of Ni to ligands present in seawater, relative to that of the phytoplankton, yields the inverse fractionation (towards light isotopes in the biomass) and limits the bioavailability of metals in the surface ocean. We demonstrate that Ni is limited for marine phytoplankton in the mid-latitude surface ocean with low Ni concentration and heavy Ni isotope composition (Wang et al., in review Nature Geoscience).