The role of zinc in the adaptive evolution of polar phytoplankton

Biogenic-to-lithogenic handoff of particulate Zn affects the Zn cycle in the Southern Ocean

Zinc (Zn) is vital to marine organisms. Its active uptake by phytoplankton results in a substantial depletion of dissolved Zn, and Zn bound to particulate organic matter replenishes dissolved Zn in the ocean through remineralization. However, we found that particulate Zn changes from Zn bound to phosphoryls in cells to recalcitrant inorganic pools that include biogenic silica, clays, and iron, manganese, and aluminum oxides in the Southern Ocean water column. The abundances of inorganic pools increase with depth and are the only phases preserved in sediments. Changes in the particulate-Zn speciation influence Zn bioavailability and explain the decoupling of Zn and phosphorus and the correlation of Zn and silicon in the water column. These findings reveal a new dimension to the ocean Zn cycle, implicating an underappreciated role of inorganic Zn particles and their impact on biological productivity.

Speciation patterns of zinc in ocean particles

Different particulate zinc forms ultimately affect marine biological productivity.

Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach

The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.

Trace and rare earth elements in phytoplankton from the Tyrrhenian Sea (Italy)

Plankton plays a very crucial role in bioaccumulation and transfer of metals in the marine food web and represents a suitable bioindicator of the occurrence of trace and rare earth elements in the ecosystem. Trace elements and REEs were analyzed by ICP-MS in phytoplankton samples from the northwestern Mediterranean Sea. Metal concentrations in phytoplankton were found strongly influenced by seasons and depth of collection (- 30 m, - 50 m). Principal component analysis (PCA) has shown that Al, As, Cr, Cu, Ga, and Sn concentrations were related to summer and autumn in samples collected at 30 m depth, while Fe, Mn, Ni, V, and Zn levels related strongly with summer and spring at 50 m depth. Fe, Al, and Zn were the most represented elements in all samples (mean values respectively in the ranges 4.2-8.2, 9.6-13, and 1.0-4.4 mg kg-1) according to their widespread presence in the environment and in the earth crust. Principal component analysis (PCA) performed on REEs showed that mostly all lanthanides' concentrations strongly correlate with summer and autumn seasons (- 30 m depth); the highest ∑REE concentration (75 µg kg-1) was found in winter. Phytoplankton REE normalized profile was comparable to those of other marine biota collected in the same area according to the suitability of lanthanides as geological tracers.

Multi-omics for studying and understanding polar life

Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.

Gene duplication and functional divergence of new genes contributed to the polar acclimation of Antarctic green algae

Psychrophilic microalgae successfully survive in the extreme and highly variable polar ecosystems, which represent the energy base of most food webs and play a fundamental role in nutrient cycling. The success of microalgae is rooted in their adaptive evolution. Revealing how they have evolved to thrive in extreme polar environments will help us better understand the origin of life in polar ecosystems. We isolated a psychrophilic unicellular green alga, Microglena sp. YARC, from Antarctic sea ice which has a huge genome. Therefore, we predicted that gene replication may play an important role in its polar adaptive evolution. We found that its protein-coding gene number significantly increased and the duplication time was dated between 37 and 48 million years ago, which is consistent with the formation of the circumpolar Southern Ocean. Most duplicated paralogous genes were enriched in pathways related to photosynthesis, DNA repair, and fatty acid metabolism. Moreover, there were a total of 657 Microglena-specific families, including collagen-like proteins. The divergence in the expression patterns of the duplicated and species-specific genes reflects sub- and neo-functionalization during stress acclimation. Overall, key findings from this study provide new information on how gene duplication and their functional novelty contributed to polar algae adaptation to the highly variable polar environmental conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00203-z.

Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Microbial rhodopsins are photoreceptor proteins that convert light into biological signals or energy. Proteins of the xanthorhodopsin family are common in eukaryotic photosynthetic plankton including diatoms. However, their biological role in these organisms remains elusive. Here we report on a xanthorhodopsin variant (FcR1) isolated from the polar diatom Fragilariopsis cylindrus. Applying a combination of biophysical, biochemical and reverse genetics approaches, we demonstrate that FcR1 is a plastid-localized proton pump which binds the chromophore retinal and is activated by green light. Enhanced growth of a Thalassiora pseudonana gain-of-function mutant expressing FcR1 under iron limitation shows that the xanthorhodopsin proton pump supports growth when chlorophyll-based photosynthesis is iron-limited. The abundance of xanthorhodopsin transcripts in natural diatom communities of the surface oceans is anticorrelated with the availability of dissolved iron. Thus, we propose that these proton pumps convey a fitness advantage in regions where phytoplankton growth is limited by the availability of dissolved iron.

Process controlling iron-manganese regulation of the Southern Ocean biological carbon pump

Iron (Fe) is a key limiting nutrient driving the biological carbon pump and is routinely represented in global ocean biogeochemical models. However, in the Southern Ocean, the potential role for other micronutrients has not received the same attention. For example, although manganese (Mn) is essential to photosynthetic oxygen production and combating oxidative stress, it is not included in ocean models and a clear understanding of its interaction with Fe in the region is lacking. This is especially important for the Southern Ocean because both Mn and Fe are strongly depleted. We use a hierarchical modelling approach to explore how the physiological traits associated with Fe and Mn contribute to driving the footprint of micronutrient stress across different phytoplankton functional types (PFTs). We find that PFT responses are driven by physiological traits associated with their physiological requirements and acclimation to environmental conditions. Southern Ocean-specific adaptations to prevailing low Fe, such as large photosynthetic antenna sizes, are of major significance for the regional biological carbon pump. Other traits more strongly linked to Mn, such as dealing with oxidative stress, may become more important under a changing Fe supply regime. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.

Optimization of the culture of Chlorella sorokiniana PA.91 by RSM: effect of temperature, light intensity, and MgAC-NPs

The unique physicochemical properties of magnesium amino clay nanoparticles (MgAC-NPs) tends to be beneficial in the application as a co-additive in treating microalgae. Also, MgAC-NPs can create oxidative stress in the environment, concurrently elective control bacteria in mixotrophic culture, and stimulate CO₂ biofixation. The condition of the cultivation of newly isolated strains, Chlorella sorokiniana PA.91, was optimized for the first time for MgAC-NPs at various temperatures and light intensities in the culture medium of municipal wastewater (MWW) by central composite design in the response surface methodology (RSM-CCD). This study examined synthesized MgAC-NP with their FE-SEM, EDX, XRD, and FT-IR characteristics. The synthesized MgAC-NPs were naturally stable, cubic shaped, and within the size range of 30-60 nm. The optimization results show that at culture conditions of 20 °C, 37 μmol m^-2 s^-1, and 0.05 g L^-1, microalga MgAC-NPs have the best growth productivity and biomass performance. Maximum dry biomass weight (55.41%), specific growth rate (30.26%), chlorophyll (81.26%), and carotenoids (35.71%) were achieved under the optimized condition. Experimental results displayed that C.S. PA.91 has a high capacity for lipid extraction (1.36 g L^-1) and significant lipid efficiency (45.1%). Also, in 0.2 and 0.05 g L^-1 of the MgAC-NPs, COD removal efficiency 91.1% and 81.34% from C.S. PA.91 showed, respectively. These results showed the potential of C.S. PA.91-MgAC-NPs for nutrient removal in wastewater treatment plants and their quality as sources of biodiesel.

Manganese Limitation of Phytoplankton Physiology and Productivity in the Southern Ocean

Although iron and light are understood to regulate the Southern Ocean biological carbon pump, observations have also indicated a possible role for manganese. Low concentrations in Southern Ocean surface waters suggest manganese limitation is possible, but its spatial extent remains poorly constrained and direct manganese limitation of the marine carbon cycle has been neglected by ocean models. Here, using available observations, we develop a new global biogeochemical model and find that phytoplankton in over half of the Southern Ocean cannot attain maximal growth rates because of manganese deficiency. Manganese limitation is most extensive in austral spring and depends on phytoplankton traits related to the size of photosynthetic antennae and the inhibition of manganese uptake by high zinc concentrations in Antarctic waters. Importantly, manganese limitation expands under the increased iron supply of past glacial periods, reducing the response of the biological carbon pump. Overall, these model experiments describe a mosaic of controls on Southern Ocean productivity that emerge from the interplay of light, iron, manganese and zinc, shaping the evolution of Antarctic phytoplankton since the opening of the Drake Passage.

Multiomics in the central Arctic Ocean for benchmarking biodiversity change

The MOSAiC ice-drift study across the Arctic Ocean is providing unprecedented opportunities to explore one of the least known ecosystems on Earth. In this Community Page, members of the EcoOmics project explain how data from MOSAiC will be used to study unique species, from viruses to multicellular animals.