Correction to: Global distribution of a chlorophyll f cyanobacterial marker.
Ontology highlight
ABSTRACT:
SUBMITTER: Antonaru LA
PROVIDER: S-EPMC9122981 | biostudies-literature | 2022 Jun
REPOSITORIES: biostudies-literature
Publications
Correction to: Global distribution of a chlorophyll f cyanobacterial marker.
Antonaru Laura A LA Cardona Tanai T Larkum Anthony W D AWD Nürnberg Dennis J DJ
The ISME journal 20220601 6
Similar Datasets
Project description:Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype's distribution.
| S-EPMC7608106 | biostudies-literature
Project description:Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
| S-EPMC10719068 | biostudies-literature
Project description:Cyanobacteria are an important component of aquatic ecosystems, with a proliferation of massive cyanobacterial blooms predicted worldwide under increasing warming conditions. In addition to temperature, other global change related variables, such as water column stratification, increases in dissolved organic matter (DOM) discharge into freshwater systems and greater wind stress (i.e., more opaque and mixed upper water column/epilimnion) might also affect the responses of cyanobacteria. However, the combined effects of these variables on cyanobacterial photosynthesis remain virtually unknown. Here we present evidence that this combination of global-change conditions results in a feed-back mechanism by which, fluctuations in solar ultraviolet radiation (UVR, 280-400 nm) due to vertical mixing within the epilimnion act synergistically with increased DOM to impair cyanobacterial photosynthesis as the water column progressively darkens. The main consequence of such a feed-back response is that these organisms will not develop large blooms in areas of latitudes higher than 30°, in both the Northern and Southern Hemispheres, where DOM inputs and surface wind stress are increasing.
| S-EPMC4586519 | biostudies-other
Project description:Subspecies in the global human gut microbiome
| PRJEB17632 | ENA
Project description:ImportancePhotosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
| S-EPMC10653834 | biostudies-literature
Project description:The necessary reduction of greenhouse gas (GHG) emissions may lead in the future to an increase in solar irradiance (solar brightening). Anthropogenic aerosols (and their precursors) that cause solar dimming are in fact often co-emitted with GHGs. While the reduction of GHG emissions is expected to slow down the ongoing increase in the greenhouse effect, an increased surface irradiance due to reduced atmospheric aerosol load might occur in the most populated areas of the earth. Increased irradiance may lead to air warming, favour the occurrence of heatwaves and increase the evaporative demand of the atmosphere. This is why effective and sustainable solar radiation management strategies to reflect more light back to space should be designed, tested and implemented together with GHG emission mitigation. Here we propose that new plants (crops, orchards and forests) with low-chlorophyll (Chl) content may provide a realistic, sustainable and relatively simple solution to increase surface reflectance of large geographical areas via changes in surface albedo. This may finally offset all or part of the expected local solar brightening. While high-Chl content provides substantial competitive advantages to plants growing in their natural environment, new plants with low-Chl content may be successfully used in agriculture and silviculture and be as productive as the green wildtypes (or even more). The most appropriate strategies to obtain highly productive and highly reflective plants are discussed in this paper and their mitigation potential is examined together with the challenges associated with their introduction in agriculture.
| S-EPMC8246939 | biostudies-literature
Project description:A survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.
| S-EPMC1489541 | biostudies-literature
Project description:Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.
| S-EPMC5923322 | biostudies-literature
Project description:Decades of research have relied on satellite-based estimates of chlorophyll-a concentration to identify oceanographic processes and plan in situ observational campaigns; however, the patterns of intrinsic temporal variation in chlorophyll-a concentration have not been investigated on a global scale. Here we develop a metric to quantify time series complexity (i.e., a measure of the ups and downs of sequential observations) in chlorophyll-a concentration and show that seemingly disparate regions (e.g., Atlantic vs Indian, equatorial vs subtropical) in the global ocean can be inherently similar. These patterns can be linked to the regularity of chlorophyll-a concentration change and the likelihood of anomalous events within the satellite record. Despite distinct spatial changes in decadal chlorophyll-a concentration, changes in time series complexity have been relatively consistent. This work provides different metrics for monitoring the global ocean and suggests that the complexity of chlorophyll-a time series can be independent of its magnitude.
| S-EPMC10876569 | biostudies-literature
Project description:Cyanobacteria possess the unique capacity to naturally produce hydrocarbons from fatty acids. Hydrocarbon compositions of thirty-two strains of cyanobacteria were characterized to reveal novel structural features and insights into hydrocarbon biosynthesis in cyanobacteria. This investigation revealed new double bond (2- and 3-heptadecene) and methyl group positions (3-, 4- and 5-methylheptadecane) for a variety of strains. Additionally, results from this study and literature reports indicate that hydrocarbon production is a universal phenomenon in cyanobacteria. All cyanobacteria possess the capacity to produce hydrocarbons from fatty acids yet not all accomplish this through the same metabolic pathway. One pathway comprises a two-step conversion of fatty acids first to fatty aldehydes and then alkanes that involves a fatty acyl ACP reductase (FAAR) and aldehyde deformylating oxygenase (ADO). The second involves a polyketide synthase (PKS) pathway that first elongates the acyl chain followed by decarboxylation to produce a terminal alkene (olefin synthase, OLS). Sixty-one strains possessing the FAAR/ADO pathway and twelve strains possessing the OLS pathway were newly identified through bioinformatic analyses. Strains possessing the OLS pathway formed a cohesive phylogenetic clade with the exception of three Moorea strains and Leptolyngbya sp. PCC 6406 which may have acquired the OLS pathway via horizontal gene transfer. Hydrocarbon pathways were identified in one-hundred-forty-two strains of cyanobacteria over a broad phylogenetic range and there were no instances where both the FAAR/ADO and the OLS pathways were found together in the same genome, suggesting an unknown selective pressure maintains one or the other pathway, but not both.
| S-EPMC3903477 | biostudies-literature