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Juan José Pierella Karlusich

Juan José Pierella Karlusich
FAS Division of Science, Harvard University

About

55
Publications
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Introduction
I am using the resources that Tara Oceans consortium obtained from samples from all major oceanic regions, which includes metabarcodes, metagenomes, metatranscriptomes, physiological determinations and environmental parameters. My aim is to get insights into the plankton adaptation/acclimation strategies towards the environment.

Publications

Publications (55)
Article
Full-text available
Oxidative stress and iron limitation represent the grim side of life in an oxygen-rich atmosphere. The versatile electron transfer shuttle ferredoxin, an iron-sulfur protein, is particularly sensitive to these hardships, and its down-regulation under adverse conditions severely compromises survival of phototrophs. Replacement of ferredoxin by a str...
Article
Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the s...
Article
Full-text available
Key message Transcriptomes of solanaceous plants expressing a plastid-targeted antioxidant protein were analysed to identify chloroplast redox networks modulating the expression of nuclear genes associated with stress acclimation. Abstract Plastid functions depend on the coordinated expression of nuclear genes, many of them associated to developme...
Article
Full-text available
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacte...
Article
Full-text available
Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll max...
Article
Full-text available
Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing an...
Article
Full-text available
A major challenge in characterizing plankton communities is the collection, identification and quantification of samples in a time-efficient way. The classical manual microscopy counts are gradually being replaced by high throughput imaging and nucleic acid sequencing. DNA sequencing allows deep taxonomic resolution (including cryptic species) as w...
Article
Full-text available
Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome‐scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so‐called metabolic niche resumes well‐kn...
Chapter
Almost half of photosynthesis on Earth occurs in marine and freshwater environments; hence, aquatic photosynthetic organisms have an enormous impact on food webs and on the biogeochemistry of the entire Earth System. In this chapter, the authors provide an overview of the main groups of aquatic photoautotrophs, exploring their complex evolutionary...
Article
Full-text available
Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121–130 base pairs, bp) and diat-...
Article
Full-text available
Eukaryotic plankton are a core component of marine ecosystems with exceptional taxonomic and ecological diversity, yet how their ecology interacts with the environment to drive global distribution patterns is poorly understood. In this work, we use Tara Oceans metabarcoding data, which cover all major ocean basins, combined with a probabilistic mod...
Article
Full-text available
Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-liv...
Preprint
Full-text available
The Arctic Ocean is being impacted by warming temperatures, increasing freshwater and highly variable ice conditions. The microalgal communities underpinning Arctic marine food webs, once thought to be dominated by diatoms, include a phylogenetically diverse range of small algal species, whose biology remains poorly understood. Here, we present gen...
Preprint
Standard niche modeling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome-scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that encompasses the whole metabolic capabilities of an organism. The so-called metabolic niche resumes well...
Preprint
Full-text available
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Phytoplankton communities are generally studied by PCR amplification of bacterial (16S), nuc...
Preprint
Full-text available
Biological nitrogen fixation is a major factor contributing to microbial primary productivity in the open ocean. The current view depicts a few cyanobacterial diazotrophs as the most relevant marine nitrogen fixers, whereas heterotrophic diazotrophs are more diverse and considered to have lower impacts on the nitrogen balance. Here, we used 891 Tar...
Article
Full-text available
Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO2 to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO2, which is vital information towards modeling their re...
Preprint
Full-text available
Marine plankton mitigate anthropogenic greenhouse gases, modulate biogeochemical cycles, and provide fishery resources. Plankton is distributed across a stratified ecosystem of sunlit surface waters and a vast, though understudied, mesopelagic 'dark ocean'. In this study, we mapped viruses, prokaryotes, and pico-eukaryotes across 32 globally-distri...
Article
Full-text available
The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model mari...
Article
Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, al...
Article
Full-text available
Marine phytoplankton are believed to account for more than 45% of photosynthetic net primary production on Earth, and hence are at the base of marine food webs and have an enormous impact on the entire Earth system. Their members are found across many of the major clades of the tree of life, including bacteria (cyanobacteria) and multiple eukaryoti...
Preprint
Full-text available
[ Now published in Nature Communications: https://doi.org/10.1038/s41467-021-24299-y ] Biological nitrogen fixation plays a critical role in marine primary production, yet, our understanding of marine N2-fixers (diazotrophs) is hindered by limited observations. Here, we developed a quantitative image analysis pipeline in concert with mapping of mo...
Article
Full-text available
Water limitation represents the main environmental constraint affecting crop yield worldwide. Photosynthesis is a primary drought target, resulting in over-reduction of the photosynthetic electron transport chain and increased production of reactive oxygen species in plastids. Manipulation of chloroplast electron distribution by introducing alterna...
Poster
Full-text available
We investigated transcriptomic features of genes regulated by chloroplast redox poise through recombinant expression of a plastid-targeted antioxidant protein (i.e., a cyanobacterial flavodoxin (Fld)) in potato and tobacco leaves. We found an important contribution of reactive oxygen species and hormone action to these transcriptional changes. In a...
Preprint
Full-text available
Water stress causes considerable yield loss in potato, usually considered a drought-sensitive crop. Photosynthesis is a primary target of abiotic stresses, and manipulation of photosynthetic electron distribution in chloroplasts by introducing the alternative electron carrier flavodoxin increased tolerance of model plants to multiple environmental...
Article
Full-text available
Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2),...
Article
Full-text available
Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron av...
Article
Full-text available
The development of oxygenic photosynthesis by primordial cyanobacteria ~2.7 billion years ago led to major changes in the components and organization of photosynthetic electron transport to cope with the challenges of an oxygen-enriched atmosphere. We review herein, following the seminal contributions as reported by Jaganathan et al. (Functional ge...
Data
List of tobacco genes belonging to clusters formed by Xcv responses exacerbated or ameliorated in the presence of Fld (Figure 5). Unigene ID and description, mapman pathway annotation, and FC (in log2 scale) for each of the four line/treatment comparisons are shown. The color code indicates statistical significance in induction (red; log2FC > 1 and...
Data
List of tobacco genes belonging to clusters formed by Xcv-responsive genes, which were already primed by Fld in the absence of Xcv inoculation (Figure 6). Unigene ID and description, mapman pathway annotation, and FC (in log2 scale) for each of the four line/treatment comparisons are shown. The color code indicates statistical significance in induc...
Data
List of tobacco genes belonging to clusters formed by Fld-regulated genes in which the effect of the flavoprotein was reverted by Xcv infection (Figure 7). Unigene ID and description, mapman pathway annotation, and FC (in log2 scale) for each of the four line/treatment comparisons are shown. The color code indicates statistical significance in indu...
Data
List of tobacco genes with altered expression patterns in response to Xcv in pfla4-2 and/or WT leaves. Unigene ID and description, mapman pathway annotation and FC (in log2 scale) are shown. The color code indicates statistical significance in induction (red; log2FC > 1 and FDR < 0.05) or repression (green; log2FC < -1 and FDR < 0.05). Genes belong...
Data
List of tobacco genes with altered expression patterns in response to Fld. Unigene ID and description, mapman pathway annotation and fold-change (FC; in log2 scale) are shown. The color code indicates statistical significance in induction (red; log2FC > 1 and FDR < 0.05) or repression (green; log2FC < -1 and FDR < 0.05). Genes belonging to various...
Data
List of tobacco genes belonging to clusters formed by Xcv-induced or Xcv-repressed genes independently of genotype (Figure 4). Unigene ID and description, mapman pathway annotation, and FC (in log2 scale) for each of the four line/treatment comparisons are shown. The color code indicates statistical significance in induction (red; log2FC > 1 and FD...
Article
Full-text available
Non-host resistance is the most ample and durable form of plant resistance against pathogen infection. It includes induction of defense-associated genes, massive metabolic reprogramming, and in many instances, a form of localized cell death (LCD) at the site of infection, purportedly designed to limit the spread of biotrophic and hemibiotrophic mic...
Conference Paper
Environmental stresses and nutrient limitation are the major causes for crop losses worldwide. Engineering strategies aimed at improving stress tolerance have mostly focused on overexpression of plant-endogenous genes belonging to molecular networks for stress perception or stress responses. Based on the stress responses observed in cyanobacteria a...
Article
Full-text available
Ferredoxins are electron shuttles harbouring iron-sulfur clusters that connect multiple oxido-reductive pathways in organisms displaying different lifestyles. Some prokaryotes and algae express an isofunctional electron carrier, flavodoxin, which contains flavin mononucleotide as cofactor. Both proteins evolved in the anaerobic environment precedin...
Article
Full-text available
Ferredoxins are electron shuttles harboring iron-sulfur clusters which participate in oxido-reductive pathways in organisms displaying very different lifestyles. Ferredoxin levels decline in plants and cyanobacteria exposed to environmental stress and iron starvation. Flavodoxin is an isofunctional flavoprotein present in cyanobacteria and algae (n...