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Changing perspectives in marine nitrogen fixation

J.P. Zehr & D.G. Capone (2020) Science

As a component of many biomolecules, nitrogen is a crucial element for life, especially in nutrient-poor environs such as the open ocean. Atmospheric dinitrogen gas (N2) is abundant but must be fixed by reduction to ammonia, a process limited to certain organisms and environments. Zehr and Capone review changes in our understanding of what marine microorganisms are fixing N2, where they live, and what environmental features influence their activity. N2 fixation is more widely distributed than previously thought, and we still have much to learn about the physiology and regulation involved. We now have better estimates of global- and basin-scale inputs and outputs, but questions remain as to whether the oceanic N cycle is balanced. New tools are enabling better understanding of ocean N2 fixation despite disruptive consequences from human activities, including ocean acidification and warming.

How microbes survive in the open ocean

Marine microbes are fundamental components of food webs and the biogeochemical cycles that maintain the habitability of the planet. In the oligotrophic open ocean, these microscopic organisms live in a dilute environment separated from other cells by large distances at the microscale while surrounded by very few essential nutrient molecules. For ubiquitous sub-micron sized and non-motile microbes, cellular growth requirements for hundreds of millions (or more) of nutrient molecules are sustained predominantly by rapid molecular diffusion. Characterizing the interactions of cells and molecules in the “empty space” of the ocean remains central to understanding the drivers and consequences of oceanic biogeochemical cycles.

Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean

Nitrogen (N) is the major limiting nutrient for phytoplankton growth and productivity in large parts of the world's oceans. Differential preferences for specific N substrates may be important in controlling phytoplankton community composition. To date, there is limited information on how specific N substrates influence the composition of naturally occurring microbial communities. We investigated the effect of nitrate, ammonium, and urea on microbial and phytoplankton community composition (cell abundances and 16S rRNA gene profiling) and functioning (photosynthetic activity, carbon fixation rates) in the oligotrophic waters of the North Pacific Ocean. All N substrates tested significantly stimulated phytoplankton growth and productivity. Urea resulted in the greatest (>300%) increases in chlorophyll a (<0.06 μg L−1 and ∼0.19 μg L−1 in the control and urea addition, respectively) and productivity (<0.4 μmol C L−1 d−1 and ∼1.4 μmol C L−1 d−1 in the control and urea addition, respectively) at two experimental stations, largely due to increased abundances of Prochlorococcus(Cyanobacteria). Two abundant clades of Prochlorococcus, High Light I and II, demonstrated similar responses to urea, suggesting this substrate is likely an important N source for natural Prochlorococcus populations. In contrast, the heterotrophic community composition changed most in response to NH4+. Finally, the time and magnitude of response to N amendments varied with geographic location, likely due to differences in microbial community composition and their nutrient status. Our results provide support for the hypothesis that changes in N supply would likely favor specific populations of phytoplankton in different oceanic regions and thus, affect both biogeochemical cycles and ecological processes.

Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A

Nitrogen fixation — the reduction of dinitrogen (N2) gas to biologically available nitrogen (N) — is an important source of N for terrestrial and aquatic ecosystems. In terrestrial environments, N2-fixing symbioses involve multicellular plants, but in the marine environment these symbioses occur with unicellular planktonic algae. An unusual symbiosis between an uncultivated unicellular cyanobacterium (UCYN-A) and a haptophyte picoplankton alga was recently discovered in oligotrophic oceans. UCYN-A has a highly reduced genome, and exchanges fixed N for fixed carbon with its host. This symbiosis bears some resemblance to symbioses found in freshwater ecosystems. UCYN-A shares many core genes with the ‘spheroid bodies’ of Epithemia turgida and the endosymbionts of the amoeba Paulinella chromatophora. UCYN-A is widely distributed, and has diversified into a number of sublineages that could be ecotypes. Many questions remain regarding the physical and genetic mechanisms of the association, but UCYN-A is an intriguing model for contemplating the evolution of N2-fixing organelles.

New insights into the ecology of the globally significant uncultured nitrogen-fixing symbiont UCYN-A

Cyanobacterial nitrogen-fixers (diazotrophs) play a key role in biogeochemical cycling of carbon and nitrogen in the ocean. In recent years, the unusual symbiotic diazotrophic cyanobacterium Atelocyanobacterium thalassa (UCYN-A) has been recognized as one of the major diazotrophs in the tropical and subtropical oceans. In this review, we summarize what is currently known about the geographic distribution of UCYN-A, as well as the environmental factors that govern its distribution. In addition, by compiling UCYN-A nifH sequences from the GenBank no. database as well as those from nifHgene amplicon next generation sequencing studies, we present an in-depth analysis of the distribution of defined UCYN-A sublineages (UCYN-A1, UCYN-A2 and UCYN-A3) and identify a novel sublineage, UCYN-A4, which may be significant in some environments. Each UCYN-A sublineage exhibited a remarkable global distribution pattern and several UCYN-A sublineages frequently co-occurred within the same sample, suggesting that if they represent different ecotypes they have overlapping niches. Recently, single cell visualization techniques using specific probes targeting UCYN-A1 and UCYN-A2 and their respective associated eukaryotic partner cells showed that the size of the consortia and the number of UCYN-A cells differed between these 2 sublineages. Combined, the results highlight that UCYN-A sublineages likely have different physiological requirements, which need to be accounted for in future studies. Furthermore, based on our increasing knowledge of the diversity of the UCYN-A lineage, we discuss some of the limitations of currently used cultivation-independent molecular techniques for the identification and quantification of UCYN-A.

How Single Cells work together

Symbiotic interactions are fundamental to life on Earth and were critical for the evolution of organelles that led to the success of eukaryotes on the planet. Such mutualistic interactions between unicellular microorganisms and multicellular plants and animals are pervasive in natural and agricultural ecosystems (1). In contrast, very little is known about symbiotic interactions between unicellular partners. Recent studies have revealed single-celled nitrogen-fixing symbioses that require different mechanisms to maintain symbiosis than seen in multicellular systems.


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Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations

Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics.

Comparative genomics reveals surprising divergence of two closely related strains of UCYN-A cyanobacteria

Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed ‘diazotrophs’) are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier. We analyzed the metagenome of this UCYN-A2 population by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A (here called UCYN-A1) and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A1 protein-coding genes (96.6%) with high synteny, yet the average amino-acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped at the same functional and ecological level. Our results suggest that UCYN-A1 and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.

Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean

Nitrogen-fixing microorganisms (diazotrophs) are keystone species that reduce atmospheric dinitrogen (N2) gas to fixed nitrogen (N), thereby accounting for much of N-based new production annually in the oligotrophic North Pacific. However, current approaches to study N2fixation provide relatively limited spatiotemporal sampling resolution; hence, little is known about the ecological controls on these microorganisms or the scales over which they change. In the present study, we used a drifting robotic gene sensor to obtain high-resolution data on the distributions and abundances of N2-fixing populations over small spatiotemporal scales. The resulting measurements demonstrate that concentrations of N2 fixers can be highly variable, changing in abundance by nearly three orders of magnitude in less than 2 days and 30 km. Concurrent shipboard measurements and long-term time-series sampling uncovered a striking and previously unrecognized correlation between phosphate, which is undergoing long-term change in the region, and N2-fixing cyanobacterial abundances. These results underscore the value of high-resolution sampling and its applications for modeling the effects of global change.

Genetic diversity of the unicellular nitrogen-fixing cyanobacteria UCYN-A and its prymnesiophyte host

Symbiotic interactions between nitrogen-fixing prokaryotes and photosynthetic eukaryotes are an integral part of biological nitrogen fixation at a global scale. One of these partnerships involves the cyanobacterium UCYN-A, which has been found in partnership with an uncultivated unicellular prymnesiophyte alga in open-ocean and coastal environments. Phylogenetic analysis of the UCYN-A nitrogenase gene (nifH) showed that the UCYN-A lineage is represented by three distinct clades, referred to herein as UCYN-A1, UCYN-A2 and UCYN-A3, which appear to have overlapping and distinct geographic distributions. The relevance of UCYN-A's genetic diversity to its symbiosis and ecology was explored through combining flow cytometric cell sorting and molecular techniques to determine the host identity, nifH expression patterns and host cell size of one newly discovered clade, UCYN-A2, at a coastal site. UCYN-A2 nifH expression peaked during daylight hours, which is consistent with expression patterns of the UCYN-A1 clade in the open ocean. However, the cell size of the UCYN-A2 host was significantly larger than UCYN-A1 and host, suggesting adaptation to different environmental conditions. Like the UCYN-A1 host, the UCYN-A2 host was closely related to the genus Braarudosphaera; however, the UCYN-A1 and UCYN-A2 host rRNA sequences clustered into two distinct clades suggesting co-evolution of symbiont and host.

Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga

Symbioses between nitrogen (N)2–fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation.


*These authors contributed equally to this work.

Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium

Nitrogen (N2)-fixing marine cyanobacteria are an important source of fixed inorganic nitrogen that supports oceanic primary productivity and carbon dioxide removal from the atmosphere1. A globally distributed2, 3, periodically abundant4 N2-fixing5 marine cyanobacterium, UCYN-A, was recently found to lack the oxygen-producing photosystem II complex6 of the photosynthetic apparatus, indicating a novel metabolism, but remains uncultivated. Here we show, from metabolic reconstructions inferred from the assembly of the complete UCYN-A genome using massively parallel pyrosequencing of paired-end reads, that UCYN-A has a photofermentative metabolism and is dependent on other organisms for essential compounds. We found that UCYN-A lacks a number of major metabolic pathways including the tricarboxylic acid cycle, but retains sufficient electron transport capacity to generate energy and reducing power from light. Unexpectedly, UCYN-A has a reduced genome (1.44 megabases) that is structurally similar to many chloroplasts and some bacteria, in that it contains inverted repeats of ribosomal RNA operons7. The lack of biosynthetic pathways for several amino acids and purines suggests that this organism depends on other organisms, either in close association or in symbiosis, for critical nutrients. However, size fractionation experiments using natural populations have so far not provided evidence of a symbiotic association with another microorganism. The UCYN-A cyanobacterium is a paradox in evolution and adaptation to the marine environment, and is an example of the tight metabolic coupling between microorganisms in oligotrophic oceanic microbial communities.

Globally Distributed Uncultivated Oceanic N2-Fixing Cyanobacteria Lack Oxygenic Photosystem II

Biological nitrogen (N2) fixation is important in controlling biological productivity and carbon flux in the oceans. Unicellular N2-fixing cyanobacteria have only recently been discovered and are widely distributed in tropical and subtropical seas. Metagenomic analysis of flow cytometry–sorted cells shows that unicellular N2-fixing cyanobacteria in “group A” (UCYN-A) lack genes for the oxygen-evolving photosystem II and for carbon fixation, which has implications for oceanic carbon and nitrogen cycling and raises questions regarding the evolution of photosynthesis and N2 fixation on Earth.

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