Biology subjects

Burns, J. A.

Publications and source records attributed to Burns, J. A..

10 recordsLinked to original sources

bioRxiv2025

Global Metagenomics Reveals Hidden Protist Diversity

Protists, defined as eukaryotes distinct from animals, plants, and fungi, are a polyphyletic group that dominates the eukaryotic tree of life, exhibiting significant phylogenetic diversity and fulfilling critical ecological roles. Historically, research has prioritized protists associated with animals and plants, particularly those of medical significance, thereby overlooking the majority of protist diversity. Conventional molecular methods, such as 18S rRNA gene amplicon sequencing, frequently encounter limitations, including primer binding bias and PCR bias caused by gene length variations, resulting in a biased representation of protistan diversity. Further, most protist lineages are notoriously difficult to cultivate. Here, we apply a cultivation-independent approach in which we analyzed over 30,000 assembled metagenomes and protist single cell genomes and 21 long 18S rRNA gene amplicon data sets from various global ecosystems, including marine, freshwater, and soil environments. We recovered 157,956 18S rRNA gene sequences ([≥]800 bp), which clustered into 103,338 operational taxonomic units (OTUs) at 97% sequence identity and 24,438 OTUs at 85% identity. Notably, 81% of 9,543 non-singleton clusters at 85% identity classified as protists consisted exclusively of environmental sequences, uncovering a wealth of novel, uncultivated, and unclassified protist diversity. A comprehensive taxonomic framework of eukaryotes based on concatenated 18S and 28S rRNA genes that incorporated most novel lineages revealed substantial underrepresentation of Amoebozoa, Discoba, and Rhizaria in reference databases, with many lacking isolate or genome sequence representation. Further, we identified 13 eukaryotic lineages with novelty on higher taxonomic ranks, such as class and phylum-level, that lack representation in public databases. The corresponding 85% OTUs were primarily affiliated with Excavata, with some branching deeply in the eukaryotic tree. Comprehensive analysis of the global distribution of protists revealed uneven microbial diversity across supergroups and ecosystems, with notable novelty particularly in soil and marine environments. We then examined co-occurrence between protists and prokaryotes, predicting putative symbiotic or predator-prey relationships, particularly among understudied protist groups with bacteria such as Verrucomicrobia and Rickettsiales. Our results substantially enhance the understanding of protistan diversity and distribution, revealing taxonomic blind spots and laying groundwork for future studies of these organisms ecological roles.

microbiology↗

bioRxiv2024

A multicellular developmental program in a close animal relative

All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of this process remain elusive. By combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii - a close relative that diverged from animals approximately 1 billion years ago - undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous developmental program of C. perkinsii, hint that such animal-like multicellular development is either much older than previously thought or evolved convergently in ichthyosporeans. One-Sentence SummaryThe ichthyosporean C. perkinsii develops via symmetry breaking, cleavage divisions, and forms spatially-organized colonies with distinct cell types.

developmental biology↗

bioRxiv2023

Functional stress responses in Glaucophyta: evidence of ethylene and ABA functions in C. paradoxa

Glaucophytes, an enigmatic group of freshwater algae, occupy a pivotal position within the Archaeplastida, providing insights into the early evolutionary history of plastids and their host cells. These algae possess unique plastids, known as cyanelles, that retain certain ancestral features, enabling a better understanding of the plastid transition from cyanobacteria. In this study, we investigated the role of ethylene, a potent hormone used by land plants to coordinate stress responses, in the glaucophyte alga Cyanophora paradoxa. We demonstrate that C. paradoxa produces gaseous ethylene when supplied with exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor in land plants. In addition, we show that cells produce ethylene natively in response to abiotic stress, and that another plant hormone, abscisic acid (ABA), interferes with ethylene synthesis from exogenously supplied ACC, while positively regulating reactive oxygen species (ROS) accumulation. ROS synthesis also occurred following abiotic stress and ACC treatment, possibly acting as a second-messenger in stress responses. A physiological response of C. paradoxa to ACC treatment is growth inhibition. Using transcriptomics, we reveal that ACC treatment induces the upregulation of senescence-associated proteases, consistent with the observation of growth inhibition. This is the first report of hormone usage in a glaucophyte alga, extending our understanding of hormone-mediated stress response coordination into the Glaucophyta, with implications for the evolution of signaling modalities across Archaeplastida.

evolutionary biology↗

bioRxiv2022

Phagocytosis underpins the biotrophic lifestyle of intracellular parasites in the class Phytomyxea (Rhizaria)

Phagocytosis is a complex multi-gene trait of eukaryotes and allegedly one of the very defining features of this group. Although well documented for free-living unicellular eukaryotes and in specific cellular types of animals, data on phagocytosis in intracellular biotrophic parasites are scant. Indeed, the definition of intracellular biotrophy as complete reliance of a parasite on a living host, with which it constantly negotiates for the exchange of nutrients, is at odd with the consumption of particulate matter suggested by phagocytosis. Phytomyxea are intracellular biotrophic parasites infecting a broad group of hosts, ranging from plants to stramenopiles. They belong to the clade Rhizaria, where phagotrophy (i.e., phagocytosis as main mode to acquire nutrients) is the main mode of nutrition. The exact mode of nutrition of the biotrophic phytomyxea, including the agriculturally impactful phytomyxid Plasmodiophora brassicae, is still unresolved; despite investigations and the availability of molecular data. For other Phytomyxea, observations are patchy and molecular data altogether lacking. Here, using available genomic and transcriptomic data for Phytomyxea and the de novo sequenced transcriptome of the brown algae parasite Maullinia ectocarpii, we investigate the likelihood that the genetic machinery underpinning phagotrophy is conserved within the clade. We further document intracellular phagocytosis in P. brassicae and M. ectocarpii by transmission electron microscopy and fluorescent in situ hybridization. Our investigations confirm that molecular signatures underpinning phagocytosis exist in Phytomyxea and hint at a smaller subset of genes used for intracellular phagocytosis, which is similar between the two parasites. Microscopic evidence confirms the existence of intracellular phagocytosis, which seems to coexist with the manipulation of host physiology typical of biotrophic interactions. In both phytomyxid parasites investigated intracellular phagocytosis has adapted to the intracellular environment and seemingly targets specific organelles. Our findings shed light on the feeding behaviour of Phytomyxea, providing new molecular data for the class; and suggest a paramount and previously unrecognised role for phagocytosis in biotrophic interactions between host and parasite.

microbiology↗

bioRxiv2022

Transformation of the symbiotic alga Oophila amblystomatis : a new toolbox for animal-algae symbiosis studies.

The ability to conduct reverse genetic studies in symbiotic systems is enabled by transgene expression and transformation of at least one partner. The symbiotic relationship between the yellow spotted salamander, Ambystoma maculatum, and the green alga, Oophila amblystomatis, is a unique model of vertebrate-algae symbiosis. Despite over 130 years of scientific study, there are still many open questions in this symbiosis. Transgene expression in one partner will accelerate research into the symbiotic relationship. In this paper we describe a tool and method for expression of foreign DNA in, and presumed transformation of, the alga O. amblystomatis. We successfully introduced heritable antibiotic resistance to algal cultures, and observed expression of a green fluorescent reporter protein in all transfected and presumably transformed algal populations. The outcomes of this work enable genetic manipulation of the symbiotic alga Oophila amblystomatis, allowing direct testing of hypotheses derived from gene expression or genomic studies that will usher in a deeper understanding of the A. maculatum-O. amblystomatis symbiotic system. Summary statementGenetic tools stimulate new possibilities for research in living systems. This work describes a new tool for transformation of a symbiotic alga that enters vertebrate tissues and cells.

molecular biology↗

bioRxiv2021

Relating genome completeness to functional predictions

Genome and transcriptome assemblies vary in their quality in terms of the connectedness of the assemblies and the amount of biological information captured. Interpreting de novo assemblies from new, poorly characterized, organisms in the context of complex traits can be challenging because, in the absence of a reference, it is difficult to know how much information is enough to claim the presence or absence of a trait. This study uses randomly downsampled proteome files to compare a genome completeness metric, BUSCO, to functional predictions of the complex trait of phagocytosis in known phagocytotic organisms broadly across the eukaryotic tree of life. We find that as additional proteins are added, BUSCO scores increase incrementally, while the phagocytosis prediction follows a sigmoidal curve. Generalizing our findings, we suggest a threshold of the number of BUSCOs detected above which one would expect an accurate prediction, positive or negative, of the complex trait of phagocytosis. While these findings are specific to a single trait, the methods can be extended to consider additional functional traits and predictive frameworks.

genomics↗

bioRxiv2020

Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge

The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north-east Asia) and Eastern Beringia (north-west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these paleoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyze mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underscore the crucial biogeographic role of the Bering Land Bridge in the distribution, turnover, and maintenance of megafaunal populations in North America.

evolutionary biology↗

bioRxiv2020

No evidence of phago-mixotropy in Micromonas polaris, the dominant picophytoplankton species in the Arctic

In the Arctic Ocean, the small green alga Micromonas polaris dominates pico-phytoplankton during the summer months. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analysed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean. Using both fluorescent beads and fluorescently labelled bacteria as prey, we found no evidence of phago-mixotrophy in any M. polaris strain by flow cytometric measurement of prey ingestion. In addition, in silico predictions reveal that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.

ecology↗

bioRxiv2020

Heterotrophic Carbon Fixation in a Salamander-Alga Symbiosis.

The unique symbiosis between a vertebrate salamander, Ambystoma maculatum, and unicellular green alga, Oophila amblystomatis, involves multiple modes of interaction. These include an ectosymbiotic interaction where the alga colonizes the egg capsule, and an intracellular interaction where the alga enters tissues and cells of the salamander. One common interaction in mutualist photosymbioses is the transfer of photosynthate from the algal symbiont to the host animal. In the A. maculatum-O. amblystomatis interaction, there is conflicting evidence regarding whether the algae in the egg capsule transfer chemical energy captured during photosynthesis to the developing salamander embryo. In experiments where we took care to separate the carbon fixation contributions of the salamander embryo and algal symbionts, we show that inorganic carbon fixed by A. maculatum embryos reaches 2% of the inorganic carbon fixed by O. amblystomatis algae within an egg capsule after 2 hours in the light. After 2 hours in the dark, inorganic carbon fixed by A. maculatum embryos is 800% of the carbon fixed by O. amblystomatis algae within an egg capsule. Using photosynthesis inhibitors we show that A. maculatum embryos and O. amblystomatis algae compete for available inorganic carbon within the egg capsule environment. Our results confirm earlier studies suggesting a role of heterotrophic carbon fixation during vertebrate embryonic development. Our results also show that the considerable capacity of developing A. maculatum embryos for inorganic carbon fixation precludes our ability to distinguish any minor role of photosynthetically transferred carbon from algal symbionts to host salamanders using bicarbonate introduced to the egg system as a marker.

ecology↗

bioRxiv2019

From intent to implementation: Factors affecting public involvement in life science research

Public involvement is key to closing the gap between research production and research use, and the only way to achieving ultimate transparency in science. The majority of life science research is not public-facing, but is funded by the public and impacts the community. We undertook a survey of researchers within the life sciences to better understand their views and perceived challenges to involving the public in their research. We had a valid response cohort of n=110 researchers, of whom 90% were primarily laboratory based. Using a mixed methods approach, we demonstrate that a top-down approach is key to motivate progression of life scientists from feeling positive towards public involvement to actually engaging in it. Researchers who viewed public involvement as beneficial to their research were more likely to have direct experience of doing it. We demonstrate that the systemic flaws in the way life sciences research enterprise is organised, including the promotion system, hypercompetition, and time pressures are major barriers to involving the public in the scientific process. Scientists are also apprehensive of being involuntarily involved in the current politicized climate, misinformation and publicity hype surrounding science nowadays makes them hesitant to share their early and in-progress research. The time required to deliberate study design and relevance, plan and build relationships for sustained involvement, provide and undertake training, and improve communication in the current research environment is often considered nonpragmatic, particularly for early career researchers. In conclusion, a top-down approach involving institutional incentives and infrastructure appears most effective at transitioning researchers from feeling positive towards public involvement to actually implementing it.

scientific communication and education↗