Biology subjects

Alexander, H.

Publications and source records attributed to Alexander, H..

22 records · Page 2Linked to original sources

bioRxiv2021

Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton

Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are not designed to consider eukaryotes, nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome assembled genomes (MAGs) from large-scale metagenomic datasets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8-2000{micro}m) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally-relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand the known marine phylogenetic diversity through the increase in coverage of likely particle- and host-associated taxa. We also demonstrate an approach to infer the putative functional mode of the recovered eukaryotic MAGs. A global survey of the TOPAZ MAGs enabled the identification of ecological cohorts, driven by specific environmental factors, and putative host-microbe associations. ImportanceDespite the ecological importance of single-celled eukaryotic organisms in marine environments, the majority are difficult to cultivate in the lab. Sequencing genetic material extracted from environmental samples enables researchers to document naturally-occurring protistan communities. However, conventional sequencing methodologies cannot separate out the genomes of individual organisms. To more completely capture the entire genomic content of mixed protistan community, we can create bins of sequences that represent the same organism. We developed a pipeline that enables scientists to bin individual organisms out of metagenomic reads, and show results that provide exciting insights into what protistan communities are present in the ocean and what roles they play in the ecosystem. Here, a global survey of both eukaryotic and prokaryotic MAGs enabled the identification of ecological cohorts, driven by specific environmental factors, and putative host-microbe associations. Accessible and scalable computational tools, such as EukHeist, are likely to accelerate the identification of meaningful genetic signatures from large datasets, ultimately expanding the eukaryotic tree of life.

microbiology↗

bioRxiv2018

A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae

Phosphorus (P) limits primary production in regions of the surface ocean, and many plankton species exhibit specific physiological responses to P-deficiency. The metabolic response of Micromonas pusilla, an ecologically relevant marine photoautotroph, to P-deficiency was investigated using environmental metabolomics and comparative genomics. The concentrations of some intracellular metabolites were elevated in the P-deficient cells (e.g., xanthine, inosine) and genes involved in the associated metabolic pathways shared a predicted conserved amino acid motif in the non-coding regions of each gene. The presence of the conserved motif suggests that these genes may be co-regulated, and the motif may constitute a regulatory element for binding a transcription factor, specifically that of Psr1 (Phosphate starvation response,), first described in the alga, Chlamydomonas reinhardtii. A putative phosphate starvation response gene (psr1-like) was identified in M. pusilla with homology to well characterized psr1/phr1 genes in algae and plants, respectively. This gene appears to be present and expressed in other marine algal taxa (e.g., Emiliania huxleyi) in field sites that are chronically phosphorus-limited. Results from the present study have implications for understanding phytoplankton taxon-specific roles in mediating P cycling in the ocean.

microbiology↗

bioRxiv2018

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

BackgroundDe novo transcriptome assemblies are required prior to analyzing RNAseq data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or \"pipelines\", on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short read data collected by the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP). The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research (NCGR).\n\nResultsNew transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics, with assemblies from the Dinoflagellata and Ciliophora phyla showing a higher percentage of open reading frames and number of contigs than transcriptomes from other phyla.\n\nConclusionsGiven current bioinformatics approaches, there is no single best reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally-intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.\n\nKey PointsO_LIRe-assembly with new tools can yield new results\nC_LIO_LIAutomated and programmable pipelines can be used to process arbitrarily many samples.\nC_LIO_LIAnalyzing many samples using a common pipeline identifies taxon-specific trends.\nC_LI

bioinformatics↗

bioRxiv2016

VIRUS-HOST INFECTION DYNAMICS OF MARINE SINGLE-CELLED EUKARYOTES RESOLVED FROM METATRANSCRIPTOMICS

Metatranscriptomics has emerged as a tool in microbial ecology that can resolve the functional landscape of both prokaryotes and eukaryotes within a community. In this study, we extend the potential of metatranscriptomics to probe active virus infections and virus-host relationships in marine systems. Polyadenylation-selected RNA-seq data were examined from microbial communities in two productive marine environments: a brown tide bloom event dominated by Aureococcus anophagefferens in Quantuck Bay, NY, and a diatom-dominated plankton community in Narragansett Bay, RI. Active infections by diverse giant viruses (NCLDVs) of algal and non-algal hosts were found at both sites. Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) were observed during both the peak and decline of the bloom. Bloom decline was also accompanied by increased activity for viruses other than AaV, including (+) ssRNA viruses. In Narragansett Bay, increased temporal resolution revealed active NCLDVs with both boom-and-bust as well as steady-state infection-like ecologies. Statistical co-occurrence examinations of the dsDNA, ssRNA and dsRNA markers within the data revealed a broad spectrum of statistically strong and significant virus-host relationships that included both known as well as novel interactions. Our approach offers a method for screening the diversity and dynamics of active viral infections in natural systems and develops links between viruses and their potential hosts in situ.\n\nSignificanceViruses are important partners in ecosystem scale ecology, yet their study to date is primarily limited to single virus-host infection models in the laboratory or limited to \"potential-actions\" derived from metagenomics analyses. Using metatranscriptomic sequences from polyadenylated-RNA selected samples, we have simultaneously captured information regarding eukaryotic diversity and active infection by viruses with dsDNA genomes, resulting in a statistical opportunity to predict \"who is infecting whom\". This approach further provides concurrent insight regarding viruses with ssRNA and dsRNA genomes, capturing dynamics for the communities of viruses infecting single-celled eukaryotes. Given the central role of these plankton in global scale processes, our efforts result in a transformational step-forward regarding the study of in situ virus-host interactions.

microbiology↗