Biology subjects

Ignacio-Espinoza, J. C.

Publications and source records attributed to Ignacio-Espinoza, J. C..

3 recordsLinked to original sources

bioRxiv2020

Ribosome-linked mRNA-rRNA chimeras reveal active novel virus-host associations.

Viruses of prokaryotes greatly outnumber their hosts1 and impact microbial processes across scales, including community assembly, evolution, and metabolism1. Metagenomic discovery of novel viruses has greatly expanded viral sequence databases, but only rarely can viral sequences be linked to specific hosts. Here, we adapt proximity ligation methods to ligate ribosomal RNA to transcripts, including viral ones, during translation. We sequenced the resulting chimeras, directly linking marine viral gene expression to specific hosts by transcript association with rRNA sequences. With a sample from the San Pedro Ocean Time-series (SPOT), we found viral-host links to Cyanobacteria, SAR11, SAR116, SAR86, OM75, and Rhodobacteracae hosts, some being the first viruses reported for these groups. We used the SPOT viral and cellular DNA database to track abundances of multiple virus-host pairs monthly over 5 years, e.g. with Roseovarius phages tracking the host. Because the vast majority of proximity ligations should occur between an organisms ribosomes and its own transcripts, we validated our method by looking for self- vs non-self mRNA-rRNA chimeras, by read recruitment to marine single amplified genomes; verifiable non-self chimeras, suggesting off-target linkages, were very rare, indicating host-virus hits were very unlikely to occur by mistake. This approach in practice could link any transcript and its associated processes to specific microorganisms.

microbiology↗

bioRxiv2019

Benchmarking metagenomic marine microbial growth prediction from codon usage bias and peak-to-trough ratios

Growth rates are fundamental to all organisms and essential for characterizing microbial ecologies. Despite this, we do not know the instantaneous nor maximum growth rates of most naturally-occurring microorganisms. Recent reports indicate DNA replication rates can be estimated from metagenomic coverage, and maximum growth rates can be estimated from genomic characteristics. We tested these approaches with native marine bacteria (<0.6 um size fraction) as 10% inoculum grown in unamended virus-free seawater from the San Pedro Channel, California. This allowed microbial growth without grazing and with greatly reduced viral infection. At multiple time points up to 48 h, we sampled for cell abundances and metagenomic analyses. We generated 101 unique Metagenome-assembled genomes (MAGs) including , {beta}, and {gamma} Proteobacteria, Flavobacteria, Actinobacteria, Verrucomicrobia, Marine Group A/SAR406, MGII archaea, and others. We tracked the growth of each as the fraction of total metagenomic reads mapped to each MAG normalized with length, completeness, and total cell counts. Some MAGs did not grow appreciably, but those we could estimate had growth rates ranging from 0.08 to 5.99 d-1; these are the first reported growth rates for several of the groups. These metagenome-determined growth rates, which often changed within experiments, were compared to (a) DNA replication estimates from the peak-to-trough ratio (PTR) as determined by three different approaches, and (b) maximum growth rates predicted from codon usage bias (CUB). For the large majority of taxa, observed growth rates were not correlated to PTR indices (r ~ -0.26 - 0.08), with exceptions being rapidly growing Oceanospirillales and Saccharospirillaceae (r ~ 0.63 - 0.92). However, CUB was moderately well correlated to observed maximum growth rates (r = 0.57). This suggests that maximum growth rates can be reasonably well-estimated from genomic information alone, but current PTR approaches poorly predict actual growth of most marine planktonic bacteria in unamended seawater.

microbiology↗

bioRxiv2017

Dynamic marine viral infections and major contribution to photosynthetic processes shown by regional and seasonal picoplankton metatranscriptomes

Viruses are an important top-down control on microbial communities, yet their direct study in natural environments has been hindered by culture limitations1-3. The advance of sequencing and bioinformatics over the last decade enabled the cultivation independent study of viruses. Many studies focus on assembling new viral genomes4-6 and studying viral diversity using marker genes amplified from free viruses7,8. We used cellular metatranscriptomics to study community-wide viral infections at three coastal California sites throughout a year. Generation of and recruitment to viral contigs (> 5kbp, N=66) allowed tracking of infection dynamics over time and space. Here we show that while these assemblies represent viral populations, they are likely biased towards clonal or low diversity assemblages. Furthermore, we demonstrate that published T4-like cyanophages (N=50) and pelagiphages (N=4), having genomic continuity between close relatives, are better tracked using marker genes. Additionally, we demonstrate determination of potential hosts by matching infection dynamics with microbial community composition. Finally, we quantify the relative contribution of various cyanobacteria and viruses to photosystem-II psbA expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression we observed is of viral origin, which highlights the proportion of infected cells and makes viruses a remarkable contributor to photosynthesis and oxygen production.

ecology↗