Biology subjects

Rasmussen, A. N.

Publications and source records attributed to Rasmussen, A. N..

4 recordsLinked to original sources

bioRxiv2026

The origin and evolution of archaeal Borg extrachromosomal elements

Borgs are giant linear extrachromosomal elements (ECEs) of methane-oxidizing Methanoperedens archaea whose evolutionary origin and ecosystem distribution remain unknown. Here we detected 240 Borgs in diverse saline, soil, and freshwater ecosystems. 27 encode methyl-coenzyme M reductases central to methane metabolism, eight have full rRNA operons related to those of Methanoperedens, and some contain up to four ribosomal proteins. We also identified 323 mini-Borgs whose proteome content and gene phylogenies classify as a distinct ECE type. Based on 105 complete and near-complete genomes, Borgs and mini-Borgs share core genes in conserved order, indicating common ancestry. Phylogenetic and diversity analyses suggest that Borgs evolved via gene acquisition into a backbone inherited from mini-Borgs. This evolutionary trajectory mirrors those proposed for giant viruses of both eukaryotes and bacteria.

microbiology↗

bioRxiv2022

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 466 high-quality publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided the first IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.

microbiology↗

bioRxiv2022

Production and cross-feeding of nitrite within Prochlorococcus populations

Prochlorococcus is an abundant photosynthetic bacterium in the oligotrophic open ocean where nitrogen (N) often limits the growth of phytoplankton. Prochlorococcus has evolved into multiple phylogenetic clades of high-light (HL) adapted and low-light (LL) adapted cells. Within these clades, cells encode a variety of N assimilation traits that are differentially distributed among members of the population. Among these traits, nitrate (NO3-) assimilation is generally restricted to a few clades of high-light adapted cells (the HLI, HLII, and HLVI clades) and a single clade of low-light adapted cells (the LLI clade). Most, if not all, cells belonging to the LLI clade have the ability to assimilate nitrite (NO2-), with a subset of this clade capable of assimilating both NO3- and NO2-. Cells belonging to the LLI clade are maximally abundant at the top of the nitracline and near the primary NO2- maximum layer. In some ecosystems, this peak in NO2- concentration may be a consequence of incomplete assimilatory NO3- reduction by phytoplankton. This phenomenon is characterized by a bottleneck in the downstream half of the NO3- assimilation pathway and the concomitant accumulation and release of NO2- by phytoplankton cells. Given the association between LLI Prochlorococcus and the primary NO2- maximum layer, we hypothesized that some Prochlorococcus exhibit incomplete assimilatory NO3- reduction. To assess this, we monitored NO2- accumulation in batch culture for 3 Prochlorococcus strains (MIT0915, MIT0917, and SB) and 2 Synechococcus strains (WH8102 and WH7803) when grown on NO3- as the sole N source. Only MIT0917 and SB accumulated external NO2- during growth on NO3-. Approximately 20-30% of the NO3-transported into the cell by MIT0917 was released as NO2-, with the balance assimilated into biomass. We further observed that co-cultures using NO3- as the sole N source could be established for MIT0917 and a Prochlorococcus strain that can assimilate NO2- but not NO3-. In these co-cultures, the NO2- released by MIT0917 was efficiently consumed by its partner strain during balanced exponential growth. Our findings highlight the potential for emergent metabolic partnerships within Prochlorococcus populations that are mediated by the production and consumption of the N cycle intermediate, NO2-. SIGNIFICANCEEarths biogeochemical cycles are substantially driven by microorganisms and their interactions. Given that N often limits marine photosynthesis, we investigated the potential for N cross-feeding within populations of Prochlorococcus, the numerically dominant photosynthetic cell in the subtropical open ocean. During growth on NO3-, some Prochlorococcus cells release up to 30% of their N uptake as extracellular NO2-. In the wild, Prochlorococcus populations are composed of multiple functional types, including those that cannot use NO3- but can still assimilate NO2-. We show that metabolic dependencies arise when Prochlorococcus strains with complementary NO2- production and consumption phenotypes are grown together on NO3-. These findings demonstrate the potential for emergent metabolic partnerships, possibly modulating ocean nutrient gradients, that are mediated by cross-feeding of N cycle intermediates.

microbiology↗

bioRxiv2020

Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation

The picocyanobacteria Prochlorococcus and Synechococcus are found throughout the oceans euphotic zone, where the daily light:dark cycle drives their physiology. Periodic deep mixing events can, however, move cells below this zone, depriving them of light for extended periods of time. Here we demonstrate that Prochlorococcus and Synechococcus can adapt to tolerate repeated periods of light energy deprivation. Cyanobacterial cultures kept in the dark for 3 days and then returned to the light initially required 18-26 days to resume growth, but after multiple rounds of dark exposure the strains began to regrow after only 1-2 days. This dark-tolerant phenotype was stable and heritable; cultures retained the trait across at least 18-21 generations even when grown in a standard 13:11 light:dark cycle. We found no genetic differences between the dark-tolerant and parental strains of Prochlorococcus NATL2A, indicating that an epigenetic change is responsible for the adaptation. To begin to explore this possibility, we asked whether DNA methylation - an epigenetic mechanism in bacteria - occurs in Prochlorococcus. LC-MS/MS analysis showed that while DNA methylations, including 6mA and 5mC, are found in some other Prochlorococcus strains, no methylations were detected in either the parental or dark-tolerant strain used in our experiments -i.e. the NATL2A strain. These findings suggest that Prochlorococcus utilizes a yet-to-be-determined epigenetic mechanism to adapt to the stress of extended light energy deprivation.

microbiology↗