Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

Abstract

Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual "inflation" of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle. marine microbiology | oligotrophic | evolution genomics | nitrogen fixation T he low availability of N (and fixed carbon) in the midlatitude upper oceans provides an important niche for autotrophic organisms that can fix atmospheric nitrogen, which can exert control over global primary production (1-3). Nitrogen fixation is a prokaryotic process with a high-energy demand, and oceanic cyanobacteria are known to be significant sources of this "new" nitrogen (nitrogen that is fixed from the atmosphere or NO 3 advected from depth) (4, 5). Molecular field data have shown that a handful of cyanobacterial diazotrophs responsible for oligotrophic nitrogen fixation can reach relatively high cell numbers (6-12) and be of significant biogeochemical importance (13-16). These include photosynthetic free-living forms, such as the filamentous Trichodesmium and the unicellular Crocosphaera and Cyanothece, and photosynthetic and nonphotosynthetic symbiotic forms, such as heterocystous Richelia and Candidatus Atelocyanobacterium thalassa (3,5,17).Trichodesmium cells can grow either as trichomes (i.e., filaments) or aggregates and form three types of classically described colonies, including radial puffs, vertically aligned fusiform tufts, and bowties (...

The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum

“…Finally, transport reactions included in the model were selected based on proteomic data or diffusion (CO 2 , H 2 O, N 2, etc.) [16]. Manual curation efforts built the model out to a maximum of 1035 reactions; closer inspection of the reactions revealed that several were predicted by the SEED algorithm but had no significant homology to the T. erythraeum genome and were non-essential, therefore they were removed.…”

“…Current characterization of Trichodesmium is limited predominantly to population level observations due to its genetic intractability and difficulty to culture. While several laboratory studies investigating the complex genome [16–18], transcriptome [19, 20], and proteome [21] have been published, most relate to populations level or sparse in situ studies in diverse, non-ideal growth conditions. A handful of other recent studies report on the morphology/structure of the cells [8, 10, 22, 23] and how cells respond to iron, nickel, and other nutrient stresses [24–27].…”

Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen‐fixing cyanobacterium Trichodesmium

“…A total of 15 652 methylated residues were detected (∼1% of total cytosines) with ∼78% and ∼22% residing in total gene and intergenic regions respectively (Supporting Information File S2). Notably, ∼60% of the Trichodesmium genome codes for protein, which is rare for the broad majority of free‐living prokaryotes that typically average ∼80% (Walworth et al ., ). Upon plotting the locations of methylated cytosines (MCs) on both forward and reverse strands, MCs within genic and intergenic exhibit broad distributions throughout the genome (Fig.…”

“…Interestingly, a handful of MCs in intergenic regions form clusters in and around repetitive elements with sequence homology to transposases. Many of these repetitive elements with MCs have been annotated as intergenic regions yet many retain transposase sequence homology suggesting them to be ancient pseudogenized transposases (Walworth et al ., ). Hence, MCs overlapping with these sequences may potentially regulate their propagation as seen in other systems (Miura et al ., ; Kato et al ., ; Lister et al ., ; see below for further discussion).…”

“…Characterizing the methylation landscape of IMS101 was facilitated using Illumina bisulfite sequencing (Walworth et al ., ) in which general bisulfite‐conversion and sequence statistics can be found in Supporting Information Table S1. Cultures of IMS101 grown in a modified Aquil medium (Hutchins et al ., ) were filtered and flash frozen in liquid nitrogen in biological triplicate during the middle of the 12 h photoperiod.…”