Comparative analysis of Chlorosarcinopsis eremi mitochondrial genome with some Chlamydomonadales algae

Facade eluates affect active and total soil microbiome

The application of biocides in building materials has become a prevalent practice to mitigate the growth of microorganisms such as algae, fungi, and bacteria on the façades. These can leach out from the material and reach the nearby soil environment. This study aimed to characterize the effect of façade eluates generated within different leaching experiments on total and metabolic active soil microbial community composition and functions. Façade eluates were produced by immersion testing DIN EN 16105 and a natural weathering experiment. Afterward, soil microcosms were treated with the respective façade eluate and incubated for 29 days. Subsequently, the active and total soil microbial community compositions were investigated. Fungal internal transcribed spacer region gene and bacterial 16S rRNA gene were sequenced for active (bromodeoxyuridine labeled DNA) microbial community and total community. Façade eluates reduced total bacterial and fungal gene copy numbers. Overall, active bacterial and fungal richness was reduced and altered in community composition in comparison to the total richness and composition, respectively. Façade eluates retrieved of façade samples without biocides did alter the soil microbial communities to the same extent as façade eluates with biocides. Additionally, members of the active microbiome that benefit from the presence of façade eluates and omitted ones could be identified. Our result demonstrated that façade eluates affect active and total soil microbial community composition and function regardless of the leaching procedure and biocides addition.

Insights from cyanobacterial genomic and transcriptomic analyses into adaptation strategies in terrestrial environments

Phylogenomic analysis of Nostoc sp. MG11, a terrestrial cyanobacterium, and some terrestrial and freshwater Nostoc strains showed that the terrestrial strains grouped together in a distinctive clade, which reveals the effect of habitat on shaping Nostoc genomes. Terrestrial strains showed larger genomes and had higher predicted CDS contents than freshwater strains. Comparative genomic analysis demonstrated that genome expansion in the terrestrial Nostoc is supported by an increase in copy number of the core genes and acquisition of shared genes. Transcriptomic profiling analysis under desiccation stress revealed that Nostoc sp. MG11 protected its cell by induction of catalase, proteases, sucrose synthase, trehalose biosynthesis and maltodextrin utilization genes and maintained its normal metabolism during this condition by up-regulation of genes related to phycobilisomes and light reactions of photosynthesis, CO₂ fixation and protein metabolism. These results provide insights into the strategies related to survival and adaptation of Nostoc strains to terrestrial environments.

Can Green Algal Plastid Genome Size Be Explained by DNA Repair Mechanisms?

A major finding in organelle biology over the past decade is that land plant mitochondrial genomes, which are the largest among eukaryotes, can have a “Jekyll and Hyde” mutational pattern: low for synonymous sites, high for intergenic ones. This has led to the theory that double-strand breaks (DSBs) in the intergenic DNA of plant mitogenomes are repaired by inaccurate mechanisms, such as break-induced replication, which can result in large insertions and, thus, could explain why these genomes are so prone to expansion. But how universal is this theory? Can it apply to other giant organelle DNAs, such as the massive plastid DNAs (ptDNAs) of chlamydomonadalean green algae? Indeed, it can. Analysis of the expanded plastomes from two distinct isolates of the unicellular chlamydomonadalean Chlorosarcinopsis eremi uncovered exceptionally low rates of synonymous substitution in the coding regions but high substitution rates, including frequent indels, in the noncoding ptDNA, mirroring the trend from land plant mitogenomes. Remarkably, nearly all of the substitutions and indels identified in the noncoding ptDNA of C. eremi occur adjacent to or within short inverted palindromic repeats, suggesting that these elements are mutational hotspots. Building upon earlier studies, I propose that these palindromic repeats are predisposed to DSBs and that error-prone repair of these breaks is contributing to genomic expansion. Short palindromic repeats are a common theme among bloated plastomes, including the largest one on record, meaning that these data could have wide-reaching implications for our understanding of ptDNA expansion.

Common Repeat Elements in the Mitochondrial and Plastid Genomes of Green Algae

Despite both originating from endosymbiotic bacteria, one does not typically expect mitochondrial DNA (mtDNA) to show strong sequence identity to plastid DNA (ptDNA). Nevertheless, a recent analysis of Haematococcus lacustris revealed exactly that. A common repeat element has proliferated throughout the mtDNA and ptDNA of this chlamydomonadalean green alga, resulting in the unprecedented situation whereby these two distinct organelle genomes are largely made up of nearly identical sequences. In this short update to the work on H. lacustris, I highlight another chlamydomonadalean species (Stephanosphaera pluvialis) for which matching repeats have spread throughout its organelle genomes (but to a lesser degree than in H. lacustris). What's more, the organelle repeats from S. pluvialis are similar to those from H. lacustris, suggesting that they have a shared origin, and perhaps existed in the mtDNA and ptDNA of the most recent common ancestor of these two species. However, my examination of organelle genomes from other close relatives of H. lacustris and S. pluvialis did not uncover further compelling examples of common organelle repeat elements, meaning that the evolutionary history of these repeats might be more complicated than initially thought.