Publications

3843

AbstractBellis perennis virescence (BellVir) phytoplasma affects ornamental daisies in Argentina. It has been previously classified within the X-disease group, subgroup III-J, which is one of the most important and widely distributed in South America, affecting diverse plant hosts. In this study, we compared 16S rRNA, ribosomal proteins rpIV and rps3, secA and immunodominant proteins imp and idpA genes of BellVir phytoplasma with previously described ‘Candidatus Phytoplasma’ species. The 16S rRNA gene of strain BellVir shared less than 97.5% with all previously described ‘Ca. Phytoplasma’ taxa except for ‘Ca. Phytoplasma pruni’. According to the recommended rules for the description of novel taxa within ‘Ca. Phytoplasma’, it should be considered as ‘Ca. P. pruni’-related strain. However, multilocus analysis showed further molecular diversity that distinguished BellVir phytoplasma from ‘Ca. Phytoplasma pruni’. Besides, BellVir phytoplasma and 16SrIII-J related strains have a geographical distribution restricted to South America, where ‘Ca. P.pruni’ has not been detected. Two insect vectors have been reported to transmit 16SrIII-J phytoplasmas, which have not been found to transmit ‘Ca. Phytoplasma pruni’. Having a wide host range, they have not been detected in Prunus persica. Therefore, based on multilocus sequence analyses, specific vector transmission and geographical distribution, we propose the recognition of the novel phytoplasma species ‘Ca. Phytoplasma platensis’, within the X-disease clade, with Bellis perennis virescence phytoplasma as the reference strain.

Abstract Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety of ecological niches and to become the most successful archaeal lineage in ocean surface waters.

“ Candidatus Accumulibacter phosphatis” is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that “ Ca . Accumulibacter phosphatis” is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.

The symbiotic N 2 -fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii , and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N 2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O 2 ) or the O 2 evolved through photosynthesis. This study showed that symbiosis between the N 2 -fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N 2 fixation, which is likely more energetically efficient than fixing N 2 at night, as found in other unicellular marine cyanobacteria.

The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat’s biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.