The ISME Journal


Publications
85

Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology

Citation
Zheng et al. (2021). The ISME Journal 15 (9)
Names
Abstract
AbstractCandidatus Izemoplasma, an intermediate in the reductive evolution from Firmicutes to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes. Unfortunately, the paucity of pure cultures has limited further insights into their physiological and metabolic features as well as ecological roles. Here, we report the first successful isolation of an Izemoplasma representative from the deep-sea methane seep, strain zrk13, using a DNA d

Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts

Citation
Taylor et al. (2021). The ISME Journal 15 (2)
Names
Perseibacter sydneyensis Ts Perseibacter Perseibacteraceae Tethybacter castelli Ts Tethybacter Tethybacteraceae Tethybacterales
Abstract
Abstract The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ

Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

Citation
Sauder et al. (2020). The ISME Journal 14 (9)
Names
Ca. Nitrosocosmicus exaquare
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

Citation
Assié et al. (2020). The ISME Journal 14 (1)
Names
“Thiobarbaceae” Ca. Thiobarba
Abstract
AbstractMost autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“CandidatusThiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems

Citation
Manzano-Marı́n et al. (2020). The ISME Journal 14 (1)
Names
“Erwinia haradaeae”
Abstract
Abstract Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutio

Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae

Citation
Salcher et al. (2019). The ISME Journal 13 (11)
Names
“Methylophilus medardensis” “Methylosemipumilus” “Methylosemipumilus turicensis” “Methylopumilus rimovensis” “Methylopumilus universalis” “Methylopumilus hibernalis” “Methylopumilus profundus” Methylopumilus Methylopumilus planktonicus Ts
Abstract
Abstract The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (“Ca. Me

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase

Citation
Kim et al. (2019). The ISME Journal 13 (9)
Names
Nanopelagicales Nanopelagicaceae “Planktophila aquatilis” “Planktophila rubra”
Abstract
Abstract The actinobacterial acI lineage is among the most successful and ubiquitous freshwater bacterioplankton found on all continents, often representing more than half of all microbial cells in the lacustrine environment and constituting multiple ecotypes. However, stably growing pure cultures of the acI lineage have not been established despite various cultivation efforts based on ecological and genomic studies on the lineage, which is in contrast to the ocean from which abun