Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure

Abstract

A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum ‘Candidatus Atribacteria’ (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography. Our observations are consistent with a classical gram-negative structure with an additional intracytoplasmic membrane. However, further studies are needed to provide conclusive evidence for this unique intracellular structure. The RT761 genome encodes proteins with features that might be related to the complex cellular structure, including: N-terminal extensions in proteins involved in important processes (such as cell-division protein FtsZ); one of the highest percentages of transmembrane proteins among gram-negative bacteria; and predicted Sec-secreted proteins with unique signal peptides. Physiologically, RT761 primarily produces hydrogen for electron disposal during sugar degradation, and co-cultivation with a hydrogen-scavenging methanogen improves growth. We propose RT761 as a new species, Atribacter laminatus gen. nov. sp. nov. and a new phylum, Atribacterota phy. nov.

Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks

“…4 and 5). However, at the flask bottom below the 3 cm column of crushed peridotite rock, anoxic conditions likely established due to a vertical O 2 gradient in the flask that commonly occurs in this experimental setup due to increased rates of aerobic respiration at the benthic-water interface [85]. Anoxic conditions in the crushed rocks at the bottom of the flasks likely promoted carbon assimilation by rock-associated strict anaerobes that also were using H 2 to increase their anabolism from the added 13 C-labeled substrates.…”

Spatial separation of ribosomes and DNA in Asgard archaeal cells

“…Considering the anticipated role of Asgard archaea in eukaryogenesis, in particular the presence of ESPs potentially involved in dynamic cytoskeleton formation [18] and membrane remodeling [4,19], the separation of DNA-and ribosome-derived signals might be indicative of cellular compartmentalization. Alternatively, the observed pattern could be the result of a membrane invagination to form a nucleoid region, similar to membrane organizations for example in Planctomycetes cells [20] or Atribacter laminatus [21].…”

Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin

“…Desulfofervidus (Figure 7A). Surface samples of cool cores 4870-2 and 4871-20 are characterized by frequent recovery of sequences attributed to the sulfate-reducing bacterial SEEP-SRB1 group (Knittel et al, 2003) which include the mesophilic syntrophic partners of ANME-1 methane-oxidizing archaea (Schreiber et al, 2010), and to the fermentative, mesophilic Atribacteria (Nobu et al, 2016a;Katayama et al, 2020) which are common inhabitants of cold seeps (Ruff et al, 2015;Chakraborty et al, 2020) and anaerobic subsurface sediments (Starnawski et al, 2017). Sequences from the aromatics-degrading sulfate-reducing Desulfatiglans lineage were recovered from all temperate cores, as well as from several hot hydrothermal and background samples, consistent with its cosmopolitan distribution (Jochum et al, 2018).…”