A widespread group of large plasmids in methanotrophic Methanoperedens archaea

Abstract

Anaerobic methanotrophic (ANME) archaea conserve energy from the breakdown of methane, an important driver of global warming, yet the extrachromosomal genetic elements that impact the activities of ANME archaea are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus. These have been maintained in two bioreactors that contain enrichment cultures dominated by different Methanoperedens species and co-occur with Methanoperedens species in other anoxic environments. By manual curation we show that two of the plasmids are large (155,607 bp and 191,912 bp), circular, and replicate bidirectionally. The group of Methanoperedens species that carry these plasmids is related to "Ca. Methanoperedens nitroreducens", "Ca. Methanoperedens ferrireducens", "Ca. Methanoperedens manganicus" and the plasmids occur in the same copy number as the main chromosome. The larger plasmid encodes transporters that potentially enhance access to Ni, which is required for the methyl-CoM reductase (Mcr), Co required for the cobalamin cofactor needed for methyltransferases, and amino acid uptake. We show that many plasmid genes are actively transcribed, including genes involved in plasmid chromosome maintenance and segregation, a Co2+/Ni2+ transporter and cell protective proteins. Notably, one plasmid carries three tRNAs and two colocalized genes encoding ribosomal protein uL16 and elongation factor eEF2. These are not encoded in the host Methanoperedens genome and uL16 and eEF2 were highly expressed, indicating an obligate interdependence between this plasmid and its host. The finding of plasmids of Methanoperedens opens the way for the development of genetic vectors that could be used to probe little understood aspects of Methanoperedens physiology. Ultimately, this may provide a route to introduce or alter genes that may enhance growth and overall metabolism to accelerate methane oxidation rates.

Nitrate leaching and its implication for Fe and As mobility in a Southeast Asian aquifer

“…Methanoperedens nitroreducens (~44%), Ca . Methylomirabilis (~26%) (Raghoebarsing et al, 2006; Schoelmerich et al, 2022). The N-DAMO(V) culture was enriched from rice paddy soil from Vercelli, Italy, and consists mainly of Ca .…”

“…The N-DAMO(V) culture was enriched from rice paddy soil from Vercelli, Italy, and consists mainly of Ca . Methanoperedens (~78%) (Schoelmerich et al, 2022; Vaksmaa et al, 2017). Both cultures are grown in a continuous bioreactor under anoxic conditions with NO 3 - as electron acceptor and CH 4 as electron donor.…”

“…Methanoperedens (~78%) (Schoelmerich et al, 2022;Vaksmaa et al, 2017). Both cultures are grown in a continuous bioreactor under anoxic conditions with NO3as electron acceptor and CH4 as electron donor.…”

Borgs are giant genetic elements with potential to expand metabolic capacity

“…We did not detect genes for plasmid partitioning or conjugative systems, rRNA loci or encoded viral proteins (Supplementary Table 3), and the genomes were markedly different from recently reported Methanoperedens spp. plasmids 20 . The distinctly lower GC content and variable copy number argue against their classification as archaeal minichromosomes 12,21 .…”

Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins

“…Based on gene content and co-occurrence patterns, Borgs associate with several species of anaerobic methanotrophic (ANME) archaea of the Methanoperedens genus [3]. A search for other ECEs associated with these archaea also led to the recent discovery of large plasmids found in members of the same genus, yet a distinct clade of Methanoperedens species [4]. ANME perform anaerobic oxidation of methane (AOM) by using the reverse methanogenesis pathway [5].…”