Publications

4420

Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO 2 -reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called “methanogenesis markers” but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.

Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine ‘Candidatus Phytoplasma asteris’ that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Anaerobic ammonium oxidation (Anammox) process is a type of biological nitrogen removal technology which is known to directly convert ammonium and nitrite to nitrogen gas. The freshwater ‘Candidatus Kuenenia stuttgartiensis’ anammox under the phylum of Planctomycetes is used to study the parameters that affect the anammox development and the metabolic pathways alongside the associated enzymes. These observations were made using state-of-the art techniques for detecting anammox bacteria based on their small-subunit ribosomal RNA genes, functional genes and unique reaction pathways. This review systematically summarizes up-to-date studies on the parameters affecting the growth of the anammox bacteria and metabolic networks driving anammox bacterial anabolism and mixotrophy beyond genome-based predictions. The K. stuttgartiensis survives in summer and winter conditions besides in the aerobic zones (dissolved oxygen >2 mg/L), which consequently contribute to better nitrogen removal in the wastewater treatment. Furthermore, the K. stuttgartiensis utilizes the Wood–Ljungdahl pathway to directly assimilate extracellular formation instead of oxidising it completely to CO2 prior reassimilation.