Lehtovirta-Morley, L. | bioRxiv Science

bioRxiv2021

Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co- occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest substrate affinity of any characterized AOA, which are similar to previously determined affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values strongly supports the hypothesis that - like for AOB - ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

microbiology↗

bioRxiv2021

Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome

Conventional methods of agricultural pest control and crop fertilisation are contributing to a crisis of biodiversity loss, biogeochemical cycle dysregulation, and ecosystem collapse. Thus, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome may contribute to this goal as microbes can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. We applied 16S rRNA gene & fungal 18S rRNA gene (ITS2 region) amplicon sequencing to profile the diversity of the bacterial, archaeal & fungal communities associated with the roots of UK elite spring bread wheat variety Triticum aestivum var. Paragon in different soils and developmental stages. This revealed that community composition shifted significantly for all three groups across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. To understand which microbes are using wheat root exudates in the rhizosphere, root exudates were labelled in a 13CO2 DNA stable isotope probing experiment. This shows that bacterial taxa within the Burkholderiaceae family among other core enriched taxa, such as Pseudomonadaceae, were able to use root exudates but Streptomycetaceae were not. Overall, this work provides a better understanding of the wheat microbiome, including the endosphere community. Understanding crop microbiome formation will contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

microbiology↗