Prosser, J. I. | bioRxiv Science

bioRxiv2024

Acidotolerant soil nitrite oxidiser 'Candidatus Nitrobacter laanbroekii' NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidisers

Nitrobacter strain NHB1 is a nitrite-oxidising bacterium previously co-enriched with the neutrophilic ammonia-oxidising bacterium Nitrosospira AHB1, a consortium that nitrifies under acidic conditions. Here we characterise the growth of isolated Nitrobacter strain NHB1 as a function of pH and nitrite (NO2-) concentration, and its influence on the activity of acidophilic soil ammonia-oxidising archaea (AOA) in co-culture. NHB1 is acidotolerant and grows optimally at pH 6.0 (range 5.0 - 7.5) at initial NO2- concentrations of 500 {micro}M. However, the optimum decreases to pH 5.0 at lower initial NO2- concentrations closer to those found in soil, with detectable growth down to pH 3.5. NHB1 has a comparatively high affinity for NO2- with an apparent-half-saturation constant (54 {micro}M) one order of magnitude lower than its closest relative, the neutrophilic strain Nitrobacter hamburgensis X14. In co-culture, NHB1 enhances the growth of acidophilic AOA. Specifically, Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2 are sensitive to NO2--derived compounds and only oxidise [~]200-300 {micro}M ammonia (NH3) in batch cultures. However, in co-culture with NHB1, pH ranges were lowered by [~]0.5 pH units and both strains could oxidise up to 2.7-2.9 mM NH3, only limited by buffering capacity. NHB1 possesses a cyanase facilitating reciprocal cross-feeding via generating cyanate-derived NH3 and utilising AOA-derived NO2-. Removal of NO2- is likely crucial for nitrifier growth in acidic soils and this study highlights the importance of considering substrate and metabolic product concentrations when characterising physiology. Genome analysis reveals that NHB1 is distinct from validated species and the name Nitrobacter laanbroekii is proposed.

microbiology↗

bioRxiv2020

Use and abuse of potential rates in soil microbiology

Potential rate assays are used in soil microbial ecology to determine the rates of a functional process in environmental samples under a defined set of conditions. While they can be used appropriately to provide mechanistic insights, potential rates are also often used to estimate the abundance of specific taxonomic groups and their in situ activity. These estimates incorrectly assume that all contributing organisms in a community are active at a maximum rate under one set of optimal incubation conditions and that potential rates reflect activity in the soil. While investigators now recognise that populations within communities are physiologically diverse, they often ignore the consequent suboptimal activity, or even inactivity, of the majority of community members performing that function. In this short perspective article, we discuss when potential assays can be informative and highlight the underlying conceptual problems under circumstances where potential assays are misused, using potential nitrification rate (PNR) as an example. PNR was originally developed to estimate the size of active ammonia oxidising communities in environmental samples. It is routinely determined in short-term shaken slurry incubations by measuring assumed maximum rates of nitrate or nitrite production under optimal, non-substrate-limiting conditions. As with other functional processes, it is now recognised that a broad diversity of organisms contribute to aerobic ammonia oxidation in terrestrial and other habitats, and this diversity represents a substantial range of physiologies, including variation in substrate affinity, ammonia tolerance, cell specific activity and substrate preference. Despite this, PNR, and other potential rate assays, are often inappropriately used in an attempt to determine an ecologically relevant measurement of activity in soil. As with any potential assay, PNR has inherent biases towards particular functional groups and its use in investigating the ecology of ammonia oxidisers in natural systems should be carefully considered.

microbiology↗