Tracing carbon and nitrogen microbial assimilation in suspended particles in freshwaters

Abstract

The dynamic interactions between dissolved organic matter (DOM) and particulate organic matter (POM) are central in nutrient cycling in freshwater ecosystems. However, the molecular-level mechanisms of such interactions are still poorly defined. Here, we study spatial differences in the chemical (i.e., individual proteinaceous amino acids) and microbial (i.e., 16S rRNA) composition of suspended sediments in the River Chew, UK. We then applied a compound-specific stable isotope probing (SIP) approach to test the potential assimilation of 13C,15N-glutamate (Glu) and 15N-NO3− into proteinaceous biomass by particle-associated microbial communities over a 72-h period. Our results demonstrate that the composition of suspended particles is strongly influenced by the effluent of sewage treatment works. Fluxes and percentages of assimilation of both isotopically labelled substrates into individual proteinaceous amino acids showed contrasting dynamics in processing at each site linked to primary biosynthetic metabolic pathways. Preferential assimilation of the organic molecule glutamate and evidence of its direct assimilation into newly synthesised biomass was obtained. Our approach provides quantitative molecular information on the mechanisms by which low molecular weight DOM is mineralised in the water column compared to an inorganic substrate. This is paramount for better understanding the processing and fate of organic matter in aquatic ecosystems.

Determining patterns in the composition of dissolved organic matter in fresh waters according to land use and management

“…Such elevated nutrient concentrations are commonly observed in UK agricultural catchments (Yates et al 2019a). Contradictory observations from Graeber et al (2012) and others (Sachse et al 2005) suggest catchments with a high proportion of agricultural activity export structurally complex DOM, characterised by elevated DOC concentrations and a dominance of humic-like fluorescent DOM, though other studies (Lloyd et al 2021;Mena-Rivera et al 2021) indicate DOM in agricultural catchments has a high proportion of lower molecular weight compounds resulting from microbial processing of terrestrially derived DOM. Similarly, both Yates et al (2019a) and Williamson et al (2021) in a pan-UK study concluded that higher DOC, higher Specific UV Absorbance (SUVA) and higher DOC:DOC ratios were consistently observed in peaty catchments than in lowland intensively farmed agricultural catchments.…”

Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions

“…Microbial nitrogen assimilation primarily occurs via the conversion of nitrate into ammonia by a series of enzymes such as nitrate reductase and nitrite reductase ( Matassa et al, 2016 ). These microorganisms then use this ammonia for amino acid synthesis and transformation ( Mena-Rivera et al, 2023 ). Amino acids are primarily used to synthesize proteins that can then be modified, sorted, transported, and stored in microbial organisms ( Xu et al, 2015 ).…”

The differential assimilation of nitrogen fertilizer compounds by soil microorganisms

“…The approach combines compound-specific gas chromatography–combustion-isotope ratio mass spectrometry (GC–C-IRMS) and 15 N-SIP in the meta-metabolome of the whole soil system (Knowles et al 2010 ; or other complex media, e.g. river water; Mena-Rivera et al 2022 ) and is essentially a targeted 15 N fluxomics approach (Cascante and Marin 2008 ). The soil protein pool is the largest (20%–50% of total soil N), and arguably most important, identifiable class of soil organic N (Stevenson 1982 ).…”