Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha-and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.

1. The deep chlorophyll maximum (DCM) harbours diverse microbial communities and regulates carbon fixation and sequestration in marine ecosystems. Although variations in the DCM microbial community diversity and composition across oceans are reported, we still have a limited knowledge about the ecological mechanism driving the biogeography of DCM microbial communities and their contributions to ecosystem functioning.2. Here, based on DNA-sequencing data (16S rRNA and 18S rRNA genes) with two size fractions collected from coastal to offshore regions of the South China sea (SCS), we found that both size-fractionated bacterial and protistan communities in the DCM exhibited a distance-decay pattern, which was strongly governed by deterministic processes (62.7%-72.2%) and mainly explained by environmental factors (34.1%-37.7%).3. Under warmer temperature and fresher salinity levels, the decreased abundance of protistan parasites induced the weakening parasitic interactions with other protists, whereas the increased abundance of protistan consumers enhanced the phagocytic interactions with bacteria. Such reconstruction of microbial communities induced by environmental variations was thought to constrain particulate organic carbon (POC) flux, as revealed by the partial least square regression model illustrating a strong correlation between the composition of functional protistan groups and POC content of DCM (R 2 = 0.48; r = 0.75; p < 10 −6 ).

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