Selective enrichment of high-affinity clade II N2O-reducers in a mixed culture
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB84459 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14149820_1.fastq.gz | Fastqsanger.gz | |||
| ERR14149820_2.fastq.gz | Fastqsanger.gz | |||
| ERR14149821_1.fastq.gz | Fastqsanger.gz | |||
| ERR14149821_2.fastq.gz | Fastqsanger.gz | |||
| ERR14149822_1.fastq.gz | Fastqsanger.gz |
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Project description:The majority of potent greenhouse gas nitrous oxide (N2O) emissions originate from microbially mediated reactions. The enzyme N2O reductase is the only known biological N2O sink and has evolved in two phylogenetically distinct lineages (clades I and II). Clade II is of particular interest for biotechnology as it is often associated with non-denitrifying N2O reducers. In this study, Laureni et al. investigated the environmental conditions that select for clade II. To do so, we enriched two N2O-respiring communities at low dilution rates, under both electron donor (acetate) and electron acceptor (N2O) limitations, in order to assess the impact of substrate affinity and N2O cytotoxicity on community assembly. We used a combination of genome-resolved metagenomics and shotgun metaproteomics to identify the taxonomy and metabolic potential of the steady-state community members. Corresponding author: Michele Laureni, contact: m.laureni@tudelft.nl
2025-01-18 | PXD047071 | Pride
Project description:Microorganisms encoding for the N2O reductase (NosZ) are the only known biological sink of the potent greenhouse gas N2O and are central to global N2O mitigation efforts. Clade II NosZ populations are of particular biotechnological interest as they usually feature high N2O affinities and often lack other denitrification genes. We focus on the yet-unresolved ecological constraints selecting for different N2O-reducers strains and controlling the assembly of N2O-respiring communities. Two planktonic N2O-respiring mixed cultures were enriched at low dilution rates under limiting and excess dissolved N2O availability to assess the impact of substrate affinity and N2O cytotoxicity, respectively. Genome-resolved metaproteomics was used to infer the metabolism of the enriched populations. Under N2O limitation, clade II N2O-reducers fully outcompeted clade I affiliates, a scenario previously only theorized based on pure-cultures. All enriched N2O-reducers encoded and expressed the sole clade II NosZ, while also possessing other denitrification genes. Two Azonexus and Thauera genera affiliates dominated the culture, and we hypothesize their coexistence to be explained by the genome-inferred metabolic exchange of cobalamin intermediates. Under excess N2O, clade I and II populations coexisted; yet, proteomic evidence suggests that clade II affiliates respired most of the N2O, de facto outcompeting clade I affiliates. The single dominant N2O-reducer (genus Azonexus) notably expressed most cobalamin biosynthesis marker genes, likely to contrast the continuous cobalamin inactivation by dissolved cytotoxic N2O concentrations (400 μM). Ultimately, our results strongly suggest the solids dilution rate to play a pivotal role in controlling the selection among NosZ clades, albeit the conditions selecting for genomes possessing the sole nosZ remain elusive. We furthermore highlight the potential significance of N2O-cobalamin interactions in shaping the composition of N2O-respiring microbiomes.
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Project description:We report here the RNA seq results of sRNA enriched Paracoccus denitrificans grown under three different N2O levels (high N2O reffered to as CuL/ low N2O reffered to as CuH/ Low N2O aerobic reffered to as CuH O2)
2016-11-16 | GSE85362 | GEO
Project description:nosZ and nosZ-II marker genes had been sequenced in order to investigate the impact of biochar on N2O reducers
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Project description:We investigated whether individual populations of freshwater bacteria in mixed experimental communities may exhibit specific responses to the presence of different bacterivorous protists. In two successive experiments, a two-stage continuous cultivation system was inoculated with nonaxenic batch cultures of the cryptophyte Cryptomonas sp. Algal exudates provided the sole source of organic carbon for growth of the accompanying microflora. The dynamics of several 16S rRNA-defined bacterial populations were followed in the experimental communities. Although the composition and stability of the two microbial communities differed, numerous members of the first assemblage could again be detected during the second experiment. The introduction of a size-selectively feeding mixotrophic nanoflagellate (Ochromonas sp.) always resulted in an immediate bloom of a single phylotype population of members of the class Actinobacteria (Ac1). These bacteria were phylogenetically affiliated with an uncultured lineage of gram-positive bacteria that have been found in freshwater habitats only. The Ac1 cells were close to the average size of freshwater bacterioplankton and significantly smaller than any of the other experimental community members. In contrast, no increase of the Ac1 population was observed in vessels exposed to the bacterivorous ciliate Cyclidium glaucoma. However, when the Ochromonas sp. was added after the establishment of C. glaucoma, the proportion of population Ac1 within the microbial community rapidly increased. Populations of a beta proteobacterial phylotype related to an Aquabacterium sp. decreased relative to the total bacterial communities following the addition of either predator, albeit to different extents. The community structure of pelagic microbial assemblages can therefore be influenced by the taxonomic composition of the predator community.
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