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In-Situ Ammonia Recovery in Anaerobic digestion via Gas Permeable Membranes: Reshaping Dominant Methanogens under Ammonia Stress through Divergent Insights from Microbiomics, Metagenomics, and Metaproteomics

ABSTRACT: Mechanistically, this study reconstructs the dominant methanogens under ammonia stress through insights from microbiomics, metagenomics, and metaproteomics. The research identifies Methanobacterium as a "pseudo dominant genus" under ammonia stress—large in population but low in contribution. The significant downregulation of electron transfer efficiency and methyl-reducing protein expression in Methanobacterium may be key factors limiting its activity. Conversely, the study confirms Methanothrix as the "true dominant genus" under ammonia inhibition—reduced in population but undiminished in contribution. Methanothrix expresses all proteins required for acetoclastic and hydrogenotrophic methanogenesis and upregulates functional proteins related to post-translational modifications, tRNA activation, and initiation complex formation during enzyme synthesis. Finally, metaproteomics unveiled the presence of "exceptionally active genera" with remarkably low community abundance—specifically, Methanolinea, Methanospirillum, and unclassified_f__Methanoregulaceae. Their protein expression levels in the methanogenesis pathway surpassed those of Methanobacterium, establishing them as the primary drivers of hydrogenotrophic methanogenesis.

ORGANISM(S): Anaerobic Bacterium Foal30

SUBMITTER: Zhiqiang Shen

PROVIDER: PXD060986 | iProX | Wed Feb 19 00:00:00 GMT 2025

REPOSITORIES: iProX

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Project description:Investigation of the whole genome gene expression level changes relative to exponential phase growth in Nitrosomonas europaea ATCC19718 after 12 hours ammonia starvation, 144 hours ammonia starvation, and 20 minutes following ammonia addition to starved cells. The ammonia monooxygenase of chemolithotrophic ammonia oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB1,2). Several AOB, including N. europaea, also posess a divergent monocistronic copy of amoC (amoC3) of unknown function. Previous work suggested a possible functional role for amoC3 in N. europaea during recovery from extended ammonia starvation as part of the σE- stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC3 is part of a general post-starvation cellular response system in N. europaea. We also found that amoC3 is required for efficient exit from prolonged ammonia starvation, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ32 global stress response regulator demonstrated that the heat shock regulon also plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC3 subunit which appears to function as a stress responsive subunit capable of maintaining ammonia oxidation activity under stress conditions. A twelve chip study using total RNA recovered from four timepoints for each of three biological replicates of wild-type cultures of Nitrosomonas europaea ATCC 19718. Total RNA was obtained from each biological culture replicate during exponential growth, following 12 hours ammonia starvation, 144 hours ammonia starvations, and 20 minutes following ammonia addition to starved cells.

Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoAÂ-carrying AOA within these sediments. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

Dataset Information

In-Situ Ammonia Recovery in Anaerobic digestion via Gas Permeable Membranes: Reshaping Dominant Methanogens under Ammonia Stress through Divergent Insights from Microbiomics, Metagenomics, and Metaproteomics

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