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Sediment metagenome

ABSTRACT: Transcriptional diversity of ammonia oxidizing archaea in estuary sediments cultivated in different temperatures and salinity

PROVIDER: PRJNA239778 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1182470.fastq.gz	Fastqsanger.gz
	SRR1182471.fastq.gz	Fastqsanger.gz
	SRR1182472.fastq.gz	Fastqsanger.gz
	SRR1182466.fastq.gz	Fastqsanger.gz
	SRR1182468.fastq.gz	Fastqsanger.gz

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Transcriptome sequencing data sets of a marine ammonia-oxidizing archaeon Nitrosopumilus zosterae NM25 to hydrogen peroxide

Project description:Marine ammonia-oxidizing archaea are known to lack the catalase gene that functions as a scavenger at high concentrations of hydrogen peroxide. Therefore, nearly isolated ammonia-oxidizing archaea require the addition of a hydrogen peroxide scavenger to their culture medium, despite being aerobic. To understand the transcriptomic response to hydrogen peroxide stress, we performed RNA-Seq analysis under two different conditions: one without the addition of a hydrogen peroxide scavenger and one with the addition of a hydrogen peroxide scavenger as a control.

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Ammonia oxidizing archaeal community composition in Gulf of Mexico sediments investigated with an amoA functional gene microarray

Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard

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Hypoosmolarity inhibits archaeal ammonia oxidation

Project description:Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on these key players in nitrogen cycling remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels (~120 µS/cm), which are comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by Nitrosomonas oligotropha, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by “Ca. Nitrosotenuis” of the Nitrosopumilaceae family, was stimulated by high salinity (~760 µS/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by N. oligotropha, significantly increased under both low (~170 µS/cm) and high salinity (~850 µS/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were found to be sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially of members of the Nitrosopumilaceae, under hypoosmolarity, unlike AOB and complete ammonia oxidizers (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress is attributed to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights the importance of hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers as well as nitrification activities in terrestrial and aquatic environments increasingly affected in their salinities by intensified water cycles due to climate change.

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Nitrosopumilus maritimus SCM1: exponential phase control vs. 24 hours starvation vs. 24 hours recovery after starvation

Project description:Transcriptional profiling of marine ammonia oxidizing archaea Nitrosopumilus maritimus cells comparing exponential phase control cells with cells under 24 hours starvation and with cells under recovery after 24 hours starvation. Goal was to determine the effects of global transcriptional responses of N. maritimus cells under ammonia starvation and recovery conditions.

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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 amoA-carrying AOA within these sediments.

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