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Bacterial communities of oligotrophic groundwater

ABSTRACT: Differential contributions of nitrifying microorganisms to nitrification in oligotrophic groundwater from the Hainich Critical Zone Exploratory

PROVIDER: PRJEB63087 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11534200_1.fastq.gz	Fastqsanger.gz
	ERR11534200_2.fastq.gz	Fastqsanger.gz
	ERR11534201_1.fastq.gz	Fastqsanger.gz
	ERR11534201_2.fastq.gz	Fastqsanger.gz
	ERR11534202_1.fastq.gz	Fastqsanger.gz

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Ammonia oxidizing communites of oligotrophic groundwater

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Hydrodynamic conditions shape ammonia-oxidizer communities in the central Baltic Sea water column

Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.

2013-08-24 | GSE50164 | GEO

Bacterial community structure in soils, seepage water and groundwater of the Hainich Critical Zone Exploratory

Project description:Bacterial community structure in soils, seepage water and groundwater of the Hainich Critical Zone Exploratory

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Project description:AquaDiva: Whole-metagenome shotgun sequencing of a groundwater ecosystem of the Hainich Critical Zone Exploratory

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Activation of 3, 4-dimethylphenol dimer production from marine Streptomyces sp. FJNU027 under oligotrophic condition

Project description:Activating the cryptic secondary metabolic gene clusters is a vital research field in Streptomyces. The marine Streptomyces sp. FJNU027 strain which could produce tirandamycins was cultured in the oligotrophic medium. Compared with normal medium, a differential product in oligotrophic culture was found by HPLC assay. After mass fermentation, 2 mg of the differential product was obtained from 30 L fermentation broth by solvent extraction, column chromatography over sephadex LH-20 and reverse phase C18, and other methods. It was identified as 4,4',5,5'-tetramethyl-[1,1'- diphenyl]-2,2'-diol by NMR and MS data. The production of this compound was enhanced with the increment of cultural time. Transcriptome sequencing analysis showed that the highest upregulated genes under oligotrophic condition were glycosidase, TraR/DksA C4-type zinc finger protein and ribonuclease encoding genes, while the expression of a MarR family transcriptional regulator was most significantly decreased under oligotrophic condition. The results indicate that oligotrophic culture is an effective method for altering the secondary metabolism of Streptomyces.

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Comammox - Complete nitrification by Nitrospira bacteria

Project description:Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.

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