Metagenomics in acid mine lake (AML)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA786738 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metagenomic raw sequence
| PRJNA787318 | ENA
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.
2026-04-06 | PXD064500 | Pride
Project description:amplicon and shotgun metagenomic sequencing of nitrate-dependent Sb(III) oxidizers
| PRJNA640466 | ENA
Project description: Not available
| S-EPMC4438317 | biostudies-literature
Project description:Marine sponges represent one of the few eukaryotic groups that ubiquitously harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of archaeal ammonia oxidizers (AOA). In this study, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and direct isotope-based functional assays. We demonstrate that the I. basta symbiont is not closely related to other genomically sequenced sponge AOA and is a member of a new genus. “Candidatus Nitrosospongia bastadiensis” is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbor nitrite-oxidizing microbes. Consistently, Ca N. bastadiensis encodes and expresses the genetic repertoire required for chemolithoautotrophic ammonia oxidation. Furthermore, we show that this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system likely involved in defense against foreign DNA, represent important adaptations of AOA to life within these ancient filter-feeding animals.
2019-11-13 | PXD012484 | Pride
Project description:soil ammonia oxidizers Raw sequence reads
| PRJNA471130 | ENA
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.
2019-03-15 | PXD013103 | Pride
Project description:Effect of nitrification inhibitors on ammonia oxidizers
| PRJDB13650 | ENA