Complete nitrification: insights into the ecophysiology of comammox Nitrospira

Koch, Hanna; Kessel, Maartje A. H. J. van; Lücker, Sebastian

doi:10.1007/s00253-018-9486-3

Cited by 261 publications

(176 citation statements)

References 105 publications

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“…Ammonia oxidizers have a versatile metabolism and can be heterotrophs 35 . In anoxic environment, comammox Nitrospira can potentially use H2, which provides an advantage in hypoxic and anoxic habitats 36 .…”

Section: Resultsmentioning

confidence: 99%

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Tran

Bachand

McIntyre

et al. 2019

Preprint

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19 Lake Tanganyika, the largest tropical freshwater lake and the second largest by volume 20 on Earth is characterized by strong oxygen and redox gradients. In spite of the majority of its 21 water column being anoxic, Tanganyika hosts some of the most diverse and prolific fisheries and 22 ecosystems on Earth. Yet, little is known about microorganisms inhabiting this lake, and their 23 impacts on biogeochemistry and nutrient cycling underlying ecosystem structure and 24 productivity. Here, we apply depth-discrete metagenomics, single-cell genomics, and 25 environmental analyses to reconstruct and characterize 3996 microbial genomes representing 802 26 non-redundant organisms from 81 bacterial and archaeal phyla, including two novel bacterial 27 candidate phyla, Tanganyikabacteria and Ziwabacteria. We found sharp contrasts in community 28 composition and metabolism between the oxygenated mixed upper layer compared to deep 29 anoxic waters, with core freshwater taxa in the former, and Archaea and uncultured Candidate 30Phyla in the latter. Microbially-driven nitrogen cycling increased in the anoxic zone, highlighting 31 microbial contribution to the productive surface layers, via production of upwelled nutrients, and 32 greenhouse gases such as nitrous oxide. Overall, we provide a window into how oxygen 33 gradients shape microbial community metabolism in widespread anoxic tropical freshwaters, and 34 advocate for the importance of anoxic freshwater habitats in the context of global 35 biogeochemical cycles and nutrient cycling. 36Tran et al.

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Section: Resultsmentioning

confidence: 99%

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Tran

Bachand

McIntyre

et al. 2019

Preprint

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“…Therefore, the identification and quantification of CAOB is of great significance to comprehensive and profound understanding of the nitrogen cycle. As CAOB do not form a monophyletic group within Nitrospira lineage II, they cannot be distinguished from the strict nitrite-oxidizing Nitrospira with 16S rRNA based analysis (Pjevac et al, 2017; Koch et al, 2018). Alternatively, the functional amoA gene formed a distinct group from the canonical AOB amoA , which become the best candidate of the specific molecular marker to identify CAOB in complex ecosystems.…”

Section: Discussionmentioning

confidence: 99%

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Zhao

Huang

Wang

et al. 2018

Preprint

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1were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal 3 2 zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that 3 3 clade A existed in all the five types of ecosystems, while clade B were only detected in soil and 3 4 sediment samples. Four sub-clusters were further classified within clade A, in which N. 3 5 nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized 3 6 soil cluster was the primary constitute in soils. Moreover, the niche specialization between 3 7 different CAOB species and the environmental conditions were supposed to be the primary 3 8 driven force to shape the diversity and community of CAOB. This study provided a strong 3 9 evidence in support of the ubiquities and high abundances of CAOB in various environmental 4 0 ecosystems and highlighted the significance of including CAOB as the new member of AOMs 4 1 to re-evaluate the biogeochemical nitrogen cycle. 4 2 4 3

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“…Other identified Clostridiales' species were also reported to use acrylate pathway to reduce arsenate and thiosulfate concomintantly fermenting organic molecules [121]. The affiliate of Nitrospirales (Nitrospira phylum), were found to reduce sulfate using H2(g) and the reaction were revealed to promote acetate oxidation [122,123]. All these metal reducing reactions were contributing to the reactor stability through providing reducing equivalents in the systems.…”

Section: )mentioning

confidence: 99%

Metagenomics survey unravels diversities of biogas’ microbiomes with potential to enhance its’ productivity in Kenya

Muturi

Muthui

Njogu

et al. 2020

Preprint

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The obstacle to optimal utilization of biogas technology is poor understanding of biogas' microbiome diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversities studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria richness dominated and composed 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, fungi and Archaea composed 5 phyla, the fungi were richer; suggesting importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Synergistales to mention but few, also catabolized macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulated PH2 and reduced metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, conveying largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas' microbiomes over wide environmental conditions and its productivity provides insights into better management and other effective strategies that ameliorate existing biochemical issues.

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Complete nitrification: insights into the ecophysiology of comammox Nitrospira

Cited by 261 publications

References 105 publications

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Metagenomics survey unravels diversities of biogas’ microbiomes with potential to enhance its’ productivity in Kenya

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