In-depth characterization of denitrifier communities across different soil ecosystems in the tundra

Pessi, Igor Stelmach; Viitamäki, Sirja; Virkkala, Anna‐Maria; Eronen-Rasimus, Eeva; Delmont, Tom O.; Marushchak, Maija E.; Luoto, Miska; Hultman, Jenni

doi:10.1186/s40793-022-00424-2

Cited by 40 publications

(29 citation statements)

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“…Indeed, annotation of protein-coding genes revealed that the two Obscuribacterales MAGs do not appear to encode proteins of the Calvin cycle (Rbc), photosystems I and II (Psa and Psb), cytochrome b6f complex (Pet), or phycobilisomes (Apc, Cpc, Cpe, and Pec) (). Interestingly, the presence of genes for the small and large subunits of nitric oxide reductase (NorC and NorB, respectively) indicates a potential role of this lineage in the production of the greenhouse gas nitrous oxide [37].…”

Section: Resultsmentioning

confidence: 99%

“…3). Interestingly, the presence of genes for the small and large subunits of nitric oxide reductase (NorC and NorB, respectively) indicates a potential role of this lineage in the production of the greenhouse gas nitrous oxide [37].…”

Section: Recovery Of Cyanobacterial Genomes From Metagenomic Datamentioning

confidence: 99%

“…The second co-assembly comprised the remaining samples from the Antarctic Peninsula, Transantarctic Mountains and East Antarctica (n=11). For each individual and co-assembly, we used anvi' o v7.0 [53] to bin contigs ≥2500 bp into metagenome-assembled genomes (MAGs) as previously described [37,38]. In brief, we used Prodigal v2.6.3 [54] to find gene calls, HMMER v.3.3 [55] to identify a set of 71 bacterial and 76 archaeal singlecopy genes [56], and DIAMOND v0.9.14 [57] to assign taxonomy to the single-copy genes according to the Genome Taxonomy Database (GTDB) release 04-RS89 [58].…”

Section: Metagenome Assembling and Binningmentioning

confidence: 99%

“…Twelve other low-quality genomes obtained by a metagenome-like assembly approach of non-axenic strains are also available [35]. Genome-resolved metagenomics has been established in recent years as a powerful approach to obtain microbial genomes, as it circumvents the difficulties associated with culturing microorganisms by reconstructing microbial genomes directly from environmental DNA [36][37][38]. Many genomes of uncultured polar Cyanobacteria have been obtained recently using this approach, including several novel lineages of early branching Cyanobacteria in the order Gloeobacterales [39][40][41].…”

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Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

et al. 2023

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Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena , Leptolyngbya , Microcoleus / Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon ; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis ; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.

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Section: Resultsmentioning

confidence: 99%

Section: Recovery Of Cyanobacterial Genomes From Metagenomic Datamentioning

confidence: 99%

Section: Metagenome Assembling and Binningmentioning

confidence: 99%

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Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

et al. 2023

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“…Siderophilus nitratireducens ”, encoded the genes for iron oxidation (cytochrome c cyc2 ) and the periplasmic nitrate reductase ( nap ), thereby supporting the hypothesis of nitrate-driven iron oxidation being its primary metabolism under the restricted availability of alternative substrates. The absence of other denitrification genes suggests a short catabolic path, which might offer a kinetic advantage in terms of higher iron oxidation rates (21) especially under N limitation (22). “ Ca.…”

Section: Discussionmentioning

confidence: 99%

“CandidatusSiderophilus nitratireducens”: a psychrophilic,nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales

Corbera-Rubio,

Stouten,

Bruins

et al. 2023

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Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-reducing iron-oxidizing (NRFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with NRFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a new Candidate order, named Siderophiliales. This new species, "Candidatus Siderophilus nitratireducens", carries central genes to iron oxidation (cytochrome c cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). To our knowledge, this is the first report of nap-based lithoautotrophic growth, and we demonstrate that iron oxidation coupled to dissimilatory reduction of nitrate to nitrite is thermodynamically favourable under realistic Fe3+/Fe2+ and NO3-/NO2- concentration ratios. Ultimately, by bridging the gap between laboratory investigations and real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NRFOs taxonomic diversity and ecological role.

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Paleometagenomics reveals environmental microbiome response to vegetation changes in northern Siberia over the millennia

et al. 2023

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The study of environmental ancient DNA provides us with the unique opportunity to link environmental with ecosystem change over a millennial timescale. Paleorecords such as lake sediments contain genetic pools of past living organisms that are a valuable source of information to reconstruct how ecosystems were and how they changed in response to climate in the past. Here, we report on paleometagenomics of a sedimentary record in northern Siberia covering the past 6700 years. We integrated taxonomic with functional gene analysis, which enabled to shed light not only on community compositions but also on eco‐physiological adaptations and ecosystem functioning. We reconstructed the presence of an open boreal forest 6700 years ago that over time was gradually replaced by tundra. This vegetation change had major consequences on the environmental microbiome, primarily enriching bacterial and archaeal ammonia oxidizers (e.g., Nitrospira, Nitrosopumilus, and Ca. Nitrosocosmicus) in the tundra ecosystem. We identified a core microbiome conserved through time and largely consisting of heterotrophic bacteria of the Bacteroidetes phylum (e.g., Mucilaginibacter) harboring numerous functional genes for degradation of plant‐biomass and abiotic and biotic stress resistance. Archaea were also a key functional guild, involved in nitrogen and carbon cycling, not only methanogenesis but possibly also degradation of plant material via enzymes such as cellulases and amylases. Overall, the paleo‐perspective offered by our study can have a profound impact on modern climate change biology, by helping to explain and predict the ecological interplay among multiple ecosystem levels based on past experiences.

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In-depth characterization of denitrifier communities across different soil ecosystems in the tundra

Cited by 40 publications

References 100 publications

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

“CandidatusSiderophilus nitratireducens”: a psychrophilic,nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales

Paleometagenomics reveals environmental microbiome response to vegetation changes in northern Siberia over the millennia

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