Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

Pinto, Otávio Henrique Bezerra; Silva, Thais F.; Vizzotto, Carla Simone; Santana, Renata Henrique; Lopes, Fabyano Álvares Cardoso; Silva, Bruno Santana da; Thompson, Fabiano L.

doi:10.1186/s12866-020-1698-x

Cited by 24 publications

(16 citation statements)

References 98 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Consistent with established conceptual geochemical theory, we showed the lower C:N ratios (< 10) of these sediments not only supported mineralization which could be a source of free ammonium in these sediments, but also nitri cation. Supporting this, ammonium was detected in all sediments (average Similarly, others have reported the prominence of nitrifying lineages from the archaeal thaumarcheotal Thermoproteota and bacterial Nitrospirota both by 16S rRNA [59] and genome-resolved metagenomics [12,13] in HZ sediments. Here we nearly doubled the genomic sampling of these river nitri ers, assigning unique gene expression patterns to 3 and 17 genomes from Nitrososphaeraceae and Nitrospiraceae respectively, including the rst genomic sampling of new genera and species (Fig.…”

Section: Microbial Metaproteomics Supports Theoretical Inferences Derived From Geochemistrysupporting

confidence: 60%

“…Metagenomic studies in river sediments have not fully inventoried carbon and nitrogen cycling metabolisms, instead focusing on speci c aspects of the nitrogen cycle (e.g., genes in denitri cation [11]). Moreover, most of these studies were not genome resolved, hindering the assignment of biogeochemical processes to speci c microorganisms, and culture independent genomic reconstructions from river sediments are limited to a handful of studies [12,13], all of which focused exclusively on nitri cation. Thus, little is known about uncultured microbial communities in river sediments, with the enzymes, interconnected chemical reactions, and microbial metabolic lifestyles mediating carbon and nitrogen transformations in river sediments not currently resolvable from existing HZ microbiome datasets.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments

Rodríguez-Ramos¹,

Borton²,

McGivern³

et al. 2021

Preprint

View full text Add to dashboard Cite

Background:Rivers serve as a nexus for nutrient transfer between terrestrial and marine ecosystems and as such, have a significant impact on global carbon and nitrogen cycles. In river ecosystems, the sediments found within the hyporheic zone are microbial hotspots that can account for a significant portion of ecosystem respiration and have profound impacts on system biogeochemistry. Despite this, studies using genome-resolved analyses linking microbial and viral communities to nitrogen and carbon biogeochemistry are limited.Results:Here, we characterized the microbial and viral communities of Columbia River hyporheic zone sediments to reveal the metabolisms that actively cycle carbon and nitrogen. Using genome-resolved metagenomics, we created the Hyporheic Uncultured Microbial and Viral (HUM-V) database, containing a dereplicated database of 55 microbial Metagenome-Assembled Genomes (MAGs), representing 12 distinct phyla. We also sampled 111 viral Metagenome Assembled Genomes (vMAGs) from 26 distinct and novel genera. The HUM-V recruited metaproteomes from these same samples, providing the first inventory of microbial gene expression in hyporheic zone sediments. Combining this data with metabolite data, we generated a conceptual model where heterotrophic and autotrophic metabolisms co-occur to drive an integrated carbon and nitrogen cycle, revealing microbial sources and sinks for carbon dioxide and ammonium in these sediments. We uncovered the metabolic handoffs underpinning these processes including mutualistic nitrification by Thermoproteota (formerly Thaumarchaeota) and Nitrospirota, as well as identified possible cooperative and cheating behavior impacting nitrogen mineralization. Finally, by linking vMAGs to microbial genome hosts, we reveal possible viral controls on microbial nitrification and organic carbon degradation.Conclusions:Our multi-omics analyses provide new mechanistic insight into coupled carbon-nitrogen cycling in the hyporheic zone. This is a key step in developing predictive hydrobiogeochemical models that account for microbial cross-feeding and viral influences over potential and expressed microbial metabolisms. Furthermore, the publicly available HUM-V genome resource can be queried and expanded by researchers working in other ecosystems to assess the transferability of our results to other parts of the globe.

show abstract

Section: Microbial Metaproteomics Supports Theoretical Inferences Derived From Geochemistrysupporting

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments

Rodríguez-Ramos¹,

Borton²,

McGivern³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…The communities are also able to metabolize urea and its products into, NH 3(g) [137,138]. The Nanoarchaeota (S31A Fig) species exploit Crenarchaeota mechanisms [139,140] to metabolize amino acids and complex sugars [141,142] while the Korarchaeotes are sole amino acid fermenters. The energy metabolism in the last two phyla is still unclear and further biochemical studies are needed to unravel their full metabolic activities.…”

Section: The Identified Archaeal Biomesmentioning

confidence: 99%

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya

et al. 2021

View full text Add to dashboard Cite

The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes 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-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate’s versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities’ metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce 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, comprising 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 variables and its’ productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.

show abstract

“…The Nanoarchaeota (SFig. 31a) species exploited Crenarchaeota mechanisms [158,159] to metabolize amino acids and complex sugars [160,161] while the Korarchaeotes were sole amino acid fermenters. The energy metabolism in the two phyla is still unclear and further biochemical studies are needed to unravel their full metabolic activities.…”

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

View full text Add to dashboard Cite

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.

show abstract

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

Cited by 24 publications

References 98 publications

Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments

Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya

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

Contact Info

Product

Resources

About