Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

Abstract Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.

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Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

Biogeosciences ◽

10.5194/bg-10-7395-2013 ◽

2013 ◽

Vol 10 (11) ◽

pp. 7395-7410 ◽

Cited By ~ 47

Author(s):

A. E. Santoro ◽

C. M. Sakamoto ◽

J. M. Smith ◽

J. N. Plant ◽

A. L. Gehman ◽

...

Keyword(s):

Ammonia Oxidation ◽

Heterotrophic Bacteria ◽

California Current ◽

Euphotic Zone ◽

Ammonia Oxidizing Bacteria ◽

Central California ◽

Oxidation Rates ◽

Ammonia Oxidizing Archaea ◽

Nitrite Production ◽

Nh3 Oxidation

Abstract. Nitrite (NO2−) is a substrate for both oxidative and reductive microbial metabolism. NO2− accumulates at the base of the euphotic zone in oxygenated, stratified open-ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2− production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria and archaea as well as assimilatory nitrate (NO3−) reduction by phytoplankton and heterotrophic bacteria. Measurements of NH3 oxidation and NO3− reduction to NO2− were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2− production in the PNM. Sensitive (< 10 nmol L−1), precise measurements of [NH4+] and [NO2−] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2− producing process, with rates of NH3 oxidation to NO2− of up to 31 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2− production from NO3− was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2− production from NO3− were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2− production agreed with production determined from 15N bottle incubations within the PNM, but a modeled net biological sink for NO2− just below the PNM was not captured in the incubations. Residence time estimates of NO2− within the PNM ranged from 18 to 470 days at the mesotrophic station and was 40 days at the oligotrophic station. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

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Archaea dominate oxic subseafloor communities over multimillion-year time scales

Science Advances ◽

10.1126/sciadv.aaw4108 ◽

2019 ◽

Vol 5 (6) ◽

pp. eaaw4108 ◽

Cited By ~ 24

Author(s):

Aurèle Vuillemin ◽

Scott D. Wankel ◽

Ömer K. Coskun ◽

Tobias Magritsch ◽

Sergio Vargas ◽

...

Keyword(s):

North Atlantic ◽

Organic Nitrogen ◽

Carbon Fixation ◽

Ammonia Oxidation ◽

North Atlantic Ocean ◽

Additional Energy ◽

Ammonia Oxidizing Archaea ◽

The North ◽

Metabolic Feature ◽

The North Atlantic

Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.

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Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

Applied and Environmental Microbiology ◽

10.1128/aem.02577-13 ◽

2013 ◽

Vol 80 (2) ◽

pp. 653-661 ◽

Cited By ~ 22

Author(s):

Trinity L. Hamilton ◽

Evangeline Koonce ◽

Alta Howells ◽

Jeff R. Havig ◽

Talia Jewell ◽

...

Keyword(s):

Nitrogen Fixation ◽

Acetylene Reduction ◽

Ammonia Oxidation ◽

Hot Spring ◽

Transcript Levels ◽

Content Type ◽

Geothermal Springs ◽

Ammonia Oxidizing Archaea ◽

Nitrite Production ◽

N Pool

ABSTRACTSource waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon “CandidatusNitrosocaldus yellowstonii” and the putatively nitrogen-fixing (diazotrophic) bacteriumThermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N2fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increasedamoAtranscript levels while it suppressed rates of acetylene reduction and decreasednifHtranscript levels. Sequencing of amplifiednifHandamoAtranscripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N2fixation are closely affiliated withCa. Nitrosocaldus yellowstonii andT. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such asCa. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable of nitrogen fixation in geothermal communities. These observations help to explain the strong pattern in the codistribution of ammonia-oxidizing archaea and diazotrophs in circumneutral-to-alkaline geothermal springs.

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Heterotrophic Thaumarchaeota with ultrasmall genomes are widespread in the ocean

10.1101/2020.03.17.996280 ◽

2020 ◽

Cited By ~ 2

Author(s):

Frank O. Aylward ◽

Alyson E. Santoro

Keyword(s):

Nutrient Dynamics ◽

Carbon Fixation ◽

Ammonia Oxidation ◽

Critical Role ◽

Deep Ocean ◽

Metagenomic Data ◽

Ancestral State ◽

Chemical Transformations ◽

Ammonia Oxidizing Archaea ◽

Transport Chain

AbstractThe Thaumarchaeota comprise a diverse archaeal phylum including numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically-characterized marine Thaumarchaeota are reported to be chemolithoautotrophic ammonia-oxidizers. In this study, we report a group of heterotrophic marine Thaumarchaeota (HMT) with ultrasmall genome sizes that is globally abundant in deep ocean waters, apparently lacking the ability to oxidize ammonia. We assemble five HMT genomes from metagenomic data derived from both the Atlantic and Pacific Oceans, including two that are >95% complete, and show that they form a deeply-branching lineage sister to the ammonia-oxidizing archaea (AOA). Metagenomic read mapping demonstrates the presence of this group in mesopelagic samples from all major ocean basins, with abundances reaching up to 6% that of AOA. Surprisingly, the predicted sizes of complete HMT genomes are only 837-908 Kbp, and our ancestral state reconstruction indicates this lineage has undergone substantial genome reduction compared to other related archaea. The genomic repertoire of HMT indicates a highly reduced metabolism for aerobic heterotrophy that, although lacking the carbon fixation pathway typical of AOA, includes a divergent form III-a RuBisCO that potentially functions in a nucleotide scavenging pathway. Despite the small genome size of this group, we identify 13 encoded pyrroloquinoline quinone (PQQ)-dependent dehydrogenases that are predicted to shuttle reducing equivalents to the electron transport chain, suggesting these enzymes play an important role in the physiology of this group. Our results suggest that heterotrophic Thaumarchaeota are widespread in the ocean and potentially play key roles in global chemical transformations.ImportanceIt has been known for many years that marine Thaumarchaeota are abundant constituents of dark ocean microbial communities, where their ability to couple ammonia oxidation and carbon fixation plays a critical role in nutrient dynamics. In this study we describe an abundant group of heterotrophic marine Thaumarchaeota (HMT) in the ocean with physiology distinct from their ammonia-oxidizing relatives. HMT lack the ability to oxidize ammonia and fix carbon via the 3-hydroxypropionate/4-hydroxybutyrate pathway, but instead encode a form III-a RuBisCO and diverse PQQ-dependent dehydrogenases that are likely used to generate energy in the dark ocean. Our work expands the scope of known diversity of Thaumarchaeota in the ocean and provides important insight into a widespread marine lineage.

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Aerobic heterotrophy and RuBisCO-mediated CO2 metabolism in marine Thaumarchaeota

10.1101/2019.12.22.886556 ◽

2019 ◽

Cited By ~ 2

Author(s):

Linta Reji ◽

Christopher A. Francis

Keyword(s):

Carbon Fixation ◽

Ammonia Oxidation ◽

Pentose Phosphate ◽

High Quality ◽

Marine Systems ◽

Carbon Cycles ◽

Ammonia Oxidizing Archaea ◽

Phylogenomic Analyses ◽

Co2 Metabolism

AbstractThaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20 % of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Unexpectedly, both genomes encoded a form III RuBisCO. Genomic composition of the MAGs is consistent with the role of RuBisCO in nucleotide salvage, as has been proposed previously for archaea harboring the form III variant. Metabolic reconstructions revealed a complete nonoxidative pentose phosphate pathway (PPP) and gluconeogenesis, which can cyclize the RuBisCO-mediated carbon metabolic pathway. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.

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Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

10.1101/2020.06.24.168906 ◽

2020 ◽

Author(s):

Melina Kerou ◽

Rafael I. Ponce-Toledo ◽

Rui Zhao ◽

Sophie S. Abby ◽

Miho Hirai ◽

...

Keyword(s):

Marine Sediments ◽

Carbon Fixation ◽

Ammonia Oxidation ◽

Sediment Cores ◽

Central Carbon Metabolism ◽

Gene Repair ◽

Fermentation Products ◽

Ammonia Oxidizing Archaea ◽

Ammonia Source ◽

Ocean Ridge

AbstractMarine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored inhabitants, that seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Ca. Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of gene repair systems that may allow to overcome challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy limiting and high-pressure environment.

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Measurements of nitrite production and nitrite-producing organisms in and around the primary nitrite maximum in the central California Current

Biogeosciences Discussions ◽

10.5194/bgd-10-5803-2013 ◽

2013 ◽

Vol 10 (3) ◽

pp. 5803-5840 ◽

Cited By ~ 6

Author(s):

A. E. Santoro ◽

C. M. Sakamoto ◽

J. M. Smith ◽

J. N. Plant ◽

A. L. Gehman ◽

...

Keyword(s):

Ammonia Oxidation ◽

Heterotrophic Bacteria ◽

California Current ◽

Euphotic Zone ◽

Ammonia Oxidizing Bacteria ◽

Central California ◽

Oxidation Rates ◽

Ammonia Oxidizing Archaea ◽

Nitrite Production ◽

Nh3 Oxidation

Abstract. Nitrite (NO2–) is a substrate for both oxidative and reductive microbial metabolism. NO2– accumulates at the base of the euphotic zone in oxygenated, stratified open ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2– production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria or archaea and assimilatory nitrate (NO3–) reduction by phytoplankton or heterotrophic bacteria. Measurements of NH3 oxidation and NO3– reduction to NO2– were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2– production in the PNM. Sensitive (< 10 nmol L−1), high-resolution measurements of [NH4+] and [NO2–] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2– producing process with rates of NH3 oxidation of up to 50 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2– production from NO3– was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2– production from NO3– were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2– profiles supported direct rate measurements of a net biological sink for NO2– just below the PNM. Residence time estimates of NO2– within the PNM were similar at the mesotrophic and oligotrophic stations and ranged from 150–205 d. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

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Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation

10.1101/2021.05.03.442362 ◽

2021 ◽

Author(s):

Spencer Diamond ◽

Adi Lavy ◽

Alexander Crits-Christoph ◽

Paula B. Matheus Carnevali ◽

Allison Sharrar ◽

...

Keyword(s):

Amino Acid ◽

Electron Transport ◽

Carbon Fixation ◽

Ammonia Oxidation ◽

Aerobic Oxidation ◽

Amino Acid Uptake ◽

Acid Uptake ◽

Copper Proteins ◽

Soils And Sediments ◽

Oxidation Of Ammonia

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarcheales. The CuMMO proteins in Ca. Angelarcheales are more similar in structure to those in ammonia-oxidizing archaea than those of bacteria, and they contain all functional residues required for activity. Similarly to the Nitrososphaerales, Ca. Angelarcheales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Angelarcheales do not have identifiable genes for methanol oxidation or carbon fixation, encode significant capacity for peptide/amino acid uptake and degradation, and share numerous electron transport mechanisms with the Nitrososphaerales. In the studied soils and sediments Ca. Angelarcheales were at least as abundant as ammonia-oxidizing Nitrososphaerales. Thus, we predict that Angelarcheales live a mixotrophic lifestyle based on oxidation of ammonia liberated from peptide and amino acid degradation. This work expands the known diversity of Thermoplasmatota and of CuMMO enzymes in archaea and suggests that these organisms are important and previously unaccounted for contributors to nitrogen cycling.

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Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

The ISME Journal ◽

10.1038/s41396-021-00962-6 ◽

2021 ◽

Author(s):

Melina Kerou ◽

Rafael I. Ponce-Toledo ◽

Rui Zhao ◽

Sophie S. Abby ◽

Miho Hirai ◽

...

Keyword(s):

Marine Sediments ◽

Carbon Fixation ◽

Ammonia Oxidation ◽

Sediment Cores ◽

Central Carbon Metabolism ◽

Fermentation Products ◽

Ammonia Oxidizing Archaea ◽

Gene Sets ◽

Ammonia Source ◽

Ocean Ridge

AbstractMarine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.

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Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean

mSystems ◽

10.1128/msystems.00415-20 ◽

2020 ◽

Vol 5 (3) ◽

Cited By ~ 5

Author(s):

Frank O. Aylward ◽

Alyson E. Santoro

Keyword(s):

Nutrient Dynamics ◽

Carbon Fixation ◽

Ammonia Oxidation ◽

Critical Role ◽

Metagenomic Data ◽

Energetic Efficiency ◽

Ancestral State ◽

Chemical Transformations ◽

Ammonia Oxidizing Archaea ◽

Transport Chain

ABSTRACT The Thaumarchaeota is a diverse archaeal phylum comprising numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically characterized marine thaumarchaea are reported to be chemolithoautotrophic ammonia oxidizers. In this study, we report a group of putatively heterotrophic marine thaumarchaea (HMT) with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia. We assembled five HMT genomes from metagenomic data and show that they form a deeply branching sister lineage to the ammonia-oxidizing archaea (AOA). We identify this group in metagenomes from mesopelagic waters in all major ocean basins, with abundances reaching up to 6% of that of AOA. Surprisingly, we predict the HMT have small genomes of ∼1 Mbp, and our ancestral state reconstruction indicates this lineage has undergone substantial genome reduction compared to other related archaea. The genomic repertoire of HMT indicates a versatile metabolism for aerobic chemoorganoheterotrophy that includes a divergent form III-a RuBisCO, a 2M respiratory complex I that has been hypothesized to increase energetic efficiency, and a three-subunit heme-copper oxidase complex IV that is absent from AOA. We also identify 21 pyrroloquinoline quinone (PQQ)-dependent dehydrogenases that are predicted to supply reducing equivalents to the electron transport chain and are among the most highly expressed HMT genes, suggesting these enzymes play an important role in the physiology of this group. Our results suggest that heterotrophic members of the Thaumarchaeota are widespread in the ocean and potentially play key roles in global chemical transformations. IMPORTANCE It has been known for many years that marine Thaumarchaeota are abundant constituents of dark ocean microbial communities, where their ability to couple ammonia oxidation and carbon fixation plays a critical role in nutrient dynamics. In this study, we describe an abundant group of putatively heterotrophic marine Thaumarchaeota (HMT) in the ocean with physiology distinct from those of their ammonia-oxidizing relatives. HMT lack the ability to oxidize ammonia and fix carbon via the 3-hydroxypropionate/4-hydroxybutyrate pathway but instead encode a form III-a RuBisCO and diverse PQQ-dependent dehydrogenases that are likely used to conserve energy in the dark ocean. Our work expands the scope of known diversity of Thaumarchaeota in the ocean and provides important insight into a widespread marine lineage.

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