Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

Manabu Nishizawa, Keisuke Koba, Akiko Makabe, Naohiro Yoshida, Masanori Kaneko, Shingo Hirao, Jun Ichiro Ishibashi, Toshiro Yamanaka, Takazo Shibuya, Tohru Kikuchi, Miho Hirai, Junichi Miyazaki, Takuro Nunoura, Ken Takai

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72°C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57°C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (σNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2-+NO3-), the total inorganic nitrogen concentration (TIN: the sum of σNH3, NO2- and NO3- concentrations) was nearly constant (250μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (≥38μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of σNH3, NO2- and NO3- of the stream water. The δ15N value of σNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial σNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of σNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of σNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.

Original languageEnglish
Pages (from-to)152-173
Number of pages22
JournalGeochimica et Cosmochimica Acta
Volume113
DOIs
Publication statusPublished - Jul 15 2013

Fingerprint

Nitrification
microbial mat
Ammonium Compounds
Metabolism
nitrification
Nitrogen
ammonium
metabolism
Ammonia
Water
nitrogen
ammonia
Nitrites
nitrite
isotopic fractionation
oxidation
Oxidation
Fractionation
water
porewater

ASJC Scopus subject areas

  • Geochemistry and Petrology

Cite this

Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream. / Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun Ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken.

In: Geochimica et Cosmochimica Acta, Vol. 113, 15.07.2013, p. 152-173.

Research output: Contribution to journalArticle

Nishizawa, M, Koba, K, Makabe, A, Yoshida, N, Kaneko, M, Hirao, S, Ishibashi, JI, Yamanaka, T, Shibuya, T, Kikuchi, T, Hirai, M, Miyazaki, J, Nunoura, T & Takai, K 2013, 'Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream', Geochimica et Cosmochimica Acta, vol. 113, pp. 152-173. https://doi.org/10.1016/j.gca.2013.03.027
Nishizawa, Manabu ; Koba, Keisuke ; Makabe, Akiko ; Yoshida, Naohiro ; Kaneko, Masanori ; Hirao, Shingo ; Ishibashi, Jun Ichiro ; Yamanaka, Toshiro ; Shibuya, Takazo ; Kikuchi, Tohru ; Hirai, Miho ; Miyazaki, Junichi ; Nunoura, Takuro ; Takai, Ken. / Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream. In: Geochimica et Cosmochimica Acta. 2013 ; Vol. 113. pp. 152-173.
@article{fe40cdb650594d60b95f8b699fd6db36,
title = "Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream",
abstract = "We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72°C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57°C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (σNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2-+NO3-), the total inorganic nitrogen concentration (TIN: the sum of σNH3, NO2- and NO3- concentrations) was nearly constant (250μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (≥38μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of σNH3, NO2- and NO3- of the stream water. The δ15N value of σNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial σNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of σNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of σNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.",
author = "Manabu Nishizawa and Keisuke Koba and Akiko Makabe and Naohiro Yoshida and Masanori Kaneko and Shingo Hirao and Ishibashi, {Jun Ichiro} and Toshiro Yamanaka and Takazo Shibuya and Tohru Kikuchi and Miho Hirai and Junichi Miyazaki and Takuro Nunoura and Ken Takai",
year = "2013",
month = "7",
day = "15",
doi = "10.1016/j.gca.2013.03.027",
language = "English",
volume = "113",
pages = "152--173",
journal = "Geochmica et Cosmochimica Acta",
issn = "0016-7037",
publisher = "Elsevier Limited",

}

TY - JOUR

T1 - Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

AU - Nishizawa, Manabu

AU - Koba, Keisuke

AU - Makabe, Akiko

AU - Yoshida, Naohiro

AU - Kaneko, Masanori

AU - Hirao, Shingo

AU - Ishibashi, Jun Ichiro

AU - Yamanaka, Toshiro

AU - Shibuya, Takazo

AU - Kikuchi, Tohru

AU - Hirai, Miho

AU - Miyazaki, Junichi

AU - Nunoura, Takuro

AU - Takai, Ken

PY - 2013/7/15

Y1 - 2013/7/15

N2 - We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72°C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57°C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (σNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2-+NO3-), the total inorganic nitrogen concentration (TIN: the sum of σNH3, NO2- and NO3- concentrations) was nearly constant (250μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (≥38μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of σNH3, NO2- and NO3- of the stream water. The δ15N value of σNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial σNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of σNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of σNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.

AB - We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72°C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57°C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (σNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2-+NO3-), the total inorganic nitrogen concentration (TIN: the sum of σNH3, NO2- and NO3- concentrations) was nearly constant (250μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (≥38μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of σNH3, NO2- and NO3- of the stream water. The δ15N value of σNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial σNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of σNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of σNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.

UR - http://www.scopus.com/inward/record.url?scp=84877031941&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84877031941&partnerID=8YFLogxK

U2 - 10.1016/j.gca.2013.03.027

DO - 10.1016/j.gca.2013.03.027

M3 - Article

VL - 113

SP - 152

EP - 173

JO - Geochmica et Cosmochimica Acta

JF - Geochmica et Cosmochimica Acta

SN - 0016-7037

ER -