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

2021 ◽  
Author(s):  
Josué A. Rodríguez-Ramos ◽  
Mikayla A. Borton ◽  
Bridget B. McGivern ◽  
Garrett J. Smith ◽  
Lindsey M. Solden ◽  
...  
Keyword(s):  
Hyporheic Zone ◽  
Ecosystem Respiration ◽  
Microbial Genome ◽  
Sources And Sinks ◽  
Carbon And Nitrogen ◽  
Cheating Behavior ◽  
Viral Communities ◽  
Nitrogen Cycles ◽  
Global Carbon ◽  
Microbial Hotspots

Abstract 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.

scholarly journals Characterization of Planctomyces limnophilus and Development of Genetic Tools for Its Manipulation Establish It as a Model Species for the Phylum Planctomycetes

2011 ◽  
Vol 77 (16) ◽  
pp. 5826-5829 ◽  
Author(s):  
Christian Jogler ◽  
Frank Oliver Glöckner ◽  
Roberto Kolter
Keyword(s):  
Eukaryotic Cells ◽  
Cellular Structures ◽  
Model Species ◽  
Content Type ◽  
Genetic Tools ◽  
Carbon And Nitrogen ◽  
Nitrogen Cycles ◽  
Global Carbon ◽  
The Phylum Planctomycetes

ABSTRACTPlanctomycetesrepresent a remarkable clade in the domainBacteriabecause they play crucial roles in global carbon and nitrogen cycles and display cellular structures that closely parallel those of eukaryotic cells. Studies onPlanctomyceteshave been hampered by the lack of genetic tools, which we developed forPlanctomyces limnophilus.

scholarly journals An integrated modeling approach to global carbon and nitrogen cycles: Balancing their budgets

1997 ◽  
Vol 11 (2) ◽  
pp. 191-215 ◽  
Author(s):  
Michel G. J. den Elzen ◽  
Arthur H. W. Beusen ◽  
Jan Rotmans
Keyword(s):  
Integrated Modeling ◽  
Carbon And Nitrogen ◽  
Modeling Approach ◽  
Nitrogen Cycles ◽  
Global Carbon

scholarly journals High Rates of Ecosytem Metabolism in Five Western Rivers

2011 ◽  
Vol 33 ◽  
pp. 115-118
Author(s):  
Robert Hall ◽  
Jennifer Tank ◽  
Michelle Baker ◽  
Emma Rosi-Marshall ◽  
Michael Grace ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Primary Production ◽  
Carbon Cycling ◽  
Carbon Balance ◽  
Carbon Fixation ◽  
Higher Plants ◽  
Ecosystem Respiration ◽  
Gross Primary Production ◽  
Total Rate ◽  
Global Carbon

Primary production and respiration are core functions of river ecosystems that in part determine the carbon balance. Gross primary production (GPP) is the total rate of carbon fixation by autotrophs such as algae and higher plants and is equivalent to photosynthesis. Ecosystem respiration (ER) measures rate at which organic carbon is mineralized to CO2 by all organisms in an ecosystem. Together these fluxes can indicate the base of the food web to support animal production (Marcarelli et al. 2011), can predict the cycling of other elements (Hall and Tank 2003), and can link ecosystems to global carbon cycling (Cole et al. 2007).

scholarly journals A global carbon and nitrogen isotope perspective on modern and ancient human diet

2021 ◽  
Keyword(s):  
Nitrogen Isotope ◽  
Human Diet ◽  
Carbon And Nitrogen ◽  
Global Carbon

Abstract The authors have requested that this preprint be withdrawn due to erroneous posting.

Global carbon sources and sinks: 2007 update

2009 ◽  
Vol 6 (8) ◽  
pp. 082001 ◽  
Author(s):  
Pep Canadell ◽  
C Lequre ◽  
M Raupach ◽  
P Ciais ◽  
T Conway ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Sources And Sinks ◽  
Global Carbon

scholarly journals Phytoplankton calcifiers control nitrate cycling and the pace of transition in warming icehouse and cooling greenhouse climates

2019 ◽  
Vol 16 (5) ◽  
pp. 1019-1034 ◽  
Author(s):  
Karin F. Kvale ◽  
Katherine E. Turner ◽  
Angela Landolfi ◽  
Katrin J. Meissner
Keyword(s):  
Carbon Cycling ◽  
Net Primary Production ◽  
Global Ocean ◽  
Type Model ◽  
Nitrate Sources ◽  
Surface Temperature Change ◽  
Sources And Sinks ◽  
Greenhouse Climate ◽  
Small Phytoplankton ◽  
Global Carbon

Abstract. Phytoplankton calcifiers contribute to global carbon cycling through their dual formation of calcium carbonate and particulate organic carbon (POC). The carbonate might provide an efficient export pathway for the associated POC to the deep ocean, reducing the particles' exposure to biological degradation in the upper ocean and increasing the particle settling rate. Previous work has suggested ballasting of POC by carbonate might increase in a warming climate, in spite of increasing carbonate dissolution rates, because calcifiers benefit from the widespread nutrient limitation arising from stratification. We compare the biogeochemical responses of three models containing (1) a single mixed phytoplankton class, (2) additional explicit small phytoplankton and calcifiers, and (3) additional explicit small phytoplankton and calcifiers with a prognostic carbonate ballast model, to two rapid changes in atmospheric CO2. The first CO2 scenario represents a rapid (151-year) transition from a stable icehouse climate (283.9 ppm) into a greenhouse climate (1263 ppm); the second represents a symmetric rapid transition from a stable greenhouse climate into an icehouse climate. We identify a slope change in the global net primary production response with a transition point at about 3.5 ∘C global mean sea surface temperature change in all models, driven by a combination of physical and biological changes. We also find that in both warming and cooling scenarios, the application of a prognostic carbonate ballast model moderates changes in carbon export production, suboxic volume, and nitrate sources and sinks, reducing the long-term model response to about one-third that of the calcifier model without ballast. Explicit small phytoplankton and calcifiers, and carbonate ballasting, increase the physical separation of nitrate sources and sinks through a combination of phytoplankton competition and lengthened remineralization profile, resulting in a significantly higher global nitrate inventory in this model compared to the single phytoplankton type model (15 % and 32 % higher for icehouse and greenhouse climates). Higher nitrate inventory alleviates nitrate limitation, increasing phytoplankton sensitivity to changes in physical limitation factors (light and temperature). This larger sensitivity to physical forcing produces stronger shifts in ocean phosphate storage between icehouse and greenhouse climates. The greenhouse climate is found to hold phosphate and nitrate deeper in the ocean, despite a shorter remineralization length scale than the icehouse climate, because of the longer residence times of the deep water masses. We conclude the global biogeochemical impact of calcifiers extends beyond their role in global carbon cycling, and that the ecological composition of the global ocean can affect how ocean biogeochemistry responds to climate forcing.

scholarly journals Crystal structures of γ-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine

2020 ◽  
pp. jbc.RA120.015952
Author(s):  
Ning Wang ◽  
Xiu-Lan Chen ◽  
Chao Gao ◽  
Ming Peng ◽  
Peng Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Trace Gas ◽  
Microbial Genomes ◽  
Carbon And Nitrogen ◽  
Tetrahedral Intermediate ◽  
Surface Ocean ◽  
Biochemical Analyses ◽  
Global Carbon

Monomethylamine (MMA) is an important climate-active oceanic trace gas and ubiquitous in the oceans. The γ-glutamylmethylamide synthetase (GmaS) catalyzes the conversion of MMA to γ-glutamylmethylamide (GMA), the first step in MMA metabolism in many marine bacteria. The gmaS gene occurs in ~23% of microbial genomes in the surface ocean and is a validated biomarker to detect MMA-utilizing bacteria. However, the catalytic mechanism of GmaS has not been studied due to the lack of structural information. Here, the GmaS from Rhodovulum sp. 12E13 (RhGmaS) was characterized, and the crystal structures of apo-RhGmaS and RhGmaS with different ligands in five states were solved. Based on structural and biochemical analyses, the catalytic mechanism of RhGmaS was explained. ATP is first bound in RhGmaS, leading to a conformational change of a flexible loop (Lys287-Ile305), which is essential for the subsequent binding of glutamate. During the catalysis of RhGmaS, the residue Arg312 participates in polarizing the γ-phosphate of ATP and in stabilizing the γ-glutamyl phosphate intermediate; Asp177 is responsible for the deprotonation of MMA, assisting the attack of MMA on γ-glutamyl phosphate to produce a tetrahedral intermediate; and Glu186 acts as a catalytic base to abstract a proton from the tetrahedral intermediate to finally generate GMA. Sequence analysis suggested that the catalytic mechanism of RhGmaS proposed in this study has universal significance in bacteria containing GmaS. Our results provide novel insights into MMA metabolism, contributing to a better understanding of MMA catabolism in global carbon and nitrogen cycles.

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