scholarly journals SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

mBio ◽  
2017 ◽  
Vol 8 (2) ◽  
Author(s):  
Zachary Landry ◽  
Brandon K. Swan ◽  
Gerhard J. Herndl ◽  
Ramunas Stepanauskas ◽  
Stephen J. Giovannoni
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Complex Mixture ◽  
Deep Ocean ◽  
Oxidative Enzymes ◽  
Flavin Mononucleotide ◽  
Biological Oxidation ◽  
Refractory Compounds ◽  
Cyclic Alkanes ◽  
Oxygen Insertion

ABSTRACTDeep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist.IMPORTANCECarbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.

scholarly journals The impact of four decades of annual nitrogen addition on dissolved organic matter in a boreal forest soil

2013 ◽  
Vol 10 (3) ◽  
pp. 1365-1377 ◽  
Author(s):  
M. O. Rappe-George ◽  
A. I. Gärdenäs ◽  
D. B. Kleja
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Soil Solution ◽  
Mineral Soil ◽  
Solution Concentration ◽  
Oxidative Enzymes ◽  
N Saturation ◽  
N Addition ◽  
Mineral N ◽  
The Impact

Abstract. Addition of mineral nitrogen (N) can alter the concentration and quality of dissolved organic matter (DOM) in forest soils. The aim of this study was to assess the effect of long-term mineral N addition on soil solution concentration of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) in Stråsan experimental forest (Norway spruce) in central Sweden. N was added yearly at two levels of intensity and duration: the N1 treatment represented a lower intensity but a longer duration (43 yr) of N addition than the shorter N2 treatment (24 yr). N additions were terminated in the N2 treatment in 1991. The N treatments began in 1967 when the spruce stands were 9 yr old. Soil solution in the forest floor O, and soil mineral B, horizons were sampled during the growing seasons of 1995 and 2009. Tension and non-tension lysimeters were installed in the O horizon (n = 6), and tension lysimeters were installed in the underlying B horizon (n = 4): soil solution was sampled at two-week intervals. Although tree growth and O horizon carbon (C) and N stock increased in treatments N1 and N2, the concentration of DOC in O horizon leachates was similar in both N treatments and control. This suggests an inhibitory direct effect of N addition on O horizon DOC. Elevated DON and nitrate in O horizon leachates in the ongoing N1 treatment indicated a move towards N saturation. In B horizon leachates, the N1 treatment approximately doubled leachate concentrations of DOC and DON. DON returned to control levels, but DOC remained elevated in B horizon leachates in N2 plots nineteen years after termination of N addition. We propose three possible explanations for the increased DOC in mineral soil: (i) the result of decomposition of a larger amount of root litter, either directly producing DOC or (ii) indirectly via priming of old SOM, and/or (iii) a suppression of extracellular oxidative enzymes.

scholarly journals Structural Characterization of Dissolved Organic Matter in Permafrost Peatland Lakes

Water ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3059
Author(s):  
Diogo Folhas ◽  
Armando C. Duarte ◽  
Martin Pilote ◽  
Warwick F. Vincent ◽  
Pedro Freitas ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Complex Mixture ◽  
Resonance Spectroscopy ◽  
Hudson Bay ◽  
Microbial Decomposition ◽  
Thermokarst Lakes ◽  
Geochemical Properties ◽  
High Concentrations ◽  
Analytical Approaches

Thermokarst lakes result from the thawing of ice-rich permafrost and are widespread across northern landscapes. These waters are strong emitters of methane, especially in permafrost peatland regions, where they are stained black by high concentrations of dissolved organic matter (DOM). In the present study, we aimed to structurally characterize the DOM from a set of peatland thermokarst lakes that are known to be intense sites of microbial decomposition and methane emission. Samples were collected at different depths from three thermokarst lakes in the Sasapimakwananisikw (SAS) River valley near the eastern Hudson Bay community of Kuujjuarapik–Whapmagoostui (Nunavik, Canada). Samples were analyzed by spectrofluorometry, Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectroscopy (NMR), and elemental analysis. Fluorescence analyses indicated considerable amounts of autochthonous DOM in the surface waters of one of SAS 1A, indicating a strong bioavailability of labile DOM, and consequently a greater methanogenic potential. The three lakes differed in their chemical composition and diversity, suggesting various DOM transformations phenomena. The usefulness of complementary analytical approaches to characterize the complex mixture of DOM in permafrost peatland waters cannot be overlooked, representing a first step towards greater comprehension of the organic geochemical properties of these permafrost-derived systems.

Efficient export of carbon to the deep ocean through dissolved organic matter

Nature ◽  
2005 ◽  
Vol 433 (7022) ◽  
pp. 142-145 ◽  
Author(s):  
Charles S. Hopkinson ◽  
Joseph J. Vallino
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Deep Ocean

scholarly journals Picocyanobacteria and deep-ocean fluorescent dissolved organic matter share similar optical properties

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Zhao Zhao ◽  
Michael Gonsior ◽  
Jenna Luek ◽  
Stephen Timko ◽  
Hope Ianiri ◽  
...  
Keyword(s):  
Organic Matter ◽  
Optical Properties ◽  
Dissolved Organic Matter ◽  
Deep Ocean ◽  
Fluorescent Dissolved Organic Matter

scholarly journals Deep-ocean dissolved organic matter reactivity along the Mediterranean Sea: does size matter?

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Alba María Martínez-Pérez ◽  
Xosé Antón Álvarez-Salgado ◽  
Javier Arístegui ◽  
Mar Nieto-Cid
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Mediterranean Sea ◽  
Deep Ocean ◽  
The Mediterranean ◽  
Size Matter

scholarly journals Fluorescence analysis allows to predict the oxidative capacity of humic quinones in dissolved organic matter: implication for pollutant degradation

2020 ◽  
Author(s):  
Davide Palma ◽  
Edith Parlanti ◽  
Mahaut Sourzac ◽  
Olivier Voldoire ◽  
Aude Beauger ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Samples ◽  
Three Dimensional ◽  
Complex Mixture ◽  
Fluorescence Analysis ◽  
Oxidative Capacity ◽  
Reactive Species ◽  
Solar Light ◽  
Pollutant Degradation

AbstractDissolved organic matter (DOM) controls the degradation and sequestration of aquatic pollutants and, in turn, water quality. In particular, pollutant degradation is performed by oxidant species that are generated by exposure of DOM to solar light, yet, since DOM is a very complex mixture of poorly known substances, the relationships between potential oxidant precursors in DOM and their oxydative capacity is poorly known. Here, we hypothesized that production of oxidant species could be predicted using fluorescence analysis. We analysed water samples from an alluvial plain by fluorescence spectroscopy; the three-dimensional spectra were then decomposed into seven individual components using a multi-way algorithm. Components include a protein-like fluorophore, e.g. tryptophan-like and tyrosine-like, three humic fluorophores, 2-naphthoxyacetic acid, and a by-product. We compared component levels with the ability of water samples to generate reactive species under solar light. The results show a strong correlation between reactive species production and the intensity of two humic-like fluorophores assigned to reduced quinones. Monitoring these fluorophores should thus allow to predict the ability of DOM degradation of pollutants in surface waters.

scholarly journals Illuminating microbial metabolic activities in the dark deep ocean with metaproteomics

2018 ◽  
Author(s):  
Zhang-Xian Xie ◽  
Shu-Feng Zhang ◽  
Hao Zhang ◽  
Ling-Fen Kong ◽  
Lin Lin ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Dissolved Organic Matter ◽  
Metabolic Activity ◽  
Deep Ocean ◽  
Viral Proteins ◽  
Life Forms ◽  
Cytoplasmic Proteins ◽  
Proteomic Study ◽  
Metabolic Activities

AbstractThe deep ocean is the largest habitat on earth and holds diverse microbial life forms. Significant advances have been made in microbial diversity and their genomic potential in the deep ocean, however, little is known about microbial metabolic activity that is crucial to regulate the bathypelagic carbon sequestration. Here, we characterized proteomes covering large particulate (>0.7 μm), small particulate (0.2-0.7 μm) and dissolved (10 kDa-0.2 μm) fractions collected at a depth of 3000 m in the South China Sea. The Rhodospirillales, SAR324, SAR11, Nitrosinae/Tectomicrobia were the major contributors in the particulate fraction whereas Alteromonadales and viruses dominated the dissolved counterpart. Frequent detection of transcription or translation proteins in the particulate fractions indicated active metabolism of SAR324, Archaea, SAR11, and possible viable surface microbes, e.g. Prochlorococcus. Transporters for diverse substrates were the most abundant functional groups, and numerous spectra of formate dehydrogenases and glycine betaine transporters unveiled the importance of methylated compounds for the survival of deep-sea microbes. Notably, abundant non-viral proteins, especially transporters and cytoplasmic proteins, were detected in the dissolved fraction, indicating their potential roles in nutrient scavenging and the stress response. Our size-based proteomic study implied the holistic microbial activity mostly acting on the labile dissolved organic matter as well as the potential activities of surface microbes and dissolved non-viral proteins in the deep ocean.ImportanceThe deep ocean produces one third of the biological CO2 in the ocean. However, little is known about metabolic activity of the bathypelagic microbial community which is crucial for understanding the biogeochemical cycling of organic matter, especially the formation of bulk refractory dissolved organic matter (DOM), one of the largest reservoirs of reduced carbon on Earth. This study provided the protein evidence firstly including both particulate and dissolved fractions to comprehensively decipher the active microbes and metabolic processes involved in the DOM recycling in the deep ocean. Our data supported the hypothesis of the carbon and energy supply from the labile DOM after the solution of sinking particles to the bathypelagic microbial community.

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