Microbial mineralization of organic matter: mechanisms of self-organization and inferred rates of precipitation of diagenetic minerals

Carbonate concretions attract study because, unlike intergranular cements, they form conspicuous spheroidal or laterally extensive bodies. However, they pose a fundamental challenge to uniformitarianism because no concretions identical to geologically preserved ones are forming today. Nevertheless, understanding their origin can be accomplished by simulation of geological processes, using present-day processes and pore-water compositions. The successive reactions (mainly microbial) degrading organic-matter during sediment burial produce inorganic species which may form carbonate and sulphide minerals and can be characterized by stable isotope and chemical compositions. Pyrite-rimmed, spheroidal carbonate carbonate concretions (Jurassic) resulted from outward diffusion of microbially produced sulphide which reacted with inwardly diffusing iron. Extensive, bedded siderite concretions (Coal Measures) were formed by microbial reduction of Fe(III) which could only proceed because the reaction was buffered by precipitation of carbonate produced by methanogens degrading more deeply buried organic matter. Byproducts of the reactions may either inhibit or promote initiation of similar precipitation reactions locally. The former case leads to situations where initial random localization of reaction sites causes self-organized reaction within the sediment (applicable to the Jurassic example). Simulations of the Jurassic concretions’ growth process, using present day pore-water solute concentrations of calcium, sulphide and iron, give results which correspond with the spatial distribution of mineral precipitates observed in geological samples. Calculated rates of mineral precipitation give minimum durations 7400 to 52000 years, much shorter than previous estimates. These results suggest that low rates of microbial sulphate reduction, relative to present day measured values, were needed and accord with the inferred depth of formation and pore-water sulphate concentrations.

Download Full-text

Biogeochemical cycling of nutrients and trace metals in anoxic freshwater sediments of the Neckar River, Germany

Marine and Freshwater Research ◽

10.1071/mf9950237 ◽

1995 ◽

Vol 46 (1) ◽

pp. 237 ◽

Cited By ~ 10

Author(s):

Y Song ◽

G Muller

Keyword(s):

Organic Matter ◽

Trace Metals ◽

Pore Water ◽

Sediment Cores ◽

Sharp Decrease ◽

Metal Sulfides ◽

Pore Waters ◽

Overlying Water ◽

Mineralization Of Organic Matter ◽

Cycling Of Nutrients

Pore-water components (SO42-, Fe2+, Mn2+), including nutrients (NH4+:, NO3-, PO43-), alkalinity and pH were determined at three sites in the Neckar River. Sequential extraction procedures and trace metals in both pore waters and sediments are reported in order to evaluate the mobility of trace metals in contaminated sediments. The results show that the mineralization of organic matter plays an important role in the cycling of nutrients and trace metals. Pore-water profiles (Zn, Cu, Pb, Cd) suggest that the element maximums at the sediment-water interface are caused by the decomposition of biomass. Low concentrations of dissolved Zn, Cu, Pb and Cd in the anoxic sediments can be explained by a sharp decrease of SO42- in pore water concomitant with HS- production. This leads to the formation of highly insoluble metal sulfides. Solubility calculations show that the sediments act as a sink for trace metals with respect to trace metal sulfides. The organic/sulfidic-bound fraction accounts for 64-81% of Cd in the sediment cores, 36-67% of Pb and 51-69% of Cu. In contrast, Cr in pore water increases with depth because of its release from Fe/Mn oxides. NH4+ and PO43- are also released into the pore water owing to the mineralization of organic matter. No significant fluxes of NH4+ and PO43- into overlying water were found because of the existence of an oxic surface layer.

Download Full-text

Labile Organic Matter-Chemical Compositions, Function, and Significance in Soil and the Environment

10.2136/sssaspecpub62 ◽

2015 ◽

Cited By ~ 4

Keyword(s):

Organic Matter ◽

Chemical Compositions ◽

Labile Organic Matter

Download Full-text

Spectral Characterization of Dissolved Organic Matter in Seawater and Sediment Pore Water from the Arctic Fjords (West Svalbard) in Summer

Water ◽

10.3390/w13020202 ◽

2021 ◽

Vol 13 (2) ◽

pp. 202

Author(s):

Meilian Chen ◽

Ji-Hoon Kim ◽

Sungwook Hong ◽

Yun Kyung Lee ◽

Moo Hee Kang ◽

...

Keyword(s):

Organic Matter ◽

Dissolved Organic Matter ◽

Pore Water ◽

Phytoplankton Bloom ◽

Ocean Surface ◽

The Arctic ◽

Sediment Pore Water ◽

Ice Edge ◽

Accumulation Trend ◽

Arctic Fjords

Fjords in the high Arctic, as aquatic critical zones at the interface of land-ocean continuum, are undergoing rapid changes due to glacier retreat and climate warming. Yet, little is known about the biogeochemical processes in the Arctic fjords. We measured the nutrients and the optical properties of dissolved organic matter (DOM) in both seawater and sediment pore water, along with the remote sensing data of the ocean surface, from three West Svalbard fjords. A cross-fjord comparison of fluorescence fingerprints together with downcore trends of salinity, Cl−, and PO43− revealed higher impact of terrestrial inputs (fluorescence index: ~1.2–1.5 in seawaters) and glaciofluvial runoffs (salinity: ~31.4 ± 2.4 psu in pore waters) to the southern fjord of Hornsund as compared to the northern fjords of Isfjorden and Van Mijenfjorden, tallying with heavier annual runoff to the southern fjord of Hornsund. Extremely high levels of protein-like fluorescence (up to ~4.5 RU) were observed at the partially sea ice-covered fjords in summer, in line with near-ubiquity ice-edge blooms observed in the Arctic. The results reflect an ongoing or post-phytoplankton bloom, which is also supported by the higher levels of chlorophyll a fluorescence at the ocean surface, the very high apparent oxygen utilization through the water column, and the nutrient drawdown at the ocean surface. Meanwhile, a characteristic elongated fluorescence fingerprint was observed in the fjords, presumably produced by ice-edge blooms in the Arctic ecosystems. Furthermore, alkalinity and the humic-like peaks showed a general downcore accumulation trend, which implies the production of humic-like DOM via a biological pathway also in the glaciomarine sediments from the Arctic fjords.

Download Full-text

Long-term changes in primary production and mineralization of organic matter in the Neva Estuary (Baltic Sea)

Journal of Marine Systems ◽

10.1016/j.jmarsys.2016.12.009 ◽

2017 ◽

Vol 171 ◽

pp. 73-80 ◽

Cited By ~ 13

Author(s):

Sergey Golubkov ◽

Mikhail Golubkov ◽

Alexei Tiunov ◽

Vera Nikulina

Keyword(s):

Organic Matter ◽

Primary Production ◽

Baltic Sea ◽

Neva Estuary ◽

Long Term Changes ◽

Mineralization Of Organic Matter

Download Full-text

Dissolution and recrystallization in modern shelf carbonates: evidence from pore water and solid phase chemistry

Philosophical Transactions of the Royal Society of London Series A Physical and Engineering Sciences ◽

10.1098/rsta.1993.0072 ◽

1993 ◽

Vol 344 (1670) ◽

pp. 27-36 ◽

Cited By ~ 75

Keyword(s):

Organic Matter ◽

Pore Water ◽

Solid Phase ◽

Chemical Exchange ◽

Isotope Composition ◽

Geochemical Data ◽

Carbonate Sediments ◽

Pore Waters ◽

Carbonate Minerals ◽

Carbonate Production

We present an overview of geochemical data from pore waters and solid phases that clarify earliest diagenetic processes affecting modern, shallow marine carbonate sediments. Acids produced by organic matter decomposition react rapidly with metastable carbonate minerals in pore waters to produce extensive syndepositional dissolution and recrystallization. Stoichiometric relations among pore water solutes suggest that dissolution is related to oxidation of H 2 S which can accumulate in these low-Fe sediments. Sulphide oxidation likely occurs by enhanced diffusion of O 2 mediated by sulphide-oxidizing bacteria which colonize oxic/anoxic interfaces invaginating these intensely bioturbated sediments. Buffering of pore water stable isotopic compositions towards values of bulk sediment and rapid 45 Ca exchange rates during sediment incubations demonstrate that carbonate recrystallization is a significant process. Comparison of average biogenic carbonate production rates with estimated rates of dissolution and recrystallization suggests that over half the gross production is dissolved and/or recrystallized. Thus isotopic and elemental composition of carbonate minerals can experience significant alteration during earliest burial driven by chemical exchange among carbonate minerals and decomposing organic matter. Temporal shifts in palaeo-ocean carbon isotope composition inferred from bulk-rocks may be seriously compromised by facies-dependent differences in dissolution and recrystallization rates.

Download Full-text

Single-particle investigation of summertime and wintertime Antarctic sea spray aerosols using low-Z particle EPMA, Raman microspectrometry, and ATR-FTIR imaging techniques

10.5194/acp-2016-584 ◽

2016 ◽

Author(s):

Hyo-Jin Eom ◽

Dhrubajyoti Gupta ◽

Hye-Rin Cho ◽

HeeJin Hwang ◽

SoonDo Hur ◽

...

Keyword(s):

Chlorophyll A ◽

Single Particle ◽

Imaging Techniques ◽

Sea Spray ◽

Chemical Compositions ◽

Research Station ◽

Ftir Imaging ◽

X Ray ◽

Inorganic Species ◽

Raman Microspectrometry

Abstract. Two aerosol samples collected at King Sejong Korean scientific research station, Antarctica on Dec. 9, 2011 in the austral summer (sample S1) and July 23, 2012 in the austral winter (sample S2), when the oceanic chlorophyll-a levels were quite different, by ~19 times (2.46 vs. 0.13 μg/L, respectively), were investigated on a single particle basis using quantitative energy-dispersive electron probe X-ray microanalysis (ED-EPMA), called low-Z particle EPMA, Raman microspectrometry (RMS), and attenuated total reflectance Fourier transform infrared (ATR-FTIR) imaging techniques to obtain their characteristics based on the elemental chemical compositions, molecular species, and mixing state. X-ray analysis showed that the supermicron summertime and wintertime Antarctic aerosol samples have different elemental chemical compositions, even though all the individual particles analyzed were sea spray aerosols (SSAs); i.e., the contents of C, O, Ca, S, and Si were more elevated, whereas Cl was more depleted, for sample S1 having a much higher chlorophyll-a level than for sample S2. Based on qualitative analysis of the chemical species present in individual SSAs by the combined application of RMS and ATR-FTIR imaging, different organic species were encountered in samples S1 and S2; i.e., Mg hydrate salts of alanine were predominant in samples S1 and S2, whereas Mg salts of fatty acids internally mixed with Mg hydrate salts of alanine were significant in sample S2. Although CaSO4 was encountered significantly in both samples S1 and S2, other inorganic species, such as Na2SO4, NaNO3, Mg(NO3)2, SiO2, and CH3SO3Mg, were encountered more significantly in sample S1, suggesting that those compounds may be related to the higher phytoplankton activity in summer.

Download Full-text

Single-particle investigation of summertime and wintertime Antarctic sea spray aerosols using low-<i>Z</i> particle EPMA, Raman microspectrometry, and ATR-FTIR imaging techniques

Atmospheric Chemistry and Physics ◽

10.5194/acp-16-13823-2016 ◽

2016 ◽

Vol 16 (21) ◽

pp. 13823-13836 ◽

Cited By ~ 18

Author(s):

Hyo-Jin Eom ◽

Dhrubajyoti Gupta ◽

Hye-Rin Cho ◽

Hee Jin Hwang ◽

Soon Do Hur ◽

...

Keyword(s):

Single Particle ◽

Imaging Techniques ◽

Attenuated Total Reflection ◽

Sea Spray ◽

Chemical Compositions ◽

Research Station ◽

Ftir Imaging ◽

X Ray ◽

Inorganic Species ◽

Raman Microspectrometry

Abstract. Two aerosol samples collected at King Sejong Korean scientific research station, Antarctica, on 9 December 2011 in the austral summer (sample S1) and 23 July 2012 in the austral winter (sample S2), when the oceanic chlorophyll a levels on the collection days of the samples were quite different, by ∼  19 times (2.46 vs. 0.13 µg L−1, respectively), were investigated on a single-particle basis using quantitative energy-dispersive electron probe X-ray microanalysis (ED-EPMA), called low-Z particle EPMA, Raman microspectrometry (RMS), and attenuated total reflection Fourier transform infrared (ATR-FTIR) imaging techniques to obtain their characteristics based on the elemental chemical compositions, molecular species, and mixing state. X-ray analysis showed that the supermicron summertime and wintertime Antarctic aerosol samples have different elemental chemical compositions, even though all the individual particles analyzed were sea spray aerosols (SSAs); i.e., the contents of C, O, Ca, S, and Si were more elevated, whereas Cl was more depleted, for sample S1 than for sample S2. Based on qualitative analysis of the chemical species present in individual SSAs by the combined application of RMS and ATR-FTIR imaging, different organic species were observed in samples S1 and S2; i.e., Mg hydrate salts of alanine were predominant in samples S1 and S2, whereas Mg salts of fatty acids internally mixed with Mg hydrate salts of alanine were significant in sample S2. Although CaSO4 was observed significantly in both samples S1 and S2, other inorganic species, such as Na2SO4, NaNO3, Mg(NO3)2, SiO2, and CH3SO3Mg, were observed more significantly in sample S1, suggesting that those compounds may be related to the higher phytoplankton activity in summer.

Download Full-text