A model for microbially induced precipitation of vadose-zone calcites in fractures at Los Alamos, New Mexico, USA

doi:10.1016/S0016-7037(97)00025-2

Geochimica et Cosmochimica Acta

Volume 61, Issue 9, May 1997, Pages 1783-1792

https://doi.org/10.1016/S0016-7037(97)00025-2 Get rights and content

Abstract

Fractures are unique environments that can concentrate the flow of water, nutrients, and contaminants. As such, fractures play an important role in controlling the flux of various substances into and through the vadose zone. Calcite fracture fillings are present in the near surface in the Bandelier Tuff Formation at Los Alamos, New Mexico, and provide a record of the geochemical and hydrologic processes that have occurred in fractures. The objective of this study was to examine calcite fracture fills in order to improve understanding of processes within fractures, and in particular those that lead to precipitation of calcite. Samples of calcite fillings were collected from vertical and horizontal fractures exposed in a shallow waste-burial pit. Scanning electron microscopy show morphologies which suggest that plants, fungi, and bacteria were important in the precipitation process. Quadrupole mass spectrometric analyses of fluid inclusion gases show predominantly methane (17–99%) and little to no oxygen (0–8%), suggesting the development of anaerobic conditions in the fractures. Ester-linked phospholipid biomarkers are evidence for a diverse microbial community in the fractures, and the presence of di-ether lipids indicate that the methane was generated by anaerobic bacteria. The calcite fillings apparently resulted from multiple biological and chemical processes in which plant roots in the fractures were converted to calcite. Roots grew into the fractures, eventually died, and were decomposed by bacteria and fungi. Anaerobic gases were generated from encapsulated organic material within the calcite via microbial decomposition, or were generated by microbes simultaneously with calcite precipitation. It is likely that the biological controls on calcite formation that occurred in the Los Alamos fractures also occurs in soils, and may explain the occurrence of other types of pedogenic calcites.

References (41)

R. Amundson
Factors and processes governing the ¹⁴C content of carbonate in desert soils
Earth Planet. Sci. Lett
(1994)
J.B. Guckert et al.
Phospholipid, ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic Community structure of estuarine sediments
FEMS Micobiol. Ecol.
(1985)
D.B. Hedrick et al.
Archaebacterial ether lipid diversity analyzed by supercritical fluid chromatography: Integration with a bacterial lipid protocol
J. Lipid Res.
(1991)
W.R. Mayberry et al.
Sequential alkaline saponification/acid hydrolysis/esterification: A one tube method with enhanced recovery of both cyclopropane and hydroxylated fatty acids
J. Microb. Method
(1993)
B.D. Newman et al.
Understanding the genesis of nonmarine calcite deposits through quadrupole mass spectrometric analysis of fluid inclusion gases
Chem. Geol.
(1996)
P.D. Nichols et al.
Analysis of archaeal phospholipid-derived di- and tetraether lipids by high temperature capillary gas chromatography
J. Microb. Method.
(1993)
D.I. Norman et al.
Analysis of volatiles in fluid inclusions by mass spectroscopy
Chem. Geol.
(1987)
M.A. Arthur et al.
R.M. Atlas et al.
Microbial Ecology
J.L. Betancourt et al.
Influence of history and climate on New Mexico piñyon-juniper woodlands

D.L. Blackwill et al.

Equivalence of microbial biomass measures based on membrane lipid and cell wall components, adenosine triphosphate, and direct counts in subsurface aquifer sediments

Microb. Ecol.

(1988)

E. Boquet et al.

Production of calcite (calcium carbonate) Crystals by soil bacteria is a general phenomenon

Nature

(1973)

G. Callot et al.

Inter-relations entre aiguilles de calcite et hyphes mycéliens

Agronomie

(1985)

T.E. Cerling et al.

Carbon isotopes in soils and paleosols as ecology and palaeoecology indicators

Nature

(1989)

K. Cromack

The role of oxalic acid and bicarbonate in calcium cycling by fungi and bacteria: Some possible implications for soil animals

Ecol. Bull.

(1977)

D.W. Davenport

Micromorphology, Mineralogy, and Genesis of Soils and Fracture Fills on the Pajarito Plateau, New Mexico

J.W. Deming et al.

The early diagenesis of organic matter: Bacterial activity

J.C. Dixon

Duricrusts

R.L. Folk

SEM imaging of bacteria and nannobacteria in carbonate sediments and rocks

J. Sediment. Petrol.

(1993)

R.C. Forster et al.

Ultrastructure of the Root-Soil Interface

(1983)

Cited by (11)

Radiocarbon dating reveals the timing of formation and development of pedogenic calcium carbonate concretions in Central Sudan during the Holocene
2018, Geochimica et Cosmochimica Acta
Citation Excerpt :
Calcitic nodules formed since the accumulation of microcrystalline calcite; the small size of crystals suggests a relatively fast precipitation of calcite, associated with high rates of evapotranspiration. In this case, the contribution of microbially induced calcite precipitation is assumed to be minimal, as micromorphological features characteristic of biological activity (Newman et al., 1997; Richter et al., 2008) are not observed. The upper Bk horizon is characterized by weak cementation and nodules are formed by microcrystalline calcite precipitated in the porosity between sand- and silt-sized quartz grains.
Calcic soil horizons are common in arid and semi-arid lands and represent the result of the progressive accumulation of calcium carbonate in the soil profile over time. This process leads to the occurrence of several pedogenic phases of calcium carbonate dissolution/precipitation. For this reason, timing the formation and development of calcic horizons through radiometric dating is not straightforward as time-averaging effects, due to the superimposition of the same process over time, occur. On this basis, this study aims to define the timing and dynamics of formation and development of pedogenic calcium carbonate concretions from semi-arid Central Sudan, highlighting the relevance of a multi-disciplinary approach and the effectiveness of radiocarbon dating (coupled to an accurate sampling strategy) applied to pedogenic carbonates. Calcic soil horizons (Bk) were sampled during the archaeological excavation of site 16-D-4 at Al Khiday (Central Sudan) and studied by optical, cathodoluminescence and scanning electron microscopy, as well as by chemical-physical and stable isotopes (C and O) analyses. Micromorphological analyses reveal the occurrence of distinctive calcitic pedofeatures, here described as calcitic-cemented nodules and calcitic-rich matrix. Radiocarbon ages obtained for these pedofeatures mostly refer to the Early Holocene for calcitic-cemented nodules (11.5, 9.9 and 9.6 cal. ka) and to the Middle Holocene for powdery calcitic-rich matrix (7.9, 7.7, 6.3 and 6.1 cal. ka) samples. Additionally, δ¹³C and δ¹⁸O values indicate major shifts of environmental conditions from the Early to the Middle Holocene, in agreement with the available information from detailed palaeoenvironmental studies carried out in the region. In particular, Early Holocene pedogenic calcitic features can be related to short arid phases during general wetter climate conditions, whereas those formed in the Middle Holocene can be related to short humid phases. Results show that Bk horizons were characterized by alternate periods of calcite accumulation (precipitation) and dissolution, and periods of quiescence or extremely slow growth rates. Thus, the formation and development of Bk horizons have been a long-lasting process significantly influenced by climatic fluctuations. This study represents a further step in the comprehension of the development of calcium carbonate concretions and (at a wider perspective) calcrete; the paper also contributes to the definition of a reliable method to radiometrically date the formation of calcic pedofeatures. On a broader perspective, this work may offer a significant tool for archaeometric studies, where the interaction between secondary calcite and archaeological material is significant (e.g., radiocarbon dating of bioapatite in bones), and palaeoenvironmental studies in arid lands, where Bk horizon development is a function of past rainfall.
Effect of source integration on the geochemical fluxes from springs
2013, Applied Geochemistry
Geochemical fluxes from watersheds are typically defined using mass-balance methods that essentially lump all weathering processes operative in a watershed into a single flux of solute mass measured in streamflow at the watershed outlet. However, it is important that we understand how weathering processes in different hydrological zones of a watershed (i.e., surface, unsaturated, and saturated zones) contribute to the total geochemical flux from the watershed. This capability will improve understanding of how geochemical fluxes from these different zones may change in response to climate change. Here, the geochemical flux from weathering processes occurring solely in the saturated zone is investigated. This task, however, remains exceedingly difficult due to the sparsity of subsurface sampling points, especially in large, remote, and/or undeveloped watersheds. In such cases, springflow is often assumed to be a proxy for groundwater (defined as water residing in fully saturated geologic formations). However, springflow generation may integrate different sources of water including, but not limited to, groundwater. The authors’ hypothesis is that long-term estimates of geochemical fluxes from groundwater using springflow proxies will be too large due to the integrative nature of springflow generation. Two conceptual models of springflow generation are tested using endmember mixing analyses (EMMA) on observations of spring chemistries and stable isotopic compositions in a large alpine watershed in the San Juan Mountains of southwestern Colorado. In the “total springflow” conceptual model, springflow is assumed to be 100% groundwater. In the “fractional springflow” conceptual model, springflow is assumed to be an integration of different sources of water (e.g., groundwater, unsaturated flow, preferential flow in the soil, etc.) and groundwater is only a fractional component. The results indicate that groundwater contributions in springflow range from 2% to 100% overall and no springs are consistently composed of 100% groundwater; providing support for the fractional springflow conceptual model. Groundwater contributions are not strongly correlated with elevation, spring contributing area, spring discharge, or seasonality. This variability has a profound effect on long-term geochemical fluxes. The geochemical fluxes for total springflow overestimate long-term solute release by 22–48% as compared to fractional springflow. These findings illustrate that springflow generation, like streamflow generation, integrates many different sources of water reflecting solute concentrations obtained along many different geochemical weathering pathways. These data suggest that springs are not always ideal proxies for groundwater. Springs may be integrating very distinct portions of the groundwater flow field and these groundwater contributions may become mixed at the spring emergence with much younger sources of water that have never resided in the groundwater system.
Bacterially mediated formation of diagenetic aragonite and native sulfur in Zechstein carbonates (Upper Permian, Central Germany)
1999, Sedimentary Geology
Neoformed diagenetic aragonite associated with organic-rich aggregations and native sulfur occur within cavities of the Ca2 and Ca3 Zechstein carbonates in Central Germany. The cavities were formerly filled with gypsum. Bacterial sulfate reduction favored the precipitation of the carbonate phase. This can be attributed to an increase in alkalinity accompanied with sulfate reduction. The high Sr concentrations of the neoformed aragonites compared to the low concentrations in the carbonate host rocks point to sulfate dissolution as the cation supplying process for the precipitation of aragonite. Low δ¹³C values (−10‰ PDB) of the aragonite indicate that some of its carbon is derived from organic matter that has been oxidized by bacterial sulfate reduction. Aragonite inclusions bear rhomb-shaped crystals of calcite, replacing former dolomite. Elevated Mg/Ca ratios due to this dedolomitization may have promoted the precipitation of aragonite instead of calcite. The aragonite precipitated in the near-surface meteoric–vadose zone in recent times. Aragonite crystals display a platy habit. SEM analyses show that two types of micro-rods are associated with these plates. The mineralized micro-rods are interpreted to be fossilized bacteria. Aragonite inclusions, most of which contain organic-rich aggregations, yield a distinctive biomarker pattern. High concentrations of specific unsaturated fatty acids are clearly indicative of newly produced organic matter and reflect the presence of a discrete microbial community being associated with the formation of the aragonite. At one of the studied localities the aragonite is accompanied by native sulfur. The formation of sulfur was mediated by H₂S-oxidizing bacteria. This is corroborated by the presence of densely packed curved rods representing permineralized bacterial cells on and within the sulfur.
Geomicrobiology: Its significance for geology
1998, Earth Science Reviews
Some microorganisms, including various kinds of bacteria, fungi, algae, and protozoa, serve as geochemical agents in the uppermost lithosphere and in the hydrosphere. Some promote rock weathering by mobilizing mineral constituents with inorganic or organic acids or ligands that they excrete. Others promote rock weathering by redox attack of mineral constituents such as Fe and Mn. Still others cause active or passive mineral formation by precipitation and subsequent nucleation of crystal formation on or in the cell, or in the bulk phase. They play a role in some phases of fossil fuel formation and accumulation. They modulate the terrestrial and marine cycles of C, N, S, and P and some other elements, and they influence the composition of the atmosphere in respect to O₂, CO₂, and CH₄. Some discriminate between stable isotopes of H, C, O, N, and S.
Conifers depend on established roots during drought: results from a coupled model of carbon allocation and hydraulics
2020, New Phytologist
Mechanisms of a coniferous woodland persistence under drought and heat
2019, Environmental Research Letters

View all citing articles on Scopus

View full text

ArticleA model for microbially induced precipitation of vadose-zone calcites in fractures at Los Alamos, New Mexico, USA

Abstract

Earth Planet. Sci. Lett

FEMS Micobiol. Ecol.

J. Lipid Res.

J. Microb. Method

Chem. Geol.

J. Microb. Method.

Chem. Geol.

Microbial Ecology

Influence of history and climate on New Mexico piñyon-juniper woodlands

Equivalence of microbial biomass measures based on membrane lipid and cell wall components, adenosine triphosphate, and direct counts in subsurface aquifer sediments

Microb. Ecol.

Production of calcite (calcium carbonate) Crystals by soil bacteria is a general phenomenon

Nature

Inter-relations entre aiguilles de calcite et hyphes mycéliens

Agronomie

Carbon isotopes in soils and paleosols as ecology and palaeoecology indicators

Nature

The role of oxalic acid and bicarbonate in calcium cycling by fungi and bacteria: Some possible implications for soil animals

Ecol. Bull.

Micromorphology, Mineralogy, and Genesis of Soils and Fracture Fills on the Pajarito Plateau, New Mexico

The early diagenesis of organic matter: Bacterial activity

Duricrusts

SEM imaging of bacteria and nannobacteria in carbonate sediments and rocks

J. Sediment. Petrol.

Ultrastructure of the Root-Soil Interface

Article
A model for microbially induced precipitation of vadose-zone calcites in fractures at Los Alamos, New Mexico, USA