Microbiology and geochemistry in a hydrogen-sulphide-rich karst environment

doi:10.1016/S0009-2541(00)00217-5

Chemical Geology

Volume 169, Issues 3–4, 1 September 2000, Pages 399-423

https://doi.org/10.1016/S0009-2541(00)00217-5 Get rights and content

Abstract

Cueva de Villa Luz, a hypogenic cave in Tabasco, Mexico, offers a remarkable opportunity to observe chemotrophic microbial interactions within a karst environment. The cave water and atmosphere are both rich in hydrogen sulphide. Measured H₂S levels in the cave atmosphere reach 210 ppm, and SO₂ commonly exceeds 35 ppm. These gases, plus oxygen from the cave air, are absorbed by freshwater that accumulates on cave walls from infiltration and condensation. Oxidation of sulphur and hydrogen sulphide forms concentrated sulphuric acid. Drip waters contain mean pH values of 1.4, with minimum values as low as 0.1.

The cave is fed by at least 26 groundwater inlets with a combined flow of 200–300 l/s. Inlet waters fall into two categories: those with high H₂S content (300–500 mg/l), mean P_CO₂=0.03–0.1 atm, and no measurable O₂; and those with less than 0.1 mg/l H₂S, mean P_CO₂=0.02 atm, and modest O₂ content (up to 4.3 mg/l). Both water types have a similar source, as shown by their dissolved solid content. However, the oxygenated water has been exposed to aerated conditions upstream from the inlets so that original H₂S has been largely lost due to outgassing and oxidation to sulphate, increasing the sulphate concentration by about 4%. Chemical modelling of the water shows that it can be produced by the dissolution of common sulphate, carbonate, and chloride minerals.

Redox reactions in the cave appear to be microbially mediated. Sequence analysis of small subunit (16S) ribosomal RNA genes of 19 bacterial clones from microbial colonies associated with water drips revealed that 18 were most similar to three Thiobacilli spp., a genus that often obtains its energy from the oxidation of sulphur compounds. The other clone was most similar to Acidimicrobium ferrooxidans, a moderately thermophilic, mineral-sulphide-oxidizing bacterium. Oxidation of hydrogen sulphide to sulphuric acid, and hence the cave enlargement, is probably enhanced by these bacteria.

Two cave-enlarging processes were identified. (1) Sulphuric acid derived from oxidation of the hydrogen sulphide converts subaerial limestone surfaces to gypsum. The gypsum falls into the cave stream and is dissolved. (2) Strongly acidic droplets form on the gypsum and on microbial filaments, dissolving limestone where they drip onto the cave floors.

The source of the H₂S in the spring waters has not been positively identified. The Villahermosa petroleum basin within 50 km to the northwest, or the El Chichón volcano ~50 km to the west, may serve as source areas for the rising water. Depletion of ³⁴S values (−11.7‰ for sulphur stabilized from H₂S in the cave atmosphere), along with the hydrochemistry of the spring waters, favour a basinal source.

Introduction

Some of the world's most notable caves, including Carlsbad Cavern and Lechuguilla Cave in New Mexico, USA, and Cupp Coutunn Cave system in Turkmenia, formed by rising acidic waters of deep-seated origin (Davis, 1980, Hill, 1987, Maltsev and Malishevsky, 1990, Palmer, 1991). Egemeier (1981) proposed that many such caves develop, at least in part, through a process he called “replacement solution”. He cited several caves in the western United States where H₂S-charged water enters air-filled caves through water-filled conduits, releasing dissolved H₂S into the cave atmosphere. The H₂S gas reacts with O₂, CaCO₃, and H₂O in a variety of reactions that lead to the deposition of elemental sulphur and gypsum on subaerial walls and ceilings. The coatings become so heavy that they cannot support their weight and fall to the floor, where streams rapidly dissolve the gypsum and remove it from the cave. Egemeier, 1969, Egemeier, 1981 noted the possible role of microbes in reducing the sulphate to H₂S in the waters before they enter the cave, but did not suggest microbial participation in oxidation reactions within the cave.

Recognition that some hypogenic caves formed, at least in part, by H₂S rising to the water table has extended to many caves throughout the world Korshunov and Semikolennyh, 1994, Galdenzi and Menichetti, 1995. Several workers have suggested that microorganisms participate in certain redox reactions in hypogenic caves, producing H₂SO₄ and elemental sulphur Spirakis and Cunningham, 1992, Sarbu et al., 1996. Cueva de Villa Luz, in southern Mexico, has recently been identified as a sulphur-rich, hypogenic cave with extremely acidic microenvironments (pH 0.1–3.0) probably attributable, in part, to biogenic oxidation reactions Pisarowicz, 1994, Hose and Pisarowicz, 1999. Acidophilic, and even hyperacidophilic bacteria growing at pH less than 2 have been described from many other habitats, including hot springs and acid mine drainage Dugan et al., 1970, Langworthy, 1978, Harrison, 1984. We suggest a microbial role in the development of acidic environments and cave enlargement in Cueva de Villa Luz.

The results of this study are preliminary, in order to meet the deadline for this special issue. However, comparison with similar field areas lends weight to the conclusions.

Section snippets

Site description

Cueva de Villa Luz is located about 2 km south of the pueblo of Tapijulapa, Municipio de Tacotalpa, Tabasco, Mexico, on the northern edge of the Chiapas Highlands (Fig. 1). A small block of massive, micritic, Lower Cretaceous limestone within a northwest–southeast-trending anticline contains the cave. A normal fault trending west–southwest to east–northeast truncates the limestone block near the spring that serves as the resurgence for the stream (INEGI, 1989). The cave developed parallel to

Cave air chemistry

The cave atmosphere shows striking temporal and spatial variations. Many of the inlets outgas H₂S, causing the nearby cave atmosphere to reach levels as high as 210 ppm. Outgassing pulses are rapid, raising atmospheric H₂S concentrations from <10 to>140 ppm within 3 min. Carbon monoxide (CO) levels as high as 85 ppm and O₂ as low as 9.6% have been recorded with an Enmet Quadrant® Four-Gas Monitor during the similarly brief events (typically about 10 min). A positive cross-interference between H₂

Redox reactions and byproducts

Sulphur-oxidizing reactions dominate in the subaerial environment in the cave. Droplets of freshwater that accumulate on the walls and ceilings by infiltration or condensation from aerosols absorb hydrogen sulphide that outgasses from the cave water. Oxygen, mainly from exchange of air through skylights, is also absorbed by the water. Oxidation of H₂S to sulphuric acid takes place in the droplets, reducing the activities of both dissolved gases and allowing more of them to be absorbed. Because

Microbial mediation of sulphur redox reactions

Microbial activity commonly mediates sulphur redox reactions. Complete oxidation of hydrogen sulphide to sulphuric acid can also be achieved through the mediation of a number of sulphur-oxidizing bacteria in the genus Thiobacillus and others (Ehrlich, 1996, p. 522). One of the most thoroughly studied, Thiobacillus thiooxidans (isolated by Waksman and Jaffe, 1922), is autotrophic, capable of fixing carbon dioxide into biomass without any organic carbon source. It produces metabolically useful

Geochemical modelling of cave streams

To clarify the nature of the two disparate stream types entering the cave, the reaction path routine of the program SI was used to model their chemistry. Aliquots of the minerals calcite, dolomite, gypsum (or anhydrite), and halite were added to water in which the field temperature and P_CO₂ were specified, until the measured concentrations of major ions were achieved. The field measurements and calculations of pH, molarity, and SI are compared to the modelled values in Table 6. Very close

Acknowledgements

The authors wish to thank the people and officials of the pueblo of Tapijulapa and the Municipio de Tacotalpa for their generous support and kindness. Our research has been financially supported by grants from the National Speleological Foundation, Richmond Area Speleological Society, National Geographic Society grant 6541-99, 6634-99, and Westminster College-Fulton, MO. Northern Films Production and PBS-NOVA provided an Enmet Quadrant Four-Gas Monitor. We thank our colleagues, Carleton Allen,

References (55)

T.J. Casadevall et al.
Crater lake and post-eruption hydrothermal activity, El Chichón volcano, Mexico
Journal of Volcanology and Geothermal Research
(1984)
K. Fuseler et al.
A common pathway of sulfide oxidation by sulphate-reducing bacteria
FEMS Microbiology Letters
(1996)
D. Langmuir
The geochemistry of certain groundwaters in central Pennsylvania
Geochimica et Cosmochimica Acta
(1971)
F. Bak et al.
Chemolithotrophic growth of Desulfovibrio sulfodismutans sp. Nov. by disproportionation of inorganic sulfur compounds
Archives of Microbiology
(1987)
S.M. Barns et al.
Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment
Proceedings of the National Academy of Sciences USA
(1994)
E.S. Bastin et al.
The presence of sulphate-reducing bacteria in oilfield waters
Science
(1926)
R.L. Brigmon et al.
Biogeochemical ecology of Thiothrix sp. in underwater limestone caves
Geomicrobiology Journal
(1994)
T.B. Britschgi et al.
Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing
Applied and Environmental Microbiology
(1991)
T.D. Brock et al.
Biology of Microorganisms
(1991)
E. Busenberg et al.
The kinetics of dissolution of dolomite in CO₂–H₂O systems at 1.5 to 65°C and 0 to 1 atm P_CO₂
American Journal of Science
(1982)

D.E. Canfield et al.

The production of 34 S-depleted sulfide during bacterial disproportionation of elemental sulfur

Science

(1994)

D.E. Canfield et al.

Isotope fractionation and sulfur metabolism by pure and enrichment cultures of elemental sulfur-disproportionating bacteria

Limnology and Oceanography

(1998)

A.R. Colmer et al.

The role of microorganisms in acid mine drainage

Science

(1947)

D.G. Davis

Cave development in the Guadalupe Mountains: a critical review of recent hypotheses

NSS Bulletin

(1980)

D.G. Davis et al.

Extraordinary subaqueous speleothems in Lechuguilla Cave, New Mexico

The NSS Bulletin

(1990)

P.R. Dugan et al.

Aerobic heterotrophic bacteria indigenous to pH 2.8 acid mine water: microscopic enumeration of acid streams

Journal of Bacteriology

(1970)

Egemeier, S.J., 1969. Cavern development by thermal waters with a possible bearing on ore deposition. PhD Thesis,...

S.J. Egemeier

Cavern development by thermal waters

NSS Bulletin

(1981)

H.L. Ehrlich

Geomicrobiology

(1996)

K. Finster et al.

Elemental sulfur and thiosulphate disproportionation by Desulfocapsa sulfoexigens sp. Nov., a new anaerobic bacterium isolated from marine surface sediment

Applied Environmental Microbiology

(1998)

K. Fuseler et al.

Elemental sulfur as an intermediate of sulfide oxidation with oxygen by Desulfolobus propionicus

Archives of Microbiology

(1995)

S. Galdenzi et al.

Occurrence of hypogenic caves in a karst region: examples from central Italy

Environmental Geology

(1995)

M.S. Gordon et al.

A cavernicolous form of the Poeciliid fish Poecilia sphenops from Tabasco, Mexico

Copeia

(1962)

D.L. Haldeman et al.

Bacterial heterogeneity in deep subsurface tunnels at Rainier Mesa, Nevada test site

Microbial Ecology

(1993)

D.L. Haldeman et al.

Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4°C

Applied Environmental Microbiology

(1994)

A. Harrison

The acidophilic thiobacilli and other acidophilic bacteria that share their habitat

Hill, C.A., 1987. Geology of Carlsbad Cavern and other caves in the Guadalupe Mountains, New Mexico and Texas. New...

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Microbiology and geochemistry in a hydrogen-sulphide-rich karst environment

Abstract

Introduction

Section snippets

Site description

Cave air chemistry

Redox reactions and byproducts

Microbial mediation of sulphur redox reactions

Geochemical modelling of cave streams

Acknowledgements

Journal of Volcanology and Geothermal Research

FEMS Microbiology Letters

Geochimica et Cosmochimica Acta

Chemolithotrophic growth of Desulfovibrio sulfodismutans sp. Nov. by disproportionation of inorganic sulfur compounds

Archives of Microbiology

Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment

Proceedings of the National Academy of Sciences USA

The presence of sulphate-reducing bacteria in oilfield waters

Science

Biogeochemical ecology of Thiothrix sp. in underwater limestone caves

Geomicrobiology Journal

Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing

Applied and Environmental Microbiology

Biology of Microorganisms

The kinetics of dissolution of dolomite in CO2–H2O systems at 1.5 to 65°C and 0 to 1 atm PCO2

American Journal of Science

The production of 34 S-depleted sulfide during bacterial disproportionation of elemental sulfur

Science

Isotope fractionation and sulfur metabolism by pure and enrichment cultures of elemental sulfur-disproportionating bacteria

Limnology and Oceanography

The role of microorganisms in acid mine drainage

Science

Cave development in the Guadalupe Mountains: a critical review of recent hypotheses

NSS Bulletin

Extraordinary subaqueous speleothems in Lechuguilla Cave, New Mexico

The NSS Bulletin

Aerobic heterotrophic bacteria indigenous to pH 2.8 acid mine water: microscopic enumeration of acid streams

Journal of Bacteriology

Cavern development by thermal waters

NSS Bulletin

Geomicrobiology

Elemental sulfur and thiosulphate disproportionation by Desulfocapsa sulfoexigens sp. Nov., a new anaerobic bacterium isolated from marine surface sediment

Applied Environmental Microbiology

Elemental sulfur as an intermediate of sulfide oxidation with oxygen by Desulfolobus propionicus

Archives of Microbiology

Occurrence of hypogenic caves in a karst region: examples from central Italy

Environmental Geology

A cavernicolous form of the Poeciliid fish Poecilia sphenops from Tabasco, Mexico

Copeia

Bacterial heterogeneity in deep subsurface tunnels at Rainier Mesa, Nevada test site

Microbial Ecology

Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4°C

Applied Environmental Microbiology

The acidophilic thiobacilli and other acidophilic bacteria that share their habitat

The kinetics of dissolution of dolomite in CO₂–H₂O systems at 1.5 to 65°C and 0 to 1 atm P_CO₂