D. Northup

Geomicrobiology of Caves: A review.

In this article, we provide a review of geomicrobiological interactions in caves, which are nutrient-limited environments containing a variety of redox interfaces. Interactions of cave microorganisms and mineral environments lead to the dissolution of, or precipitation on, host rock and speleothems (secondary mineral formations). Metabolic processes of sulfur-, iron-, and manganese-oxidizing bacteria can generate considerable acidity, dissolving cave walls and formations. Examples of possible microbially influenced corrosion include corrosion residues (e.g., Lechuguilla and Spider caves, New Mexico, USA), moonmilk from a number of caves (e.g., Spider Cave, New Mexico, and caves in the Italian Alps), and sulfuric acid speleogenesis and cave enlargement (e.g., Movile Cave, Romania, and Cueva de Villa Luz, Mexico). Precipitation processes in caves, as in surface environments, occur through active or passive processes. In caves, microbially induced mineralization is documented in the formation of carbonates, moonmilk, silicates, clays, iron and manganese oxides, sulfur, and saltpeter at scales ranging from the microscopic to landscape biokarst. Suggestions for future research are given to encourage a move from descriptive, qualitative studies to more experimental studies.In this article, we provide a review of geomicrobiological interactions in caves, which are nutrient-limited environments containing a variety of redox interfaces. Interactions of cave microorganisms and mineral environments lead to the dissolution of, or precipitation on, host rock and speleothems (secondary mineral formations). Metabolic processes of sulfur-, iron-, and manganese-oxidizing bacteria can generate considerable acidity, dissolving cave walls and formations. Examples of possible microbially influenced corrosion include corrosion residues (e.g., Lechuguilla and Spider caves, New Mexico, USA), moonmilk from a number of caves (e.g., Spider Cave, New Mexico, and caves in the Italian Alps), and sulfuric acid speleogenesis and cave enlargement (e.g., Movile Cave, Romania, and Cueva de Villa Luz, Mexico). Precipitation processes in caves, as in surface environments, occur through active or passive processes. In caves, microbially induced mineralization is documented in the formation of carbonates, ...

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

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 H 2 S levels in the cave atmosphere reach 210 ppm, and SO 2 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 H 2 S content (300–500 mg/l), mean P CO 2 =0.03–0.1 atm, and no measurable O 2 ; and those with less than 0.1 mg/l H 2 S, mean P CO 2 =0.02 atm, and modest O 2 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 H 2 S 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 (16 S ) 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 H 2 S in the spring waters has not been positively identified. The Villahermosa petroleum basin within 50 km to the northwest, or the El Chichon volcano ~50 km to the west, may serve as source areas for the rising water. Depletion of 34 S values (−11.7‰ for sulphur stabilized from H 2 S in the cave atmosphere), along with the hydrochemistry of the spring waters, favour a basinal source.

Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire.

ABSTRACT This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH3-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.

Geomicrobiology of Cave Ferromanganese Deposits: A Field and Laboratory Investigation

Abstract Unusual ferromanganese deposits are found in several caves in New Mexico. The deposits are enriched in iron and manganese by as much as three orders of magnitude over the bedrock, differing significantly in mineralogy and chemistry from bedrock-derived insoluble residue. The deposits contain metabolically active microbial communities. Enrichment cultures inoculated from the ferromanganese deposits produced manganese oxides that were initially amorphous but developed into crystalline minerals over an 8-month period and beyond; no such progression occurred in killed controls. Phylogenetic analyses of sequences from clone libraries constructed from culture DNA identified two genera known to oxidize manganese, but most clones represent previously unknown manganese oxidizers. We suggest that this community is breaking down the bedrock and accumulating iron and manganese oxides in an oligotrophic environment.

Evidence for Microbial Involvement in Pool Finger Precipitation, Hidden Cave, New Mexico

Although speleothems are usually considered inorganic precipitates, recent work has demonstrated hitherto unsuspected biogenic influence in some twilight areas. We have expanded this notion to the dark zone, examining pool fingers from Hidden Cave, New Mexico, to test for possible bacterial involvement. The pool fingers in Hidden Cave are pendant speleothems that formed subaqueously in paleo-pools. They are 1 to 4 cm in diameter and 5 to 50 cm long. A knobby, irregular external shape is underlaid by a layered interior on two scales, a 0.5 to 1.0 cm alternation between dense and porous layers and a mm-scale alternation between dark micritic calcite and clear dogtooth spar. The micrite is similar to microbialites identified in modern and ancient carbonates. Fossil bacteria were found in all layers. These include (1) calcified filaments 1 w m in diameter and 5–50 w m long and (2) micro-rods 0.1 w m by 1–2 w m. Most filaments are curved rods with a smooth surface but rare examples display a diamond crosshatch surface. The micro-rods occur as isolated crystals to dense meshes. We interpret the micro-rods as calcified bacilliform bacteria and the filaments as calcified filamentous bacteria. Carbon isotopic data are slightly more negative (by - 0.5 to - 1.0% in micritic layers than in dogtooth spar layers, suggesting a greater microbial influence in the micritic layers. Based on these similarities to known microbialites (e.g., petrographic fabrics, the presence of fossil bacteria, and the suggestive carbon isotopic data), we conclude that microbial activity was an intimate part of pool finger formation in Hidden Cave. The significance of such involvement goes beyond speleological contexts to wider questions of identification of biosignatures in rocks on earth and beyond.

Reticulated filaments in cave pool speleothems: microbe or mineral?

We report on a reticulated filament found in modern and fossil cave samples that cannot be correlated to any known microorganism or organism part. These filaments were found in moist environments in five limestone caves (four in New Mexico, U.S.A., one in Tabasco, Mexico), and a basalt lava tube in the Cape Verde Islands. Most of the filaments are fossils revealed by etching into calcitic speleothems but two are on the surface of samples. One hundred eighty individual reticulated filaments were imaged from 16 different samples using scanning electron microscopy. The filaments are up to 75 mm (average 12 mm) long, but all filaments appear broken. These reticulated filaments are elongate, commonly hollow, tubes with an open mesh reminiscent of a fish net or honeycomb. Two different cross-hatched patterns occur; 77% of filaments have hexagonal chambers aligned parallel to the filament and 23% of filaments have diamond-shaped chambers that spiral along the filament. The filaments range from 300 nm to 1000 nm in diameter, but there are two somewhat overlapping populations; one 200–400 nm in size and the other 500–700 nm. Individual chambers range from 40 to 100 nm with 30–40 nm thick walls. Similar morphologies to the cave reticulated filaments do exist in the microbial world, but all can be ruled out due to the absence of silica (diatoms), different size (diatoms, S-layers), or the presence of iron (Leptothrix sp.). Given the wide range of locations that contain reticulated filaments, we speculate that they are a significant cave microorganism albeit with unknown living habits.

A biosignature suite from cave pool precipitates, Cottonwood Cave, New Mexico.

Calcite cave pool precipitates often display a variety of potential biosignatures from the macroscopic to the submicroscopic. A fossil cave pool in Cottonwood Cave, New Mexico, exhibits older stalactites and stalagmites that are completely coated in brown, laminated calcitic crust that extends down as pool fingers and u-loops. The pool fingers and u-loops are mainly micrite to clotted micrite, some recrystallized to microspar, with some isopachous spar layers. Micrite, particularly clotted micrite, is usually interpreted by carbonate workers as microbial in origin. Scanning electron microscopy examination of etched pool fingers, u-loops, and the brown crust revealed abundant calcified microbial filaments and biofilm. Energy dispersive X-ray analysis showed that these features have excess carbon, above that found in pure calcite. Independent carbon analysis indicated that these same samples contain up to 0.2% organic carbon. Since pool fingers hang down but form underwater, we hypothesize they are biogenic with hanging microbial filaments or biofilm acting as nuclei for calcite precipitation. Because of the abundance of micrite and fossil filaments, we further hypothesize that these pendant features formed during a period of plentiful nutrients and active hydrological activity when the pool was literally dripping with microbial slime. Although each of these lines of evidence could be interpreted in other ways, their combined weight strongly suggests the cave pool precipitates in Cottonwood Cave are biogenic. These investigations can be used to help inform extraterrestrial life-detection studies.

Ultraviolet Radiation Sensitivity in Cave Bacteria: Evidence of Adaptation to the Subsurface?

We hypothesize that a reduced capacity to withstand or repair cellular damage from ultraviolet radiation may be present in caveadapted microorganisms that never experience such conditions. However, a small number of previous studies have shown that some subsurface bacteria do not show greater sensitivity to ultraviolet radiation (UVR) than surface bacteria. To estimate UVR sensitivity in cave bacteria, bacterial isolates were collected from Carlsbad Cavern, New Mexico, U.S.A., and percent survival following exposure to various UVC and UVA radiation doses was determined. Cave bacteria from Left Hand Tunnel in Carlsbad Cavern and surface bacteria from soil and rocks above Carlsbad Cavern were grown on low and high nutrient media then exposed to 0, 10,000 and 20,000 μWs/ cm 2 of UVR in a laboratory biological safety cabinet. Incubations were conducted at 15°C or 37oC, in accordance with the isolates’ natural temperature environments. In addition, DNA repair capacity was estimated by exposing the organisms to various doses of UVC radiation and measuring survivability. Gram status and pigmentation also were determined. Results showed that most of the cave isolates were more sensitive to UVR than the surface isolates, but survivability data suggest that cave microbes retain some of their capacity to repair UV-induced DNA damage. Selection appears to have favored bacteria that can survive in this low nutrient environment, while not maintaining (or paying the cost of maintaining) unneeded traits such as UVR resistance. Cave bacteria appear to have maintained DNA repair capacity, most likely because of the need to repair damage to their DNA from other environmental stressors found in caves.

The transport of nonindigenous microorganisms into caves by human visitation: a case study at Carlsbad Caverns National Park

A series of atmospheric investigations was conducted in Carlsbad Cavern to determine if human visitation is a possible cause for the contamination of the cave system with non-indigenous microorganisms. In 2004, site-specific culture-based data demonstrated that Staphylococcus spp. colony-forming units (CFUs) were the most prevalent members of the atmospheric community along the paved visitor trail (avg. 18.8% of CFU), while Knoellia spp. CFUs dominated off-trail locations (40.1% of CFU). Fungal culture data revealed that Penicillium and Aspergillus were prevalent in the Lunch Room where food is stored, sold, and consumed. Ubiquitous genera such as Cladosporium and Alternaria were prevalent near the Natural Entrance of the cave, and the general trend was a decrease in fungal CFUs with progression into the cave system, except for the area near the Lunch Room. Management practices such as prohibition of crumb-generating types of foods could be considered to protect cave health. In 2009, nonculture-based analyses demonstrated that Enterobacteriaceae were the dominant microbiota at sites along the descent trail and within the Lunch Room. Dominance of Enterobacteriaceae has not been previously demonstrated in caves. Either they are naturally occurring indigenous members, or their presence is a marker of anthropogenic contamination.

Anthropogenic lead as a tracer of rock varnish growth: Implications for rates of formation

Rock varnish is a thin dark coating best known from deserts, and is believed to grow extremely slowly. Varnish samples from near Socorro, New Mexico (United States), contain as much as 3.7% PbO, derived from nearby smelters operating from A.D. 1870 to 1931. Additional varnish, measuring as much as 4 μm beyond the Pb-rich layer, indicates continued growth from 1931 to 2003. Comparison with other varnish confirms that the Pb is not an artifact. Based on Pb layer thickness, and the period of smelter operation, these very young rock varnishes yield growth rates of 28–639 μm/k.y., substantially higher than previously documented fastest rates of 40 μm/k.y. These rates imply that the average 1–2 μm/k.y. rate for older varnish is not the active growth rate. Rather, it is a long-term value including periods of nondeposition, erosion, and active growth. Therefore, models of rock varnish formation should be reevaluated with consideration of much faster maximum growth rates.