Origins of Subsurface Microbiology

Origins of Subsurface Microbiology

By William C. Ghiorse,
Department of Microbiology, Cornell University

Humans have long benefited from the activities of subsurface microbes without knowing anything about them. Traditionally, we have ignored, or taken for granted, the many microbe-mediated biogeochemical processes that help to maintain the quality of groundwater in springs and wells. Archaeological evidence shows that early urban settlements like Jericho (8000-7000 B.C.E.) were located near springs used as water supplies. Neolithic groundwater wells from 6500 B.C.E. have been found in the Jezreel Valley in Israel (Ashkenazi, 2012). The ancient Egyptians drank from wells in the Nile River Delta during the time of Rameses II (1279-1213 B.C.E.) (Franzmeier, 2008). Wells dating back thousands of years have been found in China where well water was the first choice for the water supply of most ancient cities (Du and Chen, 2007). The Greeks perfected the use of groundwater-fed springs and fountains to water their communities, and the Romans, with their extended spring water-supplied aqueduct systems and gravity-fed distribution systems, brought public water supplies fed by groundwater sources to the pinnacle of reliability in the ancient world (Mays, 2010).

During the Middle Ages, the Roman-era water supply systems in Europe were modified by religious and royal houses along with city governments to develop the municipal water supply systems vital to the growth of medieval cities. Eventually there was a shift from traditional high-quality groundwater sources to more abundant, but lower-quality surface sources (Magnusson, 2001). In China, the same pattern of increased demand for water occurred as cities grew during and after the Tang dynasty (618-907 C.E.) (Du and Chen, 2007). Traditional groundwater sources were replaced by dams, reservoirs and water distribution systems,and water quality suffered until large-scale water purification methods were devised. Thus, in both Europe and Asia, as human communities became more concentrated in cities, traditional groundwater sources were gradually abandoned in favor of lower quality surface water sources. However, it is important to note that during all of this time the purity of groundwater was never seriously questioned. And this blind attitude toward groundwater purity continued right on through the Renaissence.

We can see from the foregoing summary that since ancient times humans blithely assumed that groundwater sources were inherrently pure. It would take centuries to achieve an understanding of the unseen and unknown subterranean processes that kept them so. Indeed, the aphorism, “out of sight, out of mind”, is an apt description of the human attitude toward these processes throughout history. Understanding these hidden subterranean processes would require the development of the modern disciplines of geology and microbiology, and their ultimate convergence with hydrology late in the 20th century.

Geology and microbiology developed in parallel during the 18th and 19th centuries (For insightful details on this history, see Chapelle, 2000). Microbiology developed later than geology because by definition it is limited to organisms that cannot be seen with the unaided eye. Thus, microbiology could not advance until high-resolution microscopes became available in the middle of the 19th century; but, once this happened, microbiology blossomed. During the last quarter of the 19th century, pioneering microbiologists invented many microscopic and cultivation techniques still in use today. They applied rigorous experimental approaches to address medical, industrial, and agricultural problems during this “Golden Age of Microbiology”. While agricultural microbiologists focused on some biogeochemical processes of interest to geologists, the mainstream of microbiology was oriented toward medical and industrial problems. Geology, an observational science, and microbiology, an experimental science, generally developed along separate paths, albeit with some important overlaps in the realms of biogeochemistry and environmental microbiology (For details, see Chapelle, 2000 and Madsen 2008). These two disciplines ultimately converged in the last half of the 20th century to form the current discipline of geomicrobiology (Ehrlich and Newman, 2009).

The convergence of geology and microbiology was not always smooth. The work of petroleum microbiologists early in the 20th century showed the presence and activity of bacteria in deep subsurface groundwater and sediments associated with petroleum deposits (Davis, 1967). However, most of the medically-oriented microbiologists of the time were either unaware of, or, at best, highly skeptical of this work. The skepticism was based on the fact that much of the microbiological work was done with selective enrichment culture techniques, and, therefore, it was open to criticism based on the lack of contamination controls during drilling and sampling procedures (Ghiorse and Wilson, 1988; Chapelle, 2000). Also, common among geologists of the time, was a degree of skepticism about biological influences on geochemical processes. Henry Ehrlich (2012), describes the nascent field of geomicrobiology during the 1950s and 1960s as a very specialized area of applied microbiology, which was viewed skeptically by individuals who doubted that microbes could contribute significantly to geological and geochemical processes. Thus, during the 1960s, when great advances were made in medical and molecular microbiology, and when the fields of environmental microbiology and microbial ecology were being established, the importance of geomicrobiology was not fully recognized. Subsurface microbiology had not yet emerged as an area of study, except, perhaps, in the minds of Soviet geomicrobiologists and petroleum microbiologists (Kuznetsov, et al, 1963; Davis, 1967; Ehrlich and Newman, 2009).

The widespread neglect of microbial life in the subsurface persisted among mainstream microbiologists outside the former Soviet Union well into the 1970s. A wake-up call came in the early 1970s with the recognition by geohydrologists that many subsurface toxic waste disposal sites across the US threatened to contaminate groundwater supplies. Despite previous work on the microbiology of groundwater in wells, springs, and caves, which are directly connected to the surface and therefore open to colonization from surface microbes, there was very little information on the microbiology of aquifer sediments (McNabb and Dunlap, 1975). Many generations had followed a conventional wisdom that assumed that burial was the best disposal practice for most forms of waste. Innumerable subsurface disposal sites were created in the form of landfills, coal tar waste depositories, chemical waste dumps, etc. It was also naively assumed that the groundwater would be protected by subsurface filtration and natural degradation processes. However, the polluted aquifers affected by buried waste showed that this was not the case. Furthermore, prevailing evidence from the work of soil microbiologists suggested that subsurface zones below the root zones of plants were, at best, very low in microbial abundance (Alexander, 1977), if not sterile. Most alarming was the realization that virtually nothing was known about the microbiology of the unsaturated zones above the water table or the shallow aquifers beneath (McNabb and Dunlap, 1975). Indeed, the ancient gnomic attitude toward these subsurface environments was still in effect. But that was about to change.

The changes came rapidly in the late 1970s and 1980s when microbial ecologists in collaboration with geologists and hydrologists specifically began to address issues of subsurface contamination and groundwater pollution (Ghiorse and Wilson, 1988; Chapelle, 2000). The early work aimed at unequivocally establishing evidence of microbial presence, abundance, and activity in pristine aquifer sediments. This effort depended entirely on obtaining sediment samples not contaminated by surface soil microbes,as well as being able to detect contamination using tracer technology. The former required that subsurface core samples and sub-samples be taken and handled as aseptically as possible to insure that they were not contaminated by ever-present microbes in the drilling fluids used to obtain subsurface core samples. The development of aseptic sampling procedures, use of chemical and biological tracers, and application of advanced microbiological techniques established a firm foundation for subsequent work in subsurface microbiology that followed during the 1990s (Ghiorse and Wobber, 1989; Ghiorse, 1997; Phelps and Fredrickson, 2001).

The initial focus of subsurface microbiology research was on groundwater contamination and the prospect of restoring the water quality of contaminated aquifers. Later, the focus broadened considerably as it was recognized that subsurface microbial activity was much more important in governing groundwater geochemistry than had been assumed in the past (Chapelle, 2000; Lovely and Chapelle, 1995). Microbes are now recognized as the principle agents of diverse biogeochemical processes in a wide range of subsurface habitats, extending into the deepest reaches of Earth’s biosphere and, possibly, in the subsurface habitats of other planets as well (Pedersen 1997; Gold, 1999; Kieft and Moser, 2006; Onstott et al, 2009).

Today, subsurface microbiology has roots in environmental microbiology (Madsen, 2008), geomicrobiology (Ehrlich and Newman, 2009), and ocean science (Colwell and D’Hondt, 2013) with alliances in a variety of other disciplines including environmental engineering, geohydrology, geology, and astrobiology. While groundwater microbiologists continue to study the microbial communities of aquifers and their effects on the fate and transport of pollutants in the subsurface (Gregory et al 2014), other subsurface microbiologists are focused on establishing the extent and diversity of microbial life in remote and extreme subsurface habitats and on the properties of deep subsurface microbial communities that might distinguish them from surface communities (Onstott et al, 2009; Edwards et al, 2012; Colwell and D’Hondt, 2013). In recent years, subsurface microbiology has reached new levels of scientific and societal relevance and awareness (Lueders and Griebler, 2012; ISSM, 2014). Indeed, it is now well established that, although subsurface microbes will always be out of sight, they are no longer out of mind.


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Roman era aqueduct, Spain

Roman era aqueduct for carrying spring water to urban populations, Spain

John Snow's statistical graphic indicating the source of a cholera epidemic to be a conaminated public well

John Snow’s 1854 statistical graphic for finding the source of a London, UK cholera epidemic. The source was a public well on Broad Street, now Broadwick Street, that was contaminated by subsurface tranpsort of Vibrio cholerae, most likely from the nearby Thames River. This was the first use of a modern epidemiological method and was the first documented case of subsurface pathogen transport. Inset on the upper left depicts the present day John Snow pub. Upper right is a portrait of John Snow, mid-nineteenth century physician. Lower left is the plaque commemorating the location of the Broad Street well.

Kuznetsov et al 1962 book cover

Russian scientists contributed substantially to the development of geomicrobiology during the 20th Century, particularly in the areas of subsurface microbiology and petroleum microbiology, as documented in the book entitled Introduction to Geological Microbiology (English translation, McGraw-Hill, New York) by S.I Kuznetsov., M.V. Ivanov, and N.N. Lyalikova, first published in Russian in 1962 and later translated into English in 1963 and Chinese in 1966.  These contributions continue to the present day.  Book cover photos courtesy of T. Nazina, Russian Academy of Sciences.

Early Russian photomicrographs in subsurface microbiology

Cells morphology and thin section of the first pure cultures of methanogens isolated from petroleum reservoirs by S.S. Belyaev, I.A. Davidova-Charackhchian and others (1982-1989). Photomicrographs: courtesy of T. Nazina, Russian Academy of Sciences.

USEPA subsurface microbiology drilling site in Lula, Oklahoma USA

USEPA subsurface microbiology drilling site in Lula, Oklahoma USA. Photo: Robert S. Kerr Environmental Research Center, USEPA, Circa 1982.

Aseptic paring device used to obtain uncontaminated subsamples of aquifer sediments from Lula, Oklahoma for subsequent characterization of the subsurface microbial community. Photo circa 1982.

Aseptic paring device used to obtain uncontaminated subsamples of aquifer sediments from Lula, Oklahoma for subsequent characterization of the subsurface microbial community. Photo US Environmental Protection Agency, circa 1982.

Handling TCE-contaminated aquifer sediment core in a sterile glovebox

TCE-contaminated aquifer sediments from Picatinny Arsenal, New Jersey USA being extruded from a core barrel into a glove box under aseptic conditions. Sediment samples were used for microcosm studies of contaminant biodegradation by the subsurface microbial communities. Photo: USGS Toxics Hydrology Program, circa 1989.

Large-scale MLS array Cape Cod for studying microbial and chemical transport in groundwater

Large-scale (150 m long) array of multilevel samplers for studying transport and interactions of microorganisms and chemicals in a sandy, drinking-water aquifer at the Cape Cod, Massachusetts USA Groundwater Research Site. Photo circa 1985 courtesy of Denis LeBlanc, US Geological Survey.

Dr. Bill Ghiorse sampling in a gold mine

Dr. Bill Ghiorse sampling at 3.2 km below land surface in a stope between levels 46 and 48 in the Driefontein mine, South Africa in 1997.   Photo credit:  Duane Moser,  Desert Research Institute.