Cited by 4,871Microbial Community Ecology and PhysiologySoil Carbon and Nitrogen DynamicsMarine Plankton and Biogeochemistry

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Prokaryotes: The unseen majority

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Whitman, William B., Coleman, David C., Wiebe, William J.·1998·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.95.12.6578PMC PMC33863

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Abstract

The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4–6 × 10 30 cells and 350–550 Pg of C (1 Pg = 10 15 g), respectively. Thus, the total amount of prokaryotic carbon is 60–100% of the estimated total carbon in plants, and inclusion of prokaryotic carbon in global models will almost double estimates of the amount of carbon stored in living organisms. In addition, the earth’s prokaryotes contain 85–130 Pg of N and 9–14 Pg of P, or about 10-fold more of these nutrients than do plants, and represent the largest pool of these nutrients in living organisms. Most of the earth’s prokaryotes occur in the open ocean, in soil, and in oceanic and terrestrial subsurfaces, where the numbers of cells are 1.2 × 10 29 , 2.6 × 10 29 , 3.5 × 10 30 , and 0.25–2.5 × 10 30 , respectively. The numbers of heterotrophic prokaryotes in the upper 200 m of the open ocean, the ocean below 200 m, and soil are consistent with average turnover times of 6–25 days, 0.8 yr, and 2.5 yr, respectively. Although subject to a great deal of uncertainty, the estimate for the average turnover time of prokaryotes in the subsurface is on the order of 1–2 × 10 3 yr. The cellular production rate for all prokaryotes on earth is estimated at 1.7 × 10 30 cells/yr and is highest in the open ocean. The large population size and rapid growth of prokaryotes provides an enormous capacity for genetic diversity.

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Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield
Itävaara, M., Nyyssönen, M., Kapanen, A., Nousiainen, A. O., Ahonen, L., & Kukkonen, I. (2011) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2011.01111.x · Cited by 135
Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge
Frossard, A., Hammes, F., & Gessner, M. O. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00903 · Cited by 131
“They recycle an extremely large fraction of organic matter (OM) in most biomes and reach an estimated total of 4–6 × 1030 cells on earth (Whitman et al., 1998).”
Background
Timing the Microbes: The Circadian Rhythm of the Gut Microbiome
Liang, X., & FitzGerald, G. A. (2017) · Journal of Biological Rhythms · doi:10.1177/0748730417729066 · Cited by 132
“Although virtually all surfaces of the human body are colonized by bacteria, the most heavily colonized organ is the gastrointestinal tract, and bacterial density in the colon reaches 1011 to 1012 per mL (Whitman et al., 1998).”
Background
Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria
Ebrahimi, A. N., Schwartzman, J. A., & Cordero, O. X. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1908512116 · Cited by 131
Life within a community: benefit to yeast long-term survival
Palková, Z., & Váchová, L. (2006) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2006.00034.x · Cited by 132
“Ninety-nine percent of these microorganisms that exist in different environments are unknown and cannot be grown on standard media in laboratories (Whitman et al., 1998).”
Background
Taxa–area relationships for microbes: the unsampled and the unseen
Woodcock, S., Curtis, T. P., Head, I. M., et al. (2006) · Ecology Letters · doi:10.1111/j.1461-0248.2006.00929.x · Cited by 131
“millilitre of seawater or a milligram of soil ( Whitman et al. 1998 ).”
Background
Soil bioaugmentation with amphibian cutaneous bacteria protects amphibian hosts from infection by Batrachochytrium dendrobatidis
Muletz‐Wolz, C. R., Myers, J. M., Domangue, R. J., Herrick, J. B., & Harris, R. N. (2012) · Biological Conservation · doi:10.1016/j.biocon.2012.03.022 · Cited by 128
Soil fungal communities of grasslands are environmentally structured at a regional scale in the A lps
Pellissier, L., Niculita‐Hirzel, H., Dubuis, A., et al. (2014) · Molecular Ecology · doi:10.1111/mec.12854 · Cited by 130
“Soil micro-organisms have already been identified as essential players in carbon, nitrogen and phosphorus cycling, and consequently in soil fertility (Whitman et al. 1998; Yang et al. 2014), as well as for the degradation and recycling of organic matter (Johnson et al. 2013).”
Background
Sources of nutrients and energy for a deep biosphere on Mars
Fisk, M., & Giovannoni, S. (1999) · Journal of Geophysical Research Atmospheres · doi:10.1029/1999je900010 · Cited by 139
Detecting Pyrolysis Products from Bacteria on Mars
Glavin, D., Schubert, M., Botta, O., Kminek, G., & Bada, J. (2001) · Earth and Planetary Science Letters · doi:10.1016/s0012-821x(00)00370-8 · Cited by 102
“coli [15], the total number of prokaryotic cells that could have been present on the surface of Mars is even larger.”
Background
How the Motility Pattern of Bacteria Affects Their Dispersal and Chemotaxis
Taktikos, J., Stark, H., & Zaburdaev, V. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081936 · Cited by 129
“Bacteria constitute a major part of the biomass on our planet [1].”
Background
Microbial Communities of Deep Marine Subsurface Sediments: Molecular and Cultivation Surveys
Teske, A. (2006) · Geomicrobiology Journal · doi:10.1080/01490450600875613 · Cited by 129
“edu estimated to constitute (1)/2 to (5)/6 of Earth’s prokaryotic biomass (Whitman et al. 1998) and (1)/10 to (1)/3 of Earth’s living biomass (Parkes et al.”
Background
Microscale ecology regulates particulate organic matter turnover in model marine microbial communities
Enke, T. N., Leventhal, G. E., Metzger, M., Saavedra, J. T., & Cordero, O. X. (2018) · Nature Communications · doi:10.1038/s41467-018-05159-8 · Cited by 130
Gut Microbiome in Obesity, Metabolic Syndrome, and Diabetes
Chen, X., & Devaraj, S. (2018) · Current Diabetes Reports · doi:10.1007/s11892-018-1104-3 · Cited by 132
A Global Census of Marine Microbes
Amaral‐Zettler, L., Artigas, L. F., Baross, J. A., Loka Bharathi, P. A., Boëtius, A., Chandramohan, D., Herndl, G. J., Kogure, K., Neal, P. R., Pedrós‐Alió, C., et al. (2010) · Wiley eBooks · doi:10.1002/9781444325508.ch12 · Cited by 131
Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA
Osburn, M. R., LaRowe, D. E., Momper, L., & Amend, J. P. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00610 · Cited by 128
“Notably, this estimate is larger than or on par with those from marine sediments (1.5–22 Pg C, Kallmeyer et al., 2012), terrestrial soil (26 Pg C, Whitman et al., 1998), or aquatic environments (2.2 Pg C, Whitman et al., 1998); however, the range is very large.”
BackgroundResultInfluential
Cold adaptation in the marine bacterium, Sphingopyxis alaskensis , assessed using quantitative proteomics
Ting, L., Williams, T. J., Cowley, M. J., Lauro, F. M., Guilhaus, M., Raftery, M. J., & Cavicchioli, R. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02235.x · Cited by 128
“Despite the predominant low temperatures, the ocean supports the growth of an estimated 60–90% of all of Earth’s microorganisms (Whitman et al., 1998).”
Background
Bacterial Transcription as a Target for Antibacterial Drug Development
Ma, C., Yang, X., & Lewis, P. J. (2016) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00055-15 · Cited by 130
“Numbered circles: streptolol (1) and monosaccharide (2) moieties of streptolydigin, squarate ring (3), benzylamine ring (4) and piperidine (5) groups of squaramides, and steroid-like carboxylic acid (6) and indolone (7) groups of DSHS0057.”
Background
Ecological drivers of bacterial community assembly in synthetic phycospheres
Fu, H., Uchimiya, M., Gore, J., & Moran, M. A. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1917265117 · Cited by 121
Stabilization of extracellular polymeric substances (Bacillus subtilis) by adsorption to and coprecipitation with Al forms
Mikutta, R., Zang, U., Chorover, J., Haumaier, L., & Kalbitz, K. (2011) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2011.03.006 · Cited by 128
A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates
Sfanos, K. S., Harmody, D. K., Dang, P. M., Ledger, A., Pomponi, S. A., McCarthy, P. J., & Lopez, J. V. (2005) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2004.12.002 · Cited by 127
“the ocean below 1000m) [66].”
Microbial cultivation and the role of microbial resource centers in the omics era
Prakash, O., Shouche, Y. S., Jangid, K., & Kostka, J. E. (2012) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-012-4533-y · Cited by 128
“Though a vast amount of microbial diversity has been revealed since the advent of omics-based approaches, a huge knowledge gap remains between assessment of genomic potential and the assignment of function to genes or proteins (Wiebe 1998; Zengler et al. 2002; Giovannoni and Stingl 2007; Cardenas and Tiedje 2008).”
Background
Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs
Mayumi, D., Dolfing, J., Sakata, S., Maeda, H., Miyagawa, Y., Ikarashi, M., Tamaki, H., Takeuchi, M., Nakatsu, C. H., & Kamagata, Y. (2013) · Nature Communications · doi:10.1038/ncomms2998 · Cited by 127
Metagenomics and novel gene discovery
Culligan, E. P., Sleator, R. D., Marchesi, J. R., & Hill, C. (2013) · Virulence · doi:10.4161/viru.27208 · Cited by 138
“It has been estimated that there are more than 10(30) microbial cells on Earth; 9 orders of magnitude greater than the number of known stars in the universe.(3,4) It is estimated that over 99% of microbes in many environments are, as yet, uncultured,(5) while cultured prokaryotic representatives are overwhelmingly fro…”
Background
Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing
Daly, R. A., Roux, S., Borton, M., Morgan, D. M., Johnston, M., Booker, A. E., Hoyt, D. W., Meulia, T., Wolfe, R. A., Hanson, A. J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0312-6 · Cited by 128
Bacteria and algae in stream periphyton along a nutrient gradient
Carr, G. M., Morin, A., & Chambers, P. A. (2005) · Freshwater Biology · doi:10.1111/j.1365-2427.2005.01401.x · Cited by 127
Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species
Handley, K. M., & Lloyd, J. R. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00136 · Cited by 126
“MINI REVIEW ARTICLE published: 22 May 2013 doi: 10.3389/fmicb.2013.00136 Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species”
BackgroundInfluential
Chapter 5 Emergence of the Th17 Pathway and Its Role in Host Defense
O’Quinn, D. B., Palmer, M. T., Lee, Y. K., & Weaver, C. T. (2008) · Advances in immunology · doi:10.1016/s0065-2776(08)00605-6 · Cited by 130
Propionibacterium acnes in shoulder surgery: true infection, contamination, or commensal of the deep tissue?
Hudek, R., Sommer, F. O., Kerwat, M., et al. (2014) · Journal of Shoulder and Elbow Surgery · doi:10.1016/j.jse.2014.05.024 · Cited by 126
“These bacteria-infecting viruses are common in nature and outnumber bacteria (10:1).(48,53) Phages could be found as prophages inserted into bacterial genomes.”
Background
Habitat structure and the evolution of diffusible siderophores in bacteria
Kümmerli, R., Schiessl, K. T., Waldvogel, T. E. E., McNeill, K., & Ackermann, M. (2014) · Ecology Letters · doi:10.1111/ele.12371 · Cited by 124
“For nc, we took three values, 10 , 10 and 10 cells mL 1 to cover the range of bacterial densities typically observed in nature (Whitman et al. 1998).”
Background
Breast and gut microbiome in health and cancer
Zhang, J., Xia, Y., & Sun, J. (2020) · Genes & Diseases · doi:10.1016/j.gendis.2020.08.002 · Cited by 130
The Alkaline Solution to the Emergence of Life: Energy, Entropy and Early Evolution
Russell, M. J. (2007) · Acta Biotheoretica · doi:10.1007/s10441-007-9018-5 · Cited by 126
“Concentrations are greater in ocean bottom sediments where methanogens and acetogens still make up a large proportion of the Earth’s biomass (Whitman et al. 1998) as they are in acid mine drainage (Baker and Banfield 2003).”
Background
Geodynamic and metabolic cycles in the Hadean
Russell, M. J., & Arndt, N. (2005) · Biogeosciences · doi:10.5194/bg-2-97-2005 · Cited by 128
“Thus the deep biosphere was born (Parkes et al., 1990, 1994; Pedersen, 1993; Thorseth et al., 1995; Wellsbury et al., 1997; Whitman et al., 1998; Kotelnikova and Pedersen, 1997; Furnes et al., 2004).”
Background
Abiogenic Origin of Hydrocarbons: An Historical Overview
Glasby, G. P. (2006) · Resource Geology · doi:10.1111/j.1751-3928.2006.tb00271.x · Cited by 126
“In Gold's defence, it should be stated that his 1992 paper was published prior to Fyfe's (1996) landmark paper on the deep biosphere and that this conclusion is supported by recent estimates of the subsurface biomass of prokaryotic bacteria of 3-5 × 1017 g of C which is equivalent to 60 to 100 % of the carbon present…”
Background
The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes
Aydin, Ö., Nieuwdorp, M., & Gerdes, V. (2018) · Current Diabetes Reports · doi:10.1007/s11892-018-1020-6 · Cited by 124
Parent material and vegetation influence bacterial community structure and nitrogen functional genes along deep tropical soil profiles at the Luquillo Critical Zone Observatory
Stone, M. M., Kan, J., & Plante, A. F. (2014) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2014.10.019 · Cited by 125
Evaluation of the ISO Standard 11063 DNA Extraction Procedure for Assessing Soil Microbial Abundance and Community Structure
Plassart, P., Terrat, S., Thomson, B., Griffiths, R., Dequiedt, S., Lelièvre, M., Régnier, T., Nowak, V., Bailey, M., Lemanceau, P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044279 · Cited by 125
“Microorganisms (particularly bacteria, archaea and fungi) comprise a significant portion of this huge biodiversity [3,4].”
Background
Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913
Qin, Q., Li, Y., Zhang, Y., Zhou, Z., Zhang, W., Chen, X., Zhang, X., Zhou, B., Wang, L., & Zhang, Y. (2010) · The ISME Journal · doi:10.1038/ismej.2010.103 · Cited by 129
“Deep-sea sediment is a dynamic geo- and biosphere that hosts rich microbial communities (”
Background
Exoplanet Biosignatures: Future Directions
Walker, S. I., Bains, W., Cronin, L., DasSarma, S., Danielache, S. O., Domagal-Goldman, S. D., Kaçar, B., Kiang, N. Y.-L., Lenardic, A., Reinhard, C. T., et al. (2018) · Astrobiology · doi:10.1089/ast.2017.1738 · Cited by 137
“Because Earth life has been exclusively microbial for the majority of Earth’s history, it is possible that primitive unicellular lifeforms are the most common and longest lasting stage of life on a planet (Whitman et al., 1998).”
Background
Microbial life on a sand grain: from bulk sediment to single grains
Probandt, D., Eickhorst, T., Ellrott, A., Amann, R., & Knittel, K. (2017) · The ISME Journal · doi:10.1038/ismej.2017.197 · Cited by 129
“The top 10 cm of marine sediments constitute a habitat for estimated 1.7 × 1028 Bacteria and Archaea (Whitman et al., 1998).”
BackgroundInfluential
Salinity Constraints on Subsurface Archaeal Diversity and Methanogenesis in Sedimentary Rock Rich in Organic Matter
Waldron, P. J., Petsch, S. T., Martini, A. M., & Nüsslein, K. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02810-06 · Cited by 131
“Subsurface sedimentary environments contain an estimated 1/10 to 1/3 of all living biomass on Earth, and the activity of subsurface microorganisms plays an important role in biogeochemical cycling of elements and the global carbon cycle (38, 51, 57).”
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis
Weinberg, Z., Perreault, J., Meyer, M. M., & Breaker, R. R. (2009) · Nature · doi:10.1038/nature08586 · Cited by 126
Ultra-diffuse hydrothermal venting supports Fe-oxidizing bacteria and massive umber deposition at 5000 m off Hawaii
Edwards, K. J., Glazer, B. T., Rouxel, O. J., Bach, W., Emerson, D., Davis, R. E., Toner, B. M., Chan, C. S., Tebo, B. M., Staudigel, H., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.48 · Cited by 123
“Assuming that aerobic autotrophs require 292 kJ to fix 1 g of biomass (Heijnen and Van Dijken, 1992) and that one cell weighs 10 13 g (Whitman et al., 1998), this energy flux could support growth of 8 108 cells cm 2 a 1 and maintain a much greater population.”
High-Pressure Biochemistry and Biophysics
Meersman, F., Daniel, I., Bartlett, D. H., Winter, R., Hazael, R., & McMillan, P. F. (2013) · Reviews in Mineralogy and Geochemistry · doi:10.2138/rmg.2013.75.19 · Cited by 130
“Considering the very large extent of the high-pressure biotopes identified to date, the deep biosphere could therefore represent a largely “unseen majority” of life on Earth, perhaps constituting up to 30% of the total living biomass, or even more (Whitman et al. 1998; Parkes et al. 2000).”
Background
The potential of probiotics in the amelioration of hyperuricemia
Zhao, H., Lu, Z., & Lu, Y. (2022) · Food & Function · doi:10.1039/d1fo03206b · Cited by 128
Earthworm invasions of ecosystems devoid of earthworms: effects on soil microbes
McLean, M. A., Migge, S., & Parkinson, D. (2006) · Biological Invasions · doi:10.1007/s10530-006-9020-x · Cited by 124
“It is estimated that half of Earth’s biomass is microbial (Whitman et al. 1998).”
Background
Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica
Tebo, B. M., Davis, R. E., Anitori, R. P., Connell, L. B., Schiffman, P. S., & Staudigel, H. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00179 · Cited by 125

Authors: Whitman, W. B., Coleman, D. C., & Wiebe, W. J.
Affiliations: University of Georgia (US)
ORCID: Whitman, William B.
Coleman, David C.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 1998-06-09
Volume: 95
Issue: 12
Pages: 6578-6583
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.95.12.6578
PMC: PMC33863
OpenAlex: W2118001436
Semantic Scholar: 321e4c5e6031364c39db3cfdb151dcc2deaac1ba
Cited by: 4,871
References: 92
Citations by year: 2026: 86 · 2025: 134 · 2024: 159 · 2023: 220 · 2022: 190 · 2021: 252 · 2020: 223 · 2019: 238 · 2018: 273 · 2017: 251 · 2016: 281 · 2015: 282 · 2014: 311 · 2013: 252 · 2012: 238
FWCI: 6.26
Type: journal article
Language: en
Open access: green
europepmc.org
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
Physical Sciences › Earth and Planetary Sciences › Oceanography › Marine Plankton and Biogeochemistry
Keywords: prokaryotes, nitrogen, phosphorus, open ocean, soil, subsurface environments, genetic diversity
MeSH terms: Prokaryotic Cells

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Prokaryotes: The unseen majority

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