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Home / Preservation & Taphonomy / Bacterial Biofilms (Microbial Mats)

Taphonomy in General
Plant Fossil Preservation and Plant Taphonomy
Collecting Bias: Our Incomplete Picture of the Past Vegetation
Three-Dimensionally Preserved Plant Compression Fossils
Pith Cast and "in situ" Preservation
Permineralized Plants and the Process of Permineralization
Petrified Forests
Molecular Palaeobotany
Pyrite Preservation
Upland and Hinterland Floras
Abscission and Tissue Separation in Fossil and Extant Plants
Leaf Litter and Plant Debris
Log Jams and Driftwood Accumulations
Wound Response in Trees
Fungal Wood Decay: Evidence from the Fossil Record

! Cyanobacteria and Stromatolites@
Teaching Documents about Plant Anatomy@
Plant Anatomy@
! Chemotaxonomy and Chemometric Palaeobotany@
Introductions to both Fossil and Recent Plant Taxa@

Bacterial Biofilms (Microbial Mats)

American Society for Microbiology: A Manual of Biofilm related exercises. An online collection of exercises which can be conducted to illustrate the formation and properties of microbial biofilms.

! Microbial Mat Research at Ames Research Center: What are Microbial Mats?
Snapshot provided by the Internet Archive´s Wayback Machine.

Loren E. Babcock et al. (2006): Starting on PDF page 4: The "Preservation Paradox": Microbes as a Key to Exceptional Fossil Preservation in the Kirkpatrick Basalt (Jurassic), Antarctica. PDF file, The Sedimentary Record, 4. See also here.
Silica-rich hydrothermal water apparently worked to fossilize organic remains rapidly and produce a "freeze-frame" of macroscopic and microscopic life forms. Microbes seem to have played a vital role in this processes.

B. Becker-Kerber et al. (2021): The role of volcanic-derived clays in the preservation of Ediacaran biota from the Itajaí Basin (ca. 563 Ma, Brazil). Open access, Scientific Reports, 11.
Note figure 4: Schematic representation of the fossilization pathway.

! P.S. Borkow and L.E. Babcock (2003): Turning Pyrite Concretions Outside-In: Role of Biofilms in Pyritization of Fossils. PDF file, The Sedimentary Record, 1.

Center for Biofilm Engineering, Montana State University, Bozeman MT: What is biofilm?
This expired link is available through the Internet Archive´s Wayback Machine.

! Alfred B. Cunningham, John E. Lennox, and Rockford J. Ross (eds.): Biofilms: The Hypertextbook. Under construction.

S.A.F. Darroch et al. (2012): Experimental formation of a microbial death mask. In PDF, Palaios, 27: 293-303. See also here (abstract).

A.W. Decho (2000): Microbial biofilms in intertidal systems: an overview. In PDF, Continental Shelf Research, 20: 1257-1273.
Now provided by the Internet Archive´s Wayback Machine.

C. Diéguez et al. (2009): A fern-bennettitalean floral assemblage in Tithonian-Berriasian travertine deposits (Aguilar Formation, Burgos-Palencia, N Spain) and its palaeoclimatic and vegetational implications. In PDF, Journal of Iberian Geology, 35: 127-140.
Specimens preserved as impressions coated with a microbial film up to 5 mm thick made up of bacteria and cyanobacteria.
See also here.

X. Duan et al. (2018): Early Triassic Griesbachian microbial mounds in the Upper Yangtze Region, southwest China: Implications for biotic recovery from the latest Permian mass extinction. Open access, PLoS ONE, 13: e0201012.

! K.A. Dunn et al. (1997): Enhancement of leaf fossilization potential by bacterial biofilms. In PDF, Geology, 25: 1119-1122. See also here (abstract).

Yoichi Ezaki et al., Department of Geosciences, Osaka City University, Sugimoto, Osaka, Japan: Earliest Triassic Microbialite Micro- to Megastructures in the Huaying Area of Sichuan Province, South China: Implications for the Nature of Oceanic Conditions after the End-Permian Extinction. Abstract, PALAIOS, Vol. 18, No. 4, pp. 388402.

J. Farmer (1999): Articel starts on page 94, PDF page 110: Taphonomic Modes in Microbial Fossilization. In PDF; In: Proceedings of the Workshop on Size Limits of Very Small Organisms, Space Studies Board, National Research Council, National Academies Press, Washington, DC.
Snapshot taken by the Internet Archive´s Wayback Machine.

D.E. Greenwalt et al. (2015): Taphonomy of the fossil insects of the middle Eocene Kishenehn Formation. In PDF, Acta Palaeontologica Polonica, 60: 931947.

NEAL S. GUPTA and RICHARD D. PANCOST: Biomolecular and Physical Taphonomy of Angiosperm Leaf During Early Decay: Implications for Fossilization. Abstract, Palaios 2004; v. 19; no. 5; p. 428-440.

! M. Iniesto et al. (2018): Plant Tissue Decay in Long-Term Experiments with Microbial Mats. Open access, Geosciences, 8.
"... Plants became trapped and progressively buried by the mat community that prevents fungal invasion, mechanical cracking, and inner tissue breakages ..."

! M. Iniesto et al. (2016): Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates. Open access, Scientific Reports, 6.

F. Käsbohrer et al. (2021): Exkursionsführer zur Geologie des Unteren Buntsandsteins (Untertrias) zwischen Harz und Thüringer Wald. PDF file, in German. Hercynia, 54: 1-64.
! Note fig. 7: Views of the giant stromatolite in the former quarry near Benzingerode.

S. Kershaw (2017): Palaeogeographic variation in the Permian-Triassic boundary microbialites: A discussion of microbial and ocean processes after the end-Permian mass extinction. Journal of Palaeogeography.

Wolfgang Elisabeth Krumbein, D.M. Paterson, Georgii Aleksandrovich Zavarzin: Fossil and Recent Biofilms: A Natural History of Life on Earth. Google books, Springer, 2003, 504 pages.

! T.M. Lenton and S.J. Daines (2016): Matworld - the biogeochemical effects of early life on land. In PDF, New Phytologist.

! E.R. Locatelli et al. (2017): Biofilms mediate the preservation of leaf adpression fossils by clays. Abstract, Palaios, 32: 708-724. See also here.
! Note fig. 10, the proposed taphonomic biofilm-clay template model.

R.J.C. McLean et al.: Biofilm Growth and Illustrations of its Role in Mineral Formation Microbial Biofilms, PDF file.

S. McMahon et al. (2018): A Field Guide to Finding Fossils on Mars. Open access, Journal of Geophysical Research: Planets, 123: 10121040.

J. Mora-Gómez et al. (2015): Limits of the biofilm concept and types of aquatic biofilms. Abstract, In: Romaní AM, Guasch H, Balaguer MD (eds) Aquatic biofilms: ecology, water quality and wastewater treatment. See also here (in PDF).

Snapshot provided by the Internet Archive´s Wayback Machine.

C.E. Morris, J. Monier and M. Jacques: Methods for Observing Microbial Biofilms Directly on Leaf Surfaces and Recovering Them for Isolation of Culturable Microorganisms. Abstract, Appl. Environ. Microbiol., 1997, 1570-1576, Vol 63, No. 4.

Penny A. MORRIS, Dept. Natural Science, Univ of Houston-Downtown, University of Houston-Downtown, Houston, TX: COMPARATIVE FOSSILIZATION PROCESSES FROM THREE HYPERSALINE ENVIRONMENTS AND THE GEOLOGICAL IMPLICATIONS. Abstract, GSA Annual Meeting, Seattle, 2003.


NASA Astrobiology Institute: What are Microbial Mats? and What are Stromatolites? See also:
Microbial Mat and Stromatolite Image gallery. (Shockwave flash presentation).

S.A. Newman et al. (2019): Experimental preservation of muscle tissue in quartz sand and kaolinite. Abstract, Palaios, 34: 437451.
See also here (in PDF).

! E.G. Nisbet and N.H. Sleep (2001): The habitat and nature of early life. PDF file, Nature, 409.
The link is to a version archived by the Internet Archive´s Wayback Machine.

Neal R. O'Brien et al.: Microbial taphonomic processes in the fossilization of insects and plants in the late Eocene Florissant Formation, Colorado. Abstract, Rocky Mountain Geology, 2002; v. 37; no. 1; p. 1-11.

! L.A. Parry et al. (2018): Soft-Bodied Fossils Are Not Simply Rotten Carcasses Toward a Holistic Understanding of Exceptional Fossil Preservation. Exceptional Fossil Preservation Is Complex and Involves the Interplay of Numerous Biological and Geological Processes.
Abstract, BioEssays, 40: 1700167. See also here (in PDF).
Note figure 1: The long journey from live organism to fossil. "... soft-bodied fossils have passed through numerous filters prior to discovery that remove, modify, or preserve anatomical characters. ..."
"... Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information".

O. Peterffy et al. (2016): Early Jurassic microbial mats - A potential response to reduced biotic activity in the aftermath of the end-Triassic mass extinction event. In PDF, Palaeogeography, Palaeoclimatology, Palaeoecology. See also here.

N. Planavsky and R.N. Ginsburg (2009): Taphonomy of Modern Marine Bahamian Microbialites. PALAIOS, 24: 517.

R.P. Reid et al. (2000): The role of microbes in accretion, lamination and early lithification of modern marine stromatolites. In PDF, Nature.
Snapshot provided by the Internet Archive´s Wayback Machine.

G.J. Retallack (2013): Ediacaran life on land. In PDF, Nature, 493: 8992.
See also here (Spaceref), and there (Xiao et al. 2014).

Robert Riding: Microbial carbonates: the geological record of calcified bacterial-algal mats and biofilms. Abstract, Sedimentology, Volume 47,Page 179; 2000.

N. Robin et al. (2015): Calcification and Diagenesis of Bacterial Colonies. In PDF, Minerals, 5: 488-506.

Jürgen Schieber, Department of Geology, University of Texas, Arlington: Microbial Mat Page.

A.C. Scott and M.E. Collinson (2003), Geology Department, Royal Holloway University of London, Egham: Non-destructive multiple approaches to interpret the preservation of plant fossils: implications for calcium-rich permineralizations. Journal of the Geological Society, 160: 857-862.
This expired link is available through the Internet Archive´s Wayback Machine.
See also here.

E.L. Simpson et al. (2015): Enigmatic spheres from the Upper Triassic Lockatong Formation, Newark Basin of eastern Pennsylvania: evidence for microbial activity in marginal-lacustrine strandline deposits. Abstract, Palaeobiodiversity and Palaeoenvironments, 95: 521529.

B.L. Teece et al. (2020): Mars Rover Techniques and Lower/Middle Cambrian Microbialites from South Australia: Con.struction, Biofacies, and Biogeochemistry. In PDF, Astrobiology, 20: See also here.

K. Thomas et al. (2016): Formation of Kinneyia via shear-induced instabilities in microbial mats. In PDF, Phil. Trans. R. Soc., A 371. See also here.
"Kinneyia are a class of microbially mediated sedimentary fossils. Characterized by clearly defined ripple structures, Kinneyia are generally found in areas that were formally littoral habitats and covered by microbial mats".

! A.M.F. Tomescu et al. (2016): Microbes and the fossil record: selected topics in paleomicrobiology. Abstract, in: Hurst C. (ed.) Their World: A Diversity of Microbial Environments. Advances in Environmental Microbiology, vol 1: 69-169. See also here (in PDF).

Ben Waggoner & Brian Speer, Bacteria: Fossil Record.

! Robert A. Spicer (1977): The pre-depositional formation of some leaf impressions. PDF file, Palaeontology, 20: 907912.

! Wikipedia, the free encyclopedia: Microbial mat, and
Biofilm. See also here (the German Wikipedia Biofilm website).

Philip R. Wilby et al.: Role of microbial mats in the fossilization of soft tissues. Abstract, Geology: Vol. 24, No. 9, pp. 787790.

Yoichi Ezaki et al., Department of Geosciences, Osaka City University, Sugimoto, Osaka, Japan: Earliest Triassic Microbialite Micro- to Megastructures in the Huaying Area of Sichuan Province, South China: Implications for the Nature of Oceanic Conditions after the End-Permian Extinction. Abstract, PALAIOS, Vol. 18, No. 4, pp. 388402.

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This index is compiled and maintained by Klaus-Peter Kelber, Würzburg,
Last updated September 10, 2021

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