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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.
Still available via Internet Archive Wayback Machine.

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

! Stanley M. Awramik, Department of Earth Science, University of California Santa Barbara:
The Record of Life on the Early Earth. Lecture notes, Powerpoint presentation.

L.E. Babcock et al. (2006): 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.

! N. Barling (2018): The Fidelity of Preservation of Insects from the Crato Formation (Lower Cretaceous) of Brazil. In PDF, Thesis, University of Portsmouth.
See also here.
"... The Nova Olinda Member fossil insects have a broad range of preservational fidelities.
[...] At their highest-fidelity, they are complete, fully-articulated, high-relief specimens with submicron-scale replication of both external and internal morphology. Cuticular structures (setae, scales, ommatidia, etc.) are sometimes replicated to the submicron-scale
[...] The remaining tissues are obliterated by pseudomorphed pseudoframboids (or pseudoframboid-like aggregates), which also protected the carcass from compaction ..."

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.

P.L. Broughton (2022): Fruit taphonomy and origin of hollow goethite spherulites in lacustrine sediments of the Maastrichtian Whitemud Formation, western Canada. Abstract, PalZ.

T. Clements and S. Gabbott (2022): Exceptional Preservation of Fossil Soft Tissues. In PDF, eLS, 2: 1–10.

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.

M.R. Downen et al. (2022): Steinkern spiders: A microbial mat-controlled taphonomic pathway in the Oligocene Aix-en-Provence Lagerstätte, France. In PDF, Palaeoentomology 005: 524–536.
See also here.
"... we examine fossil spiders preserved as molds to uncover a second taphonomic pathway based on microbial mats. Evidence of microbial mats include wrinkles, pustular textures, and possible microbial mat chips on the bedding surfaces ..."

M.L. Droser et al. (2022): What Happens Between Depositional Events, Stays Between Depositional Events: The Significance of Organic Mat Surfaces in the Capture of Ediacara Communities and the Sedimentary Rocks That Preserve Them. Front. Earth Sci., 10: 826353. doi: 10.3389/feart.2022.826353.
Note figure 5: Schematic of depositional scenarios with thick sediment packages and with thin sediment packages.
Figure 7: Schematic of the two scenarios through which complex Funisia dorothea TOS [textured organic surfaces] is hypothesized to have formed.

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).

! C. Dupraz et al. (2009): Processes of carbonate precipitation in modern microbial mats. In PDF, Earth-Science Reviews, 96: 141-162. See also here.
Note figure 1: The microbially-mediated carbon cycle.
! Figure 2: Classification of mineralization terms and processes showing the different types of mineralization as they relate to living (biotic) and non-living (abiotic) organic matter.
"... Preservation of microbial mats in the fossil record can be enhanced through carbonate precipitation, resulting in the formation of lithified mats, or microbialites.
[...] we review the specific role of microbes and the EPS matrix in various mineralization processes and discuss examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites ..."

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. 388–402.

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.

B.M. Gibson et al. (2023): The role of iron in the formation of Ediacaran ‘death masks’. Free access, Geobiology.
"... In this study, we perform decay experiments
[...] we demonstrate the first convincing “death masks” produced under experimental laboratory conditions ..."

M.L. Gomes et al. (2021): Sedimentary pyrite sulfur isotope compositions preserve signatures of the surface microbial mat environment in sediments underlying low-oxygen cyanobacterial mats. Open access, Geobiology, 20: 60-78. See also here (in PDF).

D.E. Greenwalt et al. (2015): Taphonomy of the fossil insects of the middle Eocene Kishenehn Formation. In PDF, Acta Palaeontologica Polonica, 60: 931–947.

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.

! K. Janssen et al. (2021): Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits. Free access, Appl. Plant Sci., 2021;9:e11444.
"... Fossilization of plant material can be induced by different chemical processes, including authigenic pre-servation, which is dependent on encrustation withminerals. It has been shown that the biofilm-forming activity of bacteria plays an important role in this process ..."

K. Janssen et al. (2022): The complex role of microbial metabolic activity in fossilization. Open access, Biol. Rev., 97: 449–465.
See also here.

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.

W.E. Krumbein (2008): Biogenerated Rock Structures Space Sci Rev, 135: 81–94.
See likewise here, and there.

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. (2022): Leaves in Iron Oxide: Remarkable Preservation of a Neogene Flora from New Caledonia. In PDF, Palaios, 37: 622–632.
See also here.
"... Leaf tissues are preserved three-dimensionally in multiple ways including casts/molds, permineralization/petrifaction, and replacement. [...] We propose a taphonomic model in which the fossil leaves, like their modern counterparts, were permeated by iron oxides due to the high availability of iron ..."

! 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.

! L.C.W. MacLean et al. (2008): A high-resolution chemical and structural study of framboidal pyrite formed within a low-temperature bacterial biofilm. In PDF, Geobiology 6: 471-480.
See also here.
"... A novel, anaerobically grown microbial biofilm, scraped from the inner surface of a borehole, 1474 m below land surface within a South African, Witwatersrand gold mine, contains framboidal pyrite
[...] Growth of individual pyrite crystals within the framboid occurred inside organic templates confirms the association between framboidal pyrite and organic materials in low-temperature diagenetic environments ..."

! B. Mähler et al. (2021): Adipocere formation in biofilms as a first step in soft tissue preservation. Open access, Scientific Reports, 12.
"... and further showed that in animals with biofilm formation calcite precipitates in finer grained crystals than in individuals without biofilm formation, and that the precipitates were denser and replicated the structures of the cuticles better than the coarse precipitates. ..."

! A.K. Martins et al. (2022): Exceptional preservation of Triassic-Jurassic fossil plants: integrating biosignatures and fossil diagenesis to understand microbial-related iron dynamics. In PDF, Lethaia, 55.
See also here.
! Note figure 8: Inferred biogeochemical cycle for the chemical stabilization of iron oxides into goethite.
! Figure 9: Inferred fossil diagenetic history for fossil plants, sunken into iron-rich lakes or small ponds of fresh water.
Worth checking out: ! Chapter "Fossil diagenesis" (on PDF-page 12).

J. Marugán-Lobón et al. (2022): The Las Hoyas Lagerstätte: a palaeontological look to an Early Cretaceous wetland. Open access, Journal of the Geological Society.
See also here (in PDF).
"... The site has yielded a particularly diverse assemblage of more than twenty thousand plant and animal fossils, many of which present unprecedented soft-tissue preservation, including microstructural details. Among the most significant discoveries are the oldest angiosperms, ..."

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: 1012–1040.

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? Still available via Internet Archive Wayback Machine.
What are Stromatolites?
See also: Microbial Mats Offer Clues To Life on Early Earth. Worth checking out:
! Life in the Extremes.

S.A. Newman et al. (2019): Experimental preservation of muscle tissue in quartz sand and kaolinite. Abstract, Palaios, 34: 437–451.
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.

! N. Noffke et al. (2022): Microbially Induced Sedimentary Structures (MISS). In PDF, Treatise Online, 162. Part B, Volume 2, Chapter 5. See also here.
Note figure 1: Biofilms in classic and modern sedimentology.
Figure 15: Various causes and types of microbially induced wrinkle structures.

N.R. O’Brien et al. (2008); Start on PDF-page 19: The role of biofilms in fossil preservation, Florissant Formation, Colorado. PDF file, In: Meyer, H.W., and Smith, D.M., eds., Paleontology of the Upper Eocene Florissant Formation, Colorado. The Geological Society of America, Special Paper 435: 19-31.
See also here.

N.R. O'Brien et al. (2002): Microbial taphonomic processes in the fossilization of insects and plants in the late Eocene Florissant Formation, Colorado. Rocky Mountain Geology, 37: 1-11.
The link is to a version archived by the Internet Archive´s Wayback Machine.
See also here.

! 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: 5–17.

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: 89–92.
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.

! M.H. Schweitzer et al. (2007): Soft tissue and cellular preservation in vertebrate skeletal elements from the Cretaceous to the present. In PDF Proc. R. Soc. B, 274: 183–197.
See also here.

! A.C. Scott and M.E. Collinson (2003): Non-destructive multiple approaches to interpret the preservation of plant fossils: implications for calcium-rich permineralizations. Journal of the Geological Society, 160: 857-862.

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: 521–529.

S. Slagter et al. (2022): Biofilms as agents of Ediacara-style fossilization. Open Access, Scientific Reports, 12.
"... we use an experimental approach to interrogate to what extent the presence of mat-forming microorganisms was likewise critical to the Ediacara-style fossilization of these soft-bodied organisms.
[...] results indicate that the occurrence of microbial mats and biofilms may have strongly shaped the preservational window for Ediacara-style fossils associated with early diagenetic silica cements ..."

! R.A. Spicer (1977): The pre-depositional formation of some leaf impressions. PDF file, Palaeontology, 20: 907–912.
This expired link is now available through the Internet Archive´s Wayback Machine.

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.

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

P.R. Wilby et al. (1996): Role of microbial mats in the fossilization of soft tissues. Abstract, Geology, 24: 787–790.

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. 388–402.

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