@misc{golovenok1982on2,
    author = "Golovenok, V. K",
    title = "On the Precambrian microbial remains in the Kirgitei Formation of the Yenisei Ridge [in Russian]",
    year = "1982",
    howpublished = "Doklady Akad. Nauk. SSSR, v. 262, no. 2, p. 394-396",
    note = "talkorigins\_source = {true}; raw\_reference = {Golovenok, V. K., 1982, On the Precambrian microbial remains in the Kirgitei Formation of the Yenisei Ridge [in Russian]: Doklady Akad. Nauk. SSSR, v. 262, no. 2, p. 394-396.}"
}

@misc{awramik1984ancient1,
    author = "Awramik, S. M",
    title = "Ancient stromatolites and microbial mats, in Cohen, Y., Castenholz, R. W., and Halvorson, H. O., eds., Microbioal Mats",
    year = "1984",
    howpublished = "New York, Alan Liss, p. 1-22",
    note = "talkorigins\_source = {true}; raw\_reference = {Awramik, S. M., 1984, Ancient stromatolites and microbial mats, in Cohen, Y., Castenholz, R. W., and Halvorson, H. O., eds., Microbioal Mats: New York, Alan Liss, p. 1-22.}"
}

@article{cloud1985microbial,
    author = "Cloud, Preston",
    title = "Microbial Mats: Stromatolites. Based on the Proceedings of the Integrated Approach to the Study of Microbial Mats, July 26-31, 1982. Yehuda Cohen, Richard W. Castenholz, Harlyn O. Halvorson",
    year = "1985",
    journal = "The Quarterly Review of Biology",
    url = "https://doi.org/10.1086/414220",
    doi = "10.1086/414220",
    number = "1",
    openalex = "W2022633273",
    pages = "83-83",
    volume = "60"
}

@article{shilo1985cohen,
    author = "Shilo, Moshe",
    title = "COHEN, Y., R. W. CASTENHOLZ, AND H. O. HALVORSON [Eds.] 1984. Microbial mats: Stromatolites. MBL Lectures in Biology, v. 3. Alan R. Liss, Inc., New York. 508 p. $88.00.",
    year = "1985",
    journal = "Limnology and Oceanography",
    url = "https://doi.org/10.4319/lo.1985.30.4.0917",
    doi = "10.4319/lo.1985.30.4.0917",
    number = "4",
    openalex = "W2131818503",
    pages = "917-918",
    volume = "30"
}

@article{stolz1990microbial,
    author = "Stolz, John F.",
    title = "Microbial Mats. Physiological Ecology of Benthic Microbial Communities. Yehuda Cohen, Eugene Rosenberg",
    year = "1990",
    journal = "The Quarterly Review of Biology",
    url = "https://doi.org/10.1086/416783",
    doi = "10.1086/416783",
    number = "2",
    openalex = "W2515586766",
    pages = "242-242",
    volume = "65"
}

@article{doi101111j146981371995tb03051x,
    author = "Stal, Lucas J.",
    title = "Physiological ecology of cyanobacteria in microbial mats and other communities",
    year = "1995",
    journal = "New Phytologist",
    abstract = "In this review some aspects of the physiological ecology of cyanobacteria are discussed by taking a microbial mat as an example. The majority of microbial mats are built and dominated by cyarsobacteria which are primary producers at the basis of the microbial foodweb in microbial mats. These micro-scale ecosystems are characterized by steep and fluctuating physico-chemical gradients of which those of light, oxygen and sulphide are the most conspicuous. Light is strongly attenuated in the sediment, and owing to constant sedimentation, the mat-forming cyanobacteria have to move upwards towards the light. However, at the sediment surface, light intensity, particularly in the u.v. part of the spectrum, is often deleterious. The gliding movement of the cyanobacteria, with photo- and chemotaxis, allows the organism to position itself in a thin layer at optimal conditions. The organic matter produced by cyanobacterial photosynthesis is decomposed by the ruicrobial community. Sulphate-reducing bacteria are important in the end-oxidation of the organic matter. These organisms are obligate anaerobes and produce sulphide. Gradients of sulphide and oxygen move up and down in the sediment as a response to diurnal variations of light intensity. Cyanobacteria, therefore, are sometimes exposed to large concentrations of the extremely toxic sulphide. Some species are capable of sulphide-dependent anoxygenic photosynthesis. Other cyanobacteria show increased rates of oxygenic photosynthesis in the presence of sulphide and have mechanisms to oxidize sulphide while avoiding sulphide toxicity. Iron might play an important role in this process. Under anoxic conditions in the dark, mat-forming cyanobacteria switch to fermentative metabolism. Many species are also capable of fermentative reduction of elemental sulphur to sulphide. The gradients of sulphide and oxygen are of particular importance for nitrogen fixation. Very few microbial mats are formed by heterocystous cyanobacteria, which are best adapted to diazntrophic growth. However, these organisms probably cannot tolerate greater concentrations of sulphide or anoxic conditions or both. Under such conditions non-heterocystous cyanobacteria become dominant as diazotrophs. These organisms avoid conditions of oxygen supersaturation. In the ecosystem, nitrogen fixation and photosynthesis might be separated temporally as well as spatially. In addition, non-heterocystous diazotrophic cyanobacteria have mechanisms at the subcellular level to protect the oxygen-sensitive nitrogenase from inaction. CONTENTS Summary 1 I. Introduction 2 II. Microbial mats 3 III. Cyanobacteria in light gradients 7 IV. Dark metabolism 10 V. Interactions with sulphide 13 VI. Nitrogen fixation 16 VII. References 28.",
    url = "https://doi.org/10.1111/j.1469-8137.1995.tb03051.x",
    doi = "10.1111/j.1469-8137.1995.tb03051.x",
    openalex = "W1963993817"
}

@article{doi101111j157469411998tb00494x,
    author = "Douglas, Susanne and Beveridge, Terry J.",
    title = "Mineral formation by bacteria in natural microbial communities",
    year = "1998",
    journal = "FEMS Microbiology Ecology",
    abstract = "This review focuses on bacteria and their role in mineral formation. As a consequence of their small size and diverse metabolic capabilities bacteria, more than any other type of living organism, are able to interact intimately with metal ions present in their environment. Some metals are required for metabolism and are taken into the cell through various mechanisms, then incorporated into the necessary physiological pathways and biosynthetic structures. This physiological aspect of metal-bacterial interaction will not be discussed but, rather, the ability of bacteria to accumulate metal ions and incorporate them into mineral phases will be described. This activity has widespread importance for the shaping of our planet and the recycling of mineral elements. Since bacteria are most frequently found as part of microbial communities it is within this context that their mineral-forming ability will be discussed.",
    url = "https://doi.org/10.1111/j.1574-6941.1998.tb00494.x",
    doi = "10.1111/j.1574-6941.1998.tb00494.x",
    openalex = "W2022688291",
    references = "doi1011300091761319880160149mibbbs23co2, doi1023073514631, doi1023073514674"
}

@article{doi1023073515360,
    author = "Gehlîng, James G.",
    title = "Microbial Mats in Terminal Proterozoic Siliciclastics: Ediacaran Death Masks",
    year = "1999",
    journal = "Palaios",
    abstract = "A variety of sedimentary structures and patterns in Proterozoic siliciclastic sedimentary rocks cannot be explained by known inorganic processes. In particular, certain bed-surface textures, and domed and disrupted sand lamination, are demonstrably the mechanical products of microbially bound sediment and microbial mats. In all but the most wave and current active marine environments of the terminal Proterozoic, the absence of effective grazing and burrowing allowed mat-communities of cyanobacteria to colonize sedimentary surfaces. The resultant microbial mats inhibited sediment erosion, formed partings when buried between sand beds, and restricted vertical migration of pore fluid and gas in both exposed and subaqueous environments. Distinctive petee laminations, known from modern mat-bound, tidal-flat sediments, are recorded for the first time in the rock record from the terminal Proterozoic Rawnsley Quartzite of South Australia. The preservation of external molds of soft-bodied Ediacaran organisms is interpreted as a function of the early diagenesis of a sole veneer. A form of death mask resulted from bacterial precipitation of iron minerals in the sand that smothered decaying microbial mats and megascopic benthic organisms. The appearance of three-dimensional trace fossils in Early Cambrian strata signaled a behavioral revolution; the evolution of efficient grazing reduced the development of benthic mat communities in all but the most extreme environments, while bioturbation disrupted buried mats and closed a taphonomic window of preservation for soft-bodied organisms.",
    url = "https://doi.org/10.2307/3515360",
    doi = "10.2307/3515360",
    openalex = "W2160919484",
    references = "allison1988the, doi10100797814757131762, doi1010160009254187901653, doi1010160034666775900056, doi1010160301926885900518, doi101016030192688590066x, doi101017s009483730001188x, doi101038376053a0, doi101038383423a0, doi101098rstb19850134, doi101126science1744011825, doi1011300091761319920200883etsapm23co2, doi101144gsjgs14940607, doi101306212f7e4b2b2411d78648000102c1865d, doi1023073514973, doi102475ajs26811, openalexw2326083785, openalexw3127114020"
}

@article{doi101046j13653091200000003x,
    author = "Riding, Robert",
    title = "Microbial carbonates: the geological record of calcified bacterial–algal mats and biofilms",
    year = "2000",
    journal = "Sedimentology",
    abstract = "Summary Deposits produced by microbial growth and metabolism have been important components of carbonate sediments since the Archaean. Geologically best known in seas and lakes, microbial carbonates are also important at the present day in fluviatile, spring, cave and soil environments. The principal organisms involved are bacteria, particularly cyanobacteria, small algae and fungi, that participate in the growth of microbial biofilms and mats. Grain‐trapping is locally important, but the key process is precipitation, producing reefal accumulations of calcified microbes and enhancing mat accretion and preservation. Various metabolic processes, such as photosynthetic uptake of CO 2 and/or HCO 3 – by cyanobacteria, and ammonification, denitrification and sulphate reduction by other bacteria, can increase alkalinity and stimulate carbonate precipitation. Extracellular polymeric substances, widely produced by microbes for attachment and protection, are important in providing nucleation sites and facilitating sediment trapping. Microbial carbonate microfabrics are heterogeneous. They commonly incorporate trapped particles and in situ algae and invertebrates, and crystals form around bacterial cells, but the main component is dense, clotted or peloidal micrite resulting from calcification of bacterial cells, sheaths and biofilm, and from phytoplankton‐stimulated whiting nucleation. Interpretation of these texturally convergent and often inscrutable fabrics is a challenge. Conspicuous accumulations are large domes and columns with laminated (stromatolite), clotted (thrombolite) and other macrofabrics, which may be either agglutinated or mainly composed of calcified or spar‐encrusted microbes. Stromatolite lamination appears to be primary, but clotted thrombolite fabrics can be primary or secondary. Microbial precipitation also contributes to hot‐spring travertine, cold‐spring mound, calcrete, cave crust and coated grain deposits, as well as influencing carbonate cementation, recrystallization and replacement. Microbial carbonate is biologically stimulated but also requires favourable saturation state in ambient water, and thus relies uniquely on a combination of biotic and abiotic factors. This overriding environmental control is seen at the present day by the localization of microbial carbonates in calcareous streams and springs and in shallow tropical seas, and in the past by temporal variation in abundance of marine microbial carbonates. Patterns of cyanobacterial calcification and microbial dome formation through time appear to reflect fluctuations in seawater chemistry. Stromatolites appeared at ∼3450 Ma and were generally diverse and abundant from 2800 to 1000 Ma. Inception of a Proterozoic decline variously identified at 2000, 1000 and 675 Ma, has been attributed to eukaryote competition and/or reduced lithification. Thrombolites and dendrolites mainly formed by calcified cyanobacteria became important early in the Palaeozoic, and reappeared in the Late Devonian. Microbial carbonates retained importance through much of the Mesozoic, became scarcer in marine environments in the Cenozoic, but locally re‐emerged as large agglutinated domes, possibly reflecting increased algal involvement, and thick micritic reef crusts in the late Neogene. Famous modern examples at Shark Bay and Lee Stocking Island are composite coarse agglutinated domes and columns with complex bacterial–algal mats occurring in environments that are both stressed and current‐swept: products of mat evolution, ecological refugia, sites of enhanced early lithification or all three?",
    url = "https://doi.org/10.1046/j.1365-3091.2000.00003.x",
    doi = "10.1046/j.1365-3091.2000.00003.x",
    openalex = "W2150772200",
    references = "bertrandsarfati1981stromatolite, doi101002gj3350050104, doi10100797814757115239, doi10100797836426651652, doi101016030192688590066x, doi101016s0012825297834848, doi101016s0070457108711373, doi101017cbo9780511601064, doi1010381911032b0, doi101038269209a0, doi101038324055a0, doi101038333313a0, doi101038377220a0, doi101038383423a0, doi101038scientificamerican017886, doi10108011035898209455245, doi101086626965, doi101111j136530911982tb01733x, doi101126science1631544, doi101126science1744011825, doi101126science28554301033, doi101130gsab481873, doi101139e79088, doi101144gsjgs14960979, doi101146annurevearth271313, doi101146annurevmi49100195003431, doi102216i003188842244561, doi1023073514631, doi1023073514674, doi1023073514973, doi102475ajs26791017, doi105860choice295709, doi105860choice304422, openalexw2026796374, openalexw2508765924, openalexw2601700276, openalexw599354073, schidlowski1988a, semikhatov2000proterozoic"
}

@article{doi101016s025462991531156x,
    author = "Stal, Lucas J.",
    title = "Coastal microbial mats: the physiology of a small-scale ecosystem",
    year = "2001",
    journal = "South African Journal of Botany",
    abstract = "Coastal inter-tidal sandy sediments, salt marshes and mangrove forests often support the development of microbial mats. Microbial mats are complex associations of one or several functional groups of microorganisms and their formation usually starts with the growth of a cyanobacterial population on a solid substrate. They are considered as analogues of fossil Precambrian stromatolites. Primary production by the cyanobacteria fuels the metabolism of sulfate reducing bacteria and the sulfide that they produce is oxidised by anoxygenic phototrophic bacteria and by colorless sulfur bacteria. Growth and metabolism of these microorganisms result in markedly fluctuating vertical gradients of oxygen and sulfide that shift during a day-night cycle. This review discusses the metabolic contributions of the different functional groups of microorganisms and how their joint effort results in the formation of the mat.",
    url = "https://doi.org/10.1016/s0254-6299(15)31156-x",
    doi = "10.1016/s0254-6299(15)31156-x",
    openalex = "W1548914201"
}

@article{doi1023071543552,
    author = "Marais, David J. Des",
    title = "Biogeochemistry of Hypersaline Microbial Mats Illustrates the Dynamics of Modern Microbial Ecosystems and the Early Evolution of the Biosphere",
    year = "2003",
    journal = "Biological Bulletin",
    abstract = "Photosynthetic microbial mats are remarkably complete self-sustaining ecosystems at the millimeter scale, yet they have substantially affected environmental processes on a planetary scale. These mats may be direct descendents of the most ancient biological communities in which even oxygenic photosynthesis might have developed. Photosynthetic mats are excellent natural laboratories to help us to learn how microbial populations associate to control dynamic biogeochemical gradients.",
    url = "https://doi.org/10.2307/1543552",
    doi = "10.2307/1543552",
    openalex = "W2111641799"
}

@article{doi101111j13653091200901083x,
    author = "Spadafora, Alessandra and Perri, Edoardo and McKenzie, Judith A. and VASCONCELOS, CRISÓGONO",
    title = "Microbial biomineralization processes forming modern Ca:Mg carbonate stromatolites",
    year = "2009",
    journal = "Sedimentology",
    abstract = "Modern Ca:Mg carbonate stromatolites form in association with the microbial mat in the hypersaline coastal lagoon, Lagoa Vermelha (Brazil). The stromatolites, although showing diversified fabrics characterized by thin or crude lamination and/or thrombolitic clotting, exhibit a pervasive peloidal microfabric. The peloidal texture consists of dark, micritic aggregates of very high-Mg calcite and/or Ca dolomite formed by an iso-oriented assemblage of sub-micron trigonal polyhedrons and organic matter. Limpid acicular crystals of aragonite arranged in spherulites surround these aggregates. Unlike the aragonite crystals, organic matter is present consistently in the dark, micritic carbonate comprising the peloids. This organic matter is observed as sub-micron flat and filamentous mucus-like structures inside the interspaces of the high-Mg calcite and Ca dolomite crystals and is interpreted as the remains of degraded extracellular polymeric substances. Moreover, many fossilized bacterial cells are associated strictly with both carbonate phases. These cells consist mainly of 0·2 to 4 μm in diameter, sub-spherical, rod-like and filamentous forms, isolated or in colony-like clusters. The co-existence of fossil extracellular polymeric substances and bacterial bodies, associated with the polyhedrons of Ca:Mg carbonate, implies that the organic matter and microbial metabolism played a fundamental role in the precipitation of the minerals that form the peloids. By contrast, the lack of extracellular polymeric substances in the aragonitic phase indicates an additional precipitation mechanism. The complex processes that induce mineral precipitation in the modern Lagoa Vermelha microbial mat appear to be recorded in the studied lithified stromatolites. Sub-micron polyhedral crystal formation of high-Mg calcite and/or Ca dolomite results from the coalescence of carbonate nanoglobules around degraded organic matter nuclei. Sub-micron polyhedral crystals aggregate to form larger ovoidal crystals that constitute peloids. Subsequent precipitation of aragonitic spherulites around peloids occurs as micro-environmental water conditions around the peloids change.",
    url = "https://doi.org/10.1111/j.1365-3091.2009.01083.x",
    doi = "10.1111/j.1365-3091.2009.01083.x",
    openalex = "W1563041753",
    references = "doi101016s0012825201000897, doi101016s0070457108711373"
}

@article{doi101111j14724669200900227x,
    author = "Bosak, Tanja and Bush, John W. M. and Flynn, M. R. and Liang, Biqing and Ono, Shuhei and Petroff, Alexander P. and Sim, Min Sub",
    title = "Formation and stability of oxygen‐rich bubbles that shape photosynthetic mats",
    year = "2009",
    journal = "Geobiology",
    abstract = "Gas release in photic-zone microbialites can lead to preservable morphological biosignatures. Here, we investigate the formation and stability of oxygen-rich bubbles enmeshed by filamentous cyanobacteria. Sub-millimetric and millimetric bubbles can be stable for weeks and even months. During this time, lithifying organic-rich laminae surrounding the bubbles can preserve the shape of bubbles. Cm-scale unstable bubbles support the growth of centimetric tubular towers with distinctly laminated mineralized walls. In environments that enable high photosynthetic rates, only small stable bubbles will be enclosed by a dense microbial mesh, while in deep waters extensive microbial mesh will cover even larger photosynthetic bubbles, increasing their preservation potential. Stable photosynthetic bubbles may be preserved as sub-millimeter and millimeter-diameter features with nearly circular cross-sections in the crests of some Proterozoic conical stromatolites, while centrimetric tubes formed around unstable bubbles provide a model for the formation of tubular carbonate microbialites that are not markedly depleted in (13)C.",
    url = "https://doi.org/10.1111/j.1472-4669.2009.00227.x",
    doi = "10.1111/j.1472-4669.2009.00227.x",
    openalex = "W1596690334",
    references = "doi101016jprecamres200601003, doi101130001676061974851869gsaavt20co2, doi102110palo2003p0396, openalexw431002082"
}

@book{crossref2010microbial,
    title = "Microbial Mats",
    year = "2010",
    booktitle = "Cellular Origin, Life in Extreme Habitats and Astrobiology",
    url = "https://doi.org/10.1007/978-90-481-3799-2",
    doi = "10.1007/978-90-481-3799-2",
    openalex = "W591462339"
}

@incollection{reitner2011microbial,
    author = "Reitner, Joachim",
    title = "Microbial Mats",
    year = "2011",
    booktitle = "Encyclopedia of Earth Sciences Series",
    url = "https://doi.org/10.1007/978-1-4020-9212-1\_145",
    doi = "10.1007/978-1-4020-9212-1\_145",
    openalex = "W4205309207",
    pages = "606-608",
    references = "doi1010079783642601477, doi101016001670379390347y, doi101016jpalaeo200410015, doi101038nature04764, doi101046j13653091200000003x, doi101111j157469761997tb00325x, doi1015159780691239477, doi1023073514674, doi1023073515363, openalexw431002082"
}

@incollection{ruiji2011microbiota,
    author = "Ruiji, Cao and Leiming, Yin",
    title = "Microbiota and Microbial Mats within Ancient Stromatolites in South China",
    year = "2011",
    booktitle = "Cellular Origin, Life in Extreme Habitats and Astrobiology",
    url = "https://doi.org/10.1007/978-94-007-0397-1\_4",
    doi = "10.1007/978-94-007-0397-1\_4",
    openalex = "W2111493927",
    pages = "65-86",
    references = "doi101016s0070457108711373, doi101046j13653091200000003x, doi101073pnas492158, doi1010970001069419650700000019, doi101111j150239311988tb02083x, doi101139e79088, doi101146annurevearth271313, doi105860choice304422, openalexw2326083785, openalexw2336572712"
}

@incollection{stal2011microbial,
    author = "Stal, Lucas J. and Noffke, Nora",
    title = "Microbial Mats",
    year = "2011",
    booktitle = "Encyclopedia of Astrobiology",
    url = "https://doi.org/10.1007/978-3-642-11274-4\_986",
    doi = "10.1007/978-3-642-11274-4\_986",
    openalex = "W4243991423",
    pages = "1042-1045"
}

@article{doi101016jpalaeo201312026,
    author = "Meyer, Mike and Xiao, Shuhai and Gill, Benjamin C. and Schiffbauer, James D. and Chen, Zhe and Zhou, Chuanming and Yuan, Xunlai",
    title = "Interactions between Ediacaran animals and microbial mats: Insights from Lamonte trevallis, a new trace fossil from the Dengying Formation of South China",
    year = "2013",
    journal = "Palaeogeography Palaeoclimatology Palaeoecology",
    url = "https://doi.org/10.1016/j.palaeo.2013.12.026",
    doi = "10.1016/j.palaeo.2013.12.026",
    openalex = "W2044564640",
    references = "crossref2010microbial, doi101016jgr201101006, doi101038nature05345, doi101038nmeth2089, doi101073pnas0708336105, doi101126science1107765, doi101126science1135013, doi101130g319691, doi101306212f89c22b2411d78648000102c1865d, doi1023073515360, doi105860choice295709, openalexw2344228935, openalexw431002082"
}

@article{doi101089ast20131030,
    author = "Noffke, Nora and Christian, Daniel and Wacey, David and Hazen, Robert M.",
    title = "Microbially Induced Sedimentary Structures Recording an Ancient Ecosystem in the ca. 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia",
    year = "2013",
    journal = "Astrobiology",
    abstract = "Microbially induced sedimentary structures (MISS) result from the response of microbial mats to physical sediment dynamics. MISS are cosmopolitan and found in many modern environments, including shelves, tidal flats, lagoons, riverine shores, lakes, interdune areas, and sabkhas. The structures record highly diverse communities of microbial mats and have been reported from numerous intervals in the geological record up to 3.2 billion years (Ga) old. This contribution describes a suite of MISS from some of the oldest well-preserved sedimentary rocks in the geological record, the early Archean (ca. 3.48 Ga) Dresser Formation, Western Australia. Outcrop mapping at the meter to millimeter scale defined five sub-environments characteristic of an ancient coastal sabkha. These sub-environments contain associations of distinct macroscopic and microscopic MISS. Macroscopic MISS include polygonal oscillation cracks and gas domes, erosional remnants and pockets, and mat chips. Microscopic MISS comprise tufts, sinoidal structures, and laminae fabrics; the microscopic laminae are composed of primary carbonaceous matter, pyrite, and hematite, plus trapped and bound grains. Identical suites of MISS occur in equivalent environmental settings through the entire subsequent history of Earth including the present time. This work extends the geological record of MISS by almost 300 million years. Complex mat-forming microbial communities likely existed almost 3.5 billion years ago.",
    url = "https://doi.org/10.1089/ast.2013.1030",
    doi = "10.1089/ast.2013.1030",
    openalex = "W2037461180",
    references = "doi1010160301926888900058, doi101016jearscirev200810005, doi101016jprecamres200601003, doi101111j136530911989tb00615x, doi101111j14724669200700118x, doi101130g222461, openalexw431002082, schopf2007earliest"
}

@article{doi101371journalpone0066662,
    author = "Schneider, Dominik and Arp, Gernot and Reimer, Andreas and Reitner, Joachim and Daniel, Rolf",
    title = "Phylogenetic Analysis of a Microbialite-Forming Microbial Mat from a Hypersaline Lake of the Kiritimati Atoll, Central Pacific",
    year = "2013",
    journal = "PLoS ONE",
    abstract = "On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth.",
    url = "https://doi.org/10.1371/journal.pone.0066662",
    doi = "10.1371/journal.pone.0066662",
    openalex = "W1971368203",
    references = "crossref2010microbial, doi101007978364273978121, doi101016jearscirev200810005, doi101016s0022283605803602, doi101038nmethf303, doi101093bioinformaticsbtq461, doi101093bioinformaticsbtr381, doi101093nargkm864, doi101128aem0300605, doi101128aem713150115062005, doi101371journalpone0007401, doi1014806ej171200"
}

@article{doi101038ismej201587,
    author = "Ruvindy, Rendy and White, Richard and Neilan, Brett A. and Burns, Brendan P.",
    title = "Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics",
    year = "2015",
    journal = "The ISME Journal",
    abstract = "Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.",
    url = "https://doi.org/10.1038/ismej.2015.87",
    doi = "10.1038/ismej.2015.87",
    openalex = "W368584921",
    references = "doi101371journalpone0066662"
}

@article{doi101038srep15607,
    author = "Wong, Hon Lun and Smith, Daniela-Lee and Visscher, Pieter T. and Burns, Brendan P.",
    title = "Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats",
    year = "2015",
    journal = "Scientific Reports",
    abstract = "Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.",
    url = "https://doi.org/10.1038/srep15607",
    doi = "10.1038/srep15607",
    openalex = "W2409740056",
    references = "doi101371journalpone0066662"
}

@article{doi101016jprecamres201804007,
    author = "Hickman‐Lewis, Keyron and Cavalazzi, Barbara and Foucher, Frédéric and Westall, Francès",
    title = "Most ancient evidence for life in the Barberton greenstone belt: Microbial mats and biofabrics of the ∼3.47 Ga Middle Marker horizon",
    year = "2018",
    journal = "Precambrian Research",
    url = "https://doi.org/10.1016/j.precamres.2018.04.007",
    doi = "10.1016/j.precamres.2018.04.007",
    openalex = "W2798197579",
    references = "crossref2010microbial, doi1010160008622382900434, doi1010160301926895000879, doi101016jcarbon200502018, doi101016s0966842x01020121, doi10103835059210, doi101038nature02888, doi101126science16138451005, doi10118614712148444, doi105860choice295709, openalexw2026796374, openalexw2508765924"
}

@article{doi101111gbi12274,
    author = "Sallstedt, Therese and Bengtson, Stefan and Broman, Curt and Crill, Patrick and Canfield, Donald E.",
    title = "Evidence of oxygenic phototrophy in ancient phosphatic stromatolites from the Paleoproterozoic Vindhyan and Aravalli Supergroups, India",
    year = "2018",
    journal = "Geobiology",
    abstract = "indicative of carbon fixation by the Calvin cycle. In addition, the mats hold a synsedimentary fossil biota characteristic of cyanobacterial and rhodophyte morphotypes. Phosphatic oncoid cone-like stromatolites from the Paleoproterozoic Aravalli Supergroup (Jhamarkotra Formation) comprise abundant mineralized bubbles enmeshed within tufted filamentous mat fabrics. Construction of these tufts is considered to be the result of filamentous bacteria gliding within microbial mats, and as fossilized bubbles within pristine mat laminae can be used as a proxy for oxygenic phototrophy, this provides a strong indication for cyanobacterial activity in the Aravalli mounds. We suggest that the activity of oxygenic phototrophs may have been significant for the formation of apatite in both Vindhyan and Aravalli stromatolites, mainly by concentrating phosphate and creating steep diurnal redox gradients within mat pore spaces, promoting apatite precipitation. The presence in the Indian stromatolites of alternating apatite-carbonate lamina may result from local variations in pH and oxygen levels caused by photosynthesis-respiration in the mats. Altogether, this study presents new insights into the ecology of ancient phosphatic stromatolites and warrants further exploration into the role of oxygen-producing biotas in the formation of Paleoproterozoic shallow-basin phosphorites.",
    url = "https://doi.org/10.1111/gbi.12274",
    doi = "10.1111/gbi.12274",
    openalex = "W2789404307",
    references = "doi1010160012825295000496, doi101016s001670370200950x, doi101038382127a0, doi101038nature04764, doi101038nature13068, doi101046j13653091200000003x, doi101098rstb20061838, doi101146annurevearth271313, doi1023073514674, openalexw2026796374, ruiji2011microbiota"
}

@article{doi101016jearscirev2020103296,
    author = "Lepot, Kévin",
    title = "Signatures of early microbial life from the Archean (4 to 2.5 Ga) eon",
    year = "2020",
    journal = "Earth-Science Reviews",
    abstract = "The Archean era (4 to 2.5 billion years ago, Ga) yielded rocks that include the oldest conclusive traces of life as well as many controversial occurrences. Carbonaceous matter is found in rocks as old as 3.95 Ga, but the oldest (graphitic) forms may be abiogenic. Due to the metamorphism that altered the molecular composition of all Archean organic matter, non-biological carbonaceous compounds such as those that could have formed in seafloor hydrothermal systems are difficult to rule out. Benthic microbial mats as old as 3.47 Ga are supported by the record of organic laminae in stromatolitic (layered) carbonates, in some stromatolitic siliceous sinters, and in some siliciclastic sediments. In these deposits, organic matter rarely preserved fossil cellular structures (e.g., cell walls) or ultrastructures (e.g., external sheaths) and its simple textures are difficult to attribute to either microfossils or coatings of cell-mimicking mineral templates. This distinction will require future nanoscale studies. Filamentous-sheath microfossils occur in 2.52 Ga rocks, and may have altered counterparts as old as 3.47 Ga. Surprisingly large spheres and complex organic lenses occur in rocks as old as 3.22 Ga and \textasciitilde\ 3.4 Ga, respectively, and represent the best candidates for the oldest microfossils. Titaniferous microtubes in volcanic or volcanoclastic rocks inferred as microbial trace fossils have been reevaluated as metamorphic or magmatic textures. Microbially-induced mineralization is supported by CaCO3 nanostructures in 2.72 Ga stromatolites. Sulfides 3.48 Ga and younger bear S-isotope ratios indicative of microbial sulfate reduction. Ferruginous conditions may have fueled primary production via anoxygenic photosynthesis–as suggested by Fe-isotope ratios–possibly as early as 3.77 Ga. Microbial methanogenesis and (likely anaerobic) methane oxidation are indicated by C-isotope ratios as early as 3.0 Ga and \textasciitilde\ 2.72 Ga, respectively. Photosynthetic production of O2 most likely started between 3.2 and 2.8 Ga, i.e. well before the Great Oxidation Event (2.45–2.31 Ga), as indicated by various inorganic tracers of oxidation reactions and consistent with morphology of benthic deposits and evidence for aerobic N metabolism in N-isotope ratios at \textasciitilde\ 2.7 Ga. This picture of a wide diversification of the microbial biosphere during the Archean has largely been derived of bulk-rock geochemistry and petrography, supported by a recent increase in studied sample numbers and in constraints on their environments of deposition. Use of high-resolution microscopy and micro- to nanoscale analyses opens avenues to (re)assess and decipher the most ancient traces of life.",
    url = "https://doi.org/10.1016/j.earscirev.2020.103296",
    doi = "10.1016/j.earscirev.2020.103296",
    openalex = "W3043883447",
    references = "doi1010079783540775874, doi101016jearscirev200810005, doi101016jearscirev201601005, doi101016jearscirev201706012, doi101016jearscirev2019102888, doi101016jprecamres201307019, doi101016jprecamres201504018, doi101016jprecamres201804007, doi101016jprecamres2019105347, doi1010292017je005478, doi101038384055a0, doi101038nature13068, doi101038nature23261, doi101038s4158601914364, doi101098rstb20150493, doi101111j14724669200700118x, doi101126science16138451005, doi101126science2605108640, doi101126science28554301033, doi101128mr5522592871991, doi101146annurevmicro61080706093130, doi102110palo2013p13005r, doi107185geochemlet1817, openalexw1965399445, openalexw2026796374"
}

@article{doi1011111462292016225,
    author = "Campbell, Matthew A. and Bauersachs, Thorsten and Schwark, Lorenz and Proemse, Bernadette C. and Eberhard, Rolan and Coolen, Marco J. L. and Grice, Kliti",
    title = "Salinity‐driven ecology and diversity changes of heterocytous cyanobacteria in Australian freshwater and coastal‐marine microbial mats",
    year = "2022",
    journal = "Environmental Microbiology",
    abstract = "-fixing heterocytous cyanobacteria are considered to play a minor role in sustaining coastal microbial mat communities developing under normal marine to hypersaline conditions. Here, we investigated microbial mats growing under different salinities from freshwater mats of Giblin River (Tasmania) to metahaline and hypersaline mats of Shark Bay (Western Australia). Analyses of genetic (rRNA and mRNA) and biological markers (heterocyte glycolipids) revealed an unexpectedly large diversity of heterocytous cyanobacteria in all the studied microbial mat communities. It was observed that the taxonomic distribution as well as abundance of cyanobacteria is strongly affected by salinity. Low salinity favoured the presence of heterocytous cyanobacteria in freshwater mats, while mats thriving in higher salinities mainly supported the growth unicellular and filamentous non-heterocytous genera. However, even though mRNA transcripts derived from heterocytous cyanobacteria were lower in Shark Bay (<6\%) microbial mats, functional analyses revealed that these diazotrophs were transcribing a substantial proportion of the genes involved in biofilm formation and nitrogen fixation. Overall, our data reveal an unexpectedly high diversity of heterocytous cyanobacteria (e.g. Calothrix, Scytonema, Nodularia, Gloeotrichia, Stigonema, Fischerella and Chlorogloeopsis) that had yet to be described in metahaline and hypersaline microbial mats from Shark Bay and that they play a vital role in sustaining the ecosystem functioning of coastal-marine microbial mat systems.",
    url = "https://doi.org/10.1111/1462-2920.16225",
    doi = "10.1111/1462-2920.16225",
    openalex = "W4297145556",
    references = "doi101016jearscirev2019102921"
}

@article{doi101111gbi12539,
    author = "Runge, Eric and Mansor, Muammar and Kappler, Andreas and Duda, Jan‐Peter",
    title = "Microbial biosignatures in ancient deep‐sea hydrothermal sulfides",
    year = "2022",
    journal = "Geobiology",
    abstract = "Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.",
    url = "https://doi.org/10.1111/gbi.12539",
    doi = "10.1111/gbi.12539",
    openalex = "W4311663556",
    references = "doi1010160016703784900899, doi101016jearscirev200810005, doi101038384055a0, doi101038nature14447, doi101038s4157901901589, doi101046j13653091200000003x, doi10108001490450490438757, doi101126science2735277924, doi101126science7008198, doi102475ajs26811, doi105860choice300286, reitner2011microbial"
}

@incollection{stal2023microbial,
    author = "Stal, Lucas J.",
    title = "Microbial Mats",
    year = "2023",
    booktitle = "Encyclopedia of Astrobiology",
    url = "https://doi.org/10.1007/978-3-662-65093-6\_5085",
    doi = "10.1007/978-3-662-65093-6\_5085",
    openalex = "W4385306023",
    pages = "1913-1917",
    references = "doi101016jearscirev200810005, doi101016s0012825202001587, doi101016s025462991531156x, doi101073pnas97136947, doi101111j146981371995tb03051x, doi1023071543552"
}

@article{doi101038s41598025901750,
    author = "Makk, Judit and Németh, Ábel Csongor and Tóth, Erika and Németh, Péter and Kovács, Ivett and Demény, Attila and Sipos, György and Borsodi, Andrea K. and Lange-Enyedi, Nóra Tünde",
    title = "Actively forming microbial mats provide insight into the development of microdigitate stromatolites",
    year = "2025",
    journal = "Scientific Reports",
    abstract = "Stromatolites can be traced back to ∼3.5 billion years. They were widespread in the shorelines of ancient oceans and seas. However, they are uncommon nowadays, and basic information is lacking about how these unique carbonate structures developed. Here we study the unusually thick (3-5 cm) biofilms of the 79.2 °C outflow from Köröm thermal well (Hungary) and demonstrate that its microbial mat - carbonate architecture is similar to fossilized microdigitate stromatolites. Our observations reveal vertically oriented fibrous mineral fabrics, typical of stromatolites, in the red biofilm and clotted mesostructures, typical of thrombolites, in the green biofilm. These layers contain carbonate peloids and show network structures, formed by filamentous microbes. The 16S rRNA gene-based amplicon sequencing implies that numerous undescribed taxa may contribute to the carbonate mineralisation. The biofilms abundantly contain the phyla Bacteroidota, Pseudomonadota and Cyanobacteria. Geitlerinema PCC-8501 and Raineya are characteristic for the green biofilm, whereas uncultured Oxyphotobacteria, unc. Saprospiraceae and unc. Cytophagales are abundant in the red biofilm. A hydrogen-oxidizing Hydrogenobacter within the phylum Aquificota and unclassified Bacteria together with the phylum Deinococcota dominate the water and carbonate samples. The morphological structure and taxonomic composition of Köröm biofilm is a unique representation of the development processes of microbialite formations.",
    url = "https://doi.org/10.1038/s41598-025-90175-0",
    doi = "10.1038/s41598-025-90175-0",
    openalex = "W4407568578",
    references = "doi101016jearscirev2019102921, doi101016jprecamres2021106496"
}

@article{doi101111gbi70034,
    author = "Ouyang, Qing and Zhou, Chuanming and Lang, Xianguo and Qu, Yuangao and Shi, Hongyi and Sun, Yunpeng and Chen, Zhe",
    title = "A Flourishing Planktonic Microbial Community in an Interglacial Offshore Environment: Silicified Microfossils From the Cryogenian Datangpo Formation, South China",
    year = "2025",
    journal = "Geobiology",
    abstract = "The Cryogenian global glaciations profoundly shaped the evolution of Earth's ecosystem. An active Cryogenian biosphere accompanied by key evolutionary innovations has been indicated by geochemical and phylogenetic studies, although fossil records from Cryogenian strata are limited. In this study, we report a silicified microfossil assemblage from the Cryogenian Datangpo Formation in an interglacial offshore setting of the Yangtze block, South China. The Datangpo assemblage majorly comprises coccoidal microfossils classified into three morphological types, with minor components of fragmented filamentous forms. Morphological and structural observations combined with Raman spectroscopic analysis indicate that this microfossil assemblage may represent a planktonic microbial community dominated by cyanobacteria. The exceptionally silicified taphonomic window in the Datangpo microfossil assemblage provides a snapshot of primary producers in an offshore environment between the two Cryogenian global glaciations.",
    url = "https://doi.org/10.1111/gbi.70034",
    doi = "10.1111/gbi.70034",
    openalex = "W4414573129",
    references = "doi105710amgh210420203331"
}

@misc{crossrefNonemicrobial,
    title = "Microbial Mats",
    year = "None",
    booktitle = "SpringerReference",
    url = "https://doi.org/10.1007/springerreference\_223242",
    doi = "10.1007/springerreference\_223242",
    openalex = "W4241511283"
}