Articoli di riviste: "Microbial mat communities"

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Tice, Michael M., Daniel C. O. Thornton, Michael C. Pope, Thomas D. Olszewski e Jian Gong. "Archean Microbial Mat Communities". Annual Review of Earth and Planetary Sciences 39, n. 1 (30 maggio 2011): 297–319. http://dx.doi.org/10.1146/annurev-earth-040809-152356.

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Franks, Jonathan, e John F. Stolz. "Flat laminated microbial mat communities". Earth-Science Reviews 96, n. 3 (ottobre 2009): 163–72. http://dx.doi.org/10.1016/j.earscirev.2008.10.004.

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Rothschild, Lynn J., e Lorraine J. Giver. "Photosynthesis below the surface in a cryptic microbial mat". International Journal of Astrobiology 1, n. 4 (ottobre 2002): 295–304. http://dx.doi.org/10.1017/s1473550403001320.

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The discovery of subsurface communities has encouraged speculation that such communities might be present on planetary bodies exposed to harsh surface conditions, including the early Earth. While the astrobiology community has focused on the deep subsurface, near-subsurface environments are unique in that they provide some protection while allowing partial access to photosynthetically active radiation. Previously we identified near-surface microbial communities based on photosynthesis. Here we assess the productivity of such an ecosystem by measuring in situ carbon fixation rates in an intertidal marine beach through a diurnal cycle, and find them surprisingly productive. Gross fixation along a transect (99×1 m) perpendicular to the shore was highly variable and depended on factors such as moisture and mat type, with a mean of ~41 mg C fixed m−2 day−1. In contrast, an adjacent well-established cyanobacterial mat dominated by Lyngbya aestuarii was ~12 times as productive (~500 mg C fixed m−2 day−1). Measurements made of the Lyngbya mat at several times per year revealed a correlation between total hours of daylight and gross daily production. From these data, annual gross fixation was estimated for the Lyngbya mat and yielded a value of ~1.3×105 g m−2 yr−1. An analysis of pulse-chase data obtained in the study in conjunction with published literature on similar ecosystems suggests that subsurface interstitial mats may be an overlooked endogenous source of organic carbon, mostly in the form of excreted fixed carbon.

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Revsbech, Niels Peter, Erik Trampe, Mads Lichtenberg, David M. Ward e Michael Kühl. "In SituHydrogen Dynamics in a Hot Spring Microbial Mat during a Diel Cycle". Applied and Environmental Microbiology 82, n. 14 (6 maggio 2016): 4209–17. http://dx.doi.org/10.1128/aem.00710-16.

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ABSTRACTMicrobes can produce molecular hydrogen (H2) via fermentation, dinitrogen fixation, or direct photolysis, yet the H2dynamics in cyanobacterial communities has only been explored in a few natural systems and mostly in the laboratory. In this study, we investigated the dielin situH2dynamics in a hot spring microbial mat, where various ecotypes of unicellular cyanobacteria (Synechococcussp.) are the only oxygenic phototrophs. In the evening, H2accumulated rapidly after the onset of darkness, reaching peak values of up to 30 μmol H2liter−1at about 1-mm depth below the mat surface, slowly decreasing to about 11 μmol H2liter−1just before sunrise. Another pulse of H2production, reaching a peak concentration of 46 μmol H2liter−1, was found in the early morning under dim light conditions too low to induce accumulation of O2in the mat. The light stimulation of H2accumulation indicated that nitrogenase activity was an important source of H2during the morning. This is in accordance with earlier findings of a distinct early morning peak in N2fixation and expression ofSynechococcusnitrogenase genes in mat samples from the same location. Fermentation might have contributed to the formation of H2during the night, where accumulation of other fermentation products lowered the pH in the mat to less than pH 6 compared to a spring source pH of 8.3.IMPORTANCEHydrogen is a key intermediate in anaerobic metabolism, and with the development of a sulfide-insensitive microsensor for H2, it is now possible to study the microdistribution of H2in stratified microbial communities such as the photosynthetic microbial mat investigated here. The ability to measure H2profiles within the mat compared to previous measurements of H2emission gives much more detailed information about the sources and sinks of H2in such communities, and it was demonstrated that the high rates of H2formation in the early morning when the mat was exposed to low light intensities might be explained by nitrogen fixation, where H2is formed as a by-product.

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Nübel, Ulrich, Ferran Garcia-Pichel, Michael Kühl e Gerard Muyzer. "Quantifying Microbial Diversity: Morphotypes, 16S rRNA Genes, and Carotenoids of Oxygenic Phototrophs in Microbial Mats". Applied and Environmental Microbiology 65, n. 2 (1 febbraio 1999): 422–30. http://dx.doi.org/10.1128/aem.65.2.422-430.1999.

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ABSTRACT We quantified the diversity of oxygenic phototrophic microorganisms present in eight hypersaline microbial mats on the basis of three cultivation-independent approaches. Morphological diversity was studied by microscopy. The diversity of carotenoids was examined by extraction from mat samples and high-pressure liquid chromatography analysis. The diversity of 16S rRNA genes from oxygenic phototrophic microorganisms was investigated by extraction of total DNA from mat samples, amplification of 16S rRNA gene segments from cyanobacteria and plastids of eukaryotic algae by phylum-specific PCR, and sequence-dependent separation of amplification products by denaturing-gradient gel electrophoresis. A numerical approach was introduced to correct for crowding the results of chromatographic and electrophoretic analyses. Diversity estimates typically varied up to twofold among mats. The congruence of richness estimates and Shannon-Weaver indices based on numbers and proportional abundances of unique morphotypes, 16S rRNA genes, and carotenoids unveiled the underlying diversity of oxygenic phototrophic microorganisms in the eight mat communities studied.

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Jesser, Kelsey J., Heather Fullerton, Kevin W. Hager e Craig L. Moyer. "Quantitative PCR Analysis of Functional Genes in Iron-Rich Microbial Mats at an Active Hydrothermal Vent System (Lō'ihi Seamount, Hawai'i)". Applied and Environmental Microbiology 81, n. 9 (13 febbraio 2015): 2976–84. http://dx.doi.org/10.1128/aem.03608-14.

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ABSTRACTThe chemolithotrophicZetaproteobacteriarepresent a novel class ofProteobacteriawhich oxidize Fe(II) to Fe(III) and are the dominant bacterial population in iron-rich microbial mats.Zetaproteobacteriawere first discovered at Lō'ihi Seamount, located 35 km southeast off the big island of Hawai'i, which is characterized by low-temperature diffuse hydrothermal venting. Novel nondegenerate quantitative PCR (qPCR) assays for genes associated with microbial nitrogen fixation, denitrification, arsenic detoxification, Calvin-Benson-Bassham (CBB), and reductive tricarboxylic acid (rTCA) cycles were developed using selected microbial mat community-derived metagenomes. Nitrogen fixation genes were not detected, but all other functional genes were present. This suggests that arsenic detoxification and denitrification processes are likely cooccurring in addition to two modes of carbon fixation. Two groups of microbial mat community types were identified by terminal restriction fragment length polymorphism (T-RFLP) and were further described based on qPCR data for zetaproteobacterial abundance and carbon fixation mode preference. qPCR variance was associated with mat morphology but not with temperature or sample site. Geochemistry data were significantly associated with sample site and mat morphology. Together, these qPCR assays constitute a functional gene signature for iron microbial mat communities across a broad array of temperatures, mat types, chemistries, and sampling sites at Lō'ihi Seamount.

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Shen, Yan, Volker Thiel, Pablo Suarez-Gonzalez, Sebastiaan W. Rampen e Joachim Reitner. "Sterol preservation in hypersaline microbial mats". Biogeosciences 17, n. 3 (7 febbraio 2020): 649–66. http://dx.doi.org/10.5194/bg-17-649-2020.

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Abstract. Microbial mats are self-sustaining benthic ecosystems composed of highly diverse microbial communities. It has been proposed that microbial mats were widespread in Proterozoic marine environments, prior to the emergence of bioturbating organisms at the Precambrian–Cambrian transition. One characteristic feature of Precambrian biomarker records is that steranes are typically absent or occur in very low concentrations. This has been explained by low eukaryotic source inputs, or degradation of primary produced sterols in benthic microbial mats (“mat-seal effect”). To better understand the preservational pathways of sterols in microbial mats, we analyzed freely extractable and carbonate-bound lipid fractions as well as decalcified extraction residues in different layers of a recent calcifying mat (∼1500 years) from the hypersaline Lake 2 on the island of Kiritimati, central Pacific. A variety of C27–C29 sterols and distinctive C31 4α-methylsterols (4α-methylgorgosterol and 4α-methylgorgostanol, biomarkers for dinoflagellates) were detected in freely extractable and carbonate-bound lipid pools. These sterols most likely originated from organisms living in the water column and the upper mat layers. This autochthonous biomass experienced progressive microbial transformation and degradation in the microbial mat, as reflected by a significant drop in total sterol concentrations, up to 98 %, in the deeper layers, and a concomitant decrease in total organic carbon. Carbonate-bound sterols were generally low in abundance compared to the freely extractable portion, suggesting that incorporation into the mineral matrix does not play a major role in the preservation of eukaryotic sterols in this mat. Likewise, pyrolysis of extraction residues suggested that sequestration of steroid carbon skeletons into insoluble organic matter was low compared to hopanoids. Taken together, our findings argue for a major mat-seal effect affecting the distribution and preservation of steroids in the mat studied. This result markedly differs from recent findings made for another microbial mat growing in the nearby hypersaline Lake 22 on the same island, where sterols showed no systematic decrease with depth. The observed discrepancies in the taphonomic pathways of sterols in microbial mats from Kiritimati may be linked to multiple biotic and abiotic factors including salinity and periods of subaerial exposure, implying that caution has to be exercised in the interpretation of sterol distributions in modern and ancient microbial mat settings.

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Brooks, Chequita N., e Erin K. Field. "Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats". mBio 11, n. 6 (15 dicembre 2020): e02720-20. http://dx.doi.org/10.1128/mbio.02720-20.

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ABSTRACTFreshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ. Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.

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Griffiths, Robert P., Bruce A. Caldwell, Kermit Cromack Jr. e Richard Y. Morita. "Douglas-fir forest soils colonized by ectomycorrhizal mats. I. Seasonal variation in nitrogen chemistry and nitrogen cycle transformation rates". Canadian Journal of Forest Research 20, n. 2 (1 febbraio 1990): 211–18. http://dx.doi.org/10.1139/x90-030.

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Monthly samples of ectomycorrhizal mat soils from a maturing Douglas-fir forest and adjacent nonmat soils were collected and analyzed for respiration, acetylene reduction activity, denitrification rates, extractable ammonium, nitrogen mineralization, microbial biomass, temperature, pH, percent moisture, total phosphate, nitrogen, and carbon. Seasonal patterns suggested complex interactions among the host tree, ectomycorrhizal fungus, and the mat microbial community as influenced by seasonal changes in moisture, temperature, and light availability. The most dramatic changes in rates were found during moisture-temperature transition periods in the spring and fall. Respiration within the mat community was highest during the period when tree growth is normally the greatest (in the spring and fall). In addition, there was a major respiration peak observed in the winter that we hypothesize was caused by the utilization of labile carbon by microheterotrophs. Differences were also observed between mat and nonmat soils in respiration rates, microbial biomass carbon, acetylene reduction activity, and levels of mineralizable nitrogen, which were all generally higher in the mat soils, and pH and denitrification rates, which were generally lower in nonmat soils. There is also evidence that suggests that nitrogen is very tightly coupled within the mat communities.

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Jungblut, Anne D., Ian Hawes, Tyler J. Mackey, Megan Krusor, Peter T. Doran, Dawn Y. Sumner, Jonathan A. Eisen, Colin Hillman e Alexander K. Goroncy. "Microbial Mat Communities along an Oxygen Gradient in a Perennially Ice-Covered Antarctic Lake". Applied and Environmental Microbiology 82, n. 2 (13 novembre 2015): 620–30. http://dx.doi.org/10.1128/aem.02699-15.

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ABSTRACTLake Fryxell is a perennially ice-covered lake in the McMurdo Dry Valleys, Antarctica, with a sharp oxycline in a water column that is density stabilized by a gradient in salt concentration. Dissolved oxygen falls from 20 mg liter−1to undetectable over one vertical meter from 8.9- to 9.9-m depth. We provide the first description of the benthic mat community that falls within this oxygen gradient on the sloping floor of the lake, using a combination of micro- and macroscopic morphological descriptions, pigment analysis, and 16S rRNA gene bacterial community analysis. Our work focused on three macroscopic mat morphologies that were associated with different parts of the oxygen gradient: (i) “cuspate pinnacles” in the upper hyperoxic zone, which displayed complex topography and were dominated by phycoerythrin-rich cyanobacteria attributable to the genusLeptolyngbyaand a diverse but sparse assemblage of pennate diatoms; (ii) a less topographically complex “ridge-pit” mat located immediately above the oxic-anoxic transition containingLeptolyngbyaand an increasing abundance of diatoms; and (iii) flat prostrate mats in the upper anoxic zone, dominated by a green cyanobacterium phylogenetically identified asPhormidium pseudopriestleyiand a single diatom,Diadesmis contenta. Zonation of bacteria was by lake depth and by depth into individual mats. Deeper mats had higher abundances of bacteriochlorophylls and anoxygenic phototrophs, includingChlorobiandChloroflexi. This suggests that microbial communities form assemblages specific to niche-like locations. Mat morphologies, underpinned by cyanobacterial and diatom composition, are the result of local habitat conditions likely defined by irradiance and oxygen and sulfide concentrations.

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Žutinić, Petar, Ines Petrić, Sanja Gottstein, Marija Gligora Udovič, Koraljka Kralj Borojević, Jasmina Kamberović, Anamarija Kolda, Anđelka Plenković-Moraj e Ivančica Ternjej. "Microbial mats as shelter microhabitat for amphipods in an intermittent karstic spring". Knowledge & Management of Aquatic Ecosystems, n. 419 (2018): 7. http://dx.doi.org/10.1051/kmae/2017061.

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Microbial mats represent complex communities where cyanobacteria and diatoms as key organisms provide shelter for diverse assemblages of aquatic invertebrates, like the small stygophilous amphipod Synurella ambulans. Studies addressing such communities in the karst springs have rarely examined springheads, and have ignored intermittent springs. During high flow conditions the stygophilic crustaceans are flushed to the surface of a temporary stream Krčić where microbial mats prevent their drift and enables their successful retreat into underground in the periods of drought. The objective of this study was to characterize the microbial mat community of the Krčić Spring as a shelter for S. ambulans during strong current and high water level. Representative samples for diatom and cyanobacterial species identification and composition, as well as the fresh mat material for potential animal activity and cyanobacterial phylogenetic analysis were collected. The most dominant diatom was Achnanthidium minutissimum, whilst Fragilaria capucina, Meridion circulare, Navicula cryptocephala and Nitzschia palea had abundance greater than 0.5%. Morphological observations of cyanobacteria revealed that Phormidium favosum was the most dominant, with Hydrocoleum muscicola as a subdominant. Cyanobacterial phylogenetic relationship revealed two distinct clusters: (i) "Phormidium cluster", confirming morphological observations in both winter and spring samples, and (ii) "Wilmottia cluster", a first report for Croatia and found exclusively in the winter sample. Laboratory observations revealed a small stygophilic amphipod S. ambulans, hiding and feeding inside the pockets of fresh microbial mat. The intermittent Krčić Spring as a predator-free and competitor-free ecosystem provides a spatiotemporal conformity between microbial mat and stygophilous amphipod.

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Nold, S. C., e D. M. Ward. "Photosynthate partitioning and fermentation in hot spring microbial mat communities." Applied and environmental microbiology 62, n. 12 (1996): 4598–607. http://dx.doi.org/10.1128/aem.62.12.4598-4607.1996.

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Griffiths, R. P., E. R. Ingham, B. A. Caldwell, M. A. Castellano e K. Cromack. "Microbial characteristics of ectomycorrhizal mat communities in Oregon and California". Biology and Fertility of Soils 11, n. 3 (giugno 1991): 196–202. http://dx.doi.org/10.1007/bf00335767.

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Peeters, Karolien, Elie Verleyen, Dominic A. Hodgson, Peter Convey, Damien Ertz, Wim Vyverman e Anne Willems. "Heterotrophic bacterial diversity in aquatic microbial mat communities from Antarctica". Polar Biology 35, n. 4 (11 settembre 2011): 543–54. http://dx.doi.org/10.1007/s00300-011-1100-4.

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Hirayama, Hisako, Michinari Sunamura, Ken Takai, Takuro Nunoura, Takuro Noguchi, Hanako Oida, Yasuo Furushima, Hiroyuki Yamamoto, Tamotsu Oomori e Koki Horikoshi. "Culture-Dependent and -Independent Characterization of Microbial Communities Associated with a Shallow Submarine Hydrothermal System Occurring within a Coral Reef off Taketomi Island, Japan". Applied and Environmental Microbiology 73, n. 23 (5 ottobre 2007): 7642–56. http://dx.doi.org/10.1128/aem.01258-07.

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ABSTRACT Microbial communities in a shallow submarine hydrothermal system near Taketomi Island, Japan, were investigated using cultivation-based and molecular techniques. The main hydrothermal activity occurred in a craterlike basin (depth, ∼23 m) on the coral reef seafloor. The vent fluid (maximum temperature, >52°C) contained 175 μM H2S and gas bubbles mainly composed of CH4 (69%) and N2 (29%). A liquid serial dilution cultivation technique targeting a variety of metabolism types quantified each population in the vent fluid and in a white microbial mat located near the vent. The most abundant microorganisms cultivated from both the fluid and the mat were autotrophic sulfur oxidizers, including mesophilic Thiomicrospira spp. and thermophilic Sulfurivirga caldicuralii. Methane oxidizers were the second most abundant organisms in the fluid; one novel type I methanotroph exhibited optimum growth at 37°C, and another novel type I methanotroph exhibited optimum growth at 45°C. The number of hydrogen oxidizers cultivated only from the mat was less than the number of sulfur and methane oxidizers, although a novel mesophilic hydrogen-oxidizing member of the Epsilonproteobacteria was isolated. Various mesophilic to hyperthermophilic heterotrophs, including sulfate-reducing Desulfovibrio spp., iron-reducing Deferribacter sp., and sulfur-reducing Thermococcus spp., were also cultivated. Culture-independent 16S rRNA gene clone analysis of the vent fluid and mat revealed highly diverse archaeal communities. In the bacterial community, S. caldicuralii was identified as the predominant phylotype in the fluid (clonal frequency, 25%). Both bacterial clone libraries indicated that there were bacterial communities involved in sulfur, hydrogen, and methane oxidation and sulfate reduction. Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant.

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Ward, David M., Michael J. Ferris, Stephen C. Nold e Mary M. Bateson. "A Natural View of Microbial Biodiversity within Hot Spring Cyanobacterial Mat Communities". Microbiology and Molecular Biology Reviews 62, n. 4 (1 dicembre 1998): 1353–70. http://dx.doi.org/10.1128/mmbr.62.4.1353-1370.1998.

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SUMMARY This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

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Grey, K., LS Moore, RV Burne, BK Pierson e J. Bauld. "Lake Thetis, Western Australia: and example of Saline Lake Sedimentation dominated by Benthic Microbial Processes". Marine and Freshwater Research 41, n. 2 (1990): 275. http://dx.doi.org/10.1071/mf9900275.

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Lake Thetis is a saline coastal lake in south-western Australia, a region of winter rainfall and summer drought. The lake demonstrates the close relationships between environmental variation and the nature of resident benthic microbial communities. Crenulate cyanobacterial mats occur in the low-lying areas adjacent to the lake. Lithified stromatolites with patches of living coccoid cyanobacterial mat characterize the littoral area, whereas a thick flocculent mat composed of phototrophic prokaryotes (principally purple sulfur bacteria) and diatoms has accumulated in the central lake basin. Lake Thetis is distinguished from other coastal saline lakes by the presence of the unusual flocculent mat and by the juxtaposition of this microbial community to the marginal lithified stromatolites. Further, some of the latter exhibit internal digitate columnar branching which, though common in Precambrian examples, is rare in modern environments.

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Ley, Ruth E., J. Kirk Harris, Joshua Wilcox, John R. Spear, Scott R. Miller, Brad M. Bebout, Julia A. Maresca, Donald A. Bryant, Mitchell L. Sogin e Norman R. Pace. "Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat". Applied and Environmental Microbiology 72, n. 5 (maggio 2006): 3685–95. http://dx.doi.org/10.1128/aem.72.5.3685-3695.2006.

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ABSTRACT We applied nucleic acid-based molecular methods, combined with estimates of biomass (ATP), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes were amplified by PCR from community genomic DNA extracted from layers, cloned, and sequenced. Bacteria dominated the mat and displayed unexpected and unprecedented diversity. The majority (1,336) of the 1,586 bacterial 16S rRNA sequences generated were unique, representing 752 species (≥97% rRNA sequence identity) in 42 of the main bacterial phyla, including 15 novel candidate phyla. The diversity of the mat samples differentiated according to the chemical milieu defined by concentrations of O2 and H2S. Bacteria of the phylum Chloroflexi formed the majority of the biomass by percentage of bulk rRNA and of clones in rRNA gene libraries. This result contradicts the general belief that cyanobacteria dominate these communities. Although cyanobacteria constituted a large fraction of the biomass in the upper few millimeters (>80% of the total rRNA and photosynthetic pigments), Chloroflexi sequences were conspicuous throughout the mat. Filamentous Chloroflexi bacteria were identified by fluorescence in situ hybridization within the polysaccharide sheaths of the prominent cyanobacterium Microcoleus chthonoplastes, in addition to free living in the mat. The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity.

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Akond, Z., M. Alam, MS Ahmed e MNH Mollah. "Multivariate statistical techniques for metagenomic analysis of microbial community recovered from environmental samples". Journal of Bio-Science 24 (18 luglio 2018): 45–53. http://dx.doi.org/10.3329/jbs.v24i0.37486.

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High-throughput big dataset generated through next generation sequencing (NGS) of DNA samples helps identify key differences in the function and taxonomy between microbial communities as well as shed light on the diversity of microbes, cooperation and evolution in any particular ecosystem. During this study, three statistical techniques namely, Random Forest (RF), Multidimensional Scaling (MDS) and Linear Discriminant Analysis (LDA) approaches were employed for functional analysis of 212 publicly available metagenomic datasets within and between 10 environments against 27 metabolic functions. RF generates the 8 most important metabolic variables along with MDS and LDA among which Photosynthesis has the highest score (70.20); Phages, prophages has the second highest score (61.31) and Membrane Transport was found to have the eighth highest score (45.29). The MDS plot was found useful to visualize the separation of the microbes from human or animal hosts from other samples along the first dimension and the separation of the aquatic and mat communities along the second dimension. LDA analyses compared the extent of the microbial samples into three broad groups: the human and animal associated samples, the microbial mats, and the aquatic samples. RF showed that phage activity is a major difference between host-associated microbial communities and free-living. The MDS and LDA techniques suggest that mat communities were unique from both the animal associated metagenomes and the aquatic samples with differences in the vitamin and cofactor metabolism.J. bio-sci. 24: 45-53, 2016

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Díez, Beatriz, Karolina Bauer e Birgitta Bergman. "Epilithic Cyanobacterial Communities of a Marine Tropical Beach Rock (Heron Island, Great Barrier Reef): Diversity and Diazotrophy". Applied and Environmental Microbiology 73, n. 11 (6 aprile 2007): 3656–68. http://dx.doi.org/10.1128/aem.02067-06.

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ABSTRACT The diversity and nitrogenase activity of epilithic marine microbes in a Holocene beach rock (Heron Island, Great Barrier Reef, Australia) with a proposed biological calcification “microbialite” origin were examined. Partial 16S rRNA gene sequences from the dominant mat (a coherent and layered pink-pigmented community spread over the beach rock) and biofilms (nonstratified, differently pigmented microbial communities of small shallow depressions) were retrieved using denaturing gradient gel electrophoresis (DGGE), and a clone library was retrieved from the dominant mat. The 16S rRNA gene sequences and morphological analyses revealed heterogeneity in the cyanobacterial distribution patterns. The nonheterocystous filamentous genus Blennothrix sp., phylogenetically related to Lyngbya, dominated the mat together with unidentified nonheterocystous filaments of members of the Pseudanabaenaceae and the unicellular genus Chroococcidiopsis. The dominance and three-dimensional intertwined distribution of these organisms were confirmed by nonintrusive scanning microscopy. In contrast, the less pronounced biofilms were dominated by the heterocystous cyanobacterial genus Calothrix, two unicellular Entophysalis morphotypes, Lyngbya spp., and members of the Pseudanabaenaceae family. Cytophaga-Flavobacterium-Bacteroides and Alphaproteobacteria phylotypes were also retrieved from the beach rock. The microbial diversity of the dominant mat was accompanied by high nocturnal nitrogenase activities (as determined by in situ acetylene reduction assays). A new DGGE nifH gene optimization approach for cyanobacterial nitrogen fixers showed that the sequences retrieved from the dominant mat were related to nonheterocystous uncultured cyanobacterial phylotypes, only distantly related to sequences of nitrogen-fixing cultured cyanobacteria. These data stress the occurrence and importance of nonheterocystous epilithic cyanobacteria, and it is hypothesized that such epilithic cyanobacteria are the principal nitrogen fixers of the Heron Island beach rock.

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Balskus, Emily P., Rebecca J. Case e Christopher T. Walsh. "The biosynthesis of cyanobacterial sunscreen scytonemin in intertidal microbial mat communities". FEMS Microbiology Ecology 77, n. 2 (12 maggio 2011): 322–32. http://dx.doi.org/10.1111/j.1574-6941.2011.01113.x.

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Green, J. W., A. H. Knoll e K. Swett. "Microfossils from silicified stromatolitic carbonates of the Upper Proterozoic Limestone-Dolomite 'Series', central East Greenland". Geological Magazine 126, n. 5 (1 settembre 1989): 567–85. http://dx.doi.org/10.1017/s0016756800022858.

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AbstractSilicified flake conglomerates andin situstratiform stromatolites of the Upper Proterozoic (c.700–800 Ma) Limestone-Dolomite ‘Series’, central East Greenland, contain well preserved microfossils. Five stratigraphic horizons within the 1200 m succession contain microbial mat assemblages, providing a broad palaeontological representation of late Proterozoic peritidal mat communities. Comparison of assemblages demonstrates that the taxonomy and diversity of mat builder, dweller, and allochthonous populations all vary considerably within and among horizons. The primary mat builder in most assemblages isSiphonophycus inornatum, a sheath-forming prokaryote of probable but not unequivocally established cyanobacterial affinities. An unusual low diversity unit in Bed 17 is dominated by a different builder,Tenuofilum septatum, while a thin cryptalgal horizon in Bed 18 is built almost exclusively bySiphonophycus kestron.Although variable taphonomic histories contribute to observed assemblage variation, most differences within and among horizons appear to reflect the differential success or failure of individual microbial populations in colonizing different tidal flat microenvironments. Twenty-two taxa are recognized, of which two are described as new:Myxococcoides stragulescensn.sp. andScissilisphaera gradatan. sp.

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23

Wang, Ning, Qi Li, Mengqi Jiang, Weizhen Zhang, Hao Zhang, Qixuan Song, Zhongda Hu, Jibiao Zhang e Zheng Zheng. "Effects of Distinct Revegetation Methods on Growth and Microbial Properties of Vallisneria natans". Water 12, n. 5 (2 maggio 2020): 1294. http://dx.doi.org/10.3390/w12051294.

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This study investigated the effects of the mud-sinking (MS) method, agar gel-sinking (AS) method and agar gel-sinking with artificial aquatic mat (ASA) method on the growth, physiological characteristics, water purification capacity, and associated microbial community of the different organs of Vallisneria natans (V. natans). Results showed that the growth of agar-based growth (group AS and ASA) were more effective than the mud-wrapped method (group MS), exhibiting longer length, higher fresh weight and biomass of agar-based V. natans with the artificial aquatic mat (group ASA) being higher than those of other groups. MS caused a stress response in the oxidative system, which then inhibited photosynthesis. Results of water quality measurements showed that the three planting methods positively affected water purification without significant differences (p > 0.05). Besides, there was no significant difference (p > 0.05) between the microbial communities in terms of the roots and those found in rhizosphere soils in the MS group with high throughput sequencing. Meanwhile, the addition of agar in the AS and ASA groups increased the diversity of rhizosphere soil microbial communities and reduced the diversity of root microbial communities. Microbial community compositions in the rhizosphere soil and root differed significantly (p < 0.05). High throughput sequencing and scanning electron microscopy (SEM) also revealed that the biofilm on the surfaces were different, with Proteobacteria and Cyanophyta consistently dominating. This study provides new insights on the more effective revegetation methods of V. natans, researched the environmental impact of the addition of agar, and provides some theoretical support for the revegetation of submerged macrophytes under ecological restoration.

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Verleyen, E., K. Sabbe, DA Hodgson, S. Grubisic, A. Taton, S. Cousin, A. Wilmotte, A. De Wever, K. Van der Gucht e W. Vyverman. "Structuring effects of climate-related environmental factors on Antarctic microbial mat communities". Aquatic Microbial Ecology 59 (11 marzo 2010): 11–24. http://dx.doi.org/10.3354/ame01378.

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25

Tkavc, Rok, Cene Gostinčar, Martina Turk, Pieter T. Visscher, Aharon Oren e Nina Gunde-Cimerman. "Bacterial communities in the ‘petola’ microbial mat from the Sečovlje salterns (Slovenia)". FEMS Microbiology Ecology 75, n. 1 (9 novembre 2010): 48–62. http://dx.doi.org/10.1111/j.1574-6941.2010.00985.x.

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26

Falcón, L. I., R. Cerritos, L. E. Eguiarte e V. Souza. "Nitrogen Fixation in Microbial Mat and Stromatolite Communities from Cuatro Cienegas, Mexico". Microbial Ecology 54, n. 2 (21 aprile 2007): 363–73. http://dx.doi.org/10.1007/s00248-007-9240-3.

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27

Kamran, Aysha, Kathrin Sauter, Andreas Reimer, Theresa Wacker, Joachim Reitner e Michael Hoppert. "Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy". Microorganisms 9, n. 1 (29 dicembre 2020): 62. http://dx.doi.org/10.3390/microorganisms9010062.

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(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

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28

Salvatore, Mark R., Schuyler R. Borges, John E. Barrett, Eric R. Sokol, Lee F. Stanish, Sarah N. Power e Paul Morin. "Remote characterization of photosynthetic communities in the Fryxell basin of Taylor Valley, Antarctica". Antarctic Science 32, n. 4 (16 marzo 2020): 255–70. http://dx.doi.org/10.1017/s0954102020000176.

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AbstractWe investigate the spatial distribution, spectral properties and temporal variability of primary producers (e.g. communities of microbial mats and mosses) throughout the Fryxell basin of Taylor Valley, Antarctica, using high-resolution multispectral remote-sensing data. Our results suggest that photosynthetic communities can be readily detected throughout the Fryxell basin based on their unique near-infrared spectral signatures. Observed intra- and inter-annual variability in spectral signatures are consistent with short-term variations in mat distribution, hydration and photosynthetic activity. Spectral unmixing is also implemented in order to estimate mat abundance, with the most densely vegetated regions observed from orbit correlating spatially with some of the most productive regions of the Fryxell basin. Our work establishes remote sensing as a valuable tool in the study of these ecological communities in the McMurdo Dry Valleys and demonstrates how future scientific investigations and the management of specially protected areas could benefit from these tools and techniques.

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Burne, Robert V., e Ken Johnson. "Sea-level variation and the zonation of microbialites in Hamelin Pool, Shark Bay, Western Australia". Marine and Freshwater Research 63, n. 11 (2012): 994. http://dx.doi.org/10.1071/mf12184.

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The application of modern methods of time-series analysis to a record of sea-level variation at Flint Cliff, Hamelin Pool, between October 1983 and April 1985, shows that astronomical tides account for only one of the following five key components of the record: a seasonal oceanic cycle; a short-term irregular cycle; the complex astronomical tidal system in the Pool; isolated major events; and less marked variations probably reflecting wind stress, still able to defeat the astronomical tide in the short-term. We have compared the inundation record with precisely surveyed elevation ranges of various microbial communities. The dominance of a seasonal cycle is the fundamental determinant of variation in the duration of immersion and exposure determining the littoral zonation of microbial mats in Hamelin Pool. The astronomical tide is not the major cause of this variation. The microbial communities fall into three zones. In Zone 3, the microbialite-forming colloform mat is virtually never exposed. In Zone 2, smooth, reticulate and mamillate mats colonise the lower littoral environment. Here, many of the exposed microbialites have been stranded by the falling sea level, and are colonised by intermittently submerged microbial communities that modify the stranded lithified microbialites. Zone 1 is inundated only under exceptional circumstances and microbial communities are ephemeral.

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30

Londry, Kathleen L., Pascal H. Badiou e Stephen E. Grasby. "Identification of a Marine Green Alga Percursaria percursa from Hypersaline Springs in the Middle of the North American Continent". Canadian Field-Naturalist 119, n. 1 (1 gennaio 2005): 82. http://dx.doi.org/10.22621/cfn.v119i1.84.

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The chlorophycean alga Percursaria percursa (Ulvaceae, Ulvales, Chlorophyceae), typical of marine inter-tidal zones, is reported for the first time from hypersaline springs located along the north-western shore of Lake Winnipegosis in Manitoba. Although not usually found inland, P. percursa is the dominant member of microbial mat communities that thrive in shallow pools at the outlets of hypersaline springs.

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31

Omoregie, Enoma O., Vincent Mastalerz, Gert de Lange, Kristina L. Straub, Andreas Kappler, Hans Røy, Alina Stadnitskaia, Jean-Paul Foucher e Antje Boetius. "Biogeochemistry and Community Composition of Iron- and Sulfur-Precipitating Microbial Mats at the Chefren Mud Volcano (Nile Deep Sea Fan, Eastern Mediterranean)". Applied and Environmental Microbiology 74, n. 10 (31 marzo 2008): 3198–215. http://dx.doi.org/10.1128/aem.01751-07.

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ABSTRACT In this study we determined the composition and biogeochemistry of novel, brightly colored, white and orange microbial mats at the surface of a brine seep at the outer rim of the Chefren mud volcano. These mats were interspersed with one another, but their underlying sediment biogeochemistries differed considerably. Microscopy revealed that the white mats were granules composed of elemental S filaments, similar to those produced by the sulfide-oxidizing epsilonproteobacterium “Candidatus Arcobacter sulfidicus.” Fluorescence in situ hybridization indicated that microorganisms targeted by a “Ca. Arcobacter sulfidicus”-specific oligonucleotide probe constituted up to 24% of the total the cells within these mats. Several 16S rRNA gene sequences from organisms closely related to “Ca. Arcobacter sulfidicus” were identified. In contrast, the orange mat consisted mostly of bright orange flakes composed of empty Fe(III) (hydr)oxide-coated microbial sheaths, similar to those produced by the neutrophilic Fe(II)-oxidizing betaproteobacterium Leptothrix ochracea. None of the 16S rRNA gene sequences obtained from these samples were closely related to sequences of known neutrophilic aerobic Fe(II)-oxidizing bacteria. The sediments below both types of mats showed relatively high sulfate reduction rates (300 nmol·cm−3·day−1) partially fueled by the anaerobic oxidation of methane (10 to 20 nmol·cm−3·day−1). Free sulfide produced below the white mat was depleted by sulfide oxidation within the mat itself. Below the orange mat free Fe(II) reached the surface layer and was depleted in part by microbial Fe(II) oxidation. Both mats and the sediments underneath them hosted very diverse microbial communities and contained mineral precipitates, most likely due to differences in fluid flow patterns.

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32

Yannarell, Anthony C., Timothy F. Steppe e Hans W. Paerl. "Genetic Variance in the Composition of Two Functional Groups (Diazotrophs and Cyanobacteria) from a Hypersaline Microbial Mat". Applied and Environmental Microbiology 72, n. 2 (febbraio 2006): 1207–17. http://dx.doi.org/10.1128/aem.72.2.1207-1217.2006.

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ABSTRACT Examination of variation in ecological communities can lead to an understanding of the forces that structure communities, the consequences of change at the ecosystem level, and the relevant scales involved. This study details spatial and seasonal variability in the composition of nitrogen-fixing and cyanobacterial (i.e., oxygenic photosynthetic) functional groups of a benthic, hypersaline microbial mat from Salt Pond, San Salvador Island, Bahamas. This system shows extreme annual variability in the salinity of the overlying water and the extent of water coverage. Analysis of molecular variance and FST tests of genetic differentiation of nifH and cyanobacterial 16S rRNA gene clone libraries allowed for changes at multiple taxonomic levels (i.e., above, below, and at the species level) to inform the conclusions regarding these functional groups. Composition of the nitrogen-fixing community showed significant seasonal changes related to salinity, while cyanobacterial composition showed no consistent seasonal pattern. Both functional groups exhibited significant spatial variation, changing with depth in the mat and horizontally with distance from the shoreline. The patterns of change suggest that cyanobacterial composition was more insensitive to water stress, and consequently, cyanobacteria dominated the nitrogen-fixing community during dry months but gave way to a more diverse community of diazotrophs in wet months. This seasonal pattern may allow the mat community to respond quickly to water-freshening events after prolonged dry conditions (system recovery) and maintain ecosystem function in the face of disturbance during the wet season (system resilience).

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Dick, Gregory J., Sharon L. Grim e Judith M. Klatt. "Controls on O2Production in Cyanobacterial Mats and Implications for Earth's Oxygenation". Annual Review of Earth and Planetary Sciences 46, n. 1 (30 maggio 2018): 123–47. http://dx.doi.org/10.1146/annurev-earth-082517-010035.

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Cyanobacterial mats are widely assumed to have been globally significant hot spots of biogeochemistry and evolution during the Archean and Proterozoic, but little is known about their quantitative contributions to global primary productivity or Earth's oxygenation. Modern systems show that mat biogeochemistry is the outcome of concerted activities and intimate interactions between various microbial metabolisms. Emerging knowledge of the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis by versatile cyanobacteria, and their interactions with sulfur-oxidizing bacteria and sulfate-reducing bacteria, highlights how ecological and geochemical processes can control O2production in cyanobacterial mats in unexpected ways. This review explores such biological controls on O2production. We argue that the intertwined effects of light availability, redox geochemistry, regulation and competition of microbial metabolisms, and biogeochemical feedbacks result in emergent properties of cyanobacterial mat communities that are all critical yet largely overlooked mechanisms to potentially explain the protracted nature of Earth's oxygenation.

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Engel, Annette Summers, Natuschka Lee, Megan L. Porter, Libby A. Stern, Philip C. Bennett e Michael Wagner. "Filamentous “Epsilonproteobacteria” Dominate Microbial Mats from Sulfidic Cave Springs". Applied and Environmental Microbiology 69, n. 9 (settembre 2003): 5503–11. http://dx.doi.org/10.1128/aem.69.9.5503-5511.2003.

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ABSTRACT Hydrogen sulfide-rich groundwater discharges from springs into Lower Kane Cave, Wyoming, where microbial mats dominated by filamentous morphotypes are found. The full-cycle rRNA approach, including 16S rRNA gene retrieval and fluorescence in situ hybridization (FISH), was used to identify these filaments. The majority of the obtained 16S rRNA gene clones from the mats were affiliated with the “Epsilonproteobacteria” and formed two distinct clusters, designated LKC group I and LKC group II, within this class. Group I was closely related to uncultured environmental clones from petroleum-contaminated groundwater, sulfidic springs, and sulfidic caves (97 to 99% sequence similarity), while group II formed a novel clade moderately related to deep-sea hydrothermal vent symbionts (90 to 94% sequence similarity). FISH with newly designed probes for both groups specifically stained filamentous bacteria within the mats. FISH-based quantification of the two filament groups in six different microbial mat samples from Lower Kane Cave showed that LKC group II dominated five of the six mat communities. This study further expands our perceptions of the diversity and geographic distribution of “Epsilonproteobacteria” in extreme environments and demonstrates their biogeochemical importance in subterranean ecosystems.

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Varin, Thibault, Connie Lovejoy, Anne D. Jungblut, Warwick F. Vincent e Jacques Corbeil. "Metagenomic profiling of Arctic microbial mat communities as nutrient scavenging and recycling systems". Limnology and Oceanography 55, n. 5 (5 agosto 2010): 1901–11. http://dx.doi.org/10.4319/lo.2010.55.5.1901.

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36

Saghaï, Aurélien, Ana Gutiérrez-Preciado, Philippe Deschamps, David Moreira, Paola Bertolino, Marie Ragon e Purificación López-García. "Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond". Environmental Microbiology 19, n. 6 (10 maggio 2017): 2405–21. http://dx.doi.org/10.1111/1462-2920.13754.

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37

Hegler, Florian, Tina Lösekann-Behrens, Kurt Hanselmann, Sebastian Behrens e Andreas Kappler. "Influence of Seasonal and Geochemical Changes on the Geomicrobiology of an Iron Carbonate Mineral Water Spring". Applied and Environmental Microbiology 78, n. 20 (3 agosto 2012): 7185–96. http://dx.doi.org/10.1128/aem.01440-12.

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ABSTRACTFuschna Spring in the Swiss Alps (Engadin region) is a bicarbonate iron(II)-rich, pH-neutral mineral water spring that is dominated visually by dark green microbial mats at the side of the flow channel and orange iron(III) (oxyhydr)oxides in the flow channel. Gradients of O2, dissolved iron(II), and bicarbonate establish in the water. Our goals were to identify the dominating biogeochemical processes and to determine to which extent changing geochemical conditions along the flow path and seasonal changes influence mineral identity, crystallinity, and microbial diversity. Geochemical analysis showed microoxic water at the spring outlet which became fully oxygenated within 2.3 m downstream. X-ray diffraction and Mössbauer spectroscopy revealed calcite (CaCO3) and ferrihydrite [Fe(OH)3] to be the dominant minerals which increased in crystallinity with increasing distance from the spring outlet. Denaturing gradient gel electrophoresis banding pattern cluster analysis revealed that the microbial community composition shifted mainly with seasons and to a lesser extent along the flow path. 16S rRNA gene sequence analysis showed that microbial communities differ between the flow channel and the flanking microbial mat. Microbial community analysis in combination with most-probable-number analyses and quantitative PCR (qPCR) showed that the mat was dominated by cyanobacteria and the channel was dominated by microaerophilic Fe(II) oxidizers (1.97 × 107± 4.36 × 10616S rRNA gene copies g−1usingGallionella-specific qPCR primers), while high numbers of Fe(III) reducers (109cells/g) were identified in both the mat and the flow channel. Phototrophic and nitrate-reducing Fe(II) oxidizers were present as well, although in lower numbers (103to 104cells/g). In summary, our data suggest that mainly seasonal changes caused microbial community shifts, while geochemical gradients along the flow path influenced mineral crystallinity.

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Varin, Thibault, Connie Lovejoy, Anne D. Jungblut, Warwick F. Vincent e Jacques Corbeil. "Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic". Applied and Environmental Microbiology 78, n. 2 (11 novembre 2011): 549–59. http://dx.doi.org/10.1128/aem.06354-11.

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ABSTRACTPolar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived fromProteobacteriaandCyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation ofActinobacteriaandAlphaproteobacteriain the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.

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Nelson, Lyle L., e Emily F. Smith. "Tubey or not tubey: Death beds of Ediacaran macrofossils or microbially induced sedimentary structures?" Geology 47, n. 10 (12 agosto 2019): 909–13. http://dx.doi.org/10.1130/g46473.1.

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Abstract Within the upper Ediacaran Esmeralda Member of the Deep Spring Formation in southeastern California, USA, an ∼3 m stratigraphic interval contains multiple clastic bedding surfaces with enigmatic, three-dimensionally preserved corrugated tubes (<60 cm in length and 6 cm in width). When viewed as fragments and in situ on bedding planes, these resemble larger versions of annulated, tubular soft-bodied macrofossils that are common in late Ediacaran biotic assemblages regionally and globally. Despite superficial similarities to casts and molds of body fossils preserved in correlative strata, we suggest these tubes are instead previously undescribed organosedimentary structures that developed through differential compaction of rippled heterolithic interbeds bound by pyritized microbial mat layers. These distinctive structures formed within peritidal settings in the latest Ediacaran Period as the result of specific ecological and environmental conditions marked by flourishing microbial mat communities and dysoxic sediments. This interpretation may inform the biogenicity of other structures previously reported as macroscopic body or trace fossils.

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Abed, Raeid M. M., Nimer M. D. Safi, Jürgen Köster, Dirk de Beer, Yasser El-Nahhal, Jürgen Rullkötter e Ferran Garcia-Pichel. "Microbial Diversity of a Heavily Polluted Microbial Mat and Its Community Changes following Degradation of Petroleum Compounds". Applied and Environmental Microbiology 68, n. 4 (aprile 2002): 1674–83. http://dx.doi.org/10.1128/aem.68.4.1674-1683.2002.

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ABSTRACT We studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (Wadi Gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. Phormidium- and Oscillatoria-like cyanobacterial morphotypes were dominant in the field. Bacteria belonging to different groups, mainly the Cytophaga-Flavobacterium-Bacteriodes group, the γ and β subclasses of the class Proteobacteria, and the green nonsulfur bacteria, were also detected. In slurry experiments, these communities efficiently degraded phenanthrene and dibenzothiophene completely in 7 days both in the light and in the dark. n-Octadecane and pristane were degraded to 25 and 34% of their original levels, respectively, within 7 days, but there was no further degradation until 40 days. Both cyanobacterial and bacterial communities exhibited noticeable changes concomitant with degradation of the compounds. The populations enriched by exposure to petroleum compounds included a cyanobacterium affiliated phylogenetically with Halomicronema. Bacteria enriched both in the light and in the dark, but not bacteria enriched in any of the controls, belonged to the newly described Holophaga-Geothrix-Acidobacterium phylum. In addition, another bacterial population, found to be a member of green nonsulfur bacteria, was detected only in the bacteria treated in the light. All or some of the populations may play a significant role in metabolizing the petroleum compounds. We concluded that the microbial mats from Wadi Gaza are rich in microorganisms with high biodegradative potential.

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Abed, Raeid M. M., Niculina Musat, Florin Musat e Marc Mußmann. "Structure of microbial communities and hydrocarbon-dependent sulfate reduction in the anoxic layer of a polluted microbial mat". Marine Pollution Bulletin 62, n. 3 (marzo 2011): 539–46. http://dx.doi.org/10.1016/j.marpolbul.2010.11.030.

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42

Elshahed, Mostafa S., John M. Senko, Fares Z. Najar, Stephen M. Kenton, Bruce A. Roe, Thomas A. Dewers, John R. Spear e Lee R. Krumholz. "Bacterial Diversity and Sulfur Cycling in a Mesophilic Sulfide-Rich Spring". Applied and Environmental Microbiology 69, n. 9 (settembre 2003): 5609–21. http://dx.doi.org/10.1128/aem.69.9.5609-5621.2003.

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ABSTRACT An artesian sulfide- and sulfur-rich spring in southwestern Oklahoma is shown to sustain an extremely rich and diverse microbial community. Laboratory incubations and autoradiography studies indicated that active sulfur cycling is occurring in the abundant microbial mats at Zodletone spring. Anoxygenic phototrophic bacteria oxidize sulfide to sulfate, which is reduced by sulfate-reducing bacterial populations. The microbial community at Zodletone spring was analyzed by cloning and sequencing 16S rRNA genes. A large fraction (83%) of the microbial mat clones belong to sulfur- and sulfate-reducing lineages within δ-Proteobacteria, purple sulfur γ-Proteobacteria, ε-Proteobacteria, Chloroflexi, and filamentous Cyanobacteria of the order Oscillatoria as well as a novel group within γ-Proteobacteria. The 16S clone library constructed from hydrocarbon-exposed sediments at the source of the spring had a higher diversity than the mat clone library (Shannon-Weiner index of 3.84 compared to 2.95 for the mat), with a higher percentage of clones belonging to nonphototrophic lineages (e.g., Cytophaga, Spirochaetes, Planctomycetes, Firmicutes, and Verrucomicrobiae). Many of these clones were closely related to clones retrieved from hydrocarbon-contaminated environments and anaerobic hydrocarbon-degrading enrichments. In addition, 18 of the source clones did not cluster with any of the previously described microbial divisions. These 18 clones, together with previously published or database-deposited related sequences retrieved from a wide variety of environments, could be clustered into at least four novel candidate divisions. The sulfate-reducing community at Zodletone spring was characterized by cloning and sequencing a 1.9-kb fragment of the dissimilatory sulfite reductase (DSR) gene. DSR clones belonged to the Desulfococcus-Desulfosarcina-Desulfonema group, Desulfobacter group, and Desulfovibrio group as well as to a deeply branched group in the DSR tree with no representatives from cultures. Overall, this work expands the division-level diversity of the bacterial domain and highlights the complexity of microbial communities involved in sulfur cycling in mesophilic microbial mats.

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Paerl, Hans W., Brad M. Bebout, Samantha B. Joye e David J. Des Marais. "Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities". Limnology and Oceanography 38, n. 6 (settembre 1993): 1150–61. http://dx.doi.org/10.4319/lo.1993.38.6.1150.

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Santoyo, Gustavo. "Unveiling Taxonomic Diversity and Functional Composition Differences of Microbial Mat Communities Through Comparative Metagenomics". Geomicrobiology Journal 38, n. 7 (24 maggio 2021): 639–48. http://dx.doi.org/10.1080/01490451.2021.1926600.

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45

Sekar, Raju, DeEtta K. Mills, Elizabeth R. Remily, Joshua D. Voss e Laurie L. Richardson. "Microbial Communities in the Surface Mucopolysaccharide Layer and the Black Band Microbial Mat of Black Band-Diseased Siderastrea siderea". Applied and Environmental Microbiology 72, n. 9 (settembre 2006): 5963–73. http://dx.doi.org/10.1128/aem.00843-06.

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ABSTRACT Microbial community profiles and species composition associated with two black band-diseased colonies of the coral Siderastrea siderea were studied by 16S rRNA-targeted gene cloning, sequencing, and amplicon-length heterogeneity PCR (LH-PCR). Bacterial communities associated with the surface mucopolysaccharide layer (SML) of apparently healthy tissues of the infected colonies, together with samples of the black band disease (BBD) infections, were analyzed using the same techniques for comparison. Gene sequences, ranging from 424 to 1,537 bp, were retrieved from all positive clones (n = 43 to 48) in each of the four clone libraries generated and used for comparative sequence analysis. In addition to LH-PCR community profiling, all of the clone sequences were aligned with LH-PCR primer sequences, and the theoretical lengths of the amplicons were determined. Results revealed that the community profiles were significantly different between BBD and SML samples. The SML samples were dominated by γ-proteobacteria (53 to 64%), followed by β-proteobacteria (18 to 21%) and α-proteobacteria (5 to 11%). In contrast, both BBD clone libraries were dominated by α-proteobacteria (58 to 87%), followed by verrucomicrobia (2 to 10%) and 0 to 6% each of δ-proteobacteria, bacteroidetes, firmicutes, and cyanobacteria. Alphaproteobacterial sequence types related to the bacteria associated with toxin-producing dinoflagellates were observed in BBD clone libraries but were not found in the SML libraries. Similarly, sequences affiliated with the family Desulfobacteraceae and toxin-producing cyanobacteria, both believed to be involved in BBD pathogenesis, were found only in BBD libraries. These data provide evidence for an association of numerous toxin-producing heterotrophic microorganisms with BBD of corals.

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Ward, David M., Mary M. Bateson, Michael J. Ferris, Michael Kühl, Andrea Wieland, Alex Koeppel e Frederick M. Cohan. "Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function". Philosophical Transactions of the Royal Society B: Biological Sciences 361, n. 1475 (6 ottobre 2006): 1997–2008. http://dx.doi.org/10.1098/rstb.2006.1919.

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We have investigated microbial mats of alkaline siliceous hot springs in Yellowstone National Park as natural model communities to learn how microbial populations group into species-like fundamental units. Here, we bring together empirical patterns of the distribution of molecular variation in predominant mat cyanobacterial populations, theory-based modelling of how to demarcate phylogenetic clusters that correspond to ecological species and the dynamic patterns of the physical and chemical microenvironments these populations inhabit and towards which they have evolved adaptations. We show that putative ecotypes predicted by the theory-based model correspond well with distribution patterns, suggesting populations with distinct ecologies, as expected of ecological species. Further, we show that increased molecular resolution enhances our ability to detect ecotypes in this way, though yet higher molecular resolution is probably needed to detect all ecotypes in this microbial community.

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47

Grünke, S., A. Lichtschlag, D. de Beer, J. Felden, V. Salman, A. Ramette, H. N. Schulz-Vogt e A. Boetius. "Mats of psychrophilic thiotrophic bacteria associated with cold seeps of the Barents Sea". Biogeosciences Discussions 9, n. 3 (28 marzo 2012): 3917–48. http://dx.doi.org/10.5194/bgd-9-3917-2012.

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Abstract. This study investigated the bacterial diversity associated with microbial mats of polar deep-sea cold seeps. The mats are associated with high upward fluxes of sulfide produced by anaerobic oxidation of methane, and grow at temperatures close to the freezing point of seawater. They ranged from small patches of 0.2–5 m in diameter (gray mats) to extensive fields covering up to 850 m2 of seafloor (white mats) and were formed by diverse sulfide-oxidizing bacteria differing in color and size. Overall, both the dominant mat-forming thiotrophs as well as the associated bacterial communities inhabiting the mats differed in composition for each mat type as determined by microscopy, 16S rRNA gene sequencing and Automated Ribosomal Intergenic Spacer Analysis. While the smaller gray mats were associated with a highly diverse composition of sulfide oxidizers, the large white mats were composed of only 1–2 types of gliding Beggiatoa filaments. Molecular analyses showed that most of the dominant mat-forming sulfide oxidizers were phylogenetically different from, but still closely related to thiotrophs known from warmer ocean realms. The psychrophilic nature of the polar mat-forming thiotrophs was tested by visual observation of active mats at in situ temperature compared to their warming to >4 °C. The temperature range of mat habitats and the variation of sulfide and oxygen fluxes appear to be the main factors supporting the diversity of mat-forming thiotrophs in cold seeps at continental margins.

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48

Grünke, S., A. Lichtschlag, D. de Beer, J. Felden, V. Salman, A. Ramette, H. N. Schulz-Vogt e A. Boetius. "Mats of psychrophilic thiotrophic bacteria associated with cold seeps of the Barents Sea". Biogeosciences 9, n. 8 (6 agosto 2012): 2947–60. http://dx.doi.org/10.5194/bg-9-2947-2012.

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Abstract (sommario):

Abstract. This study investigated the bacterial diversity associated with microbial mats of polar deep-sea cold seeps. The mats were associated with high upward fluxes of sulfide produced by anaerobic oxidation of methane, and grew at temperatures close to the freezing point of seawater. They ranged from small patches of 0.2–5 m in diameter (gray mats) to extensive fields covering up to 850 m2 of seafloor (white mats) and were formed by diverse sulfide-oxidizing bacteria differing in color and size. Overall, both the dominant mat-forming thiotrophs as well as the associated bacterial communities inhabiting the mats differed in composition for each mat type as determined by microscopy, 16S rRNA gene sequencing and automated ribosomal intergenic spacer analysis. While the smaller gray mats were associated with a highly diverse composition of sulfide oxidizers, the larger white mats were composed of only 1–2 types of gliding Beggiatoa filaments. Molecular analyses showed that most of the dominant mat-forming sulfide oxidizers were phylogenetically different from, but still closely related to, thiotrophs known from warmer ocean realms. The psychrophilic nature of the polar mat-forming thiotrophs was tested by visual observation of active mats at in situ temperature compared to their warming to >4 °C. The temperature range of mat habitats and the variation of sulfide and oxygen fluxes appear to be the main factors supporting the diversity of mat-forming thiotrophs in cold seeps at continental margins.

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49

Emerson, David, Jeremy A. Rentz, Timothy G. Lilburn, Richard E. Davis, Henry Aldrich, Clara Chan e Craig L. Moyer. "A Novel Lineage of Proteobacteria Involved in Formation of Marine Fe-Oxidizing Microbial Mat Communities". PLoS ONE 2, n. 8 (1 agosto 2007): e667. http://dx.doi.org/10.1371/journal.pone.0000667.

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50

Golet, D. S., e B. B. Ward. "Vertical distribution of denitrification potential, denitrifying bacteria, and benzoate utilization in intertidal microbial mat communities". Microbial Ecology 42, n. 1 (giugno 2001): 22–34. http://dx.doi.org/10.1007/s002489900184.

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