Section 8 update: Use of microelectrodes to measure in situ microbial activities in biofilms, sediments, and microbial mats

2008 ◽  
pp. 3483-3514 ◽  
Author(s):  
Armin Gieseke ◽  
Dirk de Beer
Keyword(s):  
Microbial Mats ◽  
Microbial Activities ◽  
Section 8

scholarly journals In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexusaggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

2021 ◽  
Vol 9 (3) ◽  
pp. 652
Author(s):  
Shigeru Kawai ◽  
Joval N. Martinez ◽  
Mads Lichtenberg ◽  
Erik Trampe ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Environmental Conditions ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Photosynthetic Bacterium ◽  
Early Morning ◽  
Metabolic Flexibility

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.

scholarly journals Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

2010 ◽  
Vol 192 (12) ◽  
pp. 3033-3042 ◽  
Author(s):  
Marcel T. J. van der Meer ◽  
Christian G. Klatt ◽  
Jason Wood ◽  
Donald A. Bryant ◽  
Mary M. Bateson ◽  
...  
Keyword(s):  
National Park ◽  
Microbial Mats ◽  
Hot Spring ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Anoxygenic Phototrophs ◽  
Lipid Biomarker ◽  
Genes Encoding

ABSTRACT Roseiflexus sp. strains were cultivated from a microbial mat of an alkaline siliceous hot spring in Yellowstone National Park. These strains are closely related to predominant filamentous anoxygenic phototrophs found in the mat, as judged by the similarity of small-subunit rRNA, lipid distributions, and genomic and metagenomic sequences. Like a Japanese isolate, R. castenholzii, the Yellowstone isolates contain bacteriochlorophyll a, but not bacteriochlorophyll c or chlorosomes, and grow photoheterotrophically or chemoheterotrophically under dark aerobic conditions. The genome of one isolate, Roseiflexus sp. strain RS1, contains genes necessary to support these metabolisms. This genome also contains genes encoding the 3-hydroxypropionate pathway for CO2 fixation and a hydrogenase, which might enable photoautotrophic metabolism, even though neither isolate could be grown photoautotrophically with H2 or H2S as a possible electron donor. The isolates exhibit temperature, pH, and sulfide preferences typical of their habitat. Lipids produced by these isolates matched much better with mat lipids than do lipids produced by R. castenholzii or Chloroflexus isolates.

scholarly journals Limitation of microbial processes at saturation-level salinities in a microbial mat covering a coastal saltflat

2021 ◽  
Author(s):  
Dimitri V. Meier ◽  
Andreas J. Greve ◽  
Arjun Chennu ◽  
Marit R. van Erk ◽  
Thirumahal Muthukrishnan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Mats ◽  
Microbial Processes ◽  
Saturation Level ◽  
Oxygenic Photosynthesis ◽  
Aerobic Respiration ◽  
Sulfur Cycling ◽  
Element Cycling ◽  
Salt Crust

Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of Early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate-reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinity ≤ 30% (w/v) in situ , at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed two days after reducing the pore water salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of Chloroflexi, photoheterotrophic Alphaproteobacteria , Bacteroidetes , and Archaea, the mat contained a distinct layer harboring filamentous Cyanobacteria , which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this saltflat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. Importance Due to their abilities to survive intense radiation and low water availability hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth the limitations imposed on microbial processes by saturation-level salinity have rarely been studied in situ . While abundance and diversity of microbial life in salt-saturated environments is well documented, most of our knowledge on process limitations stems from culture-based studies, few in situ studies, and theoretical calculations. Especially oxygenic photosynthesis has barely been explored beyond 5M NaCl (28% w/v). By applying a variety of biogeochemical and molecular methods we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations.

scholarly journals Taphonomy and ecology of deep-water Ediacaran organisms from northwestern Canada

1992 ◽  
Vol 6 ◽  
pp. 219-219 ◽  
Author(s):  
Guy M. Narbonne ◽  
Robert W. Dalrymple
Keyword(s):  
Shallow Water ◽  
Deep Water ◽  
Microbial Mats ◽  
Bedding Plane ◽  
Thin Layers ◽  
Sea Bottom ◽  
Windermere Supergroup ◽  
Storm Wave ◽  
Upper Slope

Although most occurrences of Ediacaran fossils are from shallow-shelf deposits, taxonomically-similar assemblages have recently been described from a 2.5 km-thick succession of dark mudstones and turbiditic sandstones in the Windermere Supergroup of the Mackenzie Mountains, northwestern Canada. The paleogeographic position (20-40 km seaward of the shelf edge), abundant evidence of mass flow, and the complete absence of in situ shallow-water features imply that deposition took place on a slope considerably below storm wave-base. Ediacaran fossils were not observed in axial trough deposits (lower parts of the Twitya and Sheepbed formations), but megafossils occur sporadically in lower to middle slope deposits higher in the same formations. Megafossils and trace fossils are present in upper slope settings (Blueflower Formation) at the top of the Ediacaran succession. The megafossil assemblage varies stratigraphically, but in all formations is dominated by discoid forms (e.g. Cyclomedusa, Ediacaria, Nimbia); frondose forms and vendomiids are very rare.Megafossils are preserved mainly as positive features on the soles of thin turbidite beds. Most fossiliferous beds begin with the rippled layer of the turbidite (Tc), but a few begin with the graded (Ta) or parallel-laminated (Tb) layer. Consistent orientation and high relief of individuals, evidence of mutual deformation during growth of adjacent organisms, and other taphonomic features imply that virtually all of the taxa represent benthic polypoid and frond-like organisms (not jellyfish). Slump structures occur commonly in the sandstone fill of fossils, suggesting that many of the organisms were buried alive by the turbidite and later decomposed. Other individuals, even on the same bedding plane, exhibit graded to laminated fill identical to that of the overlying turbidite bed, indicating that the depressions on the sea bottom produced by these individuals were empty at the time of turbidite deposition. Escape structures are absent, suggesting that the Ediacaran organisms were not capable of burrowing up through even thin layers of sand.Ediacaran megafossils are invariably preserved on black, wrinkled surfaces similar to those elsewhere interpreted as microbial mats. Molding of delicate features (including tentacles), preservation of open molds as negative epireliefs, and sedimentological evidence of considerable cohesion of these surfaces relative to the underlying turbiditic muds (Td,e) supports this interpretation, and suggests that microbial mats were as important in the preservation of these deep-water Ediacara faunas as they were in their shallow-water equivalents. The presence of the wrinkled mats and their associated Ediacaran fossils almost exclusively in the pyritic intervals of the succession suggests that both may have lived under exaerobic conditions in this deep-water setting.

Section 8 - Molecular tools to assess microbial activities

2006 ◽  
pp. 1563-1774 ◽  
Author(s):  
Pieter Breeuwer ◽  
Tjakko Abee
Keyword(s):  
Molecular Tools ◽  
Microbial Activities ◽  
Section 8

Sulfur speciation monitored in situ with solid state gold amalgam voltammetric microelectrodes: polysulfides as a special case in sediments, microbial mats and hydrothermal vent waters

2001 ◽  
Vol 3 (1) ◽  
pp. 61-66 ◽  
Author(s):  
George W. Luther, III ◽  
Brian T. Glazer ◽  
Laura Hohmann ◽  
Jeannette I. Popp ◽  
Martial Taillefert ◽  
...  
Keyword(s):  
Solid State ◽  
Hydrothermal Vent ◽  
Microbial Mats ◽  
Sulfur Speciation ◽  
Special Case

Impact of an oil field effluent on microbial activities in a Wyoming river

1984 ◽  
Vol 30 (6) ◽  
pp. 786-792 ◽  
Author(s):  
Michael A. Heitkamp ◽  
B. Thomas Johnson
Keyword(s):  
Carbon Dioxide Production ◽  
Oil Field ◽  
Microbial Activities ◽  
Discharge Point ◽  
Physiological Diversity ◽  
Oil Residue ◽  
Riverine Environment ◽  
Residue Levels ◽  
Oil Wastewater

The survival, functions, and physiological diversity of autochthonous sediment microbiota were examined in situ at five stations along the Little Popo Agie River, WY; one station above, one at, and three below a discharge point for oil wastewater from Union Oil Company's Dallas Field. Below the oil wastewater discharge point there were increases in electron-transport activity, carbon dioxide production, and microbial populations of heterotrophs, ammonifiers, hexadecane degraders, starch hydrolyzers, protein hydrolyzers, and sulfate reducers. At a station 1420 m below the discharge point, however, overall sediment microbial activities and all of the physiological groups of bacteria, except hexadecane-degrading microbiota, were at levels comparable with those at the control station above the discharge point. Similarly, mineralization of glucose, amino acids, hexanoic acid, and hexadecane was elevated at stations directly below the discharge point, but appeared to subside rapidly. Xenobiotic biodegradation potential of the sediments varied with the chemical and the sample location and was not directly related to oil residue levels in the sediment. Microorganisms thus appeared to maintain physiological diversity and increased in numbers and activity in a riverine environment that contained petroleum hydrocarbon concentrations known to be deleterious to freshwater fish and macrobenthic communities.

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