Diversity and distribution of a key sulpholipid biosynthetic gene in marine microbial assemblages

Sulphoquinovosyldiacylglycerols (SQDG) are polar sulphur‐containing membrane lipids, whose presence has been related to a microbial strategy to adapt to phosphate deprivation. In this study, we have targeted the sqdB gene coding the uridine 5′‐diphosphate‐sulphoquinovose (UDP‐SQ) synthase involved in the SQDG biosynthetic pathway to assess potential microbial sources of SQDGs in the marine environment. The phylogeny of the sqdB‐coding protein reveals two distinct clusters: one including green algae, higher plants and cyanobacteria, and another one comprising mainly non‐photosynthetic bacteria, as well as other cyanobacteria and algal groups. Evolutionary analysis suggests that the appearance of UDP‐SQ synthase occurred twice in cyanobacterial evolution, and one of those branches led to the diversification of the protein in members of the phylum Proteobacteria. A search of homologues of sqdB‐proteins in marine metagenomes strongly suggested the presence of heterotrophic bacteria potential SQDG producers. Application of newly developed sqdB gene primers in the marine environment revealed a high diversity of sequences affiliated to cyanobacteria and Proteobacteria in microbial mats, while in North Sea surface water, most of the detected sqdB genes were attributed to the cyanobacterium Synechococcus sp. Lipid analysis revealed that specific SQDGs were characteristic of microbial mat depth, suggesting that SQDG lipids are associated with specific producers.     

Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy

We studied the interaction between phototrophic and chemolithoautotrophic sulphide-oxidizing microorganisms in natural microbial mats forming in sulphidic streams. The structure of these mats varied between two end-members: one characterized by a layer dominated by large sulphur-oxidizing bacteria (SOB; mostly Beggiatoa-like) on top of a cyanobacterial layer (B/C mats) and the other with an inverted structure (C/B mats). C/B mats formed where the availability of oxygen from the water column was limited (<5 μm). Aerobic chemolithotrophic activity of the SOB depended entirely on oxygen produced locally by cyanobacteria during high light conditions. In contrast, B/C mats formed at locations where oxygen in the water column was comparatively abundant (>45 μM) and continuously present. Here SOB were independent of the photosynthetic activity of cyanobacteria and outcompeted the cyanobacteria in the uppermost layer of the mat where energy sources for both functional groups were concentrated. Outcompetition of photosynthetic microbes in the presence of light was facilitated by the decoupling of aerobic chemolithotrophy and oxygenic phototrophy. Remarkably, the B/C mats conserved much less energy than the C/B mats, although similar amounts of light and chemical energy were available. Thus ecosystems do not necessarily develop towards optimal energy usage. Our data suggest that, when two independent sources of energy are available, the structure and activity of microbial communities is primarily determined by the continuous rather than the intermittent energy source, even if the time-integrated energy flux of the intermittent energy source is greater.     

Pigments, light penetration, and photosynthetic activity in the multi-layered microbial mats of Great Sippewissett Salt Marsh, Massachusetts

The multi-layered microbial mats in the sand flats of Great Sippewissett Salt Marsh were found to have five distinct layers of phototrophic organisms. The top 1–3 mm contained oxygenic phototrophs. The lower 3–4 mm contained anoxygenic phototrophic bacteria. The uppermost gold layer contained diatoms and cyanobacteria, and chlorophyll a was the major chlorophyll. The next layer down was green and was composed of primarily filamentous cyanobacteria containing chlorophyll a. This was followed by a bright pink layer of bacteriochlorophyll b-containing purple sulfur bacteria. The lowest layer was a thin dull green layer of green sulfur bacteria containing bacteriochlorophyll c. The distribution of the chlorophylls with depth revealed that two-thirds of the total chlorophyll in the mat was composed of bacteriochlorophylls present in the anoxygenic phototrophys. The cyanobacterial layers and both purple sulfur bacterial layers had photoautotrophic activity. Light was attenuated in the uppermost layers so that less than 5% of the total radiation at the surface penetrated to the layers of anoxygenic phototrophys.     

LIPOPHILIC PIGMENTS FROM CYANOBACTERIAL (BLUE-GREEN ALGAL) AND DIATOM MATS IN HAMELIN POOL,SHARK BAY,WESTERN AUSTRALIA1

Lipophilic pigments were examined in microbial mat communities dominated by cyanobacteria in the intertidal zone and by diatoms in the subtidal and sublittoral zones of Hamelin Pool, Shark Bay, Western Australia. These microbial mats have evolutionary significance because of their similarity to lithified stromatolites from the Proterozoic and Early Paleozoic eras. Fucoxanthin, diatoxanthin, diadinoxanthin, β-carotene, and chlorophylls a and c characterized the diatom mats, whereas cyanobacterial mats contained myxoxanthophyll zeaxanthin, echinenone, β-carotene, chlorophyll a and, in some cases, sheath pigment. The presence of bacteriochlorophyll a with in the mats suggest a close association of photosynthetic bacteria with diatoms and cyanobacteria. The high carotenoids: chlorophyll a ratios (0.84–2.44 wt/wt) in the diatom mats suggest that carotenoids served a photoprotective function in this high light environment. By contrast, cyanobacterial sheath pigment may have largely supplanted the photoprotective role of carotenoids in the intertidal mats.     

ANTARCTIC CYANOBACTERIA: LIGHT,NUTRIENTS, AND PHOTOSYNTHESIS IN THE MICROBIAL MAT ENVIRONMENT1

The microenvironmental and photosynthetic characteristics of Antarctic microbial mats were measured in a series of ponds near McMurdo Sound. As elsewhere in Antarctica, these cold-water benthic communities were dominated by oscillatoriacean cyanobacteria. Despite large variations in mat thickness, surface morphology, and color, all of the communities had a similar pigment organization, with a surface carotenoid-rich layer that overlaid a deep chlorophyll maximum (DCM) enriched in phycocyanin as well as chlorophyll a. Spectroradiometric analyses showed that the DCM population inhabited an orange-red shade environment. In several of the mats, the deep-living trichomes migrated up to the surface of the mat within 2 h in response to a 10-fold decrease in surface irradiance. The euphotic layer of the mats was supersaturated in oxygen and contained ammonium and dissolved reactive phosphorus concentrations in excess of 100 mg N·m^?3 or P·m^?3. Integral photosynthesis by core samples was saturated at low irradiances and varied two- to threefold throughout the continuous 24-h radiation cycle. Oxygen microelectrode analyses showed that the photosynthetic rates were slow to negligible near the surface and maximal in the DCM. These compressed, nutrient-rich euphotic zones have some properties analogous to planktonic systems, but the integrated photosynthetic responses of the community reflect the strong self-shading within the mat and physiological dominance by the motile, DCM populations.     

Photosynthesis versus Exopolymer Degradation in the Formation of Microbialites on the Atoll of Kiritimati,Republic of Kiribati,Central Pacific

Aragonitic microbialites, characterized by a reticulate fabric, were discovered beneath lacustrine microbial mats on the atoll of Kiritimati, Republic of Kiribati, Central Pacific. The microbial mats, with cyanobacteria as major primary producers, grow in evaporated seawater modified by calcium carbonate and gypsum precipitation and calcium influx via surface and/or groundwaters. Despite the high aragonite supersaturation and a high photosynthetic activity, only minor aragonite precipitates are observed in the top parts of the microbial mats. Instead, major aragonite precipitation takes place in lower mat parts at the transition to the anoxic zone. The prokaryotic community shows a high number of phylotypes closely related to halotolerant taxa and/or taxa with preference to oligotrophic habitats. Soil- and plant- inhabiting bacteria underline a potential surface or subsurface influx from terrestrial areas, while chitinase-producing representatives coincide with the occurrence of insect remains in the mats. Strikingly, many of the clones have their closest relatives in microorganisms either involved in methane production or consumption of methane or methyl compounds. Methanogens, represented by the methylotrophic genus Methanohalophilus, appear to be one of the dominant organisms in anaerobic mat parts. All this points to a significant role of methane and methyl components in the carbon cycle of the mats. Nonetheless, thin sections and physicochemical gradients through the mats, as well as the ¹²C-depleted carbon isotope signatures of carbonates indicate that spherulitic components of the microbialites initiate in the photosynthesis-dominated orange mat top layer, and further grow in the green and purple layer below. Therefore, these spherulites are considered as product of an extraordinary high photosynthesis effect simultaneous to a high inhibition by pristine exopolymers. Then, successive heterotrophic bacterial activity leads to a condensation of the exopolymer framework, and finally to the formation of crevice-like zones of partly degraded exopolymers. Here initiation of horizontal aragonite layers and vertical aragonite sheets of the microbialite occurs, which are considered as a product of high photosynthesis at decreasing degree of inhibition. Finally, at low supersaturation and almost lack of inhibition, syntaxial growth of aragonite crystals at lamellae surfaces leads to thin fibrous aragonite veneers. While sulfate reduction, methylotrophy, methanogenesis and ammonification play an important role in element cycling of the mat, there is currently no evidence for a crucial role of them in CaCO₃ precipitation. Instead, photosynthesis and exopolymer degradation sufficiently explain the observed pattern and fabric of microbialite formation.     

Cyanobacterial mats from hot springs produce antimicrobial compounds and quorum-sensing inhibitors under natural conditions

Polar (water) and non-polar (ethyl acetate) extracts from the cyanobacterial layer (top 1–3 mm) of four hot spring microbial mats in the Sultanate of Oman were tested for their antibacterial, antidiatom and quorum-sensing inhibitory activities under natural conditions. The chemical composition of the active extracts was analysed using gas chromatography–mass spectrometry (GC-MS). Cyanobacteria within these mats were identified by direct microscopy while the total bacterial community composition was compared using automated ribosomal intergenic spacer analysis (ARISA). Only the extracts from Bowshar and Nakhl mats showed antibacterial properties against Bacillus sp., Micrococcus luteus, Shigella sonnei, Salmonella enterica and Klebsiella pneumoniae. All tested extracts inhibited the growth of the benthic diatom Amphora coffeaeformis. Extracts from Bowshar, Rustaq and Nakhl inhibited quorum-sensing of the reporter strains Chromobacterium violaceum CV017 and Agrobacterium tumefaciens NTL4. The highest bioactivity was recorded for ethyl acetate extracts from Nakhl mats, which had the lowest number of operational taxonomic units (OTUs). Using GC-MS, 74 chemical compounds were obtained, however with different distribution among the four mat extracts (similarity < 43%). Various cyanobacteria, belonging mainly to Chroococcus, Phormidium, Leptolyngbya, Spirulina and Lyngbya were detected in the different mats, and each mat had its unique bacterial community, as confirmed by ARISA profiles. We conclude that antimicrobial and quorum-sensing inhibitory compounds can be produced by hot spring mat microorganisms under natural conditions and the differences in these compounds could be attributed to the differences in the mats’ bacterial composition as well as the physical–chemical conditions of the springs.     

Effects of microbial mats on germination and seedling survival of typical dune slack species in the Netherlands

The role of microbial mats in wet dune slack succession is often discussed. We tested if presence of microbial mats may retard dune slack succession by lowering the germination and seeding survival of successor species. This hypothesis was tested on a set of typical dune slack species of the Frisian Islands in two climate chamber experiments. The species were separated into early-, intermediate- and late successional species. There were large differences in germination rates between species (2% – >200% compared to the reference), but within a species the high germination rates were mostly found on sand without a microbial mat. Only the germination of Agrostis stolonifera appeared to be stimulated by the presence of a well-developed microbial mat, they were even higher than in the reference. Seedling survival also did not show different responses between successional stages. Seedlings placed on top of a microbial mat showed for most species lower survival rates compared to seedlings that were planted or placed on top of the sand. Growth was the only measured variable that differed between successional groups. Species of the early- and intermediate successional stages grew significantly better if a microbial mat was present whereas late successional species were not stimulated. Early and intermediate successional species seem to be favored by the presence of a microbial mat. An explanation for this may be that they can profit from the enhanced nitrogen availability caused by N₂-fixation by cyanobacteria in the microbial mat. This revised version was published online in June 2006 with corrections to the Cover Date.     

Growth of elaborate microbial pinnacles in Lake Vanda,Antarctica

Microbial pinnacles in ice‐covered Lake Vanda, McMurdo Dry Valleys, Antarctica, extend from the base of the ice to more than 50 m water depth. The distribution of microbial communities, their photosynthetic potential, and pinnacle morphology affects the local accumulation of biomass, which in turn shapes pinnacle morphology. This feedback, plus environmental stability, promotes the growth of elaborate microbial structures. In Lake Vanda, all mats sampled from greater than 10 m water depth contained pinnacles with a gradation in size from <1‐mm‐tall tufts to pinnacles that were centimeters tall. Small pinnacles were cuspate, whereas larger ones had variable morphology. The largest pinnacles were up to ~30 cm tall and had cylindrical bases and cuspate tops. Pinnacle biomass was dominated by cyanobacteria from the morphological and genomic groups Leptolyngbya, Phormidium, and Tychonema. The photosynthetic potential of these cyanobacterial communities was high to depths of several millimeters into the mat based on PAM fluorometry, and sufficient light for photosynthesis penetrated ~5 mm into pinnacles. The distribution of photosynthetic potential and its correlation to pinnacle morphology suggests a working model for pinnacle growth. First, small tufts initiate from random irregularities in prostrate mat. Some tufts grow into pinnacles over the course of ~3 years. As pinnacles increase in size and age, their interiors become colonized by a more diverse community of cyanobacteria with high photosynthetic potential. Biomass accumulation within this subsurface community causes pinnacles to swell, expanding laminae thickness and creating distinctive cylindrical bases and cuspate tops. This change in shape suggests that pinnacle morphology emerges from a specific distribution of biomass accumulation that depends on multiple microbial communities fixing carbon in different parts of pinnacles. Similarly, complex patterns of biomass accumulation may be reflected in the morphology of elaborate ancient stromatolites.     

Bioinformatic,phylogenetic and chemical analysis of the UV-absorbing compounds scytonemin and mycosporine-like amino acids from the microbial mat communities of Shark Bay,Australia

Shark Bay, Western Australia is a World Heritage area with extensive microbial mats and stromatolites. Microbial communities that comprise these mats have developed a range of mitigation strategies against changing levels of photosynthetically active and ultraviolet radiation, including the ability to biosynthesise the UV-absorbing natural products scytonemin and mycosporine-like amino acids (MAAs). To this end, the distribution of photoprotective pigments within Shark Bay microbial mats was delineated in the present study. This involved amplicon sequencing of bacterial 16S rDNA from communities at the surface and subsurface in three distinct mat types (smooth, pustular and tufted), and correlating this data with the chemical and molecular distribution of scytonemin and MAAs. Employing UV spectroscopy and MS/MS fragmentation, mycosporine-glycine, asterina and an unknown MAA were identified based on typical fragmentation patterns. Marker genes for scytonemin and MAA production (scyC and mysC) were amplified from microbial mat DNA and placed into phylogenetic context against a broad screen throughout 363 cyanobacterial genomes. Results indicate that occurrence of UV screening compounds is associated with the upper layer of Shark Bay microbial mats, and the occurrence of scytonemin is closely dependent on the abundance of cyanobacteria.     

Formation of laminate travertines at bagno vignone,Italy

Travertine at Bagno Vignoni, Tuscany, is deposited from thermal CO₂‐rich water up‐welling from an artificial pool, Bagno Grande, which contains a thick benthic mat of cyanobacteria. The travertine mound, over 40 m in height, consists of calcite feather crystals and micrite. Over much of the mound, but particularly in the lower part, the travertine is finely banded, with pale bands of feather crystals alternating with dark bands containing micrite. Deposition rate measurements showed that the bands were formed daily, with the slightly narrower and darker bands formed at night. These nocturnal bands also contained wind‐borne dust. It is postulated that the dust caused heterogeneous nucleation of micrite and reduced the development of feather crystals. The deposition rate of travertine ranged from 127 to 348 μm/day and was highest at the top of the mound. Water analysis conducted over 27 h demonstrated a pronounced diurnal variation in the dissolved carbon dioxide of Bagno Grande, consistent with the photosynthetic activity of the benthic cyanobacteria. This variation could be traced to the base of the travertine mound but was not alone responsible for the higher deposition rate during the day. Water temperature on the mound also increased during the day and would have aided CO₂ evasion. Photosynthetic activity on the mound itself appeared to have far less influence on the carbon dioxide flux than Bagno Grande. The upper mound supported unlithified mats of the cyanobacteria Lyngbya (Phormidium) laminosum and Spirulina labyrinthiformis. These mats sometimes possessed fine travertine laminae resulting from cyanobacterium phototaxis and may have been responsible for some lamination in the upper mound. The CO₂ flux measurements indicated that overall, atmospheric evasion of carbon dioxide was more significant to travertine deposition than photosynthetic activity.     

Lipid biomarker and carbon isotopic signatures for stromatolite-forming, microbial mat communities and Phormidium cultures from Yellowstone National Park

The molecular and isotopic compositions of lipid biomarkers from cultured filamentous cyanobacteria (Phormidium, also known as Leptolyngbya) have been used to investigate the community and trophic structure of photosynthetic mats from alkaline hot springs of the Lower Geyser Basin at Yellowstone National Park. We studied a shallow‐water coniform mat from Octopus Spring (OS) and a submerged, tufted mat from Fountain Paint Pots (FPP) and found that 2‐methylhopanepolyols and mid‐chain branched methylalkanes were diagnostic for cyanobacteria, whereas abundant wax esters were representative of the green non‐sulphur bacterial population. The biomarker composition of cultured Phormidium‐isolates varied, but was generally representative of the bulk mat composition. The carbon isotopic fractionation for biomass relative to dissolved inorganic carbon (DIC; ?_CO2) for cultures grown with 1% CO₂ ranged from 21.4 to 26.1 and was attenuated by diffusion limitation associated with filament aggregation (i.e. cell clumping). Isotopic differences between biomass and lipid biomarkers, and between lipid classes, depended on the cyanobacterial strain, but was positively correlated with overall fractionation. Acetogenic lipids (alkanes and fatty acids) were generally more depleted than isoprenoids (phytol and hopanoids). The δ¹³C_TOC for OS and FPP mats were somewhat heavier than for cultures (?16.9 and ?23.6, respectively), which presumably reflects the lower availability of DIC in the natural environment. The isotopic dispersions among cyanobacterial biomarkers, biomass and DIC reflected those established for culture experiments. The 7‐methyl‐ and 7,11‐dimethylheptadecanes were from 9 to 11 depleted relative to the bulk organic carbon, whereas 2‐methylhopanols derived from the oxidation‐reduction of bacteriohopanepolyol were enriched relative to branched alkanes by approximately 5–7. These isotopic relationships survived with depth and indicated that the relatively heavy isotopic composition of the OS mat resulted from diffusion limitation. This study supports the suggestion that culture studies can establish valid isotopic relationships for interpretation of trophic structure in modern and ancient microbial ecosystems.     

Bioremediation of oil by marine microbial mats

Cyanobacterial mats developing in oil-contaminated sabkhas along the African coasts of the Gulf of Suez and in the pristine Solar Lake, Sinai, were collected for laboratory studies. Samples of both mats showed efficient degradation of crude oil in the light, followed by development of an intense bloom of Phormidium spp. and Oscillatoria spp. Isolated cyanobacterial strains, however, did not degrade crude oil in axenic cultures. Strains of sulfate-reducing bacteria and aerobic heterotrophs were capable of degrading model compounds of aliphatic and aromatic hydrocarbons. Results indicate that degradation of oil was done primarily by aerobic heterotrophic bacteria. The oxygenic photosynthesis of oil-insensitive cyanobacteria supplied the molecular oxygen for the efficient aerobic metabolism of organisms, such as Marinobacter sp. The diurnal shifts in environmental conditions at the mat surface, from highly oxic conditions in the light to anaerobic sulfide-rich habitat in the dark, may allow the combined aerobic and anaerobic degradation of crude oil at the mat surface. Hence, coastal cyanobacterial mats may be used for the degradation of coastline oil spills. Oxygen microelectrodes detected a significant inhibition of photosynthetic activity subsequent to oil addition. This prevailed for a few hours and then rapidly recovered. In addition, shifts in bacterial community structure following exposure to oil were determined by denaturing gradient gel electrophoresis of PCR-amplified fractions of 16S rRNA from eubacteria, cyanobacteria and sulfate-reducing bacteria. Since the mats used for the present study were obtained from oil-contaminated environments, they were believed to be preequilibrated for petroleum remediation. The mesocosm system at Eilat provided a unique opportunity to study petroleum degradation by mats formed under different salinities (up to 21%). These mats, dominated by cyanobacteria, can serve as close analogues to the sabkhas contaminated during the Gulf War in Kuwait and Saudi Arabia. Electronic Publication     

Biomarker studies on microbial carbonates: Extractable lipids of a Calcifying Cyanobacterial mat (Everglades, USA)

Summary Biomarker investigations are applied to the free lipid fractions of a naturally grown freshwater microbial mat, constructed by calcifying cyanobacteria (Scytonema sp. andSchizothrix sp.). The absolute and relative concentrations of hydrocarbons, free alcohols and carboxylic acids are studied and their probable biological precursors are discussed. A significant signal of cyanobacterial lipids is recognized by the strong predominance ofn-heptadecane (C₁₇),n-heptadecene, two monomethyl-heptadecanes, and the pentacyclic triterpenoid diploptene. Their occurrences parallel the lipid distributions found in pure cultured cyanobacteria and in recent cyanobacterial mats grown in particular environments (hypersaline, lagoonal, hot spring). The observed compound signature appears to be a suitable reference for environments, where cyanobacteria are directly associated with theloci of carbonate precipitation and thus, rock formation. In the studied material, a significant contribution of organic matter from other sources, especially higher plants is characterized by the occurrence of several specific marker compounds, namely lup-20(29)-ene-3-ol, high molecular weightn-alkanes and carboxylic acids. Although these components comprise a notably high portion of the sample’s lipid inventory, they are shown to be distinguished easily from the signal left by the predominant mat building organisms.     

Spatial variability in photosynthetic and heterotrophic activity drives localized δ13Corg fluctuations and carbonate precipitation in hypersaline microbial mats

Modern laminated photosynthetic microbial mats are ideal environments to study how microbial activity creates and modifies carbon and sulfur isotopic signatures prior to lithification. Laminated microbial mats from a hypersaline lagoon (Guerrero Negro, Baja California, Mexico) maintained in a flume in a greenhouse at NASA Ames Research Center were sampled for δ¹³C of organic material and carbonate to assess the impact of carbon fixation (e.g., photosynthesis) and decomposition (e.g., bacterial respiration) on δ¹³C signatures. In the photic zone, the δ¹³C_org signature records a complex relationship between the activities of cyanobacteria under variable conditions of CO₂ limitation with a significant contribution from green sulfur bacteria using the reductive TCA cycle for carbon fixation. Carbonate is present in some layers of the mat, associated with high concentrations of bacteriochlorophyll e (characteristic of green sulfur bacteria) and exhibits δ¹³C signatures similar to DIC in the overlying water column (?2.0‰), with small but variable decreases consistent with localized heterotrophic activity from sulfate‐reducing bacteria (SRB). Model results indicate respiration rates in the upper 12 mm of the mat alter in situ pH and concentrations to create both phototrophic CO₂ limitation and carbonate supersaturation, leading to local precipitation of carbonate minerals. The measured activity of SRB with depth suggests they variably contribute to decomposition in the mat dependent on organic substrate concentrations. Millimeter‐scale variability in the δ¹³C_org signature beneath the photic zone in the mat is a result of shifting dominance between cyanobacteria and green sulfur bacteria with the aggregate signature overprinted by heterotrophic reworking by SRB and methanogens. These observations highlight the impact of sedimentary microbial processes on δ¹³C_org signatures; these processes need to be considered when attempting to relate observed isotopic signatures in ancient sedimentary strata to conditions in the overlying water column at the time of deposition and associated inferences about carbon cycling.     

Ecological studies of Chloroflexis,a gliding photosynthetic bacterium

Summary Chloroflexis, a gliding, filamentous, photosynthetic bacterium, is present in the stratified algal-bacterial mats which occur in the 50°–70°C temperature range of alkaline hot spring effluents. The organism is in association with the alga in the upper, algal layer, and also forms thick, orange mats beneath the algal layer. Natural populations of Chloroflexis from these mats demonstrated light-stimulated uptake of some ¹⁴C-labelled organic compounds. Photosynthetic ¹⁴CO₂ fixation by natural samples of Chloroflexis was investigated with respect to temperature, light intensity and mat depth. Bacterial photosynthesis was determined in samples in which algae were present by use of the inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). Bacterial photosynthesis was maximal at depths down to about 3 mm and then decreased rapidly to very low levels at greater depths. The greatest amounts of bacteriochlorophyll pigments were also concentrated in the top 3–4 mm of the mat. The optimum light intensity for bacterial photosynthesis (about 400 ft-c) was considerably lower than the normal summer light intensity at the surface of the mat (5000-8000 ft-c).The temperature optima for photosynthesis by the bacterial component of natural mat samples from several sites of different temperatures in a hot spring thermal gradient were determined. Temperature optima approximated the environmental temperatures, indicative of the occurrence of strains of Chloroflexis adapted to different temperatures. Although bacterial standing crop was greatest in the temperature range 50°–55°C, maximum photosynthetic efficiency was observed at about 45°C. Sulfide was stimulatory to photosynthetic ¹⁴CO₂ fixation by naturally occurring populations of Chloroflexis under field conditions. These data are consistent with the hypothesis that Chloroflexis may utilize sulfide as an electron donor for photosynthetic CO₂ reduction. However, it is also likely that Chloroflexis grows photoheterotrophically in these mats, obtaining organic compounds from algal excretory products.     

Chloroflexus-like organisms from marine and hypersaline environments: Distribution and diversity

We report the presence of a diverse number ofChloroflexus-like organisms in intertidal marine and submerged hypersaline microbial mats using light, infrared fluorescence, and electron microscopy. The intertidal organisms appear morphologically very similar to thermophilicC. aurantiacus while the 2 hypersaline strains are larger and have a more complex ultrastructure composed of chlorosome-bearing internal membranes that appear to arise as invaginations of the cell membrane. By comparing spectroradiometry of microbial mat layers with microscopic observations, we have confirmed that theChloroflexus-like organisms are major constituents of the hypersaline microbial mat communities. In situ studies on mat layers dominated byChloroflexus-like organisms showed that sulfide-dependent photoautotrophic activity sustained by near infrared radiation prevailed. Autoradiographic analyses revealed that autotrophy was sustained in the filaments by 750 nm radiation. Three morphologically distinct strains are now maintained in mixed culture. One of these appears to be growing photoautotrophically.     

Horizontal gene transfer and the rock record: comparative genomics of phylogenetically distant bacteria that induce wrinkle structure formation in modern sediments

Wrinkle structures are sedimentary features that are produced primarily through the trapping and binding of siliciclastic sediments by mat‐forming micro‐organisms. Wrinkle structures and related sedimentary structures in the rock record are commonly interpreted to represent the stabilizing influence of cyanobacteria on sediments because cyanobacteria are known to produce similar textures and structures in modern tidal flat settings. However, other extant bacteria such as filamentous representatives of the family Beggiatoaceae can also interact with sediments to produce sedimentary features that morphologically resemble many of those associated with cyanobacteria‐dominated mats. While Beggiatoa spp. and cyanobacteria are metabolically and phylogenetically distant, genomic analyses show that the two groups share hundreds of homologous genes, likely as the result of horizontal gene transfer. The comparative genomics results described here suggest that some horizontally transferred genes may code for phenotypic traits such as filament formation, chemotaxis, and the production of extracellular polymeric substances that potentially underlie the similar biostabilizing influences of these organisms on sediments. We suggest that the ecological utility of certain basic life modes such as the construction of mats and biofilms, coupled with the lateral mobility of genes in the microbial world, introduces an element of uncertainty into the inference of specific phylogenetic origins from gross morphological features preserved in the ancient rock record.     

Biogeochemical cycling and microbial diversity in the thrombolitic microbialites of Highborne Cay,Bahamas

Thrombolites are unlaminated carbonate build‐ups that are formed via the metabolic activities of complex microbial mat communities. The thrombolitic mats of Highborne Cay, Bahamas develop in close proximity (1–2 m) to accreting laminated stromatolites, providing an ideal opportunity for biogeochemical and molecular comparisons of these two distinctive microbialite ecosystems. In this study, we provide the first comprehensive characterization of the biogeochemical activities and microbial diversity of the Highborne Cay thrombolitic mats. Morphological and molecular analyses reveal two dominant mat types associated with the thrombolite deposits, both of which are dominated by bacteria from the taxa Cyanobacteria and Alphaproteobacteria. Diel cycling of dissolved oxygen (DO) and dissolved inorganic carbon (DIC) were measured in all thrombolitic mat types. DO production varied between thrombolitic types and one morphotype, referred to in this study as ‘button mats’, produced the highest levels among all mat types, including the adjacent stromatolites. Characterization of thrombolite bacterial communities revealed a high bacterial diversity, roughly equivalent to that of the nearby stromatolites, and a low eukaryotic diversity. Extensive phylogenetic overlap between thrombolitic and stromatolitic microbial communities was observed, although thrombolite‐specific cyanobacterial populations were detected. In particular, the button mats were dominated by a calcified, filamentous cyanobacterium identified via morphology and 16S rRNA gene sequencing as Dichothrix sp. The distinctive microbial communities and chemical cycling patterns within the thrombolitic mats provide novel insight into the biogeochemical processes related to the lithifying mats in this system, and provide data relevant to understanding microbially induced carbonate biomineralization.