Photosynthetic action spectra and adaptation to spectral light distribution in a benthic cyanobacterial mat

Seasonal shifts in community composition and proteome expression in a sulphur-cycling cyanobacterial mat

Seasonal changes in light and physicochemical conditions have strong impacts on cyanobacteria, but how they affect community structure, metabolism, and biogeochemistry of cyanobacterial mats remains unclear. Light may be particularly influential for cyanobacterial mats exposed to sulphide by altering the balance of oxygenic photosynthesis and sulphide-driven anoxygenic photosynthesis. We studied temporal shifts in irradiance, water chemistry, and community structure and function of microbial mats in the Middle Island Sinkhole (MIS), where anoxic and sulphate-rich groundwater provides habitat for cyanobacteria that conduct both oxygenic and anoxygenic photosynthesis. Seasonal changes in light and groundwater chemistry were accompanied by shifts in bacterial community composition, with a succession of dominant cyanobacteria from Phormidium to Planktothrix, and an increase in diatoms, sulphur-oxidizing bacteria, and sulphate-reducing bacteria from summer to autumn. Differential abundance of cyanobacterial light-harvesting proteins likely reflects a physiological response of cyanobacteria to light level. Beggiatoa sulphur oxidation proteins were more abundant in autumn. Correlated abundances of taxa through time suggest interactions between sulphur oxidizers and sulphate reducers, sulphate reducers and heterotrophs, and cyanobacteria and heterotrophs. These results support the conclusion that seasonal change, including light availability, has a strong influence on community composition and biogeochemical cycling of sulphur and O2 in cyanobacterial mats.

Early impacts of climate change on a coastal marine microbial mat ecosystem

Among the earliest consequences of climate change are extreme weather and rising sea levels-two challenges to which coastal environments are particularly vulnerable. Often found in coastal settings are microbial mats-complex, stratified microbial ecosystems that drive massive nutrient fluxes through biogeochemical cycles and have been important constituents of Earth's biosphere for eons. Little Ambergris Cay, in the Turks and Caicos Islands, supports extensive mats that vary sharply with relative water level. We characterized the microbial communities across this variation to understand better the emerging threat of sea level rise. In September 2017, the eyewall of category 5 Hurricane Irma transited the island. We monitored the impact and recovery from this devastating storm event. New mat growth proceeded rapidly, with patterns suggesting that storm perturbation may facilitate the adaptation of these ecosystems to changing sea level. Sulfur cycling, however, displayed hysteresis, stalling for >10 months after the hurricane and likely altering carbon storage potential.

Growth of microaerophilic Fe(II)-oxidizing bacteria using Fe(II) produced by Fe(III) photoreduction

Iron(II) (Fe(II)) can be formed by abiotic Fe(III) photoreduction, particularly when Fe(III) is organically complexed. Light-influenced environments often overlap or even coincide with oxic or microoxic geochemical conditions, for example, in sediments. So far, it is unknown whether microaerophilic Fe(II)-oxidizing bacteria are able to use the Fe(II) produced by Fe(III) photoreduction as electron donor. Here, we present an adaption of the established agar-stabilized gradient tube approach in comparison with liquid cultures for the cultivation of microaerophilic Fe(II)-oxidizing microorganisms by using a ferrihydrite-citrate mixture undergoing Fe(III) photoreduction as Fe(II) source. We quantified oxygen and Fe(II) gradients with amperometric and voltammetric microelectrodes and evaluated microbial growth by qPCR of 16S rRNA genes. We showed that gradients of dissolved Fe(II) (maximum Fe(II) concentration of 1.25 mM) formed in the gradient tubes when incubated in blue or UV light (400-530 nm or 350-400 nm). Various microaerophilic Fe(II)-oxidizing bacteria (Curvibacter sp. and Gallionella sp.) grew by oxidizing Fe(II) that was produced in situ by Fe(III) photoreduction. Best growth for these species, based on highest gene copy numbers, was observed in incubations using UV light in both liquid culture and gradient tubes containing 8 mM ferrihydrite-citrate mixtures (1:1), due to continuous light-induced Fe(II) formation. Microaerophilic Fe(II)-oxidizing bacteria contributed up to 40% to the overall Fe(II) oxidation within 24 h of incubation in UV light. Our results highlight the potential importance of Fe(III) photoreduction as a source of Fe(II) for Fe(II)-oxidizing bacteria by providing Fe(II) in illuminated environments, even under microoxic conditions.

Selection of LED lighting systems for the reduction of the biodeterioration of speleothems induced by photosynthetic biofilms in the Nerja Cave (Malaga, Spain)

Electrical lighting favours the development of photosynthetic biofilms in caves which can induce biodeterioration in the colonized substrates. The use of specific lights as a limiting factor for biofilm growth could be effective in their control and represents an alternative to chemical methods since they can damage the substrate. However, studies about lighting and the photosynthetic activity of organisms in caves are scarce. In order to select the most effective LED light source in reducing photosynthesis and therefore, in reducing the growth rates of microalgae and cyanobacteria, four biofilms in the Nerja Cave were illuminated by several light emitted diodes (LEDs) with different spectral compositions and the photobiological responses were measured both by empirical and theoretical methodologies. The empirical approach was based on the photosynthetic efficiency, by measuring the in vivo chlorophyll a (Chl a) fluorescence and the theoretical approach was based on the photonic assimilation performance related to the proportion of the light quality used for photosynthesis, according to the action spectra for photosynthesis available in the literature. The photobiological responses showed differences between the empirical and theoretical approach mainly in biofilms dominated by cyanobacteria and red algae, probably because the available action spectra were not useful for monitoring these Nerja Cave biofilms. However, the expected spectral responses of photosynthesis were observed in green microalgal biofilms with maximum photosynthetic efficiency in red and blue light although the green light was also unexpectedly high. The high photosynthetic efficiency in green light could be explained by the predictable high chlorophyll content due to a very dark environment. The results were not conclusive enough for all the biofilm types to be able to recommend a specific lighting system for the photocontrol of biofilm expansion. Therefore, new action spectra for photosynthesis of the extremophile organisms of the Nerja Cave are required. This approach, based on theoretical and empirical methodologies, is a useful tool to obtain information to allow the design of the most adequate lighting systems to reduce photosynthetic activity and favour the conservation of the caves.

Viral rhodopsins 1 are an unique family of light-gated cation channels

Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structural characterization of two proteins of viral rhodopsin group 1, OLPVR1 and VirChR1. Functional analysis of VirChR1 shows that it is a highly selective, Na⁺/K⁺-conducting channel and, in contrast to known cation channelrhodopsins, it is impermeable to Ca²⁺ ions. We show that, upon illumination, VirChR1 is able to drive neural firing. The 1.4 Å resolution structure of OLPVR1 reveals remarkable differences from the known channelrhodopsins and a unique ion-conducting pathway. Thus, viral rhodopsins 1 represent a unique, large group of light-gated channels (viral channelrhodopsins, VirChR1s). In nature, VirChR1s likely mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, might play a major role in global phytoplankton dynamics. Moreover, VirChR1s have unique potential for optogenetics as they lack possibly noxious Ca²⁺ permeability.

Nucleocytoplasmic Large DNA Viruses (NCLDV) that infect algae encode two distinct families of microbial rhodopsins. Here, the authors characterise two proteins form the viral rhodopsin group 1 OLPVR1 and VirChR1, present the 1.4 Å crystal structure of OLPVR1 and show that viral rhodopsins 1 are light-gated cation channels.

Blue light induces major changes in the gene expression profile of the cyanobacterium Synechocystis sp. PCC 6803

Although cyanobacteria absorb blue light, they use it less efficiently for photosynthesis than other colors absorbed by their photosynthetic pigments. A plausible explanation for this enigmatic phenomenon is that blue light is not absorbed by phycobilisomes and, hence, causes an excitation shortage at photosystem II (PSII). This hypothesis is supported by recent physiological studies, but a comprehensive understanding of the underlying changes in gene expression is still lacking. In this study, we investigate how a switch from artificial white light to blue, orange or red light affects the transcriptome of the cyanobacterium Synechocystis sp. PCC 6803. In total, 145 genes were significantly regulated in response to blue light, whereas only a few genes responded to orange and red light. In particular, genes encoding the D1 and D2 proteins of PSII, the PSII chlorophyll-binding protein CP47 and genes involved in PSII repair were upregulated in blue light, whereas none of the photosystem I (PSI) genes responded to blue light. These changes were accompanied by a decreasing PSI:PSII ratio. Furthermore, many genes involved in gene transcription and translation and several ATP synthase genes were transiently downregulated, concurrent with a temporarily decreased growth rate in blue light. After 6-7 days, when cell densities had strongly declined, the growth rate recovered and the expression of these growth-related genes returned to initial levels. Hence, blue light induces major changes in the transcriptome of cyanobacteria, in an attempt to increase the photosynthetic activity of PSII and cope with the adverse growth conditions imposed by blue light.

Blue-/Green-Light-Responsive Cyanobacteriochromes Are Cell Shade Sensors in Red-Light Replete Niches

Cyanobacteriochrome (CBCRs) photoreceptors show various photochemical properties, but their ecophysiological functions remain elusive. Here, we report that the blue/green CBCRs SesA/B/C can serve as physiological sensors of cell density. Because cyanobacterial cells show lower transmittance of blue light than green light, higher cell density gives more green-light-enriched irradiance to cells. The cell-density-dependent suppression of cell aggregation under blue-/green-mixed light and white light conditions support this idea. Such a sensing mechanism may provide information about the cell position in cyanobacterial mats in hot springs, the natural habitat of Thermosynechococcus. This cell-position-dependent SesA/B/C-mediated regulation of cellular sessility (aggregation) might be ecophysiologically essential for the reorganization and growth of phototrophic mats. We also report that the green-light-induced dispersion of cell aggregates requires red-light-driven photosynthesis. Blue/green CBCRs might work as shade detectors in a different niche than red/far-red phytochromes, which may be why CBCRs have evolved in cyanobacteria.

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Blue- and green-light-sensing cyanobacteriochromes can be sensors of cell density

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They may provide information about the cell position in microbial mats

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Green-light-induced dispersion of aggregates needs red-light-driven photosynthesis

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Cyanobacteriochromes might work in a different niche than red/far-red phytochromes

Radiative Energy Budgets in a Microbial Mat Under Different Irradiance and Tidal Conditions

Irradiance and temperature variations during tidal cycles modulate microphytobenthic primary production potentially by changing the radiative energy balance of photosynthetic mats between immersion and emersion and thus sediment daily net metabolism. To test the effect of tidal stages on the radiative energy budget, we used microsensor measurements of oxygen, temperature, and scalar irradiance to estimate the radiative energy budget in a coastal photosynthetic microbial mat during immersion (constant water column of 2 cm) and emersion under increasing irradiance. Total absorbed light energy was higher in immersion than emersion, due to a lower reflectance of the microbial mat, while most (> 97%) of the absorbed light energy was dissipated as heat irrespective of tidal conditions. During immersion, the upward heat flux was higher than the downward one, whereas the opposite occurred during emersion. At highest photon irradiance (800 μmol photon m^-2 s^-1), the sediment temperature increased ~ 2.5 °C after changing the conditions from immersion to emersion. The radiative energy balance showed that less than 1% of the incident light energy (PAR, 400-700 nm) was conserved by photosynthesis under both tidal conditions. At low to moderate incident irradiances, the light use efficiency was similar during the tidal stages. In contrast, we found an ~ 30% reduction in the light use efficiency during emersion as compared to immersion under the highest irradiance likely due to the rapid warming of the sediment during emersion and increased non-photochemical quenching. These changes in the photosynthetic efficiency and radiative energy budget could affect both primary producers and temperature-dependent bacterial activity and consequently daily net metabolism rates having important ecological consequences.

Blue light reduces photosynthetic efficiency of cyanobacteria through an imbalance between photosystems I and II

Several studies have described that cyanobacteria use blue light less efficiently for photosynthesis than most eukaryotic phototrophs, but comprehensive studies of this phenomenon are lacking. Here, we study the effect of blue (450 nm), orange (625 nm), and red (660 nm) light on growth of the model cyanobacterium Synechocystis sp. PCC 6803, the green alga Chlorella sorokiniana and other cyanobacteria containing phycocyanin or phycoerythrin. Our results demonstrate that specific growth rates of the cyanobacteria were similar in orange and red light, but much lower in blue light. Conversely, specific growth rates of the green alga C. sorokiniana were similar in blue and red light, but lower in orange light. Oxygen production rates of Synechocystis sp. PCC 6803 were five-fold lower in blue than in orange and red light at low light intensities but approached the same saturation level in all three colors at high light intensities. Measurements of 77 K fluorescence emission demonstrated a lower ratio of photosystem I to photosystem II (PSI:PSII ratio) and relatively more phycobilisomes associated with PSII (state 1) in blue light than in orange and red light. These results support the hypothesis that blue light, which is not absorbed by phycobilisomes, creates an imbalance between the two photosystems of cyanobacteria with an energy excess at PSI and a deficiency at the PSII-side of the photosynthetic electron transfer chain. Our results help to explain why phycobilisome-containing cyanobacteria use blue light less efficiently than species with chlorophyll-based light-harvesting antennae such as Prochlorococcus, green algae and terrestrial plants.

Partitioning light spectra: Adaptive stratification of phytobenthic communities in Antarctic lakes

Competition for light has an important influence for phototrophic community structures, especially, along the perpendicular axis. Here we develop a mathematical model for perpendicular community buildup of phototrophic species that differ in light absorption spectra and compete for incident light. Details of photon capture efficiencies and the roles of photoinhibition were taken into consideration to define species' fitness. Our theory showed that, if there is strong light irradiation due, for example, to the high transparency of the water in freshwater lakes in Antarctica, protective absorption of light should occur near the surface and photosynthetic absorption should gradually increase with depth. These results were then validated in comparison with observed vertical distributions of pigments in phytobenthic-mat communities from Antarctic lakes.

Rise and fall of toxic benthic freshwater cyanobacteria (Anabaena spp.) in the Eel river: Buoyancy and dispersal

Benthic cyanobacteria in rivers produce cyanotoxins and affect aquatic food webs, but knowledge of their ecology lags behind planktonic cyanobacteria. The buoyancy of benthic Anabaena spp. mats was studied to understand implications for Anabaena dispersal in the Eel River, California. Field experiments were used to investigate the effects of oxygen bubble production and dissolution on the buoyancy of Anabaena dominated benthic mats in response to light exposure. Samples of Anabaena dominated mats were harvested from the South Fork Eel River and placed in settling columns to measure floating and sinking velocities, or deployed into in situ ambient and low light treatments to measure the effect of light on flotation. Floating and sinking occurred within minutes and were driven by oxygen bubbles produced during photosynthesis, rather than intracellular changes in carbohydrates or gas vesicles. Light experiment results showed that in a natural ambient light regime, mats remained floating for at least 4days, while in low light mats begin to sink in <24h. Floating Anabaena samples were collected from five sites in the watershed and found to contain the cyanotoxins anatoxin-a and microcystin, with higher concentrations of anatoxin-a (median 560, max 30,693ng/gDW) than microcystin (median 30, max 37ng/gDW). The ability of Anabaena mats to maintain their buoyancy will markedly increase their downstream dispersal distances. Increased buoyancy also allows toxin-containing mats to collect along shorelines, increasing threats to human and animal public health.

Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr's Lake, the Bahamas

Microbialites found in the low-light-intensity, hypersaline waters of Storr's Lake (SL), San Salvador Island, the Bahamas, were investigated with respect to their morphology, mineralogy, and microbial diversity. Previously described microbialite morphologies, as well as a newly identified "multi-cuspate" morphology, were observed at various depths. Electron microscopy analysis revealed the presence of angular, blocky, and needle-shaped crystals with mineralized cyanobacterial filaments and remains of exopolymeric substances. X-ray diffraction studies confirmed the presence of both Mg-calcite and aragonite in the plateau-mushroom and pinnacle mound microbialites, whereas only Mg-calcite was identified in the other microbialite morphotypes. A comprehensive molecular analysis using barcoded pyrosequencing of five different microbial mat communities identified at least 12 dominant bacterial phyla. Cyanobacteria were generally low in abundance and ranged from ∼0.01% in the deeper pinnacle mounds to ∼3.2% in the shallow calcareous knobs. Other photosynthetic members included green nonsulfur bacteria of the phylum Chloroflexi and purple sulfur bacteria of the class Gammaproteobacteria. All mat types contained significant amounts of sulfate-reducing and dehalogenating bacteria. The low light intensity reaching the deeper microbialites, the lack of dominant cyanobacteria, and the abundance of sulfate reducers and Chloroflexi collectively suggest that sulfate reduction and anoxygenic photosynthetic processes influence the carbonate biomineralization process in these systems.

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

Biostabilization of cohesive sediments: revisiting the role of abiotic conditions, physiology and diversity of microbes, polymeric secretion, and biofilm architecture

In aquatic habitats, micro-organisms successfully adhere to and mediate particles, thus changing the erosive response of fine sediments to hydrodynamic forcing by secreting glue-like extracellular polymeric substances (EPS). Because sediment dynamics is vital for many ecological and economic aspects of watersheds and coastal regions, biostabilization of cohesive sediments is one of the important ecosystem services provided by biofilms. Although the research on biostabilization has gained momentum over the last 20 years, we still have limited insights principally due to the complex nature of this topic, the varying spatial, temporal, and community scales examined, oversimplified ecohydraulic experiments with little natural relevance, and the often partial views of the disciplines involved. This review highlights the current state of our knowledge on biostabilization and identifies important areas for future research on: (A) the influence of abiotic conditions on initial colonization and subsequent biofilm growth, focusing on hydrodynamics, substratum, salinity, nutrition, and light climate; (B) the response of microbes in terms of physiological activity and species diversity to environmental settings as well as biotic conditions such as competition and grazing; and (C) the effects of the former on the EPS matrix, its main constituents, their composition, functional groups/substitutes, and structures/linkages. The review focuses specifically on how the numerous mutual feedback mechanisms between abiotic and biotic conditions influence microbial stabilization capacity, and thus cohesive sediment dynamics.

Timescales of growth response of microbial mats to environmental change in an ice-covered antarctic lake

Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has been rising, creating a “natural experiment” on development of mat communities on newly flooded substrates and the response of deeper mats to declining irradiance. Mats in recently flooded depths accumulate one lamina (~0.3 mm) per year and accrue ~0.18 µg chlorophyll-a cm⁻² y⁻¹. As they increase in thickness, vertical zonation becomes evident, with the upper 2-4 laminae forming an orange-brown zone, rich in myxoxanthophyll and dominated by intertwined Leptolyngbya trichomes. Below this, up to six phycobilin-rich green/pink-pigmented laminae form a subsurface zone, inhabited by Leptolyngbya, Oscillatoria and Phormidium morphotypes. Laminae continued to increase in thickness for several years after burial, and PAM fluorometry indicated photosynthetic potential in all pigmented laminae. At depths that have been submerged for >40 years, mats showed similar internal zonation and formed complex pinnacle structures that were only beginning to appear in shallower mats. Chlorophyll-a did not change over time and these mats appear to represent resource-limited “climax” communities. Acclimation of microbial mats to changing environmental conditions is a slow process, and our data show how legacy effects of past change persist into the modern community structure.

Photosynthetic activity and community shifts of microphytobenthos covered by green macroalgae

Macroalgae blooms, a frequent consequence of eutrophication in coastal areas, affect the photosynthetic activity of sediments dominated by microphytobenthos (MPB). Light spectra, steady-state (after 1 h) microprofiles of O2 , gross photosynthesis (Pg ), community respiration in light (RL ) and net community photosynthesis (Pn ) were measured in diatom- and cyanobacteria-dominated communities below increasing layers of Ulva. Photosynthetic photon flux (PPF) decreased exponentially with increasing layers of algae and the light spectrum was increasingly enriched in the green and deprived in blue and red regions. Sediment Pg , Pn and RL decreased as the number of Ulva layers increased; however, 1.6 times higher macroalgal density was necessary to fully inhibit cyanobacteria Pg compared with diatoms, indicating that cyanobacteria were better adapted to this light environment. Long-term (3 weeks) incubations of diatom-dominated sediments below increasing layers of Ulva resulted in a shift in the taxonomic composition of the MPB towards cyanobacteria. Hence, changes in the light climate below macroalgal accumulations can negatively affect the photosynthetic activity of sediments. However, spectral niche differentiation of MPB taxonomic groups and concurrent changes in the MPB community may provide sediments with increased resilience to the detrimental effects of eutrophication.

Light utilization efficiency in photosynthetic microbial mats

Based on combined microsensor measurements of irradiance, temperature and O(2) , we compared light energy budgets in photosynthetic microbial mats, with a special focus on the efficiency of light energy conservation by photosynthesis. The euphotic zones in the three studied mats differed in their phototrophic community structure, pigment concentrations and thickness. In all mats, < 1% of the absorbed light energy was conserved via photosynthesis at high incident irradiance, while the rest was dissipated as heat. Under light-limiting conditions, the photosynthetic efficiency reached a maximum, which varied among the studied mats between 4.5% and 16.2% and was significantly lower than the theoretical maximum of 27.7%. The maximum efficiency correlated linearly with the light attenuation coefficient and photopigment concentration in the euphotic zone. Higher photosynthetic efficiency was found in mats with a thinner and more densely populated euphotic zone. Microbial mats exhibit a lower photosynthetic efficiency compared with ecosystems with a more open canopy-like organization of photosynthetic elements, where light propagation is not hindered to the same extent by photosynthetically inactive components; such components contributed about 40-80% to light absorption in the investigated microbial mats, which is in a similar range as in oceanic planktonic systems.

Effects of macroalgal blooms on carbon and nitrogen biogeochemical cycling in photoautotrophic sediments: an experimental mesocosm

The effects of floating macroalgae (250 g DW m(-2)) on photoautotrophic microbenthos were studied in a flow-through mesocosm with a parallel mesocosm without macroalgae serving as Control. Vertical microprofiles of O(2) at the sediment-water interface showed a immediate and complete suppression of photosynthetic activity of microphytobenthos (MPB) under the macroalgal canopy, resulting in a shift of benthic metabolism from autotrophic to heterotrophic. MPB abundance and chlorophyll a content decreased and a change from a diatom-dominated to cyanobacteria-dominated community was observed. Inorganic nitrogen nutrients' concentrations increased in the porewater as a result of the inhibition of MPB nutrient demand, leading to an increase in net ammonification and anaerobic NO(x)(-) consumption rates. No organic matter transfer from macroalgae to the sediment was detected, resulting in a net consumption of the carbon and nitrogen stored in the sediment. In consequence, sediment was progressively impoverished in nitrogen, reducing sediment nutrient regeneration.

Diel Migrations of Microorganisms within a Benthic, Hypersaline Mat Community

We studied the diel migrations of several species of microorganisms in a hypersaline, layered microbial mat. The migrations were quantified by repeated coring of the mat with glass capillary tubes. The resulting minicores were microscopically analyzed by using bright-field and epifluorescence (visible and infrared) microscopy to determine depths of coherent layers and were later dissected to determine direct microscopic counts of microorganisms. Microelectrode measurements of oxygen concentration, fiber optic microprobe measurements of light penetration within the mat, and incident irradiance measurements accompanied the minicore sampling. In addition, pigment content, photosynthesis and irradiance responses, the capacity for anoxygenic photosynthesis, and gliding speeds were determined for the migrating cyanobacteria. Heavily pigmented Oscillatoria sp. and Spirulina cf. subsalsa migrated downward into the mat during the early morning and remained deep until dusk, when upward migration occurred. The mean depth of the migration (not more than 0.4 to 0.5 mm) was directly correlated with the incident irradiance over the mat surface. We estimated that light intensity at the upper boundary of the migrating cyanobacteria was attenuated to such an extent that photoinhibition was effectively avoided but that intensities which saturated photosynthesis were maintained through most of the daylight hours. Light was a cue of paramount importance in triggering and modulating the migration of the cyanobacteria, even though the migrating phenomenon could not be explained solely in terms of a light response. We failed to detect diel migration patterns for other cyanobacterial species and filamentous anoxyphotobacteria. The sulfide-oxidizing bacterium Beggiatoa sp. migrated as a band that followed low oxygen concentrations within the mat during daylight hours. During the nighttime, part of this population migrated toward the mat surface, but a significant proportion remained deep.

Conversion and conservation of light energy in a photosynthetic microbial mat ecosystem

Here we present, to the best of our knowledge, the first balanced light energy budget for a benthic microbial mat ecosystem, and show how the budget and the spatial distribution of the local photosynthetic efficiencies within the euphotic zone depend on the absorbed irradiance (J(abs)). Our approach uses microscale measurements of the rates of heat dissipation, gross photosynthesis and light absorption in the system, and a model describing light propagation and conversion in a scattering-absorbing medium. The energy budget was dominated by heat dissipation on the expense of photosynthesis: in light-limiting conditions, 95.5% of the absorbed light energy dissipated as heat and 4.5% was channeled into photosynthesis. This energy disproportionation changed in favor of heat dissipation at increasing irradiance, with >99% of the absorbed light energy being dissipated as heat and <1% used by photosynthesis at J(abs)>700 micromol photon m(-2) s(-1) (>150 J m(-2) s(-1)). Maximum photosynthetic efficiencies varied with depth in the euphotic zone between 0.014-0.047 O(2) per photon. Owing to steep light gradients, photosynthetic efficiencies varied differently with increasing irradiances at different depths in the euphotic zone; for example, at J(abs)>700 micromol photon m(-2) s(-1), they reached around 10% of the maximum values at depths 0-0.3 mm and progressively increased toward 100% below 0.3 mm. This study provides the base for addressing, in much more detail, the photobiology of densely populated photosynthetic systems with intense absorption and scattering. Furthermore, our analysis has promising applications in other areas of photosynthesis research, such as plant biology and biotechnology.

Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes

The filamentous, non-heterocystous cyanobacterium Microcoleus chthonoplastes is a cosmopolitan organism, known to build microbial mats in a variety of different environments. Although most of these cyanobacterial mats are known for their capacity to fix dinitrogen, M. chthonoplastes has not been assigned as a diazotrophic organism. None of the strains that were correctly identified as M. chthonoplastes has been shown to fix dinitrogen and it has repeatedly been reported that these organisms lacked the cyanobacterial nifH, the structural gene for dinitrogenase reductase. In this study, we show that a complete nif-gene cluster is present in the genome of M. chthonoplastes PCC 7420 and that the three structural nitrogenase genes, nifHDK, are present in a collection of axenic strains of M. chthonoplastes from distant locations. Phylogenetic analysis of nifHDK revealed that they cluster with the Deltaproteobacteria and that they are closely related to Desulfovibrio. The nif operon is flanked by typical cyanobacterial genes, suggesting that it is an integral part of the M. chthonoplastes genome. In this study, we provide evidence that the nif operon of M. chthonoplastes is acquired through horizontal gene transfer. Moreover, the presence of the same nif-cluster in M. chthonoplastes isolates derived from various sites around the world suggests that this horizontal gene transfer event must have occurred early in the evolution of M. chthonoplastes. We have been unable to express nitrogenase in cultures of M. chthonoplastes, but we show that these genes were expressed under natural conditions in the field.

Diversity and stratification of archaea in a hypersaline microbial mat

The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.

Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment

This study has utilized the tools of lipid biomarker chemistry and molecular phylogenetic analyses to assess the archaeal contribution to diversity and abundance within a microbial mat and underlying sediment from a hypersaline lagoon in Baja California. Based on abundance of ether-linked isoprenoids, archaea made up from 1 to 4% of the cell numbers throughout the upper 100 mm of mat and sediment core. Below this depth archaeal lipid was two times more abundant than bacterial. Archaeol was the primary archaeal lipid in all layers. Relatively small amounts of caldarchaeol (dibiphytanyl glyceroltetraether) were present at most depths with phytanyl to biphytanyl molar ratios lowest (approximately 10 : 1) in the 4-17 mm and 100-130 mm horizons, and highest (132 : 1) in the surface 0-2 mm. Lipids with cyclic biphytanyl cores were only detected below 100 mm. A novel polar lipid containing a C(30) isoprenoid (squalane) moiety was isolated from the upper anoxic portion of the core and partially characterized. Hydrocarbon biomarker lipids included pentamethylicosane (2-10 mm) and crocetane (primarily below 10 mm). Archaeal molecular diversity varied somewhat with depth. With the exception of samples at 0-2 mm and 35-65 mm, Thermoplasmatales of marine benthic group D dominated clone libraries. A significant number of phylotypes representing the Crenarchaeota from marine benthic group B were generally present below 17 mm and dominated the 35-65 mm sample. Halobacteriaceae family made up 80% of the clone library of the surface 2 mm, and consisted primarily of sequences affiliated with the haloalkaliphilic Natronomonas pharaonis.

Biogeochemistry of hypersaline microbial mats illustrates the dynamics of modern microbial ecosystems and the early evolution of the biosphere

Photosynthetic microbial mats are remarkably complete self-sustaining ecosystems at the millimeter scale, yet they have substantially affected environmental processes on a planetary scale. These mats may be direct descendents of the most ancient biological communities in which even oxygenic photosynthesis might have developed. Photosynthetic mats are excellent natural laboratories to help us to learn how microbial populations associate to control dynamic biogeochemical gradients.

Analysis of lipophilic pigments from a phototrophic microbial mat community by high performance liquid chromatography

As assay for lipophilic pigments in phototrophic microbial mat communities using reverse phase-high performance liquid chromatography was developed which allows the separation of 15 carotenoids and chloropigments in a single 30 min program. Lipophilic pigments in a laminated mat from a commercial salina near Laguna Guerrero Negro, Baja California Sur, Mexico reflected their source organisms. Myxoxanthophyll, echinenone, canthaxanthin, and zeaxanthin were derived from cyanobacteria; chlorophyll c, and fucoxanthin from diatoms; chlorophyll a from cyanobacteria and diatoms; bacteriochlorophylls a and c, bacteriophaeophytin a, and gamma-carotene from Chloroflexus spp.; and beta-carotene from a variety of phototrophs. Sensitivity of detection was 0.6-6.1 ng for carotenoids and 1.7-12 ng for most chloropigments. This assay represents a significant improvement over previous analyses of lipophilic pigments in microbial mats and promises to have a wider application to other types of phototrophic communities.

Monitoring of oxygenic and anoxygenic photosynthesis in a unicyanobacterial biofilm, grown in benthic gradient chamber

In order to assess the role of cyanobacteria in the formation and dynamics of microenvironments in microbial mats, we studied an experimental biofilm of a benthic, halotolerant strain, belonging to the Halothece cluster of cyanobacteria. The 12-week-old biofilm developed in a sand core incubated in a benthic gradient chamber under opposing oxygen and sulfide vertical concentration gradients. At the biofilm surface, and as a response to high light irradiances, specific accumulation of myxoxanthophyll was detected in the cells, consistent with the typical vertical distribution of sun versus shade species in nature. The oxygen turn-over in terms of gross photosynthesis and net productivity rates was comparable to oxygen dynamics in natural microbial mats. Sulfide blocked O(2) production at low irradiances in deep biofilm layers but the dynamics of H(2)S and pH demonstrated that sulfide removal by anoxygenic photosynthesis was taking place. At higher irradiances, as soon as H(2)S was depleted, the cells switched to oxygenic photosynthesis as has been postulated for natural communities. The similarities between this experimental biofilm and natural benthic microbial mats demonstrate the central role of cyanobacteria in shaping microenvironmental gradients and processes in other complex microbial communities.

Anaerobic bacteria from hypersaline environments

Strictly anaerobic halophiles, namely fermentative, sulfate-reducing, homoacetogenic, phototrophic, and methanogenic bacteria are involved in the oxidation of organic carbon in hypersaline environments. To date, six anaerobic fermentative genera, containing nine species, have been described. Two of them are homoacetogens. Six species belong to the family Haloanaerobiaceae, as indicated by their unique 16S rRNA oligonucleotide sequences. Desulfohalobium retbaense and Desulfovibrio halophilus represent the only two moderately halophilic sulfate reducers so far reported. Among anoxygenic phototrophic anaerobes, a few purple bacteria with optimal growth at salinities between 6 and 11% NaCl have been isolated from hypersaline habitats. They belong to the genera Rhodospirillum, Chromatium, Thiocapsa, and Ectothiorhodospira. The commonest organisms isolated so far are Chromatium salexigens, Thiocapsa halophila, and Rhodospirillum salinarum. Extremely halophilic purple bacteria have most commonly been isolated from alkaline brines and require about 20 to 25% NaCl for optimal growth. They belong to the family Ectothiorodhospiraceae. Their osmoregulation involves synthesis or uptake of compatible solutes such as glycine-betaine that accumulate in their cytoplasm. The existence of methanogens in hypersaline environments is related to the presence of noncompetitive substrates such as methylamines, which originate mainly from the breakdown of osmoregulatory amines. Methanogenesis probably does not contribute to the mineralization of carbohydrates at NaCl concentrations higher than 15%. Above this concentration, sulfate reduction is probably the main way to oxidize H2 (although at rates too low to use up all the H2 formed) and occupies a terminal function kn the degradation of carbohydrates. Three genera and five species of halophilic methylotrophic methanogens have been reported. A bloom of phototrophic bacteria in the marine salterns of Salins-de-Giraud, located on the Mediterranean French coast in the Rhone Delta, is also described.

Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat

Complete budgets for carbon and oxygen have been constructed for cyanobacterial mats dominated by Microcoleus chthonoplastes from the evaporating ponds of a salt works located in Guerrero Negro, Baja California Sur, Mexico. Included in the budget are measured rates of O2 production, sulfate reduction, and elemental exchange across the mat/brine interface, day and night, at various temperatures and times of the year. We infer from this data the various sinks for O2, as well as the sources of carbon for primary production. To summarize, although seasonal variability exists, a major percentage of the O2 produced during the day did not diffuse out of the mat but was used within the mat to oxidize both organic carbon and the sulfide produced by sulfate reduction. At night, most of the O2 that diffused into the mat was used to oxidize sulfide, with O2 respiration of minor importance. During the day, the internal mat processes of sulfate reduction and O2 respiration generated as much or more inorganic carbon (DIC) for primary production as diffusion into the mat. Also, oxygenic photosynthesis was the most important process of carbon fixation, although anoxygenic photosynthesis may have been important at low light levels during some times of the year. At night, the DIC lost from the mat was mostly from sulfate reduction. Elemental fluxes across the mat/brine interface indicated that carbon with an oxidation state of greater than zero was taken up by the mat during the day and liberated from the mat at night. Overall, carbon with an average oxidation state of near zero accumulated in the mat. Both carbon fixation and carbon oxidation rates varied with temperature by a similar amount. These mats are thus closely coupled systems where rapid rates of photosynthesis both require and fuel rapid rates of heterotrophic carbon oxidation.

Aerobic sulfate reduction in microbial mats

Measurements of bacterial sulfate reduction and dissolved oxygen (O2) in hypersaline bacterial mats from Baja California, Mexico, revealed that sulfate reduction occurred consistently within the well-oxygenated photosynthetic zone of the mats. This evidence that dissimilatory sulfate reduction can occur in the presence of O2 challenges the conventional view that sulfate reduction is a strictly anaerobic process. At constant temperature, the rates of sulfate reduction in oxygenated mats during daytime were similar to rates in anoxic mats at night: thus, during a 24-hour cycle, variations in light and O2 have little effect on rates of sulfate reduction in these mats.

Spectral Irradiance and Distribution of Pigments in a Highly Layered Marine Microbial Mat

The spectral irradiance from 400 to 1,100 nm was measured with depth in the intertidal sand mats at Great Sippewissett Salt Marsh, Mass. These mats contained at least four distinct layers, composed of cyanobacteria, purple sulfur bacteria containing bacteriochlorophyll a (Bchl a), purple sulfur bacteria containing Bchl b, and green sulfur bacteria. Spectral irradiance was measured directly by layering sections of mat on a cosine receptor. Irradiance was also approximated by using a calibrated fiber-optic tip. With the tip, irradiance measurements could be obtained at depth intervals less than 250 mum. The irradiance spectra were correlated qualitatively and quantitatively with the distribution of the diverse chlorophyll pigments in this mat and were compared with spectra recorded in plain sand lacking pigmented phototrophs. We found that the shorter wavelengths (400 to 550 nm) were strongly attenuated in the top 2 mm of the mat. The longer wavelengths (red and near infrared) penetrated to much greater depths, where they were attenuated by Bchl a, b, and c-containing anoxygenic phototrophic bacteria. The specific attenuation bands in the irradiance spectra correlated with the specific in vivo absorption bands of the Bchl-protein complexes in the bacteria. We concluded that the pigments in the phototrophs had a profound affect on the light environment within the mat. It seems likely that the diverse Bchl-protein complexes found in the anoxygenic phototrophs evolved in dense mat environments as a result of competition for light.

Microbial mats and the early evolution of life

Microbial mats have descended from perhaps the oldest and most widespread biological communities known. Mats harbor microbes that are crucial for studies of bacterial phylogeny and physiology. They illustrate how several oxygen-sensitive biochemical processes have adapted to oxygen, and they show how life adapted to dry land long before the rise of plants. The search for the earliest grazing protists and metazoa in stromatolites is aided by observations of mats: in them, organic compounds characteristic of ancient photosynthetic protists can be identified. Recent mat studies suggest that the 13C/12C increase observed over geological time in stromatolitic organic matter was driven at least in part by a long-term decline in atmospheric carbon dioxide levels.

Distribution of phototrophic microbes in the flat laminated microbial mat at Laguna Figueroa, Baja California, Mexico

The microbial mat community in the saltmarsh/evaporate flat interface at Laguna Figueroa involved in the deposition of laminated sediments was investigated. Pigment analysis, light microscopy and transmission electron microscopy were used to determine the relative abundance and distribution of phototrophic species. The community is vertically stratified into four distinct phototrophic populations. The layering could be distinguished by pigment and species composition. The two layers closest to the surface contained mostly oxygenic phototrophs and chlorophyll a as the primary photosynthetic pigment. Anoxic phototrophs predominated in the bottom two layers with bacteriochlorophylls a and c in the third layer and bacteriochlorophyll a and b in the bottom layer. The surface yellow layer was composed primarily of Navicula, Rhopalodia and other diatom species as well as the cyanobacteria Aphanothece sp. and Phormidium sp. Microcoleus chthonoplasces and Chroococcidiopsis sp. were the major cyanobacteria in the green colored second layer. In the third layer, pinkish-purple in color, purple photographs (Chromatium sp., Thiocapsa roseoparsicina) and filamentous green phototrophs (Chloroflexus sp., Oscillochloris sp.) were abundant. The fourth and deepest photosynthetic layer was salmon colored and composed primarily of Thiocapsa pfennigii, and other purple sulfur phototrophs. The pattern of alternating light (oxygenic community) and dark (anoxygenic community) layering preserved in older laminae is a consequence of this community structure. Study of the flat laminated mat over the 10-year period (1978-1988) including and after its destruction by catastrophic flooding events in 1978 and 1980, showed a succession of stratified communities culminating in the return of Microcoleus and the full compliment of layers by the fall of 1984.

Methanogenesis from Methylated Amines in a Hypersaline Algal Mat

Methane ebullition and high rates of methane production were observed in sediments of a hypersaline pond (180 per thousand) which contained sulfate in excess of 100 mM. The highest rates of methane production were observed in surface sediments associated with an algal mat dominated by a Spirulina sp. The mat contained a methylated amine, glycine betaine (GBT), at levels which accounted for up to 20% of the total mat nitrogen. GBT was apparently the source of trimethylamine (TMA), which was also present in the sediment at relatively high concentrations. Patterns of substrate metabolism by the methanogenic populations in sediment slurries suggested that TMA was a major methane precursor. Neither exogenous hydrogen nor acetate stimulated methanogenesis, while addition of a variety of amines including TMA, trimethylamine oxide, GBT, and choline resulted in substantial increases with yields of >70%. The temperature optimum for methanogenesis in this system was 45 to 55 degrees C, which coincided with the observed sediment temperature. Patterns and rates of methane production in this and other hypersaline algal mats may be determined by a complex interaction between salinity, the use of methylated amines for osmoregulation by algae, and the formation of TMA by fermentation.

Photosynthetic Potential and Light-Dependent Oxygen Consumption in a Benthic Cyanobacterial Mat

The potential to carry out oxygenic photosynthesis after prolonged burial below the photic zone was studied at 0.1-mm depth intervals in the thick, laminated Microcoleus chthonoplastes mats growing in Solar Lake, Sinai. The buried mat community lost about 20% of its photosynthetic potential with depth per annual layer down to 8- to 10-year-old layers at a 14-mm depth. In some of the older layers, below a 30-mm depth, light-dependent oxygen consumption which increased with increasing light intensity was observed. Possible mechanisms for this phenomenon are (i) pseudocyclic electron transport (Mehler reaction), (ii) interactions between respiratory electron transport and photosynthetic electron transport, (iii) photorespiration, and (iv) photooxidation.