Nonphotosynthetic Bacteria and the Formation of Carbonates and Evaporites Through Time

Abstract

Nonskeletal sedimentary carbonate rocks are an important component of the Precambrian geological record, but consensus on their origin is lacking. Phanerozoic carbonates are almost exclusively biogenic products of shelly fossils, but it has generally been assumed that carbonate rocks deposited before a shelly biota evolved in the marine environment formed by direct precipitation from supersaturated solution in seawater. However, there is no unequivocal empirical evidence that calcium carbonate or dolomite precipitates directly from modern seawater, and it has been suggested that kinetic inhibitors to carbonate precipitation, related to the low concentration and activity of the carbonate ion, cation hydration and ion complexing, are especially effective in saline waters. On the other hand, there is increasing evidence that these inhibitors can be overcome through microbial mediation.

Bacteria have been implicated in calcium carbonate precipitation since the Archaean, and though best known in seas and lakes, microbial carbonates are also important in fluviatile, spring, cave, and soil environments. The mechanisms of microbial mineral precipitation appear diverse, but many bacteria exhibit an ability to change solution chemistry and control pH at the microscale, passively or actively, thereby creating the ambient conditions for both oversaturation of Ca^{2 +} and CO₃ ^{2 ?} ions, and removal of kinetic inhibitors. Bacteria dominated the ecosystems of Precambrian shallow marine environments, enhancing their potential involvement in widespread carbonate formation.

Chemical precipitation of evaporite minerals is generally accepted, but the involvement of microbes may be significant and underestimated. This review evaluates current knowledge and attempts to define some of the many questions that await resolution.     

Similar controls on calcification under ocean acidification across unrelated coral reef taxa

Ocean acidification (OA) is a major threat to marine ecosystems, particularly coral reefs which are heavily reliant on calcareous species. OA decreases seawater pH and calcium carbonate saturation state (Ω), and increases the concentration of dissolved inorganic carbon (DIC). Intense scientific effort has attempted to determine the mechanisms via which ocean acidification (OA) influences calcification, led by early hypotheses that calcium carbonate saturation state (Ω) is the main driver. We grew corals and coralline algae for 8–21 weeks, under treatments where the seawater parameters Ω, pH, and DIC were manipulated to examine their differential effects on calcification rates and calcifying fluid chemistry (Ω_cf, pH_cf, and DIC_cf). Here, using long duration experiments, we provide geochemical evidence that differing physiological controls on carbonate chemistry at the site of calcification, rather than seawater Ω, are the main determinants of calcification. We found that changes in seawater pH and DIC rather than Ω had the greatest effects on calcification and calcifying fluid chemistry, though the effects of seawater carbonate chemistry were limited. Our results demonstrate the capacity of organisms from taxa with vastly different calcification mechanisms to regulate their internal chemistry under extreme chemical conditions. These findings provide an explanation for the resistance of some species to OA, while also demonstrating how changes in seawater DIC and pH under OA influence calcification of key coral reef taxa.     

海洋酸化对微藻关键生理过程的调控机制及环境因素的影响

人类活动排放大量的CO₂通过海气界面进入海洋,打破原有海水碳酸盐平衡进而造成海洋酸化(OA)。OA会影响海水和海洋污染物的理化性质,进而对生活在海洋表层的浮游藻类生理过程产生显著调控作用。海洋微藻作为海洋中主要的初级生产者,其生理功能与过程的正常进行对于海洋生态系统具有重要作用。本文综述了OA对海洋微藻光合固碳、钙化过程、固氮作用3个关键生理过程的调控作用和具体机制,总结了OA条件下,环境因素(如太阳辐射、温度、营养元素)对微藻生理过程和生长的影响,以及OA通过改变典型海洋污染物(如有机污染物、重金属、微塑料)的环境行为而对微藻生理过程的调控作用。最后,结合研究现状,对未来需要开展的研究方向进行展望。本文为进一步了解OA对海洋生态系统的潜在影响提供了重要信息。     

Enhancement of adhesion of the marine Chlorella vulgaris to glass.

The adhesion of washed cells of a marine Chlorella vulgaris to solid surfaces was enhanced by non-diffusible material recovered from Chlorella exudate, marine bacterial cultures, natural seawater, and fouled marine surfaces. Materials isolated from certain bacterial cultures and from particulate materials filtered from seawater were three orders of magnitude more active than Chlorella exudate per unit weight. Active polymer materials from several sources were chromatographed on DEAE cellulose. The major fraction eluted with dilute base contained both protein and carbohydrate and enhanced adhesion more than the unchromatographed material.     

Persistent infectivity of a disease-associated herpesvirus in green turtles after exposure to seawater

Herpesviruses are associated with several diseases of marine turtles including lung-eye-trachea disease (LETD) and gray patch disease (GPD) of green turtles (Chelonia mydas) and fibropapillomatosis (FP) of green, loggerhead (Caretta caretta), and olive ridley turtles (Lepidochelys olivacea). The stability of chelonian herpesviruses in the marine environment, which may influence transmission, has not been previously studied. In these experiments, LETD-associated herpesvirus (LETV) was used as a model chelonian herpesvirus to test viral infectivity after exposure to seawater. The LETV virus preparations grown in terrapene heart (TH-1) cells were dialyzed for 24 to 120 hr against aerated artificial or natural seawater or Hank's balanced salt solution (HBBS). Fresh TH-1 cells were inoculated with dialyzed LETV, and on day 10 post-infection cells were scored for cytopathic effect. Virus samples dialyzed up to 120 hr were positive for the herpesvirus DNA polymerase gene by polymerase chain reaction. Electron microscopy revealed intact LETV nucleocapsids after exposure of LETV to artificial seawater or HBSS for 24 hr at 23 C. LETV preparations remained infectious as long as 120 hr in natural and artificial seawater at 23 C. Similar results were obtained with a second culturable chelonian herpesvirus, HV2245. LETV infectivity could not be detected after 48 hr exposure to artificial seawater at 30 C. Since LETV and HV2245 remain infectious for extended periods of time in the marine environment, it is possible that FP-associated and GPD-associated herpesviruses also may be stable. These findings are significant both for researchers studying the epidemiological association of herpesviruses with diseases of marine turtles and for individuals who handle turtles in marine turtle conservation efforts.     

Local paleoenvironmental controls on the carbon‐isotope record defining the Bitter Springs Anomaly

Large magnitude (>10‰) carbon‐isotope (δ¹³C) excursions recorded in carbonate‐bearing sediments are increasingly used to monitor environmental change and constrain the chronology of the critical interval in the Neoproterozoic stratigraphic record that is timed with the first appearance and radiation of metazoan life. The ~10‰ Bitter Springs Anomaly preserved in Tonian‐aged (1000–720 Ma) carbonate rocks in the Amadeus Basin of central Australia has been offered as one of the best preserved examples of a primary marine δ¹³C excursion because it is regionally reproducible and δ¹³C values covary in organic and carbonate carbon arguing against diagenetic exchange. However, here we show that δ¹³C values defining the excursion coincide with abrupt lithofacies changes between regularly cyclic grainstone and microbial carbonates, and desiccated red bed mudstones with interbedded evaporite and dolomite deposits, recording local environmental shifts from restricted marine conditions to alkaline lacustrine and playa settings that preserve negative (?4‰) and positive (+6‰) δ¹³C values, respectively. The stratigraphic δ¹³C pattern in both organic and carbonate carbon recurs within the basin in a similar way to associated sedimentary facies, reflecting the linkage of local paleoenvironmental conditions and δ¹³C values. These local excursions may be time transgressive or record a relative sea‐level influence manifest through exposure of sub‐basins isolated by sea‐level fall below shallow sills, but are independent of secular seawater variation. As the shallow intracratonic setting of the Bitter Springs Formation is typical of other Neoproterozoic carbonate successions used to construct the present δ¹³C seawater record, it identifies the potential for local influences on δ¹³C excursions that are neither diagenetic nor representative of the global exogenic cycle.     

Significance of Na+ in the fish pathogen, Vibrio anguillarum, under energy depleted condition

Vibrio anguillarum kills various kinds of fish over salinities ranging from seawater to freshwater. In this study, we investigated the role of Na(+) in V. anguillarum, especially under energy-depleted conditions such as in natural seawater. V. angustum S14, which is a typical marine vibrio, was used for comparison. V. anguillarum only required Na(+) for starvation-survival, but in contrast, V. angustum S14 always required Na(+) for both growth and starvation-survival. In marine vibrios, Na(+) is used in the Na(+)-dependent respiratory chain that produces the sodium motive force (SMF) across the cell membrane. It has been considered that marine vibrios always need a SMF produced by Na(+), however in the case of V. anguillarum, the SMF is not required for growth, but becomes more important for starvation-survival.     

Characteristics of Cyclic AMP Transport by Marine Bacteria

Uptake and autoradiography experiments with natural populations of marine bacteria, seawater cultures, and cultured isolates showed that the high-affinity cyclic AMP transport system in marine bacteria has stringent structural requirements, is found in a minority of cells in mixed bacterial assemblages, and appears to be related to the culture growth state.     

Cathodic protection and microbially induced corrosion

Cathodic protection, using sacrificial anodes or impressed current, has been recognized for a long time as an effective way to prevent marine corrosion. Cathodic polarization leads to the formation of a protective calcareous layer on the surfaces. It is well documented that the attachment of bacteria to metal surfaces and subsequent biofilm formation changes some physical and chemical parameters at the interface and influences the corrosion process. The objective of this study was to determine whether there is a relationship between cathodic polarization and development of biofilms on surfaces exposed to both synthetic and natural seawater. Experiments were conducted on clean surfaces, biofilmed surfaces, in natural or synthetic seawater using bacterial monocultures and cocultures. In marine sediments, cathodically produced hydrogen encouraged growth of hydrogenase-containing sulphate-reducing bacteria while in aerated seawater biofilms competed with the magnesium and calcium deposition. Both low pH induced by bacterial metabolism and exopolymers affect the deposition process and the stability of the calcareous layer.     

Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota

Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources.     

The influence of sunlight on the localized corrosion of UNS S31600 in natural seawater

Tests were conducted on the performance of UNS S31600 stainless steel (SS) in a natural day/night cycle vs full darkness under conditions of natural marine biofilm accumulation. In quiescent flowing seawater tests in the laboratory as well as under natural immersion in the sea, diffuse sunlight (～10% of natural) counteracted the influence of marine biofilms and produced substantial inhibition of the corrosion of SS. Thus, the probabilities (percentage attack) and propagation rates (depths of attack) in multiple crevice tests were substantially lower in the day/night cycle than in the dark. A benefit was also observed for welded SS in terms of the time to corrosion initiation and the mass loss. SS in the passive state showed broader passive regions, well-defined breakdown potentials and markedly smaller anodic and cathodic current densities under the diurnal cycle. The overall reduction in corrosion is attributed to a combination of electrochemical photoinhibition and simultaneous photoinactivation of microbially mediated metal redox reactions linked to cathodic kinetics. These data offer fresh insights into the behaviour of SS under practical seawater situations and the proposed potential use of illumination in the mitigation of biologically influenced consequences.     

Immunofluorescent Assay for the Marine Ammonium-Oxidizing Bacterium Nitrosococcus oceanus

Nitrification is one of the important microbiological transformations of nitrogen in the ocean. Traditional enrichment-culture methods for enumerating the autotrophic bacteria which oxidize ammonium to nitrite are very time consuming (months) and are believed to seriously underestimate natural abundances. A fluorescent-antibody assay for a marine ammonium-oxidizing bacterium was developed to provide a rapid and direct means of identifying these microorganisms. Antibodies to Nitrosococcus oceanus were prepared and tested against pure cultures of marine, freshwater, and soil ammonium oxidizers and against bacteria from natural seawater samples. Cell counts of culture samples determined by the fluorescent-antibody assay agreed with hemacytometer and acridine orange counts. Our results demonstrated that the immunofluorescent assay is a powerful tool for the detection of Nitrosococcus in the marine environment.     

A review of microbial-environmental interactions recorded in Proterozoic carbonate-hosted chert

The record of life during the Proterozoic is preserved by several different lithologies, but two in particular are linked both spatially and temporally: chert and carbonate. These lithologies capture a snapshot of dominantly peritidal environments during the Proterozoic. Early diagenetic chert preserves some of the most exceptional Proterozoic biosignatures in the form of microbial body fossils and mat textures. This fossiliferous and kerogenous chert formed in shallow marine environments, where chert nodules, layers, and lenses are often surrounded by and encased within carbonate deposits that themselves often contain kerogen and evidence of former microbial mats. Here, we review the record of biosignatures preserved in peritidal Proterozoic chert and chert-hosting carbonate and discuss this record in the context of experimental and environmental studies that have begun to shed light on the roles that microbes and organic compounds may have played in the formation of these deposits. Insights gained from these studies suggest temporal trends in microbial-environmental interactions and place new constraints on past environmental conditions, such as the concentration of silica in Proterozoic seawater, interactions among organic compounds and cations in seawater, and the influence of microbial physiology and biochemistry on selective preservation by silicification.     

The influence of sunlight on the localized corrosion of UNS S31600 in natural seawater

Tests were conducted on the performance of UNS S31600 stainless steel (SS) in a natural day/night cycle vs full darkness under conditions of natural marine biofilm accumulation. In quiescent flowing seawater tests in the laboratory as well as under natural immersion in the sea, diffuse sunlight (～10% of natural) counteracted the influence of marine biofilms and produced substantial inhibition of the corrosion of SS. Thus, the probabilities (percentage attack) and propagation rates (depths of attack) in multiple crevice tests were substantially lower in the day/night cycle than in the dark. A benefit was also observed for welded SS in terms of the time to corrosion initiation and the mass loss. SS in the passive state showed broader passive regions, well-defined breakdown potentials and markedly smaller anodic and cathodic current densities under the diurnal cycle. The overall reduction in corrosion is attributed to a combination of electrochemical photoinhibition and simultaneous photoinactivation of microbially mediated metal redox reactions linked to cathodic kinetics. These data offer fresh insights into the behaviour of SS under practical seawater situations and the proposed potential use of illumination in the mitigation of biologically influenced consequences.     

Metabolic and ultrastructural response to glucose of two eurytrophic bacteria isolated from seawater at different enriching concentrations

Two marine bacteria, an Acinetobacter sp. (strain GO1) and a vibrio sp. (strain G1), were isolated by extinction dilution and maintained in natural seawater supplemented with nitrogen, phosphorus, and glucose at 0.01 and 10 mg of glucose carbon per liter above ambient monosaccharide concentrations, respectively. After 3 days in unsupplemented natural seawater, growth in batch culture with glucose supplements was determined by changes in cell numbers and glucose concentration. The exponential growth of the Acinetobacter strain with added glucose was indistinguishable from that in natural seawater alone, whereas that of the Vibrio strain was more rapid in the presence of glucose supplements, suggesting that the Acinetobacter strain preferred the natural organic matter in seawater as a carbon source. The ultrastructure for both isolates was unaffected by glucose supplements during exponential growth, but there were marked changes in stationary-phase cells. The Vibrio strain formed polyphosphate at 10 mg of glucose carbon per liter, whereas poly-beta-hydroxybutyrate formation occurred at 100 mg and became excessive at 1,000 mg, disrupting the cells. In contrast, the Acinetobacter strain elongated at 100 and 1,000 mg of glucose carbon per liter but failed to show poly-beta-hydroxybutyrate formation. The diversity of responses shown here would not have been detected with a single concentration of substrate, often used in the literature to characterize both pure and natural populations of marine bacteria.     

Metabolic and ultrastructural response to glucose of two eurytrophic bacteria isolated from seawater at different enriching concentrations.

Two marine bacteria, an Acinetobacter sp. (strain GO1) and a vibrio sp. (strain G1), were isolated by extinction dilution and maintained in natural seawater supplemented with nitrogen, phosphorus, and glucose at 0.01 and 10 mg of glucose carbon per liter above ambient monosaccharide concentrations, respectively. After 3 days in unsupplemented natural seawater, growth in batch culture with glucose supplements was determined by changes in cell numbers and glucose concentration. The exponential growth of the Acinetobacter strain with added glucose was indistinguishable from that in natural seawater alone, whereas that of the Vibrio strain was more rapid in the presence of glucose supplements, suggesting that the Acinetobacter strain preferred the natural organic matter in seawater as a carbon source. The ultrastructure for both isolates was unaffected by glucose supplements during exponential growth, but there were marked changes in stationary-phase cells. The Vibrio strain formed polyphosphate at 10 mg of glucose carbon per liter, whereas poly-beta-hydroxybutyrate formation occurred at 100 mg and became excessive at 1,000 mg, disrupting the cells. In contrast, the Acinetobacter strain elongated at 100 and 1,000 mg of glucose carbon per liter but failed to show poly-beta-hydroxybutyrate formation. The diversity of responses shown here would not have been detected with a single concentration of substrate, often used in the literature to characterize both pure and natural populations of marine bacteria.     

Permian and early Triassic isotopic records of carbon and strontium in Australia and a scenario of events about the Permian‐Triassic boundary

The negative shift in δ¹³C values of carbonate carbon at the Permian/Triassic boundary is one of the better documented geochemical signatures of a mass extinction event. The similar negative shift in δ¹³C values in organic carbon from Permian/Triassic boundary marine sediments in Austria and Canada is shown to occur also in marine and non‐marine sediments from Australian sedimentary basins. This negative shift in δ¹³C values is used to calibrate Australian sections lacking diagnostic faunal elements identifying the Permian/Triassic boundary. The minimum in the carbonate ⁸⁷Sr/⁸⁶Sr seawater curve from carbonates across the Guadalupian/Ochoan Stage boundary, mainly from North America, is shown to occur also in brachiopod calcite mainly from the Bowen Basin of eastern Australia, hence providing a second calibration point in the Australian sedimentary record. These two geochemical events support a model of a runaway greenhouse developing about the Permian/Triassic boundary; this is inferred to have contributed to the end‐Permian mass extinction.     

Carbonate Production by Benthic Communities on Shallow Coralgal Reefs of Abrolhos Bank,Brazil

The abundance of reef builders, non-builders and the calcium carbonate produced by communities established in Calcification Accretion Units (CAUs) were determined in three Abrolhos Bank shallow reefs during the period from 2012 to 2014. In addition, the seawater temperature, the irradiance, and the amount and composition of the sediments were determined. The inner and outer reef arcs were compared. CAUs located on the inner reef shelf were under the influence of terrigenous sediments. On the outer reefs, the sediments were composed primarily of marine biogenic carbonates. The mean carbonate production in shallow reefs of Abrolhos was 579 ± 98 g m^-2 y^-1. The builder community was dominated by crustose coralline algae, while the non-builder community was dominated by turf. A marine heat wave was detected during the summer of 2013–2014, and the number of consecutive days with a temperature above or below the summer mean was positively correlated with the turf cover increase. The mean carbonate production of the shallow reefs of Abrolhos Bank was greater than the estimated carbonate production measured for artificial structures on several other shallow reefs of the world. The calcimass was higher than the non-calcareous mass, suggesting that the Abrolhos reefs are still in a positive carbonate production balance. Given that marine heat waves produce an increase of turf cover on the shallow reefs of the Abrolhos, a decrease in the cover represented by reef builders and shifting carbonate production are expected in the near future.     

Solar UV radiation does not inactivate marine birnavirus in coastal seawater

We examined the inactivation kinetics of marine birnavirus (MABV) in a coastal sea, in seawater samples collected from 50 cm depth. MABV was added to both natural and autoclaved seawater at a concentration of 6 x 10(6.43) TCID50 (50% tissue culture infectious dose) ml(-1), put in dialysis tubes and incubated at the original depth. The inactivation of MABV by solar UV radiation was examined using light and dark tubes. The infectivity titer of MABV was measured by the TCID50 method using CHSE-214 cells. Virus infectivity in natural seawater decreased quickly and was below the detection limit by 270 min in both light and dark conditions; however, virus infectivity was maintained in the autoclaved seawater until 420 min. These results suggest that the loss of virus infectivity is not caused by sunlight UV radiation.     

Ocean acidification refugia of the Florida reef tract

Ocean acidification (OA) is expected to reduce the calcification rates of marine organisms, yet we have little understanding of how OA will manifest within dynamic, real-world systems. Natural CO₂, alkalinity, and salinity gradients can significantly alter local carbonate chemistry, and thereby create a range of susceptibility for different ecosystems to OA. As such, there is a need to characterize this natural variability of seawater carbonate chemistry, especially within coastal ecosystems. Since 2009, carbonate chemistry data have been collected on the Florida Reef Tract (FRT). During periods of heightened productivity, there is a net uptake of total CO₂ (TCO₂) which increases aragonite saturation state (Ω_arag) values on inshore patch reefs of the upper FRT. These waters can exhibit greater Ω_arag than what has been modeled for the tropical surface ocean during preindustrial times, with mean (± std. error) Ω_arag-values in spring = 4.69 (±0.101). Conversely, Ω_arag-values on offshore reefs generally represent oceanic carbonate chemistries consistent with present day tropical surface ocean conditions. This gradient is opposite from what has been reported for other reef environments. We hypothesize this pattern is caused by the photosynthetic uptake of TCO₂ mainly by seagrasses and, to a lesser extent, macroalgae in the inshore waters of the FRT. These inshore reef habitats are therefore potential acidification refugia that are defined not only in a spatial sense, but also in time; coinciding with seasonal productivity dynamics. Coral reefs located within or immediately downstream of seagrass beds may find refuge from OA.