Biogeochemical modelling of the rise in atmospheric oxygen

Understanding the evolution of atmospheric molecular oxygen levels is a fundamental unsolved problem in Earth's history. We develop a quantitative biogeochemical model that simulates the Palaeoproterozoic transition of the Earth's atmosphere from a weakly reducing state to an O₂‐rich state. The purpose is to gain an insight into factors that plausibly control the timing and rapidity of the oxic transition. The model uses a simplified atmospheric chemistry (parameterized from complex photochemical models) and evolving redox fluxes in the Earth system. We consider time‐dependent fluxes that include organic carbon burial and associated oxygen production, reducing gases from metamorphic and volcanic sources, oxidative weathering, and the escape of hydrogen to space. We find that the oxic transition occurs in a geologically short time when the O₂‐consuming flux of reducing gases falls below the flux of organic carbon burial that produces O₂. A short timescale for the oxic transition is enhanced by a positive feedback due to decreasing destruction of O₂ as stratospheric ozone forms, which is captured in our atmospheric chemistry parameterization. We show that one numerically self‐consistent solution for the rise of O₂ involves a decline in flux of reducing gases driven by irreversible secular oxidation of the crust caused by time‐integrated hydrogen escape to space in the preoxic atmosphere, and that this is compatible with constraints from the geological record. In this model, the timing of the oxic transition is strongly affected by buffers of reduced materials, particularly iron, in the continental crust. An alternative version of the model, where greater fluxes of reduced hydrothermal cations from the Archean seafloor consume O₂, produces a similar history of O₂ and CH₄. When climate and biosphere feedbacks are included in our model of the oxic transition, we find that multiple ‘Snowball Earth’ events are simulated under certain circumstances, as methane collapses and rises repeatedly before reaching a new steady‐state.     

Light‐dependent oxygen consumption in nitrogen‐fixing cyanobacteria plays a key role in nitrogenase protection1

All colonial diazotrophic cyanobacteria are capable of simultaneously evolving O₂ through oxygenic photosynthesis and fixing nitrogen via nitrogenase. Since nitrogenase is irreversibly inactivated by O₂, accommodation of the two metabolic pathways has led to biochemical and/or structural adaptations that protect the enzyme from O₂. In some species, differentiated cells (heterocysts) are produced within the filaments. PSII is absent in the heterocysts, while PSI activity is maintained. In other, nonheterocystous species, however, a “division of labor” occurs whereby individual cells within a colony appear to ephemerally fix nitrogen while others evolve oxygen. Using membrane inlet mass spectrometry (MIMS) in conjunction with tracer ¹⁸O₂ and inhibitors of photosynthetic and respiratory electron transport, we examined the light dependence of O₂ consumption in Trichodesmium sp. IMS 101, a nonheterocystous, colonial cyanobacterium, and Anabaena flos‐aquae (Lyngb.) Bréb. ex Bornet et Flahault, a heterocystous species. Our results indicate that in both species, intracellular O₂ concentrations are maintained at low levels by the light‐dependent reduction of oxygen via the Mehler reaction. In N₂‐fixing Trichodesmium colonies, Mehler activity can consume ～75% of gross O₂ production, while in Trichodesmium utilizing nitrate, Mehler activity declines and consumes ～10% of gross O₂ production. Moreover, evidence for the coupling between N₂ fixation and Mehler activity was observed in purified heterocysts of Anabaena, where light accelerated O₂ consumption by 3‐fold. Our results suggest that a major role for PSI in N₂‐fixing cyanobacteria is to effectively act as a photon‐catalyzed oxidase, consuming O₂ through pseudocyclic electron transport while simultaneously supplying ATP in both heterocystous and nonheterocystous taxa.     

Using chlorophyll a and cyanobacteria in the ecological classification of lakes

Phytoplankton is one of the four key biological quality elements to be used in the ecological classification of lakes in Europe according to the Water Framework Directive (WFD). Chlorophyll a (Chla) has so far been used as the main – and sometimes only – metric to define class boundaries. Chla is often a key metric for lake managers and is used to determine whether and how much action should be taken to reduce the external nutrient loading. In this paper we present the analyses of empirical relationships between nutrient (total phosphorus, TP, total nitrogen, TN) concentrations versus Chla and the proportion of cyanobacteria of total phytoplankton biomass based on data from 440 Danish lakes (1800 lake years). These data represent one eco-region sampled using standardised methodology, thereby minimising the heterogeneity often seen in large datasets. Sampling frequency is important for the precision by which Chla can be determined and the precision is always low with less than 15 summer measurements. As expected Chla was related significantly to TP, but the variability was high, with R² reaching only 0.47, 0.59 and 0.61 in shallow, stratified and siliceous lakes, respectively, based on summer averages. The correlation was strongest in late summer (R² up to 0.80) and weak in winter. Chla is also related to TN, but the correlation coefficients were low throughout the year, and in a multiple regression with TP included, TN only added little to the total variability. Similarly, the proportion of cyanobacteria increased significantly with TP, but the correlation was weak. Seasonal and yearly data from five lakes with relatively stable TP show considerable variations in Chla and cyanobacteria abundance during a 20-year monitoring period. It is concluded that despite clear nutrient phytoplankton relationships it will be difficult to define the proposed WFD ecological classes – particularly regarding cyanobacteria. To ensure a high degree of certainty for meeting a specific water quality threshold, lake managers must reduce the external phosphorus loading more strongly than expected from existing simple empirical external loading-inlake TP–Chla relationships.     

Treeline form – a potential key to understanding treeline dynamics

Aim Treelines occur globally within a narrow range of mean growing season temperatures, suggesting that low‐temperature growth limitation determines the position of the treeline. However, treelines also exhibit features that indicate that other mechanisms, such as biomass loss not resulting in mortality (dieback) and mortality, determine treeline position and dynamics. Debate regarding the mechanisms controlling treeline position and dynamics may be resolved by identifying the mechanisms controlling prominent treeline spatial patterns (or ‘form’) such as the spatial structure of the transition from closed forest to the tree limit. Recent treeline studies world‐wide have confirmed a close link between form and dynamics. Location The concepts presented refer to alpine treelines globally. Methods In this review, we describe how varying dominance of three general ‘first‐level’ mechanisms (tree performance: growth limitation, seedling mortality and dieback) result in different treeline forms, what ‘second‐level’ mechanisms (stresses, e.g. freezing damage, photoinhibition) may underlie these general mechanisms, and how they are modulated by interactions with neighbours (‘third‐level’ mechanisms). This hierarchy of mechanisms should facilitate discussions about treeline formation and dynamics. Results We distinguish four primary treeline forms: diffuse, abrupt, island and krummholz. Growth limitation is dominant only at the diffuse treeline, which is the form that has most frequently responded as expected to growing‐season warming, whereas the other forms are controlled by dieback and seedling mortality and are relatively unresponsive. Main conclusions Treeline form provides a means for explaining the current variability in treeline position and dynamics and for exploring the general mechanisms controlling the responses of treelines to climatic change. Form indicates the relative dependence of tree performance on various aspects of the external climate (especially summer warmth versus winter stressors) and on internal feedbacks, thus allowing inferences on the type as well as strength of climate‐change responses.     

Landscape fluidity – a unifying perspective for understanding and adapting to global change

Rapid, human-induced global change presents major challenges to researchers, policy-makers and land managers. Addressing these challenges requires an appreciation of the dynamics of ecological systems. Here, we propose 'landscape fluidity' as a perspective and research agenda from which to consider landscapes in the process of changing rapidly through both time and space. We define landscape fluidity as the ebb and flow of different organisms within a landscape through time. A range of existing ideas, themes and practical approaches are relevant to landscape fluidity, and we use a case study of scattered tree landscapes in south-eastern Australia to illustrate the benefits of a landscape fluidity perspective. We suggest that a focus on landscape fluidity can bring a renewed emphasis on change in landscapes and so help unify a range of currently separate research themes in biogeography, ecology, palaeoecology and conservation biology.     

The role of land plants,phosphorus weathering and fire in the rise and regulation of atmospheric oxygen

The evolution of vascular plants and their spread across the land surface, beginning ～420 Ma, progressively increased the rate of weathering of phosphorus from rocks. This phosphorus supply promoted terrestrial and marine productivity and the burial of organic carbon, which has been the major source of O₂ over geological timescales. Hence, it is predicted that the rise of plants led to an increase in the O₂ content of the atmosphere from ～12 vol %, 570–400 Ma to its present level of ～21 vol % by ～340 Ma. Previous modelling studies suggest that O₂ then rose to ～35 vol % ～300 Ma. Such high concentrations are difficult to reconcile with the known persistence of forests, because rising O₂ increases the frequency and intensity of vegetation fires, tending to decrease biomass and cause ecological shifts toward faster regenerating ecosystems. Rising O₂ also directly inhibits C3 photosynthetic carbon assimilation and increases the production of toxic reactive oxygen species in cells. These effects suppress plant‐induced phosphorus weathering and hence organic carbon burial, providing a sensitive negative feedback on O₂. A revised model predicts that this mechanism could have regulated atmospheric O₂ within the range 15–25 vol % for the last 350 million years.     

Refuge availability: a key to understanding the summer disappearance of Daphnia

SUMMARY. 1. The mid-summer declines of Daphnia species in three small lakes were investigated to examine the relative roles of reduced natality and increased mortality. Reduced natality (assessed by quantifying clutch size, lipid index, and available food) could not account for the decline in daphnid abundance in any of the populations examined.
2. The role of increased mortality imposed by zooplanktivorous fish was assessed by estimating the sizes of the mid-water refuge areas where daphnids could escape fish predation. The boundaries of the refuge areas were estimated from field measurements and literature values and were based on gradients of temperature, dissolved oxygen and light. Observed decreases in refuge thicknesses correlated well with the mid-summer declines of large-bodied Daphnia species in all three lakes. Intermediatesized daphnids were less affected as the refuges thinned and small-bodied species increased in abundance.
3. The importance of refuge thickness in modifying zooplanktivore-induced mortality was further tested in large enclosures where refuge thickness was experimentally modified. In the presence of zooplanktivorous fish, large-bodied Daphnia , which used the refuge, persisted when the refuge was thick but disappeared when it thinned. Daphnia galeata mendotae , which did not occupy the refuge zone, was rapidly eliminated regardless of refuge thickness. We conclude that refuge availability plays a major role in Daphnia population dynamics.     

Parallel adaptations to nectarivory in parrots,key innovations and the diversification of the Loriinae

Specialization to nectarivory is associated with radiations within different bird groups, including parrots. One of them, the Australasian lories, were shown to be unexpectedly species rich. Their shift to nectarivory may have created an ecological opportunity promoting species proliferation. Several morphological specializations of the feeding tract to nectarivory have been described for parrots. However, they have never been assessed in a quantitative framework considering phylogenetic nonindependence. Using a phylogenetic comparative approach with broad taxon sampling and 15 continuous characters of the digestive tract, we demonstrate that nectarivorous parrots differ in several traits from the remaining parrots. These trait‐changes indicate phenotype–environment correlations and parallel evolution, and may reflect adaptations to feed effectively on nectar. Moreover, the diet shift was associated with significant trait shifts at the base of the radiation of the lories, as shown by an alternative statistical approach. Their diet shift might be considered as an evolutionary key innovation which promoted significant non‐adaptive lineage diversification through allopatric partitioning of the same new niche. The lack of increased rates of cladogenesis in other nectarivorous parrots indicates that evolutionary innovations need not be associated one‐to‐one with diversification events.     

The slow S to M fluorescence rise in cyanobacteria is due to a state 2 to state 1 transition

In dark-adapted plants and algae, chlorophyll a fluorescence induction peaks within 1s after irradiation due to well documented photochemical and non-photochemical processes. Here we show that the much slower fluorescence rise in cyanobacteria (the so-called "S to M rise" in tens of seconds) is due to state 2 to state 1 transition. This has been demonstrated in particular for Synechocystis PCC6803, using its RpaC(-) mutant (locked in state 1) and its wild-type cells kept in hyperosmotic suspension (locked in state 2). In both cases, the inhibition of state changes correlates with the disappearance of the S to M fluorescence rise, confirming its assignment to the state 2 to state 1 transition. The general physiological relevance of the SM rise is supported by its occurrence in several cyanobacterial strains: Synechococcus (PCC 7942, WH 5701) and diazotrophic single cell cyanobacterium (Cyanothece sp. ATCC 51142). We also show here that the SM fluorescence rise, and also the state transition changes are less prominent in filamentous diazotrophic cyanobacterium Nostoc sp. (PCC 7120) and absent in phycobilisome-less cyanobacterium Prochlorococcus marinus PCC 9511. Surprisingly, it is also absent in the phycobiliprotein rod containing Acaryochloris marina (MBIC 11017). All these results show that the S to M fluorescence rise reflects state 2 to state 1 transition in cyanobacteria with phycobilisomes formed by rods and core parts. We show that the pronounced SM fluorescence rise may reflect a protective mechanism for excess energy dissipation in those cyanobacteria (e.g. in Synechococcus PCC 7942) that are less efficient in other protective mechanisms, such as blue light induced non-photochemical quenching. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

Organizational levels analysis: a key to understanding processes in natural systems

Recent research conducted on a hypothetical four-parameter system generated by two stochastic processes has shown that errors of interpretation are likely to result when the relative importance of an underlying generating process is inferred from the analysis of an emergent pattern of a natural system. This paper presents an approach which substantially reduces that error for the hypothetical system, taken as an analog for a natural system. This approach is based on recognition of the organizational levels composing the system and utilizes observations on structure at a lower organizational level to resolve the properties of the generating processes at the lower level. The resulting knowledge of those underlying structures and the processes which created them are then used to determine the relative importance of those processes in affecting the emergent pattern of the system at a higher organizational level. It is concluded that in order to understand the role of a process in a natural system, measurements of system structure must be performed at a frequency which isolates the process from the other processes in the system.     

Application of transgenic plants in understanding responses to atmospheric change

Acclimation of plants to an increase in atmospheric carbon dioxide concentration is a well described phenomenon. It is characterized by an increase in leaf carbohydrates and a degradation of ribulose 1, 5-bisphosphate carboxylase protein (Rubisco) leading in the long term to a lower rate of CO₂ assimilation than expected from the kinetic constants of Rubisco. This article summarizes studies with transgenic plants grown in elevated pCO₂ which are modified in their capacity of CO₂ fixation, of sucrose and starch synthesis, of triosephosphate and sucrose transport and of sink metabolism of sucrose. These studies show that a feedback accumulation of carbohydrates in leaves play only a minor role in acclimation, because leaf starch synthesis functions as an efficient buffer for photoassimilates. There is some evidence that in elevated pCO₂, plants grow faster and senescence is induced earlier.     

PII,the key regulator of nitrogen metabolism in the cyanobacteria

PII proteins are a protein family important to signal transduction in bacteria and plants. PII plays a critical role in regulation of carbon and nitrogen metabolism in cyanobacteria. Through conformation change and covalent modification, which are regulated by 2-oxoglutarate, PII interacts with different target proteins in response to changes of cellular energy status and carbon and nitrogen sources in cyanobacteria and regulates cellular metabolism. This article reports recent progress in PII research in cyanobacteria and discusses the mechanism of PII regulation of cellular metabolism .     

Cell biology in model systems as the key to understanding corals

Corals provide the foundation of important tropical reef ecosystems but are in global decline for multiple reasons, including climate change. Coral health depends on a fragile partnership with intracellular dinoflagellate symbionts. We argue here that progress in understanding coral biology requires intensive study of the cellular processes underlying this symbiosis. Such study will inform us on how the coral symbiosis will be affected by climate change, mechanisms driving coral bleaching and disease, and the coevolution of this symbiosis in the context of other host-microbe interactions. Drawing lessons from the broader history of molecular and cell biology and the study of other host-microbe interactions, we argue that a model-systems approach is essential for making effective progress in understanding coral cell biology.     

Fossil evidence for key innovations in the evolution of insect diversity

Explaining the taxonomic richness of the insects, comprising over half of all described species, is a major challenge in evolutionary biology. Previously, several evolutionary novelties (key innovations) have been posited to contribute to that richness, including the insect bauplan, wings, wing folding and complete metamorphosis, but evidence over their relative importance and modes of action is sparse and equivocal. Here, a new dataset on the first and last occurrences of fossil hexapod (insects and close relatives) families is used to show that basal families of winged insects (Palaeoptera, e.g. dragonflies) show higher origination and extinction rates in the fossil record than basal wingless groups (Apterygota, e.g. silverfish). Origination and extinction rates were maintained at levels similar to Palaeoptera in the more derived Polyneoptera (e.g. cockroaches) and Paraneoptera (e.g. true bugs), but extinction rates subsequently reduced in the very rich group of insects with complete metamorphosis (Holometabola, e.g. beetles). Holometabola show evidence of a recent slow-down in their high net diversification rate, whereas other winged taxa continue to diversify at constant but low rates. These data suggest that wings and complete metamorphosis have had the most effect on family-level insect macroevolution, and point to specific mechanisms by which they have influenced insect diversity through time.     

Antibacterial properties of extracts from selected planktonic freshwater cyanobacteria – a comparative study of bacterial bioassays

Aqueous and methanol extracts from five selected cyanobacteria were examined for antibacterial properties in six different bacterial bioassays. All five cyanobacteria revealed antibacterial properties. Methanol extracts made from Tychonema bourrellyi, Aphanizomenon flos-aquae and Cylindrospermopsis raciborskii showed the most pronounced inhibitory effects. Aqueous extracts made from Microcystis aeruginosa and T. bourrellyi possessed evident antibacterial properties. The bacterial bioassays were based on agar diffusion tests and included pour-plate methods commonly used to detect residues of antibacterial substances in food. In addition, a pour-plate bioassay with Aeromonas hydrophila was developed and described. Antibacterial effects were observed in five of the six bacterial bioassays. No antibacterial effect was observed in the Micrococcus luteus bioassay. Bioassays based on Aer. hydrophila, Bacillus cereus and B. subtilis grown in Antibiotic Medium 8, pH 5·85, seemed to be sensitive and suitable. The MIC value of diluted MeOH extracts made from C. raciborskii and T. bourrellyi against Aer. hydrophila corresponded to 38 mg freeze-dried cyanobacteria. Bacillus subtilis was more sensitive when grown in a culture medium with pH 5·85 than 7·9. The antibacterial properties of extracts from the cyanobacteria examined differed from defined cyanotoxins and antibacterial substances. The pattern of inhibition in the bacterial bioassays indicated that various antibacterial substances are involved.     

Genomics and genetics of Cryptosporidium parvum: the key to understanding cryptosporidiosis

This paper focuses on recent advances in the genetics and genomics of Cryptosporidium parvum. The approach to and the relevance of sequencing the genomes of C. parvum type 1 and type 2 are discussed, as well as new insights into the genetic heterogeneity of this species.