Pigment production and isotopic fractionations in continuous culture: okenone producing purple sulfur bacteria Part II

Okenone is a carotenoid pigment unique to certain members of Chromatiaceae, the dominant family of purple sulfur bacteria (PSB) found in euxinic photic zones. Diagenetic alteration of okenone produces okenane, the only recognized molecular fossil unique to PSB. The in vivo concentrations of okenone and bacteriochlorophyll a (Bchl a) on a per cell basis were monitored and quantified as a function of light intensity in continuous cultures of the purple sulfur bacterium Marichromatium purpuratum (Mpurp1591). We show that okenone‐producing PSB have constant bacteriochlorophyll to carotenoid ratios in light‐harvesting antenna complexes. The in vivo concentrations of Bchl a, 0.151 ± 0.012 fmol cell^?1, and okenone, 0.103 ± 0.012 fmol cell^?1, were not dependent on average light intensity (10–225 Lux) at both steady and non‐steady states. This observation revealed that in autotrophic continuous cultures of Mpurp1591, there was a constant ratio for okenone to Bchl a of 1:1.5. Okenone was therefore constitutively produced in planktonic cultures of PSB, regardless of light intensity. This confirms the legitimacy of okenone as a signature for autotrophic planktonic PSB and by extrapolation water column euxinia. We measured the δ¹³C, δ¹⁵N, and δ³⁴S bulk biomass values from cells collected daily and determined the isotopic fractionations of Mpurp1591. There was no statistical relationship in the bulk isotope measurements or stable isotope fractionations to light intensity or cell density under steady and non‐steady‐state conditions. The carbon isotope fractionation between okenone and Bchl a with respect to overall bulk biomass (¹³ε_{pigment – biomass}) was 2.2 ± 0.4‰ and ?4.1 ± 0.9‰, respectively. The carbon isotopic fractionation () for the production of pigments in PSB is more variable than previously thought with our reported values for okenone at ?15.5 ± 1.2‰ and ?21.8 ± 1.7‰ for Bchl a.     

Hydrogen, carbon and nitrogen isotopic fractionations during chlorophyll biosynthesis in C3 higher plants

We determined hydrogen, carbon and nitrogen isotopic compositions of chlorophylls a and b isolated from leaves of five C3 higher plant species (Benthamidia japonica, Prunus japonica, Acer carpinifolium, Acer argutum and Querus mongloica), and hydrogen and carbon isotopic compositions of phytol and chlorophyllides in the chlorophylls to understand isotopic fractionations associated with chlorophyll biosynthesis in these species. Chlorophylls are depleted in D relative to ambient water by approximately 189 per thousand and enriched in (13)C relative to bulk tissue by approximately 1.6 per thousand. These data can be explained by the contribution of isotopic fractionations during phytol and chlorophyllide biosyntheses. Phytol is more depleted in both D (by approximately 308 per thousand) and (13)C (by approximately 4.3 per thousand), while chlorophyllides are less depleted in D (by approximately 44 per thousand) and enriched in (13)C (by approximately 4.8 per thousand). Such inhomogeneous distribution of isotopes in chlorophylls suggests that (1) the phytol in chlorophylls reflects strong D- and (13)C-depletions due to the isotopic fractionations during the methylerythritol phosphate pathway followed by hydrogenation, and (2) the chlorophyllides reflect D- and (13)C-enrichments in tricarboxylic acid cycle. On the other hand, chlorophylls are slightly ( approximately 1.2 per thousand) depleted in (15)N relative to the bulk tissue, indicating that net isotopic fractionation of nitrogen during chlorophyll biosynthesis is small compared with those of hydrogen and carbon.     

Reading shell shape: implications for palaeoenvironmental reconstructions. A case study for bivalves from the marine Quaternary of Argentina (south-western Atlantic)

Most research on bivalves from the south-western Atlantic used morphological (shell) characters for taxonomic discriminations. Dominant Veneroids from Argentinian Quaternary coastal deposits exhibit wide morphological variation – often making objective discriminations difficult/impossible, which could be objectively described and compared through geometric morphometrics techniques. This work focuses on comparison of geometric morphometrics methods applied to fossil and modern shells, to assess inter- and intra-generic variations. Three approaches were considered: landmarks (L), semi-landmarks (SL) and outlines. Shell shape analyses for different time spans (Pleistocene, fossil Holocene and modern) and areas (Patagonia and Bonaerensian) showed that Elliptic Fourier analysis (EFA), Landmarks and Landmarks plus Semilandmarks (L+SL) can discriminate at generic levels: Mactra, Mulinia (Mactridae) vs. Pitar, Protothaca, Eurhomalea, Clausinella (Veneridae). L and L+SL are powerful for inter/intraspecific distinctions of Mactra. Variability of Mactra isabelleana includes the remaining nominal ‘species’ (transitional morphs). Causal environmental factors of (phenotype) variation could be addressed for modern environments (substrate, salinity and energy). Subtrigonal-inflated shells predominate in muddy, quieter, shallow mixo-polyhaline waters; ovate-elongate-compressed in sandy, poly-euhaline, deeper habitats. Differential spatial distribution (and abundance) across time responds to Late Quaternary high sea-level stands: transgressive maxima allowed higher salinity in marginal-marine areas and optimal conditions for Mactra isabelleana contrasting with scarcer records in the Mar Argentino today.     

Late quaternary variations in oxygen and carbon isotopic compositions in Canadian Arctic marine bivalves

The oxygen and carbon isotopic composition of arctic marine bivalves Mya truncata, Hiatella arctica, and Mytilus edulis are reported on samples from raised marine deposits in Hudson Bay and eastern Baffin Island. The shells range in age from modern, through the Holocene, to “old” marine units. During the Holocene the ¹⁸O/¹⁶O ratio in shells rose to a maximum about 3,500 B.P. which coincides in time with the period of maximum growth rates of bivalves, maximum size and maximum faunal diversity. The change is interpreted to indicate that about 3,500 years ago arctic waters may have reached a salinity ≈ 1–2% greater than present. Comparison of Holocene shell-carbonate isotopic compositions with those from the “old” marine shells (that are characteristically extremely thick) suggests that during the early Wisconsin advance on eastern Baffin Island, surface and near-surface waters were more saline than at present. This may have been related to low meltwater discharge. Paradoxically, positive values of ¹⁸O/¹⁶O and ¹³O/¹²C in marine shells occurred during the Holocene marine optimum and during the early Wisconsin ice advance.     

Hydrogen isotopic fractionations during desaturation and elongation associated with polyunsaturated fatty acid biosynthesis in marine macroalgae

Compound-specific hydrogen isotopic compositions (deltaD) of saturated, monounsaturated and polyunsaturated fatty acids have been determined for natural marine macroalgae including two brown algae (Heterokontophyta) and two red algae (Rhodophyta). deltaD values of individual fatty acids from four macroalgae exhibit a wide variation ranging from -189% to +48%. Generally, stearic (18:0), arachidic (20:0) and behenic acids (22:0) are much more enriched in D by up to approximately 180% relative to myristic (14:0), palmitic (16:0), octatetraenoic [18:4(n-3)] and eicosapentaenoic acids [20:5(n-3)]. Other fatty acids such as oleic [18:1(n-9)], lenoleic [18:2(n-6)] and linolenic acids [18:3(n - 3)] fall isotopically between these fatty acids. This wide deltaD variation of fatty acids is probably explained by the hydrogen isotopic fractionation during desaturation being much larger than that during elongation in the network of polyunsaturated fatty acid biosynthesis. A large hydrogen isotopic fractionation during desaturation may cause D-enrichment in the remaining hydrogen of the residual fatty acids, which could be controlled by the relative flux into their desaturates.     

Parasitism in bivalves from an Arctic ecosystem

In arctic ecosystems parasitism seems less conspicuous than in more diverse tropical ecosystems. However, several host-parasite relations may be a burden in Arctic ecosystems and modify energy-flow patterns. Four different localities of the shallow shelf off Godhavn, West Greenland, were studied with regard to biomass, production and life cycles of selected bivalve and polychaete species. The following important parasite-bivalve associations were found: the athecate hydroidMonobrachium parasitum onMacoma calcarea; the digenetic trematodeGymnophallus somateriae inHiatella byssifera; an unidentified species of turbellarian inHiatella byssifera; and the nemerteanMalacobdella grossa inMya truncata. In the bivalvesMytilus edulis, Serripes groenlandicus andCardium ciliatum only few parasites were detected. Parasitism seems to follow the general trend observed in Arctic ecosystems which exhibit low species diversities and high numbers of individuals.     

Invasive bivalves in fresh waters: impacts from individuals to ecosystems and possible control strategies

Invasive bivalves may cause great ecological, evolutionary, and economic impacts in freshwater ecosystems. Species such as Corbicula fluminea, Dreissena bugensis, Dreissena polymorpha, Limnoperna fortunei, and Sinanodonta woodiana are widely distributed hyper-successful invaders, but several others not yet invasive (or at least not considered as such) may become so in the near future. These species can affect hydrology, biogeochemical cycling, and biotic interactions through several mechanisms, with impacts ranging from individuals to ecosystems. Freshwater invasive bivalves can create no-analog ecosystems, posing serious difficulties for management, but new techniques are becoming available which may enhance options to detect early introductions and mitigate impacts. Although knowledge about the biology of these bivalves has increased considerably in the last two decades, several fundamental gaps still persist; we suggest new research directions that are worth exploring in the near future.     

Dermal bone in early tetrapods: a palaeophysiological hypothesis of adaptation for terrestrial acidosis

The dermal bone sculpture of early, basal tetrapods of the Permo-Carboniferous is unlike the bone surface of any living vertebrate, and its function has long been obscure. Drawing from physiological studies of extant tetrapods, where dermal bone or other calcified tissues aid in regulating acid-base balance relating to hypercapnia (excess blood carbon dioxide) and/or lactate acidosis, we propose a similar function for these sculptured dermal bones in early tetrapods. Unlike the condition in modern reptiles, which experience hypercapnia when submerged in water, these animals would have experienced hypercapnia on land, owing to likely inefficient means of eliminating carbon dioxide. The different patterns of dermal bone sculpture in these tetrapods largely correlates with levels of terrestriality: sculpture is reduced or lost in stem amniotes that likely had the more efficient lung ventilation mode of costal aspiration, and in small-sized stem amphibians that would have been able to use the skin for gas exchange.     

Stealing bivalves from common eiders: kleptoparasitism by glaucous gulls in spring

Here I report on glaucous gulls (Larus hyperboreus), an opportunistic, generalist predator, stealing bivalves from a diving duck, the common eider (Somateria mollissima). The study took place in spring, the pre-breeding period of the common eider, in an Arctic fjord (Adventfjorden) at western Spitsbergen, Svalbard. Eiders were abundant, their presence predictable, and they fed on large prey requiring surface handling—all factors facilitating food theft. Only adult glaucous gulls attended the eider flocks. The glaucous gulls brought stolen prey ashore. Amongst these the bivalve Mya neoovata (Myidae) was common. The probability that an eider flock was attended by glaucous gulls declined as the season progressed and increased with the foraging activity of the eiders. Eider flock size and the degree of aggregation within flocks were poor predictors of gull presence. However, eider flocks attended by a single gull were smaller than flocks attended by more than one gull. Common eiders are capital breeders which build up large energy reserves prior to breeding. Kleptoparasitism, therefore, may have a negative impact on eider energy acquisition in early spring. For the glaucous gull, kleptoparasitism may be important as few other food sources are available this time of the season.     

Sticky bivalves from the Mesozoic: clues to the origin of the anomalodesmatan arenophilic system

Arenophilic glands represent the only molluscan example of multicellular organs solely concerned with adhesion of foreign particles to the external surfaces of an organism. The glands are exclusive to the bivalve clade Anomalodesmata, but do not occur in all component taxa, having been declared absent in a number of families, including Pholadomyidae. This paper records and describes for the first time the arenophilic apparatus of Pholadomya candida G. B. Sowerby I, 1823, and demonstrates that secretion from these glands is at times preserved in the fossil record. In P. candida , arenophilic glands in the middle mantle folds discharge their products on top of the shell as the animal grows, forming radial lines of secretion that comprise a meandering main strand and numerous thin threads projecting in tufts. The arrangement is similar to that of other families, corroborating the hypothesis that the glands are a synapomorphy of crown-group anomalodesmatans. Instances of preserved secretion in fossil Pholadomya , ranging in age almost to the initial appearance of the genus in the Late Triassic, suggest that fossilized arenophilic secretion may aid systematic studies of problematic fossil groups traditionally included in Anomalodesmata.     

Linking past cultural developments to palaeoenvironmental changes in Estonia

Connections between environmental and cultural changes are analysed in Estonia during the past c. 4,500 years. Records of cereal-type pollen as (agri)cultural indices are compared with high-resolution palaeohydrological and annual mean temperature reconstructions from a selection of Estonian bogs and lakes (and Lake Igelsjön in Sweden). A broad-scale comparison shows increases in the percentage of cereal-type pollen during a decreasing trend in annual mean temperatures over the past c. 4,300 years, suggesting a certain independence of agrarian activities from environmental conditions at the regional level. The first cereal-type pollen in the region is found from a period with a warm and dry climate. A slow increase in pollen of cultivated land is seen around the beginning of the late Bronze Age, a slight increase at the end of the Roman Iron Age and a significant increase at the beginning of the Middle Ages. In a few cases increases in agricultural pollen percentages occur in the periods of warming. Stagnation and regression occurs in the periods of cooling, but regression at individual sites may also be related to warmer climate episodes. The cooling at c. 400–300 cal b.p., during the ‘Little Ice Age’ coincides with declines in cereal-type and herb pollen curves. These may not, however, be directly related to the climate change, because they coincide with war activities in the region.     

Biologically plausible learning in neural networks: a lesson from bacterial chemotaxis

Learning processes in the brain are usually associated with plastic changes made to optimize the strength of connections between neurons. Although many details related to biophysical mechanisms of synaptic plasticity have been discovered, it is unclear how the concurrent performance of adaptive modifications in a huge number of spatial locations is organized to minimize a given objective function. Since direct experimental observation of even a relatively small subset of such changes is not feasible, computational modeling is an indispensable investigation tool for solving this problem. However, the conventional method of error back-propagation (EBP) employed for optimizing synaptic weights in artificial neural networks is not biologically plausible. This study based on computational experiments demonstrated that such optimization can be performed rather efficiently using the same general method that bacteria employ for moving closer to an attractant or away from a repellent. With regard to neural network optimization, this method consists of regulating the probability of an abrupt change in the direction of synaptic weight modification according to the temporal gradient of the objective function. Neural networks utilizing this method (regulation of modification probability, RMP) can be viewed as analogous to swimming in the multidimensional space of their parameters in the flow of biochemical agents carrying information about the optimality criterion. The efficiency of RMP is comparable to that of EBP, while RMP has several important advantages. Since the biological plausibility of RMP is beyond a reasonable doubt, the RMP concept provides a constructive framework for the experimental analysis of learning in natural neural networks.     

Botcinolide: A Biologically Active Natural Product from Botrytis cinerea

A novel biologically active natural product was isolated from a strain of Botrytis cinerea found on cultivated raspberry fruit (Rubus ideaus) upon fermentation in a liquid medium. Following a bioassay-directed purification process, the final product was an amorphous solid with the molecular formula C₂₀H₃₄O₈, and is trivially named botcinolide. It significantly inhibited etiolated wheat coleoptile growth at 10^?3 and 10^?4 M by 100 and 82% respectively, relative to the controls. Greenhouse-grown bean, corn, and tobacco plants were affected by treating with botcinolide, and exhibited chlorosis and severe necrosis at 10^?2 and 10^?3 M. The structure is a new hydroxylated nonalactone that is esterified with 4-hydroxy-2-octenoic acid.     

Spikey bivalves: intra-periostracal crystal growth in anomalodesmatans

The external shell surfaces of most anomalodesmatan bivalves are studded with small spikes, particularly at the posterior end. We have studied the morphology, mode of growth, and distribution among taxa of these spikes. In this study we found that spikes vary widely in morphology, from acute spikes to flat plaques. Optical and electron microscopy has revealed that the periostraca of Laternula, Myadora, and Thraciopsis consist of an outer dense layer and an inner translucent layer. The dense layer grows at the expense of the inner layer as it progresses toward the shell edge. The spikes begin to grow in the free periostracum, within the translucent periostracal layer, immediately below the dense layer. With growth, they push the dense periostracal layer upward but without penetrating it. Those parts of the spike in contact with this layer cease to grow, which explains the typical conical shape of spikes. When fully grown, spikes reach the base of the translucent layer, becoming incorporated into the outer shell layer. Scanning electron microscopy and electron backscatter diffraction analysis reveal that the spikes of Lyonsia norwegica and Lyonsiella abyssicola are prisms of aragonite composed of twinned crystals, with the c-axis vertical. A survey of the occurrence of spikes within the anomalodesmatans shows that they are present in all but a few families. Elsewhere within the closely related palaeoheterodonts, intra-periostracal calcification is also known in Neotrigonia and unionids, which indicates that this character may be plesiomorphic for these bivalves. The present data do not support the homology of spikes in other bivalve groups (e.g., veneroids) or in the aplacophorans or polyplacophorans.     

Consumer‐driven nutrient dynamics in freshwater ecosystems: from individuals to ecosystems

The role of animals in modulating nutrient cycling [hereafter, consumer‐driven nutrient dynamics (CND)] has been accepted as an important influence on both community structure and ecosystem function in aquatic systems. Yet there is great variability in the influence of CND across species and ecosystems, and the causes of this variation are not well understood. Here, we review and synthesize the mechanisms behind CND in fresh waters. We reviewed 131 articles on CND published between 1973 and 1 June 2015. The rate of new publications in CND has increased from 1.4 papers per year during 1973–2002 to 7.3 per year during 2003–2015. The majority of investigations are in North America with many concentrating on fish. More recent studies have focused on animal‐mediated nutrient excretion rates relative to nutrient demand and indirect impacts (e.g. decomposition). We identified several mechanisms that influence CND across levels of biological organization. Factors affecting the stoichiometric plasticity of consumers, including body size, feeding history and ontogeny, play an important role in determining the impact of individual consumers on nutrient dynamics and underlie the stoichiometry of CND across time and space. The abiotic characteristics of an ecosystem affect the net impact of consumers on ecosystem processes by influencing consumer metabolic processes (e.g. consumption and excretion/egestion rates), non‐CND supply of nutrients and ecosystem nutrient demand. Furthermore, the transformation and transport of elements by populations and communities of consumers also influences the flow of energy and nutrients across ecosystem boundaries. This review highlights that shifts in community composition or biomass of consumers and eco‐evolutionary underpinnings can have strong effects on the functional role of consumers in ecosystem processes, yet these are relatively unexplored aspects of CND. Future research should evaluate the value of using species traits and abiotic conditions to predict and understand the effects of consumers on ecosystem‐level nutrient dynamics across temporal and spatial scales. Moreover, new work in CND should strive to integrate knowledge from disparate fields of ecology and environmental science, such as physiology and ecosystem ecology, to develop a comprehensive and mechanistic understanding of the functional role of consumers. Comparative and experimental studies that develop testable hypotheses to challenge the current assumptions of CND, including consumer stoichiometric homeostasis, are needed to assess the significance of CND among species and across freshwater ecosystems.     

Koninginin C: A Biologically Active Natural Product from Trichoderma koningii

Koninginin C, a congener of koninginins A and B, was isolated from Trichoderma koningii fermented on a shredded wheat medium. The compound inhibited the growth of etiolated wheat coleoptiles by 100% at 10^?3 M. It was a fine, white cystalline substance with a molecular formula of C₁₆H₂₈O₄ and a melting point of 70–72°C.     

Megarhizoliths in Pleistocene aeolian deposits from Gran Canaria (Spain): Ichnological and palaeoenvironmental significance

The Pleistocene dune field of Tufia, located on the east of Gran Canaria (Spain), contains different stratigraphic levels of indurated pillar-like structures that are interpreted as megarhizoliths. The megarhizoliths occur at the top of different aeolian sets and reach 31.5 cm in diameter and over 1 m in height. These scattered, free-standing, vertical, cylindrical-to-slightly conical columns usually appear as hollow cylinders, displaying elliptical cross-sections aligned with the prevailing wind. On the leeward side of some specimens the external wall shows a tail of rock matrix resembling a sort of “wind shadow”. These tails and other remains of the associated rock matrix show a texture composed of long, horizontal, parallel cylinders orientated with the wind.Internally the most complete structures show five concentrically arranged zones: Zone (a), is a central pore corresponding to the cavity originally occupied by the root; Zones (b) and (c), which include alveolar and laminated carbonate textures indicating that carbonate precipitation was mostly induced by the roots and their associated microorganisms; and Zones (d) and (e), consisting mostly of aeolian sands. In (d) the sand grains show thin micritic coatings whereas in (e) vadose aragonite cements can be seen on the grain surface suggesting a less biogenic influence in their formation. The degree of cementation and the time of the precipitation of carbonate around the roots controlled the preservation of these zones. Thus, in some cases, Zones b, c and/or d are not preserved. Cylinders are up to 30× the diameter of the root that nucleated them.The presence of the megarhizoliths at the top of the aeolianite beds indicates that aeolian sedimentation halted several times, allowing soil formation and plant colonisation during slightly more humid periods. The occurrence of megarhizoliths is further proof of the alternation of arid and slightly more humid climates in the north Atlantic during the last glacial period. It is also noted that they may be misinterpreted as animal trace fossils or tree trunk casts, resulting in incorrect ichnological or palaeoenvironmental interpretations.