Antiquity and evolutionary status of bacterial sulfate reduction: sulfur isotope evidence

The presently available sedimentary sulfur isotope record for the Precambrian seems to allow the following conclusions: (1) In the Early Archaean, sedimentary delta 34S patterns attributable to bacteriogenic sulfate reduction are generally absent. In particular, the delta 34S spread observed in the Isua banded iron formation (3.7 x 10(9) yr) is extremely narrow and coincides completely with the respective spreads yielded by contemporaneous rocks of assumed mantle derivation. Incipient minor differentiation of the isotope pattersn notably of Archaean sulfates may be accounted for by photosynthetic sulfur bacteria rather than by sulfate reducers. (2) Isotopic evidence of dissimilatory sulfate reduction is first observed in the upper Archaean of the Aldan Shield, Siberia (approximately 3.0 x 10(9) yr) and in the Michipicoten and Woman River banded iron formations of Canada (2.75 x 10(9) yr). This narrows down the possible time of appearance of sulfate respirers to the interval 2.8--3.1 x 10(9) yr. (3) Various lines of evidence indicate that photosynthesis is older than sulfate respiration, the SO4(2-) Utilized by the first sulfate reducers deriving most probably from oxidation of reduced sulfur compounds by photosynthetic sulfur bacteria. Sulfate respiration must, in turn, have antedated oxygen respiration as O2-respiring multicellular eucaryotes appear late in the Precambrian. (4) With the bulk of sulfate in the Archaean oceans probably produced by photosynthetic sulfur bacteria, the accumulation of SO4(2-) in the ancient seas must have preceded the buildup of appreciable steady state levels of free oxygen. Hence, the occurrence of sulfate evaporites in Archaean sediments does not necessarily provide testimony of oxidation weathering on the ancient continents and, consequently, of the existence of an atmospheric oxygen reservoir.     

Oxygen isotopic evidence for the depth stratification of tertiary and cretaceous planktic foraminifera

Oxygen isotope analyses of Tertiary and Cretaceous planktic foraminifera indicate that species have been stratified with respect to depth in the water column at least since Albian time. There is a relationship between morphology and depth habitat. Species with globigerine morphology have consistently occupied shallower depths than have species with globorotalid morphology. Biserially arranged species occupied both shallow and deep levels in the water column. On the average, it appears that ancient species with shallow habitats have been more susceptible to dissolution and have been preserved less well than species dwelling in deeper habitats. This relationship is similar to that observed for Recent planktic foraminifera. Comparison of carbon isotope ratios of adult and juvenile forms indicates that either the source of the carbon found in the shell or the carbon isotopic fractionations which occur during calcite secretion change during the development of individual foraminifera. The carbon isotopic ratios do not provide a reliable means for reconstructing the depth habitats of ancient species. Temperature-depth profiles for tropical Tertiary oceans have been reconstructed from the isotopic temperatures of planktic and benthic foraminifera. The vertical thermal structure of Oligocene oceans resembled that of modern oceans most closely. Those of Paleocene and Maastrichtian times differed most from that of modern oceans.     

Exocytosis of pinocytosed fluid in cultured cells: kinetic evidence for rapid turnover and compartmentation

The uptake and fate of pinocytosed fluid were investigated in monolayers of pulmonary alveolar macrophages and fetal lung fibroblasts using the fluid-phase marker, [14C]sucrose. Initial experiments revealed that cellular accumulation of chromatographically repurified [14C]sucrose was not linear with incubation time. Deviation from linearity was shown to be due to constant exocytosis of accumulating marker. Chromatographic analysis revealed that the cells were unable to metabolize sucrose and were releasing it intact by a process that was temperature-sensitive but not dependent on extracellular calcium and magnesium. A detailed analysis of the kinetics of exocytosis was undertaken by preloading cells with [14C]sucrose for various lengths of time and then monitoring the appearance of radioactivity into isotope- free medium. Results indicated that modeling the process of fluid-phase pinocytosis and subsequent exocytosis required at least two intracellular compartments in series, one compartment being of small size and turning over very rapidly (t1/2 = 5 min in macrophages, 6--8 min in fibroblasts) and the other compartment being apparently larger in size and turning over very slowly (t1/2 = 180 min in macrophages, 430--620 min in fibroblasts). Computer-simulation based on this model confirmed that the kinetics of efflux faithfully reflected the kinetics of influx and that the rate of efflux completely accounted for the deviation from linearity of accumulation kinetics. Moreover, the sizes of the compartments and magnitude of the intercompartment fluxes were such that the majority of fluid internalized in pinocytic vesicles was rapidly returned to the extracellular space via exocytosis. This result provides direct experimental evidence for a process previously thought necessary based solely on morphological and theoretical considerations. Furthermore, the turnover of pinocytosed fluid was so dynamic that accumulation deviated from linearity even within the first few minutes of incubation. We were able to show that the kinetics of exocytosis allowed calculation of the actual pinocytic rate, a rate that was nearly 50% greater than the apparent initial rate obtained from the slope of the uptake curve over the first 10 min.     

Stable sulfur isotopic distributions and sulfate reduction in lake sediments of the Adirondack Mountains,New York

Cores from five lakes of the Adirondack Mountains, New York, were analyzed for sedimentary sulfur concentrations and stable sulfur isotopic compositions. Isotopic values of total sedimentary sulfur were as much as 6 to 8 lower than isotopic values of sulfur sources (soils, tree leaves and lake water sulfate) which showed little isotopic variation in the Adirondacks. The low isotopic values of recent sediments indicate increased sulfate reduction, probably in response to increased sulfate loading and acid deposition. Detailed historical reconstruction of sulfate loading histories from sedimentary sulfur profiles is premature, however, since model calculations indicate that sulfur can be added to deeper older sediments by ongoing, contemporary sulfate reduction.     

Lunar rhythms in the deep sea: evidence from the reproductive periodicity of several marine invertebrates

While lunar rhythms are commonly documented in plants and animals living in terrestrial and shallow-water environments, deep-sea organisms have essentially been overlooked in that respect. This report describes evidence of lunar periodicity in the reproduction of 6 deep-sea species belonging to 2 phyla. Occurrences of gamete release in free spawners and larval release in brooders exhibited significant peaks around the new and full moons, respectively. The exact nature of this lunar period (endogenous or exogenous rhythm) and its adaptive significance in the deep sea remain elusive. Current knowledge suggests that proxies of moon phases at depth may include fluxes in particulate matter deposition, cyclic currents, and moonlight for species living in the disphotic zone.     

The ionic composition of the plasma and erythrocytes of deep sea fish

Summary This paper reports measurements of the plasma osmolarities, the main inorganic ions and the concentrations of plasma proteins in nine species of deep sea fish from depths of 900–4,000 m. Chloride and magnesium values are high compared to those of shallow water fish. These ions may be contaminants from sea water either contributing to, or resulting from, the animals' moribund condition. They may also contribute to the failure of isolated erythrocytes to show ionic regulation even after being restored to their normal high pressure.     

Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea

Two patterns of plant defense gene evolution are emerging from molecular population genetic surveys. One is that specialist defenses experience stronger selection than generalist defenses. The second is that specialist defenses are more likely to be subject to balancing selection, i.e., evolve in a manner consistent with balanced-polymorphism or trench-warfare models of host-parasite coevolution. Because most of the data of specialist defenses come from Arabidopsis thaliana, we examined the genetic diversity and evolutionary history of three defense genes in two outcrossing species, the autotetraploid Zea perennis and its most closely related extant relative the diploid Z. diploperennis. Intraspecific diversity at two generalist defenses, the protease inhibitors wip1 and mpi, were consistent with a neutral model. Like previously studied genes in these taxa, wip1 and mpi harbored similar levels of diversity in Z. diploperennis and Z. perennis. In contrast, the specialist defense hm2 showed strong although distinctly different departures from a neutral model in the two species. Z. diploperennis appears to have experienced a strong and recent selective sweep. Using a rejection-sampling coalescent method, we estimate the strength of selection on Z. diploperennis hm2 to be approximately 3.0%, which is approximately equal to the strength of selection on tb1 during maize domestication. Z. perennis hm2 harbors three highly diverged alleles, two of which are found at high frequency. The distinctly different patterns of diversity may be due to differences in the phase of host-parasite coevolutionary cycles, although higher hm2 diversity in Z. perennis may also reflect reduced efficacy of selection in the autotetraploid relative to its diploid relative.     

Changes in sulfate transport characteristics and protein composition of Anacystis nidulans R2 during sulfur deprivation.

Sulfur-starved cells of Anacystis nidulans have an increased capacity to take up sulfate. The apparent Vmax for sulfate uptake increased at least 10-fold after 24 h of sulfur deprivation, whereas the K1/2 remained unchanged at approximately 1.35 microM. The initial rate of sulfate uptake increased between 2 and 6 h after transfer of the cells to sulfur-free medium, in concert with elevated levels of three cytoplasmic membrane polypeptides with molecular masses of 43, 42, and 36 kilodaltons (kDa). The amounts of these polypeptides did not increase in response to nitrogen or phosphorus deprivation. A fourth cytoplasmic membrane polypeptide of 17 kDa did not appear until 24 h after transfer to sulfur-deficient medium. In the total soluble fraction, three polypeptides with masses of 36.5, 33.5, and 28.5 kDa increased dramatically in response to sulfur deprivation, but not in response to nitrogen or phosphorus deprivation. The specificity and abundance of these polypeptides indicate that they could play an important role in the response of A. nidulans to sulfur deprivation.     

Multiple deep-water sources and trophic regimes in the latest Cretaceous deep sea: evidence from benthic foraminifera

Benthic foraminifera from 24 DSDP/ODP sites were investigated to assess their global horizontal and vertical distribution in the deep-sea environment at the end of the Cretaceous period. The samples analyzed are from the late Maastrichtian and within the planktic forammiferal Abathomphalus mayaroensis Zone from a wide range of oceans and paleolatitudes, including the low-latitude Sites 10 and 384 (Atlantic Ocean), 47, 171, 305, and 465 (Pacific Ocean), the mid-latitude Sites 20, 111, 356, 363, 516, 525, 527, 548, and 605 (Atlantic Ocean), 216, 217, and 758 (Indian Ocean), and the high-latitude Sites 208 (Pacific Ocean), 689, 698, 700, 738 and 750 (Southern Ocean).Correspondence analysis, based on the 75 most common taxa, shows a clear biogeographic trend along the first correspondence axis by arranging the sites in paleolatitudinal order. The assemblages from the Tethyan Realm (i.e., low latitudes) are marked by abundant heavily calcified buliminids (such as Bulimina incisa B. trinitatensis B. velascoensis, and Reussella szajnochae) and Aragonia spp., whereas high-latitude faunas are characterized by abundant Alabamina creta, Gyroidinoides quadratus, and Pullenia coryelli.The results indicate that the faunas at low and high latitudes, respectively, were influenced by quite different environmental conditions. This is based on the much higher abundance of infaunal morphotypes at low and mid latitudes compared to high latitudes, suggesting that the biogeographic trend found in the data set coincides with the trophic regime at the various sites. The results also provide support for the hypothesis that postulates two simultaneous sources and mechanisms for deep-water formation during the Late Cretaceous, including warm, saline deep water produced by evaporation at low (equatorial) latitudes in contrast to the formation of cold deep waters at high (southern) latitudes.     

酸性硫酸盐土中的硫及其形态演变探讨

研究了酸性硫酸盐土中S及其形态演变。结果表明,酸性硫酸盐土S含量高,以无机态为主;S积累和S形态演变与酸性硫酸盐土形成、发育与利用密切相关。与红树林盐渍沼泽土(潜在酸性硫酸盐土)比较,酸性硫酸盐水稻土黄钾铁矾S含量较高,但FeS2含量较低。酸性硫酸盐水稻土S形态剖面分布明显,其氧化层的黄钾铁矾S含量较高,pH值较低;其还原层的FeS2含量较高。防治酸害是酸性硫酸盐土持续利用要解决的关键问题。     

Dissimilatory sulfur cycling in oxygen minimum zones: an emerging metagenomics perspective

Biological diversity in marine OMZs (oxygen minimum zones) is dominated by a complex community of bacteria and archaea whose anaerobic metabolisms mediate key steps in global nitrogen and carbon cycles. Molecular and physiological studies now confirm that OMZs also support diverse micro-organisms capable of utilizing inorganic sulfur compounds for energy metabolism. The present review focuses specifically on recent metagenomic data that have helped to identify the molecular basis for autotrophic sulfur oxidation with nitrate in the OMZ water column, as well as a cryptic role for heterotrophic sulfate reduction. Interpreted alongside marker gene surveys and process rate measurements, these data suggest an active sulfur cycle with potentially substantial roles in organic carbon input and mineralization and critical links to the OMZ nitrogen cycle. Furthermore, these studies have created a framework for comparing the genomic diversity and ecology of pelagic sulfur-metabolizing communities from diverse low-oxygen regions.     

Carbon isotopic composition of lipid biomarkers from an endoevaporitic gypsum crust microbial mat reveals cycling of mineralized organic carbon

Microbial mats that inhabit gypsum deposits in ponds at Guerrero Negro, Baja California Sur, Mexico, developed distinct pigmented horizons that provided an opportunity to examine the fixation and flow of carbon through a trophic structure and, in conjunction with previous phylogenetic analyses, to assess the diagenetic fates of molecular δ¹³C biosignatures. The δ¹³C values of individual biomarker lipids, total carbon, and total organic carbon (TOC) were determined for each of the following horizons: tan‐orange (TO) at the surface, green (G), purple (P), and olive‐black (OB) at the bottom. δ¹³C of individual fatty acids from intact polar lipids (IPFA) in TO were similar to δ¹³C of dissolved inorganic carbon (DIC) in the overlying water column, indicating limited discrimination by cyanobacteria during CO₂ fixation. δ¹³C_TOC of the underlying G was 3‰ greater than that of TO. The most δ¹³C‐depleted acetogenic lipids in the upper horizons were the cyanobacterial biomarkers C₁₇ n‐alkanes and polyunsaturated fatty acids. Bishomohopanol was 4 to 7‰ enriched, relative to alkanes and intact polar fatty acids (IPFA), respectively. Acyclic C₂₀ isoprenoids were depleted by 14‰ relative to bishomohopanol. Significantly, ?[δ¹³C_TOC ? δ¹³C_∑IPFA] increased from 6.9‰ in TO to 14.7‰ in OB. This major trend might indicate that ¹³C‐enriched residual organic matter accumulated at depth. The permanently anoxic P horizon was dominated by anoxygenic phototrophs and sulfate‐reducing bacteria. P hosted an active sulfur‐dependent microbial community. IPFA and bishomohopanol were ¹³C‐depleted relative to upper crust by 7 and 4‰, respectively, and C₂₀ isoprenoids were somewhat ¹³C‐enriched. Synthesis of alkanes in P was evidenced only by ¹³C‐depleted n‐octadecane and 8‐methylhexadecane. In OB, the marked increase of total inorganic carbon δ¹³C (δ¹³C_TIC) of >6‰ perhaps indicated terminal mineralization. This δ¹³C_TIC increase is consistent with degradation of the osmolyte glycine betaine by methylotrophic methanogens and loss of ¹³C‐depleted methane from the mat.     

Cytoplasmic sulfurtransferases in the purple sulfur bacterium Allochromatium vinosum: evidence for sulfur transfer from DsrEFH to DsrC

While the importance of sulfur transfer reactions is well established for a number of biosynthetic pathways, evidence has only started to emerge that sulfurtransferases may also be major players in sulfur-based microbial energy metabolism. Among the first organisms studied in this regard is the phototrophic purple sulfur bacterium Allochromatium vinosum. During the oxidation of reduced sulfur species to sulfate this Gammaproteobacterium accumulates sulfur globules. Low molecular weight organic persulfides have been proposed as carrier molecules transferring sulfur from the periplasmic sulfur globules into the cytoplasm where it is further oxidized via the "Dsr" (dissimilatory sulfite reductase) proteins. We have suggested earlier that the heterohexameric protein DsrEFH is the direct or indirect acceptor for persulfidic sulfur imported into the cytoplasm. This proposal originated from the structural similarity of DsrEFH with the established sulfurtransferase TusBCD from E. coli. As part of a system for tRNA modification TusBCD transfers sulfur to TusE, a homolog of another crucial component of the A. vinosum Dsr system, namely DsrC. Here we show that neither DsrEFH nor DsrC have the ability to mobilize sulfane sulfur directly from low molecular weight thiols like thiosulfate or glutathione persulfide. However, we demonstrate that DsrEFH binds sulfur specifically to the conserved cysteine residue DsrE-Cys78 in vitro. Sulfur atoms bound to cysteines in DsrH and DsrF were not detected. DsrC was exclusively persulfurated at DsrC-Cys111 in the penultimate position of the protein. Most importantly, we show that persulfurated DsrEFH indeed serves as an effective sulfur donor for DsrC in vitro. The active site cysteines Cys78 of DsrE and Cys20 of DsrH furthermore proved to be essential for sulfur oxidation in vivo supporting the notion that DsrEFH and DsrC are part of a sulfur relay system that transfers sulfur from a persulfurated carrier molecule to the dissimilatory sulfite reductase DsrAB.     

Freeze-etch and histochemical evidence for cycling in crayfish photoreceptor membranes

Summary Freeze-etched rhabdoms and adjacent cytoplasmic organelles from crayfish compound eyes have been studied for evidence of photoreceptor membrane cycling. The protoplasmic leaflet face (PF) of split photoreceptor membrane of the microvilli is richly particulate. The particles (92±16 A in diameter in surface fractures; 70±9 A in cross fractures; density about 8000/m²) probably indicate rhodopsin molecule localization. Closely similar particles appear in membranes of pinocytotic vesicles, multivesicular bodies (MVB) and secondary lysosomes. In contrast other retinular cell membranes like plasma membrane remote from the rhabdom are quite distinct (60±23 A particle diameter, density ca 1000/m²). Histochemical tests for acid phosphatase demonstrate its presence in well-developed (but not early stage) MVBs, mixed lamellar vesicular bodies (LVB) and lamellar bodies. Density of PF particles decreases from 8000 in MVB to roughly 4500/m² in LVB indicating a degradative sequence from rhabdom to lamellar bodies. Membrane leaflet orientations show that primary endocytosis from microvilli must be followed by secondary endocytosis of fused coated vesicles to form MVB. Morphological evidence for photoreceptor membrane resynthesis has not been found yet in crayfish but some has been obtained in other crustaceans.This research was supported by grants from the U.S. National Institutes of Health (EY 00405), the National Geographic Society and the Japan Society for the Promotion of ScienceThe authors are grateful to Mr. Washioka of the JEOL Co. Research Laboratory for his essential help in effecting the freeze-etch preparations. They also thank Professor Ryoji Kikuchi of Tokyo Women's Medical College for welcome cooperation and hospitality as well as Dr. Karl Pfenninger of Yale University for his generous assistance in interpreting the freeze-etch data. Technical advice and help were also kindly provided on the acid phosphatase histochemistry by Professor Marilyn Farquhar and others in the Yale Cell Biology Section     

Student-centered introductory biology course: evidence for deep learning

Our interpretative study that was carried out in a science and engineering oriented university examined the ways students in an introductory biology course perceived their learning in the course that was substantially changed to allow student-centered learning. The instructional change was framed by the view of learning as a sociocultural activity as well as a cognitive process that can take place face-to-face or through online interaction. Most of the lectures were substituted with individual learning and project-based, small-group learning that lasted one month. Data were collected through interviews with students and instructors, and through observations. In the paper, we show evidence for deep learning that was associated by the students and the instructors with short-term, meaningful activities in a setting that included collaborative peer learning; and replacing most lectures by small group learning that ended in a mini-conference. Deep learning was evidenced by the ways students reflected on how they organised and applied knowledge using deep learning strategies.     

First evidence for adoption in California sea lions

Demographic parameters such as birth and death rates determine the persistence of populations. Understanding the mechanisms that influence these rates is essential to developing effective management strategies. Alloparental behavior, or the care of non-filial young, has been documented in many species and has been shown to influence offspring survival. However, the role of alloparental behavior in maintaining population viability has not been previously studied. Here, we provide the first evidence for adoption in California sea lions and show that adoption potentially works to maintain a high survival rate of young and may ultimately contribute to population persistence. Alloparental behavior should have a positive effect on the population growth rate when the sum of the effects on fitness for the alloparent and beneficiary is positive.     

Performance evaluation of thermal cyclers for PCR in a rapid cycling condition

The performance of thermal cyclers for polymerase chain reactions (PCR) is of great concern in terms of the reliability of PCR-based assays, particularly when rapid cycling conditions are applied to small volume reactions. In this work, the precision of the temperature controls during rapid thermal cycling was measured in 19 commercial thermal cyclers of 8 different models. The temperatures of test solutions in specific locations in each thermal block were simultaneously monitored at 1 s intervals during thermal cycling. A temperature-sensitive multiplex PCR was run in parallel to assess undesirable PCR results caused by poor temperature control. Under the given conditions (20 s of annealing time and 20 microL reaction volume), a majority of the tested instruments showed prominent curving, undershooting, and/or overshooting in their temperature profiles, which substantially influenced the results of the temperature-sensitive multiplex PCR. Variations between wells were also observed in most instruments. It is strongly hoped that these problems will be addressed by manufacturers and that they will make substantial improvements in the precision and efficiency of thermal cyclers. In the meantime, users of thermal cyclers might be able to avoid unexpected poor outcomes of sensitive PCR-based assays by designing their PCR protocols with these findings in mind.