Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

Abstract Two chronosequences of unsaturated, buried loess sediments, ranging in age from <10,000 years to >1 million years, were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession was inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Core samples were collected at two sites 40 km apart in the Palouse region of eastern Washington State, near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the Winona site elevation is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was approximately 250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: approximately 1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Same-age sediments had equal quantities of microorganisms, but different community types. Differences in community makeup between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the microbial community age can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be considerably older than the porewater ages, since microbial transport is severely restricted in unsaturated sediments. This is particularly true at the Winona site, which was never flooded.     

Global distribution of the European species of the lichen genus Melanelia Essl.

Aim The global distribution of the European species of Melanelia Essl. (Lichenes: Parmeliaceae) was investigated in order to understand their distribution patterns against the background of ecogeographical and historical factors. Location The location of the study is global, with a local emphasis on Europe. Methods Geographical distribution and ecology of the species were investigated on the basis of herbarium studies and data from the literature as well as field observations. Distribution maps were created with ArcView GIS. The distribution patterns are expressed as three‐dimensional ‘areal formulas’, regarding zonal distribution, altitudinal range and oceanicity, using a previously described method. The observed distribution patterns are discussed on the basis of their analogies with vascular plants and with respect to the ecogeographical vs. historical factors reflected by them. Results With the exception of one species that is endemic to Europe, all species studied occur in both northern continents. A number of species have tropical‐alpine outposts, and two species occur also in extratropical zones of the southern hemisphere. Arctic and boreal distributions are circumpolar, while in the southern holarctic zones an affinity to the western sides of both northern continents is frequent. Main conclusions The distribution patterns appear to be mainly determined by contemporary ecogeographical factors. Most species probably have largely filled their potential distribution, at least within the Holarctic. Thus, the geographical origin and dispersal history of a species cannot reliably be reconstructed; they can be dissimilar in different species with similar distributions.     

<Emphasis Type="Italic">Chlamydia pneumoniae</Emphasis> aggravates vein graft intimal hyperplasia in a rat model

Background  

Along with angioplasty, autologus vein grafts are commonly used for artery bypass grafting in patients with advanced arterial stenosis and drug-resistant angina pectoris. Although initially a successful procedure, long-term functionality is limited due to proliferation and migration of smooth muscle cells. Like in atherosclerosis, common chronic infections caused by viruses and bacteria may contribute to this process of vein graft failure. Here we investigated the possible role of Chlamydia pneumoniae (Cpn) in the pathogenesis of venous graft failure in an experimental animal model. In 2 groups (n = 10 rats/group), an epigastric vein-to-common femoral artery interposition graft was placed. Immediately thereafter, rats were infected with Cpn (5*10⁸ IFU) or injected with control solutions. Rats were sacrificed three weeks after surgery and the grafts were harvested for morphometrical and immunohistochemical analysis.     

Cyclic 3'', 5''-AMP relay in dictyostelium discoideum. IV. Recovery of the cAMP signaling response after adaptation to cAMP

In dictyoselium discoideum, an increase in extracellular cAMP activates adenylate cyclase, leading to an increase in intracellular cAMP and the rate of cAMP secretion. Cells adapt to any constant cAMP stimulus after several minutes, but still respond to an increase in the concentration of the stimulus. We have now characterized the decay of adaptation (deadaptation) after the removal of cAMP stimuli. Levels of adaptation were established by the perfusion of [(3)H]adenosine-labeled amoebae with a defined cAMP stimulus. After a variable recovery period, the magnitude of the signaling response to a second stimulus was measured; its attenuation was taken as a measure of residual adaption to the first stimulus. The level of adaptation established by the first stimulus depended on both its magnitude and duration. Deadaptation began as soon as the first stimulus was removed. The magnitude of the response to the second stimulus increased with the recovery time in a first-order fashion, with a t(1/2)=3-4 min for stimuli of 10(-8) M to 10(-5) M cAMP. Responses to test stimuli, although reduced in magnitude, had an accelerated time-course when they closely followed a prior response that had not completely subsided. This effect is called priming; we believe it reveals a reversible, rate-limiting step that modulates the onset and termination of the signaling responses of amoebae that have not recently responded to a cAMP stimulus. We have suggested that the cAMP signaling response is controlled by two antagonistic cellular processes, excitation and adaptation. The data reported here imply that both the rate of rise in the adaptation process and the final level reached depend on the occupancy of cAMP surface receptors and that the decay of adaptation when external cAMP is removed proceeds with first-order kinetics.     

Miocene divergence,phenotypically cryptic lineages,and contrasting distribution patterns in common lichen‐forming fungi (Ascomycota: Parmeliaceae)

Despite the recent advancements in recognizing diversity in lichen‐forming fungi, assessing the timing of diversification remains largely unexplored in these important fungal symbionts. To better understand the evolutionary processes driving diversification in common lichen‐forming fungi, we investigated the phylogeny and biogeography of the broadly distributed Melanelixia fuliginosa/M. glabratula group, using molecular data from six nuclear markers. Phylogenetic analyses of individual gene alignments and combined data provide strong evidence for five species‐level lineages within this species complex. Three of these lineages correspond to the previously described species M. fuliginosa, M. glabratula, and M. subaurifera. The remaining two lineages, ‘M. sp. 1’ and ‘M. sp. 2’, merit species recognition based on genealogical concordance. Both M. glabratula and M. subaurifera had broad intercontinental distributions, sharing identical haplotypes among intercontinental populations. Based on the current sampling, M. fuliginosa s.s. was represented exclusively by European material and was not collected in North America. ‘M. sp. 1’ was represented by collections from Scotland and Spain; and ‘M. sp. 2’ was represented by collections in California, USA. Environmental factors driving the contrasting distribution patterns in this group remain unknown. Divergence times estimated using a coalescence‐based multilocus species‐tree approach suggest that diversification within the M. fuliginosa/M. glabratula group occurred exclusively during the Miocene. The results of the present study indicate that phenotypically cryptic lichen‐forming fungal species‐level lineages may be relatively ancient and do not necessarily reflect recent divergence events. Furthermore, diagnosable phenotypic differences may be absent even millions of years after the initial divergence. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●●, ●●–●●.     

Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane

This article describes a simple and quick in silico method for the prediction of cytochrome P450 (CYP)-mediated hydroxylation of drug-like compounds. Testosterone and progesterone, two known substrates of CYP3A4, are used to test the method. Further, we apply the procedure to predict sites of hydroxylation of isomers of the flame retardant hexabromocyclododecane by CYP3A4. Within the method, the compound is rotated in the binding pocket of the cytochrome, so that each hydrogen under consideration is placed near the active centre. Afterwards, short molecular dynamics simulations are provided for each step of the rotation. All steps of the simulation are compared concerning the distances between the hydrogens and the active centre and the corresponding energies. The computational results correlate well with experimental results.     

Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen‐forming family Parmeliaceae (Ascomycota)

Microbial symbionts are instrumental to the ecological and long‐term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species‐rich lichen‐forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.     

Biogeographical research on European species of the lichen genus Physconia

Abstract Aim The (world) distribution of the European species of Physconia Poelt (Lichenes: Physciaceae) [except Ph. distorta (With.) J. R. Laundon and Ph. americana Essl.] was investigated. The study was complemented by data on the ecological behaviour of the species. Location The location of the study is the whole world with a local emphasis on Europe. Methods The geographical distribution of the lichen species under consideration was investigated from collection data of herbaria and field studies in a databank. Additional data were taken from existing literature and critically considered. Distribution maps were created with ArcView GIS. The distribution patterns are expressed as three‐dimensional areal formulas, regarding zonal distribution, altitudinal range and oceanity of the species distributions, using the method of Meusel et al. (1965 ). Results The distribution patterns of the ten Physconia taxa considered are represented in detailed maps and expressed as three‐dimensional areal formulas. The ecological behaviour was discussed. Physconia muscigena and Ph. perisidiosa are species of bipolar distribution type, the other species are holarctic types. Physconia detersa and Ph. enteroxantha occur in both Eurasia and North America, the remaining species (Ph.grisea ssp. grisea, Ph. grisea ssp. lilacina, Ph. petraea, Ph. servitii, Ph. subpulverulenta and Ph.venusta) are pure Old world taxa with a much more limited distribution.The majority of the European Physconia taxa are distributed meridionally to submeridionally and occur preferentially in suboceanic areas. Main conclusions Some of the species under consideration have a wide distribution, nevertheless they show clear affinities to ecological conditions that influence their distribution patterns. A number of species show not only zonal and regional restrictions, but also affinities to the western climatic type. The Mediterranean is the centre of diversity of the genus Physconia in Europe.     

Trends and Carrying Capacity of Sea Otters in Southeast Alaska

Sea otter populations in Southeast Alaska, USA, have increased dramatically from just over 400 translocated animals in the late 1960s to >8,000 by 2003. The recovery of sea otters to ecosystems from which they had been absent has affected coastal food webs, including commercially important fisheries, and thus information on expected growth and equilibrium abundances can help inform resource management. We compile available survey data for Southeast Alaska and fit a Bayesian state-space model to estimate past trends and current abundance. Our model improves upon previous analyses by partitioning and quantifying sources of estimation error, accounting for over-dispersion of aerial count data, and providing realistic measurements of uncertainty around point estimates of abundance at multiple spatial scales. We also provide estimates of carrying capacity (K) for Southeast Alaska, at regional and sub-regional scales, and analyze growth rates, current population status and expected future trends. At the regional scale, the population increased from 13,221 otters in 2003 to 25,584 otters in 2011. The average annual growth rate in southern Southeast Alaska (7.8%) was higher than northern Southeast Alaska (2.7%); however, growth varied at the sub-regional scale and there was a negative relationship between growth rates and the number of years sea otters were present in an area. Local populations vary in terms of current densities and expected future growth; the mean estimated density at K was 4.2 ± 1.58 sea otters/km² of habitat (i.e., the sub-tidal benthos between 0 m and 40 m depth) and current densities correspond on average to 50% of projected equilibrium values (range = 1–97%) with the earliest-colonized sub-regions tending to be closer to K. Assuming a similar range of equilibrium densities for currently un-occupied habitats, the projected value of K for all of Southeast Alaska is 74,650 sea otters. Future analyses can improve upon the precision of K estimates by employing more frequent surveys at index sites and incorporating environmental covariates into the process model to generate more accurate, location-specific estimates of equilibrium density. © 2019 The Authors. The Journal of Wildlife Management Published by Wiley Periodicals, Inc.