Proxy comparison in ancient peat sediments: pollen,macrofossil and plant DNA

We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.     

A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline

Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north–south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single‐tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site‐specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition.     

The vegetational history of the northern Apennines, Italy: information from three new sequences and a review of Regional vegetational change

Abstract. The results of pollen analysis and radiocarbon dating are presented from three northern Apennine sequences; Lago Padule in northern Tuscany and Lago Pratignano and Ospitale in the Emilia-Romagnan Apennines. This is the first detailed pollen stratigraphic information from sites in Emilia-Romagna and north Tuscany and extends eastwards the area from which information on vegetational history is available. The sequence from Lago Padule is one of the most complete Holocene records known from the northern Apennine region. Lago Pratignano has the deepest sequence of organic sediments (1544 cm) and the fastest rates of sediment accumulation (up to 28 cm per 100 years) providing the highest resolution record for the mid to late Holocene periods in the region. High rates of sedimentation have also occurred at Ospitale where organic sediments are 780 cm deep and began to form at approximately 5500 bp. The record from Lago Padule is compared with Holocene records from two nearby sites and a series of Regional Pollen Assemblage Zones is defined for the eastern area of the northern Apennines. The main features of vegetational change identified are: (i) a‘pioneer’phase of rapid forest development during the early Holocene followed by the establishment of an upper forest belt dominated by Abies, and a belt of mixed deciduous forest at lower altitudes; (ii) the appearance and rapid expansion of Fagus between approximately 5200 bp and 2900 bp forming a mixed Abies-Fagus association in the upper forest belt; and (iii) the overall reduction of forest cover, and dominance of Fagus in the arboreal vegetation from around 2900 bp. The scheme of Regional PAZs for the eastern area is used as a framework for the review of pollen stratigraphic information and radiocarbon dates from other sites in the northern Apennine region. Characteristics of pollen records which can be identified in sequences from across the region are identified and the chronology of similar changes in pollen stratigraphy is examined. The scheme of four regional PAZs for the Holocene period is shown to be valid for the entire northern Apennine region. The examination of a series of pollen records shows that Fagus appeared earlier in the western than the eastern part of the region during the mid Holocene and became dominant in the northern Apennine forests post 3000 bp. The impact of anthropogenic activity and climatic change on the spread and development of Fagus are discussed. The palynological evidence which is now available from the northern Apennines is compared with information for the region shown in the‘European pollen maps’of Huntley & Birks (1983). This study provides an updated review of the representation of different tree taxa in Holocene pollen records from the northern Apennines and illustrates the role of the northern Apennines as a refugium for trees during the Wurmian Lateglacial.     

Mercury-resistant bacteria from permafrost sediments and prospects for their use in comparative studies of mercury resistance determinants

Mercury-resistant bacteria were isolated from permafrost sediments of Kolyma lowland and Canada existing over five thousand to two million years. Their content was shown to vary within the range 0.001-2.9% and to depend on the amount of mercury in sampling sites (coefficient of correlation 0.75). A collection of mercury-resistant bacterial strains was created. In this collection, various representatives of both Gram-positive bacteria (Bacillus, Exiguobacterium, Micrococcus, Arthrobacter) and Gram-negative bacteria (Pseudomonas, Acinetobacter, Plesiomonas, Myxobacteriales) were identified. Most resistant bacteria were found to contain determinants homologous to mer-operons of contemporary bacteria. The isolated strains of paleobacteria are proposed to be used for a comparative structural study of contemporary and ancient plasmids and transposons carrying mercury resistance determinants.     

A taphonomic study of modern pollen assemblages from dung and surface sediments in arid environments of Spain

Coastal plant communities in arid southeastern Spain are characterized by insect-pollinated scrub species, which fail to occur in Quaternary pollen sequences from valleys, marshlands and marine cores. We investigate pollen–vegetation relationships in samples from soil surfaces, animal dung, and sediments in depressions or basins that, in theory, should have pollen spectra that are comparable to those from sedimentary basins elsewhere. Pollen spectra from basins or depressions are very susceptible to long-distance wind and water transport. This can mask representation of pollen from the surrounding insect-pollinated vegetation, as can over-representation of basin-margin halophilous and hydrophilous pollen. Pollen spectra from biogenic materials of animal origin are the best analogues of local and regional vegetation, and show the best analytical potential in terms of pollen concentration and taxon diversity. Pollination properties of the species studied indicate they will rarely be found in most conventional pollen records. It cannot be stressed too strongly that insight into Quaternary vegetation of arid regions demands complementary pollen analysis of coprolites, urine-cemented deposits, and cave sediments with preserved biotic remains, in addition to water-lain sediments.     

Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia

The methane oxidation potential of active layer profiles of permafrost soils from the Lena Delta, Siberia, was studied with regard to its respond to temperature, and abundance and distribution of type I and type II methanotrophs. Our results indicate vertical shifts within the optimal methane oxidation temperature and within the distribution of type I and type II methanotrophs. In the upper active layer, maximum methane oxidation potentials were detected at 21 degrees C. Deep active layer zones that are constantly exposed to temperatures below 2 degrees C showed a maximum potential to oxidize methane at 4 degrees C. Our results indicate a dominance of psychrophilic methanotrophs close to the permafrost table. Type I methanotrophs dominated throughout the active layer profiles but their number strongly fluctuated with depth. In contrast, type II methanotrophs were constantly abundant through the whole active layer and displaced type I methanotrophs close to the permafrost table. No correlation between in situ temperatures and the distribution of type I and type II methanotrophs was found. However, the distribution of type I and type II methanotrophs correlated significantly with in situ methane concentrations. Beside vertical fluctuations, the abundance of methane oxidizers also fluctuated according to different geomorphic units. Similar methanotroph cell counts were detected in samples of a flood plain and a polygon rim, whereas cell counts in samples of a polygon centre were up to 100 times lower.     

A comparative study of the thermal stability of formate dehydrogenases from microorganisms and plants

A comparative study of the thermostability of NAD⁺-dependent formate dehydrogenases (FDHs; EC 1.2.1.2) from both methylotrophic bacteria Pseudomonas sp. 101 and Moraxella sp. C1, the methane-utilizing yeast Candida boidinii, and plants Arabidopsis thaliana and Glycine max (soybean) was performed. All the enzymes studied were produced by expression in E. coli cells. The enzymes were irreversibly inactivated in one stage according to first-order reaction kinetics. The FDH from Pseudomonas sp. 101 appeared as the most thermostable enzyme; its counterpart from Glycine max exhibited the lowest stability. The enzymes from Moraxella sp. C1, C. boidinii, and Arabidopsis thaliana showed similar thermostability profiles. The temperature dependence of the inactivation rate constant of A. thaliana FDH was studied. The data of differential scanning calorimetry was complied with the experimental results on the inactivation kinetics of these enzymes. Values of the melting heat were determined for all the enzymes studied.     

A comparative study of the alpha-subdomains of bovine and human alpha-lactalbumin reveals key differences that correlate with molten globule stability

The alpha-lactalbumins form stable molten globule states under a range of conditions, with the low pH form being the best characterized. The stability of the molten globule varies among different members of this family, but the origin of the stability difference is not clear. We compare the folding and stability of alpha-subdomain constructs of human and bovine alpha-lactalbumin. Previous studies have demonstrated that the isolated alpha-subdomain of human alpha-lactalbumin folds and forms a molten globule state. The minimum core construct has been defined to include the A, B, and D alpha-helices and the C-terminal 3(10) helix. A construct corresponding to the same region of bovine alpha-lactalbumin is much less structured and less stable than the human alpha-lactalbumin construct. Addition of the C-helix to generate a 75-residue bovine construct does not lead to a significant increase in structure or stability. This construct (AB-CD/3(10)) contains the entire alpha-subdomain of bovine alpha-lactalbumin. Thus molten globule formation in the human protein, but not in the bovine protein, can be rationalized on the basis of a stable alpha-subdomain. Interactions involving more of the protein chain are required to generate a well structured molten globule in the bovine protein. Comparison of AB-CD/3(10) to the molten globule formed by the intact protein and to the protein with the 6-120 disulfide reduced indicates that both the beta-subdomain and the 6-120 disulfide play a role in stabilizing the bovine alpha-lactalbumin molten globule.     

A comparative study of pollen trends in Genoa and Sanremo (Italy) from 1981 to 1989

Summary Trends of the atmospheric dispersion of the pollens of Urticaceae, Poaceae, Asteraceae,Plantago, Chenopodiaceae-Amaranthaceae, Polygonaceae, Oleaceae, Betulaceae-Corylaceae,Quercus, Castanea, and Cupressaceae-Taxaceae were studied from 1981 to 1989 in two localities (Genoa and Sanremo) about 120 km apart on the coast of Liguria in Italy. Statistical analysis revealed, in particular, and overall increase in pollen rain in Genoa during the period considered. The following observations were carried out on the pollens of greatest allergological interest: Urticaceae, a slightly increasing trend in Genoa; Poaceae, a moderately increasing trend in Sanremo; Oleaceae, almost parallel, uniform trendsin both centres. The values of this study lies in its ability to point out any increase which may occur over the years in the dispersal of certain allergenic pollens.     

A long-term study of winter and early spring tree pollen in the Tulsa, Oklahoma atmosphere

Since 1986 the atmosphere in Tulsa, Oklahoma has been monitored for airborne pollen and spores with a Burkard 7-day spore trap situated on the roof of a building at The University of Tulsa. The present study specifically examined the early spring tree pollen season for several local taxa and the occurrence of pre-season pollen during December and January. Knowledge of the local pollen season will help identify the presence of out-of-season pollen and possible long distance transport (LDT) events. Average daily concentrations of airborne pollen for species ofBetula, Quercus, Ulmus, and Cupressaceae were determined for each year from 1987 to 1996. The data showed that during the early spring the precise pollination periods for these allergenic tree species are highly variable. There were considerable variations in start date, season length, peak concentration, date of peak, and cumulative season total. The start dates forUlmus, Betula, andQuercus varied by 30 days or more, while the early spring Cupressaceae pollen showed the least variation in start date (only 23 days). More research is needed to understand the mechanisms which govern the onset and magnitude of pollen release. Although several reports have documented episodes of long distance transport (LDT) of pollen, the actual contribution of out-of-season or out-of-region pollen to local air spora is poorly known. The current study also re-examined the LDT ofJuniperus ashei pollen in Oklahoma.Juniperus pollen appeared in the Tulsa atmosphere on 40% of the days in December and January with concentrations as high as 2400 pollen grains/m³ of air; however, no local populations ofJuniperus pollinate at this time of the year. High concentrations occurred on days with southerly winds suggesting thatJuniperus ashei populations in southern Oklahoma and Texas were the pollen source. Since no local pollen is present in the Tulsa atmosphere in December and January, this example of LDT has been easy to document.     

Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations

Background

The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.

Methodology/Principal Findings

We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.

Conclusion/Significance

Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.     

Isobaric tags for relative and absolute quantification- based comparative proteomics reveals the features of plasma membrane-associated proteomes of pollen grains and pollen tubes from Lilium davidii

Mature pollen grains (PGs) from most plant species are metabolically quiescent. However, once pollinated onto stigma, they quickly hydrate and germinate. A PG can give rise to a vegetative cell-derived polarized pollen tube (PT), which represents a specialized polar cell. The polarized PT grows by the tip and requires interaction of different signaling molecules localized in the apical plasma membrane and active membrane trafficking. The mechanisms underlying the interaction and membrane trafficking are not well understood. In this work, we purified PG and PT plasma-membrane vesicles from Lilium davidii Duch. using the aqueous two-phase partition technique, then enriched plasma membrane proteins by using Brij58 and KCl to remove loosely bound contaminants. We identified 223 integral and membrane-associated proteins in the plasma membrane of PGs and PTs by using isobaric tags for relative and absolute quantification (iTRAQ) and 2-D high-performance liquid chromatography-tandem mass spectrometry. More than 68% of the proteins have putative transmembrane domains and/or lipid-modified motifs. Proteins involved in signal transduction, membrane trafficking and transport are predominant in the plasma-membrane proteome. We revealed most components of the clathrin-dependent endocytosis pathway. Statistical analysis revealed 14 proteins differentially expressed in the two development stages: in PTs, six upregulated and eight downregulated are mainly involved in signaling, transport and membrane trafficking. These results provide novel insights into polarized PT growth.     

An application of scanning electron microscopy to the study of ancient sedimentary rocks from the Saionia Scarp,Sierra Leone

Quartz grains taken from the lithologies of the Late Ordovician Saionia Scarp Group of Sierra Leone have been examined by scanning electron microscopy. The results show that diagenetic changes do not completely destroy original surface textures and that the scanning electron microscope technique of environmental discrimination is of use in revealing the depositional history of these ancient sedimentary rocks. Past environmental interpretations of the Saionia Scarp Group based on more conventional sedimentary studies have been confirmed by this study.     

A comparative study on the allergenicity, structure, and ultrastructure of two Acacia pollen grains in guinea pigs

Acacia saligna and Acacia victoria are native to Australia brought to and grown in Southern Iran. They have since had a widespread distribution and become native in Iran. As people of the region are exposed to the pollen grains from these plants during a 5 months period, this study aimed at investigating the allergenicity of their mature pollen grains. In addition, the structural and ultrastructural as well as the total protein content of the mature pollen grains were analyzed. Pollen grains of A. saligna and A. victoria were collected from the suburbs of Ahvaz, Iran. Pollen extracts (15 % concentration) were prepared in PBS (pH 7.2), and 4- to 6-week-old male guinea pigs (Hartly) were used for allergenicity tests. Skin tests showed a significant increase in flare diameter. Clinical tests also showed a significant change in the levels of eosinophils, neutrophils, and IgE. Comparative analysis of the allergenicity of A. saligna and A. victoria pollen grains revealed a higher IgE level in the latter. Comparative analysis of pollen characteristics was performed using both light and electron microscopy for sporoderm structure and ultrastructure, respectively. Twelve percent PAGE analysis of the total protein content of mature pollen grains showed a greater number of bands in A. victoria, while four bands were common in both species. In conclusion, this study demonstrates that both A. saligna and A. victoria pollen grains are allergenic, with a greater allergenicity of A. victoria pollen grains. In addition, the structural and ultrastructural as well as the total protein content of the mature pollen grains are revealed, and a potential protein allergen is proposed.     

A comparative study of nuclear and chloroplast DNA dependent RNA polymerases from wheat leaves

• 1.1. Three DNA dependent RNA polymerases have been purified from chromatin and chloroplast fractions of wheat leaves.
• 2.2. The purified enzymes were completely dependent on exogenous DNA after purification by glycerol gradient, DEAE-Sephadex and phosphocellulose chromatography.
• 3.3. The nuclear enzymes, I and II, showed a strong preference for denatured nuclear DNA, whereas the chloroplast enzyme preferred denatured chloroplast DNA.
• 4.4. The three enzymes require either Mg²⁺ or Mn²⁺ for activity.
• 5.5. α-amanitin specifically inhibited RNA polymerase II but has no effect on polymerase I and chloroplast polymerase.
• 6.6. Enzyme I is most active at very low ionic strength (0.10 mM KC1), whereas enzyme II and chloroplast enzyme show maximum activity at 150mM and 50 mM KC1 respectively.

     

The diatoms of contemporary and ancient sediments from Lake Waiau,Hawaii, and their geochemical environment

Lake Waiau, a shallow, heart-shaped water body, is located at 3969 m on the summit plateau of Mauna Kea, a now extinct volcano, on the island of Hawaii. Sediment core from the lake bottom contains remnants of diatom populations spanning a period of more than 5000 years. The presence of diatom frustules in conjunction with an analysis of the major chemical constituents of core and modern sediments provided a unique opportunity to assess changes with time in a highly isolated environment.     

Oxygen concentration profiles in sediments of two ancient lakes: Lake Baikal (Siberia,Russia) and Lake Malawi (East Africa)

Oxygen concentration profiles have been measured, by means of with microelectrodes in sediments of Lake Baikal and Lake Malawi, along transects allowing to give a survey of two major ancient Rift lakes: Lake Baikal (Eastern Siberia) and Lake Malawi (East Africa), along depth transects in the constitutive basins of the lakes and/or of relevant depths with regard to oxygen (including including the deepest point, 1680 m, in Lake Baikal). Sediment oxygen penetration depths (SOPs) display very different patterns, depending on the lake in the two lakes. In Lake Baikal, SOPs are variable, show no significant relationship with bathymetric depth and are surprisingly deep on Akademichesky ridge (> 50.0 mm), emphasizing the distinctive feature of this region in the lake. While the Selenga river is an important source of eutrophication, the similarity of SOP-values in the Selenga shallow with those of most other sites suggests either a dilution of organic material by allochthonous matter, or a strong south-to-north transport of particles. In Lake Malawi, available oxygen is restricted to a maximum of three millimetres of the sediment, and there is a negative relationship with bathymetric depth, as a result of a steady decline of oxygen concentration with depth through the water column. Amongst the few parameters known to affect SOPs, the oxygen consumption by the sediment seems the most significant in both lakes. SOP-values furthermore confirm differences in the trophic status of Baikal and Malawi, respectively. The importance of oxygen as a factor likely to create ecological segregation for benthic organisms is discussed. Lake Malawi offers possibilities of bathymetric segregation but no vertical segregation in the sediment. In contrast, no bathymetric segregation related to oxygen is possible in Lake Baikal, but vertical segregation in the sediment is very likely. This revised version was published online in July 2006 with corrections to the Cover Date.