| 1. |
- Abarenkov, Kessy, et al.
(författare)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 2. |
- Erséus, Christer, 1951, et al.
(författare)
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New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida)
- 2017
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 7:23, s. 10421-10439
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Tidskriftsartikel (refereegranskat)abstract
- Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate-specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.
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| 3. |
- Heyman, Jakob, 1979-, et al.
(författare)
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A paleoglaciological reconstruction for Bayan Har Shan, NE Tibetan Plateau
- 2009
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Konferensbidrag (refereegranskat)abstract
- The paleoglaciology of the Tibetan Plateau has remained elusive because extensive areas still lack detailed scrutiny. We here present a paleoglaciological reconstruction for the Bayan Har Shan region, NE Tibetan Plateau, which could serve as a working model to investigate other poorly investigated regions. The reconstruction is primarily based on three methods for revealing the glacial history; 1) remote sensing (geomorphology), 2) field studies (stratigraphy), and 3) numerical dating techniques. Remote sensing (SRTM elevation data, Landsat ETM+ satellite imagery and Google Earth) of a 136 500 km2 area reveals an abundance of glacial landforms in the highest mountain areas and an absence of glacial landforms on intervening plateau surfaces. Stratigraphical data collected during three field seasons supplement the picture emerging from remote sensing. Glacial deposits (including erratic boulders and till) occur in the elevated mountain areas but are absent on the intervening plateau areas. Marginal moraines in central Bayan Har can be grouped to represent at least three separate glacial extents and scattered observations of glacial deposits indicate the presence of a fourth (and maximum) glacial extent. To tie the glacial geological record to a chronology we have employed terrestrial cosmogenic nuclide (TCN) exposure and optically stimulated luminescence (OSL) dating. Beryllium apparent exposure ages of 65 glacial boulders, surface cobbles/pebbles and depth profile samples yield minimum ages for the three youngest glacial extents of 40-65 ka, 60-100 ka, and 95-165 ka (with the wide age ranges due to TCN dating uncertainties). A preliminary OSL age of c. 160 ka from glacial sediments of the oldest of these glacial extents supports our interpretation based on TCN dating. The glacial extent presented here is more restricted than most previous reconstructions, most notably with very restricted glaciers over at least the last 40-65 ka. These results indicate that while continental-scale ice sheets evolved and disappeared in North America and Eurasia over the last half of the last glacial cycle, the NE corner of the Tibetan Plateau experienced relatively minor glacial fluctuations.
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| 4. |
- Heyman, Jakob, 1979-, et al.
(författare)
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An evaluation of multiple working hypotheses to explain cosmogenic exposure age data from glacial deposits in the Bayan Har Shan, NE Tibetan Plateau
- 2009
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Ingår i: Proceedings.
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Konferensbidrag (refereegranskat)abstract
- Many questions remain unanswered regarding the Quaternary glaciations of the Tibetan Plateau. We have used terrestrial cosmogenic nuclide (TCN) exposure age dating of glacial deposits to examine the style, extent, and timing of past glaciations of the Bayan Har Shan, a mountain region on the northeastern Tibetan Plateau. This area lies within a transition zone between the dry interior of the Tibetan Plateau and the wetter eastern margin affected by the Asian monsoon. Bayan Har Shan has many glacial landforms and deposits that provide evidence for former glaciation ranging from cirque and valley glaciers to ice-fields and ice caps.In an attempt to constrain the timing of glaciations in Bayan Har Shan, we have performed TCN exposure dating on 65 samples in central Bayan Har Shan from glacial deposits. boulders (39 samples), on surface pebbles/cobbles (12 samples), and on pebbles in sediment depth profiles (14 samples from four profiles) allow us to examine the timing and extent of glaciations in this area. As is often the case, there are some challenges in interpreting the range of TCN apparent exposure ages that is found in data from several samples and sample types on a single deposit and from samples taken at various sites. Thus we evaluate multiple working hypotheses to explain apparent exposure ages on glacial deposits, which in this case range from 3 ka to 129 ka. We consider three different hypotheses; 1) some samples have erroneously old exposure ages due to inheritance, 2) samples have been preserved under cold-based, non-erosive ice, and 3) samples have experienced only post-glacial shielding. Only when we adopt a hypothesis that assumes no prior exposure, and thus that maximum apparent exposure ages constrain the minimum age of formation of a feature (working hypotheses 3), do we find broad consistency between apparent exposure ages from different sample types (erratic boulders, surface pebbles/cobbles and pebbles from depth profiles). This leads to the conclusion that all of the sites of former glaciations we examined are at least 50ka in age, and that there has been no large-scale expansion of glaciers in the central Bayan Har Shan over the last 50ka.
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| 5. |
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| 6. |
- Heyman, Jakob, 1979-, et al.
(författare)
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Palaeoglaciation of Bayan Har Shan, northeastern Tibetan Plateau: glacial geology indicates maximum extents limited to ice cap and ice field scales
- 2009
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Ingår i: Journal of Quaternary Science. - : John Wiley & Sons. - 0267-8179 .- 1099-1417. ; 24:7, s. 710-727
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Tidskriftsartikel (refereegranskat)abstract
- Key locations within an extensive area of the northeastern Tibetan Plateau, centred on Bayan Har Shan, have been mapped to distinguish glacial from non-glacial deposits. Prior work suggests palaeo-glaciers ranging from valley glaciers and local ice caps in the highest mountains to a regional or even plateau-scale ice sheet. New field data show that glacial deposits are abundant in high mountain areas in association with large-scale glacial landforms. In addition, glacial deposits are present in several locations outside areas with distinct glacial erosional landforms, indicating that the most extensive palaeo-glaciers had little geomorphological impact on the landscape towards their margins. The glacial geological record does indicate extensive maximum glaciation, with local ice caps covering entire elevated mountain areas. However, absence of glacial traces in intervening lower-lying plateau areas suggests that local ice caps did not merge to form a regional ice sheet on the northeastern Tibetan Plateau around Bayan Har Shan. No evidence exists for past ice sheet glaciation.
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| 7. |
- Li, Yingkui, et al.
(författare)
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Patterns of landscape evolution on the central and northern Tibetan Plateau investigated using in-situ produced Be-10 concentrations from river Sediments
- 2014
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Ingår i: Earth and Planetary Science Letters. - : Elsevier BV. - 0012-821X .- 1385-013X. ; 398, s. 77-89
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Tidskriftsartikel (refereegranskat)abstract
- Quantifying long-term erosion rates across the Tibetan Plateau and its bordering mountains is of critical importance to an understanding of the interaction between climate, tectonic movement, and landscape evolution. We present a new dataset of basin-wide erosion rates from the central and northern Tibetan Plateau derived using in-situ produced Be-10 concentrations of river sediments. Basin-wide erosion rates from the central plateau range from 10.1 +/- 0.9 to 36.8 +/- 3.2 mm/kyr, slightly higher than published local erosion rates measured from bedrock surfaces. These values indicate that long-term downwearing of plateau surfaces proceeds at low rates and that the landscape is demonstrably stable in the central plateau. In contrast, basin-wide erosion rates from the Kunlun Shan on the northern Tibetan Plateau range from 19.9 +/- 1.7 to 163.2 +/- 15.9 mm/kyr. Although the erosion rates of many of these basins are much higher than the rates from the central plateau, they are lower than published basin-wide erosion rates from other mountains fringing the Tibetan Plateau, probably because the basins in the Kunlun Shan include both areas of low-relief plateau surface and high-relief mountain catchments and may also result from retarded fluvial sediment transport in an arid climate. Significantly higher basin-wide erosion rates derived from the Tibetan Plateau margin, compared to the central plateau, reflect a relatively stable plateau surface that is being dissected at its margins by active fluvial erosion.
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| 8. |
- Li, Yingkui, et al.
(författare)
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Timing and extent of Quaternary glaciations in the Tianger Range, eastern Tian Shan, China, investigated using Be-10 surface exposure dating
- 2014
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 98, s. 7-23
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Tidskriftsartikel (refereegranskat)abstract
- Reconstructing glacial chronologies with consistent methods is critical for efforts to examine the timing and pattern of past climate change. Cosmogenic Be-10 surface exposure dating has been widely used to constrain the timing of glacial events on the Tibetan Plateau and in Central Asia. However, few such studies have been conducted in the Chinese Tian Shan and available Be-10 ages from this region have only provided evidence for glacial events during the global Last Glacial Maximum (gLGM) and Lateglacial. Here, we present 45 Be-10 surface exposure ages from glacial landforms in the Ala and Daxi valleys, two formerly glaciated valleys draining the Tianger Range, eastern Tian Shan. Combined with previously published Be-10 surface exposure ages from the Daxi Valley in the source area of the Urumqi River, the new ages record five major glacial events during Marine Oxygen Isotope Stages (MIS) 6 or older, 4, 3, 2, and 1 (during the Little Ice Age, LIA). Landforms from glacial events since MIS 2 are found on the northern slope of the Tianger Range (Daxi Valley), whereas evidence for the older glacial events is only preserved on its southern slope (Ala Valley). This disparity may be caused by different preservation- and micro-climatic conditions on the northern and southern slopes of this mountain range, due to differences in gradient and aspect. The LIA glacial advances are apparently the only Holocene glacial event recorded in this area. Earlier Holocene glacial events were probably so restricted in extent that they were destroyed by subsequent LIA advances.
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| 9. |
- Liang, Jiawei, et al.
(författare)
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Performance and microbial communities of a novel integrated industrial-scale pulp and paper wastewater treatment plant
- 2021
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Ingår i: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526. ; 278
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Tidskriftsartikel (refereegranskat)abstract
- Ltd Paper production generates pulp and paper wastewater (PPW), and it is difficult to remove the high-level pollutants in PPW efficiently. Herein, an efficient industrial-scale pulp and paper wastewater treatment plant (PP-WWTP) that integrated physicochemical and biological processes is investigated and reported. This PP-WWTP treated 2.3 Mt of wastewater with 17,388 ± 1436 mg/L chemical oxygen demand (COD) annually. The PP-WWTP can effectively remove over 99.81% of the COD. In detail, the physical, anaerobic, aerobic and chemical steps accounted for 41.6%, 40.0%, 11.9%, and 6.5% of COD removal, respectively. The microbial communities of the bioreactors removed the pollutants efficiently and contained diverse microbes. Further metagenomic analyses of the bioreactors identified more than 90,000 genes/gene fragments encoding for carbohydrate-active enzymes (CAZys), demonstrating high lignocellulose degradation ability of the bioreactors at molecular level. The xylanase activity assay showed some lignocellulase in the bioreactors were functional. Recycling the residual heat from the PPW along with energy recovered from biological treatment of the PPW, in the form of biogas (20,000 m³/d), could generate more than 1.5 M USD benefits/y. The results of this study demonstrated that the integrated physicochemical and biological process for PPWW treatment could effectively remove pollutants while generating revenue.
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| 10. |
- Liu, Yingkui, et al.
(författare)
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Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae)
- 2017
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Ingår i: Organisms Diversity and Evolution. - : Springer Science and Business Media LLC. - 1439-6092 .- 1618-1077. ; 17:2, s. 477-495
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Tidskriftsartikel (refereegranskat)abstract
- Limnodrilus hoffmeisteri Claparède, 1862 is a common freshwater worm, often regarded as an indicator of organic pollution. The taxonomic status of this species is controversial due to great variation in morphological features. Numerous morphological forms of L. hoffmeisteri are recorded in the literature, especially from Europe and North America. Today, DNA-based species delimitation assumes that species boundaries can be more objectively and effectively estimated using genetic data rather than with morphological data alone. To investigate if L. hoffmeisteri is a single species, 295 worms identified as either L. hoffmeisteri or other similar (congeneric) morphospecies, using currently accepted morphological criteria, were collected from 82 locations in the northern hemisphere. The number of primary species hypotheses (PSHs) was first explored with cytochrome oxidase subunit I (COI), the proposed DNA barcode for animal species, and with data for all specimens. Both automatic barcoding gap discovery (ABGD) and the Bayesian general mixed Yule coalescent (bGMYC) model revealed the existence of ≥25 distinct PSHs (COI lineages) in our dataset. Then, smaller samples of individuals representing major COI lineages were used for exploration of a nuclear locus, the internal transcribed spacer (ITS) region. In the ITS gene tree (81 sequences), generated by BEAST, 16 well-supported terminal groups were found, but not all of these groups were congruent with the PSHs found in the COI tree. As results across these different analyses were inconsistent, we resorted to analyzing reciprocal monophyly between gene trees and used a minimum consensus of all evidence, suggesting that there are 13 separately evolving lineages (=13 species) within our sample. The smallest uncorrected COI p-distance between these species is 12.1%, and the largest intraspecific p-distance is 16.4%, illustrating the problem of species delimitation with a DNA-barcoding gap as the sole criterion. Ten of these species are morphologically identified as “L. hoffmeisteri,” the remaining three can be attributed to morphologically distinct congeneric species. An individual from the type locality in Switzerland was designated as a neotype of L. hoffmeisteri sensu stricto. This worm belongs to one of the ten species, and this lineage is widely distributed in Europe, Asia, and North America. The remaining nine species show a mixed distribution pattern; some appear to be endemic to a restricted area, others are Holarctic. Our results provide clues to the future revalidation of some of the nominal species today placed in synonymy with L. hoffmeisteri. A BEAST analysis, based on previously published and newly generated 16S data, suggested that this complex contains also other species than those studied by us. By integrating additional genetic data, it will be possible to identify these and additional specimens in future studies of Limnodrilus, and the neotype provides a baseline for further revisions of the taxonomy of the L. hoffmeisteri complex.
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