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Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species
No full textBackgroundEven though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a critical issue for ecological and evolutionary studies. However, the extent to which assembly strategy, read length, sequencing depth, and library layout produce a measurable effect on microsatellite marker development remains unclear. Here, we use six frog species for genome skimming and two frog species for transcriptome sequencing to develop microsatellite markers, and investigate the effect of different isolation strategies on the yield of microsatellites.ResultsThe results revealed that the number of isolated microsatellites increases with increased data quantity and read length. Assembly strategy could influence the yield and the polymorphism of microsatellite development. Larger k-mer sizes produced fewer total number of microsatellite loci, but these loci had a longer repeat length, suggesting greater polymorphism. However, the proportion of each type of nucleotide repeats was not affected; dinucleotide repeats were always the dominant type. Finally, the transcriptomic microsatellites displayed lower levels of polymorphisms and were less abundant than genomic microsatellites, but more likely to be functionally linked loci.ConclusionsThese observations provide deep insight into the evolution and distribution of microsatellites and how different isolation strategies affect microsatellite development using NGS
Different Selectivity in Fungal Communities Between Manure and Mineral Fertilizers: A Study in an Alkaline Soil After 30 Years Fertilization
No full textFertilizer application has contributed substantially to increasing crop yield. Despite the important role of soil fungi in agricultural production, we still have limited understanding of the complex responses of fungal taxonomic and functional groups to organic and mineral fertilization in long term. Here we report the responses of the fungal communities in an alkaline soil to 30-year application of mineral fertilizer (NP), organic manure (M) and combined fertilizer (NPM) by the Illumina HiSeq sequencing and quantitative real-time PCR to target fungal internal transcribed spacer (ITS) genes. The results show: (1) compared to the unfertilized soil, fertilizer application increased fungal diversity and ITS gene copy numbers, and shifted fungal community structure. Such changes were more pronounced in the M and NPM soils than in the NP soil (except for fungal diversity), which can be largely attributed to the manure induced greater increases in soil total organic C, total N and available P. (2) Compared to the unfertilized soil, the NP and NPM soils reduced the proportion of saprotrophs by 40%, the predominant taxa of which may potentially affect cellulose decomposition. (3) Indicator species analysis suggested that the indicator operational taxonomic units (OTUs) in the M soil occupied 25.6% of its total community, but that only accounted for 0.9% in the NP soil. Our findings suggest that fertilization-induced changes of total fungal community were more responsive to organic manure than mineral fertilizer. The reduced proportion of cellulose decomposition-related saprotrophs in mineral fertilizer treatments may potentially contribute to increasing their soil C stocks
Response of anaerobic mineralization of different depths peat carbon to warming on Zoige plateau
No full textWarming greatly reshapes carbon cycle of peatlands where soil is water saturated with anaerobic condition prevailing all the year round. However, little is known about the response of anaerobic mineralization of peatlands carbon to global warming, especially when considering the difference of soil from above water table (AWT) and below water table (BWT). This study measured variations in soil carbon anaerobic mineralization as a function of warming and depth by sampling 100-cm soil columns in Zoige plateau. Warming enhanced carbon anaerobic mineralization significantly with different increments among the whole depths. The response of CO2-C and CH4-C to warming varied with depth: at surface soil, both CO2-C and CH4-C emission increased with higher increment; at deep soil, CO2-C emission increased with small increment and CH4-C emission decreased. Substrate availability influenced carbon anaerobic mineralization rate and pathway. Substantial resistant carbon at deep soil lowered CO2 increment and varied CH4 production pathway. The temperature sensitivity of peat carbon anaerobic mineralization varied with depth, suggesting the heterogeneous distribution of soil substrate among the whole depths. AWT soil was higher in temperature sensitivity than BWT soil for the substantial simple carbon and higher microbial/enzyme activity at AWT. BWT soil was a major contributor of the amount of carbon emission and the total increased carbon caused by warming. Further, for the management of peatlands, we should conduct advanced research by focusing more towards the soil of whole depth, especially on the temperature sensitivity of AWT soil and the contribution to total carbon emission of BWT soil
Paris in the spring: A review of the trade, conservation and opportunities in the shift from wild harvest to cultivation of Paris polyphylla (Trilliaceae)
No full textEthnopharmacological relevance: P. polyphylla Smith is used in traditional medicine in China, India and Nepal and is likely to be similarly used through most of its geographic range. China is at the centre of demand for P. polyphylla where it is used as an ingredient in several very successful Chinese medicinal herbal formulations. The Chinese e-commerce platform 'alibaba.com', for example, lists 97 P. polyphylla items offered by 46 Asian suppliers, of which 21 are situated in the Chinese mainland, 12 in Nepal, 7 in India, 2 in Pakistan, and 1 each in Bhutan, Hong Kong, Thailand, and Vietnam. Products offered include the crude drug (dried whole or cut rhizomes), extracts and formulations containing this herbal drug. Aims of the review: The aims of this review were to assess the scale of the P. polyphylla trade, reviewing evidence on the impacts of wild harvest on P. polyphylla populations and on the role of cultivation as an alternative to wild harvest. Materials and methods: Firstly, we reviewed published information on Paris population biology and studies on impacts of wild P. polyphylla harvest from across the geographic range of this species. Secondly, global trade data for P. polyphylla were analysed. Thirdly, we reviewed published information on P. polyphylla cultivation and made field visits to P. polyphylla cultivation areas in Yunnan and Sichuan. Results: Since the 1980s, there has been a 400-fold increase in the market price paid in China for P. polyphylla rhizomes, from 2.7 Chinese Yuan (CNY) per kg in the 1980s to market prices up to 1100 CNY per kg in 2017. Cross-border trade in dried P. polyphylla rhizomes occurs at three different scales. Firstly, an internal, national trade of P. polyphylla rhizomes within countries (such as India, Nepal and China). Secondly, trade in P. polyphylla rhizomes from Nepal (and possibly from Bhutan) to the two range states that have the largest traditional medicine trade in the world: China and India. Thirdly, trade in processed herbal products. In China, for example, P. polyphylla is widely used as an ingredient in several very successful herbal products, including a famous first aid treatment to stop bleeding. Some of these products are exported globally, in addition to entering into regional trade. Trade data in our review shows that c. 800-1050 t of P. polyphylla rhizomes are sold annually, significantly more than recorded in earlier studies. China is the only country where P. polyphylla is cultivated on a significant scale, although small-scale cultivation is taking place in India and Nepal. Conclusions: Based on the criteria for the inclusion of species in CITES Appendix II (Art. IV 2(a)), there is compelling evidence for adding Paris polyphylla. At the same time, cultivation of P. polyphylla outside of high conservation value habitats needs to be encouraged and supported. One way of doing this may be to develop separate, traceable supply chains for cultivated supplies in order to distinguish them from wild harvested stocks
Gut Microbiota in Tibetan Herdsmen Reflects the Degree of Urbanization
No full textUrbanization is associated with shifts in human lifestyles, thus possibly influencing the diversity, interaction and assembly of gut microbiota. However, the question regarding how human gut microbiota adapts to varying lifestyles remains elusive. To understand the relationship between gut microbiota and urbanization, we compared the diversity, interaction and assembly of gut microbial communities of herdsmen from three regions with different levels of urbanization, namely traditional herdsmen (TH), semi-urban herdsmen (SUH) and urban herdsmen (UH). The relative abundance of Prevotella decreased with the degree of urbanization (from TH to UH), whereas that of Bacteroides, Faecalibacterium, and Blautia showed an opposite trend. Although the alpha diversity measures (observed OTUs and phylogenetic diversity) of gut microbiota were unaffected by urbanization, the beta diversity (Jaccard or Bray-Curtis distances) was significantly influenced by urbanization. Metagenome prediction revealed that the gene functions associated with metabolism (i.e., carbohydrate and lipid metabolism) had significant differences between TH and UH. Network analysis showed that the modularity increased with the degree of urbanization, indicating a high extent of niche differentiation in UH. Meanwhile the trend of network density was opposite, indicating a more complex network in TH. Notably, the relative importance of environmental filtering that governed the community assembly increased with the degree of urbanization, which indicated that deterministic factors (e.g , low-fiber diet) play more important roles than stochastic factors (e.g., stochastic dispersal) in shaping the gut microbiota. A quantification of ecological processes showed a stronger signal of variable selection in UH than TH, implying that different selective pressures cause divergent gut community compositions due to urban lifestyles. Our results suggest that beta diversity, network interactions and ecological processes of gut microbiota may reflect the degree of urbanization, and highlight the adaptation of human gut microbiota to lifestyle changes
Structural Insight into the Allosteric Coupling of Cu1 Site and Trinuclear Cu Cluster in CotA Laccase
No full textIn laccase, type1 copper (Cu1) was connected to the trinuclear copper center (TNC) by the conserved Cys-His bridge. An allosteric coupling between the two redox sites has been reported; however, the molecular mechanism underlining the allosteric coupling is unknown. In this study, ligands of the two type3 copper sites, including His491 and His493, in CotA were mutated to Cys or Ala. The crystal structures revealed that mutations at His491 and His493 caused rearrangement of the hydrogen-bond network and geometric distortion of the TNC, which severely impaired the activities of mutants H493A, H493C, and H491C. In addition, the change in TNC affected hydrogen bonds around Cys492 in the mutants and led to Cu1 being partially reduced. These results not only decipher the mechanism of allosteric coupling between Cu1 and TNC in laccase, but also pave the way for laccase protein engineering
Cd resistant characterization of mutant strain irradiated by carbon-ion beam
No full textHeavy metal pollution is harmful to the environment and to human health. Resistant strains can grow in adverse conditions and store heavy metals to reduce their damage. The Cd2+ resistant mutant strain C2, which was irradiated by the C-12(6+) beams, can grow in Cd medium ranging from 20 to 100 mg L-1 when compared with the original strain. Attempting to discern the cause of the resistance, the phenotype and antioxidant defense system were analyzed. SEM images showed that when exposed to Cd2+, gaps on the cell surface were filled with a complex granular compound. FT-IR demonstrated that the alcoholic hydroxyl group, amino, and amide groups combined with ions. Moreover, responses of antioxidant defense system were different in the Cd2+ groups. The expression of SOD peaked at 24 h in high concentrations of Cd2+; the content of GSH increased gradually and was significantly affected by cultivation time. The MDA and CAT had the strongest response to 20 mg L-1 Cd2+ and the related metabolic pathway of CAT might play a key role in the resistance to high concentrations of Cd2+, The result indicated that the applicability of C2 could provide potential biotechnology for treatment of waste-waters and soils with Cd pollutions.</p
Hymenasplenium perriei (Aspleniaceae), a new fern species from Fiji
No full textA new fern species, Hymenasplenium perriei (Aspleniaceae), from very shaded and wet rocks in southeastern Fiji, is described and illustrated based on our morphological and recent phylogenetic studies. The new species is distinguished by its phyllopodia 2-3(-10) mm apart, marginal teeth irregular and usually with notches, veins usually terminating in marginal teeth below the notch or sometimes in the teeth, and sori inframedial
Stair-Step Pattern of Soil Bacterial Diversity Mainly Driven by pH and Vegetation Types Along the Elevational Gradients of Gongga Mountain, China
No full textEcological understandings of soil bacterial community succession and assembly mechanism along elevational gradients in mountains remain not well understood. Here, by employing the high-throughput sequencing technique, we systematically examined soil bacterial diversity patterns, the driving factors, and community assembly mechanisms along the elevational gradients of 1800-4100 m on Gongga Mountain in China. Soil bacterial diversity showed an extraordinary stair-step pattern along the elevational gradients. There was an abrupt decrease of bacterial diversity between 2600 and 2800 m, while no significant change at either lower (1800-2600 m) or higher (2800-4100 m) elevations, which coincided with the variation in soil pH. In addition, the community structure differed significantly between the lower and higher elevations, which could be primarily attributed to shifts in soil pH and vegetation types. Although there was no direct effect of MAP and MAT on bacterial community structure, our partial least squares path modeling analysis indicated that bacterial communities were indirectly influenced by climate via the effect on vegetation and the derived effect on soil properties. As for bacterial community assembly mechanisms, the null model analysis suggested that environmental filtering played an overwhelming role in the assembly of bacterial communities in this region. In addition, variation partition analysis indicated that, at lower elevations, environmental attributes explained much larger fraction of the beta-deviation than spatial attributes, while spatial attributes increased their contributions at higher elevations. Our results highlight the importance of environmental filtering, as well as elevation-related spatial attributes in structuring soil bacterial communities in mountain ecosystems
Next-generation sequencing yields a nearly complete mitochondrial genome of the Variegated Racerunner (Eremias Vermiculata) from Dunhuang Basin
No full textThe Variegated Racerunner, Eremias vermiculata, is widespread in Northwest China, southern Mongolia, and Zaisan Basin of Kazakhstan. In this study, a nearly complete mitochondrial genome (17,972 bp in length) of E. vermiculata from the Dunhuang Basin in Northwest China was determined by next-generation sequencing. Similar to the typical mtDNA of vertebrates, it contained two ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region (CR). With exception to the CR, all of the 37 genes were completely recovered. The concatenated PCGs were used to conduct Bayesian phylogenetic analyses together with mitogenome data of lacertids in GenBank. The resulting phylogenetic tree confirmed the monophyly of genus Eremias and its viviparous species as well as E. vermiculata, respectively. The mitogenome presented here will contribute to the examination of phylogeographic structure for E. vermiculata and understanding of mitochondrial DNA evolution in Eremias