| 31. |
- Strand, Malin, et al.
(författare)
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Size of genera - biology or taxonomy?
- 2015
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 44, s. 106-116
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Annan publikation (refereegranskat)
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| 32. |
- Subhash, Santhilal, 1987, et al.
(författare)
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Sperm Originated Chromatin Imprints and LincRNAs in Organismal Development and Cancer
- 2020
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Ingår i: iScience. - : Elsevier BV. - 2589-0042. ; 23:6
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Tidskriftsartikel (refereegranskat)abstract
- Importance of sperm-derived transcripts and chromatin imprints in organismal development is poorly investigated. Here using an integrative approach, we show that human sperm transcripts are equally important as oocyte. Sperm-specific and sperm-oocyte common transcripts carry distinct chromatin structures at their promoters correlating with corresponding transcript levels in sperm. Interestingly, sperm-specific H3K4me3 patterns at the lincRNA promoters are not maintained in the germ layers and somatic tissues. However, bivalent chromatin at the sperm-specific protein-coding gene promoters is maintained throughout the development. Sperm-specific transcripts reach their peak expression during zygotic genome activation, whereas sperm-oocyte common transcripts are present during early preimplantation development but decline at the onset of zygotic genome activation. Additionally, there is an inverse correlation between sperm-specific and sperm-oocyte lincRNAs throughout the development. Sperm-lincRNAs also show aberrant activation in tumors. Overall, our observations indicate that sperm transcripts carrying chromatin imprints may play an important role in human development and cancer.
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| 33. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
- 2018
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Ingår i: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 34:23
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Tidskriftsartikel (refereegranskat)abstract
- Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.
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| 34. |
- Borchert, Erik, et al.
(författare)
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Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort
- 2021
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Ingår i: mSystems. - 2379-5077 .- 2379-5077. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- The marine bone biome is a complex assemblage of macro- and microor- ganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic colla- gen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of micro- bial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia con- tained the most diverse gene repertoires. We postulate that demineralization of inor- ganic bone components is achieved by a timely succession of a closed sulfur biogeo- chemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone sur- face communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia. IMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.
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| 35. |
- Drennan, Regan, et al.
(författare)
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Annelid Fauna of the Prince Gustav Channel, a Previously Ice-Covered Seaway on the Northeastern Antarctic Peninsula
- 2021
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The Prince Gustav Channel is a narrow seaway located in the western Weddell Sea on the northeastern-most tip of the Antarctic Peninsula. The channel is notable for both its deep (>1200 m) basins, and a dynamic glacial history that most recently includes the break-up of the Prince Gustav Ice Shelf, which covered the southern portion of the channel until its collapse in 1995. However, the channel remains mostly unsampled, with very little known about its benthic biology. We present a preliminary account of the benthic annelid fauna of the Prince Gustav Channel in addition to samples from Duse Bay, a sheltered, glacier-influenced embayment in the northwestern portion of the channel. Samples were collected using an Agassiz Trawl, targeting megafaunal and large macrofaunal sized animals at depths ranging between 200–1200 m; the seafloor and associated fauna were also documented in situ using a Shallow Underwater Camera System (SUCS). Sample sites varied in terms of depth, substrate type, and current regime, and communities were locally variable across sites in terms of richness, abundance, and both taxonomic and functional composition. The most diverse family included the motile predator/scavenger Polynoidae, with 105 individuals in at least 12 morphospecies, primarily from a single site. This study provides first insights into diverse and spatially heterogeneous benthic communities in a dynamic habitat with continuing glacial influence, filling sampling gaps in a poorly studied region of the Southern Ocean at direct risk from climate change. These specimens will also be utilized in future molecular investigations, both in terms of describing the genetic biodiversity of this site and as part of wider phylogeographic and population genetic analyses assessing the connectivity, evolutionary origins, and demographic history of annelid fauna in the region.
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| 36. |
- Ritter, Camila, et al.
(författare)
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High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.
- 2018
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.We used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.Soil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).In spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world's largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.
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| 37. |
- Tedersoo, Leho, et al.
(författare)
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Novel soil-inhabiting clades fill gaps in the fungal tree of life
- 2017
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
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| 38. |
- Zanne, Amy E, et al.
(författare)
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Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
- 2020
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Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
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Tidskriftsartikel (refereegranskat)abstract
- Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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| 39. |
- Lanzén, Anders, et al.
(författare)
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Benthic eDNA metabarcoding provides accurate assessments of impact from oil extraction, and ecological insights
- 2021
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Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X. ; 130
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Tidskriftsartikel (refereegranskat)abstract
- Apart from its contribution to climate change, offshore oil and gas extraction is also a potential threat to the diversity and function of marine ecosystems. Routine monitoring of the environmental status of affected areas is therefore critical for effective management. While current morphology-based monitoring is relatively time consuming, costly and prone to identification bias, environmental DNA metabarcoding offers an attractive alternative for assessing the impacts of oil drilling, extraction or spills. However, to be ready for routine monitoring, its performance needs to be demonstrated through agreement with assessments based on physicochemical measurements and current bioindicators. To this end, we applied metabarcoding to sequence the metazoan (COI) and total eukaryotic (18S) benthic components. We targeted a range of sites, with a gradient of low to high level of impact, located near active production installations and reference sites, in the North and Barents Seas. Alpha diversity and community structure of both datasets correlated strongly with a physicochemical pressure index (PI) based on total hydrocarbons (THC), PAH16, Ba and Cu. Calculations of the macroinvertebrate-based Norwegian Sensitivity Index (NSI) based on COI metabarcoding data agreed well with corresponding morpho-taxonomy values and with the PI. Further, we identified a set of bioindicator taxa from both metabarcoding datasets, to develop novel biotic indices and demonstrate their predictive performance using cross-validation. Finally, we compared co-occurrence networks from impacted vs. non-impacted sites, to improve the understanding of the ecological consequences of impacts. Our study demonstrates that metabarcoding can act as a meaningful and relatively accurate complement to the current morpho-taxonomic approach.
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| 40. |
- Abbott, Jessica K., et al.
(författare)
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The microevolutionary response to male-limited X-chromosome evolution in Drosophila melanogaster reflects macroevolutionary patterns
- 2020
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Ingår i: Journal of Evolutionary Biology. - : Wiley-Blackwell. - 1010-061X .- 1420-9101. ; 33:6, s. 738-750
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Tidskriftsartikel (refereegranskat)abstract
- Due to its hemizygous inheritance and role in sex determination, the X-chromosome is expected to play an important role in the evolution of sexual dimorphism and to be enriched for sexually antagonistic genetic variation. By forcing the X-chromosome to only be expressed in males over >40 generations, we changed the selection pressures on the X to become similar to those experienced by the Y. This releases the X from any constraints arising from selection in females and should lead to specialization for male fitness, which could occur either via direct effects of X-linked loci or trans-regulation of autosomal loci by the X. We found evidence of masculinization via up-regulation of male-benefit sexually antagonistic genes and down-regulation of X-linked female-benefit genes. Potential artefacts of the experimental evolution protocol are discussed and cannot be wholly discounted, leading to several caveats. Interestingly, we could detect evidence of microevolutionary changes consistent with previously documented macroevolutionary patterns, such as changes in expression consistent with previously established patterns of sexual dimorphism, an increase in the expression of metabolic genes related to mito-nuclear conflict and evidence that dosage compensation effects can be rapidly altered. These results confirm the importance of the X in the evolution of sexual dimorphism and as a source for sexually antagonistic genetic variation and demonstrate that experimental evolution can be a fruitful method for testing theories of sex chromosome evolution.
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