| 1. |
- Field, Dawn, et al.
(författare)
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The minimum information about a genome sequence (MIGS) specification.
- 2008
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Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 26:5, s. 541-7
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Tidskriftsartikel (refereegranskat)abstract
- With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
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| 2. |
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| 3. |
- Heijboer, Amber, et al.
(författare)
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Plant biomass, soil microbial community structure and nitrogen cycling under different organic amendment regimes; a 15N tracer-based approach
- 2016
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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393. ; 107, s. 251-260
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Tidskriftsartikel (refereegranskat)abstract
- Sustainable agriculture requires nutrient management options that lead to a profitable crop yield with relatively low nitrogen (N) losses to the environment. We studied whether the addition of contrasting organic amendments together with inorganic fertilizer can promote both requirements simultaneously. In particular we studied how the chemical composition of organic amendments affects the biomass, activity and composition of the soil microbial community and subsequently carbon (C) and N mineralization, microbial N immobilization and plant growth and nutrient uptake. In a pot experiment, Brussels sprouts (Brassica oleracea, cvar. Cyrus) were grown on arable soil, mixed with 15N-labelled mineral fertilizer and different kinds of organic amendments (cattle manure solid fraction, maize silage, lucerne silage, wheat straw) differing in C:N ratio and lignin content. After 69 and 132 days, destructive sampling took place to assess the effects of the different treatments on soil microbial biomass (microscopic measurements), microbial community composition (phospholipid fatty acid profiles), soil microbial activity (14C-leucine incorporation), C and N mineralization, plant biomass and 15N retrieval in soil pools, microbial biomass and plant biomass. Addition of organic amendments increased soil microbial biomass, activity and fungal/bacterial ratio and created distinct microbial community compositions, whereby high C:N ratio organic amendments had stronger effects compared to low C:N ratio amendments. Structural equation modelling showed that higher values of soil microbial activity were associated with increased N mineralization rates, increased plant biomass and plant 15N uptake, while microbial 15N immobilization was associated with soil microbial community composition. The outcomes of this study highlight the importance of the chemical composition and the amount of the organic amendments for finding a balance between plant N uptake, microbial N immobilization and N retention in labile and stable soil pools through the effects on the composition and activity of the soil microbial community. The results provide insights that can be used in designing combined input (nutrient and organic) nutrient management strategies for a more sustainable agriculture.
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| 4. |
- Rinnan, Riikka, et al.
(författare)
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Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming
- 2009
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 15:11, s. 2615-2625
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Tidskriftsartikel (refereegranskat)abstract
- Soil microorganisms, the central drivers of terrestrial Antarctic ecosystems, are being confronted with increasing temperatures as parts of the continent experience considerable warming. Here we determined short-term temperature dependencies of Antarctic soil bacterial community growth rates, using the leucine incorporation technique, in order to predict future changes in temperature sensitivity of resident soil bacterial communities. Soil samples were collected along a climate gradient consisting of locations on the Antarctic Peninsula ( Anchorage Island, 67 degrees 34'S, 68 degrees 08'W), Signy Island (60 degrees 43'S, 45 degrees 38'W) and the Falkland Islands (51 degrees 76'S 59 degrees 03'W). At each location, experimental plots were subjected to warming by open top chambers (OTCs) and paired with control plots on vegetated and fell-field habitats. The bacterial communities were adapted to the mean annual temperature of their environment, as shown by a significant correlation between the mean annual soil temperature and the minimum temperature for bacterial growth (T-min). Every 1 degrees C rise in soil temperature was estimated to increase T-min by 0.24-0.38 degrees C. The optimum temperature for bacterial growth varied less and did not have as clear a relationship with soil temperature. Temperature sensitivity, indicated by Q(10) values, increased with mean annual soil temperature, suggesting that bacterial communities from colder regions were less temperature sensitive than those from the warmer regions. The OTC warming (generally <1 degrees C temperature increases) over 3 years had no effects on temperature relationship of the soil bacterial community. We estimate that the predicted temperature increase of 2.6 degrees C for the Antarctic Peninsula would increase T-min by 0.6-1 degrees C and Q(10) (0-10 degrees C) by 0.5 units.
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| 5. |
- Sarneel, Judith M., et al.
(författare)
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Alternative transient states and slow plant community responses after changed flooding regimes
- 2019
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Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 25:4, s. 1358-1367
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Tidskriftsartikel (refereegranskat)abstract
- Climate change will have large consequences for flooding frequencies in freshwater systems. In interaction with anthropogenic activities (flow regulation, channel restoration and catchment land-use) this will both increase flooding and drought across the world. Like in many other ecosystems facing changed environmental conditions, it remains difficult to predict the rate and trajectory of vegetation responses to changed conditions. Given that critical ecosystem services (e.g. bank stabilization, carbon subsidies to aquatic communities or water purification) depend on riparian vegetation composition, it is important to understand how and how fast riparian vegetation responds to changing flooding regimes. We studied vegetation changes over 19 growing seasons in turfs that were transplanted in a full-factorial design between three riparian elevations with different flooding frequencies. We found that (a) some transplanted communities may have developed into an alternative stable state and were still different from the target community, and (b) pathways of vegetation change were highly directional but alternative trajectories did occur, (c) changes were rather linear but faster when flooding frequencies increased than when they decreased, and (d) we observed fastest changes in turfs when proxies for mortality and colonization were highest. These results provide rare examples of alternative transient trajectories and stable states under field conditions, which is an important step towards understanding their drivers and their frequency in a changing world.
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| 6. |
- Sarneel, Judith M., et al.
(författare)
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Species traits interact with stress level to determine intraspecific facilitation and competition
- 2022
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Ingår i: Journal of Vegetation Science. - : John Wiley & Sons. - 1100-9233 .- 1654-1103. ; 33:5
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Tidskriftsartikel (refereegranskat)abstract
- Questions: Flooding and drought stress are expected to increase significantly across the world and plant responses to these abiotic changes may be mediated by plant–plant interactions. Stress tolerance and recovery often require a biomass investment that may have consequences for these plant–plant interactions. Therefore, we questioned whether phenotypic plasticity in response to flooding and drought affected the balance between competition and facilitation for species with specific adaptations to drought or flooding.Location: Utrecht University. Methods: Stem elongation, root porosity, root:shoot ratio and biomass production were measured for six species during drought, well-drained and submerged conditions when grown alone or together with conspecifics. We quantified competition and facilitation as the ‘neighbour intensity effect’ directly after the 10-day treatment and again after a seven-day recovery period in well-drained conditions.Results: Water stress, planting density and species identity interactively affected standardized stem elongation in a way that could lead to facilitation during submergence for species that preferably grow in wet soils. Root porosity was affected by the interaction between neighbour presence and time-step. Plant traits were only slightly affected during drought. The calculated neighbour interaction effect indicated facilitation for wetland species during submerged conditions and, after a period to recover from flooding, for species that prefer dry habitats.Conclusions: Our results imply that changing plant–plant interactions in response to submergence and to a lesser extent to drought should be considered when predicting vegetation dynamics due to changing hydroclimatic regimes. Moreover, facilitation during a recovery period may enable species maladapted to flooding to persist.
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| 7. |
- Yergeau, Etienne, et al.
(författare)
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Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils
- 2010
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 12:8, s. 2096-2106
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Tidskriftsartikel (refereegranskat)abstract
- P>Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities.
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