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51. Soil phosphorus and relationship to phosphorus balance under long-term fertilization.

Author

BENHUA SUN, QUANHONG CUI, YUN GUO, XUEYUN YANG, SHULAN ZHANG, MINGXIA GAO, and HOPKINS, DAVID W.

Subjects
PHOSPHORUS in soils, SOIL testing, ORGANIC fertilizers, PLANT-soil relationships, SOIL composition, POTASSIUM
Abstract

Temporal changes in the concentrations of plant-available phosphorus (P) in soil (Olsen-P), total soil-P and P activation coefficient (the ratio of Olsen-P to residual-P (i.e. an approximation to total-P)) were measured in plots that received consistent inorganic nitrogen, phosphorus and potassium plus organic fertilizers annually. Maize and winter wheat crops were grown in rotation for 24 years. Olsen-P and P activation coefficient declined significantly in the earlier years (< 12 years) for treatments that did not include any P fertilizer, and increased over the same period for the P-fertilized treatments. The rates of change in the Olsen-P and P activation coefficient values were positively related to P balance. In the later years, the Olsen-P and P activation coefficient plateau values were positively related to the P balance. [ABSTRACT FROM AUTHOR]

Published
2018
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53. Genetically modified lignin below ground

Author

Hopkins, David W., Webster, Elizabeth A., Boerjan, Wout, Pilate, Gilles, Halpin, Claire, Scottish Crop Research Institute, School of Biological and Environmental Sciences, University of Stirling, Department of plant systems biology, Flanders Institute for Biotechnology, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Plant Research Unit, and University of Dundee at SCRI

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, dégradation du bois, Biotechnologies, transformation génétique, lignine
Published
2007

54. Gelifluction and Thixotropy of Maritime Antarctic Soils: Small-Scale Measurements with a Rotational Rheometer.

Author

Sun, Benhua, Dennis, Paul G., Newsham, Kevin K., Hopkins, David W., and Hallett, Paul D.

Subjects
THIXOTROPY, RHEOMETERS, SHEARING force, SOIL stabilization
Abstract

Gelifluction, thixotropy and yield stress were measured from < 5 g soil samples taken from Signy, Alectoria, Greenwich, Wiencke and Livingston islands in the maritime Antarctic using a temperature-controlled rotational rheometer. The small sample size that this method permitted is compatible with sampling from sensitive sample locations. An oscillating 10 Pa shear stress was applied to samples at -0.5 kPa water potential. Two freeze-thaw cycles had temperature ramps from 5°C to -10°C over 2 h, followed by -10°C to 5°C over 2 h and finally at 5°C for 1 h. At freezing onset, the shear modulus, G, dropped to 4-50 per cent of thawed G, with no differences between locations. At thawing onset, G dropped to 8-32 per cent of thawed G, with significant differences between locations ( P < 0.001). Thixotropy was then measured by applying a 2 kPa oscillating shear stress for 10 min, followed by relaxation at 10 Pa for 2 h. The increased shear stress caused G to drop to less than 8 per cent of the pre-stressed value, with no difference between locations. After 0.1 and 2 h, G was 18-65 per cent and 31-82 per cent of the pre-stressed value, respectively. A shear ramp determined yield stresses ranging from 494-2217 Pa. These findings demonstrate the potential risk of more frequent freeze-thaw cycles or the occurrence of thawed soil to the stability of polar soils. Gelifluction through more frequent freeze-thaw cycles could result in increased slope movement, whereas thixotropy caused by trampling of thawed soils could exacerbate mechanical damage of surface soils. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Published
2017
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73. Ecosystem feedbacks and cascade processes: understanding their role in the responses of Arctic and alpine ecosystems to environmental change

Author

WOOKEY, PHILIP A., primary, AERTS, RIEN, additional, BARDGETT, RICHARD D., additional, BAPTIST, FLORENCE, additional, BRÅTHEN, KARI ANNE, additional, CORNELISSEN, JOHANNES H. C., additional, GOUGH, LAURA, additional, HARTLEY, IAIN P., additional, HOPKINS, DAVID W., additional, LAVOREL, SANDRA, additional, and SHAVER, GAIUS R., additional

Published
2009
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74. Strategies for monitoring and managing mass populations of toxic cyanobacteria in recreational waters: a multi-interdisciplinary approach

Author

Tyler, Andrew N, primary, Hunter, Peter D, additional, Carvalho, Laurence, additional, Codd, Geoffrey A, additional, Elliott, J Alex, additional, Ferguson, Claire A, additional, Hanley, Nick D, additional, Hopkins, David W, additional, Maberly, Stephen C, additional, Mearns, Kathryn J, additional, and Scott, E Marion, additional

Published
2009
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84. Field and pulping performances of transgenic trees with altered lignification

Author

Pilate, Gilles, primary, Guiney, Emma, additional, Holt, Karen, additional, Petit-Conil, Michel, additional, Lapierre, Catherine, additional, Leplé, Jean-Charles, additional, Pollet, Brigitte, additional, Mila, Isabelle, additional, Webster, Elizabeth A., additional, Marstorp, Håkan G., additional, Hopkins, David W., additional, Jouanin, Lise, additional, Boerjan, Wout, additional, Schuch, Wolfgang, additional, Cornu, Daniel, additional, and Halpin, Claire, additional

Published
2002
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87. Relationship between soil fungal diversity and temperature in the maritime Antarctic

Author

Newsham, Kevin K., Hopkins, David W., Carvalhais, Lilia C., Fretwell, Peter T., Rushton, Steven P., O’Donnell, Anthony G., and Dennis, Paul G.

Abstract

Soil fungi have pivotal ecological roles as decomposers, pathogens and symbionts. Alterations to their diversity arising from climate change could have substantial effects on ecosystems, particularly those undergoing rapid warming that contain few species. Here, we report a study using pyrosequencing to assess fungal diversity in 29 soils sampled from a 1,650 km climatic gradient through the maritime Antarctic, the most rapidly warming region in the Southern Hemisphere. Using a ‘space-for-time’ substitution approach, we show that soil fungal diversity is higher in warmer habitats, with increases of 4.7 (observed) and 11.3 (predicted) fungal taxa per degree Celsius rise in surface temperature along the transect. Among 22 predictor variables, air temperature was the strongest and most consistent predictor of diversity. We propose that the current rapid warming in the maritime Antarctic (0.34 °C per decade) will facilitate the colonization of soil by a wider diversity of fungi than at present, with data from regression models suggesting 20–27% increases in fungal species richness in the southernmost soils by 2100. Such increases in diversity, which provide a sentinel for changes at lower latitudes, are likely to have substantial effects on nutrient cycling and, ultimately, productivity in the species-poor soils of maritime Antarctica.

Published
2016
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90. Easy data layout: DataShaper

Author

Hopkins, David W.

Subjects
Evaluation, Software Packages, Desktop Utility, BenWare Inc. -- Product information, Aldus PageMaker (DTP software), DataShaper (DTP software)
Published
1990

91. Distribution of soil carbon and microbial biomass in arable soils under different tillage regimes.

Author

Benhua Sun, Hallett, Paul D., Caul, Sandra, Daniell, Tim J., and Hopkins, David W.

Subjects
HUMUS, CARBON compounds, NO-tillage, MINIMUM tillage, SINGLE cell lipids, SOILS
Abstract

We have measured total soil organic carbon (SOC), dissolved organic carbon (DOC), and microbial lipid contents (as indices of microbial biomass and community structure), and their distributions to 60 cm depth in soils from replicated medium-term (2003-2008) experimental arable plots subject to different tillage regimes in Scotland. The treatments were zero tillage (ZT), minimum tillage (MT; cultivation to 7 cm), the conventional tillage (CT) practice of ploughing to 20 cm, and deep ploughing (DP) to 40 cm depth. In the 0-30 cm depth range, SOC content (corrected for bulk density differences between tillage treatments) was greatest under ZT and MT, but over 0-60 cm depth the SOC contents of these treatments were similar to the CT and DP treatments. DOC concentrations declined with increasing depth in ZT and MT above 20 cm, but there were no significant differences with depth in the CT and DP treatments. Beneath 20 cm, there was little change in DOC concentration with depth for all treatments, although for the MT treatment, there was less DOC beneath the depth of cultivation. The total microbial biomass decreased with increasing depth over the 0-60 cm range in the ZT and MT treatments, whereas it decreased with depth only below 30-40 cm in the CT and DP treatments. The microbial biomass was significantly different only between 0-5 cm in the ZT, CT and DP treatments, but not for other depths between all treatments. The bacterial biomass was greater in the ZT treatment than in MT, CT and DP near the soil surface, but not significantly different over the whole profile (0-60 cm). The fungal biomass decreased with depth in the ZT and MT treatments over the whole 0-60 cm depth range, whereas it decreased with depth only below 20 cm in the CT and DP treatments. [ABSTRACT FROM AUTHOR]

Published
2011
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92. Microbial community structure in soils with decomposing residues from plants with genetic modifications to lignin biosynthesis.

Author

Hénault, Catherine, English, Lorna C., Halpin, Claire, Andreux, Francis, and Hopkins, David W.

Subjects
SOIL microbiology, LIGNINS, SOIL testing, PLANT-soil relationships, TRANSGENIC plants, FATTY acids
Abstract

Lignin is a major determinant of the decomposition of plant materials in soils. Advances in transgenic technology have led to the possibility of modifying lignin to improve the pulping properties of plant materials for papermaking. Previous studies have shown that lignin modifications also affect the rate of plant material decay in soil. The aim of this work was to investigate short-term changes in soil microbial community structures when tobacco residues with reduced activity of enzymes in the monolignol pathway decompose. The residues from lignin-modified plants all decomposed faster than unmodified plant materials. The relative proportions of some of the structural groups of microbial phospholipid fatty acids were affected by genetic modifications, especially the proportion of double unsaturated chain fatty acids, indicative of fungi. [ABSTRACT FROM AUTHOR]

Published
2006
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93. A potential loss of carbon associated with greater plant growth in the European Arctic

Author

Hartley, Iain P., Garnett, Mark H., Sommerkorn, Martin, Hopkins, David W., Fletcher, Benjamin J., Sloan, Victoria L., Phoenix, Gareth K., and Wookey, Philip A.

Abstract

Rapid warming is expected to increase plant growth in the Arctic, and result in trees gradually colonizing tundra. Models predict that enhanced carbon (C) storage in plant biomass may help offset atmospheric CO2increases and reduce rates of climate change. However, in some Arctic ecosystems, high plant productivity is associated with rapid cycling and low storage of soil C (refs , , ); thus, as plant growth increases, soil C may be lost through enhanced decomposition. Here we show that, in northern Sweden, total ecosystem C storage is greater in tundra heath (owing to greater soil C stocks) than in more productive mountain-birch forest. Furthermore, we demonstrate that in the forest, high plant activity during the middle of the growing season stimulates the decomposition of older soil organic matter. Such a response, referred to as positive priming, helps explain the low soil C storage in the forest when compared with the tundra. We suggest that, as more productive forest communities colonize tundra, the decomposition of the large C stocks in tundra soils could be stimulated. Thus, counter-intuitively, increased plant growth in the European Arctic could result in C being released to the atmosphere, accelerating climate change.

Published
2012
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94. Assessment of Titratable Acidity in Fruit Using Short Wave near Infrared Spectroscopy. Part B: Intact Fruit Studies

Author

Subedi, Phul P., Walsh, Kerry B., and Hopkins, David. W.

Abstract

Interactance spectra (700–1100 nm) of intact fruit possess features interpreted as being due to the dilution and perturbation of water OH stretching and combination bands (with the second and third overtones of OH stretching at 960 nm and 740 nm, respectively), while the contribution from citric acid CH_2 and OH stretching and combination bands are not obvious. A model developed using interactance spectra collected from the cut surfaces of lime fruit (mean ± SD of 7.3 ± 0.51 g citric acid equivalents 100 mL^−1, units subsequently presented as% w/v) achieved prediction results of RMSEP=0.16%, r_p^2 = 0.79, bias = −0.03%. However, for intact lime fruit, model calibration results (RMSECV=0.16, r_cv^2 = 0.85) were markedly better than prediction results (RMSEP=0.30, r_p^2 = 0.49). For a low total titratable acidity (TTA) product, peach (with spectra collected across fruit maturity stages; mean ± SD of 0.88 ± 0.17%), calibration results were relatively poor (RMSECV=0.09%, r_cv^2 = 0.79) and the model failed in prediction (RMSEP=0.10%, r_p^2 = 0.00, bias = 0.02%). It is concluded that interactance geometry shortwave (700–1100 nm) near infrared spectroscopy using diode array instrumentation and an interactance optical geometry suited to on-line or field-portable instrumentation used for Brix and DM assessment is not appropriate for assessment of the acidity of intact low TTA fruit and has limited use for high TTA fruit.

Published
2012

99. No evidence for compensatory thermal adaptation of soil microbial respiration in the study of Bradford et al. (2008).

Author

Hartley, Iain P., Hopkins, David W., Garnett, Mark H., Sommerkorn, Martin, and Wookey, Philip A.

Subjects
*SOIL respiration, *ACCLIMATIZATION, *SOIL microbial ecology, *SOIL temperature, *MICROBIAL respiration, *GLOBAL warming, *SUCROSE, *BIOMASS & the environment, *CHLOROFORM
Abstract

Bradford et al. (2008) conclude that thermal adaptation will reduce the response of soil microbial respiration to rising global temperatures. However, we question both the methods used to calculate mass-specific respiration rates and the interpretation of the results. No clear evidence of thermal adaptation reducing soil microbial activity was produced. [ABSTRACT FROM AUTHOR]

Published
2009
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100. Metagenomic analyses of marine new production under elevated CO2 conditions

Author

Meakin, Nicholas G., Wyman, Michael, and Hopkins, David W.

Subjects
551.46, Metagenomics, Biochemistry, New Production, Marine Microorganisms, Plankton, Algae, Carbon Fixation, Nitrogen Fixation, Diazotrophs, Phosphorus, RuBisCO, NifH, PstS, Genomics, Proteomics, Elevated CO2, PCR, Sequencing, Gel Electrophoresis, Real-Time PCR, Environmental Microbiology, Climatic changes, Atmospheric carbon dioxide, Chemical oceanography
Abstract

A mesocosm experiment was carried out in a Norwegian fjord near Bergen in May 2006, with the main objective being the study of the effects of increasing concentrations of atmospheric CO2 (and associated effects such as increased acidification) on blooms of natural marine coastal plankton. Three mesocosms were bubbled with CO2(g) to achieve a high (~700ppm) CO2 concentration (pH ~7.8) to simulate predicted future conditions as a result of rising atmospheric CO2 concentrations. Another three mesocosms were treated as controls and bubbled with ambient air to represent a near pre-industrial scenario (atmospheric CO2 concentration ~300ppm, surface seawater pH ~8.15). Blooms in the mesocosms were stimulated by the addition of nutrients at a near-Redfield ratio ([N:P] ≈ [16:1]), and scientific measurements and analyses were carried out over the course of the blooms for approximately one month. Of particular interest in this study were the autotrophic plankton. The diversity and activities of these microorganisms under the two treatments was therefore investigated. By designing and using new degenerate primers specifically targeting ‘Green-type’ (Form IA and IB), ‘Red-type’ (Form IC and ID) and Form II RuBisCO, analysis of primary producers was carried out using PCR and either gDNA or cDNA (mRNA) templates from key time points spanning the complete duration of the blooms throughout the mesocosm experiment. Over 1250 novel RuBisCO large subunit sequences have been fully annotated and deposited in the NCBI GenBank® database. These sequences revealed distinct changes in the diversity of primary producers both over the courses of the blooms and between treatments. Particularly striking was the effect of acidification on the community structure of the eukaryotic picoplankton, Prasinophytes. A clade of prasinophytes closely related to Micromonas pusilla showed a distinct preference for the high CO2 conditions; a laboratory-based experiment confirmed the high tolerance of Micromonas pusilla to lower pH. Conversely, a clade related to Bathycoccus prasinos was almost entirely excluded from the high CO2 treatments. Clades of form II RuBisCO-containing dinoflagellates were also abundant throughout the experiment in both treatments. The high similarity of some of these clades to the toxin-producing species Heterocapsa triquetra and Gonyaulax polyedra, and apparent high tolerance of some clades to high CO2 conditions, is perhaps cause for concern in a high CO2 world and demands further research. In parallel with the RubisCO work, new primers were designed that target the gene encoding the Fe protein of nitrogenase (NifH). 82 Bergen genomic nifH sequences have been annotated and submitted to GenBank®. These sequences include those from organisms related to Alpha, Beta, and Gammaproteobacteria, and Cluster II and Cluster III sequences that align most closely with anaerobic Bacteria, Gram positive, and/or sulphur-reducing Bacteria. The biggest surprise, however, was the apparent abundance and significance of a Rhodobacter sphaeroides-like microorganism throughout the duration of the experiment in both treatments. Whilst this clade was unsurprisingly absent in the RuBisCO cDNA libraries, all but two of 128 nifH cDNA clones analysed were identical to the gene from Rhodobacter sphaeroides. This shows that this clade was potentially fixing N2 throughout the entire experiment, even in the presence of combined N added to both sets of mesocosms at the start of the experiment. A group of Rhodobacter sphaeroides-like microorganisms present at Bergen may therefore have been an unexpected source of new N during the experiment and contributed to the maintenance of the mesocosm communities as nutrients became depleted. One organism dominated the autotrophic communities after the blooms in both treatments. Synechococcus spp. Form IA rbcL clones most closely related to the coastal strain Synechococcus sp. strain CC9902 were recovered throughout the experiment but were particularly numerous toward the end of the experiment and dominated the “Green-type” libraries at this time. Initially, rbcL clones from these cyanobacteria were mostly derived from the ambient CO2 mesocosms but were equally distributed between treatments by the end of the experiment. This suggests that cyanobacteria related to strain CC9902 may be less tolerant of elevated CO2 (which was greatest at the beginning rather than the end of the experiment). However, despite the mesocosms being Pi-limited at the end of the experiment, several Synechococcus species (including those related to strain CC9902 and another coastal strain, CC9311) thrived. Following on from this observation, Pi uptake and assimilation mechanisms in a Synechococcus species were investigated in the laboratory. This led to the sequencing and characterisation of a pstS gene from the marine cyanobacterium Synechococcus sp. WH 8103. Unlike conventional pstS, it was discovered that the pstS II gene in this organism is constitutively expressed and unresponsive to or only weakly regulated by Pi supply. The use of PstS/pstS as a marker for P-limitation in natural samples, therefore, should be interpreted with caution.

Published
2009

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