A generic framework to assess the representation and protection of benthic ecosystems in European marine protected areas
Greathead, Clare ; Magni, Paolo ; Vanaverbeke, Jan ; Buhl‐Mortensen, Lene ; Janas, Urszula ; Blomqvist, Mats ; Craeymeersch, Johan A. ; Dannheim, Jennifer ; Darr, Alexander ; Degraer, Steven ; Desroy, Nicolas ; Donnay, Annick ; Griffiths, Yessica ; Guala, Ivan ; Guerin, Laurent ; Hinchen, Hayley ; Labrune, Celine ; Reiss, Henning ; Hoey, Gert Van; Birchenough, Silvana N.R. - \ 2020
Aquatic conservation: marine and freshwater ecosystems 30 (2020)7. - ISSN 1052-7613 - p. 1253 - 1275.
There is concern across the International Council for the Exploration of the Sea (ICES) region that a consideration of vulnerable components and the wider support mechanisms underpinning benthic marine ecosystems may be lacking from the process of marine protected area (MPA) designation, management and monitoring. In this study, MPAs across six European ecoregions were assessed from a benthic ecology perspective. The study included 102 MPAs, designated by 10 countries, and focused on three aspects regarding the role of the benthos in: (i) the designation of MPAs; (ii) the management measures used in MPAs; and (iii) the monitoring and assessment of MPAs. Qualitative entries to a questionnaire based on an existing framework (EU project ‘Monitoring Evaluation of Spatially Managed Areas’, (MESMA) were collected by 19 benthic experts of the ICES Benthic Ecology Working Group. A pedigree matrix was used to apply a numerical scale (score) to these entries. The results showed clear differences in scores between ecoregions and between criteria. The designation‐phase criteria generally achieved higher scores than the implementation‐phase criteria. Poor designation‐phase scores were generally reiterated in the implementation‐phase scores, such as scores for assessment and monitoring. Over 70% of the MPA case studies were found to consider the benthos to some extent during selection and designation; however, this was not followed up with appropriate management measures and good practice during the implementation phase.
Poor spatial and temporal coverage of monitoring and ineffective indicators is unlikely to pick up changes caused by management measures in the MPA. There is concern that without adequate monitoring and adaptive management frameworks, the MPAs will be compromised. Also, there could be an increased likelihood that, with regard to the benthos, they will fail to meet their conservation objectives. This assessment was successful in highlighting issues related to the representation and protection of the benthos in MPAs and where changes need to be made, such as expanding the characterization and monitoring of benthic species or habitats of interest. These issues could be attributable to an ongoing process and/or an indication that some MPAs only have ‘paper protection’.
An Assessment of Climate Induced Increase in Soil Water Availability for Soil Bacterial Communities Exposed to Long-Term Differential Phosphorus Fertilization
Randall, Kate C. ; Brennan, Fiona ; Clipson, Nicholas ; Creamer, Rachel E. ; Griffiths, Bryan S. ; Storey, Sean ; Doyle, Evelyn - \ 2020
Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
bacteria - climate change - phosphorus - rhizosphere - soil moisture
The fate of future food productivity depends primarily upon the health of soil used for cultivation. For Atlantic Europe, increased precipitation is predicted during both winter and summer months. Interactions between climate change and the fertilization of land used for agriculture are therefore vital to understand. This is particularly relevant for inorganic phosphorus (P) fertilization, which already suffers from resource and sustainability issues. The soil microbiota are a key indicator of soil health and their functioning is critical to plant productivity, playing an important role in nutrient acquisition, particularly when plant available nutrients are limited. A multifactorial, mesocosm study was established to assess the effects of increased soil water availability and inorganic P fertilization, on spring wheat biomass, soil enzymatic activity (dehydrogenase and acid phosphomonoesterase) and soil bacterial community assemblages. Our results highlight the significance of the spring wheat rhizosphere in shaping soil bacterial community assemblages and specific taxa under a moderate soil water content (60%), which was diminished under a higher level of soil water availability (80%). In addition, an interaction between soil water availability and plant presence overrode a long-term bacterial sensitivity to inorganic P fertilization. Together this may have implications for developing sustainable P mobilization through the use of the soil microbiota in future. Spring wheat biomass grown under the higher soil water regime (80%) was reduced compared to the constant water regime (60%) and a reduction in yield could be exacerbated in the future when grown in cultivated soil that have been fertilized with inorganic P. The potential feedback mechanisms for this need now need exploration to understand how future management of crop productivity may be impacted.
Addressing the need for improved land cover map products for policy support
Szantoi, Zoltan ; Geller, Gary N. ; Tsendbazar, Nandin-Erdene ; See, Linda ; Griffiths, Patrick ; Fritz, Steffen ; Gong, Peng ; Herold, Martin ; Mora, Brice ; Obregón, André - \ 2020
Environmental Science & Policy 112 (2020). - ISSN 1462-9011 - p. 28 - 35.
The continued increase of anthropogenic pressure on the Earth’s ecosystems is degrading the natural environment and then decreasing the services it provides to humans. The type, quantity, and quality of many of those services are directly connected to land cover, yet competing demands for land continue to drive rapid land cover change, affecting ecosystem services. Accurate and updated land cover information is thus more important than ever, however, despite its importance, the needs of many users remain only partially attended. A key underlying reason for this is that user needs vary widely, since most current products – and there are many available – are produced for a specific type of end user, for example the climate modelling community. With this in mind we focus on the need for flexible, automated processing approaches that support on-demand, customized land cover products at various scales. Although land cover processing systems are gradually evolving in this direction there is much more to do and several important challenges must be addressed, including high quality reference data for training and validation and even better access to satellite data. Here, we 1) present a generic system architecture that we suggest land cover production systems evolve towards, 2) discuss the challenges involved, and 3) propose a step forward. Flexible systems that can generate on-demand products that match users’ specific needs would fundamentally change the relationship between users and land cover products – requiring more government support to make these systems a reality.
A global database of soil nematode abundance and functional group composition
Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
Scientific Data 7 (2020)1. - ISSN 2052-4463
As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
Inactivation of H-type and L-type bovine spongiform encephalopathy following recommended autoclave decontamination procedures
Chapman, Gail E. ; Lockey, Richard ; Beck, Katy E. ; Vickery, Chris ; Arnold, Mark ; Thorne, Leigh ; Thorne, Jemma K. ; Walker, Sarah R. ; Keulen, Lucien van; Casalone, Cristina ; Griffiths, Peter C. ; Simmons, Marion M. ; Terry, Linda A. ; Spiropoulos, John - \ 2020
Transboundary and Emerging Diseases (2020). - ISSN 1865-1674
bovine spongiform encephalopathy - H-type - inactivation - L-type - transmissible spongiform encephalopathie
The resistance of H-type and L-type BSE prions to autoclaving under EU regulation conditions for specified risk material is unknown. We employed transgenic mouse (bovinized line tg1896) bioassay to assess the efficacy of such decontamination on L- and H-type BSE. For each source, titre calculation was based on the comparison of incubation period and attack rate prior to and after decontamination. The infectious titre of L-type BSE was reduced by at least 9.40 log10 and of H-type BSE by at least 3.94 log10. In fact, no infectivity was detected for L-type or H-type BSE post-inactivation even at a 10–1 dilution.
A qualitative exploration of the experiences of community health animation on malaria control in rural Malawi
Malenga, Tumaini ; Griffiths, Frances E. ; Berg, Marrit Van Den; Berg, Henk Van Den; Vugt, Michèle Van; Phiri, Kamija Samuel ; Manda-Taylor, Lucinda ; Umar, Eric - \ 2020
Globalization and Health 16 (2020)1. - ISSN 1744-8603
Behaviour change communication - Community engagement - Community health animator - Health animation - Health education - Malaria
Background: While great strides have been achieved in fighting malaria through the Roll Back Malaria (RBM) strategy, the recent world malaria report shows an increase in malaria-related deaths compared to previous years. Malaria control tools are efficacious and effective in preventing the disease; however, the human behaviour aspect of the intervention strategies is weak due to heavy reliance on positive human health behaviour. The challenge lies in adoption of control interventions by the target population which, to an extent, may include access to prevention and treatment tools. We present a qualitative assessment of the use of the Health Animator (HA) model for Information, Education and Communication (IEC) to improve adoption and use of malaria control by promoting positive health behaviours. Results: We conducted 3 Focus Group Discussions (FGDs) and 23 individual in-depth interviews (IDIs) with HAs. Each FGD consisted of 8 participants. Data was analysed using QSR International NVivo 10 software. There are four main themes emerging regarding HA experiences. The perceptions include; collaborative work experience, personal motivation and growth, community participation with health animation and challenges with implementation. Results suggest that HAs were pleased with the training as they gained new information regarding malaria, which affected their use of malaria control interventions within their families. Knowledge was well assimilated from the trainings and influenced personal growth in becoming a community leader. Support from the leadership within the village and the health system was important in legitimising the main messages. The community responded positively to the workshops valued the information imparted. The voluntary nature of the work in a poverty-stricken community affected sustainability. Conclusions: There is need to empower communities with strategies within their reach. Functioning traditional social support structures are a crucial element in sustainability. Voluntarism is also key for sustainability, especially for rural and remote communities with limited sources of income.
Global patterns and drivers of ecosystem functioning in rivers and riparian zones
Tiegs, Scott D. ; Costello, David M. ; Isken, Mark W. ; Woodward, Guy ; McIntyre, Peter B. ; Gessner, Mark O. ; Chauvet, Eric ; Griffiths, Natalie A. ; Flecker, Alex S. ; Acuña, Vicenç ; Albariño, Ricardo ; Allen, Daniel C. ; Alonso, Cecilia ; Andino, Patricio ; Arango, Clay ; Aroviita, Jukka ; Barbosa, Marcus V.M. ; Barmuta, Leon A. ; Baxter, Colden V. ; Bell, Thomas D.C. ; Bellinger, Brent ; Boyero, Luz ; Brown, Lee E. ; Bruder, Andreas ; Bruesewitz, Denise A. ; Burdon, Francis J. ; Callisto, Marcos ; Canhoto, Cristina ; Capps, Krista A. ; Castillo, María M. ; Clapcott, Joanne ; Colas, Fanny ; Colón-Gaud, Checo ; Cornut, Julien ; Crespo-Pérez, Verónica ; Cross, Wyatt F. ; Culp, Joseph M. ; Danger, Michael ; Dangles, Olivier ; Eyto, Elvira De; Derry, Alison M. ; Villanueva, Veronica Díaz ; Douglas, Michael M. ; Elosegi, Arturo ; Encalada, Andrea C. ; Entrekin, Sally ; Espinosa, Rodrigo ; Ethaiya, Diana ; Ferreira, Verónica ; Ferriol, Carmen ; Flanagan, Kyla M. ; Fleituch, Tadeusz ; Follstad Shah, Jennifer J. ; Barbosa, André Frainer ; Friberg, Nikolai ; Frost, Paul C. ; Garcia, Erica A. ; Lago, Liliana García ; Soto, Pavel Ernesto García ; Ghate, Sudeep ; Giling, Darren P. ; Gilmer, Alan ; Gonçalves, José Francisco ; Gonzales, Rosario Karina ; Graça, Manuel A.S. ; Grace, Mike ; Grossart, Hans Peter ; Guérold, François ; Gulis, Vlad ; Hepp, Luiz U. ; Higgins, Scott ; Hishi, Takuo ; Huddart, Joseph ; Hudson, John ; Imberger, Samantha ; Iñiguez-Armijos, Carlos ; Iwata, Tomoya ; Janetski, David J. ; Jennings, Eleanor ; Kirkwood, Andrea E. ; Koning, Aaron A. ; Kosten, Sarian ; Kuehn, Kevin A. ; Laudon, Hjalmar ; Leavitt, Peter R. ; Lemes Da Silva, Aurea L. ; Leroux, Shawn J. ; LeRoy, Carri J. ; Lisi, Peter J. ; MacKenzie, Richard ; Marcarelli, Amy M. ; Masese, Frank O. ; McKie, Brendan G. ; Medeiros, Adriana Oliveira ; Meissner, Kristian ; Miliša, Marko ; Mishra, Shailendra ; Miyake, Yo ; Moerke, Ashley ; Mombrikotb, Shorok ; Mooney, Rob ; Moulton, Tim ; Muotka, Timo ; Negishi, Junjiro N. ; Neres-Lima, Vinicius ; Nieminen, Mika L. ; Nimptsch, Jorge ; Ondruch, Jakub ; Paavola, Riku ; Pardo, Isabel ; Patrick, Christopher J. ; Peeters, Edwin T.H.M. ; Pozo, Jesus ; Pringle, Catherine ; Prussian, Aaron ; Quenta, Estefania ; Quesada, Antonio ; Reid, Brian ; Richardson, John S. ; Rigosi, Anna ; Rincón, José ; Rîşnoveanu, Geta ; Robinson, Christopher T. ; Rodríguez-Gallego, Lorena ; Royer, Todd V. ; Rusak, James A. ; Santamans, Anna C. ; Selmeczy, Géza B. ; Simiyu, Gelas ; Skuja, Agnija ; Smykla, Jerzy ; Sridhar, Kandikere R. ; Sponseller, Ryan ; Stoler, Aaron ; Swan, Christopher M. ; Szlag, David ; Teixeira-De Mello, Franco ; Tonkin, Jonathan D. ; Uusheimo, Sari ; Veach, Allison M. ; Vilbaste, Sirje ; Vought, Lena B.M. ; Wang, Chiao Ping ; Webster, Jackson R. ; Wilson, Paul B. ; Woelfl, Stefan ; Xenopoulos, Marguerite A. ; Yates, Adam G. ; Yoshimura, Chihiro ; Yule, Catherine M. ; Zhang, Yixin X. ; Zwart, Jacob A. - \ 2019
Science Advances 5 (2019)1. - ISSN 2375-2548 - p. 14966 - 14973.
River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
First international descriptive and interventional survey for cholesterol and non-cholesterol sterol determination by gas- and liquid-chromatography–Urgent need for harmonisation of analytical methods
Lütjohann, Dieter ; Björkhem, Ingemar ; Friedrichs, Silvia ; Kerksiek, Anja ; Lövgren-Sandblom, Anita ; Geilenkeuser, Wolf Jochen ; Ahrends, Robert ; Andrade, Isabel ; Ansorena, Diana ; Astiasarán, Iciar ; Baila-Rueda, Lucía ; Barriuso, Bianca ; Becker, Susen ; Bretillon, Lionel ; Browne, Richard W. ; Caccia, Claudio ; Ceglarek, Uta ; Cenarro, Ana ; Crick, Peter J. ; Fauler, Günter ; Garcia-Llatas, Guadalupe ; Gray, Robert ; Griffiths, William J. ; Gylling, Helena ; Harding, Scott ; Helmschrodt, Christin ; Iuliano, Luigi ; Janssen, Hans Gerd ; Jones, Peter ; Kaipiainen, Leena ; Kannenberg, Frank ; Lagarda, María Jesús ; Leoni, Valerio ; Lottenberg, Ana Maria ; MacKay, Dylan S. ; Matysik, Silke ; McDonald, Jeff ; Menendez-Carreño, Maria ; Myrie, Semone B. ; Sutti Nunes, Valéria ; Ostlund, Richard E. ; Polisecki, Eliana ; Ramos, Fernando ; Rideout, Todd C. ; Schaefer, Ernst J. ; Schmitz, Gerd ; Wang, Yuqin ; Zerbinati, Chiara ; Diczfalusy, Ulf ; Schött, Hans Frieder - \ 2019
Journal of Steroid Biochemistry and Molecular Biology 190 (2019). - ISSN 0960-0760 - p. 115 - 125.
Atherosclerosis - Cholesterol absorption - Cholesterol balance - Cholesterol synthesis - Phytosterols - Surrogate marker
Serum concentrations of lathosterol, the plant sterols campesterol and sitosterol and the cholesterol metabolite 5α-cholestanol are widely used as surrogate markers of cholesterol synthesis and absorption, respectively. Increasing numbers of laboratories utilize a broad spectrum of well-established and recently developed methods for the determination of cholesterol and non-cholesterol sterols (NCS). In order to evaluate the quality of these measurements and to identify possible sources of analytical errors our group initiated the first international survey for cholesterol and NCS. The cholesterol and NCS survey was structured as a two-part survey which took place in the years 2013 and 2014. The first survey part was designed as descriptive, providing information about the variation of reported results from different laboratories. A set of two lyophilized pooled sera (A and B) was sent to twenty laboratories specialized in chromatographic lipid analysis. The different sterols were quantified either by gas chromatography-flame ionization detection, gas chromatography- or liquid chromatography-mass selective detection. The participants were requested to determine cholesterol and NCS concentrations in the provided samples as part of their normal laboratory routine. The second part was designed as interventional survey. Twenty-two laboratories agreed to participate and received again two different lyophilized pooled sera (C and D). In contrast to the first international survey, each participant received standard stock solutions with defined concentrations of cholesterol and NCS. The participants were requested to use diluted calibration solutions from the provided standard stock solutions for quantification of cholesterol and NCS. In both surveys, each laboratory used its own internal standard (5α-cholestane, epicoprostanol or deuterium labelled sterols). Main outcome of the survey was, that unacceptably high interlaboratory variations for cholesterol and NCS concentrations are reported, even when the individual laboratories used the same calibration material. We discuss different sources of errors and recommend all laboratories analysing cholesterol and NCS to participate in regular quality control programs.
Earthworms Coordinate Soil Biota to Improve Multiple Ecosystem Functions
Liu, Ting ; Chen, Xiaoyun ; Gong, Xin ; Lubbers, Ingrid M. ; Jiang, Yangyang ; Feng, Wen ; Li, Xianping ; Whalen, Joann K. ; Bonkowski, Michael ; Griffiths, Bryan S. ; Hu, Feng ; Liu, Manqiang - \ 2019
Current Biology 29 (2019)20. - ISSN 0960-9822 - p. 3420 - 3429.
bacterial-dominated channel - earthworm - ecosystem engineer - ecosystem service - soil fauna - soil microbe - sustainable agriculture
Liu et al. study a 13-year-old field experiment to show that earthworms are beneficial to agroecosystems from a multifunctional perspective. This work incorporates the concerns of negative effects of earthworms in recently published syntheses and highlights the potential pathways in which earthworms contribute to sustainable agriculture.
Persistence of dissolved organic matter explained by molecular changes during its passage through soil
Roth, Vanessa Nina ; Lange, Markus ; Simon, Carsten ; Hertkorn, Norbert ; Bucher, Sebastian ; Goodall, Timothy ; Griffiths, Robert I. ; Mellado-Vázquez, Perla G. ; Mommer, Liesje ; Oram, Natalie J. ; Weigelt, Alexandra ; Dittmar, Thorsten ; Gleixner, Gerd - \ 2019
Nature Geoscience 12 (2019). - ISSN 1752-0894 - p. 755 - 761.
Dissolved organic matter affects fundamental biogeochemical processes in the soil such as nutrient cycling and organic matter storage. The current paradigm is that processing of dissolved organic matter converges to recalcitrant molecules (those that resist degradation) of low molecular mass and high molecular diversity through biotic and abiotic processes. Here we demonstrate that the molecular composition and properties of dissolved organic matter continuously change during soil passage and propose that this reflects a continual shifting of its sources. Using ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, we studied the molecular changes of dissolved organic matter from the soil surface to 60 cm depth in 20 temperate grassland communities in soil type Eutric Fluvisol. Applying a semi-quantitative approach, we observed that plant-derived molecules were first broken down into molecules containing a large proportion of low-molecular-mass compounds. These low-molecular-mass compounds became less abundant during soil passage, whereas larger molecules, depleted in plant-related ligno-cellulosic structures, became more abundant. These findings indicate that the small plant-derived molecules were preferentially consumed by microorganisms and transformed into larger microbial-derived molecules. This suggests that dissolved organic matter is not intrinsically recalcitrant but instead persists in soil as a result of simultaneous consumption, transformation and formation.
Soil bacterial community structure and functional responses across a long-term mineral phosphorus (Pi) fertilisation gradient differ in grazed and cut grasslands
Randall, Kate ; Brennan, Fiona ; Clipson, Nicholas ; Creamer, Rachel ; Griffiths, Bryan ; Storey, Sean ; Doyle, Evelyn - \ 2019
Applied Soil Ecology 138 (2019). - ISSN 0929-1393 - p. 134 - 143.
Agricultural management - Bacteria - Grassland - Phosphorus - Soil
Grasslands form a significant proportion of land used across the globe and future management is important. The objective of this study was to compare the long-term impact of inorganic phosphorus (Pi) fertilisation rates (P0, P15 and P30 ha−1 yr−1) under two grass management trials (grazed vs. cut and removed) on soil physicochemical properties, microbial biomass, phosphomonoesterase activity, bacterial community structure and abundance of a phosphorus (P) mineralising gene (phoD). Under grazing, microbial biomass and soil phosphorus concentrations (total and Pi) generally increased with Pi fertilisation rate, accompanied by significant differences in bacterial community structure between unfertilised (P0) and P30 soil. At the cut and removed site, although Pi was significantly greater in P30 soil, P concentrations (total and Pi) did not increase to the same extent as for grazing, with microbial biomass and bacterial community structures unresponsive to Pi fertilisation. Despite differences in soil P concentrations (total and Pi) and microbial biomass between sites, the abundance of bacterial phoD increased with increasing soil Pi across both sites, while phosphomonoesterase activity decreased. Amplicon sequencing revealed Acidobacteria were the dominant bacterial phylum across both grasslands, but significant differences in relative abundances of bacterial genera were detected at the grazed site only. The bacterial genera Gp6 and Gp16 increased significantly with Pi fertilisation under grazing. Conversely, Bradyrhizobium as well as unclassified genus-type groups belonging to Actinobacteria and Acidimicrobiales significantly decreased with Pi fertilisation, suggesting potential roles in P mobilisation when soil Pi concentrations are low. This study highlights the importance of long-term Pi fertilisation rates and aboveground vegetation removal in shaping soil bacterial community structure and microbial biomass, which in turn may impact soil fertility and plant productivity within agricultural soils.
Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect
Plassart, Pierre ; Prévost-Bouré, Nicolas Chemidlin ; Uroz, Stéphane ; Dequiedt, Samuel ; Stone, Dorothy ; Creamer, Rachel ; Griffiths, Robert I. ; Bailey, Mark J. ; Ranjard, Lionel ; Lemanceau, Philippe - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322
To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
Assignment of a dubious gene cluster to melanin biosynthesis in the tomato fungal pathogen Cladosporium fulvum
Griffiths, Scott A. ; Cox, Russell J. ; Overdijk, Elysa J.R. ; Mesarich, Carl H. ; Saccomanno, Benedetta ; Lazarus, Colin M. ; Wit, Pierre J.G.M. de; Collemare, Jérôme - \ 2018
PLoS ONE 13 (2018)12. - ISSN 1932-6203
Pigments and phytotoxins are crucial for the survival and spread of plant pathogenic fungi. The genome of the tomato biotrophic fungal pathogen Cladosporium fulvum contains a predicted gene cluster (CfPKS1, CfPRF1, CfRDT1 and CfTSF1) that is syntenic with the characterized elsinochrome toxin gene cluster in the citrus pathogen Elsinoë fawcettii. However, a previous phylogenetic analysis suggested that CfPks1 might instead be involved in pigment production. Here, we report the characterization of the CfPKS1 gene cluster to resolve this ambiguity. Activation of the regulator CfTSF1 specifically induced the expression of CfPKS1 and CfRDT1, but not of CfPRF1. These co-regulated genes that define the CfPKS1 gene cluster are orthologous to genes involved in 1,3-dihydroxynaphthalene (DHN) melanin biosynthesis in other fungi. Heterologous expression of CfPKS1 in Aspergillus oryzae yielded 1,3,6,8-tetrahydroxynaphthalene, a typical precursor of DHN melanin. Δcfpks1 deletion mutants showed similar altered pigmentation to wild type treated with DHN melanin inhibitors. These mutants remained virulent on tomato, showing this gene cluster is not involved in pathogenicity. Altogether, our results showed that the CfPKS1 gene cluster is involved in the production of DHN melanin and suggests that elsinochrome production in E. fawcettii likely involves another gene cluster.
Applying soil health indicators to encourage sustainable soil use : The transition from scientific study to practical application
Griffiths, Bryan S. ; Faber, Jack ; Bloem, Jaap - \ 2018
Sustainability 10 (2018)9. - ISSN 2071-1050
Earthworms - Ecosystem services - Monitoring - Soil food web - Water infiltration
The sustainable management of land for agricultural production has at its core a healthy soil, because this reduces the quantity of external inputs, reduces losses of nutrients to the environment, maximises the number of days when the soil can be worked, and has a pore structure that maximises both the retention of water in dry weather and drainage of water in wet weather. Soil health encompasses the physical, chemical, and biological features, but the use of biological indicators is the least well advanced. Sustainability also implies the balanced provision of ecosystem services, which can be more difficult to measure than single indicators. We describe how the key components of the soil food web contribute to a healthy soil and give an overview of the increasing number of scientific studies that have examined the use of biological indicators. A case study is made of the ecosystem service of water infiltration, which is quite an undertaking to measure directly, but which can be inferred from earthworm abundance and biodiversity which is relatively easy to measure. This highlights the difficulty of putting any monitoring scheme into practice and we finish by providing the considerations in starting a new soil health monitoring service in the UK and in maintaining biological monitoring in The Netherlands.
The need for standardisation: Exemplified by a description of the diversity, community structure and ecological indices of soil nematodes
Griffiths, B.S. ; Groot, G.A. de; Laros, I. ; Stone, D. ; Geisen, S. - \ 2018
Ecological Indicators 87 (2018). - ISSN 1470-160X - p. 43 - 46.
Biodiversity - DNA extraction - Metabarcoding - Microscopy - Molecular approaches - Nematodes - Standardisation
Molecular approaches are offering a supplement to, or even the possibility of replacing morphological identification of soil fauna, because of advantages for throughput, coverage and objectivity. We determined ecological indices of nematode community data from four sets of duplicate soil cores, based on morphological identification of nematodes after elutriation from 200 g soil and high throughput sequencing (HTS) targeting nematodes both after being elutriated from soils and DNA extracted directly from 10 g soil. HTS (at genus and species level) increased the taxonomic resolution compared to morphology (at family level). DNA extracted from elutriated nematodes identified more nematode taxa than when extracted from soil, due to an enrichment in nematode sequences. Each method also gave a different ecological footprint for the nematode community. Standardisation to previously determined indices based on morphological identification is needed in order to provide more meaningful information about soil quality and for ecological monitoring.
Detecting macroecological patterns in bacterial communities across independent studies of global soils
Ramirez, Kelly S. ; Knight, Christopher G. ; Hollander, Mattias de; Brearley, Francis Q. ; Constantinides, Bede ; Cotton, Anne ; Creer, Si ; Crowther, Thomas W. ; Davison, John ; Delgado-Baquerizo, Manuel ; Dorrepaal, Ellen ; Elliott, David R. ; Fox, Graeme ; Griffiths, Robert I. ; Hale, Chris ; Hartman, Kyle ; Houlden, Ashley ; Jones, David L. ; Krab, Eveline J. ; Maestre, Fernando T. ; McGuire, Krista L. ; Monteux, Sylvain ; Orr, Caroline H. ; Putten, Wim H. van der; Roberts, Ian S. ; Robinson, David A. ; Rocca, Jennifer D. ; Rowntree, Jennifer ; Schlaeppi, Klaus ; Shepherd, Matthew ; Singh, Brajesh K. ; Straathof, Angela L. ; Bhatnagar, Jennifer M. ; Thion, Cécile ; Heijden, Marcel G.A. van der; Vries, Franciska T. de - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 189 - 196.
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Specific Hypersensitive Response–Associated Recognition of New Apoplastic Effectors from Cladosporium fulvum in Wild Tomato
Mesarich, Carl H. ; Ӧkmen, Bilal ; Rovenich, Hanna ; Griffiths, Scott A. ; Wang, Changchun ; Karimi Jashni, Mansoor ; Mihajlovski, Aleksandar ; Collemare, Jérôme ; Hunziker, Lukas ; Deng, Cecilia H. ; Burgt, Ate Van Der; Beenen, Henriek G. ; Templeton, Matthew D. ; Bradshaw, Rosie E. ; Wit, Pierre J.G.M. De - \ 2018
Molecular Plant-Microbe Interactions 31 (2018)1. - ISSN 0894-0282 - p. 145 - 162.
Tomato leaf mold disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged. To combat these strains, new Cf genes are required. An effectoromics approach was employed to identify wild tomato accessions carrying new Cf genes. Proteomics and transcriptome sequencing were first used to identify 70 apoplastic in planta–induced C. fulvum SSPs. Based on sequence homology, 61 of these SSPs were novel or lacked known functional domains. Seven, however, had predicted structural homology to antimicrobial proteins, suggesting a possible role in mediating antagonistic microbe-microbe interactions in planta. Wild tomato accessions were then screened for HR-associated recognition of 41 SSPs, using the Potato virus X–based transient expression system. Nine SSPs were recognized by one or more accessions, suggesting that these plants carry new Cf genes available for incorporation into cultivated tomato.
Down-regulation of cladofulvin biosynthesis is required for biotrophic growth of Cladosporium fulvum on tomato : A secondary metabolite prevents fungal biotrophy
Griffiths, Scott ; Mesarich, Carl H. ; Overdijk, Elysa J.R. ; Saccomanno, Benedetta ; Wit, Pierre J.G.M. De; Collemare, Jérôme - \ 2018
Molecular Plant Pathology 19 (2018)2. - ISSN 1464-6722 - p. 369 - 380.
Fungal biotrophy is associated with a reduced capacity to produce potentially toxic secondary metabolites (SMs). Yet, the genome of the biotrophic plant pathogen Cladosporium fulvum contains many SM biosynthetic gene clusters, with several related to toxin production. These gene clusters are, however, poorly expressed during colonisation of tomato. The sole detectable SM produced by C. fulvum during in vitro growth is the anthraquinone cladofulvin. Although this pigment is not detected in infected leaves, cladofulvin biosynthetic genes are expressed throughout the pre-penetration phase and during conidiation at the end of the infection cycle, but they are repressed during the biotrophic phase of tomato colonization. It was suggested that tight regulation of SM gene clusters is required for C. fulvum to behave as a biotrophic pathogen, while retaining potential fitness determinants for growth and survival outside its host. To address this hypothesis, we analysed the disease symptoms caused by mutant C. fulvum strains that do not produce or over-produce cladofulvin during the biotrophic growth phase. Non-producers infected tomato similar to wild type, suggesting that cladofulvin is not a virulence factor. In contrast, the cladofulvin over-producers caused strong necrosis and desiccation of tomato leaves, which in turn, arrested conidiation. Consistent with the role of pigments in survival against abiotic stresses, cladofulvin protects conidia against UV light and low temperature stress. Overall this study demonstrates that repression of cladofulvin production is required for C. fulvum to sustain its biotrophic lifestyle in tomato, while its production is important for survival outside its host.
Isolation by oceanic distance and spatial genetic structure in an overharvested international fishery
Truelove, Nathan K. ; Box, Stephen J. ; Aiken, Karl A. ; Blythe-Mallett, Azra ; Boman, Erik M. ; Booker, Catherine J. ; Byfield, Tamsen T. ; Cox, Courtney E. ; Davis, Martha H. ; Delgado, Gabriel A. ; Glazer, Bob A. ; Griffiths, Sarah M. ; Kitson-Walters, Kimani ; Kough, Andy S. ; Pérez Enríquez, Ricardo ; Preziosi, Richard F. ; Roy, Marcia E. ; Segura-García, Iris ; Webber, Mona K. ; Stoner, Allan W. - \ 2017
Diversity and Distributions 23 (2017)11. - ISSN 1366-9516 - p. 1292 - 1300.
Connectivity - Conservation - Dispersal - Fisheries - Genetics - Spatial
Aim: A detailed understanding of spatial genetic structure (SGS) and the factors driving contemporary patterns of gene flow and genetic diversity are fundamental for developing conservation and management plans for marine fisheries. We performed a detailed study of SGS and genetic diversity throughout the overharvested queen conch (Lobatus gigas) fishery. Caribbean countries were presented as major populations to examine transboundary patterns of population differentiation. Location: Nineteen locations in the greater Caribbean from Anguilla, the Bahamas, Belize, Caribbean Netherlands, Honduras, Jamaica, Mexico, Turks and Caicos, and the USA. Methods: We genotyped 643 individuals with nine microsatellites. Population genetic and multivariate analyses characterized SGS. We tested the alternate hypotheses: (1) SGS is randomly distributed in space or (2) pairwise genetic structure among sites is correlated with oceanic distance (IBOD). Results: Our study found that L. gigas does not form a single panmictic population in the greater Caribbean. Significant levels of genetic differentiation were identified between Caribbean countries (FCT = 0.011; p = .0001), within Caribbean countries (FSC = 0.003; p = .001), and among sites irrespective of geographic location (FST = 0.013; p = .0001). Gene flow across the greater Caribbean was constrained by oceanic distance (p = .0009; Mantel r = .40), which acted to isolate local populations. Main conclusions: Gene flow over the spatial scale of the entire Caribbean basin is constrained by oceanic distance, which may impede the natural recovery of overfished L. gigas populations. Our results suggest a careful blend of local and international management will be required to ensure long-term sustainability for the species.
Priorities for research in soil ecology
Eisenhauer, Nico ; Antunes, Pedro M. ; Bennett, Alison E. ; Birkhofer, Klaus ; Bissett, Andrew ; Bowker, Matthew A. ; Caruso, Tancredi ; Chen, Baodong ; Coleman, David C. ; Boer, Wietse de; Ruiter, Peter de; DeLuca, Thomas H. ; Frati, Francesco ; Griffiths, Bryan S. ; Hart, Miranda M. ; Hättenschwiler, Stephan ; Haimi, Jari ; Heethoff, Michael ; Kaneko, Nobuhiro ; Kelly, Laura C. ; Leinaas, Hans Petter ; Lindo, Zoë ; Macdonald, Catriona ; Rillig, Matthias C. ; Ruess, Liliane ; Scheu, Stefan ; Schmidt, Olaf ; Seastedt, Timothy R. ; Straalen, Nico M. van; Tiunov, Alexei V. ; Zimmer, Martin ; Powell, Jeff R. - \ 2017
Pedobiologia 63 (2017). - ISSN 0031-4056 - p. 1 - 7.
Aboveground-belowground interactions - Biodiversity–ecosystem functioning - Biogeography - Chemical ecology - Climate change - Ecosystem services - Global change - Microbial ecology - Novel environments - Plant-microbe interactions - Soil biodiversity - Soil food web - Soil management - Soil processes
The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.