Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Modulation of litter decomposition by the soil microbial food web under influence of land use change
    Heijboer, Amber ; Ruiter, Peter C. de; Bodelier, Paul L.E. ; Kowalchuk, George A. - \ 2018
    Frontiers in Microbiology 9 (2018)NOV. - ISSN 1664-302X
    Agricultural abandonment - Carbon cycle - Decomposition - PLFA-SIP - Soil food web - Soil microbial community

    Soil microbial communities modulate soil organic matter (SOM) dynamics by catalyzing litter decomposition. However, our understanding of how litter-derived carbon (C) flows through the microbial portion of the soil food web is far from comprehensive. This information is necessary to facilitate reliable predictions of soil C cycling and sequestration in response to a changing environment such as land use change in the form of agricultural abandonment. To examine the flow of litter-derived C through the soil microbial food web and it’s response to land use change, we carried out an incubation experiment with soils from six fields; three recently abandoned and three long term abandoned fields. In these soils, the fate of 13C-labeled plant litter was followed by analyzing phospholipid fatty acids (PLFA) over a period of 56 days. The litter-amended soils were sampled over time to measure 13CO2 and mineral N dynamics. Microbial 13C-incorporation patterns revealed a clear succession of microbial groups during litter decomposition. Fungi were first to incorporate 13C-label, followed by G− bacteria, G+ bacteria, actinomycetes and micro-fauna. The order in which various microbial groups responded to litter decomposition was similar across all the fields examined, with no clear distinction between recent and long-term abandoned soils. Although the microbial biomass was initially higher in long-term abandoned soils, the net amount of 13C-labeled litter that was incorporated by the soil microbial community was ultimately comparable between recent and long-term abandoned fields. In relative terms, this means there was a higher efficiency of litter-derived 13C-incorporation in recent abandoned soil microbial communities compared to long-term abandoned soils, most likely due to a net shift from SOM-derived C toward root-derived C input in the soil microbial food web following land-abandonment.

    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.

    Soil protists: A fertile frontier in soil biology research
    Geisen, Stefan ; Mitchell, Edward A.D. ; Adl, Sina ; Bonkowski, Michael ; Dunthorn, Micah ; Ekelund, Flemming ; Fernández, Leonardo D. ; Jousset, Alexandre ; Krashevska, Valentyna ; Singer, David ; Spiegel, Frederick W. ; Walochnik, Julia ; Lara, Enrique - \ 2018
    FEMS Microbiology Reviews 42 (2018)3. - ISSN 0168-6445 - p. 293 - 323.
    Biogeography - Functional diversity - Plant performance - Soil food web - Soil microbiome - Taxonomic diversity

    Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

    An overview of microplastic and nanoplastic pollution in agroecosystems
    Ng, Ee Ling ; Huerta Lwanga, Esperanza ; Eldridge, Simon M. ; Johnston, Priscilla ; Hu, Hang Wei ; Geissen, Violette ; Chen, Deli - \ 2018
    Science of the Total Environment 627 (2018). - ISSN 0048-9697 - p. 1377 - 1388.
    Ecotoxicology - Plant response - Plastic degradation - Soil food web - Soils
    Microplastics and nanoplastics are emerging pollutants of global importance. They are small enough to be ingested by a wide range of organisms and at nano-scale, they may cross some biological barriers. However, our understanding of their ecological impact on the terrestrial environment is limited. Plastic particle loading in agroecosystems could be high due to inputs of some recycled organic waste and plastic film mulching, so it is vital that we develop a greater understanding of any potentially harmful or adverse impacts of these pollutants to agroecosystems. In this article, we discuss the sources of plastic particles in agroecosystems, the mechanisms, constraints and dynamic behaviour of plastic during aging on land, and explore the responses of soil organisms and plants at different levels of biological organisation to plastic particles of micro and nano-scale. Based on limited evidence at this point and understanding that the lack of evidence of ecological impact from microplastic and nanoplastic in agroecosystems does not equate to the evidence of absence, we propose considerations for addressing the gaps in knowledge so that we can adequately safeguard world food supply.
    Methodological advances to study the diversity of soil protists and their functioning in soil food webs
    Geisen, Stefan ; Bonkowski, Michael - \ 2018
    Applied Soil Ecology 123 (2018). - ISSN 0929-1393 - p. 328 - 333.
    Biodiversity - Functional diversity - High throughput sequencing - Soil food web - Soil protists

    Soils host the most complex communities of organisms, which are still largely considered as an unknown 'black box'. A key role in soil food webs is held by the highly abundant and diverse group of protists. Traditionally, soil protists are considered as the main consumers of bacteria in soils. However, recent insights obtained using new methodologies, provide clear evidence for the trophic diversity of microbial eukaryotes, showing that non-bacterivorous soil protists (fungivores, omnivores, predators of other protists and nematodes), photosynthetic taxa and plant-as well as animal parasites might be equally important.Here we provide an overview of methodologies to study these important soil organisms. Major gaps of knowledge are highlighted, which can be addressed using a combination of now available methods These studies will undeniably reveal an even higher functional diversity of protists and likely raise awareness of their ecological importance in soils.

    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.
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