148 research outputs found
Does diversity matter? : Soil microbial functioning and greenhouse gas fluxes in cover crop mixtures
No full textSustainable agricultural management is needed to reduce negative effects of current intensive agricultural practices. Intensification of agricultural land use management can lead to reduced soil organic matter (SOM) and microbial functional diversity in the soil. One of the options to increase sustainability in agricultural practices is the diversification of the cropping system via the use of wider crop rotations, intercropping and growing of cover crops. A major reason to grow cover crops is to reduce nutrient losses during the fallow period of the soil. Furthermore, cover crops are used to suppress weeds, plant pathogens, as well as to protect against erosion and stimulate nutrient cycling in the soil. There are indications that cover crops are beneficial by enhancing SOM content, aggregate stability and microbial functioning. Reducing the fallow period of the soil can be beneficial to enhance microbial diversity and main crop yields. It is hypothesized that using cover crop mixtures instead of cover crop monocultures will have an extra positive effect as mixtures will increase complementarity, possibly leading to increased biomass production and chemically more diverse root exudates and plant residues. In this PhD project, I studied if cover crop mixtures are beneficial compared to cover crop monocultures both during cover crop growth and after cover crop incorporation in the soil. Field and pot experiments were executed to determine if cover crop mixtures enhance nutrient cycling in the soil, reduce GHG emissions, stimulate a diverse microbial community and enhance yield of the main crop. To determine long term effects, the field experiment was conducted for four years.First, we studied in a pot experiment if diversity of cover crop residues will increase microbial functional diversity during decomposition (Chapter 2). Cover crop residues of single species and diverse mixtures of 3 or 15 species were mixed with arable soil. Addition of cover crop residues rapidly increased microbial biomass in the soil during the first two weeks of the experiment. However, microbial biomass increase did not differ between monocultures and mixtures. With the use of Biolog ECO plates, we tested if residue diversity increased microbial metabolic potential as a proxy of functional diversity. Microbial communities extracted from pots amended with residue mixtures were able to use significantly more substrates than the ones extracted from pots with amended with residues derived from a single cover crop species. Microbial communities from pots with residues of Vicia sativa showed high functional diversity as well. However, metabolic activity of the microbes from the V. sativa amended pots was mainly associated with easily degradable substrates while microbial communities from mixed residue amended pots were able to consume a wider set of substrates. This indicates that residues from cover crop mixtures increase the substrate utilization range and therefore the number of niches for microbes compared to residues derived from a single species. Furthermore, we found that the C:N ratio of cover crop residues rather than residue diversity influences greenhouse gas (CO2 and N2O) fluxes. This indicates that composition of the residues is important for nutrient cycling while diversity of cover crop residues influences the soil microbial functional diversity.To be able to evaluate the potential of organic residues, including cover crops, to mitigate greenhouse gasses (GHGs), pot experiments in controlled climate chambers were set up to determine if residues can minimize emissions. The aim of Chapter 3 was to test differences between organic amendments (compost, sewage sludge, digestate and cover crop mixture) and understand how (combinations of) organic amendments influence the global warming potential (GWP) of an agricultural soil. Organic residues were added to the soil in two different amounts (5 and 20 ton*ha-1) at different soil moisture levels (40% and 65% of soil water holding capacity). GHG fluxes (CO2, CH4 and N2O) were measured over time while abundance of microbial groups involved in nutrient cycling (nosZ, bacterial and archaeal amoA, nifH, mcrA and pmoA) was measured at the beginning and at the end of the incubation. Compost resulted in the lowest GHG balance while the mixture of cover crop residues showed the highest GHG emissions. However, the used compost is poor in mineral nutrients and can reduce yield of the main crop. To overcome this problem, combining compost with nutrient rich organic amendment (e.g. sewage sludge or digestate) can minimize the trade-off between obtaining high yields and minimizing GHG emissions. Additionally, all amendments increased microbial communities involved in nutrient cycling and GHG consumption. Mixed cover crop residues led to the highest increase. However, this is dependent on the amount of the added residues. Applying 20 ton per hectare of residues strongly increased microbial groups, while 5 ton per hectare did not significantly increase these microbial groups compared to un-amended soil.Apart from studying the effect of plant diversity of cover crop residues, microbial diversity itself can influence processes like decomposition and nutrient cycling. As fungi play a major role in decomposition, the aim of Chapter 4 was to determine if fungal diversity enhance decomposition, which was assessed by executing a meta-analysis. An extensive literature search was performed to find papers that studied decomposition with a fungal diversity gradient both in manipulated and field experiments and in aquatic and terrestrial environments. Increased fungal diversity coincided with increased decomposition rate of plant residues (leaf litter and wood). However, in artificially manipulated experiments, fungal diversity rapidly reached a saturation level at two fungal species and further increase of diversity did not enhance decomposition. In field experiments, however, fungal diversity was positively correlated with decomposition regardless of the diversity level. This suggests that manipulated experiments are not representative for field situations and that it is necessary to study microbial diversity in the field. Furthermore, plant residue quality influences the fungal diversity – decomposition relationship. Increasing the C:N ratio of the residue reduced the positive effect of diversity on decomposition. These results indicate that both microbial diversity and residue quality are important to estimate decomposition rates of plant residues.In Chapter 5, results of cover crop diversity effects of a multiannual field experiment are described both during cover crop growth and after cover crop incorporation in the soil. We hypothesized that cover crop mixtures reduce greenhouse gas (GHG) fluxes and increase soil microbial diversity compared to cover crop monocultures. Three cover crop species (Avena strigosa, Vicia sativa and Raphanus sativus) were grown in randomized block design with all possible combinations of the three species. GHG fluxes were measured regularly throughout the year. We found increased emissions in the plots with cover crops compared to fallow plots, both during cover crop growth and after cover crop incorporation. Cover crop mixtures did not reduce GHG fluxes compared to cover crop monocultures. N2O emission peaked after cover crop incorporation and was correlated with increased denitrification and nitrification rates. Furthermore, contrasting to our hypothesis, we did not find effects of cover crops on microbial biomass or - diversity in the field. This indicates that, in this field experiment, cultivating mixtures of cover crops for four years did not develop benefits compared to monocultures with respect to GHG fluxes and microbial biomass, - diversity and - activity.Overall, my thesis research compared performance of mixtures and monocultures of cover crops both in pot experiments during decomposition and in a four-year field experiment. The results show that residues of cover crop mixtures have the potential to increase microbial functional diversity and stimulate microbial groups involved in nutrient cycling. This indicates a promising perspective to use cover crop mixtures in the field. However, in our field experiment, mixtures did not result in reduced GHG emissions or increased microbial biomass or diversity. Continuation of field experiments for a longer period is needed to determine if mixtures are advantageous compared to monocultures to increase sustainability in agricultural systems
Nitrification and denitrification in the root zone of Glyceria maxima: 'The plant gives ... the plant takes'
No full textContains fulltext :
mmubn000001_251022889.pdf (Publisher’s version ) (Open Access)Promotores : H. Laanbroek en C. Blom159 p
Archaeal ammonia oxidation in volcanic grassland soils of Iceland. Effects of elevated temperature and N availability on processes and organisms
No full textThaumarchaea are recognized today as the most abundant and ubiquitously distributed archaeal organisms, especially in the oceans and soil. Their phylogenetic placement as a phylum, the capability of all cultivated Thaumarchaea to oxidize ammonia for energy conservation as well as many further aspects concerning their ecology, physiology and evolution are discoveries of the last decade only. Still, conceptual knowledge on the role of Thaumarchaea in soil ammonia oxidation is lacking and their ecological significance in soils is poorly understood. The work presented in this thesis is concerned with archaeal ammonia-oxidizing communities in volcanic grassland soil in Grændalur, Iceland. The study site was chosen as it is remote enough from continental Europe to experience very little atmospheric N deposition and because it contains grassland soils with different in situ temperatures as a result of geothermal heating.
Several lines of evidence were gathered that Thaumarchaea are most likely of primary importance for ammonia oxidation in Grændalur, while ammonia-oxidizing bacteria (AOB) are present in numbers below the detection limit of conventional PCR (chapter 2, 4 and 5). Supposedly, this finding resembles a high ecological importance of AOA in terrestrial environments with low ammonia availability (chapter 4). Thaumarchaea could be stimulated in growth and activity by N deposition in the form of ammonium, but only in low and medium concentrations of ~ 45 - 150 μg NH4+ - N per ∙ g dry soil-1. AOB however, were only responsive to medium and higher applications of ammonium (chapter 4).
Through microcosm incubations it was identified that gross nitrification (i.e. the two step process by which ammonia is converted to nitrate with nitrite as intermediary product) is functionally coupled to gross N mineralization in soils of Grændalur (chapter 3). By exposing the soils to short-term temperature changes however, this coupling of gross nitrification and gross N mineralization was lost and nitrifiers performed less well. This finding led to the conclusion that the nitrifying communities in Grændalur’s soils are adapted to function best at the temperature they experience in situ (chapter 3).
In a stable-isotope labeling experiment with soil from Grændalur evidence for autotrophic growth of Nitrosopumilus-like Thaumarchaea, likely coupled to ammonia oxidation, was collected (chapter 5). Additionally, the results strongly suggested a syntrophic association between the autotrophically growing Thaumarchaea and nitrite-oxidizing bacteria (NOB) of the Nitrospira sublineages I and II. The work of chapter 5 furthermore showed that the autotrophically active nitrifiers in this soil (i.e. Thaumarchaea and Nitrospira-like NOB) are stimulated by application of inorganic N in form of ammonium, but suppressed by the presence of active methane-oxidizing bacteria (MOB). Likely, this negative interaction is a result of competition for common resources like inorganic N and oxygen. Intriguingly, growth of the total Thaumarchaeal community did not seize under conditions of suppressed net nitrification and autotrophic growth. In addition, the Thaumarchaeal community structure did not change. The data collected in this thesis therefore suggests that at least some Thaumarchaea possess the metabolic plasticity to choose for an energetically more advantageous mode of growth than lithoautotrophy by growing mixotrophically, possibly in association with mineralizers (chapters 3 and 5)
Interactions between nitrogenous fertilizers and methane cycling in wetland and upland soils
No full textRecent dynamics and uncertainties in global methane budgets
necessitate research of controls of sources and sinks of
atmospheric methane. Production of methane by
methanogenic archaea in wetlands is a major source while
consumption by methane oxidizing bacteria in upland soils is a
major sink. Methane formation as well as consumption is
affected by nitrogenous fertilizers as has been studied
intensively. This review synthesizes the results of these studies
which are contradictory and await mechanistic explanations.
These can be found in the community composition and the
traits of the microbes involved in methane cycling. Molecular
microbial investigations, use of stable isotope labeling
techniques, discoveries and isolation of new species and
pathways offer new insight into interactions between nitrogen
and methane cycling.
Disentangling microbial decomposition networks : linking detritus-based soil microbial food webs to ecosystem processes
No full textSoils are crucial for a large number of ecosystem services and occupy an important position in driving the Earth’s biogeochemical cycles. Soils are therefore essential for e.g. agricultural food production, carbon sequestration, water purification and nutrient cycling. These soil functions are to a large extent governed by the huge biodiversity of soil life, which can be depicted in the form of a soil food web: a model that describes the feeding relationships among groups of species that live in the soil. A number of soil ecosystem services, as governed by soil life, are currently under considerable threat due to e.g. soil degradation, atmospheric nitrogen deposition and land use change. A proper understanding of the mechanisms underlying soil ecosystem functioning, in relation to global change, is important to anticipate these threats and to help ensure optimal functioning of our soils. Soil food web models have proven to be highly useful in the study of the long-term consequences of environmental change on soil communities and associated ecosystem functioning. Perhaps the most important ecosystem process driven by the soil food web is the decomposition of detritus: plant residues and soil organic matter. Via the decomposition of detritus, soil organisms determine the critical balance between sequestration and mineralization of carbon (C) and nutrients, affecting soil CO2 emissions to the atmosphere and nutrient availability for plants. Soil microbes (bacteria, fungi and protozoa) play a very important role in the decomposition of detritus by being the first consuming trophic level and by making up more than 90% of the total belowground biomass. In this way, soil microbes are the main influencers of C and nitrogen (N) dynamics in soil. However, detailed information on the microbial processing of different types of organic substrates in soil food webs is still missing. Due to the important role of soil microbial communities in C and N cycling, this information is crucial to incorporate in soil food web models in order to study the long-term consequences of global change on ecosystem functioning. This is especially important if one wants to use this information for targeted management of soil life, which is seen as a promising management tool to target optimal soil functioning in anticipation of a changing world. The main research aim of this thesis was therefore to disentangle the soil microbial food web in relation to an important type of environmental change: land use change. In chapter 2, I start with discussing how state-of-the-art empirical techniques can be used to collect trophic information that is needed to construct different types of empirically-based food webs: connectedness webs, semi-quantitative webs, energy flow webs and functional webs. I explain what types of information is needed from molecular and biogeochemical studies to create such soil food web models. I thereby give a comprehensive overview of the available empirical techniques with respect to the type of information they can provide for soil food web models. In chapter 3, I study litter-derived C flows through the soil microbial food web in six different ex-arable soils. In a 56-day incubation experiment, I compared the fate of litter-derived C flows through the soil microbial communities of recent and long-term abandoned soils. Soils were amended with 13C-labelled plant litter and microbial C flows were studied by tracing the labelling of biomarkers in the form of Phospholipid Fatty Acids Stable Isotope Probing (PLFA-SIP). PLFA-SIP revealed that soil microbial communities are less efficient in decomposing litter-derived C in long-term compared to recently abandoned soils. The reduced efficiency of litter-derived C decomposition is most likely due to a net shift of organic matter-derived C to root-derived C input in relation to time since abandonment of agricultural practices. The study further revealed a clear succession of microbial decomposers, both in time and quantity that was similar across all examined fields: fungi > G- bacteria > G+ bacteria ≥ actinomycetes > micro-fauna. This information gives a first quantitative insight in how litter-derived C flows through the detritus-based soil microbial food web. In chapter 4, I continue assessing C flows through the soil microbial community in more detail, by tracing the fate of three contrasting types of organic substrates. The same set of ex-arable soils as examined in chapter 3 were incubated for 28 days after the addition of a mixture of glycine, cellulose and vanillin. In each of the treatments one or none of these compounds was 13C-labelled, to trace the fate of a specific organic compound. Application of both PLFA-SIP and RNA-SIP analyses allowed me to 1) quantify substrate-derived C flows through the soil microbial food web and 2) assess soil microbial resource partitioning beyond the concepts of the bacterial and fungal energy channels. The analyses revealed the emergence of a specific microbial community that deals with the decomposition of recalcitrant material in long-term abandoned soils. Furthermore, the existence of soil microbial decomposer succession was further confirmed by revealing both intra-kingdom microbial decomposer successional patterns and intra-kingdom microbial resource partitioning on the taxonomic level of fungal and bacterial classes. These results further enhance the view that the understanding of soil microbial decomposition goes beyond the concepts of bacterial and fungal energy channels. In chapter 5, I assess the effects of contrasting types of organic matter inputs on microbial biomass, activity and community structure, as well as related ecosystem processes like N mineralization, microbial N immobilization, plant growth and nutrient uptake. In a pot experiment, Brussels sprouts were grown on arable soils that were mixed with 15N-labelled mineral fertilizer and a contrasting type of organic amendments. The experiment revealed that a number of ecosystem processes were directly related to soil microbial activity, while microbial N immobilization was mostly dependent on the soil microbial community structure. These outcomes support the idea that soil microbial community structure is important to take into account when assessing the effects of the soil organic inputs on soil ecosystem functioning and can be used to design nutrient management strategies for more sustainable agriculture. In chapter 6, I study the drivers of both soil microbial community structure and function on two spatial scales (landscape and local scale). It is shown that these two soil microbial community characteristics are controlled by a distinct set of drivers at local versus landscape scale. I show that soil microbial community structure is driven on the landscape level by phosphorous related variables, whereas soil microbial functioning is driven locally through vegetation patterns. It is therefore important that management strategies consider the scale-dependent action of soil microbial community drivers and take both soil microbial community function and structure into account to target the desired biogeochemical functioning of soils. Overall, this thesis gives the first high-resolution and quantitative image of detritus-based microbial food webs as affected by land use change and advances our understanding of soil food webs. Studying soil microbial food webs in a chronosequence of ex-arable fields revealed that a good understanding of soil microbial C flows, beyond the level of bacterial and fungal energy channels, is crucial to understand the effect of land-abandonment on the functioning of soil food webs. A thorough understanding of intra-kingdom variation in soil microbial C processing is therefore of vital importance to enhance our understanding of soil microbial functioning in response to global change, which is the key to success for targeted management of soil life in a changing world
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