1,721,027 research outputs found
Spatio-temporal patterns and potential trade-offs in the promotion of aphid and seed predation in agroforestry systems
Full text linkAbstract Agricultural intensification and simplification compromise biodiversity and can destabilize populations of important ecosystem service providers. By promoting invertebrate and vertebrate predators that deliver important ecosystem services such as pest and weed control, agroforestry systems may reconcile ecological benefits and agriculture productivity, making them a promising land-use system for the transition towards sustainable agriculture. However, the spatio-temporal regulation of ecosystem services and potential disservices provided by predators in agroforestry systems remains poorly studied. We compared aphid, weed seed, and crop seed predation in the crop rows between temperate alley cropping systems and open croplands without trees. In addition, we analyzed the extent to which effects of tree rows extended into the crop rows at two different time periods in spring. Aphid predation was higher at sampling locations close to the tree rows. Seed predation was spatially more variable but showed, similar to aphid predation, particularly low rates in open croplands. The distance-dependence of aphid and crop seed predation changed in magnitude across sampling periods, while weed seed predation was more temporally constant. Moreover, crop seeds were consumed nearly twice as much as weed seeds, indicating varying food preferences among invertebrate and vertebrate seed predators and a potential trade-off between ecosystem services and disservices. Our results suggest that alley cropping agroforestry benefits pest and weed control. However, differences in spatio-temporal patterns of aphid and seed predation indicate varying dependencies of different predator groups on the tree rows, while high crop seed predation suggests a concurrent promotion of a disservice. Our study emphasizes that understanding the spatial and temporal patterns of predation-related ecosystem services and disservices is needed to develop management practices promoting natural pest control and reducing the amount of plant protection products used in agriculture. Therefore, knowing how and when to support beneficial organisms and at the same time control pests is key for the development of sustainable agricultural systems.German Federal Ministry of Education and ResearchGeorg-August-Universität Göttingen http://dx.doi.org/10.13039/50110000338
Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities
Full text linkBackground Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities. Methods SRS consists of two steps. In the scaling step, the counts for all species or operational taxonomic units (OTUs) are divided by a scaling factor chosen in such a way that the sum of scaled counts equals the selected total number of counts Cmin. The relative frequencies of all OTUs remain unchanged. In the subsequent ranked subsampling step, non-integer count values are converted into integers by an algorithm that minimizes subsampling error with regard to the population structure (relative frequencies of species or OTUs) while keeping the total number of counts equal Cmin. SRS and rarefying were compared by normalizing a test library representing a soil bacterial community. Common parameters of biodiversity and population structure (Shannon index H’, species richness, species composition, and relative abundances of OTUs) were determined for libraries normalized to different size by rarefying as well as SRS with 10,000 replications each. An implementation of SRS in R is available for download (https://doi.org/10.20387/BONARES-2657-1NP3). Results SRS showed greater reproducibility and preserved OTU frequencies and alpha diversity better than rarefying. The variance in Shannon diversity increased with the reduction of the library size after rarefying but remained zero for SRS. Relative abundances of OTUs strongly varied among libraries generated by rarefying, whereas libraries normalized by SRS showed only negligible variation. Bray–Curtis index of dissimilarity among replicates of the same library normalized by rarefying revealed a large variation in species composition, which reached complete dissimilarity (not a single OTU shared) among some libraries rarefied to a small size. The dissimilarity among replicated libraries normalized by SRS remained negligibly low at each library size. The variance in dissimilarity increased with the decreasing library size after rarefying, whereas it remained either zero or negligibly low after SRS. Conclusions Normalization of OTU or species counts by scaling with ranked subsampling preserves the original community structure by minimizing subsampling errors. We therefore propose SRS for the normalization of biological count data
Early response of soil fungal communities to the conversion of monoculture cropland to a temperate agroforestry system
No full textBackground Alley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of these systems. Agroforestry systems that are established for more than 10 years have shown to increase the fungal biomass and impact the composition of soil fungal communities. Investigations of soil fungi in younger temperate agroforestry systems are scarce and the temporal dynamic of these changes is not understood. Methods Our study was conducted in a young poplar-based alley cropping and adjacent monoculture cropland system in an Arenosol soil in north-west Germany. We investigated the temporal dynamics of fungal populations after the establishment of agroforestry by collecting soil samples half, one, and one and a half years after conversion of cropland to agroforestry. Samples were collected within the agroforestry tree row, at 1, 7, and 24 m distance from the tree row within the crop row, and in an adjacent conventional monoculture cropland. The biomass of soil fungi, Asco-, and Basidiomycota was determined by real-time PCR. Soil fungal community composition and diversity were obtained from amplicon sequencing. Results Differences in the community composition of soil fungi in the tree row and arable land were detected as early as half a year following the conversion of monoculture cropland to agroforestry. In the tree row, soil fungal communities in the plots strongly diverged with the age of the system. The presence of young trees did not affect the biomass of soil fungi. Conclusions The composition of soil fungal communities responded rapidly to the integration of trees into arable land through agroforestry, whereas the fungal biomass was not affected during the first one and a half years after planting the trees. Fungal communities under the trees gradually diversified. Adaptation to spatially heterogeneous belowground biomass of the trees and understory vegetation or stochastic phenomena due to limited exchange among fungal populations may account for this effect; long-term monitoring might help unravelling the cause
Single versus repeated applications of CuO and Ag nanomaterials and their effect on soil microflora
No full textAbstractNanomaterials enter the terrestrial environment via the repeated application of sludge to soils over many years. The goal of this investigation was to compare the effects of CuO and Ag nanomaterials on soil microorganisms after a single application and after repeated applications ultimately resulting in the same test concentrations. The effect on soil microorganisms was determined using the ammonium oxidation (ISO 15685), enzymatic activity patterns (ISO 22939) and MicroResp™ tests on days 28, 56 and 84. The comparability of single and repeated applications of ion-releasing nanomaterials depended on the test endpoint and duration. No significant differences between single and repeated applications were observed when testing nitrifying microorganisms and exoenzymes, but differences were observed in the substrate-induced respiration test. The three test systems used together provide more comprehensive information about the impact of different nanomaterials on the soil microflora and its diversity
Tree rows in temperate agroforestry croplands alter the composition of soil bacterial communities.
No full textBackgroundTree-based intercropping (agroforestry) has been advocated to reduce adverse environmental impacts of conventional arable cropping. Modern agroforestry systems in the temperate zone are alley-cropping systems that combine rows of fast-growing trees with rows of arable crops. Soil microbial communities in these systems have been investigated intensively; however, molecular studies with high taxonomical resolution are scarce.MethodsHere, we assessed the effect of temperate agroforestry on the abundance, diversity and composition of soil bacterial communities at three paired poplar-based alley cropping and conventional monoculture cropland systems using real-time PCR and Illumina sequencing of bacterial 16S rRNA genes. Two of the three systems grew summer barley (Hordeum vulgare); one system grew maize (Zea mays) in the sampling year. To capture the spatial heterogeneity induced by the tree rows, soil samples in the agroforestry systems were collected along transects spanning from the centre of the tree rows to the centre of the agroforestry crop rows.ResultsTree rows of temperate agroforestry systems increased the abundance of soil bacteria while their alpha diversity remained largely unaffected. The composition of the bacterial communities in tree rows differed from those in arable land (crop rows of the agroforestry systems and conventional monoculture croplands). Several bacterial groups in soil showed strong association with either tree rows or arable land, revealing that the introduction of trees into arable land through agroforestry is accompanied by the introduction of a tree row-associated microbiome.ConclusionThe presence of tree row-associated bacteria in agroforestry increases the overall microbial diversity of the system. We speculate that the increase in biodiversity is accompanied by functional diversification. Differences in plant-derived nutrients (root exudates and tree litter) and management practices (fertilization and tillage) likely account for the differences between bacterial communities of tree rows and arable land in agroforestry systems
N2O flux dynamics and production pathways modulated by soil organic matter and litter turnover
Full text linkAddition of organic material, such as plant litter, can strongly alter C and N turnover in soils and promote CO2 and N2O formation. This study aimed to elucidate the role of C availability on N turnover processes leading to N2O formation under moderately dry conditions. We measured CO2, NO, and N2O fluxes and contributing processes from an arable and a grassland soil with four different treatments: 50% water-filled pore space (WFPS), 50% WFPS + Maize litter, 60% WFPS, 60% WFPS + Maize litter. CO2 fluxes were partitioned into SOM- and litter-derived, and N2O-forming processes were estimated applying a Bayesian mixing and fractionation model to infer source contributions and N2O reduction rates. Further, we quantified bacterial and fungal population size, as well as genes involved in nitrification and denitrification at the end of the experiment. N2O flux dynamics and contributing processes strongly differed between the C-limited arable soil and the C-rich grassland soil. In the arable soil, bacterial denitrification was consistently the main source of N2O and strongly increased with addition of maize litter. In contrast, nitrification accounted for 51% of N2O formation in the grassland soil without litter, while litter addition promoted fungal denitrification. We found higher N2O emissions with higher total and SOM-derived CO2 emissions confirming that availability of organic C from SOM and litter are important controls of N2O losses. However, neither soil organic C content, nor litter addition, nor soil moisture alone were appropriate to predict the main N2O-forming process. Therefore, our study emphasizes the need to disentangle and quantify N2O-forming processes to develop successful mitigation strategies
Temperate alley‐cropping agroforestry improves pest control potential by promoting spider abundance and functional diversity
Full text linkAbstract Intensive agricultural land use negatively impacts biodiversity, including arthropod predator diversity and their pest control potential. Alley‐cropping agroforestry systems (integration of tree rows into arable land) are increasingly considered an economically viable alternative for more sustainable and biodiversity‐friendly agriculture. However, their effectiveness in promoting generalist predator diversity and pest control, especially as a function of space (distance from tree rows) and time (across the growing season) remains poorly understood. We assessed how spider abundance, taxonomic and functional diversity (as proxies of pest control potential) respond to temperate alley‐cropping agroforestry systems as compared to open croplands. Additionally, we analysed whether spiders with different habitat preferences (eurytopic, forest and open‐habitat specialists) show distinct responses. Lastly, we analysed whether the influence of agroforestry changes with decreasing tree proximity and across the growing season. Tree row proximity generally benefited the abundance, as well as taxonomic and functional diversity of the overall spider communities. Alley‐cropping promoted the abundance and taxonomic diversity of forest specialists and eurytopic spiders, without negatively affecting open‐habitat specialists. The positive effect of alley cropping was strongest within tree rows and their immediate vicinity, but was still detectable at considerably farther distances. These patterns were temporally dynamic with spider abundance and taxonomic diversity being highest within tree rows in early spring and spiders spilling over to adjacent crop rows in subsequent periods. Synthesis and applications : Overall, our findings highlight that the inclusion of tree rows benefited spiders across the entirety of the 48 m crop rows, independent of crop type. Since the peak in spider abundance and taxonomic diversity in crop rows coincided with crop pest arrival, alley‐cropping agroforestry is expected to benefit agricultural production through increased pest control potential. Alley‐cropping agroforestry may therefore be an important management strategy to develop more sustainable agricultural systems benefiting farmers and biodiversity alike.Zusammenfassung Intensive landwirtschaftliche Landnutzung wirkt sich negativ auf die Biodiversität aus, einschließlich der Vielfalt räuberischer Arthropoden und ihres Schädlingskontrollpotenzials. Alley Cropping Agroforstsysteme (Integration von Baumreihen in Ackerland) gelten zunehmend als wirtschaftlich sinnvolle Alternative für eine nachhaltigere und biodiversitätsfreundlichere Landwirtschaft. Allerdings ist ihre Wirksamkeit bei der Förderung der Vielfalt generalistischer Prädatoren und der Schädlingskontrolle, insbesondere in Abhängigkeit von Raum (Entfernung von Baumreihen) und Zeit (über die Vegetationsperiode hinweg), noch wenig untersucht. Wir haben untersucht, wie Spinnenabundanz, taxonomische und funktionelle Vielfalt (stellvertretend für das Schädlingskontrollpotenzial) auf Alley Cropping Agroforstsysteme im Vergleich zu offenen Ackerflächen reagieren. Darüber hinaus haben wir analysiert, ob Spinnen mit unterschiedlichen Lebensraumpräferenzen (Eurytop‐, Wald‐ und Offenhabitat‐Spezialisten) unterschiedliche Reaktionen zeigen. Abschließend haben wir analysiert, ob sich der Einfluss der Agroforstwirtschaft mit abnehmender Nähe zu den Bäumen und über die Vegetationsperiode hinweg ändert. Die Nähe der Baumreihen wirkte sich grundsätzlich positiv auf die Abundanz sowie auf die taxonomische und funktionelle Vielfalt der gesamten Spinnengemeinschaften aus. Alley Cropping förderte die Abundanz und die taxonomische Vielfalt von Waldspezialisten und eurytopen Spinnen, ohne Offenhabitat‐Spezialisten negativ zu beeinflussen. Der positive Effekt von Alley Cropping war innerhalb der Baumreihen und deren unmittelbarer Umgebung am stärksten, aber auch in deutlich größerer Entfernung noch nachweisbar. Diese Muster waren zeitlich dynamisch, wobei die Spinnenabundanz und die taxonomische Vielfalt in den Baumreihen im zeitigen Frühjahr am höchsten waren und die Spinnen in den Folgeperioden in benachbarte Ackerreihen abwanderten. Synthese und Anwendung: Insgesamt unterstreichen unsere Ergebnisse, dass die Implementierung von Baumreihen den Spinnen über die gesamte Länge der 48 m breiten Ackerreihen zugutekam, unabhängig von der Kulturpflanzenart. Da der Höhepunkt der Spinnenabundanz und der taxonomischen Vielfalt in den Ackerreihen zeitlich mit dem Auftreten von Pflanzenschädlingen zusammenfiel, kann angenommen werden, dass Alley Cropping Agroforstwirtschaft die landwirtschaftliche Produktion durch ein erhöhtes Schädlingskontrollpotenzial unterstützt. Alley Cropping Agroforstwirtschaft kann daher eine wichtige Managementstrategie zur Entwicklung nachhaltigerer landwirtschaftlicher Systeme sein, die Landwirt*innen und der Artenvielfalt gleichermaßen zugutekommt.Abstract Intensive agricultural land use negatively impacts biodiversity, including arthropod predator diversity and their pest control potential. Alley‐cropping agroforestry systems (integration of tree rows into arable land) are increasingly considered an economically viable alternative for more sustainable and biodiversity‐friendly agriculture. However, their effectiveness in promoting generalist predator diversity and pest control, especially as a function of space (distance from tree rows) and time (across the growing season) remains poorly understood. We assessed how spider abundance, taxonomic and functional diversity (as proxies of pest control potential) respond to temperate alley‐cropping agroforestry systems as compared to open croplands. Additionally, we analysed whether spiders with different habitat preferences (eurytopic, forest and open‐habitat specialists) show distinct responses. Lastly, we analysed whether the influence of agroforestry changes with decreasing tree proximity and across the growing season. Tree row proximity generally benefited the abundance, as well as taxonomic and functional diversity of the overall spider communities. Alley‐cropping promoted the abundance and taxonomic diversity of forest specialists and eurytopic spiders, without negatively affecting open‐habitat specialists. The positive effect of alley cropping was strongest within tree rows and their immediate vicinity, but was still detectable at considerably farther distances. These patterns were temporally dynamic with spider abundance and taxonomic diversity being highest within tree rows in early spring and spiders spilling over to adjacent crop rows in subsequent periods. Synthesis and applications : Overall, our findings highlight that the inclusion of tree rows benefited spiders across the entirety of the 48 m crop rows, independent of crop type. Since the peak in spider abundance and taxonomic diversity in crop rows coincided with crop pest arrival, alley‐cropping agroforestry is expected to benefit agricultural production through increased pest control potential. Alley‐cropping agroforestry may therefore be an important management strategy to develop more sustainable agricultural systems benefiting farmers and biodiversity alike.Zusammenfassung Intensive landwirtschaftliche Landnutzung wirkt sich negativ auf die Biodiversität aus, einschließlich der Vielfalt räuberischer Arthropoden und ihres Schädlingskontrollpotenzials. Alley Cropping Agroforstsysteme (Integration von Baumreihen in Ackerland) gelten zunehmend als wirtschaftlich sinnvolle Alternative für eine nachhaltigere und biodiversitätsfreundlichere Landwirtschaft. Allerdings ist ihre Wirksamkeit bei der Förderung der Vielfalt generalistischer Prädatoren und der Schädlingskontrolle, insbesondere in Abhängigkeit von Raum (Entfernung von Baumreihen) und Zeit (über die Vegetationsperiode hinweg), noch wenig untersucht. Wir haben untersucht, wie Spinnenabundanz, taxonomische und funktionelle Vielfalt (stellvertretend für das Schädlingskontrollpotenzial) auf Alley Cropping Agroforstsysteme im Vergleich zu offenen Ackerflächen reagieren. Darüber hinaus haben wir analysiert, ob Spinnen mit unterschiedlichen Lebensraumpräferenzen (Eurytop‐, Wald‐ und Offenhabitat‐Spezialisten) unterschiedliche Reaktionen zeigen. Abschließend haben wir analysiert, ob sich der Einfluss der Agroforstwirtschaft mit abnehmender Nähe zu den Bäumen und über die Vegetationsperiode hinweg ändert. Die Nähe der Baumreihen wirkte sich grundsätzlich positiv auf die Abundanz sowie auf die taxonomische und funktionelle Vielfalt der gesamten Spinnengemeinschaften aus. Alley Cropping förderte die Abundanz und die taxonomische Vielfalt von Waldspezialisten und eurytopen Spinnen, ohne Offenhabitat‐Spezialisten negativ zu beeinflussen. Der positive Effekt von Alley Cropping war innerhalb der Baumreihen und deren unmittelbarer Umgebung am stärksten, aber auch in deutlich größerer Entfernung noch nachweisbar. Diese Muster waren zeitlich dynamisch, wobei die Spinnenabundanz und die taxonomische Vielfalt in den Baumreihen im zeitigen Frühjahr am höchsten waren und die Spinnen in den Folgeperioden in benachbarte Ackerreihen abwanderten. Synthese und Anwendung: Insgesamt unterstreichen unsere Ergebnisse, dass die Implementierung von Baumreihen den Spinnen über die gesamte Länge der 48 m breiten Ackerreihen zugutekam, unabhängig von der Kulturpflanzenart. Da der Höhepunkt der Spinnenabundanz und der taxonomischen Vielfalt in den Ackerreihen zeitlich mit dem Auftreten von Pflanzenschädlingen zusammenfiel, kann angenommen werden, dass Alley Cropping Agroforstwirtschaft die landwirtschaftliche Produktion durch ein erhöhtes Schädlingskontrollpotenzial unterstützt. Alley Cropping Agroforstwirtschaft kann daher eine wichtige Managementstrategie zur Entwicklung nachhaltigerer landwirtschaftlicher Systeme sein, die Landwirt*innen und der Artenvielfalt gleichermaßen zugutekommt.BonaRes https://doi.org/10.13039/50110002257
Digging deeper: microbial communities in subsoil are strongly promoted by trees in temperate agroforestry systems
No full textAbstract
Aims
Temperate alley-cropping agroforestry systems maintain agricultural production while offering several environmental benefits. Central benefits of agroforestry systems such as the ‘safety-net’-role of the trees for leached nutrients are mainly due to processes occurring below the soil surface: the subsoil. Microorganisms in the subsoil may play a key role in the ‘safety-net’-function as they can improve the capturing and uptake of nutrients by the trees. Systematic investigations of microbial communities in temperate agroforestry systems, however, are restricted to topsoil.
Methods
We quantified bacteria, fungi, and functional groups of microorganisms in the topsoil and subsoil of two alley-cropping systems using real-time PCR. Topsoil and subsoil samples were collected in the tree rows and at multiple distances from the trees within the crop rows of the agroforestry systems as well as at an adjacent monoculture cropland.
Results
Microbial population size decreased with soil depth likely due to limited resource availability in subsoil. Tree rows in agroforestry systems not only promote soil microbial populations in both the topsoil and subsoil but the promotion also extends gradually into the crop rows of the systems. The promotion of microorganisms through trees is stronger in subsoil than topsoil, pointing at more intense resource scarcity in the subsoil than topsoil.
Conclusions
We propose that tree root-derived resources and root litter, which are scarce in agricultural subsoils, triggered the strong positive response of the subsoil community to the trees. Finally, we provide initial evidence that subsoil microorganisms contribute to the ‘safety-net’-role of the trees in agroforestry systems
Relative Abundances of Species or Sequence Variants Can Be Misleading: Soil Fungal Communities as an Example
No full textPlant production systems that are more sustainable than conventional monoculture croplands are the vision of future agriculture. With numerous environmental benefits, agroforestry is among the most promising alternatives. Although soil fungi are key drivers of plant productivity and ecosystem processes, investigations of these microorganisms in temperate agroforestry systems are scarce, leaving our understanding of agricultural systems under agroforestry practice incomplete. Here, we assessed the composition and diversity of the soil fungal community as well as the frequency (relative abundance) of fungal groups in three paired temperate poplar-based alley cropping (agroforestry) and monoculture cropland systems by amplicon sequencing. Analysis of microbiomes using relative abundances of species or sequence variants obtained from amplicon sequencing ignores microbial population size, which results in several problems. For example, species stimulated by environmental parameters may appear unaffected or suppressed in amplicon counts. Therefore, we determined absolute abundances of selected fungal groups as well as total fungal population size by real-time polymerase chain reaction (PCR). Tree rows strongly affected the community composition and increased the population size and species richness of soil fungi. Furthermore, ectomycorrhiza were strongly promoted by the tree rows. We speculate that mycorrhiza improved the nutrient acquisition in unfertilized tree rows, thereby contributing to the total productivity of the system. Comparison of relative and absolute abundances revealed dramatic discrepancies, highlighting that amplicon sequencing alone cannot adequately assess population size and dynamics. The results of our study highlight the necessity of combining frequency data based on amplicon sequencing with absolute quantification
‘SRS’ R Package and ‘q2-srs’ QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)
No full textSeveral ecological data types, especially microbiome count data, are commonly sample-wise normalized before analysis to correct for sampling bias and other technical artifacts. Recently, we developed an algorithm for the normalization of ecological count data called ‘scaling with ranked subsampling (SRS)’, which surpasses the widely adopted ‘rarefying’ (random subsampling without replacement) in reproducibility and in safeguarding the original community structure. Here, we describe an implementation of the SRS algorithm in the ‘SRS’ R package and the ‘q2-srs’ QIIME 2 plugin. We also provide accessory functions for dataset exploration to guide the choice of parameters for SRS
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