Landscape perspectives on agricultural intensification and biodiversity – ecosystem service management

Understanding the negative and positive effects of agricultural land use for the conservation of biodiversity, and its relation to ecosystem services, needs a landscape perspective. Agriculture can contribute to the conservation of high‐diversity systems, which may provide important ecosystem services such as pollination and biological control via complementarity and sampling effects. Land‐use management is often focused on few species and local processes, but in dynamic, agricultural landscapes, only a diversity of insurance species may guarantee resilience (the capacity to reorganize after disturbance). Interacting species experience their surrounding landscape at different spatial scales, which influences trophic interactions. Structurally complex landscapes enhance local diversity in agroecosystems, which may compensate for local high‐intensity management. Organisms with high‐dispersal abilities appear to drive these biodiversity patterns and ecosystem services, because of their recolonization ability and larger resources experienced. Agri‐environment schemes (incentives for farmers to benefit the environment) need to broaden their perspective and to take the different responses to schemes in simple (high impact) and complex (low impact) agricultural landscapes into account. In simple landscapes, local allocation of habitat is more important than in complex landscapes, which are in total at risk. However, little knowledge of the relative importance of local and landscape management for biodiversity and its relation to ecosystem services make reliable recommendations difficult.     

Contrasting responses of arable spiders to the landscape matrix at different spatial scales

Aim Animal communities can be influenced by the composition of the surrounding landscape through immigration. Depending on habitat preferences, however, the effect of the landscape matrix can be positive or negative and can vary with scale. We tested this idea with arable spiders and tried to infer dispersal distances from relationships between local density and landscape composition at different spatial scales. Location Thirty‐eight landscapes around the cities of Göttingen and Giessen, Germany. Methods Spiders were captured with pitfall traps in one field of winter wheat in each landscape. Landscape composition around the fields was characterized at 11 scales from 95 m to 3 km radius by land‐use mapping and subsequent GIS analysis. Correlation tests were performed between landscape composition and local densities or species richness. Results In both study regions, local species richness was enhanced by non‐crop habitats on a landscape scale. The overall densities of wolf spiders (Lycosidae), long‐jawed spiders (Tetragnathidae), crab spiders (Thomisidae), and dwarf sheet spiders (Hahniidae) increased significantly in landscapes with high percentages of non‐crop habitats. Out of the 40 species tested, 19 responded positively to the percentage of non‐crop habitats in the surrounding landscape, and five responded negatively. Depending on the species, the spatial scales with the highest explanatory power ranged from 95 m to 3 km radius around the study fields, potentially reflecting dispersal distances. Main conclusions Arable spider species showed contrasting responses to the landscape context with respect both to the direction and to the spatial scale of the relationship. The variation in landscape requirements among species ensures high spider densities in a wide range of situations, which contributes to ecosystem resilience. However, species richness of arable spiders depends on heterogeneous landscapes with high percentages of non‐crop habitats.     

Long-term orchard groundcover management systems affect soil microbial communities and apple replant disease severity

Apple replant disease (ARD) is a soil-disease syndrome of complex etiology that affects apple tree roots in replanted orchards, resulting in stunted tree growth and reduced yields. To investigate whether different groundcover management systems (GMSs) influence subsequent ARD severity, we grew apple seedlings in an outdoor nursery in pots containing orchard soil from field plots where four GMSs had been maintained for 14 years in an orchard near Ithaca, NY, USA. The GMS treatments were: (1) pre-emergence herbicide (Pre-H), bare soil strips maintained by applying tank-mixed glyphosate, norflurazon and diuron herbicides annually; (2) post-emergence herbicide (Post-H), sparse weed cover maintained by applying glyphosate in May and July each year; (3) mowed sod grass (Mowed Sod); and (4) bark mulch (Mulch). Soils were also sampled from the grass drive lane maintained between the trees in the orchard (Grass Lane). Sampled soils (Orchard soil) were either pasteurized or left untreated, placed into 4-L pots, and planted with one apple seedling per pot. After 3 months of growth, soil (Bioassay soil) and apple tree roots (Bioassay roots) were sampled from each pot and microbial populations colonizing samples were characterized. Seedling growth was reduced in soils sampled from all four GMS treatments compared to the Grass Lane soils. Among the GMS treatments, seedling biomass was greater in Pre-H than in the Post-H soil. Soil microbial communities and nutrient availability differed among all four GMS treatments and the Grass Lane. Root-lesion (Pratylenchus sp.) nematode populations were higher in the Mowed Sod than in the other GMS treatments. Soil bacterial and fungal community composition was assessed in Orchard and Bioassay soils and Bioassay roots with a DNA fingerprinting method (T-RFLP). Redundancy analysis indicated that soils sampled from the different GMS treatments differentially influenced seedling biomass. A clone library of 267 soil bacteria was developed from sampled Orchard soils and Bioassay roots. These communities were dominated by Acidobacteria (25% of sequences), Actinobacteria (19%), δ-Proteobacteria (12%), β-Proteobacteria (10%), and these ratios differed among the GMS soils. Members of the family Comamonadaceae were detected only in tree-row soil, not in the Grass Lanes. The dominant sequences among 145 cloned fungi associated with apple seedling roots were Fusarium oxysporum (16% of sequences), an uncultured soil fungus submitted under DQ420986 (12%), and Rhodotorula mucilaginosa (9%). In a redundancy analysis, factors including fungal and oomycete community compositions, soil respiration rates, population sizes of culturable bacteria and fungi, soil organic matter content, and nutrient availability, were not significant predictors of apple seedling biomass in these soils. Different GMS treatments used by apple growers may influence subsequent ARD severity in replanted trees, but edaphic factors commonly associated with soil fertility may not reliably predict tree-root health and successful establishment of replanted orchards.     

let‐7 regulates radial migration of new‐born neurons through positive regulation of autophagy

During adult neurogenesis, newly formed olfactory bulb (OB) interneurons migrate radially to integrate into specific layers of the OB. Despite the importance of this process, the intracellular mechanisms that regulate radial migration remain poorly understood. Here, we find that microRNA (miRNA) let‐7 regulates radial migration by modulating autophagy in new‐born neurons. Using Argonaute2 immunoprecipitation, we performed global profiling of miRNAs in adult‐born OB neurons and identified let‐7 as a highly abundant miRNA family. Knockdown of let‐7 in migrating neuroblasts prevented radial migration and led to an immature morphology of newly formed interneurons. This phenotype was accompanied by a decrease in autophagic activity. Overexpression of Beclin‐1 or TFEB in new‐born neurons lacking let‐7 resulted in re‐activation of autophagy and restored radial migration. Thus, these results reveal a miRNA‐dependent link between autophagy and adult neurogenesis with implications for neurodegenerative diseases where these processes are impaired.     

The clubroot pathogen Plasmodiophora brassicae: A profile update

Background

Plasmodiophora brassicae is the causal agent of clubroot disease of cruciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide.

Disease symptoms

In the advanced stages of clubroot disease wilting, stunting, yellowing, and redness are visible in the shoots. However, the typical symptoms of the disease are the presence of club-shaped galls in the roots of susceptible hosts that block the absorption of water and nutrients.

Host range

Members of the family Brassicaceae are the primary host of the pathogen, although some members of the family, such as Bunias orientalis, Coronopus squamatus, and Raphanus sativus, have been identified as being consistently resistant to P. brassicae isolates with variable virulence profile.

Taxonomy

Class: Phytomyxea; Order: Plasmodiophorales; Family: Plasmodiophoraceae; Genus: Plasmodiophora; Species: Plasmodiophora brassicae (Woronin, 1877).

Distribution

Clubroot disease is spread worldwide, with reports from all continents except Antarctica. To date, clubroot disease has been reported in more than 80 countries.

Pathotyping

Based on its virulence on different hosts, P. brassicae is classified into pathotypes or races. Five main pathotyping systems have been developed to understand the relationship between P. brassicae and its hosts. Nowadays, the Canadian clubroot differential is extensively used in Canada and has so far identified 36 different pathotypes based on the response of a set of 13 hosts.

Effectors and resistance

After the identification and characterization of the clubroot pathogen SABATH-type methyltransferase PbBSMT, several other effectors have been characterized. However, no avirulence gene is known, hindering the functional characterization of the five intercellular nucleotide-binding (NB) site leucine-rich-repeat (LRR) receptors (NLRs) clubroot resistance genes validated to date.

Important Link

Canola Council of Canada is constantly updating information about clubroot and P. brassicae as part of their Canola Encyclopedia: https://www.canolacouncil.org/canola-encyclopedia/diseases/clubroot/ .

Phytosanitary categorization

PLADBR: EPPO A2 list; Annex designation 9E.     

Perturbed angular correlation studies of the metal-binding sites in ovotransferrin and its C- and N-terminal halves

The perturbed angular correlation (PAC) technique has been applied to study the electric quadrupole interaction of ¹⁸¹Hf nuclei at the binding sites of ovotransferrin (OTF) molecules. Two specific electric field gradients were observed. Their relative intensities depend on the pH value and the temperature of the samples, whereas the electric quadrupole interaction parameters themselves remain unaffected. In order to compare the binding sites in OTF, experiments with N- and C-terminal half-molecules were performed. Both specific configurations are observed at the N-terminal and at the C-terminal binding site with similar quadrupole parameters as for the intact protein. Remarkably, the stability of the hafnium binding to the C-terminal fragment appears to be reduced as compared with the N-terminal half and the intact protein.     

Diatom-inferred productivity changes in the eastern equatorial Pacific: The quaternary record of ODP leg 111, site 677

Recent marine planktonic diatom assemblages from 47 sediment surface samples retrieved from the eastern equatorial Pacific yielded four significant Q-mode factors that are related to surface water properties. They include a northern subtropical (Factor 1), a southern subtropical (Factor 2), a Peru Current (Factor 3) and an eastern Equatorial Pacific (Factor 4) factor.A transfer function (based on 42 surface sediment samples) with a productivity range of 109 to 210 gC m^–2 y^–1 was defined using the geographic distribution of the northern and southern subtropical assemblages (Factor 1 and 2) and their relation to mapped surface water primary productivity. This transfer function has a standard error of estimate of 11.9 gC m^–2 y^–1 and it is used to estimate late Pleistocene paleo-productivity changes at ODP Leg 111 Site 677 off Ecuador.The Site 677 samples (usually spaced 10 cm apart and with a linear sedimentation rate of 4.3 cm y^–3) were the same samples that were used for stable oxygen/carbon isotopic analysis from planktonic Foraminifera. The well constrained oxygen isotope stratigraphy permitted assignment of accurate ages to downcore samples.The interval between oxygen isotope stages 3 and 9 had variable productivity that is generally higher than present values of 175 gC m^–2 y^–1 A major decline in paleo-productivity below the present value occurred in stage 9, the early part of stage 8 and in the early and late stage 5.     

Subgroups of the Cowpea Miscellany: Symbiotic Specificity within Bradyrhizobium spp. for Vigna unguiculata, Phaseolus lunatus, Arachis hypogaea, and Macroptilium atropurpureum

Rhizobia classified as Bradyrhizobium spp. comprise a highly heterogeneous group of bacteria that exhibit differential symbiotic characteristics on hosts in the cowpea miscellany cross-inoculation group. To delineate the degree of specificity exhibited by four legumes in the cowpea miscellany, we tested the symbiotic characteristics of indigenous cowpea bradyrhizobia on cowpea (Vigna unguiculata), siratro (Macroptilium atropurpureum), lima bean (Phaseolus lunatus), and peanut (Arachis hypogaea). The most-probable-number counts of indigenous bradyrhizobia at three sites on Maui, Hawaii, were substantially different on the four hosts: highest on siratro, intermediate on cowpea, and significantly lower on both lima bean and peanut. Bradyrhizobia from single cowpea nodules from the most-probable-number assays were inoculated onto the four hosts. Effectiveness patterns of these rhizobia on cowpea followed a normal distribution but were strikingly different on the other legumes. The effectiveness profiles on siratro and cowpea were similar but not identical. The indigenous cowpea-derived bradyrhizobia were of only moderate effectiveness on siratro and were in all cases lower than the inoculant-quality reference strain. Between 5 and 51% of the bradyrhizobia, depending on site, failed to nodulate peanut, whereas 0 to 32% failed to nodulate lima bean. No significant correlation was observed between the relative effectiveness of the bradyrhizobia on cowpea and their corresponding effectiveness on either lima bean or peanut. At all sites, bradyrhizobia that were ineffective on cowpea but that effectively nodulated lima bean, peanut, or both were found. Eighteen percent or fewer of the bradyrhizobia were as effective on lima bean as the reference inoculant strain; 44% or fewer were as effective on peanut as the reference strain. Only 18% of all cowpea-derived bradyrhizobia tested were able to form N(2)-fixing nodules on both lima bean and peanut. These results indicate the need to measure indigenous bradyrhizobial population characteristics directly with the crop of interest to obtain an accurate assessment of the need to inoculate.     

Influence of protein dynamics on the metal-sites of ovotransferrin

Using the perturbed angular correlations (PAC) technique, the formation of hafnium-ovotransferrin complexes has been studied. Two binding configurations at each of the two specific binding-sites of the protein have been observed. They are characterized by well-defined electric quadrupole frequencies. Information about the dynamics of the protein was derived from temperature dependent measurements of the relaxation constant. The well-resolved spectra taken with fast BaF₂-detectors allow a precise determination of the relaxation behaviour of the protein. The results are compared with the predictions from a hydrodynamic model for the reorientation of macromolecules. Thus the hydrodynamic volume of ovotransferrin and its N-terminal half-molecule were determined. The ovotransferrin volume is in agreement with a value derived for human serum transferrin from small angle neutron scattering. From experiments with immobilized protein material there is evidence for internal protein dynamics which is probed by the Hf-ion bound to the specific metal-sites.Abbreviations PAC perturbed angular correlations technique - TF serum transferrin - LF lactoferrin - OTF ovotransferrin - OTF/2N N-terminal half-molecule of ovotransferrin - NQR nuclear quadrupole resonance - EFG electric field gradient - NQI nuclear quadrupole interaction - NTA nitrilotriacetate - MES 2-(N-morpholino)ethanesulphonic acid - HEPPS N-2-hydroxyethyl-piperazine-N-3-propanesulphonic acid - TRIS tris(hydroxymethyl)aminomethane Correspondence to: F. J. Schwab.     

Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection

MOTIVATION: The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions. We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks. The proposed approach is based on both microarray data and available biological knowledge. RESULTS: The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series). The number of clusters was optimized using various evaluation criteria. For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge. Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes. For the construction of hypothetical network structures singular value decomposition (SVD) based methods and a newly introduced heuristic Network Generation Method here were compared. It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. CONTACT: Reinhard.Guthke@hki-jena.de.