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opencc-zeroApr 2022View details →

Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

opencc-zeroApr 2022View details →

Community composition of bacteria isolated from Swiss banknotes varies depending on collection environment

Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae and Staphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.

opencc-zeroDec 2021View details →

Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings

The assembly of root-associated microbes during the seedling stage has strong impact on subsequent performance of crops. Major factors influencing this assembly are crop species identity and composition of potential root-colonizing microbes in the bulk soil. The latter can be modified by soil management, such as organic amendments. The incorporation of residues of cover crops before the start of the growing season of cash crops presents an interesting option for steering of root-associated seedling microbiomes as there is a wide range of cover crops species with different properties available for farmers. In a greenhouse study, we examined the effect of soil amendments with milled shoot and root materials of seven cover crop species (niger seed, phacelia, rapeseed, radish, vetch, black oat and buckwheat) on the soil nitrogen and biomass of seedlings of four cash crop species (asparagus, carrot, onion and sugar beet) and their root-associated bacteria and fungi. Field-grown cover crops material used for the study was collected at two time points (before and after winter) which had strong impact on plant elemental composition. Since the soil used for the study was a mixture of sandy arable soils with a history of soil-borne fungal diseases (Fusarium and Rhizoctonia), we also examined whether decomposing cover crop residues had an influence on the severity of damping-off diseases. Within the context of a strong selection of root-associated microbes by cash crop species, we found significant modifying effects by cover crop materials. High-quality residues (with low C/N ratio) caused profound shifts within root-associated Proteobacteria and increases in relative abundance of certain microbial groups such as Bacillaceae and Mortierellomycetes. These changes coincided with differences in establishment and survival of cash crop seedlings. This indicates that fine-tuning of cover crops amendments for different cash crops is required to realize enhanced functioning of root microbiomes.

opencc-zeroDec 2021View details →

Dataset for: Interactive effects of tree species composition and water availability on growth and direct and indirect defences in Quercus ilex

Plant diversity has often been reported to decrease insect herbivory in plants. Of the numerous mechanisms that have been proposed to explain this phenomenon, how plant diversity influences plant defences via effects on growth has received little attention. In addition, plant diversity effects may be contingent on abiotic conditions (e.g., resource and water availability). Here, we used a long-term experiment to explore the interactive effects of tree species composition and water availability on growth, direct (i.e. phenolics) and indirect (i.e. Volatile Organic Compounds – VOCs) defences and leaf herbivory in Quercus ilex. We quantified herbivory by chewing insects, phenolic compounds and VOCs in Q. ilex trees growing in stands differing in tree species composition (Q. ilex, Q. ilex + Betula Pendula, Q. ilex + Pinus pinaster and Q. ilex + B. pendula + P. pinaster) and water availability (irrigated vs control). Both direct and indirect defences were affected by tree species composition, but such changes were not mediated by changes in tree stem diameter. Q. ilex trees growing in stands with P. pinaster had the lowest concentration of both direct and indirect defences. Importantly, the effects of tree species composition on VOCs were exacerbated on irrigated blocks. Despite variation in defences, tree species composition did not affect herbivory in Q. ilex. Accordingly, we did not find any association between defences and insect herbivory. Our results suggest that changes in the micro-environment rather than growth-defence associations may mediate tree diversity effects on defences. In addition, reduced defensive investment in more diverse stands could negatively impact tree resistance masking the beneficial effects of species diversity at reducing insect herbivory.

opencc-by-4.0Apr 2022View details →

Fire exclusion changes belowground bud bank and bud-bearing organ composition jeopardizing open savanna resilience

Dataset from the article: Bombo, A.B.; Appezzato-da-Glória, B.; Fidelis, A. (2022) Fire exclusion changes belowground bud bank and bud-bearing organ composition jeopardizing open savanna resilience. Oecologia DOI 10.1007/s00442-022-05172-1, Article type: Community ecology – original research.

opencc-zeroDec 2017View details →

Data from: The mesic savannas of the Bateke Plateau: carbon stocks and floristic composition

The Bateke Plateau in the Republic of Congo is one of the last frontiers for ecology, with little known about its floristics and physiognomy. Despite occupying 89,800 km2 and its importance for local livelihoods, its ecology and ecosystem functions are poorly understood. Situated on Kalahari sands, the Bateke has a complex evolutionary history, mainly isolated from other savannas for much of its past, with currently unresolved ecological implications. Here we assess the biomass and floristic diversity of this savanna. We established four 25 ha permanent sample plots at two savanna sites, inventoried all trees, and assessed shrub, forb and grass species and biomass, and characterised the soils. Total plant carbon stocks (aboveground and belowground) were only 6.5 ± 0.3 MgC/ha, despite precipitation of 1600 mm/yr. Over half the biomass was grass, with the remainder divided between trees and shrubs. The carbon stock of the system is mostly contained in the top layer of the soil (16.7 ± 0.9 MgC/ha in 0-20 cm depth). We identified 49 plant species (4 trees, 13 shrubs, 4 sedges, 17 forbs and 11 grass species), with an average species richness of 23 per plot. There is tree hyperdominance of Hymenocardia acida (Phyllanthaceae), and a richer herbaceous species composition dominated by Loudetia simplex and Hyparrhenia diplandra. The low carbon stocks and tree biodiversity, compared to other African savannas, is surprising considering the high rainfall. We speculate it is due to low nutrient soils, high fire frequency and the effect of a temporally variable and restricted connection to the main southern African savanna complex.

opencc-zeroApr 2022View details →

Lichen holobionts show compositional structure along elevation

Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here we assess how the major components of lichen holobionts – fungal hosts, green algal symbionts, and the bacterial community – collectively respond to an elevational gradient. We analyze populations of two lichen symbioses, Umbilicaria pustulata and U. hispanica, along an elevational gradient spanning 2100 altitudinal meters and covering three major biomes. Our study shows (i) discontinuous genomic variation in fungal hosts with one abrupt genomic differentiation within each of the two host species, (ii) altitudinally structured bacterial communities with pronounced turnover within and between hosts, and (iii) altitude-specific presence of algal symbionts. Alpha diversity of bacterial communities decreased with increasing elevation. A marked turnover in holobiont diversity occurred across two altitudinal belts: at 11-13°C average annual temperature (here: 800-1200m a.s.l.), and at 7-9°C average annual temperature (here: 1500-1800m a.s.l.). The two observed zones mark a clustering of distribution limits and community shifts. The three ensuing altitudinal classes, i.e. the most frequent combinations of species in holobionts, approximately correspond to the Mediterranean, cool-temperate, and alpine climate zones. We conclude that multitrophic microecosystems, such as lichen holobionts, respond with concerted compositional changes to climatic factors that also structure communities of macroorganisms, e.g. vascular plants.

opencc-by-4.0May 2022View details →

Photographic data on the influence of the composition, preparation method, time and fuel system on the size of water droplets in a fuel-water emulsion

This data was collected during the research aimed at understanding the influence of the composition, mixing time and time between the production and application of the fuel-water emulsion, as well as the influence of the fuel pump of the miniature gas turbine GTM-120 on the droplet size of the water-fuel emulsion. An emulsion with a water content of 3% to 15% and an emulsifier content of 1% to 3% was tested. The basic fuel in the conducted tests was Jet-A1 with 5% oil additive.

opencc-zeroMay 2022View details →

Data from: Ant community composition and functional traits in newly established grasslands within agricultural landscapes

Ongoing intensification and fragmentation of European agricultural landscapes dramatically reduce biodiversity and associated functions. Enhancing perennial non-crop areas holds great potential to support ecosystem services such as ant mediated pest control. To study the potential of newly established grassland strips to enhance ant diversity and associated functions, we used hand collection data and predation experiments to investigate differences in (a) ant community composition (b) biocontrol related functional traits, and (c) natural pest control across habitats in cereal fields, old grasslands, and new grassland transects of three years age. Whilst all data regarding biocontrol related functional traits of ant species (b) are available within the publication and its supporting information files, we provide here our raw data of ant species activity and diversity surveys (a) and further the results of sticky card experiments as a proxy for biocontrol potential (c).

FIGURE 59 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURE 59. Abundance of Steneotarsonemus spinki vs S. subfurcatus within the species complex of rice sheath mites across the different agroecological zones of West Bengal. Equal letters for each species category do not differ significantly at p<0.05.

FIGURE 58 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURE 58. Results of Non-metric multidimensional scaling (NMDS), using Bary Curtis matrix, applied to test similarity in morphological variant composition of Steneotarsonemus spinki males in Eastern India (The states are colour coded as green: West Bengal; Blue: Orissa; Yellow: Tripura; Red: Manipur).

FIGURE 57 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURE 57. Abundance of morphological variants (mean±S.E.) of Steneotarsonemus spinki male in Eastern India. Mean followed by same letter do not differ significantly at 5% level of Significance.

FIGURES 41.—47. Steneotarsonemus spinki 41 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURES 41.—47. Steneotarsonemus spinki 41—Dorsal surface (female), 42—Ventral surface (female), 43. Dorsal surface (male), 44—Ventral surface (male), 45. Leg IV (male, variant S), 46. Leg IV (male, variant I), 47. Leg IV (male, variant L).

FIGURES 38.—40 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURES 38.—40. Three variants of Steneotarsonemus spinki (male Leg IV). 38.Variant S, 49. Variant I and 40. Variant L (top to bottom).

FIGURES 53.—56. Steneotarsonemus subfurcatus 53 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURES 53.—56. Steneotarsonemus subfurcatus 53—Dorsal surface (female), 54—Ventral surface (female), 55. Dorsal surface (male), 56—Ventral surface (male).

FIGURES 28.—31 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURES 28.—31. Steneotarsonemus subfurcatus (female). 28.—leg I, 29.—leg II, 30.—leg III, 31.—leg IV.

FIGURES 34.—37 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURES 34.—37. Steneotarsonemus subfurcatus (male). 34.—leg I, 35.—leg II, 36.—leg III, 37.—leg IV.

FIGURES 48.—52. Steneotarsonemus furcatus 48 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURES 48.—52. Steneotarsonemus furcatus 48—Dorsal surface (female), 49—Ventral surface (female), 50. Dorsal surface (male), 51—Dorsal surface (male), 52. Ventral surface (male).

FIGURE 1 in Complementary description of three species of Steneotarsonemus (Acari: Tarsonemidae) from rice agroecosystems of Eastern India with notes on their taxonomic status, spatial distribution, intraspecific variation and species composition

FIGURE 1. Map of India depicting the locations of survey areas from where the specimens were collected.