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Data from: Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7–38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

Data from: Initial colonization, community assembly, and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate

Priority effects are an important ecological force shaping biotic communities and ecosystem processes, in which the establishment of early colonists alters the colonization success of later-arriving organisms via competitive exclusion and habitat modification. However, we do not understand which biotic and abiotic conditions lead to strong priority effects and lasting historical contingencies. Using saprotrophic fungi in a model leaf decomposition system, we investigated whether compositional and functional consequences of initial colonization were dependent on initial colonizer traits, resource availability or a combination thereof. To test these ideas, we factorially manipulated leaf litter biochemistry and initial fungal colonist identity, quantifying subsequent community composition, using neutral genetic markers, and community functional characteristics, including enzyme potential and leaf decay rates. During the first 3 months, initial colonist respiration rate and physiological capacity to degrade plant detritus were significant determinants of fungal community composition and leaf decay, indicating that rapid growth and lignolytic potential of early colonists contributed to altered trajectories of community assembly. Further, initial colonization on oak leaves generated increasingly divergent trajectories of fungal community composition and enzyme potential, indicating stronger initial colonizer effects on energy-poor substrates. Together, these observations provide evidence that initial colonization effects, and subsequent consequences on litter decay, are dependent upon substrate biochemistry and physiological traits within a regional species pool. Because microbial decay of plant detritus is important to global C storage, our results demonstrate that understanding the mechanisms by which initial conditions alter priority effects during community assembly may be key to understanding the drivers of ecosystem-level processes.

Data from: A deteriorating state of affairs: how endogenous and exogenous factors determine plant decay rates

Woody plants store large quantities of carbon (C) and nutrients. As plants senesce and decay, these stores transfer to the soil or other organisms or are released to the atmosphere. Exogenous factors such as topographic position and microclimatic and edaphic conditions tied to locations affect decay rates; however, we know less about how exogenous relative to endogenous factors such as morphological, anatomical and chemical construction tied to plant species affect these rates, especially across different tissue types. We monitored stem, fine branch and leaf decay over 1 year in 'rot plots' distributed across four watersheds in ridge top and valley bottom habitats in a temperate deciduous oak-hickory forest at Tyson Research Center, MO, USA, in the Ozark Highlands for 21 species of woody plants that vary in their constructions. We found poor coordination across tissues in construction and decay, which likely reflects how functional constraints on living tissues influence recalcitrance to decay. Additionally, for all three tissues, species membership and construction were better predictors of decay than was location. Of the construction traits, chemical composition including total fibre, lignin, cellulose, hemicellulose and concentrations of multiple microelements were the best predictors of decay, although the strength of these relationships differed among tissues. Synthesis. We have long known that rates of biogeochemical cycling are influenced by exogenous factors, such as climatic and edaphic factors. Here, we show across plant tissues that endogenous factors, including species identity and tissue construction, can have stronger controls on rates of decay within our study system than do exogenous factors. However, it is likely that the relative strengths of these different controls change through time and among tissues. We predict that anatomical and morphological controls may be more important at early stages and exogenous factors may be more important at later stages of decay.

opencc-zeroDec 2017View details →

Data from: Agri-environmental schemes promote ground-dwelling predators in adjacent oilseed rape fields: diversity, species traits and distance-decay functions

1. Rising demands for agricultural products and high environmental costs of intensive agriculture reinforce the need for ecological replacements in agricultural management. In Europe, agri-environmental schemes (AES) are implemented to enhance species richness and provision of ecosystem services, but the effectiveness of different AES types and the spatial extent of possible beneficial effects are little understood. In this study we assessed the effects of different AES types on diversity, species traits and distance-decay functions of ground- dwelling predators in adjacent crop fields. 2. On 31 study sites with winter oilseed rape (OSR) adjacent to four types of AES differing in management intensity and habitat age we recorded ground-dwelling predators (carabid beetles, staphylinid beetles and spiders) during OSR growth from April to July. Effects of the AES on species richness, activity densities and different traits of these taxa were examined with transects of pitfall traps running along a continuous distance gradient from the AES across the habitat border into the OSR fields. 3. Ground-dwelling predator communities benefitted similarly from the different AES types. In adjacent OSR, activity densities, carabid species richness and the proportion of predatory carabid beetles declined from the field edge while mean body size increased. Adjacent AES increased the proportion of predatory species and simultaneously decreased the proportion of granivorous or frugivorous species in adjacent OSR fields. 4. Synthesis and applications. Our results indicate a beneficial effect of adjacent agri-environmental schemes (AES) on ground-dwelling predators in oilseed rape (OSR), mostly irrespective of AES type and therefore management intensity and habitat age. The short-ranged distance decay effects on natural enemies in OSR underpin that a strategic spatial placement of AES in agricultural landscapes is required to maximise biological pest control. This could help replace anthropogenic input in modern agriculture and secure adequate yields.

opencc-zeroDec 2016View details →

Data from: The mutational decay of male-male and hermaphrodite-hermaphrodite competitive fitness in the androdioecious nematode C. elegans

Androdioecious Caenorhabditis have a high frequency of self-compatible hermaphrodites and a low frequency of males. The effects of mutations on male fitness are of interest for two reasons. First, when males are rare, selection on male-specific mutations is less efficient than in hermaphrodites. Second, males may present a larger mutational target than hermaphrodites because of the different ways in which fitness accrues in the two sexes. We report the first estimates of male-specific mutational effects in an androdioecious organism. The rate of male-specific inviable or sterile mutations is ≤ 5 x 10-4/generation, below the rate at which males would be lost solely due to those kinds of mutations. The rate of mutational decay of male competitive fitness is ~0.17%/generation; that of hermaphrodite competitive fitness is ~0.11%/generation. The point estimate of ~1.5X faster rate of mutational decay of male fitness is nearly identical to the same ratio in Drosophila. Estimates of mutational variance (VM) for male mating success and competitive fitness are not significantly different from zero, whereas VM for hermaphrodite competitive fitness is similar to that of non-competitive fitness. Two independent estimates of the average selection coefficient against mutations affecting hermaphrodite competitive fitness agree to within two-fold, 0.33%-0.5%.

opencc-zeroDec 2009View details →

Data from: Nonsense-mediated decay enables intron gain in Drosophila

Intron number varies considerably among genomes, but despite their fundamental importance, the mutational mechanisms and evolutionary processes underlying the expansion of intron number remain unknown. Here we show that Drosophila, in contrast to most eukaryotic lineages, is still undergoing a dramatic rate of intron gain. These novel introns carry significantly weaker splice sites that may impede their identification by the spliceosome. Novel introns are more likely to encode a premature termination codon (PTC), indicating that nonsense-mediated decay (NMD) functions as a backup for weak splicing of new introns. Our data suggest that new introns originate when genomic insertions with weak splice sites are hidden from selection by NMD. This mechanism reduces the sequence requirement imposed on novel introns and implies that the capacity of the spliceosome to recognize weak splice sites was a prerequisite for intron gain during eukaryotic evolution.

Data from: Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization

Exceptionally preserved fossils provide major insights into the evolutionary history of life. Microbial activity is thought to play a pivotal role in both the decay of organisms and the preservation of soft tissue in the fossil record, though this has been the subject of very little experimental investigation. To remedy this, we undertook an experimental study of the decay of the brine shrimp Artemia, examining the roles of autolysis, microbial activity, oxygen diffusion and reducing conditions. Our findings indicate that endogenous gut bacteria are the main factor controlling decay. Following gut wall rupture, but prior to cuticle failure, gut-derived microbes spread into the body cavity, consuming tissues and forming biofilms capable of mediating authigenic mineralization, that pseudomorph tissues and structures such as limbs and the haemocoel. These observations explain patterns observed in exceptionally preserved fossil arthropods. For example, guts are preserved relatively frequently, while preservation of other internal anatomy is rare. They also suggest that gut-derived microbes play a key role in the preservation of internal anatomy and that differential preservation between exceptional deposits might be because of factors that control autolysis and microbial activity. The findings also suggest that the evolution of a through gut and its bacterial microflora increased the potential for exceptional fossil preservation in bilaterians, providing one explanation for the extreme rarity of internal preservation in those animals that lack a through gut.

opencc-zeroDec 2016View details →

Data from: Quantifying and modelling decay in forecast proficiency indicates the limits of transferability in land-cover classification

1. The ability to provide reliable projections for the current and future distribution patterns of land-covers is fundamental if we wish to protect and manage our diminishing natural resources. Two inter-related revolutions made map productions feasible at unprecedented resolutions- the availability of high-resolution remotely-sensed data and the development of machine-learning algorithms. However, the ground-truth data needed for training models is in most cases spatially and temporally clustered. Therefore, map production requires extrapolation of models from one place to another and the uncertainty cost of such extrapolation is rarely explored. In other words, we focus mainly on projections, and less on quantifying how reliable they are. 2. Following the concept of 'forecast horizon', we suggest that the predictability of land-cover classification models should be methodologically explored with quantitative tools as a continuum against distances measured along multiple dimensions. Focusing on ten agricultural sites from England and using models specifically designed to predict multivariate decay-curves we ask: how does a model's predictive performance decay with distance? More specifically, we explored if we could predict the proficiency (kappa statistics) of a model trained in one site when making predictions in another site based on the spatial, temporal, spectral and environmental distances between sites. 3. We found that model proficiency decays with spatial, temporal, spectral and environmental distance between sites. More importantly, we found for the first time that it is possible to predict the performance a model transferred to or from a novel site will have, based on its distances from known sites. The spatial distance variables where the most important when predicting model transferability. 4. Exploring model transferability as a continuum may have multiple usages including predicting uncertainty values in space and time, prioritization of strategies for ground-truth data collection, and optimizing model characteristics for defined tasks.

opencc-zeroDec 2015View details →

Data from: Decaying of Artemia salina in clay colloids: 14-month experimental formation of subfossils

The mechanism that guides the formation of exceptionally preserved fossils with soft tissues variously displayed is a paramount challenge to paleontology. The key question for exceptional preservation is the nature of the slowdown of decay and acceleration of soft tissue mineralization. Here we report the experimental formation of subfossils of the brine shrimp Artemia salina (Crustacea, Branchiopoda), which were produced during 14 months of aging in a kaolinite clay sediment. EDS/SEM elemental analyses showed that the subfossils were preserved as thin clay-organic replicas that displayed fine anatomical details. Decomposition in the clay-colloidal solution established highly heterogeneous acidic conditions, with the lowest pH typically found in the vicinity of the buried organisms, and visually manifested in patchy coloration of the sediment. Elevated acidity is likely what ultimately slowed the decay. An acidic environment increases the rate of clay destruction and, consequently, the diffusion rate decline. As a result, the acidic products quickly accumulate around a buried body; this in turn inhibits bacterial proliferation, accelerates the acidic hydrolysis of clay and, accordingly, the release of tanning and mineralizing agents. The subfossils remained stable under experimental high pressure and temperature. These model subfossils exhibit features that are typical of some Lagerstätten fossils preserved in fine-grained sediments.

opencc-by-4.0Mar 2024View details →

Dataset: Modelling Seepage Erosion in Porous Media with a Linear Decay Function

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opennotspecifiedSep 2014View details →

Fig. 1 in Stephanopachys conicolaFisher (Coleoptera: Bostrichidae) Feeding on Decaying Western Juniper (Juniperus occidentalisHooker) Berries: A Novel Association for Bostrichidae

Fig. 1. Stephanopachys conicola, lateral and dorsal views.

opencc-by-4.0Nov 2023View details →

Fluorescence decay kinetics at 516nm

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opencc-by-4.0Nov 2023View details →

Fluorescence decay kinetics at 610nm

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opennotspecifiedDec 2015View details →

Figure 1 in Radon and material radiopurity assessment for the NEXT double beta decay experiment

Figure 1 Geogcaphic position of Ciecca NanchititSa NatucaS Pack (CNNP) in centcaS Mexico.

Figure 2 from: Shen H-W, Bao D-F, Boonmee S, Lu Y-Z, Su X-J, Li Y-X, Luo Z-L (2024) Diversity of Distoseptispora (Distoseptisporaceae) taxa on submerged decaying wood from the Red River in Yunnan, China. MycoKeys 102: 1-28. https://doi.org/10.3897/mycokeys.102.116096

Figure 2 Distoseptispora bambusae (HKAS 125826) a, b colonies on woody substrates c–e conidiophores f, g conidiogenous cells h–m conidia n germinated conidium o culture on PDA. Scale bars: 50 μm (c–e); 10 μm (f, g); 20 μm (h–n).

Figure 1 from: Shen H-W, Bao D-F, Boonmee S, Lu Y-Z, Su X-J, Li Y-X, Luo Z-L (2024) Diversity of Distoseptispora (Distoseptisporaceae) taxa on submerged decaying wood from the Red River in Yunnan, China. MycoKeys 102: 1-28. https://doi.org/10.3897/mycokeys.102.116096

Figure 1 Maximum likelihood (ML) tree is based on combined LSU, ITS, tef1-α and rpb2 sequence data. Bootstrap support values with a ML greater than 65% and Bayesian posterior probabilities (PP) greater than 0.95 are given above the nodes, shown as "ML/PP". The tree is rooted to Aquapteridospora fusiformis (MFLUCC 18–1606) and A. lignicola (MFLUCC 15–0377). New species are indicated in blue and type strains are in bold.

Figure 5 from: Shen H-W, Bao D-F, Boonmee S, Lu Y-Z, Su X-J, Li Y-X, Luo Z-L (2024) Diversity of Distoseptispora (Distoseptisporaceae) taxa on submerged decaying wood from the Red River in Yunnan, China. MycoKeys 102: 1-28. https://doi.org/10.3897/mycokeys.102.116096

Figure 5 Distoseptispora pachyconidia (HKAS 125824) a, b colonies on woody substrates c conidiophores e conidiophores with conidia d conidiogenous cells f, g conidia h germinated conidium i culture on PDA. Scale bars: 20 μm (c, d); 60 μm (e–h).

Figure 7 from: Shen H-W, Bao D-F, Boonmee S, Lu Y-Z, Su X-J, Li Y-X, Luo Z-L (2024) Diversity of Distoseptispora (Distoseptisporaceae) taxa on submerged decaying wood from the Red River in Yunnan, China. MycoKeys 102: 1-28. https://doi.org/10.3897/mycokeys.102.116096

Figure 7 Distoseptispora suae (ex-type culture KUNCC 22–12476) a culture on PDA, obverse (left) and reverse (right) b, c colonies on PDA d mycelium from PDA e mycelium, conidiophores and conidia f conidiophore g–j conidiophores with conidia (Arrow in i, j indicate the gelatinous sheath) k conidia. Scale bars: 10 μm (d); 40 μm (e); 20 μm (f–k).

Figure 4 from: Shen H-W, Bao D-F, Boonmee S, Lu Y-Z, Su X-J, Li Y-X, Luo Z-L (2024) Diversity of Distoseptispora (Distoseptisporaceae) taxa on submerged decaying wood from the Red River in Yunnan, China. MycoKeys 102: 1-28. https://doi.org/10.3897/mycokeys.102.116096

Figure 4 Distoseptispora obpyriformis (HKAS 125823) a, b colonies on woody substrates c conidiophores d, e conidiophores with conidia f conidiogenous cell g–j conidia k germinating conidium l culture on PDA. Scale bars: 30 μm (c–e, g–k); 20 μm (j).

Figure 6 from: Shen H-W, Bao D-F, Boonmee S, Lu Y-Z, Su X-J, Li Y-X, Luo Z-L (2024) Diversity of Distoseptispora (Distoseptisporaceae) taxa on submerged decaying wood from the Red River in Yunnan, China. MycoKeys 102: 1-28. https://doi.org/10.3897/mycokeys.102.116096

Figure 6 Distoseptispora suae (HKAS 125819, holotype) a, b colonies on woody substrates c–e conidiophores and conidiogenous cells f–k conidia l germinated conidium m culture on PDA. Scale bars: 10 μm (c–l).