Browsing by Subject "TURNOVER"

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  • Becker, Isabelle C.; Scheller, Inga; Wackerbarth, Lou M.; Beck, Sarah; Heib, Tobias; Aurbach, Katja; Manukjan, Georgi; Gross, Carina; Spindler, Markus; Nagy, Zoltan; Witke, Walter; Lappalainen, Pekka; Bender, Markus; Schulze, Harald; Pleines, Irina; Nieswandt, Bernhard (2020)
    Rearrangements of the microtubule (MT) and actin cytoskeleton are pivotal for platelet biogenesis. Hence, defects in actin- or MT-regulatory proteins are associated with platelet disorders in humans and mice. Previous studies in mice revealed that loss of the actin-depolymerizing factor homology (ADF-H) protein Cofilin1 (Cof1) in megakaryocytes (MKs) results in a moderate macrothrombocytopenia but normal MK numbers, whereas deficiency in another ADF-H protein, Twinfilin1 (Twf1), does not affect platelet production or function. However, recent studies in yeast have indicated a critical synergism between Twf1 and Cof1 in the regulation of actin dynamics. We therefore investigated platelet biogenesis and function in mice lacking both Twf1 and Cof1 in the MK lineage. In contrast to single deficiency in either protein, Twf1/Cof1 double deficiency (DKO) resulted in a severe macrothrombocytopenia and dramatically increased MK numbers in bone marrow and spleen. DKO MKs exhibited defective proplatelet formation in vitro and in vivo as well as impaired spreading and altered assembly of podosome-like structures on collagen and fibrinogen in vitro. These defects were associated with aberrant F-actin accumulation and, remarkably, the formation of hyperstable MT, which appears to be caused by dysregulation of the actin- and MT-binding proteins mDia1 and adenomatous polyposis coli. Surprisingly, the mild functional defects described for Cof1-deficient platelets were only slightly aggravated in DKO platelets suggesting that both proteins are largely dispensable for platelet function in the peripheral blood. In summary, these findings reveal critical redundant functions of Cof1 and Twf1 in ensuring balanced actin/microtubule crosstalk during thrombopoiesis in mice and possibly humans.
  • Wioland, Hugo; Guichard, Berengere; Senju, Yosuke; Myram, Sarah; Lappalainen, Pekka; Jegou, Antoine; Romet-Lemonne, Guillaume (2017)
    Actin-depolymerizing factor (ADF)/cofilins contribute to cytoskeletal dynamics by promoting rapid actin filament disassembly. In the classical view, ADF/cofilin sever filaments, and capping proteins block filament barbed ends whereas pointed ends depolymerize, at a rate that is still debated. Here, by monitoring the activity of the three mammalian ADF/cofilin isoforms on individual skeletal muscle and cytoplasmic actin filaments, we directly quantify the reactions underpinning filament severing and depolymerization from both ends. We find that, in the absence of monomeric actin, soluble ADF/cofilin can associate with bare filament barbed ends to accelerate their depolymerization. Compared to bare filaments, ADF/cofilin-saturated filaments depolymerize faster from their pointed ends and slower from their barbed ends, resulting in similar depolymerization rates at both ends. This effect is isoform specific because depolymerization is faster for ADF-than for cofilin-saturated filaments. We also show that, unexpectedly, ADF/cofilin-saturated filaments qualitatively differ from bare filaments: their barbed ends are very difficult to cap or elongate, and consequently undergo depolymerization even in the presence of capping protein and actin monomers. Such depolymerizing ADF/cofilin-decorated barbed ends are produced during 17% of severing events. They are also the dominant fate of filament barbed ends in the presence of capping protein, because capping allows growing ADF/cofilin domains to reach the barbed ends, thereby promoting their uncapping and subsequent depolymerization. Our experiments thus reveal how ADF/cofilin, together with capping protein, control the dynamics of actin filament barbed and pointed ends. Strikingly, our results propose that significant barbed-end depolymerization may take place in cells.
  • Bitu, Carolina C.; Kauppila, Joonas H.; Bufalino, Andreia; Nurmenniemi, Sini; Teppo, Susanna; Keinanen, Meeri; Vilen, Suvi-Tuuli; Lehenkari, Petri; Nyberg, Pia; Coletta, Ricardo D.; Salo, Tuula (2013)
  • Keronen, Satu; Martola, Leena; Finne, Patrik; Burton, Inari S.; Kröger, Heikki; Honkanen, Eero (2019)
    Background and objectives Over the past decade, the management of CKD-mineral and bone disorder has changed substantially, altering the pattern of bone disease in CKD. We aimed to evaluate the natural history of kidney bone disease in contemporary kidney transplant recipients and patients on dialysis. Design, settings, participants, & measurements Sixty one patients on dialysis who were referred to kidney transplantation participated in this prospective cohort study during November 2009 and December 2010. We performedbaseline bone biopsieswhile thepatientswere ondialysis andrepeatedthe procedure in 56 patients at 2 years after kidney transplantation or 2 years after baseline if transplantationwas not performed. Measurements of mineral metabolism and bone turnover, as well as dual energy x-ray absorptiometry scans, were obtained concurrently. Results A total of 37 out of 56 participants received a kidney transplant, of which 27 underwent successful repeat bone biopsy. The proportion of patients with high bone turnover declined from 63% at baseline to 19% at 2 years after kidney transplantation, whereas the proportion of thosewith lowbone turnover increased from26% to 52%. Of 19 participants remaining on dialysis after 2 years, 13 underwent successful repeat biopsy. The proportion of patients remaining on dialysis with high bone turnover decreased from 69% to 31%, and low bone turnover increased from8% to 38%. Abnormal bonemineralization increased in transplant recipients from33% to 44%, but decreased in patients remaining on dialysis from 46% to 15%. Trabecular bone volume showed little change after transplantation, but low bone volume increased in patients remaining on dialysis. Bone mineral density did not correlate with histomorphometric findings. Conclusions Bone turnover decreased over time both in patients remaining on dialysis and in kidney transplant recipients. Bone mineral density and bone biomarkers were not associated with bone metabolism changes detected in bone biopsy specimens.
  • Leboucher, Thibault; Budnick, William R.; Passy, Sophia; Boutry, Sebastien; Jannoneau, Aurelien; Soininen, Janne; Vyverman, Wim; Tison-Rosebery, Juliette (2019)
    Aim To quantify the relative contributions of local community assembly processes versus gamma-diversity to beta-diversity, and to assess how spatial scale and anthropogenic disturbance (i.e. nutrient enrichment) interact to dictate which driver dominates. Location France and the United States. Time period 1993-2011. Major taxa studied Freshwater stream diatoms. Methods beta-diversity along a nutrient enrichment gradient was examined across multiple spatial scales. beta-diversity was estimated using multi-site Sorensen dissimilarity. We assessed the relative importance of specialists versus generalists using Friedley coefficient, and the contribution of local community assembly versus gamma-diversity to beta-diversity across spatial scales, with a null model. Finally, we estimated the response of beta-diversity to environmental and spatial factors by testing the correlations between community, environmental and geographical distance matrices with partial Mantel tests. Results beta-diversity generally increased with spatial scale but the rate of increase depended on nutrient enrichment level. beta-diversity decreased significantly with increasing nutrient enrichment level due to the loss of specialist species. Local assembly was an important driver of beta-diversity especially under low nutrient enrichment. Significant partial Mantel correlations were observed between diatom beta-diversity and pure environmental distances under these conditions, highlighting the role of species sorting in local assembly processes. Conversely, in heavily enriched sites, only spatial distances were significantly correlated with beta-diversity, which indicated a substantial role of dispersal processes. Main conclusions Nutrient concentration mediated the expected increase in beta-diversity with spatial scales. Across spatial scales, beta-diversity was more influenced by local assembly processes rather than by gamma-diversity. Nutrient enrichment was associated with an overall decline in diatom beta-diversity and a shift in assembly processes from species sorting to dispersal, notably due to the elimination of some specialists and their subsequent replacement by generalists.
  • Milardi, Marco; Gavioli, Anna; Soininen, Janne; Castaldelli, Giuseppe (2019)
    Exotic species invasions often result in native biodiversity loss, i.e. a lower taxonomic diversity, but current knowledge on invasions effects underlined a potential increase of functional diversity. We thus explored the connections between functional diversity and exotic species invasions, while accounting for their environmental drivers, using a fine-resolution large dataset of Mediterranean stream fish communities. While functional diversity of native and exotic species responded similarly to most environmental constraints, we found significant differences in the effects of altitude and in the different ranking of constraints. These differences suggest that invasion dynamics could play a role in overriding some major environmental drivers. Our results also showed that a lower diversity of ecological traits in communities (about half of less disturbed communities) corresponded to a high invasion degree, and that the exotic component of communities had typically less diverse ecological traits than the native one, even when accounting for stream order and species richness. Overall, our results suggest that possible outcomes of severe exotic species invasions could include a reduced functional diversity of invaded communities, but analyzing data with finer ecological, temporal and spatial resolutions would be needed to pinpoint the causal relationship between invasions and functional diversity.
  • Mikkonen, Elisa; Haglund, Caj; Holmberg, Carina I. (2017)
    The ubiquitin-proteasome system (UPS) plays a crucial part in normal cell function by mediating intracellular protein clearance. We have previously shown that UPS-mediated protein degradation varies in a cell type-specific manner in C. elegans. Here, we use formalin-fixed, paraffin-embedded C. elegans sections to enable studies on endogenous proteasome tissue expression. We show that the proteasome immunoreactivity pattern differs between cell types and within subcellular compartments in adult wild-type (N2) C. elegans. Interestingly, widespread knockdown of proteasome subunits by RNAi results in tissue-specific changes in proteasome expression instead of a uniform response. In addition, long-lived daf-2 (e1370) mutants with impaired insulin/IGF-1 signaling (IIS) display similar proteasome tissue expression as aged-matched wild-type animals. Our study emphasizes the importance of alternate approaches to the commonly used whole animal lysate-based methods to detect changes in proteasome expression occurring at the sub-cellular, cell or tissue resolution level in a multicellular organism.
  • Koskinen, Mikko; Hotulainen, Pirta (2014)
  • Viljakainen, Heli T.; Koistinen, Heikki A.; Tervahartiala, Taina; Sorsa, Timo; Andersson, Sture; Mäkitie, Outi (2017)
    High leptin concentration, low-grade inflammation, and insulin resistance often coexist in obese subjects; this adverse metabolic milieu may be the main culprit for increased fracture risk and impaired bone quality seen in patients with type 2 diabetes. We examined the associations of leptin, hs (high sensitivity)-CRP and insulin resistance with bone turnover markers (BTMs) and bone characteristics in 55 young obese adults (median BMI 40 kg/m(2)) and 65 non-obese controls. Mean age of the subjects was 19.5 +/- 2.5 years (mean +/- SD). Concentrations of leptin, adiponectin, hs-CRP, MMP-8 and TIMP-1, fasting plasma glucose and insulin (to calculate HOMA), BTMs (BAP, P1NP, CTX-1, and TRAC5b) were measured. Bone characteristics were determined with pQCT at radius and tibia, and with DXA for central sites. Leptin, hs-CRP and HOMA correlated inversely with BTMs: the partial coefficients were 1.5-1.9 fold higher in males than in females. After adjusting for age, BMI, and other endocrine factors, leptin displayed an independent effect in males on radial bone mass (p = 0.019), tibial trabecular density (p = 0.025) and total hip BMD (p = 0.043), with lower densities in males with high leptin. In females, the model adjusting for age, BMI, and other endocrine factors, revealed that hs-CRP had independent effects on radial bone mass (p = 0.034) and lumbar spine BMD (p = 0.016), women with high hs-CRP having lower values. Partial correlations of adiponectin and TIMP-1 with bone characteristics were discrepant; MMP-8 showed no associations. In conclusion, in young obese adults and their controls, leptin, hs-CRP and HOMA associate inversely with BTMs and bone characteristics. Leptin appears to be the key independent effector in males, whereas hs-CRP displayed a predominant role in females.
  • Richter, Uwe; Ng, Kah Ying; Suomi, Fumi; Marttinen, Paula; Turunen, Taina; Jackson, Christopher; Suomalainen, Anu; Vihinen, Helena; Jokitalo, Eija; Nyman, Tuula A.; Isokallio, Marita A.; Stewart, James B.; Mancini, Cecilia; Brusco, Alfredo; Seneca, Sara; Lombes, Anne; Taylor, Robert W.; Battersby, Brendan J. (2019)
    Mitochondria have a compartmentalized gene expression system dedicated to the synthesis of membrane proteins essential for oxidative phosphorylation. Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function. Pathogenic mutations that impede the function of the mitochondrial matrix quality control protease complex composed of AFG3L2 and paraplegin cause a multifaceted clinical syndrome. At the cell and molecular level, defects to this quality control complex are defined by impairment to mitochondrial form and function. Here, we establish the etiology of these phenotypes. We show how disruptions to the quality control of mitochondrial protein synthesis trigger a sequential stress response characterized first by OMA1 activation followed by loss of mitochondrial ribosomes and by remodelling of mitochondrial inner membrane ultrastructure. Inhibiting mitochondrial protein synthesis with chloramphenicol completely blocks this stress response. Together, our data establish a mechanism linking major cell biological phenotypes of AFG3L2 pathogenesis and show how modulation of mitochondrial protein synthesis can exert a beneficial effect on organelle homeostasis.
  • Wesołowska, Karolina; Elovainio, Marko; Komulainen, Kaisla; Hietapakka, Laura; Heponiemi, Tarja (2020)
    Abstract Aim To examine: 1) whether nativity status was associated with workplace discrimination, 2) whether this association was mediated through psychosocial work characteristics (job strain, job demands and job control) among registered female nurses. Design Cross-sectional survey with a self-report questionnaire was conducted. Methods A random sample of 610 native Registered Nurses and a total sample of 188 foreign-born Registered Nurses working in Finland were used. Data were collected between September - November of 2017 and analyzed using a counterfactual approach in the causal mediation framework. Results After adjusting for several potential confounders, foreign-born nurses scored higher on workplace discrimination than native nurses. Approximately 20% of the association between nativity status and workplace discrimination was mediated through job control. Job demands and job strain were unlikely to mediate this association. Conclusion The study provides further evidence that migrant status is associated with a higher risk of workplace discrimination among nurses. Lower levels of control over one's own job may partly contribute to the higher risk of workplace discrimination in foreign-born women nurses. Impact Our study addresses the relationship between nativity status and workplace discrimination among female nurses and its mediating factors. The findings suggest that health care organization leaders need to be aware of the increased risk of workplace discrimination among migrant nurses. Moreover, health care organizations need to consider psychosocial work characteristics, including job control, in the efforts aimed to prevent and reduce discrimination against their foreign-born employees.
  • Zeleznik, Peter; Westergren, Marjana; Bozik, Gregor; Eler, Klemen; Bajc, Marko; Helmisaari, Heljä-Sisko Marketta; Horvath, Aniko; Kraigher, Hojka (2019)
    European beech (Fagus sylvatica L.) is commercially and ecologically important tree species in Central European forests but its intra-specific variability in drought and temperature tolerance might endanger its future distribution in Europe. Beech phenological and growth traits have been studied in large-scale international beech provenance trials, yet the growth and turnover of its fine roots (FR) has not been included among the observations. FR growth dynamics and FR architectural traits of three beech provenances in the international beech provenance trial Straza/Kamenski hrib, established in Slovenia in 1998, and from a natural beech regeneration site growing at its border, were studied from 2007 to 2010. We studied FR biomass using soil cores (SC), root production using ingrowth soil cores (IC), and root longevity using minirhizotrons (MR). Significant differences in FR biomass (live and dead) between the provenance P37 and other provenances were discovered in SC, FR biomass of P37 being significantly higher than FR biomass of latter, which could be connected with overall excellent growth performance of P37 due to favourable environmental conditions at trial. Values of specific root length (SRL) in IC varied significantly among P37 and P54. The turnover rates in IC were at the end of the experiment close to MR results. Median MR-based longevities of FR varied between 625 and 934 days. Survival curve of the slowest growing provenance (considering its aboveground characteristics) was significantly different from the other two, median longevities of the latter being higher. Death of FR, older than two years, occurred most likely in the winter. Our results suggest that there are significant differences in FR longevity among provenances, which might contribute to their adaptation to future environmental conditions. Furthermore, the calculated annual C investment into FR growth per ha differs up to twofold between provenances, contributing to different C dynamics of their future stands.
  • Lewandowska, Aleksandra; Jonkers, Lukas; Auel, Holger; Freund, Jan A.; Hagen, Wilhelm; Kucera, Michal; Hillebrand, Helmut (2020)
    Aim Biodiversity dynamics comprise evolutionary and ecological changes on multiple temporal scales from millions of years to decades, but they are often interpreted within a single time frame. Planktonic foraminifera communities offer a unique opportunity for analysing the dynamics of marine biodiversity over different temporal scales. Our study aims to provide a baseline for assessments of biodiversity patterns over multiple time-scales, which is urgently needed to interpret biodiversity responses to increasing anthropogenic pressure. Location Global (26 sites). Time period Five time-scales: multi-million-year (0-7 Myr), million-year (0-0.5 Myr), multi-millennial (0-15 thousand years), millennial (0-1,100 years) and decadal (0-32 years). Major taxa studied Planktonic foraminifera. Methods We analysed community composition of planktonic foraminifera at five time-scales, combining measures of standing diversity (richness and effective number of species, ENS) with measures of temporal community turnover (presence-absence-based, dominance-based). Observed biodiversity patterns were compared with the outcome of a neutral model to separate the effects of sampling resolution (the highest in the shortest time series) from biological responses. Results Richness and ENS decreased from multi-million-year to millennial time-scales, but higher standing diversity was observed on the decadal scale. As predicted by the neutral model, turnover in species identity and dominance was strongest at the multi-million-year time-scale and decreased towards the millennial scale. However, contrary to the model predictions, modern time series show rapid decadal variation in the dominance structure of foraminifera communities, which is of comparable magnitude as over much longer time periods. Community turnover was significantly correlated with global temperature change, but not on the shortest time-scale. Main conclusions Biodiversity patterns can be to some degree predicted from the scaling effects related to different durations of time series, but changes in the dominance structure observed over the last few decades reach higher magnitude, probably forced by anthropogenic effects, than those observed over much longer durations.
  • Karhu, Kristiina; Hilasvuori, Emmi; Jarvenpaa, Marko; Arppe, Laura; Christensen, Bent T.; Fritze, Hannu; Kulmala, Liisa; Oinonen, Markku; Pitkanen, Juha-Matti; Vanhala, Pekka; Heinonsalo, Jussi; Liski, Jari (2019)
    Most of the carbon (C) stored in temperate arable soils is present in organic matter (OM) intimately associated with soil minerals and with slow turnover rates. The sensitivity of mineral-associated OM to changes in temperature is crucial for reliable predictions of the response of soil C turnover to global warming and the associated flux of carbon dioxide (CO2) from the soil to the atmosphere. We studied the temperature sensitivity of C in <63 mu m fractions rich in mineral-associated organic matter (MOM) and of C in > 63 mu m fractions rich in particulate organic matter (POM). The fractions were isolated by physical separation of two light-textured arable soils where the C4-plant silage maize had replaced C3-crops 25 years ago. Differences in C-13 abundance allowed for calculation of the age of C in the soil-size fractions (old C, C3-C > 25 years; recent C, C4-C <25 years). We incubated bulk soils ( <2 mm) and size fractions sequentially at 6, 18, 26 and 34 degrees C (ramping up and down the temperature scale) and calculated the temperature sensitivity of old and recent C from (CO2)-C-12 and (CO2)-C-13 evolution rates. The temperature sensitivity was similar or slightly higher for POM than for MOM. Within the POM fraction, old C3-C was more sensitive to changes in temperature than recent C4-C. For the MOM fraction, the temperature sensitivity was unrelated to the age of C. Quantitative PCR analysis indicated that the proportions of bacteria, archaea and fungi did not change during incubation. Our results suggest that while OM stabilizing mechanisms affect the temperature sensitivity of soil C, temperature sensitivity appears unrelated to the age of mineral-associated OM.
  • Soinne, Helena; Keskinen, Riikka; Räty, Mari; Kanerva, Sanna; Turtola, Eila; Kaseva, Janne; Nuutinen, Visa; Simojoki, Asko; Salo, Tapio (2021)
    To achieve appropriate yield levels, inherent nitrogen (N) supply and biological N fixation are often complemented by fertilization. To avoid economic losses and negative environmental impacts due to over-application of N fertilizer, estimation of the inherent N supply is critical. We aimed to identify the roles of soil texture and organic matter in N mineralization and yield levels attained in cereal cultivation with or without N fertilization in boreal mineral soils. First, the net N mineralization and soil respiration were measured by laboratory incubation with soil samples varying in clay and organic carbon (C) contents. Secondly, to estimate the inherent soil N supply under field conditions, both unfertilized and fertilized cereal yields were measured in fields on clay soils (clay 30-78%) and coarse-textured soils (clay 0-28%). In clay soils (C 2.5-9.0%), both the net N mineralization and the cereal yields (without and with fertilization) decreased with increasing clay/C ratio. Moreover, in soils with high clay/C ratio, the agronomic N use efficiency (additional yield per kg of fertilizer N) varied considerably, indicating the presence of growth limitations other than N. In coarse-textured soils, the yield increase attained by fertilization increased with increasing organic C. Our results indicate that for clay soils in a cool and humid climate, the higher the clay content, the more organic C is needed to produce reasonable yields and to ensure efficient use of added nutrients without high N losses to the environment. For coarse soils having a rather high mean organic C of 2.3%, the organic C appeared to improve agronomic N use efficiency. For farmers, simple indicators such as the clay/C ratio or the use of non-N-fertilized control plots may be useful for site-specific adjustment of the rates of N fertilization. Highlights We aimed to identify simple indicators of inherent soil N supply applicable at the farm level. In clay soils, the net N mineralization was found to correlate negatively with the clay/C ratio. In coarse-textured soils, agronomic N use efficiency improved with increasing soil organic C. Clay soils with high clay/C ratio are at risk of low yield levels.
  • Kaarlejarvi, Elina; Salemaa, Maija; Tonteri, Tiina; Merila, Paivi; Laine, Anna-Liisa (2021)
    Aim The diversity and composition of natural communities are rapidly changing due to anthropogenic disturbances. Magnitude of this compositional reorganization varies across the globe, but reasons behind the variation remain largely unknown. Disturbances induce temporal turnover by stimulating species colonizations, causing local extinctions, altering dominance structure, or all of these. We test which of these processes drive temporal community changes, and whether they are constrained by natural environmental gradients. Moreover, we assess to what degree identity shifts translate to changes in dominance structure. Location Finland. Time period Observations 1985-2006, disturbance history > 140 years. Major taxa studied Vascular plants. Methods We investigated temporal turnover of boreal forest understorey in response to disturbance, here forest management, along a soil fertility gradient. We disentangle the roles of species gains, losses and abundance changes in driving temporal turnover in response to and after disturbance by comparing turnover rates in different forest age categories along a fertility gradient. We quantify temporal turnover using richness-based complement of Jaccard's similarity index and proportional-abundance based dissimilarity index. We also test whether disturbance history or fertility influence the relationship between identity shifts and dominance structure. Results We found that the impact of disturbance on temporal turnover depends on soil fertility. The greatest turnover occurred in the most fertile forests immediately after disturbance. There, species gains and losses strongly altered dominance structure leading to high turnover, whereas undisturbed old forests and nutrient-poor habitats were characterized by stable dominant species even when the majority of species shifted their identity. Main conclusions Our results suggest that human impacts on temporal biodiversity change vary along environmental gradients. In boreal forests, the fertile habitats have a higher probability than nutrient-poor sites of changing their composition in response to anthropogenic disturbances. Resource availability and disturbance history may thus influence consequences of temporal turnover for ecosystem functioning.
  • Solly, Emily F.; Brunner, Ivano; Helmisaari, Heljä-Sisko Marketta; Herzog, Claude; Leppälammi-Kujansuu, Jaana; Schöning, Ingo; Schrumpf, Marion; Schweingruber, Fritz H; Trumbore, Susan E.; Hagedorn, Frank (2018)
    Fine roots support the water and nutrient demands of plants and supply carbon to soils. Quantifying turnover times of fine roots is crucial for modeling soil organic matter dynamics and constraining carbon cycle–climate feedbacks. Here we challenge widely used isotopebased estimates suggesting the turnover of fine roots of trees to be as slow as a decade. By recording annual growth rings of roots from woody plant species, we show that mean chronological ages of fine roots vary from <1 to 12 years in temperate, boreal and sub-arctic forests. Radiocarbon dating reveals the same roots to be constructed from 10 ± 1 year (mean ± 1 SE) older carbon. This dramatic difference provides evidence for a time lag between plant carbon assimilation and production of fine roots, most likely due to internal carbon storage. The high root turnover documented here implies greater carbon inputs into soils than previously thought which has wide-ranging implications for quantifying ecosystem carbon allocation.
  • Ovaskainen, Otso; Rybicki, Joel; Abrego, Nerea (2019)
    A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non-manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent-based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta-diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche-based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral-based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.