Browsing by Subject "DECOMPOSITION"

Sort by: Order: Results:

Now showing items 1-20 of 37
  • Daub, Christopher D.; Halonen, Lauri (2019)
    The deprotonation of formic acid is investigated using metadynamics in tandem with Born-Oppenheimer molecular dynamics simulations. We compare our findings for formic acid in pure water with previous studies before examining formic acid in aqueous solutions of lithium bromide. We carefully consider different definitions for the collective variable(s) used to drive the metadynamics, emphasizing that the variables used must include all of the possible reactive atoms in the system, in this case carboxylate oxygens and water hydrogens. This ensures that all the various possible proton exchange events can be accommodated and the collective variable(s) can distinguish the protonated and deprotonated states, even over rather long ab initio simulation runs (ca. 200-300 ps). Our findings show that the formic acid deprotonation barrier and the free energy of the deprotonated state are higher in concentrated lithium bromide, in agreement with the available experimental data for acids in salt solution. We show that the presence of Br- in proximity to the formic acid hydroxyl group effectively inhibits deprotonation. Our study extends previous work on acid deprotonation in pure water and at air-water interfaces to more complex multicomponent systems of importance in atmospheric and marine chemistry.
  • Fernandez-Martinez, M.; Vicca, S.; Janssens, I. A.; Ciais, P.; Obersteiner, M.; Bartrons, M.; Sardans, J.; Verger, A.; Canadell, J. G.; Chevallier, F.; Wang, X.; Bernhofer, C.; Curtis, P. S.; Gianelle, D.; Gruewald, T.; Heinesch, B.; Ibrom, A.; Knohl, A.; Laurila, T.; Law, B. E.; Limousin, J. M.; Longdoz, B.; Loustau, D.; Mammarella, I.; Matteucci, G.; Monson, R. K.; Montagnani, L.; Moors, E. J.; Munger, J. W.; Papale, D.; Piao, S. L.; Penuelas, J. (2017)
    Concentrations of atmospheric carbon dioxide (CO2) have continued to increase whereas atmospheric deposition of sulphur and nitrogen has declined in Europe and the USA during recent decades. Using time series of flux observations from 23 forests distributed throughout Europe and the USA, and generalised mixed models, we found that forest-level net ecosystem production and gross primary production have increased by 1% annually from 1995 to 2011. Statistical models indicated that increasing atmospheric CO2 was the most important factor driving the increasing strength of carbon sinks in these forests. We also found that the reduction of sulphur deposition in Europe and the USA lead to higher recovery in ecosystem respiration than in gross primary production, thus limiting the increase of carbon sequestration. By contrast, trends in climate and nitrogen deposition did not significantly contribute to changing carbon fluxes during the studied period. Our findings support the hypothesis of a general CO2-fertilization effect on vegetation growth and suggest that, so far unknown, sulphur deposition plays a significant role in the carbon balance of forests in industrialized regions. Our results show the need to include the effects of changing atmospheric composition, beyond CO2, to assess future dynamics of carbon-climate feedbacks not currently considered in earth system/climate modelling.
  • Fraixedas, Sara; Burgas, Daniel; Robson, David; Camps, Joachim; Barriocanal, Carles (2020)
    Mediterranean European rice fields provide important habitats for migrating waterbirds. In winter. one waterbird species that particularly benefits from rice fields is the Northern Lapwing (VaneIlus vanellas), a species threatened in Europe. To assess the effect of agii-environmental measures on rice field selection and use by wintering lapwings, bird counts were conducted in northeastern Spain during two consecutive winters (2005-2006 and 2006-2007). Information on two mandatory post-harvest management prescriptions of the agri-environment schemes was collected, namely winter flooding (percent ground surface covered by water) and whether fields were rolled or not. The number of lapwings in rolled fields was significantly higher compared to non-rolled fields. For instance. an average rolled field with 50% water cover (percentage at which lapwing abundance more or less peaked) would host an estimated 12.03 +/- 0.52 SE lapwings versus 0.18 +/- 0.58 in a non-rolled field. While the maximum abundance of lapwings in rolled fields was found at an intermediate percentage of water cover (about 25 to 75%), the number of lapwings increased steadily with water cover in non-rolled fields. Rice post-harvest practices derived from the agri-environment schemes are beneficial for biodiversity, promoting the conservation of suitable habitats for waterbirds.
  • Picazo, Felix; Vilmi, Annika; Aalto, Juha; Soininen, Janne; Casamayor, Emilio O.; Liu, Yongqin; Wu, Qinglong; Ren, Lijuan; Zhou, Jizhong; Shen, Ji; Wang, Jianjun (2020)
    Background Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China. Results We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively. Conclusions We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change.
  • Lehikoinen, Markku; Arffman, Martti; Manderbacka, Kristiina; Elovainio, Marko; Keskimaki, Ilmo (2016)
    Background: Large cities are often claimed to display more distinct geographical and socioeconomic health inequalities than other areas due to increasing residential differentiation. Our aim was to assess whether geographical inequalities in mortality within the capital (City of Helsinki) both exceeded that in other types of geographical areas in Finland, and whether those differences were dependent on socioeconomic inequalities. Methods: We analysed the inequality of distribution separately for overall, ischemic heart disease and alcohol-related mortality, and mortality amenable (AM) to health care interventions in 1992-2008 in three types of geographical areas in Finland: City of Helsinki, other large cities, and small towns and rural areas. Mortality data were acquired as secondary data from the Causes of Death statistics from Statistics Finland. The assessment of changing geographical differences over time, that is geographical inequalities, was performed using Gini coefficients. As some of these differences might arise from socioeconomic factors, we assessed socioeconomic differences with concentration indices in parallel to an analysis of geographical differences. To conclude the analysis, we compared the changes over time of these inequalities between the three geographical areas. Results: While mortality rates mainly decreased, alcohol-related mortality in the lowest income quintile increased. Statistically significant differences over time were found in all mortality groups, varying between geographical areas. Socioeconomic differences existed in all mortality groups and geographical areas. In the study period, geographical differences in mortality remained relatively stable but income differences increased substantially. For instance, the values of concentration indices for AM changed by 54 % in men (p <0.027) and by 62 % in women (p <0.016). Only slight differences existed in the time trends of Gini or in the concentration indices between the geographical areas. Conclusions: No geographical or income-related differences in the distribution of mortality existed between Helsinki and other urban or rural areas of Finland. This suggests that the effect of increasing residential differentiation in the capital may have been mitigated by the policies of positive discrimination and social mixing. One of the main reasons for the increase in health inequalities was growth of alcohol-related mortality, especially among those with the lowest incomes.
  • Mäki, Mari; Mali, Tuulia; Hellén, Heidi; Heinonsalo, Jussi; Lundell, Taina; Bäck, Jaana (2021)
    Wood-decaying fungi in the phylum Basidiomycota play a significant role in the global carbon cycle, as they decompose deadwood effectively. Fungi may compete for utilizable substrate and growth space by producing soluble metabolites and by releasing volatile organic compounds (VOCs). We determined the role of wood substrate (Scots pine or Norway spruce) on the generation of hyphal biomass, secreted metabolites and enzyme activities, wood decomposition rate, and fungal species-species interactions on VOC release. We studied one brown-rot species (Fomitopsis pinicola) and two white-rot species (Phlebia radiata and Trichaptum abietinum) cultivated individually or in combinations. Wood substrate quality influences VOC release by the wood-decaying fungi, with signature differences caused by the decomposition trait (brown rot or white rot) and species-species interactions. VOC release was higher in the cultures of Basidiomycota than in uncolonized sawdust. Fungal biomass, decomposition activity, iron reduction, enzyme activities, oxalate anion content, and oxalic acid production explained VOC release from decaying wood.
  • Kaila, Annu; Lauren, Ari; Sarkkola, Sakari; Koivusalo, Harri; Ukonmaanaho, Liisa; O'Driscoll, Connie; Xiao, Liwen; Asam, Zaki; Nieminen, Mika (2015)
    Calibration-period/control-area approach was used to study nitrogen and phosphorus export from drained and productive Norway-spruce-dominated peatland forests following conventional stem-only and whole-tree harvesting. The study indicated high nitrogen and particulate phosphorus exports and lack of significant differences between the harvest treatments during the first 3-4 years after harvesting. The high extra nitrogen exports, increasing to a maximum level of about 10 kg ha(-1) during the third year after harvesting, were partly caused by the higher nitrate export than in previous studies. The study has a practical outcome that management of harvest residues (i.e. left on site or harvested) may not be an efficient means of mitigation of nitrogen and phosphorus exports. The high exports following harvesting underline the importance of using the best available water protection methods, such as sufficiently large wetland buffer areas, to decrease nutrient exports to watercourses from productive Norway spruce dominated peatland catchments.
  • Hagner, Marleena; Mikola, Juha; Saloniemi, Irma; Saikkonen, Kari; Helander, Marjo (2019)
  • Bosch, Sina; Leminen, Alina (2018)
    The aim of this review is to provide a selective overview of priming studies which have employed the event-related brain potential (ERP) technique in order to investigate bilingual language processing. The priming technique can reveal an implicit memory effect in which exposure to one stimulus influences the processing of another stimulus. Behavioral approaches, such as measuring reaction times, may not always be enough for providing a full view on the exact mechanisms and the time-course of language comprehension. Instead, ERPs have a time-resolution of a millisecond and hence they offer a precise temporal overview of the underlying neural processes involved in language processing. In our review, we summarize experimental research that has combined priming with ERP measurements, thus creating a valuable tool for examining the neurophysiological correlates of language processing in the bilingual brain.
  • Tupek, Boris; Launiainen, Samuli; Peltoniemi, Mikko; Sievanen, Risto; Perttunen, Jari; Kulmala, Liisa; Penttila, Timo; Lindroos, Antti-Jussi; Hashimoto, Shoji; Lehtonen, Aleksi (2019)
    We can curb climate change by improved management decisions for the most important terrestrial carbon pool, soil organic carbon stock (SOC). However, we need to be confident we can obtain the correct representation of the simultanous effect of the input of plant litter, soil temperature and water (which could be altered by climate or management) on the decomposition of soil organic matter. In this research, we used regression and Bayesian statistics for testing process-based models (Yasso07, Yasso15 and CENTURY) with soil heterotrophic respiration (Rh) and SOC, measured at four sites in Finland during 2015 and 2016. We extracted climate modifiers for calibration with Rh. The Rh values of Yasso07, Yasso15 and CENTURY models estimated with default parameterization correlated with measured monthly heterotrophic respiration. Despite a significant correlation, models on average underestimated measured soil respiration by 43%. After the Bayesian calibration, the fitted climate modifier of the Yasso07 model outperformed the Yasso15 and CENTURY models. The Yasso07 model had smaller residual mean square errors and temperature and water functions with fewer, thus more efficient, parameters than the other models. After calibration, there was a small overestimate of Rh by the models that used monotonic moisture functions and a small generic underestimate in autumn. The mismatch between measured and modelled Rh indicates that the Yasso and CENTURY models should be improved by adjusting climate modifiers of decomposition or by accounting for missing controls in, for example, microbial growth.
  • Heinonsalo, Jussi; Sun, Hui; Santalahti, Minna; Bäcklund, Kirsi; Hari, Pertti; Pumpanen, Jukka (2015)
    Ectomycorrhizal (ECM) symbiosis has been proposed to link plant photosynthesis and soil organic matter (SOM) decomposition through the production of fungal enzymes which promote SOM degradation and nitrogen (N) uptake. However, laboratory and field evidence for the existence of these processes are rare. Piloderma sp., a common ECM genus in boreal forest soil, was chosen as model mycorrhiza for this study. The abundance of Piloderma sp. was studied in root tips and soil over one growing season and in winter. Protease production was measured from ectomycorrhiza and soil solution in the field and pure fungal cultures. We also tested the effect of Piloderma olivaceum on host plant organic N nutrition in the laboratory. The results showed that Piloderma sp. was highly abundant in the field and produced extracellular proteases, which correlated positively with the gross primary production, temperature and soil respiration. In the laboratory, Piloderma olivaceum could improve the ability of Pinus sylvestris L. to utilize N from extragenous proteins. We suggest that ECM fungi, although potentially retaining N in their hyphae, are important in forest C and N cycling due to their ability to access proteinaeous N. As Piloderma sp. abundance appeared to be seasonally highly variable, recycling of fungal-bound N after hyphal death may therefore be of primary importance for the N cycling in boreal ecosystems.
  • Minwegen, Heiko; Döntgen, Malte; Hemken, Christian; Büttgen, Rene Daniel; Leonhard, Kai; Heufer, Karl Alexander (2019)
    Recently the possibility of hot beta-scission pathways gained attention. These reactions give a shortcut during the important fuel consumption phase in combustion processes leading from H-atom abstraction directly to the beta-scission products without fuel radical thermalization. Methyl formate (MF) was shown to be prone to hot beta-scission due to a low beta-scission barrier height. Furthermore, MF as smallest methyl ester can be considered as biodiesel surrogate and it is an important intermediate product during combustion of various ethers. In this work a predominantly ab-initio derived detailed kinetic model of MF combustion is developed including hot beta-scission pathways and compared to a sophisticated literature model based on classical estimation methods. For this, new stoichiometric MF in air ignition delay time measurements in a shock tube and a rapid compression machine over a wide temperature range (790 K-1250 K) and pressures of 10, 20 and 40 bar served as validation targets. The experimental ignition delay times (IDT) show Arrhenius type behavior in both facilities at all conditions. The newly developed quantum-based model catches the pressure dependency and low-temperature reactivity well although overpredicting the IDT at higher temperatures. It was found that hot beta-scission is the major depletion pathway of formate group-centered MF radicals. This, however, does not change the overall reactivity of MF combustion due to the low stability of the alkyl peroxide (RO2) at the formate group. For species with competing thermal beta-scission and RO2 formation, however, hot beta-scission may have a significant impact. (C) 2018 The Combustion Institute. Published by Elsevier Inc. All rights reserved.
  • Aaltonen, Heidi; Koster, Kajar; Koster, Egle; Berninger, Frank; Zhou, Xuan; Karhu, Kristiina; Biasi, Christina; Bruckman, Viktor; Palviainen, Marjo; Pumpanen, Jukka (2019)
    Wildfires burn approximately 1% of boreal forest yearly, being one of the most significant factors affecting soil organic matter (SOM) pools. Boreal forests are largely situated in the permafrost zone, which contains half of global soil carbon (C). Wildfires advance thawing of permafrost by burning the insulating organic layer and decreasing surface albedo, thus increasing soil temperatures. Fires also affect SOM quality through chemical and physical changes, such as the formation of resistant C compounds. The long-term post-fire effects on SOM quality, degradability and isotopic composition are not well known in permafrost forests. We studied the effect of forest fires on the proportional sizes of SOM pools with chemical fractionation (extracting with water, ethanol and acid) of soil samples (5, 30 and 50cm depths) collected from a fire chronosequence in the upland mineral soils of the Canadian permafrost zone. We also determined the C-13 and N-15 isotopic composition of soil after fire. In the topsoil horizon (5cm) recent fire areas contained a smaller fraction of labile SOM and were slightly more enriched with N-15 and C-13 than older fire areas. The SOM fraction ratios reverted towards pre-fire status with succession. Changes in SOM were less apparent deeper in the soil. Best predictors for the size of recalcitrant SOM fraction were active layer depth, vegetation biomass and soil C/N ratio, whereas microbial biomass was best predicted by the size of the recalcitrant SOM fraction. Results indicated that SOM in upland mineral soils at the permafrost surface could be mainly recalcitrant and its decomposition not particularly sensitive to changes resulting from fire.
  • Odriozola, Inaki; Abrego, Nerea; Tlaskal, Vojtech; Zrustova, Petra; Morais, Daniel; Vetrovsky, Tomas; Ovaskainen, Otso; Baldrian, Petr (2021)
    Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood's properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.
  • Daly, Paul; Peng, Mao; Di Falco, Marcos; Lipzen, Anna; Wang, Mei; Ng, Vivian; Grigoriev, Igor; Tsang, Adrian; Makela, Miia R.; de Vries, Ronald P. (2019)
    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of plant biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant biomass would benefit from derepressed or constitutively CAZyme-expressing strains. IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant biomass utilization in the white-rot fungus Dichomitus squalens. This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.
  • Riikonen, Anu; Pumpanen, Jukka; Mäki, Mari Jasmiina; Nikinmaa, Eero (2017)
    We assessed the net carbon (C) sequestration dynamics of street tree plantings based on 10 years of measurements at two case study sites each with different tree species in Helsinki, Finland. We assessed C loss from tree soils and tree C accumulation, tested the applicability of pre-existing growth and biomass equations against observations, and estimated the time point for the beginning of net C sequestration for the studied street tree plantings. The tree woody biomass C accumulation in the first 10 years after planting was 18-32 kg per tree. At the same time the C loss from the growth media was at least 170 kg per growth media volume (25 m(3)) per tree. If this soil C loss was accounted for, the net C sequestration would begin, at best, approximately 30 years after planting. Biomass equations developed for traditional forests predicted more stem biomass and less leaf and branch biomass than measured for the species examined, but total aboveground biomass was generally well predicted.
  • Lopez, Sara Casado; Peng, Mao; Issak, Tedros Yonatan; Daly, Paul; de Vries, Ronald P.; Mäkelä, Miia R. (2018)
    Fungi can decompose plant biomass into small oligo-and monosaccharides to be used as carbon sources. Some of these small molecules may induce metabolic pathways and the production of extracellular enzymes targeted for degradation of plant cell wall polymers. Despite extensive studies in ascomycete fungi, little is known about the nature of inducers for the lignocellulolytic systems of basidiomycetes. In this study, we analyzed six sugars known to induce the expression of lignocellulolytic genes in ascomycetes for their role as inducers in the basidiomycete white-rot fungus Dichomitus squalens using a transcriptomic approach. This identified cellobiose and L-rhamnose as the main inducers of cellulolytic and pectinolytic genes, respectively, of D. squalens. Our results also identified differences in gene expression patterns between dikaryotic and monokaryotic strains of D. squalens cultivated on plant biomass-derived monosaccharides and the disaccharide cellobiose. This suggests that despite conservation of the induction between these two genetic forms of D. squalens, the fine-tuning in the gene regulation of lignocellulose conversion is differently organized in these strains. IMPORTANCE Wood-decomposing basidiomycete fungi have a major role in the global carbon cycle and are promising candidates for lignocellulosic biorefinery applications. However, information on which components trigger enzyme production is currently lacking, which is crucial for the efficient use of these fungi in biotechnology. In this study, transcriptomes of the white-rot fungus Dichomitus squalens from plant biomass-derived monosaccharide and cellobiose cultures were studied to identify compounds that induce the expression of genes involved in plant biomass degradation.
  • Adamczyk, Bartosz; Sietio, Outi-Maaria; Biasi, Christina; Heinonsalo, Jussi (2019)
    See also the Commentary on this article by Hattenschwiler et al., 223: 5-7.
  • Miyauchi, Shingo; Kiss, Eniko; Kuo, Alan; Drula, Elodie; Kohler, Annegret; Sanchez-Garcia, Marisol; Morin, Emmanuelle; Andreopoulos, Bill; Barry, Kerrie W.; Bonito, Gregory; Buee, Marc; Carver, Akiko; Chen, Cindy; Cichocki, Nicolas; Clum, Alicia; Culley, David; Crous, Pedro W.; Fauchery, Laure; Girlanda, Mariangela; Hayes, Richard D.; Keri, Zsofia; LaButti, Kurt; Lipzen, Anna; Lombard, Vincent; Magnuson, Jon; Maillard, Francois; Murat, Claude; Nolan, Matt; Ohm, Robin A.; Pangilinan, Jasmyn; Pereira, Maira de Freitas; Perotto, Silvia; Peter, Martina; Pfister, Stephanie; Riley, Robert; Sitrit, Yaron; Stielow, J. Benjamin; Szoellosi, Gergely; Zifcakova, Lucia; Stursova, Martina; Spatafora, Joseph W.; Tedersoo, Leho; Vaario, Lu-Min; Yamada, Akiyoshi; Yan, Mi; Wang, Pengfei; Xu, Jianping; Bruns, Tom; Baldrian, Petr; Vilgalys, Rytas; Dunand, Christophe; Henrissat, Bernard; Grigoriev, Igor V.; Hibbett, David; Nagy, Laszlo G.; Martin, Francis M. (2020)
    Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.