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Soil microbial carbon-use efficiency (CUE), described as the ratio of growth over total carbon (C) uptake, i.e. the sum of growth and respiration, is a key variable in all soil organic matter (SOM) models and critical to ecosystem C cycling. However, there is still a lack of consensus on microbial CUE when estimated using different methods. Furthermore, the significance of many fundamental drivers of CUE remains largely unknown and inconclusive, especially for tropical ecosystems. For these reasons, we determined CUE and microbial indicators of soil nutrient availability in seven tropical forest soils along an altitudinal gradient (circa 900–2200 m a.s.l) occurring at Taita Hills, Kenya. We used this gradient to study the soil nutrient (N and P) availability and its relation to microbial CUE estimates. For assessing the soil nutrient availability, we determined both the soil bulk stoichiometric nutrient ratios (soil C:N, C:P and N:P), as well as SOM degradation related enzyme activities. We estimated soil microbial CUE using two methods: substrate independent 18O-water tracing and 13C-glucose tracing method. Based on these two approaches, we estimated the microbial uptake efficiency of added glucose versus native SOM, with the latter defined by 18O-water tracing method. Based on the bulk soil C:N stoichiometry, the studied soils did not reveal N limitation. However, soil bulk P limitation increased slightly with elevation. Additionally, based on extracellular enzyme activities, the SOM nutrient availability decreased with elevation. The 13C-CUE did not change with altitude indicating that glucose was efficiently taken up and used by the microbes. On the other hand, 18O-CUE, which reflects the growth efficiency of microbes growing on native SOM, clearly declined with increasing altitude and was associated with SOM nutrient availability indicators. Based on our results, microbes at higher elevations invested more energy to scavenge for nutrients and energy from complex SOM whereas at lower elevations the soil nutrients may have been more readily available.

Warming will likely stimulate Arctic primary production, but also soil C and N mineralization, and it remains uncertain whether the Arctic will become a sink or a source for CO2. Increasing insect herbivory may also dampen the positive response of plant production and soil C input to warming. We conducted an open-air warming experiment with Subarctic field layer vegetation in North Finland to explore the effects of warming (+3 degrees C) and reduced insect herbivory (67% reduction in leaf damage using an insecticide) on soil C and N dynamics. We found that plant root growth, soil C and N concentrations, microbial biomass C, microbial activity, and soil NH4+ availability were increased by both warming and reduced herbivory when applied alone, but not when combined. Soil NO3- availability increased by warming only and in-situ soil respiration by reduced herbivory only. Our results suggest that increasing C input from vegetation under climate warming increases soil C concentration, but also stimulates soil C turnover. On the other hand, it appears that insect herbivores can significantly reduce plant growth. If their abundance increases with warming as predicted, they may curtail the positive effect of warming on soil C concentration. Moreover, our results suggest that temperature and herbivory effects on root growth and soil variables interact strongly, which probably arises from a combination of N demand increasing under lower herbivory and soil mineral N supply increasing under higher temperature. This may further complicate the effects of rising temperatures on Subarctic soil C dynamics.

Primary biological aerosol particles (PBAPs) play an important role in the interaction between biosphere, atmosphere, and climate, affecting cloud and precipitation formation processes. The presence of pollen, plant fragments, spores, bacteria, algae, and viruses in PBAPs is well known. In order to explore the complex interrelationships between airborne and particulate chemical tracers (amino acids, saccharides), gene copy numbers (16S and 18S for bacteria and fungi, respectively), gas phase chemistry, and the particle size distribution, 84 size-segregated aerosol samples from four particle size fractions (< 1.0, 1.0–2.5, 2.5–10, and > 10 µm) were collected at the SMEAR II station, Finland, in autumn 2017. The gene copy numbers and size distributions of bacteria, Pseudomonas, and fungi in biogenic aerosols were determined by DNA extraction and amplification. In addition, free amino acids (19) and saccharides (8) were analysed in aerosol samples by hydrophilic interaction liquid chromatography–mass spectrometry (HILIC-MS). Different machine learning (ML) approaches, such as cluster analysis, discriminant analysis, neural network analysis, and multiple linear regression (MLR), were used for the clarification of several aspects related to the composition of biogenic aerosols. Clear variations in composition as a function of the particle size were observed. In most cases, the highest concentration values and gene copy numbers (in the case of microbes) were observed for 2.5–10 µm particles, followed by > 10, 1–2.5, and < 1.0 µm particles. In addition, different variables related to the air and soil temperature, the UV radiation, and the amount of water in the soil affected the composition of biogenic aerosols. In terms of interpreting the results, MLR provided the greatest improvement over classical statistical approaches such as Pearson correlation among the ML approaches considered. In all cases, the explained variance was over 91 %. The great variability of the samples hindered the clarification of common patterns when evaluating the relation between the presence of microbes and the chemical composition of biogenic aerosols. Finally, positive correlations were observed between gas-phase VOCs (such as acetone, toluene, methanol, and 2-methyl-3-buten-2-ol) and the gene copy numbers of microbes in biogenic aerosols.

The boreal forests are significant sinks for carbon, and the majority of the carbon present in boreal forests is stored in the soils. Especially in the organic layers of the boreal forest soils, a significant amount of the carbon is stored as complex polymers, which are rather stable and have a long residence time. In addition, these soils are considered to be nutrient poor since important nutrients, such as nitrogen and phosphorus, are complexed with soil particles or stored in organic forms, which are inaccessible to the plants. For acquiring nutrients from the complex substrate, plants form mutualistic associations with fungi. In boreal forest ecosystems, where above-ground vegetation is dominated by coniferous trees, shrubs and mosses, the most common fungi associated with plant roots are ectomycorrhizal and ericoid mycorrhizal. In return for the enhanced water and nutrient uptake, the plants provide energy to their fungal symbionts in the form of recently photosynthesized carbon. As it is predicted that the amount of atmospheric CO2 levels will rise and the climate will warm, the growing season will be extended in the boreal zones and the input of photosynthetic C from the plants to the soil will increase. This increase in the input of photosynthates from the plants can accelerate the below-ground processes and enhance the degradation of the older, stable soil organic matter through a phenomenon called the “priming effect”. Thus, a more thorough understanding of the dynamics of plant-fungal interactions and their importance to the functioning of the whole boreal forest ecosystem is essential when predicting ecosystem level responses to the changing environment. This PhD thesis aimed to enlighten the effect of plant-derived photosynthetic carbon to the fungal community structures and soil organic matter decomposition. Two studies of this thesis are based on a laboratory scale microcosm experiment, and the third study is based on a multiyear field experiment. Fungal community structure was assessed using high throughput sequencing. In addition, the first study provided new insights on the root-associated fungal communities which utilized photosynthates directly from the plant, as well as their host preference via a stable isotope probing technique. The common boreal forest plants, ericoid shrubs Calluna vulgaris (common heather), Vaccinium myrtillus (bilberry), and Vaccinium vitis-idaea (lingonberry), and the conifer Pinus sylvestris (Scots pine) shaped their root and surrounding soil associated fungal communities differently from each other, while they also shared many fungal species. In addition, the ericoid shrubs and their associated microbes had different effects on the soil chemistry and enzymatic activities compared to the conifer P. sylvestris. The results from the laboratory scale experiment described in the first two studies of this thesis indicate that ericoid plants have an important influence on fungal community structures and processes in boreal forest soils. The manipulation of the carbon flow from the plant to the soil induced moderate changes to the fungal community structure in humus during a three-year field experiment. According to the ecological theory known as the “Gadgil effect”, decomposition should be enhanced when saprotrophic fungi are alleviated from competition with ectomycorrhizal fungi. However, the results of the third study of this thesis did not support the Gadgil theory, indicating that the competitive outcome between the saprotrophic and ectomycorrhizal fungi is substrate dependent and these two fungal guilds have preference towards different ecological niches. In addition, the results suggest that the members of the soil microbial community are rather flexible and can adapt to temporary disturbances. This PhD thesis provided further insights into the role of plants in determining the fungal community structure on their own roots and surrounding soils as well as shaping the soil chemical profile. The results underline that for predicting how the changing climate affects soil processes in the boreal forest ecosystem, more knowledge on plant microbe interactions and their impact on soil processes is needed. Boreaaliset metsät ovat merkittäviä hiilivarastoja ja suurin osa niihin varastoidusta hiilestä on maaperässä. Erityisesti maaperän orgaanisessa kerroksessa hiili on muuntunut hitaasti hajoavaksi humusaineeksi, joka muodostaa boreaalisen metsämaan pysyvimmän hiilivaraston. Koska metsämaassa vain pieni osa tärkeistä ravinteista on kasveille helposti hyödynnettävissä muodoissa, turvatakseen ravinteiden saannin kasvit muodostavat sienijuurisymbiooseja niiden juuristoissa elävien sienten kanssa. Boreaalisissa metsissä havupuut ovat yleisiä ja metsän aluskasvillisuus koostuu pääasiassa varpukasveista sekä sammaleista. Havupuut muodostavat tyypillisesti sienijuurisymbioosin pintasienijuurisienten kanssa (ektomykorritsasienet) ja varpukasvit kanervasienijuurisienien (erikoidimykorritsasienet) kanssa. Vastineeksi turvatusta ravinteiden- ja vedenotosta, sienijuurisienet saavat energiansa isäntäkasveilta erilaisina hiiliyhdisteinä eli sokereina. Ihmisen toiminnan aiheuttaman kasvihuoneilmiön voimistumisen ja ilmakehän CO2-pitoisuuden noustessa myös kasvukaudet pidentyvät ja sen myötä kasvien maahan allokoiman hiilen määrien on arveltu kasvavan. Helppokäyttöiset hiiliyhdisteet antavat mikrobeille mahdollisuuden tuottaa tavallista enemmän orgaanisen materiaalin hajotukselle välttämättömiä entsyymejä ja näin lisäävän myös vaikeasti hajotettavien hiiliyhdisteiden, kuten humuksen, hajotusta. Parempi tietämys kasvi-sieni-vuorovaikutuksen merkityksestä boreaalisen metsäekosysteemin toiminnalle on tärkeää, jotta voidaan arvioida muuttuvan ilmaston vaikutuksia maaperän hiilenkierrolle ja hiilivarastoille. Tämän väitöskirjatyön tarkoituksena oli tutkia kasvien maahan syöttämien hiiliyhdisteiden merkitystä juuriston ja maaperän sieniyhteisön monimuotoisuudelle sekä maaperän hiilenkierrolle. Tämän työn kaksi ensimmäistä osajulkaisua perustuivat laboratoriomittakaavan mikrokosmoskokeeseen ja viimeinen monivuotiseen kenttäkokeeseen. Sieniyhteisöjä ja niiden monimuotoisuutta tutkittiin molekyylibiologisin menetelmin ja syväsekvensoinnilla. Lisäksi ensimmäisessä osajulkaisussa tunnistettiin isäntäkasvin (kanerva, mustikka, puolukka ja mänty) kanssa suorassa vuorovaikutuksessa olleet sienet hyödyntäen DNA:n isotooppileimaukseen perustuvaa tekniikkaa. Tutkittujen boreaalisen metsän kasvien (kanerva, mustikka, puolukka ja mänty) juuristojen ja ympäröivän maan sieniyhteisöjen rakenteet erosivat toisistaan, mutta niistä löytyi myös keskenään samoja lajeja. Lisäksi varpukasveilla (kanerva, mustikka ja puolukka) oli erilainen vaikutus ympäröivän maan kemialliseen koostumukseen kuin männyllä. Tämän laboratoriomittakaavan mikrokosmoskokeen tulosten perusteella kanervakasveilla on merkittävä vaikutus boreaalisen metsämaan prosesseihin ja mikrobien monimuotoisuuden ylläpitämiseen. Kasvien maahan syöttämien hiiliyhdisteiden pääsyn rajoittaminen aiheutti muutoksia humusmaan sieniyhteisön rakenteeseen kolmivuotisen kenttäkokeen aikana. Lahottajasienten ja ektomykorritsasienten on arveltu kilpailevan maaperässä samoista ravinteista. Jos kasvien hiilisyöte ektomykorritsasienille lakkaa, lahottajasienten on arveltu yleistyvän ja estävän ektomykorritsasienten kasvua. Tämän sieniryhmien välisen oletetun kilpailun taustalla olevaa mekanismia kutsutaan Gadgil-ilmiöksi. Tässä väitöskirjatyössä kuvatun kolmivuotisen kenttäkokeen tulokset eivät kuitenkaan tue Gadgil-ilmiötä vaan viittaavat siihen, että lahottajasienet ja ektomykorritsasienet suosivat erilaisia ravinteiden lähteitä ja eri ekolokeroita. Lisäksi tuloksien perusteella maaperän mikrobit ovat sopeutuvaisia ja kykenevät mukautumaan tilapäisiin häiriöihin. Tässä väitöskirjatyössä saatiin uusia näkökulmia kasvin vaikutuksesta juuriston ja maaperän sieniyhteisön rakenteeseen ja toimintaan sekä maaperän kemialliseen koostumukseen. Tämän väitöskirjatyön tulokset viittaavat siihen, että tarvitsemme lisätietoa kasvien ja mikrobien vuorovaikutuksesta sekä näiden vuorovaikutusten merkityksestä maaperän prosesseille, jotta voimme ennustaa muuttuvan ilmaston vaikutusta boreaalisen metsämaan hiilenkierrossa.

The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.

Isolation of high quantity and quality RNA is a crucial step in the detection of meaningful gene expression data. Obtaining intact fungal RNA from complex lignocellulosic substrates is often difficult, producing low integrity RNA which perform poorly in downstream applications. In this study we developed an RNA extraction method using CsCl centrifugation procedure, modified from previous reports and adapted for isolation of RNA from plant biomass. This method provided high level of integrity and good quantity of RNA which were suitable for reliable analyses of gene expression and produced consistent and reproducible results.

The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analysed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat. This article is protected by copyright. All rights reserved.

Oxalic acid is a prevalent fungal metabolite with versatile roles in growth and nutrition, including degradation of plant biomass. However, the toxicity of oxalic acid makes regulation of its intra- and extracellular concentration crucial. To increase the knowledge of fungal oxalate metabolism, a transcriptional level study on oxalate-catabolising genes was performed with an effective lignin-degrading white-rot fungus Dichomitus squalens, which has demonstrated particular abilities in production and degradation of oxalic acid. The expression of oxalic-acid decomposing oxalate decarboxylase (ODC) and formic-acid decomposing formate dehydrogenase (FDH) encoding genes was followed during the growth of D. squalens on its natural spruce wood substrate. The effect of high proton concentration on the regulation of the oxalate-catabolising genes was determined after addition of organic acid (oxalic acid) and inorganic acid (hydrochloric acid) to the liquid cultures of D. squalens. In order to evaluate the co-expression of oxalate-catabolising and manganese peroxidase (MnP) encoding genes, the expression of one MnP encoding gene, mnp1, of D. squalens was also surveyed in the solid state and liquid cultures. Sequential action of ODC and FDH encoding genes was detected in the studied cultivations. The odc1, fdh2 and fdh3 genes of D. squalens showed constitutive expression, whereas ODC2 and FHD1 most likely are the main responsible enzymes for detoxification of high concentrations of oxalic and formic acids. The results also confirmed the central role of ODC1 when D. squalens grows on coniferous wood. Phylogenetic analysis revealed that fungal ODCs have evolved from at least two gene copies whereas FDHs have a single ancestral gene. As a conclusion, the multiplicity of oxalate-catabolising genes and their differential regulation on wood and in acid-amended cultures of D. squalens point to divergent physiological roles for the corresponding enzymes.