Search

The study of 16 alpine ecosystems in Europe highlights that temperature increases may lead to changes on plant and fungal communities resulting in fungal biomass and topsoil carbon content loss. Alpine tundra ecosystems suffer from ongoing warming-induced tree encroachment and vegetation shifts. While the effects of tree line expansion on the alpine ecosystem receive a lot of attention, there is also an urgent need for understanding the effect of climate change on shifts within alpine vegetation itself, and how these shifts will consequently affect soil microorganisms and related ecosystem characteristics such as carbon storage. For this purpose, we explored relationships between climate, soil chemistry, vegetation, and fungal communities across seven mountain ranges at 16 alpine tundra locations in Europe. Among environmental factors, our data highlighted that plant community composition had the most important influence on variation in fungal community composition when considered in combination with other factors, while climatic factors had the most important influence solely. According to our results, we suggest that rising temperature, associated with a replacement of ericoid-dominated alpine vegetation by non-mycorrhizal or arbuscular mycorrhizal herbs and grasses, will induce profound changes in fungal communities toward higher dominance of saprotrophic and arbuscular mycorrhizal fungi at the expense of fungal root endophytes. Consequently, topsoil fungal biomass and carbon content will decrease. This work was supported by the Czech Science Foundation (21- 20802 M).

Labile carbon (C) input to soils is expected to affect soil organic matter (SOM) decomposition and soil organic C (SOC) stocks in temperate coniferous forests. We hypothesized that the SOM decomposition rate, C content in soil fractions, and microbial and faunal abundance and activity were increased along the gradient in labile C input around wood ant nests. Three distances from the nest that differed in annual labile C input to soil were selected: 4 m with 6379 mg C m−2, 30 m with 9060 mg C m−2, and 70 m with 9215 mg C m−2. Soil from the organic horizon (Oe+Oa), surface mineral horizon (A), and subsoil mineral horizon (B) was analyzed for C content in soil fractions and for activity and abundance of soil microorganisms and fauna. In addition, a 1-year litter-bag and soil-bag decomposition experiment was conducted. Although the rate of soil decomposition did not differ along the labile C input gradient, the rate of litter decomposition in the B horizon increased as labile C input increased with distance from the nest. Correspondingly, the C content in bulk soil and in the labile and less-protected soil fractions in the B horizon decreased as labile C input increased. We infer that, because the O and A horizons are less C-limited than the B horizon, the changes in the labile C input along the gradient affected the B horizon more than the surface O and A horizons. However, soil microbial and faunal activity and abundances were not consistently affected by the gradient. Apparently, C stocks in soil fractions are more important for microbial and faunal communities than labile C inputs. Although the results indicate that SOC content changes very slowly in the coniferous forest soil of the current study, increases in the input of natural labile C leads to decreases in the SOC stock in the B horizon. By increasing the labile C input to temperate forest soils, future increases in atmospheric CO2 concentration may therefore lead to a significant loss of SOC in deep soil layers.

The formation of soil aggregates is related to the stability of soil organic carbon, which distinguishes the living conditions of microbial communities in different micro-niches. Here, we investigated fungal and bacterial community structure, networks, biomass and respiration in individual micro-niches between and within soil aggregates using seven different chronosequences (both primary and secondary successions from pioneer stages to well-developed ecosystems) on a European-scale gradient from a maritime climate in Belgium to a more continental climate in Hungary. We showed that geographical location was the most important factor (74% for bacterial community, 53% for fungal community) affecting microbial community composition, while soil aggregates (5% for bacterial community and 12% for fungal community) were the second most important factor followed by age of succession and vegetation. Moreover, aggregates (52%) were the most important factor influencing the biomass of major microbial groups, followed by location (37%) and age of succession (6%). Interestingly, macro-aggregates had less interconnected microbial networks and low microbial respiration rates compared to other aggregate sizes. We therefore hypothesize that the embedding of organic particles in the mineral matrix of macro-aggregates is a crucial point in microbial community organization, as evidenced by microbial community connectivity and microbial respiration. Our results demonstrate the importance of soil aggregates for microbial community organization and soil carbon stabilization.

In this study, the diversity of bphA genes was assessed in a 13C-enriched metagenome upon stable isotope probing (SIP) of microbial populations in legacy PCB-contaminated soil with 13C-biphenyl (BP). In total, 13 bphA sequence variants (SVs) were identified in the final amplicon dataset. Of these, one SV comprised 59% of all sequences, and when it was translated into a protein sequence, it exhibited 87, 77.4, and 76.7% identity to its homologs from Pseudomonas furukawaii KF707, Cupriavidus sp. WS, and Pseudomonas alcaliphila B-367, respectively. This same BphA sequence also contained unusual amino acid residues, Alanine, Valine, and Serine in region III, which had been reported to be crucial for the substrate specificity of the corresponding biphenyl dioxygenase (BPDO), and was accordingly designated BphA_AVS. The DNA locus of 18 kbp containing the BphA_AVS-coding sequence retrieved from the metagenome was comprised of 16 ORFs and was most likely borne by Paraburkholderia sp. The BPDO corresponding to bphAE_AVS was cloned and heterologously expressed in E. coli, and its substrate specificity toward PCBs and a spectrum of flavonoids was assessed. Although depleting a rather narrow spectrum of PCB congeners, the efficient transformation of flavone and flavanone was demonstrated through dihydroxylation of the B-ring of the molecules. The homology-based functional assignment of the putative proteins encoded by the rest of ORFs in the AVS region suggests their potential involvement in the transformation of aromatic compounds, such as flavonoids. In conclusion, this study contributes to the body of information on the involvement of soil-borne BPDOs in the metabolism of flavonoid compounds, and our paper provides a more advanced context for understanding the interactions between plants, microbes and anthropogenic compounds in the soil.

The creamy white to beige, aerobic, non-motile, ovoid to rod-shaped, Gram-stain-negative strain, Cd-10(T), was isolated from heavy-metal-contaminated sludge from a decantation basin of a heavy metal processing factory based on its ability to tolerate CdCl2 in the cultivation medium. In the reconstruction of its phylogeny based on 16S rRNA gene sequences, strain Cd-10(T) clustered with species of the genera Gemmobacter, Xinfangfangia, Tabrizicola and Rhodobacter within the family Rhodobacteraceae. Its 16S rRNA gene sequence exhibited 96.32% pairwise similarity to the type strain of Xinfangfangia soli, 95.3 % to that of Gemmobacter intermedius, followed by Tabrizicola fusiformis (95.10 %), Rhodobacter sediminis (94.88 %), Gemmobacter nectariphilus and Rhodobacter capsulatus (both 94.81%). The major respiratory quinone was Q-10 accompanied by Q-9, the fatty acid profile consisted predominantly of C-18:1 omega 7C, C-18:0, C-16:0 and C-16:1 omega 7c, the major polar lipids were phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and diphosphatidylglycerol. An analysis of the percentage of conserved proteins deduced from draft or complete genomic sequences of strain Cd-10(T) and representatives of its closest relatives suggested that strain Cd-10(T) is a member of a novel genus within the Rhodobacteraceae family for which we propose the name Pseudogemmobacter. Strain Cd-10(T) (=DSM 103618(T)=NCCB 100645(T)) is the type strain of Pseudogemmobacter bohemicus gen. nov., sp. nov., the type species of the genus Pseudogemmobacter gen. nov.

Soil microbial communities involved in 13C-labeled cellulose utilization from two contrasting (in terms of vegetation and climatic conditions) forest sites at different elevations were studied by using a laboratory microcosm experiment and a PLFA (phospholipid fatty acid)-SIP (stable isotope probing) approach considering the effects of incubation temperature (0, 10 and 20 °C) and time (1–4 weeks). The amounts of cellulose-13C assimilated by soil microorganisms and the composition of microbial communities utilizing cellulose were site-dependent. Total, bacterial and actinobacterial biomass incorporated higher amounts of 13C in soil from the deciduous forest site (at the lower elevation), while fungal biomass contained increased amounts of 13C in soil from the coniferous forest site (at the higher elevation). Increasing temperatures resulted in increased amounts of 13C assimilated by the different PLFA-based microbial groups, except fungi, and in significant changes in the community structure of cellulose utilizers. Fungi were better adapted to cold conditions than bacteria. Longer incubation times determined an increase in the amount of 13C incorporated into total and bacterial PLFAs but had no effect on the composition of labeled microbial communities.

The involvement of bacterial aromatic ring-hydroxylating dioxygenases (ARHDs) in the degradation of aromatic pollutants, such as polychlorinated biphenyls (PCBs), has been well studied. However, there is considerable speculation as to the origin of this ability. One hypothesis is centered on a connection between the ability to degrade aromatic pollutants and the necessity of soil bacteria to cope with and/or utilize secondary plant metabolites (SPMs). To investigate this connection, we researched the involvement of biphenyl 2,3-dioxygenase (BPDO), an ARHD essential for the degradation of PCBs, in the metabolism of SPMs in the soil bacterium Pseudomonas alcaliphila JAB1, a versatile degrader of PCBs. We demonstrated the ability of the strain JAB1 to transform a variety of SPMs, namely the flavonoids apigenin, flavone, flavanone, naringenin, fisetin, quercetin, morin, and catechin, caffeic acid, trans-cinnamic acid, and the monoterpenes (S)-limonene and (R)-carvone. Of those, the transformation of flavone, flavanone, and (S)-limonene was conditioned by the activity of JAB1-borne BPDO and thus was researched in more detail, and we found evidence for the limonene monooxygenase activity of the BPDO. Furthermore, the bphA gene in the strain JAB1 was demonstrated to be induced by a wide range of SPMs, with monoterpenes being the strongest inducers of the SPMs tested. Thus, our findings contribute to the growing body of evidence that ARHDs not only play a role in the catabolism of aromatic pollutants, but also of natural plant-derived aromatics, and this study supports the hypothesis that ARHDs participate in ecological processes mediated by SPMs.

Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers., Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils. IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.

Many of the world’s peatlands have been affected by water table drawdown and subsequent loss of organic matter. Rewetting has been proposed as a measure to restore peatland functioning and to halt carbon loss, but its effectiveness is subject to debate. An important prerequisite for peatland recovery is a return of typical microbial communities, which drive key processes. To evaluate the effect of rewetting, we investigated 13 fen peatland areas across a wide (>1500 km) longitudinal gradient in Europe, in which we compared microbial communities between drained, undrained, and rewetted sites. There was a clear difference in microbial communities between drained and undrained fens, regardless of location. Community recovery upon rewetting was substantial in the majority of sites, and predictive functional profiling suggested a concomitant recovery of biogeochemical peatland functioning. However, communities in rewetted sites were only similar to those of undrained sites when soil organic matter quality (as expressed by cellulose fractions) and quantity were still sufficiently high. We estimate that a minimum organic matter content of ca. 70% is required to enable microbial recovery. We conclude that peatland recovery after rewetting is conditional on the level of drainage-induced degradation: severely altered physicochemical peat properties may preclude complete recovery for decades.

Chlorhexidine (CHX) and octenidine (OCT), antimicrobial compounds used in oral care products (toothpastes and mouthwashes), were recently revealed to interfere with human sex hormone receptor pathways. Experiments employing model organisms&mdash, white-rot fungi Irpex lacteus and Pleurotus ostreatus&mdash, were carried out in order to investigate the biodegradability of these endocrine-disrupting compounds and the capability of the fungi and their extracellular enzyme apparatuses to biodegrade CHX and OCT. Up to 70% &plusmn, 6% of CHX was eliminated in comparison with a heat-killed control after 21 days of in vivo incubation. An additional in vitro experiment confirmed manganese-dependent peroxidase and laccase are partially responsible for the removal of CHX. Up to 48% &plusmn, 7% of OCT was removed in the same in vivo experiment, but the strong sorption of OCT on fungal biomass prevented a clear evaluation of the involvement of the fungi or extracellular enzymes. On the other hand, metabolites indicating the enzymatic transformation of both CHX and OCT were detected and their chemical structures were proposed by means of liquid chromatography&ndash, mass spectrometry. Complete biodegradation by the ligninolytic fungi was not achieved for any of the studied analytes, which emphasizes their recalcitrant character with low possibility to be removed from the environment.

Forest soils represent important terrestrial carbon (C) pools where C is primarily fixed in the plant-derived biomass but it flows further through the biomass of fungi and bacteria before it is lost from the ecosystem as CO(2) or immobilized in recalcitrant organic matter. Microorganisms are the main drivers of C flow in forests and play critical roles in the C balance through the decomposition of dead biomass of different origins. Here, we track the path of C that enters forest soil by following respiration, microbial biomass production, and C accumulation by individual microbial taxa in soil microcosms upon the addition of (13)C-labeled biomass of plant, fungal, and bacterial origin. We demonstrate that both fungi and bacteria are involved in the assimilation and mineralization of C from the major complex sources existing in soil. Decomposer fungi are, however, better suited to utilize plant biomass compounds, whereas the ability to utilize fungal and bacterial biomass is more frequent among bacteria. Due to the ability of microorganisms to recycle microbial biomass, we suggest that the decomposer food web in forest soil displays a network structure with loops between and within individual pools. These results question the present paradigms describing food webs as hierarchical structures with unidirectional flow of C and assumptions about the dominance of fungi in the decomposition of complex organic matter.

Wood ants maintain a stable, high temperature in their nests from spring to autumn. Much of the heat is generated by the nest's microbial community, which might be differently affected by the addition of available carbon (C) sources in spring, when the nest temperature increases, than in summer, when the nest temperature is maintained at a high level. We used an incubation experiment to examine the effects of honeydew and resin on microbial activity and biomarkers' contents in ant nest and forest floor substrates. The effects of resin lasted longer than those of honeydew. Microbial activity was higher in the ant nest substrate than in the forest floor substrate, indicating that the microorganisms in the ant nest substrate were better adapted to utilize both C sources. Although bacteria were expected to be dominant after honeydew addition, this was not the case probably because the available C from honeydew had been depleted by the end of the incubation. Fungal biomarkers dominated at 10 °C with both C sources probably because fungi are better able than bacteria to remain active at low temperatures.

The study of soil microbial communities and chemical properties of soil organic matter (SOM) over altitudinal mountain gradients have been regarded as especially useful to better predict and help mitigate the effects of climate change. However, there is a lack of surveys considering altitudinal, seasonal and interannual variations at the same time. Here, we investigated four forest sites, along an altitude gradient (545–2000 m a.s.l.), in spring and autumn during two consecutive years (2014 and 2015) regarding i) soil temperature and physicochemical properties; ii) SOM chemical composition using pyrolysis; iii) soil microbial activity (basal respiration, potential enzyme activities, community level physiological profiles (CLPP)); iv) archaeal, bacterial and fungal abundance (qPCR, phospholipid fatty acid (PLFA) analysis, numbers of culturable heterotrophic bacteria); and v) microbial community structure (PLFA analysis). Sites at high altitudes (alpine, subalpine) showed lower mean, maximum and minimum soil temperatures respect to those at lower altitudes (montane, submontane) and were characterized by increased levels of SOM and nutrients, higher archaeal, bacterial and fungal abundance as well as higher microbial activities. Soils at the sites at higher altitudes presented a higher humification degree of SOM, as demonstrated by an enhanced content of aromatic compounds and fatty acids. The seasonal effect determined a rise in the content of SOM, some soil nutrients, basal respiration and microbial abundance in autumn respect to spring over the altitudinal gradient as well as a change in the structure of microbial community and SOM molecular composition. Interannuality had a significant effect on the relative abundance of various chemical groups of SOM compounds and on the ratios of microbial groups, and produced an increase in microbial abundance in the second study year, as a consequence of the increased soil maximum temperatures recorded in this year. CLPP showed to be site-specific with limited seasonal and interannual variations. Altitudinal, seasonal and interannual changes in chemical composition of SOM were explained by variations in PLFA-based microbial community structure as well as in the abundance of bacteria and fungi, which, in turn, were affected by climatic conditions.

Respiration is a simple method to describe the overall condition of soils. Most usually, it is suggested CO2 evaluation after 7 days. Our study compared the relationship between soil respiration measured at different periods of times (one and eight weeks and cumulative respiration), as well as basic soil properties and the quantification microbial and fungal communities and their activity. We located our research on three sites with post-mine soils in Poland afforested by pine, birch and oak. Each site had soil derived from different substrate. The samples were taken from the fermentation layer (Oe) and mineral soil layer (A – at 0–5 cm beneath the Oe). In both studied layers basic soil properties such as: pH and C, N contents were analysed while soil texture was determined in A layer only. Microbial respiration was measured after each week of the eighth weeks incubation period. Microbial analyses included determination of ergosterol and phospholipid fatty acid (PLFA) profiles. Microbial respiration was nearly two time higher after the first week than the eighth week in both soil layers. Forest type and soil substrate had an effect on respiration in the Oe layer at both measurement times. Respiration in the A layer measured in the eighth week was affected only by the soil substrate. In the Oe layer, fungal decomposers play a lead role, and their activity was affected both by tree species and soil substrate. In the A layer, however, bacteria activity was predominated and was affected by tree species and substrate composition.

The objective of this work was to test the PCB-degrading abilities of two white-rot fungi, namely Pleurotus ostreatus and Irpex lacteus, in real contaminated soils with different chemical properties and autochthonous microflora. In addition to the efficiency in PCB removal, attention was given to other important parameters, such as changes in the toxicity and formation of PCB transformation products. Moreover, structural shifts and dynamics of both bacterial and fungal communities were monitored using next-generation sequencing and phospholipid fatty acid analysis. The best results were obtained with P. ostreatus, which resulted in PCB removals of 18.5, 41.3 and 50.5% from the bulk, top (surface) and rhizosphere, respectively, of dumpsite soils after 12 weeks of treatment. Numerous transformation products were detected (hydoxylated and methoxylated PCBs, chlorobenzoates and chlorobenzyl alcohols), which indicates that both fungi were able to oxidize and decompose the aromatic moiety of PCBs in the soils. Microbial community analysis revealed that P. ostreatus efficiently colonized the soil samples and suppressed other fungal genera. However, the same fungus substantially stimulated bacterial taxa that encompass putative PCB degraders. The results of this study finally demonstrated the feasibility of using this fungus for possible scaled-up bioremediation applications.

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past. Electronic supplementary material The online version of this article (doi:10.1007/s00248-016-0904-8) contains supplementary material, which is available to authorized users.

Investigations on how tree species modify decomposition of understory litter have rarely been conducted, although potentially having impacts on soil carbon stocks and stability. The aim of our study was to disentangle the effects different tree species (alder, spruce, oak, and willow) exert on litter decomposition by comparing decomposition patterns and microbial measures (phospholipid fatty acids and microbial DNA) of both tree and understory (Calamagrostis epigejos) litter exposed at the respective tree species stands of a common garden experiment. An initially uniform mass loss of understory litter exposed at the stands suggests that inherent litter quality (assessed by C:N ratios and lignin content) was the major driver in early decomposition. However, in later stages of our experiment, decomposition of understory litter began to differ among the stands, suggesting a delayed tree species effect. Here, differences in microbial community composition caused by tree species identity (e.g., through varying N supply or phenolics leached from low-quality litter) were likely the major determinants affecting the decomposition of understory litter. However, in these advanced decomposition stages, tree species identity only partly altered microbial communities associated with understory litter. These results indicate that the development of microbial communities on understory litter (and its decay) is likely a combined result of inherent chemical composition and tree species identity.

The study addresses the role of microbial community and soil properties development on species replacement during succession. During succession, plants directly and indirectly affect microbial communities and soil properties. Such belowground changes then feedback on plants. Although of both substrate-plant and microflora–plant interactions have been studied, the joint interactions of all three remain underexplored. We studied the effects of the microbial community and substrate on plants in a full-factorial experiment. Substrates from 10- and 50-year-old post-mining sites were sterilized. Suspensions from the early and late substrate, each applied in two dilutions (high and low diversity), were used to inoculate each substrate. Substrates were sown with three early and three late successional plant species both with one grass and two herbs. Aboveground plant biomass was higher in the late than early successional substrate. Grasses were not stimulated by higher diversity of microbial community while herbs grew better with the more diverse microbial community. Late successional herbs grew better with the late successional microbial community but early successional herbs grew well with both early and late microbial community. Grasses were thus very responsive to substrate quality and were not stimulated by microbial diversity while herbs responded positively to microbial diversity. This may affect species replacement during succession, from early succession herbs not showing strong responses to microbial community composition to late succession herbs showing specific responses to microbial communities, with grasses responding to nutrient conditions. Also nutrient supply and reduction of microbial community is likely to support grasses over herbs.

Oxidative stress induced by zero-valent iron nanoparticles (nZVIs) was used to improve lipid accumulation in various oleaginous and non-oleginous yeasts-Candida sp., Kluyveromyces polysporus, Rhodotorula glutinis, Saccharomyces cerevisiae, Torulospora delbrueckii, Trichosporon cutaneum, and Yarrowia lipolytica. The highest lipid yields occurred at 9-13 mg/L nZVIs. Gas chromatography-mass spectrometry was used for the quantitative and qualitative analysis of the fatty acids. It showed an increasing abundance of polyunsaturated fatty acids, especially essential linoleic acid, in the presence of nZVIs. Our results suggest that nZVIs can be used to improve not only lipid production by oleaginous microorganisms but also the nutritional value of biosynthesized unsaturated fatty acids.

To understand why excrements of soil macrofauna often decompose more slowly than leaf litter, we fed Bibio marci larvae the litter of tree species differing in litter quality ( Alnus glutinosa , Salix caprea , and Quercus robur ) and then measured respiration induced by litter and excrements. We also measured respiration induced by the same litter artificially modified to mimic faunal effects; the litter was modified by grinding, grinding with alkalinization to pH = 11, grinding with coating by kaolinite, and grinding with both alkalinization and coating. Decomposition of excrements tended to be slower for willow and was significantly slower for oak and alder than for the corresponding litter. With oak, decomposition was slower for all artificially modified litter than for non-modified litter. The reduction in the decomposition was similar for excrements and for alder and willow litter that was ground, coated, and alkalinized. In alder, a similar reduction was found in ground and alkalinized litter. 13 C NMR indicated that gut passage increases aliphatic components and decreases polysaccharides. Pyrolysis indicated that gut passage increases the ratio of guaiacyl to hydroxymethyl derivatives in lignin. Our findings indicate that the decreased decomposition rate of excrements might result from the removal of easily available polysaccharides, the increase in aliphatic components, an increase in the resistant components of lignin, the accumulation of microbial cell walls, and the binding of nitrogen into complexes with aromatic components. Several of these mechanisms are supported or determined by litter alkalinization during gut passage.

Digestate from biogas production contains a significant amount in organic matter and N, whereas fly ash from biomass combustion is rich in P and other nutrients. The use of both, as suitable fertilizers, has been shown to improve crop yields and soil properties. A Chernozem soil was used in a pot experiment in which wheat was grown to evaluate the impact of digestate (organic amendment) and fly ash (inorganic amendment) application on soil microbial activity, biomass and community structure. Soil samples were collected after two time-term treatments (30 and 60 days). Digestate application significantly improved soil chemical variables, microbial activity, the substrate average well colour development (SAWCD) and physiological diversity. Bacterial, actinobacterial, and fungal communities were positively affected by digestate addition, as well as microbial biomass. These effects were evident after a short period (30 days), but were more significant after long-term treatment (60 days). However, fly ash did not provoke significant changes in soil microbial activities, qPCR or PLFA at any time of treatment. Nevertheless, with this amendment, some chemical variables were positively affected after 60 days of treatment and the SAWCD revealed different patterns in the use of C sources compared with un-amended and digestate-amended soil at both treatment times. These results suggest that the chemical properties present in digestate may determine its use as a suitable organic amendment because it improves soil health and quality, whereas fly ash did not have a relevant impact on soil microbial activities, qPCR, or PLFA.

Small twigs represent a substantial input of organic carbon into forest soils, but potential influencing factors on their decomposition have rarely been investigated. Here, we studied potential effects of twig size on decomposition and associated composition and activity of microbial communities during decomposition. Because the surface area for microbial colonization and the volume of accessible substrate increases with decreasing twig size, we hypothesized that twig size affects both microbial community and decomposition rate. Litterbags with twigs (Salix caprea) of two different diameters were placed within the litter layer and consecutively collected over a seven-year period. We determined the mass loss and microbial measures after each sampling event. The observed microbial parameters suggested a faster microbial colonization of thin twigs, where the proportion of bacteria was higher than in thick twigs. The development of the microbial community in thick twigs was more gradual and the proportion of fungi was higher. Despite this differential and successional development of microbial communities (and against our hypothesis), the mass loss among different twig diameters did not differ after our seven-year experiment, indicating that surface-to-volume ratios, though a primary control on microbial succession, may have limited predictive power for twig decomposition rates.

Wood ant nests are hotspots of nutrients and microbial activity in nutrient-limited coniferous forest ecosystems, as ants accumulate honeydew and nutrients in their nests due to foraging and building activities. In this study we carried out a microcosm experiment focussing on the role of bacteria and protozoa on carbon and nitrogen turnover in nutrient-rich and nutrient-poor litter materials. Two types of litter material, (i) ant nest material or (ii) surrounding forest floor material were sterilized and inoculated either with bacteria alone (B treatment) or with bacteria and protozoa in combination (BP treatment). The litter materials were subsequently incubated in laboratory microcosms for 21 days. Respiration of the microcosms was measured during the whole incubation period and leachates were sampled every week and analysed for ammonium and nitrate. Our results showed lower ammonium leaching and increased respiration in the BP treatment, which could be explained by higher microbial biomass in this treatment. The negative effect of protozoa on ammonium leaching was independent of the type of litter material suggesting that available carbon in nest material supported fixation of nitrogen in the bacterial biomass. Our data show that protozoan grazing can play a critical role in retaining nitrogen in ant nests by increasing microbial activity and biomass, and thereby preventing nitrogen leaching.

Wood ants build large, long-lasting nests and maintain stable high temperatures in nest centers from April to September to support brood development. Similar nest temperatures have been recorded regardless of latitude and altitude, suggesting that nests from colder environments produce more heat than nests from warmer environments. We measured changes in temperature and in situ respiration in nests from 700 and 1000 m a.s.l. We also sampled ants and nest materials from the same nests and measured their respiration at 10 and 20 °C in the laboratory. Both ant and microbial respiration increased greatly as temperature increased in spring, especially at 1000 m, resulting in the increase in nest temperature in spring. Metabolic activity greatly increased for ants in March and for nest microorganisms in April when nutrient contents also increased because of input of plant material and food. Nests from 1000 m maintained similar temperatures as nests from 700 m in summer but were colder in winter. Ants were responsible for the maintenance of high temperatures during summer but metabolic activity did not differ between the two altitudes, suggesting that the increased respiration and heat production in summer by ants at the higher altitude resulted from an increase in numbers of ants per colony.

Without any doubt, endocrine-disrupting compounds (EDCs) represent an environmental risk for wildlife and human beings. Endocrine-disrupting effects were found for many chemicals in products for personal use, industrial compounds and even in classical persistent organic pollutants (POPs). In order to understand the fate of EDCs in the environment, it is highly important to identify and to clarify the biodegradation mechanisms that can lead to their decomposition. Ligninolytic fungi (LF) are interesting microorganisms that are capable of participating in a variety of versatile decomposition mechanisms. The microorganisms represent a useful model group and, moreover, LF or their enzymes can be actively used for decontamination. Potential optimization of the decontamination process provides another important reason why it is necessary for understanding the mechanisms of EDC transformation. This minireview summarizes current knowledge about the LF biodegradation mechanisms of the most important micropollutants (xenoestrogens), including nonylphenols, bisphenol A and 17α-ethinylestradiol and polychlorinated biphenyls as POPs with endocrine-disrupting potency. Generally, LF exhibit the ability to either polymerize the target pollutants or to substantially decompose the original structure using ligninolytic enzymes and cytochrome P-450. Moreover, most of the transformation processes are accompanied by reduction of the endocrine-disrupting activity or ecotoxicity.

The aim of this study was to describe the decomposition of litter along a successive series of sites developed at a post-mining overburden deposit over 12, 21 and 45 years, representing the early, mid and late stages of succession. Litter decomposition was largely dependent on the initial composition of the litters. The tree litter of the mid and late stages decomposed faster than the grass litter of the early stage, with 64, 60 and 35 % of mass lost over 2 years, respectively. The contents of hot-water-soluble C and N, which were the best predictors of litter decay rates, were relatively stable over time in all litters. Neither the nutrient content nor the plant biopolymer composition exhibited convergence during decay, indicating that the litter-derived soil organic matter most likely carries a legacy of the original vegetation. In contrast to the litter chemistry, the development of the microbial community was largely specific to the decay stage and consistent among the litters, showing decreasing fungal dominance in time. Extracellular enzymes were found to be of limited value in the prediction of litter decay rates, chemical transformation or microbial community composition.

The purpose of this study was to develop a fungal bioremediation method that could be used for soils heavily contaminated with persistent organic compounds, such as polyaromatic hydrocarbons (PAHs). Sawmill soil, contaminated with PAHs, was mixed with composted green waste (1:1) and incubated with or without fungal inoculum. The treatments were performed at the laboratory and field scales. In the laboratory scale treatment (starting concentration 3500 mg kg −1 , sum of 16 PAH) the high molecular weight PAHs were degraded significantly more in the fungal-inoculated microcosms than in the uninoculated ones. In the microcosms inoculated with Phanerochaete velutina , 96% of 4-ring PAHs and 39% of 5- and 6-ring PAHs were removed in three months. In the uninoculated microcosms, 55% of 4-ring PAHs and only 7% of 5- and 6-ring PAHs were degraded. However, during the field scale (2 t) experiment at lower starting concentration (1400 mg kg −1 , sum of 16 PAH) the % degradation was similar in both the P. velutina -inoculated and the uninoculated treatments: 94% of the 16 PAHs were degraded in three months. In the field scale experiment the copy number of gram-positive bacteria PAH-ring hydroxylating dioxygenase genes was found to increase 1000 fold, indicating that bacterial PAH degradation also played an important role.

Exotic plant invasions often change ecosystem properties with subsequent impacts on the structure of invaded communities. Despite an increasing knowledge of post-invasion ecosystem changes, these modifications are only rarely studied within the temporal context of ongoing invasions. In this study we investigated 19 soil chemical and biological characteristics, as well as light conditions, in uninvaded grassland sites and compared them with those from sites invaded by giant hogweed (Heracleum mantegazzianum) for different times (from 11 to 48 years). We further related variation in these soil and light characteristics to richness and productivity of native plant species and hogweed cover measured in the field, and to common-garden performance of hogweed grown in soil inocula from the same sites. Hogweed presence significantly reduced red/far-red light ratios but increased soil pH. Longer invasion history was associated with increasing soil conductivity and content of extractable phosphorus. There were also parameters that displayed opposite trends in different periods of invasion such as fungal/bacterial ratios or relative amount of photosynthetically active radiation (ΔPAR). These parameters initially increased (fungal/bacterial ratio) or decreased (ΔPAR), but after reaching a certain breakpoint they tended to return to pre-invasion conditions. Differences in native species richness were best correlated with light availability and soil pH, and productivity with composition of soil microbial communities. Differences in hogweed cover were associated with soil pH and conductivity. The variation in hogweed performance in a common garden was related to the composition of soil microbial communities, soil conductivity and light availability of sites from which soil inocula were collected. This study documents that ecosystem properties can be altered not only by an invasion event but are further modified as the invasion proceeds. These ecosystem changes likely underlie long-term impacts of invasive plants on native communities.

Soil biota were studied at four post-mining areas along a climatic gradient in the USA. The natural climax vegetation was hardwood forest (TN, IN), tallgrass prairie (IL), or shortgrass prairie (WY). Two chronosequences were used in each state, each contained young (2–5 y) and old (15–20 y) post-mining and a site with the area's climax vegetation. All sites were sampled in spring 2008 and 2011. Microbial biomass, microbial respiration, ergosterol, composition of microbial community (using phospholipid fatty acids), community composition of soil nematodes and macrofauna, soil chemistry, and soil microstructure (using thin soil sections) were studied. Total carbon and nitrogen content increased with successional age, while total phosphorus was often greater in young post-mining sites than in climax sites. Microbial biomass in forest chronosequences increased with age, actinobacteria were associated with prairie sites, and fungi were associated with forest sites. Root-feeding nematodes and macroflora were dominant in the shortgrass prairie sites. Earthworms were absent in such shortgrass sites but were present in the wetter, eastern sites. In forest chronosequences, other saprophages, litter transformers, and microphagous groups were also abundant. Absence of saprophagous groups, and especially earthworms, resulted in the absence of bioturbation in shortgrass prairie sites while worm casts and other biogenic structures formed an important part of the soil profile in other chronosequences. Both young and old restoration sites were much closer to the climax condition in shortgrass prairie than in the other sites. The shortgrass prairie soil community contained abundant root-feeding organisms, which may establish quicker than the more saprophagous soil biota that were abundant at the other sites. In chronosequences other than the one in shortgrass prairie, bioturbation played an important role in topsoil formation, which result to complex soil profile development compare to shortgrass prairie which may contribute to faster recovery communities in shortgrass prairie in comparison with tallgrass prairie and forest.

Flumequine, a fluoroquinolone antibiotic, is applied preferably in veterinary medicine, for stock breeding and treatment of aquacultures. Formation of drug resistance is a matter of general concern when antibiotics such as flumquine occur in the environment. Thus, biodegradation of flumequine in solution was investigated using five different ligninolytic fungi. Irpex lacteus, Dichomitus squalens, and Trametes versicolor proved most efficient and transformed more than 90% of flumequine within 6 or even 3 days. Panus tigrinus and Pleurotus ostreatus required up to 14 days to remove >90% of flumequine. Analyses of the metabolites by liquid chromatography-mass spectrometry suggest different transformation pathways for the different fungal strains. Structure proposals were elaborated for 8 metabolites. 7-Hydroxy-flumequine and flumequine ethyl ester were identified as common metabolites produced by all ligninolytic fungi. The largest variety of metabolites was formed by D. squalens. Residual antibacterial activity of the metabolite mixtures was tested using gram-positive and gram-negative bacteria. While for the less efficient P. tigrinus and P. ostreatus cultures the antibacterial activities corresponded to the residual concentrations of flumequine, a remarkable antibacterial activity remained in the D. squalens cultures although flumequine was transformed to more than 90%. Obviously, antibacterially active transformation products were formed by this fungal strain.

We conducted a factorial microcosm experiment to determine whether the effects of soil fauna on N dynamics differ in tilled vs. non-tilled soil with and without a legume. Soil monoliths were taken from two neighboring fields that had been continually tilled or non-tilled for the past 15 years; the soil was defaunated, and meso- and macrofauna were added back to half the monoliths. In addition, half of the monoliths were planted with a legume ( Lotus corniculatus ), and the other half were maintained without vegetation. Nitrogen losses by leaching from soil were periodically determined. After 3 months, the plants were harvested, and the soil and plants in each treatment were analyzed for, plant biomass, microbial respiration and biomass, PLFA. Fauna significantly increased N loss only in the tilled soil with legume and significantly decreased N loss in the non-tilled soil without legume. When fauna were absent, legume biomass was higher in the non-tilled soil than in the tilled soil, but when fauna were present, legume biomass did not differ between tilled and non-tilled soil. Our results show that non-tilled soil with fauna conserves soil N and enhances the efficient use of N by plants.

The activities of extracellular enzymes that participate in the decomposition of litter and organic matter in forest soils depend on, among other factors, temperature and soil moisture content and also reflect the quality of litter, which changes dramatically after a short litterfall period. Here, we explored the effects of soil temperature and seasonality on the sizes of extracellular enzyme pools and activities in a temperate hardwood forest soil with dominant Quercus petraea (cambisol, mean annual temperature 9.3 °C). We hypothesized that the most significant variation of enzyme activity would occur in the litter, which faces greater variations in temperature, moisture content and chemical quality during the season, which decrease with soil depth. The site exhibited relatively large seasonal temperature differences and moderate changes in soil moisture content. Enzyme activity, microbial biomass, soil moisture content, temperature and pH were monitored for three years in the litter (L), organic horizon (O) and upper mineral horizon (Ah). Enzyme activity in vitro strongly increased with temperature until 20–25 °C, the highest temperatures recorded in situ. While no significant differences in the pools of most extracellular enzymes and in the content of microbial biomass were found among the seasons, enzyme activity typically increased during the warm period of the year, especially in the O and Ah horizons. Approximately 63%, 64%, and 69% of total annual activity was recorded during the warm period of the year in the L, O, and Ah horizons, respectively. Significant positive correlations were observed between soil moisture content and fungal biomass, but not bacterial biomass, indicating a decrease of the fungal/bacterial biomass ratio under dry conditions. The effect of moisture on enzyme activities was not significant except for endoxylanase in the litter. If soil temperature rises as predicted due to global climate change, enzyme activity is predicted to rise substantially in this ecosystem, especially in winter, when decomposition is not limited by drought and fresh litter that can decompose rapidly is present.

The aim of this work was to quantify the effects of vegetation on the activity of extracellular enzymes in the litter and soil. To achieve this, we investigated a set of post-mining sites in a brown-coal mine deposit area near Sokolov, Czech Republic. The sites were 22–33 years old and had been established on the same initial substrate by planting with six tree genera or leaving for spontaneous revegetation, with four replicate sites per vegetation type. The activity of extracellular hydrolytic and oxidative enzymes and the microbial community composition of the litter and topsoil were compared in the spring, summer and autumn using the dominant tree, pH, soil nutrient content and soil moisture as the explanatory variables. Sites under individual trees exhibited significant differences in the chemical properties of both the litter and soil, and the tree effect was identified as the most important factor affecting the activity of extracellular enzymes either directly or in the interaction with seasonal effects, although not all pairs of tree species were significantly different from each other. Seasonal effects on enzyme activity were only important in the litter. The effects of dominant trees and of seasons contributed equally to the variation in the microbial community composition at individual sites. Only a minor part of the tree effect could be explained by differences in the litter or soil chemistry. Among the chemical variables, the N content most affected the microbial biomass content, increasing fungal (but not bacterial) biomass in the litter and bacterial (but not fungal) biomass in the soil. The results indicate that other factors, such as nutrient quality or the specific association of microorganisms with rhizospheres of different trees or the understory, are likely important mediators of the vegetation effects. When comparing the revegetated sites with sites under spontaneous succession, the enzyme activities and microbial biomass were similar except for the sites revegetated with Alnus which may indicate similar rates of soil development at revegetated and succession sites. Spontaneous succession in temperate Europe may thus be a suitable option for land restoration.

The white rot fungus Pleurotus ostreatus is able to completely remove the synthetic hormone 17α-ethinylestradiol (EE2, 200 μg in 20 mL) from a liquid complex or mineral medium in 3 or 14 days, respectively. Its efficiency has also been documented in the removal of estrogenic activity that correlated with the EE2 degradation. A set of in vitro experiments using various cellular and enzyme fractions has been performed and the results showed that EE2 was degraded by isolated laccase (about 90% within 24 h). The degradation was also tested with concentrated extracellular liquid where degradation reached 50% mainly due to the laccase activity; however, after a supplementation with H₂O₂ and Mn²⁺, residual manganese-dependent peroxidase activities (40 times lower than Lac) raised the degradation to 100%. Moreover, the intracellular fraction and also laccase-like activity associated with fungal mycelium were found to be efficient in the degradation too. Isolated microsomal proteins appeared to also be involved in the process. The degradation was completely suppressed in the presence of cytochrome P-450 inhibitors, piperonylbutoxide and carbon monoxide, indicating a role of this monooxygenase in the degradation process. Attention was also paid to monitoring of changes in the estrogenic activity during these particular in vitro experiments when mainly degradations related to ligninolytic enzymes were found to decrease the estrogenic activity with EE2 removal proportionally. Several novel metabolites of EE2 were detected using different chromatographic method with mass spectrometric techniques (LC-MS, GC-MS) including also [¹³C]-labeled substrates. The results document the involvement of various different simultaneous mechanisms in the EE2 degradation by P. ostreatus by both the ligninolytic system and the eukaryotic machinery of cytochromes P-450.

The white rot fungus Pleurotus ostreatus HK 35, which is also an edible industrial mushroom commonly cultivated in farms, was tested in the degradation of typical representatives of endocrine disrupters (EDCs; bisphenol A, estrone, 17β-estradiol, estriol, 17α-ethinylestradiol, triclosan and 4-n-nonylphenol); its degradation efficiency under model laboratory conditions was greater than 90% within 12 days and better than that of another published strain P. ostreatus 3004. A spent mushroom substrate from a local farm was tested for its applicability in various batch and trickle-bed reactors in degrading EDCs in model fortified and real communal wastewater. The reactors were tested under various regimes including a pilot-scale trickle-bed reactor, which was finally tested at a wastewater treatment plant. The result revealed that the spent substrate is an efficient biodegradation agent, where the fungus was usually able to remove about 95% of EDCs together with suppression of the estrogenic activity of the sample. The results showed the fungus was able to operate in the presence of bacterial microflora in wastewater without any substantial negative effects on the degradation abilities. Finally, a pilot-scale trickle-bed reactor was installed in a wastewater treatment plant and successfully operated for 10days, where the bioreactor was able to remove more than 76% of EDCs present in the wastewater.

The feasibility of decontaminating creosote-treated wood (CTW) by co-composting with agricultural wastes was investigated using two bulking agents, grass cuttings (GC) and broiler litter (BL), each employed at a 1:1 ratio with the matrix. The initial concentration of total polycyclic aromatic hydrocarbons (PAHs) in CTW (26,500 mg kg(-1)) was reduced to 3 and 19% after 240 d in GC and BL compost, respectively. PAH degradation exceeded the predicted bioaccesible threshold, estimated through sequential supercritical CO2 extraction, together with significant detoxification, assessed by contact tests using Vibrio fisheri and Hordeum vulgare. GC composting was characterized by high microbial biomass growth in the early phases, as suggested by phospholipid fatty acid analyses. Based on the 454-pyrosequencing results, fungi (mostly Saccharomycetales) constituted an important portion of the microbial community, and bacteria were characterized by rapid shifts (from Firmicutes (Bacilli) and Actinobacteria to Proteobacteria). However, during BL composting, larger amounts of prokaryotic and eukaryotic PLFA markers were observed during the cooling and maturation phases, which were dominated by Proteobacteria and fungi belonging to the Ascomycota and those putatively related to the Glomeromycota. This work reports the first in-depth analysis of the chemical and microbiological processes that occur during the co-composting of a PAH-contaminated matrix.

This study examined laccase production by the fungus Trametes versicolor while it was degrading Delor 103, a commercial mixture of polychlorinated biphenyls (PCBs). Delor 103 (10 mg l−1) caused a significant increase in laccase activity in the culture supernatants in nitrogen-limited medium cultures (the maximum activity of 1439 U g−1 was 42 times that of the controls) where the induction effect was suppressed in a malt extract – glucose medium. Similarly, laccase activity stimulation depended on the growth phase of the fungal cultures. Higher laccase activities that developed in Delor 103 treated with non-growing fungal cultures correlated with an up to 2.6-fold greater laccase gene expression, which was analysed by the quantitative polymerase chain reaction (qPCR). Simultaneously, laccases of different pIs were formed in response to Delor 103 treatment. When analysing laccase gene expression by degenerated primers and denaturing gradient gel electrophoresis, differences between transcript profiles of Delor 103-treated and untreated control cultures were observed. Despite all the differences in laccase production, no PCB removal was observed in the non-growing T. versicolor cultures. This makes the connection between laccase production and PCB degradation uncertain.

We investigated the abilities of several perspective ligninolytic fungal strains to degrade 12 mono-, di- and trichloro representatives of chlorobenzoic acids (CBAs) under model liquid conditions and in contaminated soil. Attention was also paid to toxicity changes during the degradation, estimated using two luminescent assay variations with Vibrio fischeri. The results show that almost all the fungi were able to efficiently degrade CBAs in liquid media, where Irpex lacteus, Pycnoporus cinnabarinus and Dichomitus squalens appeared to be the most effective in the main factors: degradation and toxicity removal. Analysis of the degradation products revealed that methoxy and hydroxy derivatives were produced together with reduced forms of the original acids. The findings suggest that probably more than one mechanism is involved in the process. Generally, the tested fungal strains were able to degrade CBAs in soil in the 85-99% range within 60 days. Analysis of ergosterol showed that active colonization is an important factor for degradation of CBAs by fungi. The most efficient strains in terms of degradation were I. lacteus, Pleurotus ostreatus, Bjerkandera adusta in soil, which were also able to actively colonize the soil. However, in contrast to P. ostreatus and I. lacteus, B. adusta was not able to significantly reduce the measured toxicity.

To investigate the link between the functionality and the diversity of microbial communities under strong selective pressure from pollutants, two types of mesocosms that simulate natural attenuation and phytoremediation were generated using soil from a site highly contaminated with jet fuel and under air-sparging treatment. An increase in the petroleum hydrocarbon concentration from 4900 to 18 500 mg kg−1 dw soil simulated a pollutant rebound (postremediation pollutant reversal due to residual contamination). Analysis of soil bacterial communities by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments showed stronger changes and selection for a phylogenetically diverse microbial population in the mesocosms with pollutant-tolerant willow trees. Enumeration of the main subfamilies of catabolic genes characteristic to the site detected a rapid increase in the degradation potential of both systems. A marked increase in the abundance of genes encoding extradiol dioxygenases with a high affinity towards various catecholic substrates was found in the planted mesocosms. The observed adaptive response to the simulated pollutant rebound, characterized by increased catabolic gene abundance, but with different changes in the microbial structure, can be explained by functional redundancy in biodegrading microbial communities.

The common grass Calamagrostis epigeions produces a large amount of dead biomass, which remain above the soil surface for many months. In this study, we determined how exposure of dead biomass above the soil affects its subsequent decomposition in soil. Collected dead standing biomass was divided in two parts, the first one (initial litter) was stored in a dark, dry place. The other part was placed in litterbags in the field. The litterbags were located in soil, on the soil surface, or hanging in the air without contact with soil but exposed to the sun and rain. After 1 year of field exposure, litter mass loss and C and N content were measured, and changes in litter chemistry were explored using NMR and thermochemolysis-GC-MS. The potential decomposability of the litter was quantified by burying the litter from the litterbags and the initial litter in soil microcosms and measuring soil respiration. Soil respiration was greater with litter that had been hanging in air than with all other kinds of litter. These finding could not be explained by changes in litter mass or C:N ratio. NMR indicated a decrease in polysaccharides relative to lignin in litter that was buried in soil but not in litter that was placed on soil surface or that was hanging in the air. Thermochemolysis indicated that the syringyl units of the litter lignin were decomposed when the litter was exposed to light. We postulate that photochemical decay of lignin increase decomposability of dead standing biomass.

The links among the changes in litter chemistry, the activity of extracellular enzymes and the microbial community composition were observed in Quercus petraea litter. Three phases of decomposition could be distinguished. In the early 4-month stage, with high activities of β-glucosidase, β-xylosidase and cellobiohydrolase, 16.4% of litter was decomposed. Hemicelluloses were rapidly removed while cellulose and lignin degradation was slow. In months 4-12, with high endocellulase and endoxylanase activities, decomposition of cellulose prevailed and 31.8% of litter mass was lost. After the third phase of decomposition until month 24 with high activity of ligninolytic enzymes, the litter mass loss reached 67.9%. After 2 years of decay, cellulose decomposition was almost complete and most of the remaining polysaccharides were in the form of hemicelluloses. Fungi largely dominated over bacteria as leaf endophytes and also in the litter immediately before contact with soil, and this fungal dominance lasted until month 4. Bacterial biomass (measured as phospholipid fatty acid content) in litter increased with time but also changed qualitatively, showing an increasing number of Actinobacteria. This paper shows that the dynamics of decomposition of individual litter components changes with time in accordance with the changes in the microbial community composition and its production of extracellular enzymes.

The small-scale distribution of activities of extracellular laccase, Mn-peroxidase, endoglucanase, cellobiohydrolase, β-glucosidase, endoxylanase, β-xylosidase, chitinase, and acid phosphatase were studied in the litter (L) and organic (H) horizons of Quercus petraea forest soil and related to the distribution of microbial biomass. Geostatistical analysis showed that the spatial autocorrelation of the enzyme activities and soil microbial biomass measured as phospholipid fatty acids (PLFA) and ergosterol content occurred at similar scales, typically in the range of tens of centimeters. The size of the spatial structures differed between the L and H horizons; for most of the studied enzymatic processes, litter exhibited a higher spatial variability (smaller autocorrelation distances). The distribution of several enzymes, including laccase, Mn-peroxidase, and some hydrolases, reflected the distribution of fungal biomass. Polysaccharide hydrolases exhibited similar spatial distribution patterns in the L horizon, and their activity coincided with a high fungal/bacterial biomass ratio.

The yellow-green alga Trachydiscus minutus (class Xanthophyta) was cultivated in a standard medium and in media without sulfur and nitrogen. Its yield after a 16-d cultivation reached 13 g dry mass per 1 L medium. The content of oligoenoic ('polyenoic') fatty acid (PUFA), i.e. eicosapentaenoic (EPA), was in excess of 35 % of total fatty acids; the productivity was thus 88 mg/L per d. This result makes the alga a very prospective organism that may serve as a new biotechnological source of single cell oil.

White-rot fungi that are efficient lignin degraders responsible for its turnover in nature have appeared twice in the center of biotechnological research - first, when the lignin degradation process started being systematically investigated and major enzyme activities and mechanisms involved were described, and second, when the huge remediation potential of these organisms was established. Originally, Phanerochaete chrysosporium became a model organism, characterized by a secondary metabolism regulatory pattern triggered by nutrient (mostly nitrogen) limitation. Last decade brought evidence of more varied regulatory patterns in white-rot fungi when ligninolytic enzymes were also abundantly synthesized under conditions of nitrogen sufficiency. Gradually, research was focused on other species, among them Irpex lacteus showing a remarkable pollutant toxicity resistance and biodegradation efficiency. Systematic research has built up knowledge of biochemistry and biotechnological applicability of this fungus, stressing the need to critically summarize and estimate these scattered data. The review attempts to evaluate the information on I. lacteus focusing on various enzyme activities and bioremediation of organopollutants in water and soil environments, with the aim of mediating this knowledge to a broader microbiological audience.

Extracellular lignocellulose-degrading enzymes are responsible for the transformation of organic matter in hardwood forest soils. The spatial variability on a 12 × 12 m plot and vertical distribution (0–8 cm) of the ligninolytic enzymes laccase and Mn-peroxidase, the polysaccharide-specific hydrolytic enzymes endoglucanase, endoxylanase, cellobiohydrolase, 1,4-β-glucosidase, 1,4-β-xylosidase and 1,4-β-N-acetylglucosaminidase and the phosphorus-mineralizing acid phosphatase were studied in a Quercus petraea forest soil profile. Activities of all tested enzymes exhibited high spatial variability in the L and H horizons. Acid phosphatase and 1,4-β-N-acetylglucosaminidase exhibited low variability in both horizons, while the variability of Mn-peroxidase activity in the L horizon, and endoxylanase and cellobiohydrolase activities in the H horizon were very high. The L horizon contained 4× more microbial biomass (based on PLFA) and 7× fungal biomass (based on ergosterol content) than the H horizon. The L horizon also contained relatively more fungi-specific and less actinomycete-specific PLFA. There were no significant correlations between enzyme activities and total microbial biomass. In the L horizon cellulose and hemicellulose-degrading enzymes correlated with each other and also with 1,4-β-N-acetylglucosaminidase and acid phosphatase activities. Laccase, Mn-peroxidase and acid phosphatase activities correlated in the H horizon. The soil profile showed a gradient of pH, organic carbon and humic compound content, microbial biomass and enzyme activities, all decreasing with soil depth. Ligninolytic enzymes showed preferential localization in the upper part of the H horizon. Differences in enzyme activities were accompanied by differences in the microbial community composition where the relative amount of fungal biomass decreased and actinomycete biomass increased with soil depth. The results also showed that the vertical gradients occur at a small scale: the upper and lower parts of the H horizon only 1 cm apart were significantly different with respect to seven out of nine activities, microbial biomass content and community composition.

Due to the production of lignocellulose-degrading enzymes, saprotrophic basidiomycetes can significantly contribute to the turnover of soil organic matter. The production of lignin- and polysaccharide-degrading enzymes and changes of the chemical composition of litter were studied with three isolates from a Quercus petraea forest. These isolates were capable of fresh litter degradation and were identified as Gymnopus sp., Hypholoma fasciculare and Rhodocollybia butyracea. Within 12 weeks of incubation, H. fasciculare decomposed 23%, R. butyracea 32% and Gymnopus sp. 38% of the substrate dry mass. All fungi produced laccase and Mn-peroxidase (MnP) and none of them produced lignin peroxidase or other Mn-independent peroxidases. There was a clear distinction in the enzyme production pattern between R. butyracea or H. fasciculare compared to Gymnopus sp. The two former species caused the fastest mass loss during the initial phase of litter degradation, accompanied by the temporary production of laccase (and MnP in H. fasciculare) and also high production of hydrolytic enzymes that later decreased. In contrast, Gymnopus sp. showed a stable rate of litter mass loss over the whole incubation period with a later onset of ligninolytic enzyme production and a longer lasting production of both lignin and cellulose-degrading enzymes. The activity of endo-cleaving polysaccharide hydrolases in this fungus was relatively low but it produced the most cellobiose hydrolase. All fungi decreased the C/N ratio of the litter from 24 to 15–19 and Gymnopus sp. also caused a substantial decrease in the lignin content. Analytical pyrolysis mass spectrometry of litter decomposed by this fungus showed changes in the litter composition similar to those caused by white-rot fungi during wood decay. These changes were less pronounced in the case of H. fasciculare and R. butyracea. All fungi also changed the mean masses of humic acid and fulvic acid fractions isolated from degraded litter. The humic acid fraction after degradation by all three fungi contained more lignin and less carbohydrates. Compared to the decomposition by saprotrophic basidiomycetes, litter degradation in situ on the site of fungal isolation resulted in the relative enrichment of lignin and differences in lignin composition revealed by analytical pyrolysis. It can most probably be explained by the participation of non-basidiomycetous fungi and bacteria during natural litter decomposition.

Bioavailability of pollutants in contaminated soils represents an important factor influencing the bioremediation process. We investigated the impact of the bioavailability of polycyclic aromatic hydrocarbons (PAHs) on the efficacy of mycoremediation of aged matrices. Two historically contaminated soils, differing in both overall PAH concentrations (2320 vs. 612 mg PAHs kg - 1 ) and in the relative amount of the non-bioavailable fraction (4.0 vs. 32%, respectively), were incubated with two white rot fungi – Irpex lacteus and Pleurotus ostreatus. When relating biodegradation results with the amount of PAH bioavailable fractions estimated by sequential supercritical fluid extractions, the correlation coefficients ranged from 0.60 to 0.83. In order to assess a possible increase of the mycoremediation efficiency, four different mobilizing agents (MAs), i.e. soybean oil, Tween 20, Tween 80 and olive-mill wastewater, were added to soil prior to fungal incubations. The addition of MAs to the soil with a negligible amount of the non-bioavailable fraction had either a limited or even a negative impact on PAH degradation. The same was true also in the case of the other soil, characterized by a larger non-bioavailable fraction. Both white rot fungi under study markedly degraded PAHs in historically contaminated soils differing significantly in PAH content and the bioavailability. However, both the fungi performed better in the soil with higher pollutant bioavailability. Consequently, a preliminary determination of non-bioavailable fraction might provide a useful indication of the performance of bioremediation treatment.