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In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound‐building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies., We have previously shown that the fungal and bacterial communities in nests of ants Formica exsecta are distinct from those in the surrounding soil. Now, the results from our three‐year study show that the nests also provide a temporally stable environment, where microbial taxa, less tolerant of climatic fluctuations, could survive through unfavorable seasons. The nest could thus act as a reservoir for such microbial inocula, promoting the divergence of the nest communities over time.

Arbuscular mycorrhizal fungi (AMF) enhance plant phosphorus uptake, increase soil water holding abilities, reduce soil erosion and can protect their hosts from soil-borne pathogens. Hence, AMF play an important part in improving sustainable agricultural practices, and information about the effects of different preceding crop species on the following crop's AMF well-being is crucial for designing crop rotations. We studied onion root and soil microbial diversity and onion root AMF colonization rates after being preceded by three AMF hosting and one non-hosting green manure crop species in a boreal climate organic field. One-season cultivation of different preceding green manure crops did not have a strong effect on AMF colonization or microbial diversity in onion roots nor in the surrounding soil. Onions had high AMF colonization and microbial diversity after all four preceding crops. The overall fungal and bacterial populations of the soil reacted more strongly to seasonal variations than preceding crops. The study suggests that one season is a too short time to influence the AMF community in boreal climate organic fields with conventional tillage. Thus, non-host preceding crops can also be used in rotations, especially together with AMF host crops.

Mycorrhizal fungi have a strong impact on soil biota. In this study, bacterial and archaeal populations in different parts of Suillus bovinus - Pinus sylvestris mycorrhizospheres in boreal forest were quantified and identified by DNA analysis. The numbers of bacterial and archaeal 16S rRNA gene copies were highest in uncolonized humus and lowest in fruiting bodies. The numbers of bacterial 16S rRNA gene copies varied from 1.3 × 107 to 3.1 × 109 copies g−1 fw and archaeal copies from 4.1 × 107 to 9.6 × 108 copies g−1 fw. The relatively high number of archaeal 16S rRNA gene copies was likely due to the cold and highly organic habitat. The presence of hyphae appeared to further promote archaeal numbers and the archaea:bacteria ratio was over one in samples containing only fungal material. Most detected archaea belonged to terrestrial Thaumarchaeota. Proteobacteria, Actinobacteria and Acidobacteria were predictably the dominating bacterial taxa in the samples with clear trend of Betaproteobacteria preferring the pine root habitats. acceptedVersion

In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenarchaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria. acceptedVersion

Isozyme expression of nutrient-mobilizing and defence-related enzymes were examined in different functional components of intact Scots pine (Pinus sylvestris L.) ectomycorrhizal root systems developed in natural unsterilized forest humus. Scots pine seedlings colonized by Suillus bovinus (L. ex Fr.) O. Kuntze or Paxillus involutus (Batsch ex Fr.) strains were grown on humus in two-dimensional Perspex⌖ microcosms to allow development of complete ectomycorrhizal root systems. Soluble proteins from uncolonized short roots, whole mycorrhizal root tips or dissected mantle and core fractions, fungal strands and the outermost soil colonizing fine hyphae were subjected to native polyacrylamide gel electrophoresis and stained to detect esterase, acid phosphatase, peroxidase and different polyphenoloxidase isozyme activities. Tissue-specific esterase isozymes were detected in all components and most, including unique Hartig net isozymes, were of fungal origin. High fungal acid phosphatase activities were detected in mycorrhiza and fine hyphae of S. bovinus, supporting earlier findings of active phosphatase activity at the fungal interface in the Hartig net region and in the fine hyphal margins of extramatrical mycelium actively colonizing the humus. All compartments in the P. involutus mycorrhizosphere had weaker acid-phosphatase activities. Peroxidases formed a large part of the soluble-protein content in non-mycorrhizal short roots. The amount of peroxidases, on a tissue f. wt basis, was similar in mycorrhizal and non-mycorrhizal roots, but differential isozyme expression was detected, indicating a change in root peroxidase activities following mycorrhiza formation. The expression of DL-3,4-dihydroxyphenylalanine metabolizing polyphenol oxidase enzymes was reduced in mycorrhizas compared with non-mycorrhizal short roots. In the extramatrical mycelial components, fine hyphae expressed the highest polyphenoloxidase activity. P. involutus displayed some polyphenol-oxidizing isoenzymes not detected in S. bovinus systems. Laccase activity was not detected in the plant and fungal components examined. It is concluded that enzyme activities and isozyme expression are differentially regulated in the different functional components of Scots pine mycorrhizospheres.

Biotic and abiotic characteristics shape the microbial communities in the soil environment. Manipulation of soil, performed by ants when constructing their nests, radically changes the soil characteristics and creates a unique environment, which differs in its composition, frequency and abundance of microbial taxa, from those in the reference soils. We sampled nests of the mound-building ant Formica exsecta, and the surrounding reference soils over a three-month period, and generated NGS (Illumina MiSeq), and T-RFLP data of the bacterial and fungal communities. We used ordination techniques and network analysis to disclose the community structure, and we assessed the variation in diversity, evenness and enrichment of taxa between the two environments. We also used indicator analysis to identify the potential core microbiome of the nests. Our results show that the bacterial and fungal communities, in the rigorously curated nest environment, are significantly different from those in the reference soils, in terms of community structure and enrichment of characteristic indicator taxa. We demonstrate that the nests represent a niche, where microbial species can adapt and diverge from the communities in the surrounding soils. Our findings contribute to our understanding of the composition and function of microbiomes in fragmented habitats.

Root-colonizing fungi can form mycorrhizal or endophytic associations with plant roots, the type of association depending on the host. We investigated the differences and similarities of the fungal communities of three boreal ericoid plants and one coniferous tree, and identified the community structure of fungi utilizing photosynthates from the plants studied. The fungal communities of roots and soils of Vaccinium myrtillus, Vaccinium vitis-idaea, Calluna vulgaris and Pinus sylvestris were studied in an 18-month-long experiment where the plants were grown individually in natural substrate. Photosynthates utilizing fungi were detected with DNA stable-isotope probing using 13 CO2 (13 C-DNA-SIP). The results indicated that the plants studied provide different ecological niches preferred by different fungal species. Those fungi which dominated the community in washed roots had also the highest 13 C-uptake. In addition, a common root endophyte without confirmed mycorrhizal status also obtained 13 C from all the plants, indicating close plant-association of this fungal species. We detect several fungal species inhabiting the roots of both ericoid mycorrhizal and ectomycorrhizal plants. Our results highlight that the ecological role of co-occurrence of fungi with different life styles (e.g. mycorrhizal or endophytic) in plant root systems should be further investigated.

Coastal ecosystems are highly dynamic and can be strongly influenced by climate change, anthropogenic activities (e.g. pollution) and a combination of the two pressures. As a result of climate change, the northern hemisphere is predicted to undergo an increased precipitation regime, leading in turn to higher terrestrial runoff and increased river inflow. This increased runoff will transfer terrestrial dissolved organic matter (tDOM) and anthropogenic contaminants to coastal waters. Such changes can directly influence the resident biology, particularly at the base of the food web, and can influence the partitioning of contaminants and thus their potential impact on the food web. Bacteria have been shown to respond to high tDOM concentration and organic pollutants loads, and could represent the entry of some pollutants into coastal food webs. We carried out a mesocosm experiment to determine the effects of: 1) increased tDOM concentration, 2) organic pollutant exposure, and 3) the combined effect of these two factors, on pelagic bacterial communities. This study showed significant responses in bacterial community composition under the three environmental perturbations tested. The addition of tDOM increased bacterial activity and diversity, while the addition of organic pollutants led to an overall reduction of these parameters, particularly under concurrent elevated tDOM concentration. Furthermore, we identified 33 bacterial taxa contributing to the significant differences observed in community composition, as well as 35 bacterial taxa which responded differently to extended exposure to organic pollutants. These findings point to the potential impact of organic pollutants under future climate change conditions on the basal coastal ecosystem, as well as to the potential utility of natural bacterial communities as efficient indicators of environmental disturbance. Errata: Rodríguez, J., Gallampois, C. M. J., Timonen, S., Andersson, A., Sinkko, H., Haglund, P., et al. Corrigendum: Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios. Front. Microbiol. 2019;10:2388. DOI: 10.3389/fmicb.2019.02388 ECOCHANGE

Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the antFormica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.

Decades of intensive discharge from industrial activities into coastal systems has resulted in the accumulation of a variety of persistent organic pollutants (POPs) in marine waters and sediments, having detrimental impacts on aquatic ecosystems and the resident biota. POPs are among the most hazardous chemicals originating from industrial activities due to their biotoxicity and resistance to environmental degradation. Bacterial communities are known to break down many of these aromatic compounds, and different members of naturally occurring bacterial consortia have been described to work in syntrophic association to thrive in heavily contaminated waters and sediments, making them potential candidates as bioindicators of environmental pollution. In this study environmental, sampling was combined with chemical analysis of pollutants and high-resolution sequencing of bacterial communities using Next Generation Sequencing molecular biology tools. The aim of the present study was to describe the bacterial communities from marine sediments containing high loads of POPs and to identify relevant members of the resident microbial communities that may act as bioindicators of contamination. Marine sediments were collected from a coastal bay area of the Baltic Sea historically influenced by intense industrial activity, including metal smelting, oil processing, and pulp and paper production. Different types of POPs were detected at high concentrations. Fiberbank sediments, resulting from historic paper industry activity, were found to harbour a clearly distinct bacterial community including a number of bacterial taxa capable of cellulolytic and dechlorination activities. Our findings indicate that specific members of the bacterial communities thrive under increasing levels of POPs in marine sediments, and that the abundances of certain taxa correlate with specific POPs (or groups), which could potentially be employed in monitoring, status assessment and environmental management purposes.

Northern peatlands are often dominated by ericaceous shrub species which rely on ericoid mycorrhizal fungi (ERM) for access to organic sources of nutrients, such as nitrogen (N) and phosphorus (P), and host abundant dark septate endophytes (DSE). Relationships between hosts and fungal symbionts may change during deposition of anthropogenic N and P. We studied the long-term effects of N and P addition on two ericaceous shrubs, Calluna vulgaris and Erica tetralix, at Whim Bog, Scotland by analyzing fungal colonization of roots, enzymatic activity, and fungal species composition. Unexpectedly, the frequency of typical ERM intracellular colonization did not change while the occurrence of ERM hyphae tended to increase and DSE hyphae to decrease. Our findings indicate that altered nutrient limitations shift root associated fungal colonization patterns as well as affecting ericaceous root enzyme activity and thereby decomposition potential. Reduction of recalcitrant fungal biomass in melanized DSE may have implications for peatland C sequestration under nutrient addition.

Rhizophagus irregularis, an arbuscular mycorrhizal fungus, and Bacillus amyloliquefaciens, a bacterium, are microorganisms that promote plant growth. They associate with plant roots and facilitate nutrient absorption by their hosts, increase resistance against pathogens and pests, and regulate plant growth through phytohormones. In this study, eight local plant species in Finland (Antennaria dioica, Campanula rotundifolia, Fragaria vesca, Geranium sanguineum, Lotus corniculatus, Thymus serpyllum, Trifolium repens, and Viola tricolor) were inoculated with R. irregularis and/or B. amyloliquefaciens in autoclaved substrates to evaluate the plant growth−promoting effects of different plant/microbe combinations under controlled conditions. The eight plant species were inoculated with R. irregularis, B. amyloliquefaciens, or both microbes or were not inoculated as a control. The impact of the microbes on the plants was evaluated by measuring dry shoot weight, colonization rate by the arbuscular mycorrhizal fungus, bacterial population density, and chlorophyll fluorescence using a plant phenotyping facility. Under dual inoculation conditions, B. amyloliquefaciens acted as a “mycorrhiza helper bacterium” to facilitate arbuscular mycorrhizal fungus colonization in all tested plants. In contrast, R. irregularis did not demonstrate reciprocal facilitation of the population density of B. amyloliquefaciens. Dual inoculation with B. amyloliquefaciens and R. irregularis resulted in the greatest increase in shoot weight and photosynthetic efficiency in T. repens and F. vesca.

In this study, the bacterial populations of roots and mycospheres of the boreal pine forest ericoid plants, heather (Calluna vulgaris), bilberry (Vaccinium myrtillus), and lingonberry (Vaccinium vitis-idaea), were studied by qPCR and next-generation sequencing (NGS). All bacterial communities of mycosphere soils differed from soils uncolonized by mycorrhizal mycelia. Colonization by mycorrhizal hyphae increased the total number of bacterial 16S ribosomal DNA (rDNA) gene copies in the humus but decreased the number of different bacterial operational taxonomic units (OTUs). Nevertheless, ericoid roots and mycospheres supported numerous OTUs not present in uncolonized humus. Bacterial communities in bilberry mycospheres were surprisingly similar to those in pine mycospheres but not to bacterial communities in heather and lingonberry mycospheres. In contrast, bacterial communities of ericoid roots were more similar to each other than to those of pine roots. In all sample types, the relative abundances of bacterial sequences belonging to Alphaproteobacteria and Acidobacteria were higher than the sequences belonging to other classes. Soil samples contained more Actinobacteria, Deltaproteobacteria, Opitutae, and Planctomycetia, whereas Armatimonadia, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia were more common to roots. All mycosphere soils and roots harbored bacteria unique to that particular habitat. Our study suggests that the habitation by ericoid plants increases the overall bacterial diversity of boreal forest soils.

Prokaryotes colonize decaying wood and contribute to the degradation process, but the dynamics of prokaryotic communities during wood decay is still poorly understood. We studied the abundance and community composition of Bacteria and Archaea inhabiting naturally decaying Picea abies logs and tested the hypothesis that the variations in archaeal and bacterial abundances and community composition are coupled with environmental parameters related to the decay process. The data set comprises >500 logs at different decay stages from five geographical locations in south and central Finland. The results show that Bacteria and Archaea are an integral and dynamic component of decaying wood biota. The abundances of bacterial and archaeal 16S rRNA genes increase as wood decay progresses. Changes in bacterial community composition are clearly linked to the loss of density of wood, while specific fungal-bacterial interactions may also affect the distribution of bacterial taxa in decaying wood. Thaumarchaeota were prominent members of the archaeal populations colonizing decaying wood, providing further evidence of the versatility and cosmopolitan nature of this phylum in the environment. The composition and dynamics of the prokaryotic community suggest that they are an active component of biota that are involved in processing substrates in decaying wood material.

The effects of the transformation of a 4-coumarate:coenzyme A ligase (4CL) gene involved in lignin biosynthesis on the interactions between transgenic plants and soil microbiota were studied in silver birch (Betula pendula Roth). Although the genetic transformation did not lead to expected changes in wood chemistry, it had significant influence on root biomass and morphology. The transgenic lines had less root biomass and lower numbers of root tips than the wild-type birch. However, the transgenic lines formed normal ectomycorrhizas with Paxillus involutus (Batsch) Fr. and no differences between the transgenic lines and the wild-type birch were detected in the colonization by mycorrhizas in vitro. In a field trial, the decomposition of the transgenic and wild-type birch litter was equally rapid, and no marked differences were found between the transgenic lines and wild-type birch in total microbial biomass (SIR) or activity (basal respiration). The effects of the genetic transformation on the ergosterol content of the leaf litter were contradictory; the litter from one transgenic line had significantly higher ergosterol content and the litters from two other transgenic lines had significantly lower ergosterol content than the litter from wild-type birch. This study shows that the 4CL antisense transformation and the pleiotropic effects of the transformation on growth characteristics of birch did not disturb the formation of ectomycorrhizas with P. involutus and had no clear influence on the biodegradability of the leaf litter.

This study assessed the effect of mycorrhizal colonization by Glomus intraradices (Gi) and G. versiforme (Gv) on the bacterial community composition in the rhizosphere of canola, clover and two tomato genotypes (wild type (76R) and its mutant with reduced mycorrhizal colonization (rmc)). Additionally, the effect of light intensity on the rhizosphere bacterial community composition of the tomato genotypes was studied. The bacterial community composition was assessed by denaturing gradient gel electrophoresis (DGGE). In canola, which is considered to be a non-mycorrhizal species, inoculation with Gi increased the shoot dw compared to Gv and the non-mycorrhizal control plants and also induced changes in the bacterial community composition in the rhizosphere. These fungal effects were observed although less than 8% of the root length of canola was colonized. On the other hand, about 50% of the root length of clover was colonized and inoculation with Gv resulted in a higher shoot dw compared to Gi or the control plants but the rhizosphere bacterial community composition was not affected by inoculation. Plant growth, mycorrhizal colonization and bacterial community composition of the two tomato genotypes were affected by a complex interaction between tomato genotype, AM fungal species and light intensity. Low light intensity (photosynthetic photon flux 200–250 μmol m −2 s −1 ) increased the shoot–root ratio in both genotypes and reduced colonization in the wild type. The differences in bacterial community composition between the two genotypes were more pronounced at low than at high light intensity (550–650 μmol m −2 s −1 ).

The distribution of heterotrophic flagellates, naked amoebae, testate amoebae and ciliates was investigated in habitats created by Scots pine-Paxillus involutus and -Suillus bovinus ectomycorrhizospheres. The protozoa living on plant and fungal surfaces preferred the non-mycorrhizal pine roots over mycorrhizal roots or external mycelium. The testate amoebae were more abundant on external mycelium than on mycorrhizae regardless of the mycorrhizal fungal species. Numbers of protozoa were higher in the different habitats provided by S. bovinus mycorrhizospheres when compared with P. involutus mycorrhizospheres. Interestingly, the quality of the bacterial flora as food for the protozoa was affected by the mycorrhizal fungi even in the soils adjacent to non-mycorrhizal root tips of pine. These results demonstrate that mycorrhizal fungi create habitats differently suitable for protozoa living in boreal forest soil.

Archaea colonising defined compartments of Scots pine Suillus bovinus or Paxillus involutus mycorrhizospheres developed in forest humus-containing microcosms were investigated by nested polymerase chain reaction (PCR), cloning, restriction fragment length polymorphism (RFLP) and sequencing. Archaea representing six RFLP groups were detected in the system. Sequence analysis of clones representing the different RFLP types confirmed the presence of novel Finnish forest soil Crenarchaeota. Archaeal sequences were identified from mycorrhizas of both P. involutus and S. bovinus, at the margins of the external mycelium and in uncolonised humus but not from non-mycorrhizal short roots. Fungal and compartment-specific crenarchaeal occupation of mycorrhizospheres is discussed in relation to bacterial community distribution in similar systems.

The tolerance to, and degradation of m-toluate by Scots pine (Pinus sylvestris), a symbiotic mycorrhizal fungus (Suillus bovinus) and Pseudomonas fluorescens strains, with or without m-toluate-degrading capacity, was determined individually and in all symbiotic/associative plant-microbe combinations. Fungal survival on medium with m-toluate was increased in co-culture with the degradative bacterial strains on agar plates (up to 0.02%, w/v). When fungi were grown in mycorrhizal association with Scots pine seedlings in test-tube microcosms containing expanded clay pellets and growth media, the fungus was able to withstand m-toluate concentrations up to 2.0%, w/v in all treatments. The seedling tolerance remained unaltered regardless of the presence or absence of mycorrhizal fungi or biodegradative bacteria. Reduction in m-toluate levels was only detected in treatments inoculated with bacterial strains harbouring TOL catabolic plasmids. The plant and fungus, alone or in mycorrhizal symbiosis, were unable to cleave m-toluate. The presence of easily available plant-derived carbon sources did not impede m-toluate degradation by the bacteria in the mycorrhizosphere.

Cellular interactions and catabolic activities of mycorrhizal root associated non-sporulating bacteria were investigated in a simplified phytoremediation simulation involving a woody plant species. Mycorrhizal Scots pine ( Pinus sylvestris ) seedlings pre-colonised by Suillus bovinus or Paxillus involutus were grown in forest humus containing microcosms amended with petroleum hydrocarbon (PHC) contaminated soil. Fungal hyphae of both species, emanating from mycorrhizal roots, colonised the PHC contaminated soil over a 16-week period and dense long-lived patches of S. bovinus hyphae formed on the PHC contaminated soil. Transmission electron microscopy revealed a microbial biofilm at the PHC soil-fungal interface composed of differentiated pseudoparenchymous patch hyphae supporting a morphologically diverse bacterial population. Certain non-sporulating bacterial isolates closely associated with the S. bovinus patch hyphae or P. involutus `web' hyphae from the PHC soil harboured similar sized mega-plasmids (approx. 150 kb). Isolates of Pseudomonas fluorescens from the `patch' mycorrhizospheres represented different biovars, displayed similar REP-PCR genomic fingerprints, grew on e.g. m -toluate and m -xylene as sole carbon sources, cleaved catechol, and harboured plasmid-borne catabolic marker genes, xylE and xylMA , involved in degradation of mono-aromatics. The plasmids were transmissible in vitro, and Pseudomonas putida transconjugants retained a similar catabolic profile. The identification of microbial biofilms containing catabolic bacteria in the external mycorrhizosphere is discussed in relation to both phytoremediation mechanisms and normal efficient nutrient mobilisation from highly lignin-rich forest soils.

cf thèse de doctorat (PhD); Arbuscular mycorrhizal (AM) symbioses may alter the competitive abilities of plant species and facilitate positive interactions such as nutrient transfer between plants. They are therefore particularly interesting components in agroforestry systems. We studied spatial variation of AM colonisation on a cut-and-carry fodder production site (agroforestry plot) of the legume tree [i]Gliricidia sepium[/i] and the fodder grass [i]Dichanthium aristatum[/i]. Roots of the two plant species were sampled under the tree canopies and on the adjacent grass plot at 1 and 3.5 m from the first tree row where [i]G. sepium[/i] roots also occur. Roots of [i]D. aristatum[/i] were also sampled on a nearby grass monocrop. Colonisation of arbuscules, vesicles and hyphae in root samples was visually determined, and AM fungal species were identified by DNA sequencing. Colonisation and frequency of types of AM formations varied statistically significantly between the species and sampling points. Arbuscular colonisation in [i]G. sepium[/i] roots was higher under the tree canopies than on the adjacent grass plot. Soil nutrient content, particularly P and N, and interspecies competition are the most probable explanations for the observed variation in AM colonisation. Both arbuscular colonisation and arbuscule: vesicle ratio in [i]D. aristatum[/i] roots was lower on the [i]D. aristatum[/i] monocrop than on the agroforestry plot under or near the tree canopies. Intercropping could stimulate AM symbiosis in [i]D. aristatum[/i]. Both plant species formed symbiosis with [i]Rhizophagus intraradices[/i], indicating potential for interplant N transfer via common mycelial networks of AM-forming fungi.

Phosphorus uptake and translocation through intact mycelial systems of Paxillus involutus and Suillus variegatus infecting Pinus contorta seedlings was monitored non-destructively using a beta-scanner. Mycorrhizal plants were grown in flat perspex chambers (20 x 6 cm(2)) and root growth was restricted to the upper portion of each chamber enabling mycelial translocation to be studied over distances of up to 15 cm. P-32 was supplied, either directly to distal parts of the extending mycelium, or to single, cut mycelial strands in feeding dishes. Two-dimensional patterns of activity were accumulated as scans with a lateral resolution of 5 mm and a longitudinal resolution of 3-4 mm. No distinct translocation front could be detected but patterns of accumulation of label in the mycorrhizal roots were not consistent with movement by simple diffusion. Activity in translocating hyphae became visible only after the activity in mycorrhizal root lips had been visible for a few days. In all cases there was a lag period of 20-50 hours before P-32 could be detected in mycorrhizal root tips. Pre-feeding with unlabelled phosphate had no effect on this lag period. This implies continuous translocation of phosphate at low concentrations and a lag period due to the time needed for detectable levels of phosphate to accumulate in mycorrhizal roots. Thus the minimum velocity of phosphate movement in the hyphae would be 7.5 mm/h, if the first molecules of P-32 arriving at the roots could be detected and the transport distance is 15 cm. Accumulation of phosphate to the roots was fairly constant, but not linear. The phosphorus uptake rate by intact mycelial margins was nearly four orders of magnitude higher than the uptake rate of cut mycorrhizal strands. The results indicate that the fine, foraging hyphae are better suited for nutrient uptake than mycelial strands and that phosphorus translocation in the hyphae occurs by active translocation of small amounts rather than by mass flow. (Less)

Group 1.1c Crenarchaeota are the predominating archaeal group in acidic boreal forest soils. In this study, we show that the detection frequency of 1.1c crenarchaeotal 16S rRNA genes in the rhizospheres of the boreal forest trees increased following colonization by the ectomycorrhizal fungus Paxillus involutus . This effect was very clear in the fine roots of Pinus sylvestris , Picea abies , and Betula pendula , the most common forest trees in Finland. The nonmycorrhizal fine roots had a clearly different composition of archaeal 16S rRNA genes in comparison to the mycorrhizal fine roots. In the phylogenetic analysis, the 1.1c crenarchaeotal 16S rRNA gene sequences obtained from the fine roots formed a well-defined cluster separate from the mycorrhizal ones. Alnus glutinosa differed from the other trees by having high diversity and detection levels of Crenarchaeota both on fine roots and on mycorrhizas as well as by harboring a distinct archaeal flora. The similarity of the archaeal populations in rhizospheres of the different tree species was increased upon colonization by the ectomycorrhizal fungus. A minority of the sequences obtained from the mycorrhizas belonged to Euryarchaeota (order Halobacteriales ).

Amino acids are major nitrogen sources in soils and they harbour a central position in the nitrogen metabolism of cells. We determined whether Hebeloma spp. and Laccaria bicolor expressed the enzyme L-amino acid oxidase (LAO), which catalyses the oxidative deamination of the alpha-amino group of L-amino acids. We measured LAO activities from the mycelial extracts of seven laboratory-grown fungal strains with three methods, and we measured how LAO activities were expressed in one Hebeloma sp. strain grown on four nitrogen sources. Hebeloma spp. and L. bicolor converted L-phenylalanine, but not D-phenylalanine, to hydrogen peroxide, 2-oxoacid, and ammonia, suggesting that they expressed LAO enzymes. The enzymes utilized five out of seven tested L-amino acids as substrates. LAO activities were maximal at pH 8, where Michaelis constant (Km) values were 2-5mm. The LAO of Hebeloma sp. was expressed on every nitrogen source analysed, and the activities were the highest in mycelia grown in nitrogen-rich conditions. We suggest that LAO is a mechanism for cellular amino acid catabolism in Hebeloma spp. and L. bicolor. Many soil bacteria and fungi also express LAO enzymes that have broad substrate specificities. Therefore, LAO is a potential candidate for a mechanism that catalyses nitrogen mineralization from amino acids at the ecosystem level.

Bacterial isolations were carried out on Pinus sylvestris – Suillus bovinus mycorrhizospheres obtained directly from boreal pine forest. When samples were taken during dry weather, the numbers of bacterial colony-forming units were significantly higher in uncolonized short roots and external mycelia than in mycorrhizal roots and soil outside the mycorrhizosphere. In contrast, the colony-forming unit counts were similar in all hypogeous samples after rainy weather. Culturable bacteria were absent from most Suillus bovinus sporocarps. The bacteria isolated from all types of mycorr hizo sphere samples, i.e. short roots, mycorrhizal roots, and external mycelia, consisted primarily of Burkholderia spp., whereas most isolates from soil outside the mycorrhizosphere were identified as Paenibacillus spp. This study shows that mycorrhizal external mycelia can expand the habitat favourable for common rhizosphere bacteria into the soil far from the immediate rhizosphere. Some of these bacteria may help the trees with nitrogen acquisition, since potentially diazotrophic bacteria harbouring nitrogenase reductase (nifH) genes were isolated from mycorrhizal root tips.Key words: boreal forest soil, Burkholderia, ectomycorrhiza, nitrogen fixation, Paenibacillus.

Rhizosphere microbial communities can be regarded as a subset of the soil microbial community. As the root tip grows through the soil, microorganisms in its pathway will be the first colonisers. During rapid root growth, the zone of elongation immediately behind the root tips is only sparsely colonised by soil microorganisms. Thereafter, microbial population densities increase rapidly in the zone behind the root tips, where high concentrations of soluble, insoluble and volatile root exudates can be utilised for microbial growth and metabolism. In contrast, along the older root parts, the compounds present in the rhizosphere are dominated by cellulose and other recalcitrant cell wall materials from sloughed root cortex tissues. Here the population density is often lower than in the younger root regions closer to the rot tip. The species composition of microbial communities in rhizosphere differs from that in the bulk soil (Foster 1986; Marilley and Aragno 1999). This is a clear indication that plants have a strong influence on the microbial populations on their roots. Indeed, in many cases the rhizosphere communities of different plant species growing in the same soil are distinct (Ibekwe and Kennedy 1998) and plants may even have very similar microbial community composition in different soils (Grayston et al. 1998; Miethling et al. 2000). Plant roots release 1–25% of the net photosynthesis as soluble and insoluble compounds into the rhizosphere (Merbach et al. 1999). Among rhizosphere microbial ecologists there is currently a consensus that differences in exudate amount and composition are likely to affect microbial community composition because microbial species differ in their ability to metabolise and compete for different carbon sources. Therefore, differences in exudate amount and composition will affect the competitiveness and hence the survival of microbial species. A wide range of factors have

Mycorrhizal short roots of Pinus contorta Dougl. ex Loud colonized by Suillus variegatus (Sow. ex Fr.) O. Kuntze or Paxillus involutus (Batsch) Fr. were collected 1–>60 days after fungal contact. The proteins of the inoculated roots were extracted, electrophoretically separated, blotted and immunostained for α-tubulin and actin. The development of the mycorrhiza was also followed microscopically. The signal of plant α-tubulin was stronger than the signal of fungal α-tubulin during the first 5 days in S. variegatus mycorrhiza and was then exceeded by fungal α-tubulin. This correlated well with the increase of fungal mycelium in the mycorrhiza. A transient drop in both plant and fungal α-tubulin signals was observed 20 days after fungal contact, suggesting a change in the metabolism of the mycorrhiza. The signals for plant and fungal actins in the mycorrhiza increased steadily during early infection and then remained at a high level as the mycorrhiza matured. Similar trends were observed in P. contorta–P. involutus mycorrhiza. The data from P. contorta–S.variegatus mycorrhizas suggests that α-tubulin is a growth-related protein, subject to changes, while the amount of actin reflects the general metabolic activity of the mycorrhiza. In both mycorrhizal systems clear α-tubulin and actin signals were detected 60 days after colonization, which indicates that the mycorrhizas were metabolically active in spite of their withered appearance.

SUMMARY The early development of indigenous and introduced Scots pine (Pinus sylvestris L.) ectomycorrhiza in natural forest humus was examined using molecular fingerprinting techniques. Non-mycorrhizal or mycorrhizal (Suillus bovinus (L. ex Fr.) O. Kuntze or Paxillus involutus (Batsch ex Fr.) Fr.) seedlings were placed in transparent two-dimensional microcosms on a thin layer of sieved humus to allow observation of ectomycorrhizal development and fungal growth. Twelve ectomycorrhizal morphotypes, mainly based on colour, gross morphology and outer mantle structure, were identified over a 3-month period. No successional trends in mycorrhiza formation were observed. For further characterization, individual ectomycorrhiza representing the different morphotypes were subjected to analyses of esterase (EST) isozyme profiles and RFLPs of the internal transcribed spacer (ITS) from fungal rRNA genes following amplification using PCR. All 10 morphotypes analysed displayed different esterase isozyme profiles, and the characteristic s. bovinus species diagnostic band (S. b. EST8) was detected in two white morphotypes. Ten Pink and Black ectomycorrhiza were all separated into one and three groups, respectively. A fast-running plant-specific polymorphic locus (Z) was also confirmed in most ectomycorrhizal morphotypes. Diagnostic species-specific (S. bovinus and Pink) EST bands were detected in intact external mycelium colonizing soil. Successful amplification of the ITS from individual ectomycorrhiza, of eight different morphotypes, was found to be mainly influenced by the DNA template concentration. Different RFLPs (Hinf I, Mbo I and Hha I) of the ITS placed the white morphotypes into two groups, one corresponding to S. bovinus, in agreement with the esterase fingerprinting. By contrast, Pink and Beige morphotypes displayed different EST profiles but nearly identical RFLP fingerprints. The ITS amplification success rate of standardized DNA template concentrations from 10 individual Pink and Black ectomycorrhiza was 90 and 50%, respectively. In all successful amplifications, the black morphotype yielded the smallest ITS fragment, similar to earlier reports for Cenococcum geophilum, that gave identical RFLPs. The ecological significance of the observed mycorrhizal diversity and combined application of these two identification methods is discussed.

summary The identity of individual ectomycorrhizas, root colonization patterns and early growth responses of interconnected Scots pine (Pinus sylvestris L.) seedlings were investigated following interactions between local genets of Suillus bovinus (L. ex Fr.) O. Kuntze (SBK4b and SBK5b) and S. variegatus (Swartz ex Fr.) O. Kuntze (SVK3b) and different host-genotype combinations. Three equidistant 39-d-old seedlings, in pots that contained sterile N-limited nursery soil, were each inoculated with one of the three genets in the multiple inoculation treatment (MIT). Single inoculation treatments (SITs), involving inoculation of only one seedling in the triad with one of the three genets, and a similarly configured uninoculated treatment (UIT), were also prepared for comparative analysis. All seedling roots in the inoculated treatments, except for one SIT/SBK4b combination, hosted large numbers (>150) of Suillus-type ectomycorrhizas after 23–25 wk growth without additional fertilization. Esterase (EST) isozyme analysis of individual ectomycorrhizas from all SIT and MIT combinations enabled efficient interspecific and intraspecific typing of fungal (genet) colonization (89 and 72 %, respectively) and identification of host genotype variation (Z locus polymorphism) at a lower rate (51 %). Species, but not 5. bovinus genet, typing within randomly sampled individual ectomycorrhizas from selected SITs was successful (50–70%) following PCR/RFLP analysis of diagnostic sequences of fungal rRNA genes. In the SITs, only the inoculated fungal genet was detected in ectomycorrhizas on all three seedlings. Roots were predominantly colonized by SBK4b in one, and SBK5b in three, of the MIT combinations, although ectomycorrhizas of the former genet were detected at low frequencies on nearly all seedlings. In the remaining MIT combination, both SBK4b and SVK3b were found to co-dominate as ectomycorrhizas on the seedling roots. Small numbers of the latter genet were detected in ectomycorrhizas of two SBK5b-dominated MIT combinations. However, no significant trends in host-mycorrhiza interactions were detected using a log-linear analysis. Compared with the UIT, significant positive mycorrhizal plant growth responses, particularly increased needle length, were recorded in all the heavily colonized seedlings in most SIT and all MIT combinations. Intermediate seedling growth was restricted to the one SIT/SBK4b combination where seedlings supported limited numbers of ectomycorrhizas. The general host-fungal colonization patterns observed provide further below-ground evidence supporting genet interactions previously detected through sporocarp population analyses in young Scots pine reforestation sites.

The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ. (C) 2015 Elsevier B.V. All rights reserved.

Phytoplankton and heterotrophic bacteria are key groups at the base of aquatic food webs. In estuaries receiving riverine water with a high content of coloured allochthonous dissolved organic matter (ADOM), phytoplankton primary production may be reduced, while bacterial production is favoured. We tested this hypothesis by performing a field study in a northerly estuary receiving nutrient-poor, ADOM-rich riverine water, and analyzing results using multivariate statistics. Throughout the productive season, and especially during the spring river flush, the production and growth rate of heterotrophic bacteria were stimulated by the riverine inflow of dissolved organic carbon (DOC). In contrast, primary production and photosynthetic efficiency (i.e. phytoplankton growth rate) were negatively affected by DOC. Primary production related positively to phosphorus, which is the limiting nutrient in the area. In the upper estuary where DOC concentrations were the highest, the heterotrophic bacterial production constituted almost 100% of the basal production (sum of primary and bacterial production) during spring, while during summer the primary and bacterial production were approximately equal. Our study shows that riverine DOC had a strong negative influence on coastal phytoplankton production, likely due to light attenuation. On the other hand DOC showed a positive influence on bacterial production since it represents a supplementary food source. Thus, in boreal regions where climate change will cause increased river inflow to coastal waters, the balance between phytoplankton and bacterial production is likely to be changed, favouring bacteria. The pelagic food web structure and overall productivity will in turn be altered. Fil: Andersson, Agneta. Universidad de Umea; Suecia. Umeå Marine Sciences Centre; Suecia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Brugel, S.. Universidad de Umea; Suecia. Umeå Marine Sciences Centre; Suecia Fil: Paczkowska, Joanna Marianna. Universidad de Umea; Suecia. Umeå Marine Sciences Centre; Suecia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Rowe, O.F.. Universidad de Umea; Suecia. Umeå Marine Sciences Centre; Suecia. University of Helsinki; Finlandia Fil: Figueroa, D.. Universidad de Umea; Suecia. Umeå Marine Sciences Centre; Suecia Fil: Kratzer, S.. Stockholms Universitet; Suecia Fil: Legrand, C.. Linnaeus University; Suecia

In the sedimental organic matter of eutrophic continental seas, such as the largest dead zone in the world, the Baltic Sea, bacteria may directly participate in nutrient release by mineralizing organic matter or indirectly by altering the sediment's ability to retain nutrients. Here, we present a case study of a hypoxic sea, which receives riverine nutrient loading and in which microbe-mediated vicious cycles of nutrients prevail. We showed that bacterial communities changed along the horizontal loading and vertical mineralization gradients in the Gulf of Finland of the Baltic Sea, using multivariate statistics of terminal restriction fragments and sediment chemical, spatial and other properties of the sampling sites. The change was mainly explained by concentrations of organic carbon, nitrogen and phosphorus, which showed strong positive correlation with Flavobacteria, Sphingobacteria, Alphaproteobacteria and Gammaproteobacteria. These bacteria predominated in the most organic-rich coastal surface sediments overlain by oxic bottom water, whereas sulphate-reducing bacteria, particularly the genus Desulfobacula, prevailed in the reduced organic-rich surface sediments in the open sea. They correlated positively with organic nitrogen and phosphorus, as well as manganese oxides. These relationships suggest that the bacterial groups participated in the aerobic and anaerobic degradation of organic matter and contributed to nutrient cycling. The high abundance of sulphate reducers in the surficial sediment layers reflects the persistence of eutrophication-induced hypoxia causing ecosystem-level changes in the Baltic Sea. The sulphate reducers began to decrease below depths of 20 cm, where members of the family Anaerolineaceae (phylum Chloroflexi) increased, possibly taking part in terminal mineralization processes. Our study provides valuable information on how organic loading affects sediment bacterial community compositions, which consequently may maintain active nutrient recycling. This information is needed to improve our understanding on nutrient cycling in shallow seas where the dead zones are continuously spreading worldwide.

Legume trees which form symbiosis with N2-fixing bacteria can help replenish and maintain soil fertility on tropical agricultural lands by supplying nitrogen to the system. However, the mechanisms of N transfer from the trees to associated crops are not well understood. The role of root exudation and common mycelial networks of mycorrhizal fungi (CMN) in interplant N transfer was analysed in this study. A cut-and-carry agroforestry system comprising a legume tree (Gliricidia sepium) and a fodder grass (Dichanthium aristatum) was used as a model system. Nitrogen transfer was measured by labelling the tree with 15N. Variation in the isotopic composition of the N sources from the tree and its effects on N transfer estimates was analysed using experimental methods and mathematical modeling. Both plant species were observed to form symbiosis with the same subgroup of Rhizophagus intraradices in the field, indicating favourable conditions for the formation of CMN. In pot culture D. aristatum obtained up to 14% of its N from G. sepium via belowground pathways over 10 weeks, which was mainly accounted for N exudation. Nitrogen transfer via CMN contributed up to 2.5% of N in D. aristatum and corresponded to 18% of total N transferred. Nitrogen transfer via CMN increased with arbuscular colonisation of the N donor and with decreasing N concentration of the N recipient. Transfer estimates varied manifold depending on the assumed isotopic composition of transferred N, which highlights the need for careful estimation of the isotopic ratios of the actual N sources. The results suggest a significant role for root exudates and CMN in transferring N from legume trees to the associated crops, as opposed to the common perception of tree prunings and mulching as the primary N sources to the crops. Design and management options of agroforestry systems could be reviewed to foster belowground N transfer and improve the sustainability of farming systems., Les arbres légumineux qui forment symbioses avec les bactéries fixatrices d’azote peuvent aider à maintenir ou à rétablir la fertilité des sols dans les agroécosystèmes tropicaux, en fournissant de l’azote au système. Cependant, les mécanismes de transfert d’azote des arbres aux plantes associées n’ont pas bien connus. Dans cette étude, on a analysé le transfert d’azote souterrain via les exsudats racinaires et les réseaux des champignons mycorhiziens (angl. Common Mycelial Networks, CMN). Un système agroforestier de production du fourrage, composé d’un arbre légumineux (Gliricidia sepium) et d’une herbe fourragère (Dichanthium aristatum), a été utilisé comme système modèle. Les arbres et l’herbe étaient régulièrement taillés ou coupée et la biomasse était exportée de la parcelle. Le transfert d’azote a été mesuré en utilisant le marquage artificiel 15N des feuilles de l’arbre. La variation de la composition isotopique des sources azotées de l’arbre et ses effets sur le transfert d’azote ont été analysés par des méthodes expérimentales et la modélisation. On a observé que Gliricidia sepium et D. aristatum forment des symbioses avec le même sous-groupe du champignon mycorhizien Rhizophagus intraradices sur la parcelle agroforestière, ce qui indique des conditions favorables pour la formation de CMN. Dans une expérimentation en pot de dix semaines, D. aristatum a obtenu jusqu’à 14% de son azote de G. sepium par le transfert souterrain, ce qui a été associé principalement à l’exsudation racinaire de l’arbre. Le transfert via le CMN a apporté jusqu’à 2.5% de l’azote de D. aristatum, ce qui correspond à 18% de l’azote total transféré. Le transfert d’azote via le CMN a été positivement corrélé avec la colonisation des arbuscules dans l’arbre donneur d’azote, et négativement corrélé avec la concentration d’azote dans la plante associée. L’évaluation du transfert dépend fortement de l’estimation de la composition isotopique des sources azotées, ce qui souligne l’importance de cerner avec fiabilité les teneurs en 15N de ces sources. Les résultats indiquent que les exsudats racinaires et le CMN ont un rôle clé dans le transfert d’azote des arbres légumineux aux plantes associées. Cette étude améliore ainsi le cadre conceptuel actuel de la problématique traitée, d’après lequel l’engrais vert (p. ex. recyclage dans le sol des tailles de l’arbre) est considéré la seule source de transfert d’azote. De nouvelles options pour la conception et la gestion des systèmes agroforestiers pourraient être envisagées afin d’optimiser le transfert souterrain d’azote et assurer la durabilité de ces systèmes.

Background External nutrient discharges have caused eutrophication in many estuaries and coastal seas such as the Baltic Sea. The sedimented nutrients can affect bacterial communities which, in turn, are widely believed to contribute to release of nutrients such as phosphorus from the sediment. Methods We investigated relationships between bacterial communities and chemical forms of phosphorus as well as elements involved in its cycling in brackish sediments using up-to-date multivariate statistical methods. Bacterial community composition was determined by terminal restriction fragment length polymorphism and cloning of the 16S rRNA gene. Results and Conclusions The bacterial community composition differed along gradients of nutrients, especially of different phosphorus forms, from the estuary receiving agricultural phosphorus loading to the open sea. This suggests that the chemical composition of sediment phosphorus, which has been affected by riverine phosphorus loading, influenced on bacterial communities. Chemical and spatial parameters explained 25% and 11% of the variation in bacterial communities. Deltaproteobacteria, presumptively sulphate and sulphur/iron reducing, were strongly associated to chemical parameters, also when spatial autocorrelation was taken into account. Sulphate reducers correlated positively with labile organic phosphorus and total nitrogen in the open sea sediments. Sulphur/iron reducers and sulphate reducers linked to iron reduction correlated positively with aluminium- and iron-bound phosphorus, and total iron in the estuary. The sulphate and sulphur/iron reducing bacteria can thus have an important role both in the mineralization and mobilization of nutrients from sediment. Significance Novelty in our study is that relationships between bacterial community composition and different phosphorus forms, instead of total phosphorus, were investigated. Total phosphorus does not necessarily bring out interactions between bacteria and phosphorus chemistry since proportions of easily usable mobile (reactive) phosphorus and immobile phosphorus forms in different sediments can vary. Our study suggested possible feedbacks between different forms of phosphorus and bacterial community composition.