Sara J. M. Holmström

The role of fungi in weathering

No rock at the Earths surface escapes weathering. This process is the primary source of all the essential elements for organisms, except nitrogen and carbon. Since the onset of terrestrial life, weathering has been accelerated under the influence of biota. The study of biological weathering started at the end of the 19th century. Although the role of bacteria (Eubacteria, Archaea) has attracted a lot of interest, until recently the role of fungi has largely been neglected. More recently, however, fungal weathering has become an increasingly important focus of biogeochemical research.

Siderophores in environmental research: roles and applications

Siderophores are organic compounds with low molecular masses that are produced by microorganisms and plants growing under low iron conditions. The primary function of these compounds is to chelate the ferric iron [Fe(III)] from different terrestrial and aquatic habitats and thereby make it available for microbial and plant cells. Siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. Their significance in these applications is because siderophores have the ability to bind a variety of metals in addition to iron, and they have a wide range of chemical structures and specific properties. For instance, siderophores function as biocontrols, biosensors, and bioremediation and chelation agents, in addition to their important role in weathering soil minerals and enhancing plant growth. The aim of this literature review is to outline and discuss the important roles and functions of siderophores in different environmental habitats and emphasize the significant roles that these small organic molecules could play in applied environmental processes.

Effects of acidification and its mitigation with lime and wood ash on forest soil processes in southern Sweden. A joint multidisciplinary study

A joint multidisciplinary investigation was undertaken to studythe effects of lime and wood ash applications on two Norway spruce forest Spodosolic soils. The two sites, typical for southern Sweden, were treated in 1994 with either 3.25 t ha-1 dolomite or 4.28 t ha-1 wood ash (Horröd site) or in 1984 with either 3.45 or 8.75 t ha-1 dolomite (Hasslöv site). Both sites show signs of acidification by atmospheric anthropogenic deposition and possessed low soil pH(4.3) and high concentrations of inorganic Al (35 μM) in theupper illuvial soil solution. The prevailing soil conditions indicated perturbed soil processes. Following treatment with lime or wood ash, the soil conditions were dramatically altered. Cation exchange capacity (CEC) and base saturation (BS) was considerable increased after addition. Four years after application most of the added Ca and Mg was still present in the mor layer. Fifteen years after application,Mg in particular, became integrated deeper in the soil profile with a greater proportion lost by leaching incomparison to Ca. The concentrations of these ions were greatestin the mor layer soil solutions and Mg had higher mobility givinghigher concentrations also deeper in the profile. Four years after treatment, the application of wood ash and limeresulted in lower pH values and higher inorganic Al in mineral subsoil solutions compared to the untreated soil. We hypothesize that this was probably due to an increased flow of hydrogen ionsfrom the upper soil as a result of displacement by Ca and Mg ionsin the enlarged exchangeable pool. In contrast, fifteen years after lime and wood ash application, the mineral subsoil horizonspossessed a higher pH and lower soil solution Al content than theuntreated plots.Liming promoted soil microbial activity increasing soil respiration 10 to 36%. This is in the same range as net carbon exchange for forests in northern Sweden and could potentially have a climatological impact. The turnover of low molecularweight organic acids (LMWOA) by the soil microbial biomass werecalculated to contribute 6 to 20% to this CO2 evolution.At Horröd, citrate and fumarate were the predominant LMWOAs with lowest concentrations found in the treated areas. In contrast, at the Hasslöv site, propionate and malonate were the most abundant LMWOAs. Higher microbial activity in the upper soil horizons was also theprobable cause of the considerably higher DOC concentrations observed in the soil solution of ash and lime treated areas. Thelime-induced increase in DOC levels at Hasslöv could be attributed to increases in the 3–10 kDa hydrophobic size fraction. Liming also promoted nitrification with high liming doses leading to extreme concentrations of NO3- (1 mM) in soil solution.At Hasslöv the community of mycorrhizal fungi was dramatically changed by the addition of lime, with only four of 24 species recorded being common to both control and treated areas.Many of the observed effects of lime and ash treatment can be viewed as negative in terms of forest sustainability. After fouryears of treatment, there was a decrease in the pH of the soil solution and higher concentrations of inorganic Al and DOC. Increased organic matter turnover, nitrification and NO3-leakage were found at Hasslöv. Considering that the weathering rate and the mineral nutrient uptake by trees is mostprobably governed by mycorrhizal hyphae etchingmineral grains in the soil, it is important to maintain this ability of the mycorrhizal fungi. The lime and ash-induced changed mycorrhizal community structure may significantly affect this capability. In light of this investigation and others, as reviewed by Lundström et al. (2003), the implications ofliming on forest health are multifaceted with complex relationships occurring over both space and time.

Impact of Lime and Ash Applications on Soil Solution Chemistry of an Acidified Podzolic Soil

Soil solution samples were taken from two sites (Horröd and Hasslöv) in the south part of Sweden to evaluate how soil solution chemistry responded to different treatmentswith dolomite and wood ash. At Horröd, samples were taken four years after application of wood ash, 4.28 ton ha-1 and dolomite, 3.25 ton ha-1. At Hasslöv dolomite, 3.45 ton ha-1 and 8.75 ton ha-1 was applied and samples were taken 15 yr later. It was found that treatment with dolomite at one site (Hasslöv) resulted in higher pH values (<2 pH units) and higher nitrification. It was also found at this site that the total Al and the inorganic Al concentrations decreased with dolomite treatment. The Ca, Mg, DOC, Fe, SO42- and Cl- concentrations, mainly in the topsoil, were found to be higher at both sites, following dolomite treatment; Ca and Mg concentrations were 2–8 times higher (<820 μM) than in controls (<70 μM). Wood ash was found to have less impact. The PO4 concentration in the O2 horizon at Hasslöv decreased due to dolomite-treatment. ANOVA (Analyse of Variance) and PLS (Partial Least Square) were used to evaluate the data from the two sites.

Novel approach to the determination of structurally similar hydroxamate siderophores by column-switching capillary liquid chromatography coupled to mass spectrometry.

In this study a new approach to determine three different siderophores (ferrichrome, ferrichrysin, ferricrocin) in natural soil solutions as well as in cultures of fungi is presented. The method includes enrichment of the analytes on a short pre-column, packed with C18 material, and subsequent highly selective separation of the analytes on a capillary porous graphitic carbon (PGC) column. In contrast to normal C18 packing materials, porous graphitic carbon offers chromatographic resolution between the three very similar analytes. The selectivity of the method is enhanced even further by the electrospray ionization (ESI) mass spectrometric detection. The combination of a short pre-column and a packed capillary separation column results in a method with high sensitivity. Reported detection limits, defined as the concentration giving the signal-to-noise ratio 3:1, is 27.7 pM for ferrichrome, 46.1 pM for ferricrocin and 37.4 pM for ferrichrysin.

Mobilization of metals from uranium mine waste: the role of pyoverdines produced by Pseudomonas fluorescens

Microorganisms produce chelating agents, such as siderophores and other ligands, which allow them to mobilize and scavenge essential elements from the environment when bioavailability is low. To better understand the effects of biologically mediated leaching of metals from mine waste, Pseudomonas fluorescens was cultivated in the presence of processed ore from the former uranium mine in Ranstad, southern Sweden. Light conditions, the concentration of the mineral source and oxygen availability were varied. The presence of ore in the culture flasks enhanced bacterial growth and raised the pH of the culture medium. Increasing the amount of ore or enhancing aeration of the medium further encouraged cell growth and pH rise. Bacteria mobilized Fe, Ni and Co from the ore. Fe-siderophore complexes were detected and estimated to be present at approximately 9 mum. In the presence of bacteria and light, dissolved Fe and U concentrations were higher compared to dark conditions. Increasing the amount of ore resulted in higher dissolved Ni concentrations but lower dissolved Fe, most likely due to precipitate formation. Data from this study support siderophore production by bacteria that allowed mobilization of essential nutrients from the processed ore. However, the availability of potentially toxic metals like Ni and U may also be enhanced. Microbial-promoted mobilization could contribute to leaching of toxic metals in current and historic mining areas. This process should be considered during design and implementation of remediation projects where trace metals are of environmental concern.

Effects of lime and ash treatments on DOC fractions and low molecular weight organic acids in soil solutions of acidified podzolic soils

Dissolved organic carbon (DOC) fractions and different low molecular weight organic acids (LMWOAs) were determined in soil solutions from two lime or ash treated Norway spruce sites in the south of Sweden. At Hasslöv, 3.45 t ha-1 or 8.75 t ha-1 dolomite were applied 15 years before sampling. Horröd was treated with 4.28 t ha-1 ash and 3.25 t ha-1 dolomite and sampled four years later. Propionate (7–268 μM) and malonate (2–34 μM) were the LMWOAsfound in the highest concentrations at Hasslöv. Two other LMWOAs dominated at Horröd, namely citrate (18–64 μM)and fumarate (5–31 μM). The differences in concentration of most of the determined LMWOAs at Hasslöv were significantly increased due to treatment. The LMWOAs comprised between 1.1–6.3% of the DOC at Hasslöv and 4.5–17.6% at Horröd. At Hasslöv normally 3–10% of the total acidity (TA) was due to LMWOAs and the average specific buffer capacity was 74 ± 22 mmol mol-1C.The total DOC concentration in the mor layer solution was ∼16 mM for the dolomite treated plots compared to ∼10 mM at the untreated plot. A major part of the increase in DOC at the treated plots apparently had a hydrophobic character and was of high molecular weight corresponding to 3–10 kDa. The concentration of DOC < 1 kDa in the control and treated plots was similar.

Pools and Fluxes of Cations, Anions and Doc in Two Forest Soils Treated With Lime and Ash

The effect of liming and ash treatment on pools, fluxes and concentrations of major solutes was investigated at two forestedsites (Norway spruce) in S. Sweden. One site was treated 15 yrprior to sampling (Hasslöv-Hs; dolomite: 3.45 and 8.75 t ha-1) and the other 4 yr before (Horröd-Hd; dolomite: 3.25 t ha-1; wood ash: 4.28 t ha-1). Effects of limingwere most pronounced in the O horizon solutions where higher pH,elevated Ca (120–700 μM) and Mg (50–600 μM) were observed as compared to control plots. The impact on the mineralsoil was more moderate. Soil solution concentrations were combined with modelled hydrological flow to calculate mass flows,which largely followed the trends of the solution composition. Liming also resulted in large increases of both exchangeable Caand Mg as well as effective cation exchange capacity (CECE;2–5 times the controls). The base saturation (BS%) was raised to 60–100% in the O horizon while in the mineral soil elevated values were only seen at the Hs site (20–60%; down to 10–15 cm depth for 8.75 t ha-1). Ash treatment did notaffect either the soil solution nor the exchangeable pool to thesame extent as lime. In general, the impact at the Hd site was less pronounced especially in the mineral soil, which might be due to shorter treatment time (4 vs. 15 yr) and also differentthickness of the O horizon. Budget calculations for Ca and Mg originating from the lime showed that a major part of the Ca (40–100%) was retained in the top 30 cm of the soil, of which30–95% was present in the O horizon. The mobility of Mg wasgreater and it was estimated that a significant part had been leached from the profile (30 and 50 cm depth) after 15 yr. Increased mass flows of NO3- due to nitrification resulting from liming at the Hs site were calculated in the range120–350 mmol m-2 yr-1 (or 1.2–3.5 kmol ha-1 yr-1). There was significant leaching of Al (25–60 mmol m-2 yr-1), of which about 70% was inorganic, in thelower B horizon at both sites with no influence of liming.

Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description

Rock varnish is a thin layer of Fe and Mn oxyhydroxides with embedded clay minerals that contain an increased Mn/Fe ratio compared to that of the Earth’s crust. Even if the study of rock varnish has important implications in several fields, the composition of epilithic bacterial communities and the distribution of taxa on varnish surfaces are still not wholly described. The aim of this study was (i) to identify the bacterial taxa which show the greatest variation between varnish and non-varnish environments, collected from the same rock, and (ii) to describe the morphology of epilithic communities through scanning electron microscopy (SEM). Triplicate samples of rock surfaces with varnish and triplicate samples without varnish were collected from five sites in Matsch Valley (South Tyrol, Italy). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing. Fifty-five ubiquitous taxa have been examined to assess variation between varnish and non-varnish. Cyanobacteria, Chloroflexi, Proteobacteria along with minor taxa such as Solirubrobacterales, Conexibaxter, and Rhodopila showed significant variations of abundance, diversity, or both responding to the ecology (presence/absence of varnish). Other taxa, such as the genus Edaphobacter, showed a more marked spatial variation responding to the sampling site. SEM images showed a multitude of bacterial morphologies and structures involved in the process of attachment and creation of a suitable environment for growth. The features emerging from this analysis suggest that the highly oxidative Fe and Mn-rich varnish environment favors anoxigenic autotrophy and establishment of highly specialized bacteria.

Putative Fossilized Fungi from the Lithified Volcaniclastic Apron of Gran Canaria, Spain

We report the discovery of fossilized filamentous structures in samples of the lithified, volcaniclastic apron of Gran Canaria, which were obtained during Leg 157 of the Ocean Drilling Program (ODP). These filamentous structures are 2-15 μm in diameter and several hundred micrometers in length and are composed of Si, Al, Fe, Ca, Mg, Na, Ti, and C. Chitin was detected in the filamentous structures by staining with wheat germ agglutinin dye conjugated with fluorescein isothiocyanate (WGA-FITC), which suggests that they are fossilized fungal hyphae. The further elucidation of typical filamentous fungal morphological features, such as septa, hyphal bridges, and anastomosis and their respective sizes, support this interpretation. Characteristic structures that we interpreted as fossilized spores were also observed in association with the putative hyphae. The fungal hyphae were found in pyroxene phenocrysts and in siderite pseudomorphs of a basalt breccia. The fungal colonization of the basalt clasts occurred after the brecciation but prior to the final emplacement and lithification of the sediment at ∼16-14 Ma. The siderite appears to have been partially dissolved by the presence of fungal hyphae, and the fungi preferentially colonized Fe-rich carbonates over Fe-poor carbonates (aragonite). Our findings indicate that fungi may be an important geobiological agent in subseafloor environments and an important component of the deep subseafloor biosphere, and that hydrothermal environments associated with volcanism can support a diverse ecosystem, including eukaryotes.