Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles.

The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by Proteobacteria, and Sulfurimonas was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H2, indicating that besides H2S, H2 could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H2S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas.

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.

"Candidatus Hydrogenisulfobacillus filiaventi" strain R50 gen. nov. sp. nov., a highly efficient producer of extracellular organic compounds from H2 and CO2.

Production of organic molecules is largely depending on fossil fuels. A sustainable alternative would be the synthesis of these compounds from CO2 and a cheap energy source, such as H2, CH4, NH3, CO, sulfur compounds or iron(II). Volcanic and geothermal areas are rich in CO2 and reduced inorganic gasses and therefore habitats where novel chemolithoautotrophic microorganisms for the synthesis of organic compounds could be discovered. Here we describe "Candidatus Hydrogenisulfobacillus filiaventi" R50 gen. nov., sp. nov., a thermoacidophilic, autotrophic H2-oxidizing microorganism, that fixed CO2 and excreted no less than 0.54 mol organic carbon per mole fixed CO2. Extensive metabolomics and NMR analyses revealed that Val, Ala and Ile are the most dominant form of excreted organic carbon while the aromatic amino acids Tyr and Phe, and Glu and Lys were present at much lower concentrations. In addition to these proteinogenic amino acids, the excreted carbon consisted of homoserine lactone, homoserine and an unidentified amino acid. The biological role of the excretion remains uncertain. In the laboratory, we noticed the production under high growth rates (0.034 h-1, doubling time of 20 h) in combination with O2-limitation, which will most likely not occur in the natural habitat of this strain. Nevertheless, this large production of extracellular organic molecules from CO2 may open possibilities to use chemolithoautotrophic microorganisms for the sustainable production of important biomolecules.

Fine Particle Adsorption Capacity of Volcanic Soil from Southern Kyushu, Japan.

"Akahoya" is a volcanic soil classified as a special soil deposited in Kyushu, Japan. Many of its properties are not yet clearly understood. We found that Akahoya had the potential to adsorb bacteria in cattle feces, which prompted us to investigate its material properties and perform experiments to comprehensively evaluate its adsorption performance for various fine particles such as acidic and basic dyes, NOx/SOx gas, and phosphoric acid ions, in addition to bacteria. Akahoya had a very high specific surface area owing to the large number of nanometer-sized pores in its structure; it exhibited a high adsorption capacity for both NO2 and SO2. Regarding the zeta potential of Akahoya, the point of zero charge was approximately pH 7.0. The surface potential had a significant effect on the adsorption of acidic and basic dyes. Akahoya had a very high cation exchange capacity when the sample surface was negatively charged and a high anion exchange capacity when the sample surface was positively charged. Akahoya also exhibited a relatively high adsorption capacity for phosphoric acid because of its high level of Al2O3, and the immersion liquid had a very high Al ion concentration. Finally, filtration tests were performed on Escherichia coli suspension using a column filled with Akahoya or another volcanic soil sample. The results confirmed that the Escherichia coli adhered on the Akahoya sample. The results of the Escherichia coli release test, after the filtration test, suggested that this adhesion to Akahoya could be phosphorus-mediated.

New Insights into the Phosphorus Acquisition Capacity of Chilean Lowland Quinoa Roots Grown under Low Phosphorus Availability.

Reducing phosphate fertilizer inputs while increasing food nutritional quality has been posited as a major challenge to decrease human undernourishment and ensure food security. In this context, quinoa has emerged as a promising crop due to its ability to tolerate different stress conditions and grow in marginal soils with low nutrient content, in addition to the exceptional nutritional quality of its grains. However, there is scarce information about the phosphorus acquisition capacity of quinoa roots. This work aimed to provide new insights into P acquisition and functional root traits, such as root biomass, rhizosphere pH, carboxylate exudation, and acid phosphatase activity of thirty quinoa genotypes grown under P limiting conditions (7 mg P kg-1). Significant genotypic variation was observed among genotypes, with average P accumulation ranging from 1.2 to 11.8 mg. The shoot biomass production varied more than 14 times among genotypes and was correlated with the P accumulation on shoots (r = 0.91). Despite showing high variability in root traits, only root biomass production highly correlated with P acquisition (r = 0.77), suggesting that root growth/morphology rather than the measured biochemical activity possesses a critical role in the P nutrition of quinoa.

Environmental Variables Including Heavy Metals Significantly Shape the Soil Bacterial Community Structure in the Tatun Volcano Group, Northern Taiwan.

Recent studies suggested the presence of magma chambers from the Tatun volcano group under northern Taiwan's surface, the result of episodic volcanism for 0.2-2.8 million years. However, the microbial community in volcanic soil has not yet been characterized. Therefore, the present study investigated the spatial distribution of microbial communities and their relationships with environmental variables, including heavy metals. Next-generation sequencing was used to analyze the microbial community structures in three areas with different land uses: Lengshuikeng (recreational area), Zhuzihu (agricultural area), and Huangzuishan (conservation area). High contents of environmental factors, such as nitrogen (0.46-1.14%) and phosphorus (2.01-13.88 ppm), were detected. Large concentrations of heavy metals, such as copper (55.90-127.60 ppm) and zinc (36.13-147.73 ppm), were found among the three sites, whereas those of lead (83.13 ppm) and chromium (48.33 ppm) were higher in the Zhuzihu area. The most prevalent phylum across all sites was Proteobacteria, followed by Actinobacteria, Acidobacteria, and Chloroflexi, while the most abundant bacterial species was Koribacteraceae: NA_01, followed by Cyanobacteria: NA. A network ana-lysis showed that Koribacteracea: NA_01 positively correlated with bacterial groups, including Flavisolibacter sp., Oxalobacteraceae: NA, and Actinomycetales: NA_01. Based on Shannon and Simpson's diversity indices, the diversity of bacteria was significantly less in the Huangzuishan area than in the Lengshuikeng and Zhuzihu areas. Bacterial assemblages also significantly differed (P<0.05) among the three sites. The present results provide clear evidence to show that environmental variables, including heavy metals, are key factors affecting the bacterial community structure in volcanic soil.

An Experimental Investigation of the Mechanical Behavior and Particle Crushing Characteristic of Volcanic Soil.

Volcanic soil is a special soil that is well-known for its distinctive texture, vesicular nature, and particle fragility. The fragility characteristic of volcanic soil is the main factor affecting the foundation stability in road engineering. This study focuses on the mechanical properties and particle crushing characteristics of volcanic soil retrieved from Northeast China. A series of triaxial consolidation and drainage shear tests are performed on volcanic coarse-grained soil (5 mm > d > 0.075 mm) under different initial relative densities and effective confining pressures. Results show the peak friction angle of volcanic soil significantly decreases with the increase of confining pressure. The particle crushing degree of volcanic soil increases with the increase of confining pressure, particle size, and relative density. The relative breakage rate of the same particle size group has a good linear relationship with a fractal dimension. Moreover, for the same particle size, the relationship between plastic work and relative breakage rate can be fitted by a power function, which is not significantly affected by relative density or effective confining pressure. From an engineering view, in addition to increasing the compaction degree of volcanic soil, volcanic soil with fine particles used as a roadbed filler can significantly reduce the deformation of the roadbed and improve the bearing capacity of the foundation.

Metagenome Assembled Genome of a Novel Verrucomicrobial Methanotroph From Pantelleria Island.

Verrucomicrobial methanotrophs are a group of aerobic bacteria isolated from volcanic environments. They are acidophiles, characterized by the presence of a particulate methane monooxygenase (pMMO) and a XoxF-type methanol dehydrogenase (MDH). Metagenomic analysis of DNA extracted from the soil of Favara Grande, a geothermal area on Pantelleria Island, Italy, revealed the presence of two verrucomicrobial Metagenome Assembled Genomes (MAGs). One of these MAGs did not phylogenetically classify within any existing genus. After extensive analysis of the MAG, we propose the name of "Candidatus Methylacidithermus pantelleriae" PQ17 gen. nov. sp. nov. The MAG consisted of 2,466,655 bp, 71 contigs and 3,127 predicted coding sequences. Completeness was found at 98.6% and contamination at 1.3%. Genes encoding the pMMO and XoxF-MDH were identified. Inorganic carbon fixation might use the Calvin-Benson-Bassham cycle since all genes were identified. The serine and ribulose monophosphate pathways were incomplete. The detoxification of formaldehyde could follow the tetrahydrofolate pathway. Furthermore, "Ca. Methylacidithermus pantelleriae" might be capable of nitric oxide reduction but genes for dissimilatory nitrate reduction and nitrogen fixation were not identified. Unlike other verrucomicrobial methanotrophs, genes encoding for enzymes involved in hydrogen oxidation could not be found. In conclusion, the discovery of this new MAG expands the diversity and metabolism of verrucomicrobial methanotrophs.

Combined Effects of Wildfire and Vegetation Cover Type on Volcanic Soil (Functions and Properties) in A Mediterranean Region: Comparison of Two Soil Quality Indices.

Mediterranean regions are the most impacted by fire in Europe. The effects of fire on soil greatly vary according to several factors such as vegetation cover type, but they are scarcely studied. Therefore, this research aimed at evaluating the combined impacts of fire and vegetation on single soil characteristics and on the overall soil quality and functionality through two soil quality indices, simple additive (SQI) and a weighted function (SQIFUNCT). In order to reach the aims, burnt and unburnt soils were collected under different vegetation cover types (herbs and shrubs, black locust, pine and holm oak) within the Vesuvius National Park. The soils were analyzed for the main abiotic (water and organic matter content, total C, N, Ca, K, Cu and Pb concentrations, C/N ratio) and biotic (microbial and fungal biomasses, basal respiration, ß-glucosidase activity) characteristics. On the basis of the investigated soil characteristics, several soil functions (water retention, nutrient supply, contamination content, microorganism habitat and activities), and the soil quality indices were calculated. The results showed that the impact of fire on soil quality and functionality was mediated by the vegetation cover type. In fact, fire occurrence led to a decrease in water and C/N ratio under herbs, a decrease in C concentration under holm oak and a decrease in Cu and Pb concentrations under pine. Although the soil characteristics showed significant changes according to vegetation cover types and fire occurrence, both the additive and weighted function soil quality indices did not significantly vary according to both fire occurrence and the vegetation cover type. Among the different vegetation cover types, pine was the most impacted one.

Analysis of Soil Fungal and Bacterial Communities in Tianchi Volcano Crater, Northeast China.

High-altitude volcanoes, typical examples of extreme environments, are considered of particular interest in biology as a possible source of novel and exclusive microorganisms. We analyzed the crater soil microbial diversity of Tianchi Volcano, northeast China, by combining molecular and morphological analyses of culturable microbes, and metabarcoding based on Illumina sequencing, in order to increase our understanding of high-altitude volcanic microbial community structure. One-hundred and seventeen fungal strains belonging to 51 species and 31 genera of Ascomycota, Basidiomycota and Mucoromycota were isolated. Penicillium, Trichoderma, Cladosporium, Didymella, Alternaria and Fusarium dominated the culturable fungal community. A considerable number of isolated microbes, including filamentous fungi, such as Aureobasidium pullulans and Epicoccum nigrum, yeasts (Leucosporidium creatinivorum), and bacteria (Chryseobacterium lactis and Rhodococcus spp.), typical of high-altitude, cold, and geothermal extreme environments, provided new insights in the ecological characterization of the investigated environment, and may represent a precious source for the isolation of new bioactive compounds. A total of 1254 fungal and 2988 bacterial operational taxonomic units were generated from metabarcoding. Data analyses suggested that the fungal community could be more sensitive to environmental and geographical change compared to the bacterial community, whose network was characterized by more complicated and closer associations.

Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island.

The genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. "Ca. Methylobacter favarea" B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments.

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages.

Basaltic rocks play a significant role in CO2 sequestration from the atmosphere during their weathering. Moreover, the primary microorganisms that colonize them, by providing mineral elements and nutrients, are shown to promote growth of diverse heterotrophic communities and plants, therefore positively impacting Earth's long-term climate balance. However, the first steps of microbial colonization and subsequent rock weathering remain poorly understood, especially regarding microbial communities over a chronological sequence. Here, we analyzed the microbial communities inhabiting the soil developed in crevices on lava flows derived from different eruptions on Fogo Island. Investigated soils show typically low carbon and nitrogen content and are relatively similar to one another regarding their phylogenetic composition, and similar to what was recorded in large soil surveys with dominance of Actinobacteria and Proteobacteria. Moreover, our results suggest a stronger effect of the organic carbon than the lava flow age in shaping microbial communities as well as the possibility of exogenous sources of bacteria as important colonizers. Furthermore, archaea reach up to 8.4% of the total microbial community, dominated by the Soil Crenarchaeotic Group, including the ammonium-oxidizer Candidatus Nitrososphaera sp. Therefore, this group might be largely responsible for ammonia oxidation under the environmental conditions found on Fogo.

Environmental Risk Assessment of Metals in the Volcanic Soil of Changbai Mountain.

Tianchi volcano is a dormant active volcano with a risk of re-eruption. Volcanic soil and volcanic ash samples were collected around the volcano and the concentrations of 21 metals (major and trace elements) were determined. The spatial distribution of the metals was obtained by inverse distance weight (IDW) interpolation. The metals' sources were identified and their pollution levels were assessed to determine their potential ecological and human health risks. The metal concentrations were higher around Tianchi and at the north to the west of the study area. According to the geo-accumulation index (Igeo), enrichment factor (EF) and contamination factor (CF) calculations, Zn pollution was high in the study area. Pearson's correlation analysis and principal component analysis showed that with the exception of Fe, Mn and As, the metals that were investigated (Al, K, Ca, Na, Mg, Ti, Cu, Pb, Zn, Cr, Ni, Ba, Ga, Li, Co, Cd, Sn, Sr) were mostly naturally derived. A small proportion of Li, Pb and Zn may have come from vehicle traffic. There is no potential ecological risk and non-carcinogenic risk because of the low concentrations of the metals; however, it is necessary to pay attention to the carcinogenic risk of Cr and As in children.

Effects of radiocesium fixation potentials on 137Cs retention in volcanic soil profiles of Fukushima forests.

Radiocesium is well-known to be stabilized by clay minerals in soils, while volcanic soils could typically be poor in micaceous clays that fix 137Cs effectively. We investigated 137Cs fixation potentials [radiocesium interception potential (RIP)] and depth distribution of 137Cs stocks in volcanic soils to analyze effects of clay content and mineralogy on soil retention and migration of 137Cs after the Fukushima nuclear accident. Clay minerals of the volcanic soils were dominated by hydroxy-interlayered vermiculite (HIV) and short-range-order minerals, irrespective of bedrocks. The soil RIPs were positively correlated with mass of clay fraction among the HIV-dominated volcanic soils, but RIP per clay content in the HIV-dominated volcanic soils were lower than in the soils rich in illite or vermiculitic clays. The small RIPs in the organic horizons resulted in rapid 137Cs migration from the organic horizons and their accumulation in the upper 0-5 cm mineral soil. Although RIPs of the studied volcanic soils fall within the lower class among major soil types, vertical 137Cs migration in the mineral soil is small unless RIP is less than 300-400 mmol kg-1 due to the low clay contents and shortage of illite or vermiculite.

Quantitative Analysis of Pedogenic Thresholds and Domains in Volcanic Soils.

Pedogenic thresholds describe where soil properties or processes change in an abrupt/nonlinear fashion in response to small changes in environmental forcing. Contrastingly, soil process domains refer to the space between thresholds where soil properties are either unchanged, or change gradually, across a broad range of environmental forcing. Here, we test quantitatively for the presence of thresholds in patterns of soil properties across a climatic gradient on soils developed from ~20 ky old basaltic substrate on the Island of Hawai'i. From multiple soil properties, we quantitatively identified a threshold at ~750 mm/y of water balance (precipitation minus potential evapotranspiration), delineating the upper water balance boundary of soil fertility in these soils. From the threshold in the ratio of exchangeable Ca to total Ca we identified the lower water balance boundary of soil fertility in these soils at -1000 mm/y, however this threshold was qualitatively described as it lies near the limit of the climate gradient data where the statistical approach can not be applied. These two results represent the first time that pedogenic thresholds have been identified using statistically rigorous methods and the limitations of said methods, respectively. Comparing the 20 ky soils to soils that developed on basaltic substrates of 1.2 ky, 7.5 ky, 150 ky, and 4100 ky in a time-climate matrix, we found that our quantitative analysis supports previous qualitatively identified thresholds in the soils developed from older substrates. We also identified the 20 ky as the transition from kinetic to supply limitation for plant nutrients in soil in this system.

May humic acids or mineral fertilisation mitigate arsenic mobility and availability to carrot plants (Daucus carota L.) in a volcanic soil polluted by As from irrigation water?

Carrot (Daucus carota L.) is a widely consumed root vegetable, whose growth and safety might be threatened by growing-medium arsenic (As) contamination. By this work, we evaluated the effects of humic acids from Leonardite and NPK mineral fertilisation on As mobility and availability to carrot plants grown for 60 days in a volcanic soil irrigated with As-contaminated water - representing the most common scenario occurring in As-affected Italian areas. As expected, the irrigation with As-contaminated water caused a serious toxic effect on plant growth and photosynthetic rate; the highest rate of As also inhibited soil enzymatic activity. In contrast, the organic and mineral fertilisation alleviated, at least partially, the toxicity of As, essentially by stimulating plant growth and promoting nutrient uptake. The mobility of As in the volcanic soil and thus its phytoavailability were differently affected by the organic and mineral fertilisers; the application of humic acids mitigated the availability of the contaminant, likely by its partial immobilisation on humic acid sorption sites - thus raising up the intrinsic anionic sorption capacity of the volcanic soil; the mineral fertilisation enhanced the mobility of As in soil, probably due to competition of P for the anionic sorption sites of the soil variable-charge minerals, very affine to available P. These findings hence suggest that a proper soil management of As-polluted volcanic soils and amendment by stable organic matter might mitigate the environmental risk of these soils, thus minimising the availability of As to biota.

[Podoconiosis, a society and medical community neglected disease]. / Podoconiosis: enfermedad olvidada por la sociedad y la comunidad médica.

Podoconiosis, mossy foot or endemic non-filarial elephantiasis, is a geochemical disease that causes lower limb lymphedema; it is directly related to walking barefoot over soils of volcanic origin, in areas with a high pluviometric annual index. It has a specific geographical distribution, affecting around 5% population in areas where it is endemic. It is debilitating and disfiguring disease, which frequently leads to social margination. Podoconiosis is totally preventable and, once a diagnosis is established, it may improve with simple therapeutic measures.

Ibuprofen adsorption in four agricultural volcanic soils.

Ibuprofen (IB) is a high environmental risk drug and one of the most frequently prescribed in human medicine. Recently, IB has been detected in Gran Canaria in reclaimed water for irrigation and in groundwater. Adsorption was studied in four volcanic soils from three islands of the Canarian Archipelago. Once the biodegradation process has been excluded from the experimental conditions, a batch method was applied using initial concentrations of 1-5-10-20-50-100-200 mg L(-1) and two soil/water ratios (w/V): 1:5 (OECD, 2000) and 1:1. Non-linear and linearized Langmuir and Freundlich equations were well fitted. The wide IB range tested in our batch studies allowed us to measure experimental adsorption values close to the maximum adsorption capacity (S(max)) as estimated by Langmuir, making it possible thereby to validate the use of the Langmuir equation when there is a burst of contamination at high concentration. The distribution coefficient (Kd), S(max) and Retardation Factor (RF) varied from 0.04 to 0.5 kg L(-1), 4-200 mgk g(-1) and 1.2-1.9, respectively. The lowest S(max) and Kd values were found for the 1:1S/W ratio whereas most batch studies employ 1:5S/W ratios, thus obtaining higher adsorption parameters than when considering field conditions (1:1). Despite the high anion retention of andic soils, similar Kd and RF to those reported for other soils were obtained in 1:5, while high S(max) was found. Our results demonstrate that IB adsorption in volcanic areas responds not only to the soil properties commonly cited in adsorption studies, but also depends on andic properties, sorbent concentration and Dissolved Organic Carbon, the higher values of which are related to the lower Kd and S(max). The low RF and low detection frequency of the IB in groundwater suggests that a) reclaimed water irrigation is not the main source of IB, and b) the existence of some uncontrolled water disposal points in the zone.