Forest Soil Samples Research Articles

Effects of source sample amount on biodiversity surveys of bacteria, fungi, and nematodes in soil ecosystems

Bacteria, fungi, and nematodes are major components of soil ecosystems, playing pivotal roles in belowground material cycles and biological community processes. A number of studies have recently uncovered the diversity and community structure of those organisms in various types of soil ecosystems based on DNA metabarcoding (amplicon sequencing). However, because most previous studies examined only one or two of the three organismal groups, it remains an important challenge to reveal the entire picture of soil community structure. We examined how we could standardize DNA extraction protocols for simultaneous DNA metabarcoding of bacteria, fungi, and nematodes. Specifically, in an Illumina sequencing analysis of forest and farmland soil samples, we performed DNA extraction at five levels of soil-amount (0.5, 2, 5, 10, and 20 g). We then found that DNA extraction with the 0.5 g soil setting, which had been applied as default in many commercial DNA extraction kits, could lead to underestimation of α-diversity in nematode community. We also found that dissimilarity (β-diversity) estimates of community structure among replicate samples could be affected by soil sample amount. Based on the assays, we conclude that DNA extraction from at least 20 g of soil is a standard for comparing biodiversity patterns among bacteria, fungi and nematodes.

Seasonal Variation of Soil Quality in a Semi-deciduous Northern Tropical Forest of Nagaland, India.

To assess the seasonal changes in soil parameters and the soil quality of a semi-deciduous forest in Nagaland, tropical forest soil samples were tested for 10 physical and chemical variables. Apart from clay content, EC, and CEC, the rest of the parameters showed a seasonal mean significant difference at p < .05 level. Based on the principal component analysis, available nitrogen (Nav) and electrical conductivity (EC) were included in a minimum data set and are regarded to best represent the system attributes. In both additive and weighted soil quality method, maximum SQI was recorded in autumn season. The research summarized that seasonal variations can influence soil characteristics and soil quality through its aggregate effects. Considering the result obtained from the present study, the approach we have used in soil quality assessment would be suitable for primarily screening the tropical forest soil status. This would ultimately pave ways for future management and mitigation plans to facilitate the improvement of forest health and aid to biodiversity conservation.

Cohnella mopanensis sp. nov., a new Gram-negative bacterium isolated from soil in Xinping Mountain National Forest Park.

A Gram-stain-negative, aerobic, rod-shaped bacteria strain, named YIM B01951T, was isolated from a forest soil sample collected from Mopan Mountain National Forest Park, Xinping City, Yunnan Province, southwest PR China (101°58'06" N, 23°03'02" E). Growth occurred at 15-40°C (optimum, 30°C), pH 5.0-8.0 (optimum, pH 6.5) and with up to ≤ 3.0% (w/v) NaCl on Nutrient Agar plates. The results of 16S rRNA gene sequence similarity analysis showed that strain YIM B01951T was closely related to the type strain of Cohnella arctica M9-62T (96.5%) and Cohnella lupini RLAHU4BT (96.3%). YIM B01951T contains anteiso-C15:0 and iso-C16:0 as the major cellular fatty acids; the main polar lipids are diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), lysylphosphatidylglycerol (PGL) and five aminophospholipids (APL). The MK-7 is the major respiratory quinone and the DNA G + C content is 49.2mol%. Based on these phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM B01951T is considered to be a novel species of the genus Cohnella, and named Cohnella mopanensis sp. nov. The type strain is YIM B01951T (= NBRC 115331T = KCTC 43370T).

Species‐specific DNA distribution in spruce–beech forest soil

AbstractEnvironmental DNA consists of species‐specific intracellular and extracellular fractions, whose content and information may not be similar in all environments. In forest soil, in particular, the biogeochemical fate of DNA originated by plant litter input has been extensively reviewed, but species‐specific persistence and distribution still await to be quantified. In the present work, based on the purification of extracellular and intracellular DNA fractions from forest soil samples representing 3 soil horizons at 36 randomized locations differing for stand composition (either beech‐ or spruce‐dominated, and mixed), followed by exDNA metabarcoding with the rbcL marker, we provide a clear picture of species‐specific plant DNA distribution, and explore plant community composition and diversity along the explored gradient and the soil profile. We did not find significant differences in intra‐ vs. extracellular total DNA distribution, with a progressive depletion with soil depth positively associated with soil organic C and N content and negatively associated with soil pH and mineral content. Species‐specific DNA distribution was horizontally dependent on beech and spruce basal area aboveground, while extracellular DNA showed peculiar species‐specific vertical patterns. Proportion of Fagus sylvatica DNA increased with depth in beech stand soil, and Picea abies DNA decreased in spruce stand soil, respectively, possibly linked to species‐specific differences in leaf litter decomposition dynamics and root litter contributions. Finally, our approach by metabarcoding provided a faithful, although incomplete, picture of the local plant diversity, suggesting that such technique could positively integrate traditional biodiversity inventory studies based on expert field assessments.

Extraction and characterization of cellulase from forest and compost soil fungal isolates for the application of straw degradation

Cellulases are complex hydrolytic enzymes working synergistically on the hydrolysis of cellulolytic materials for the production of simple sugars. These enzymes have tremendous environmental, industrial and agricultural applications including enhancement of the degradability of lignocellulosic materials for cattle’s feed. The aim of this study was to isolate fungus and extract cellulose enzyme from forest and compost soil samples and examine the extent to which these enzymes enhance the degradability of finger millet and oat straw for making palatable cattle’s feed. Accordingly, a total of 53 fungal isolates were isolated from forest and compost soil. On 1% CMC media resulted 40% were cellulolytic fungal species. Six were selected based on their clear zone. These isolates belonged to the genera Trichoderma, Aspergillus and Penicillium based on their morphological characteristics. Cultivation of fungal isolates for cellulase production using submerged fermentation and Solid-state fermentation was undertaken through make the variation on their levels of different growth conditions such as temperature, pH, minerals and substrates. The results showed that the highest cellulase production i.e CMCase 83.12 ± 3.18 U/dL and FPase 44.51± 0.391FPU/dL were obtained from FSI6 in FMS supplemented SSF at 280C and a pH of 6.

Paraburkholderia gardini sp. nov. and Paraburkholderia saeva sp. nov.: Novel aromatic compound degrading bacteria isolated from garden and forest soil samples

Three forest and four botanical garden top soil isolates with unique MALDI-TOF mass spectra were identified as Paraburkholderia strains closely related to Paraburkholderia sartisoli through recA gene sequence analysis. OrthoANIu, digital DNA-DNA hybridization analyses and phylogenomic analyses demonstrated that the five strains represented two new Paraburkholderia species closely related to P. sartisoli. The genome of strain LMG 31841T had a cumulative size of 6.3 Mb and a G + C content of 62.64 mol%; strain LMG 32171T had a genome size of 5.8 Mb and a G + C content of 62.91 mol%. Hemolysis on horse blood agar, beta-galactosidase and phosphoamidase activity, and assimilation of adipic acid and trisodium citrate allowed phenotypic differentiation of strains LMG 31841T, LMG 32171T and P. sartisoli LMG 24000T. An analysis of the genomic potential for aromatic compound degradation yielded additional differences among strains representing these three species, but also highlighted some discrepancies between the presence of genes and pathways, and the phenotype revealed through growth experiments using a mineral salts medium supplemented with single aromatic compounds as carbon sources. We propose to classify all isolates from the present study into two novel Paraburkholderia species, for which we propose the names Paraburkholderia gardini with LMG 32171T (=CECT 30344T) as the type strain, and Paraburkholderia saeva with LMG 31841T (=CECT 30338T) as the type strain.

Forest soil biotic communities show few responses to wood ash applications at multiple sites across Canada

There is interest in utilizing wood ash as an amendment in forestry operations as a mechanism to return nutrients to soils that are removed during harvesting, with the added benefit of diverting this bioenergy waste material from landfill sites. Existing studies have not arrived at a consensus on what the effects of wood ash amendments are on soil biota. We collected forest soil samples from studies in managed forests across Canada that were amended with wood ash to evaluate the effects on arthropod, bacterial and fungal communities using metabarcoding of F230, 16S, 18S and ITS2 sequences as well as enzyme analyses to assess its effects on soil biotic function. Ash amendment did not result in consistent effects across sites, and those effects that were detected were small. Overall, this study suggests that ash amendment applied to managed forest systems in amounts (up to 20 Mg ha−1) applied across the 8 study sties had little to no detectable effects on soil biotic community structure or function. When effects were detected, they were small, and site-specific. These non-results support the application of wood ash to harvested forest sites to replace macronutrients (e.g., calcium) removed by logging operations, thereby diverting it from landfill sites, and potentially increasing stand productivity.

Ecological Assessment of Non-Target Impact on the Intensity of Human-Induced Changes in Gray Forest Soils

This article presents studies on determining the rate of anthropogenic influences on the gray forest soils sustainability. At present, various pollutants from the atmosphere affect soils. This leads to a decrease in soil fertility, water and air pollution, a decrease in crop yields, and deterioration of product quality. A study of the gray forest soils sustainability to anthropogenic influences incompatible with natural processes is of particular interest to select groups by the degree of anthropogenic transformation. Therefore, the objective of this study was to determine the rate of anthropogenic influences on the grey forest soils sustainability and the degree of their anthropogenic transformation. This requires determining the change in the agrochemical indicators of the fertility of gray forest soils disturbed by overburdened quarrying. Identifying the nature of changes in the texture and micro-aggregate composition of the disturbed soils. Assess the nature of changes in the heavy metals content in gray forest soils of the areas chemically polluted by unauthorized disposal of industrial wastes. Reveal the nature of technogenic load and ecological hazard of industrial waste on the fertile layer of gray forest soils in the chemically polluted area. The research was conducted on an agricultural land site, where soil samples of gray forest soils were extracted. As a result, the gray forest soils’ sustainability to anthropogenic impact, incompatible with natural processes, was assessed. The rates of organic content reduction due to violation of the humus layer were proved. The decrease level of available phosphorus was proved, significant fluctuations for potassium in the soils were revealed. A significant decrease in soil acidity has been confirmed. The influence of chemical pollution of the soil cover by heavy metals has been found out. The intensity of anthropogenic load of industrial waste on the soil depending on the soil contamination levels of heavy metals was revealed.

Viridibacillus soli sp. nov., isolated from forest soil in Ailaoshan National Nature Reserve.

A Gram stain-positive, rod-shaped, and subterminal endospore-forming bacterium, designated strain YIM B01967T, was isolated from a forest soil sample collected in Ailaoshan National Nature Reserve, Yuxi City, Xinpin county, Yunnan province, China. Strain YIM B01967T showed the highest 16S rRNA gene sequence similarity with Viridibacillus arvi (99.1%) and Viridibacillus arenosi (98.9%). Based on the phylogenetic and 16S rRNA gene sequence results, strain YIM B01967T was affiliated to the genus Viridibacillus. The growth of YIM B01967T was observed at 15-35°C (optimum, 28°C), pH 7.0-9.0 (optimum, pH 7.5) and in the presence of 0-2% (w/v) NaCl (optimum in 2% NaCl). The cell wall sugars include ribose, glucose, arabinose, galactose, and mannose. The quinone system consisted of the major compound MK-8 and moderate amounts of MK-7. The major fatty acids (> 10%) included iso-C15:0, anteiso-C15:0, C16:1 ω10c. The major polar lipids profile included DPG, PME. The cell wall peptidoglycan was most likely of the type A4α with an L-Lys-D-Asp interpeptide bridge. The genomic DNA G + C content of strain YIM B01967T was 36.3mol%. The ANI and digital DNA-DNA hybridization (dDDH) values between strain YIM B01967T and Viridibacillus arvi DSM 16317T, Viridibacillus arenosi DSM 16319T were 61.0% and 32.1%, 60.0% and 33.1% based on the draft genome sequence. The results support the conclusion that strain YIM B01967T represents a novel species of the genus Viridibacillus, for which the name Viridibacillus soli sp. nov., is proposed. The type strain is YIM B01967T (= KCTC 43249T = CGMCC 1.18436T).

Propioniciclava soli sp. nov., isolated from forest soil, Yunnan, China, and reclassification of the genus Brevilactibacter into the genus Propioniciclava, and Brevilactibacter sinopodophylli, Brevilactibacter flavus, and Brevilactibacter coleopterorum as Propioniciclava sinopodophylli comb. nov., Propioniciclava flava comb. nov., and Propioniciclava coleopterorum comb. nov., respectively.

A Gram-stain-positive, coccus-shaped, facultatively anaerobic, non-motile bacterial strain, designated YIM S02567T, was isolated from a forest soil sample collected from Gejiu City, Yunnan Province, southwest PR China. Growth was observed at 10-45°C, at pH 6.0-9.5, in the presence of up to 4.0% (w/v) NaCl on R2A medium. The results of 16S rRNA gene sequence similarity analysis showed that strain YIM S02567T was most closely related to the type strain of Brevilactibacter sinopodophylli (95.4%) and Propioniciclava tarda (94.7%), and phylogenetic analysis based on genome data showed that strain YIM S02567T should be assigned to the genus Propioniciclava. The cell-wall diamino acid was meso-diaminopimelic acid. The major cellular fatty acids were identified as anteiso-C15:0 and C16:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and two unidentified glycolipids. The predominant menaquinone was MK-9(H4). The genomic DNA G + C content was 71.2mol%. Based on the polyphasic taxonomic evidence, strain YIM S02567T is assigned to a novel member of the genus Propioniciclava, for which the name Propioniciclava soli sp. nov., (type strain YIM S02567T = CCTCC AB 2020128T = CGMCC 1.18504T = KCTC 49478T) is proposed. Furthermore, we propose the reclassification of Brevilactibacter as Propioniciclava gen. nov.

Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov., two novel species isolated from forest soil.

Three aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains RXD178T, RXD172-2 and RLT1W51T, were isolated from two forest soil samples of Nanling National Nature Reserve in Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that they belonged to the genus Collimonas, and were most closely related to four validly published species with similarities ranging from 99.4 to 98.2 %. The genomic DNA G+C contents of strains RXD178T, RXD172-2 and RLT1W51T were 57.1, 59.5 and 59.4 mol%, respectively. The genome-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel strains and closely related type species were below 37.90 and 89.34 %, respectively. Meanwhile, the ANI and dDDH values between strains RXD172-2 and RLT1W51T were 98.27 and 83.50 %, respectively. The three novel strains contained C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) as the major fatty acids, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) comprised a relative higher proportion in strain RXD178T than in other strains. Both strains RXD172-2 and RLT1W51T had phosphatidylglycerol (PG), phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG) and an unidentified aminophospholipid (APL) as the main polar lipids while only PE and APL were detected in strain RXD178T. Ubiquinone 8 was the predominant quinone. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, strain RXD178T should be considered as representing one novel species within the genus Collimonas and strains RXD172-2 and RLT1W51T as another one, for which the names Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov. are proposed, with RXD178T (=GDMCC 1.1925T=KACC 21987T) and RLT1W51T (=GDMCC 1.1923T=KACC 21985T) as the type strains, respectively.

Dyella telluris sp. nov. and Dyella acidiphila sp. nov., isolated from forest soil of Dinghushan Biosphere Reserve, China.

Cells of bacterial strains G9T and 7MK23T, isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China, were Gram-stain-negative, aerobic and rod-shaped. Strain G9T was motile with single polar flagellum and grew at 12-37 °C (optimum, 28 °C), pH 4.5-8.0 (optimum, pH 6.0-7.5) and in the presence of 0-3.5 % NaCl (optimum, 1.5%, w/v); while strain 7MK23T was non-motile and grew at 12-42 °C (optimum, 28-33 °C), pH 2.5-8.5 (optimum, pH 4.5-6.5) and NaCl levels of 0-1.0 % (optimum, 0-0.5 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates fell within the cluster of the genus Dyella. The closely related species (with a 16S rRNA gene sequence similarity >98.65%) of strain G9T were Dyella terrae JS14-6T (99.0 %), D. kyungheensis THG-B117T (98.8 %) and D. amyloliquefaciens DHC06T (98.7 %) while that of strain 7MK23T were D. mobilis DHON07T (99.2 %) and D. flava DHOC52T (99.1 %), but the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains G9T, 7MK23T and the closely related Dyella species listed above were in the ranges of 77.5-83.8 % and 22.0-27.0 %, much lower than the species demarcation lines of 95.5 and 70 %, respectively. Phylogenomic analyses using UBCG and Phylophlan also supported that these two strains represent two novel species of Dyella. The major fatty acids of strain G9T were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 while that of strain 7MK23T were iso-C15 : 0 and anteiso-C15 : 0. Ubiquinone-8 was the only respiratory quinone detected in both strains. The polar lipids of strain G9T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and several unknown phospholipids, aminophospholipids, aminolipids and lipid while strain 7MK23T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and several unknown phospholipids and aminophospholipids. The DNA G+C contents of strains G9T and 7MK23T were 64.7 and 63.4 mol%, respectively. On the basis of 16S rRNA gene sequence phylogenetic and phylogenomic analyses as well as phenotypic data obtained, we propose that strains G9T and 7MK23T represent two novel species of the genus Dyella, for which the names Dyella telluris sp. nov. (type strain G9T=KACC 21725T=GDMCC 1.2132T) and Dyella acidiphila sp. nov. (type strain 7MK23T=KCTC 62739T=GDMCC 1.1446T) are proposed.

Impact of copper mining wastes in the Amazon: Properties and risks to environment and human health

Improper disposal of copper mining wastes can threaten the ecosystem and human health due to the high levels of potentially toxic elements released into the environment. The objective of this study was to determine the properties of Cu mining wastes generated in the eastern Amazon and their potential risks to environment and human health. Samples of forest soil and artisanal/industrial Cu mining wastes were collected and subjected to characterization of properties and pseudo-total concentrations of Al, As, Ba, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, and Zn, in addition to chemical fractionation of Cu. The pH ranged from near neutrality to alkaline. Pseudo-total concentrations of Cu were high in all wastes, mainly in the artisanal rock waste, with 19,034 mg kg−1, of which 61% is concentrated in the most reactive fractions. Pollution indices indicated that the wastes are highly contaminated by Cu and moderately contaminated by Cr and Ni. However, only the artisanal rock waste is associated with environmental risk. Non-carcinogenic and carcinogenic human health risks were detected, especially from exposure to Cr in the artisanal rock waste. Prevention actions and monitoring of the artisanal mining area are necessary to avoid impacts to the local population.

Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures.

Simple SummaryThe study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community’s information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications. This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

Application of Low-Cost MEMS Spectrometers for Forest Topsoil Properties Prediction.

Increasing temperatures and drought occurrences recently led to soil moisture depletion and increasing tree mortality. In the interest of sustainable forest management, the monitoring of forest soil properties will be of increasing importance in the future. Vis-NIR spectroscopy can be used as fast, non-destructive and cost-efficient method for soil parameter estimations. Microelectromechanical system devices (MEMS) have become available that are suitable for many application fields due to their low cost as well as their small size and weight. We investigated the performance of MEMS spectrometers in the visual and NIR range to estimate forest soil samples total C and N content of Ah and Oh horizons at the lab. The results were compared to a full-range device using PLSR and Cubist regression models at local (2.3 ha, n: Ah = 60, Oh = 50) and regional scale (State of Saxony, Germany, 184,000 km, n: Ah = 186 and Oh = 176). For each sample, spectral reflectance was collected using MEMS spectrometer in the visual (Hamamatsu C12880MA) and NIR (NeoSpetrac SWS62231) range and using a conventional full range device (Veris Spectrophotometer). Both data sets were split into a calibration (70%) and a validation set (30%) to evaluate prediction power. Models were calibrated for Oh and Ah horizon separately for both data sets. Using the regional data, we also used a combination of both horizons. Our results show that MEMS devices are suitable for C and N prediction of forest topsoil on regional scale. On local scale, only models for the Ah horizon yielded sufficient results. We found moderate and good model results using MEMS devices for Ah horizons at local scale ( 0.71, RPIQ 2.41) using Cubist regression. At regional scale, we achieved moderate results for C and N content using data from MEMS devices in Oh ( 0.57, RPIQ ≥ 2.42) and Ah horizon ( 0.54, RPIQ ). When combining Oh and Ah horizons, we achieved good prediction results using the MEMS sensors and Cubist ( 0.85, RPIQ ≥ 4.69). For the regional data, models using data derived by the Hamamatsu device in the visual range only were least precise. Combining visual and NIR data derived from MEMS spectrometers did in most cases improve the prediction accuracy. We directly compared our results to models based on data from a conventional full range device. Our results showed that the combination of both MEMS devices can compete with models based on full range spectrometers. MEMS approaches reached between 68% and 105% of the corresponding full ranges devices values. Local models tended to be more accurate than regional approaches for the Ah horizon. Our results suggest that MEMS spectrometers are suitable for forest soil C and N content estimation. They can contribute to improved monitoring in the future as their small size and weight could make in situ measurements feasible.

Contamination of Slovak Bilberry (Vaccinium Myrtillus L.) with Radiocaesium 137Cs in Selected Slovak Locations

Abstract The aim of this study was to determine the activity of post-Chernobyl 137Cs in Slovak bilberry (Vaccinium myrtillus L.) from selected locations of Slovakia depending upon: the season, location and the soil-plant transfer factor (TF). The 137Cs activity was determined in samples of forest soil and bilberry bushes (stems, leaves and fruits) growing on the soil in three locations: Arboretum Mlyňany (1), Hodruša-Hámre (2) and Javorníky (3). Altogether we collected 35 samples; namely 15 samples from Arboretum Mlyňany, 10 samples from Hodruša-Hámre and 10 from Javorníky. The samples of soil were examined also for the activity of 40K. The samples were collected in the spring, summer and autumn in the years 2019 and 2020 and were analysed by a gamma-ray spectrometry method. The highest levels of 137Cs activity concentrations were determined in Hodruša-Hámre in September where they reached 161 ± 13 Bq.kg−1 in the soil, 3.95 ± 1.07 Bq.kg−1 in the stems and 14.7 ± 4.26 Bq.kg−1 in the leaves. The lowest levels were determined in the Arboretum Mlyňany in October where the 137Cs activity in the soil reached 13.1 ± 1 15 Bq.kg−1, while in the stems, leaves and fruits it was lower than the minimum detectable level. In the latter location, we also determined the highest activity of 40K, the radioactive isotope physiologically and metabolically similar to 137Cs. The mass activity of 137Cs in all samples of bilberries were lower than the minimum detectable activity (MDA). The comparison of the results obtained in this study with the limit for total mass activity of radiocaesium (134Cs + 137Cs) in the food (600 Bq.kg−1) allowed us to conclude that the fruits, stems and leaves of Slovak bil-berries present neither health nor environmental risk.

Impact of common sample pre-treatments on key soil microbial properties

Pre-treatment of soil samples prior to analysis is acknowledged to affect microbial activity and community parameters, but recommendations are diverging and there are no best-practice or standardised laboratory protocols. For the microbial carbon use efficiency (CUE) as a ratio parameter of C allocated to anabolism over total metabolised C, the effects of sample pre-treatment are unpredictable because the underlying parameters of microbial metabolism may be affected differently. In treatment or land use comparisons, it is important to know whether soils are affected in a similar way by pre-treatment. Based on five different paired sites (each with cropland and forest), the effects of six common pre-treatments were evaluated on 18O-CUE and associated parameters, i.e. respiration rate, soil microbial biomass C, total DNA extracted, and estimated abundances of fungi, bacteria and archaea. The six common pre-treatments were: (i) immediate analysis of field-fresh soil samples, and analysis following 14 d pre-incubation of soil samples that were (ii) field-fresh, (iii) air-dried, (iv) oven-dried (40 °C), (v) frozen at −20 °C and (vi) frozen in-situ (dry ice and subsequently liquid N2). The experiment revealed two main findings. The first was that pre-incubation of 14 d had the most pronounced effect and reduced microbial respiration rate, growth rate and microbial biomass C by between 28% and 63% on average compared with field-fresh samples, suggesting an impact of the reduction in readily available substrates on microbial activity. The second finding was that even after 14 days of pre-incubation, drying & rewetting caused an increase in the microbial respiration rate in forest soil samples of 64 ± 53% (air-drying) and 86 ± 65% (oven-drying), known as the Birch effect. However, CUE as a ratio parameter was found to be unaffected by sample pre-treatment, with only minor changes after 14 d of pre-incubation. Pre-treatment (including pre-incubation) affected cropland and forest samples similarly, with one exception: the estimated abundance of fungi increased only with drying & rewetting in forest soils. This suggests that dried cropland soils could potentially yield appropriate community data, while forest soils respond to soil drying in a more complex way. It was concluded that CUE values can be derived from soil samples regardless of whether they were dried & rewetted, frozen & thawed, or stored fresh.

Combining Vis–NIR spectroscopy and advanced statistical analysis for estimation of soil chemical properties relevant for forest road construction

AbstractA thorough quantification of soil chemical properties is essential for assessing the engineering properties of forest soils for road design, construction, and maintenance. Here, we investigate the applicability of visible–near‐infrared (Vis–NIR) spectroscopy in conjunction with advanced statistical analysis for estimation of soil chemical properties. Sixty forest soil samples were collected and analyzed for pH, electrical conductivity (EC), CaCO3, organic matter (OM), and cation exchange capacity (CEC) with established laboratory methods. The spectral measurements were performed with a Vis–NIR spectrometer within a range of 350–2,500 nm. To estimate abovementioned soil properties from reflectance spectra, advanced statistical techniques including partial least squares regression (PLSR), hybrid partial least squares and artificial neural networks (PLS–DI–ANN) models, hybrid partial least squares and adaptive neural fuzzy inference system (PLS–DI–ANFIS) models, as well as narrow band spectral indices were applied. The obtained results ​​indicate that the PLS–DI–ANFIS models show great potential for the estimation of pH, EC, OM, and CEC from reflectance spectra and their first derivatives, exhibiting higher R2 values and lower RMSE than the other investigated models. The estimation accuracy for CaCO3, however, was low for all applied methods. The results confirm that Vis–NIR spectroscopy may be applied as a rapid and cost‐efficient alternative to standard chemical soil analysis techniques, aiding forest road design, construction, and maintenance.

Soil biota and fertility along a gradient of forest degradation in a temperate ecosystem

Soil biota populations are good indicators for the evaluation of soil quality, which is in line with the nutrient cycles in forest ecosystems. To the best of the authors’ knowledge, responses of belowground biota to forest removal intensity have received little attention. The present study aimed to study the effect of low, moderate and high intensities of forest degradation, based on the density of standing trees, in lands covered by Carpinus betulus and Parrotia persica tree species in northern Iran on forest floor, soil properties and fauna and flora activities. In the summer season, a total of 15 forest floor and soil samples (30 × 30 × 10 cm) from each site were transferred to the laboratory. To achieve the temporal pattern of soil biota, sampling was also performed in the fall season. The activities of earthworm groups (i.e. epigeic, anecic, and endogeic) were significantly decreased in order of low > moderate > high levels of forest degradation, with higher populations in the fall season (especially epigeic earthworms). Similarly, greater activity of soil Acarina, Collembola, nematode, protozoa (especially in the fall season), bacteria and fungi (especially in the summer season) were found in forests with low intensity of degradation. Principal component analysis (PCA) indicated higher soil biological activities and fertility in the forest areas with low degradation which can be attributed to the higher density of trees, forest floor mass and quality. This research provides evidence of the strong dependence of below-ground communities on aboveground tree density in temperate forests.

Sources of Magnetic Particles from Air Pollution in Mountainous Area

Measurement of magnetic susceptibility of topsoil represents a very useful tool for the detection of atmospherically depositedmagnetic particles. The samples of forest soils from the Moravian-Silesian Beskydy Mountains (the Czech Republic) were used foridentification of emissions sources of particles with magnetic ordering. Magnetic susceptibility was measured at bulk samples ofgrain size class under 2 mm. Microanalysis using electron microscope with an energy dispersive X-ray spectrometer was used forthe determination of particles in the magnetic fraction. The samples of dust from the sintering plant of the Iron Works in the townof Třinec were analysed. The values of magnetic susceptibility of forest soils in the Třinec region are increased. In the relatively nearvicinity of the industrial area, the average value for Javorový Mount was 7.90×10-6 m3/kg, for Ostrý Mount it was 6.69×10-6 m3/kg. It was proved that they were higher than the average values from the Beskydy Mountains (4.64×10-6 m3/kg). The concentrationsof lead and magnetic susceptibility in soils showed significant correlation dependence (rs = 0.85). The iron and steel industryrepresent the primary source of the pollution load in forest soils of the studied area. Statistically, significant dependences betweenthe organic matter content and the lead and zinc concentrations as well as between the magnetic susceptibility values and the ironconcentrations in forest soils were found. It was confirmed that the airborne particles are deposited on vegetation and accumulatedin the organic horizon of forest soils.