The taxonomic status of two filamentous actinobacteria, isolates NF23 and NL8
, recovered from the litter layer of a pine forest soil in Poland was established in a genome-based polyphasic study. The ...isolates showed a combination of chemotaxonomic, morphological and physiological properties associated with their classification in the genus
. They formed a well supported lineage within the
16S rRNA gene tree and were most closely related to the type strains of
(99.1%),
(99.9 %) and
(99.1 %), and like them, were found to have large genomes (10.8 and 11.5 Mbp, respectively). A phylogenomic tree based on the draft genomes of isolates NF23 and NL8
and their phylogenetic neighbours showed that they formed a distinct branch in the
clade that was most closely related to
DSM 111109
. The isolates shared a combination of genomic, genotypic and phenotypic features, and had high average nucleotide index (ANI) and digital DNA:DNA hybridization (dDDH) similarities consistent with their assignment to the same species. The isolates were distinguished from the
and
strains by a wealth of taxonomic data and by low ANI (84.9-93.9 %) and dDDH (29.6-54.7 %) values. It is proposed that the isolates be classified in the genus
as
sp. nov. with isolate NL8
(=DSM 111110
=PCM 3045
) as the type strain. The genomes of strains NF23 and NL8
are rich in natural product-biosynthetic gene clusters hence these strains have the potential to synthesize new specialised metabolites.
Three aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains RXD178
, RXD172-2 and RLT1W51
, 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
, 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 RXD178
, RXD172-2 and RLT1W51
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 RLT1W51
were 98.27 and 83.50 %, respectively. The three novel strains contained C
, C
cyclo and summed feature 3 (C
6
and/or C
7
) as the major fatty acids, and summed feature 8 (C
6
and/or C
7
) comprised a relative higher proportion in strain RXD178
than in other strains. Both strains RXD172-2 and RLT1W51
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 RXD178
. Ubiquinone 8 was the predominant quinone. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, strain RXD178
should be considered as representing one novel species within the genus
and strains RXD172-2 and RLT1W51
as another one, for which the names
sp. nov. and
sp. nov. are proposed, with RXD178
(=GDMCC 1.1925
=KACC 21987
) and RLT1W51
(=GDMCC 1.1923
=KACC 21985
) as the type strains, respectively.
In soil incubation experiments we examined if there are differences in the kinetic parameters of atmospheric methane (CH
4) oxidation in soils of upland forests and forested peatlands. All soils ...showed net uptake of atmospheric CH
4. One of the upland forests included also managed (clear-cut with or without previous liming or N-fertilization) study plots. The CH
4 oxidation in the forested peat soil had a higher
K
m (510 μl l
−1) and
V
max (6.2
nmol CH
4
cm
−3
h
−1) than the upland forest soils (
K
m from 5 to 18 μl l
−1 and
V
max from 0.15 to 1.7
nmol CH
4
cm
−3
h
−1). The forest managements did not affect the
K
m-values. At atmospheric CH
4 concentration, the upland forest soils had a higher CH
4 oxidation activity than the forested peat soil; at high CH
4 concentrations the reverse was true. Most of the soils oxidised CH
4 in the studied pH range from 3 to 7.5. The pH optimum for CH
4 oxidation varied from 4 to 7.5. Some of the soils had a pH optimum for CH
4 oxidation that was above their natural pH. The CH
4 oxidation in the upland forest soils and in the peat soil did not differ in their sensitivities to (NH
4)
2SO
4 or K
2SO
4 (used as a non-ammonium salt control). Inhibition of CH
4 oxidation by (NH
4)
2SO
4 resulted mainly from a general salt effect (osmotic stress) though NH
4
+ did have some additional inhibitory properties. Both salts were better inhibitors of CH
4 oxidation than respiration. The differences in the CH
4 oxidation kinetics in the forested peat soil and in the upland forest soils reveal that there are differences in the physiologies of the CH
4 oxidisers in these soils.
► Forest coppicing modifies soil chemical, biochemical and microbiological properties. ► Microbial biomass and its activities were increased by trees cutting. ► Functional diversity measured with ...enzymes and CLPP was affected by management. ► Enzymes and CLPP may target different components of microbial functional diversity.
Among the bioindicators used to determine soil quality a vast interest is devoted to those related to soil biodiversity; in fact, the ability of a system to withstand stress and abiotic and biotic disturbances depends on its level of biodiversity which is the basis of the functionality of ecosystems. Functional diversity is widely used to gain insight into microbial performances, particularly in presence of a factor of disturbance. In this study we present the changes of microbial functional diversity and other soil chemical and biochemical properties following forest coppicing. The study was conducted in central Italy, in a natural reservation under Quercus cerris spp. plant cover; soils were sampled after three years from coppicing and in an aged coppice taken as control. Trees cutting provoked a decrease of soil total organic carbon (TOC) and a pH increase suggesting a priming effect on native organic matter and qualitative changes in soil solution composition. Microbial indicators (microbial biomass carbon, MBC), basal and cumulative respiration, and indexes (microbial and metabolic quotients) were significantly affected by forest management. Enzyme activities and microbial catabolic activity measured by means of community level physiological profile (CLPP) techniques (MicroResp and Biolog) increased in coppiced plots indicating higher decomposition processes promoted by plant debris and rhizodepositions released after cutting.
The calculation of the diversity indexes using both techniques (enzyme activities and CLPP) suggested interesting speculations and perspectives on possible interpretations of these results.
Sawdust and wood residues are considered to be stimulators of microbiological change in soil and could be used in post-arable sites designed for afforestation. In this study, we discuss changes in ...bacteria numbers within selected groups in relation to soil type (arable and forest) and method of sawdust application. Sawdust was spread along planting rows and mixed with the soil or put directly under roots of planted seedlings. Applying sawdust under the roots increased the number of cellulolytic bacteria in all experimental treatments. On post-arable soil, adding sawdust in rows increased the number of copiotrophic bacteria and reduced the number of fluorescent bacteria and actinomycetes (ACT). In control forest soils, the number of copiotrophic, oligotrophic and spore-forming bacteria decreased simultaneously with increased ACT in all treatments. The number of fluorescent bacteria increased when sawdust was applied on forest sites under planted trees and decreased when sawdust was spread in planting rows. Oligotrophic bacteria also decreased in the latter case. We present a list of bacteria identified by DNA - 16S rRNA gene sequences. Adding sawdust to arable soils significantly changed the quantitative and qualitative composition of microbial communities.
•Effects of stump harvesting and soil disturbance on C and N mineralization were studied in clear-felled Norway spruce stands.•No significant effects on soil and C and N mineralization rates were ...found 11–12years after stump harvesting.•No significant effect of stump harvesting on soil C and N pools were discovered•Stump harvesting increased soil mixing, as indicated by changes in pH and C/N ratios.
The use of forest-derived biomass has steadily increased in Finland and Sweden during the past decades leading to more intensive forest management practices in the region, such as whole-tree harvesting, both above- and belowground. Stump harvesting results in a direct removal of stump and coarse-root carbon (C) from the stand and can cause extensive soil disturbance, which has been suggested to increase C mineralization. In this study, the effects of stump harvesting on soil C and nitrogen (N) mineralization, and soil surface disturbance were studied in two different clear-felled Norway spruce (Picea abies) sites in Central Finland. The treatments were whole-tree harvesting (WTH, removal of stems and logging residues), and WTH and stump harvesting (WTH+S). Both sites, Honkola (2 stands) and Haukilahti (6 stands) were mounded. In both treatments, soil samples were taken from different soil layers down to a total depth of 20cm in the mineral soil from (i) mounds, (ii) undisturbed soil and (iii) pits. The sampling was performed 11–12years after treatments. Soil C and N mineralization rates were determined in laboratory incubation experiments. In addition, total C and N pools (gm−2) were estimated for each disturbance class and soil layer. Soil C and N pools had a tendency to be lower following stump harvesting, but no statistically significant treatment effect was detected. Stump harvesting increased soil mixing as indicated by a significant decrease in C concentration in the mound disturbance class. There was no significant effect of stump harvesting on soil C mineralization rates. A combination of mineralization rates and soil pool data showed that field C mineralization (g CO2-Cm−2yr−1) did not significantly differ between stands where stumps were removed or were retained. Further, stump harvesting did not seem to have any stimulating effect on soil CO2 efflux 11–12years after treatment.
Chloride is often considered as the main chlorine form in soils. However, recent studies show that chlorine is mostly present in soils as naturally produced organically bound molecules. The relative ...contribution of biotic, including microbial, and abiotic processes to formation of organically bound chlorine remains poorly understood. We performed a37Cl spiking batch experiment with a forest soil incubated under abiotic and biotic conditions over two time periods to simultaneously monitor the formation of organically bound chlorine from natural and tracer chlorine. To compare biotic and abiotic conditions without biased effect of sterilization technique for abiotic control, the soil was irradiated and reinoculated or not with soil microflora. Fifteen days after microbial inoculation, the natural non-extractable organic chlorine content in the inoculated soil was significantly higher than in the sterile soil, showing that microbial activity contributed to formation of organically bound chlorine. However, no significant difference was noted between the two incubation periods. The same trend was noted for tracer chlorine, yet without a significant difference. The present study shows that chlorination is mediated by microbial activity, but there is also some indication of abiotic formation of organically bound chlorine, with a non-extractable organic tracer chlorine formation of about 6% just after spiking in abiotic conditions.
•Inorganic 37Cl was used to trace organically bound chlorine formation in soil incubation.•Irradiated forest soil was inoculated or not with soil microflora.•Organically bound chlorine was higher in inoculated than in sterile soil.•Abiotic processes also contribute to organic chlorine formation.
Litter is an important source of nutrients for trees and can improve the quality of degraded soils. The objective of this study was to describe the dynamics of carbon mineralization in litter soils ...using nonlinear models, estimating half-life times. Soil carbon mineralization under three types of forest cover was evaluated: Atlantic forest fragment (capoeira), Acacia auriculiformis trees (acacia), and Mimosa caesalpiniifolia (sabiá) from a reforested area with a history of degradation. Twelve measurements of the mineralized carbon were made up to 222 days after the beginning of the incubation of litter soils. Stanford and Smith, Juma, and Cabrera models were fitted by the least squares method using the Gauss-Newton algorithm in the R software. The Stanford and Smith model was more appropriate in describing all treatments, based on the Akaike Information Criterion, with estimates of half-life for Acácia, Capoeira, and Sabiá soils at 25, 44, and 51 days, respectively. The Stanford and Smith and Juma nonlinear models satisfactorily described the carbon mineralization of soils of all treatments.
The objective of this study is to better quantify the occurrence, intake, and potential risk from Hg in fungi traditionally foraged in SW China. The concentrations and intakes of Hg were measured ...from 42 species including a “hard” flesh type polypore fungi and a” soft” flesh type edible species that are used in traditional herbal medicine, collected during the period 2011–2017. Three profiles of forest topsoil from the Zhenyuan site in 2015 and Changning and Dulong sites in 2016 were also investigated. The concentrations of Hg in composite samples of polypore fungi were usually below 0.1 mg kg
−1
dry weight (dw) but higher levels, 0.11 ± 0.01 and 0.24 ± 0.00 mg kg
−1
dw, were noted in
Ganoderma applanatum
and
Amauroderma niger
respectively, both from the Nujiang site near the town of Lanping in NW Yunnan. Hg concentrations in
Boletaceae
species were usually well above 1.0 mg kg
−1
dw and as high as 10 mg kg
−1
dw. The quality of the mushrooms in this study in view of contamination with Hg showed a complex picture. The “worst case” estimations showed probable intake of Hg from 0.006 μg kg
−1
body mass (bm) (“hard” type flesh) to 0.25 μg kg
−1
bm (“soft” flesh) on a daily basis for capsulated products, from 17 to 83 μg kg
−1
bm (“soft” flesh) in a meal (“hard” type flesh mushrooms are not cooked while used in traditional herbal medicine after processing), and from 0.042 to 1.7 and 120 to 580 μg kg
−1
bm on a weekly basis, respectively.
Graphical abstract
Key points
•
Polypore species were slightly contaminated with Hg.
•
Hg maximal content in the polypore was < 0.25 mg kg
−1
dry weight.
•
Many species from Boletaceae family in Yunnan showed elevated Hg.
•
Locals who often eat Boletus may take Hg at a dose above the daily reference dose.
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