Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Eastern Canadian boreal forest soil and foliar chemistry show evidence of resilience to long-term nitrogen addition

The boreal forest is one of the world's largest terrestrial biome and plays crucial roles in global biogeochemical cycles, such as carbon (C) sequestration in vegetation and soil. However, the impacts of decades of N deposition on N-limited ecosystems, like the eastern Canadian boreal forest, remain unclear. For 13 years, N deposition was simulated by periodically adding ammonium nitrate on soils of two boreal coniferous forests (i.e., balsam fir and black spruce) of eastern Canada, at low (LN) and high (HN) rates, corresponding to 3 and 10 times the ambient N deposition, respectively. We show that more than a decade of N addition had no strong effects on mineral soil C, N, P, and cation concentrations and on foliar total Ca, K, Mg, and Mn concentrations. In organic soil, C stock was not affected by N addition while N stock increased, and exchangeable Ca2+ and Mg2+ decreased at the balsam fir site under HN treatment. At both sites, LN treatment had nearly no impact on foliage and soil chemistry but foliar N and N:P significantly increased under HN treatment, potentially leading to foliar nutrient imbalance. Overall, our work indicates that, in the eastern Canadian boreal forest, soil and foliar nutrient concentrations and stocks are resilient to increasing N deposition potentially because, in the context of N limitation, extra N would be rapidly immobilized by soil micro-organisms and vegetation. These findings could improve modeling future boreal forest soil C stocks and biomass growth and could help in planning forest management strategies in eastern Canada.

Decoding seasonal changes: soil parameters and microbial communities in tropical dry deciduous forests

In dry deciduous tropical forests, both seasons (winter and summer) offer habitats that are essential ecologically. How these seasonal changes affect soil properties and microbial communities is not yet fully understood. This study aimed to investigate the influence of seasonal fluctuations on soil characteristics and microbial populations. The soil moisture content dramatically increases in the summer. However, the soil pH only gradually shifts from acidic to slightly neutral. During the summer, electrical conductivity (EC) values range from 0.62 to 1.03 ds m-1, in contrast to their decline in the winter. The levels of soil macronutrients and micronutrients increase during the summer, as does the quantity of soil organic carbon (SOC). A two-way ANOVA analysis reveals limited impacts of seasonal fluctuations and specific geographic locations on the amounts of accessible nitrogen (N) and phosphorus (P). Moreover, dehydrogenase, nitrate reductase, and urease activities rise in the summer, while chitinase, protease, and acid phosphatase activities are more pronounced in the winter. The soil microbes were identified in both seasons through 16S rRNA and ITS (Internal Transcribed Spacer) gene sequencing. Results revealed Proteobacteria and Ascomycota as predominant bacterial and fungal phyla. However, Bacillus, Pseudomonas, and Burkholderia are dominant bacterial genera, and Aspergillus, Alternaria, and Trichoderma are dominant fungal genera in the forest soil samples. Dominant bacterial and fungal genera may play a role in essential ecosystem services such as soil health management and nutrient cycling. In both seasons, clear relationships exist between soil properties, including pH, moisture, iron (Fe), zinc (Zn), and microbial diversity. Enzymatic activities and microbial shift relate positively with soil parameters. This study highlights robust soil-microbial interactions that persist mainly in the top layers of tropical dry deciduous forests in the summer and winter seasons. It provides insights into the responses of soil-microbial communities to seasonal changes, advancing our understanding of ecosystem dynamics and biodiversity preservation.

nov., isolated forest soil

A milky-white-coloured, aerobic, Gram-stain-positive, rod-shaped and motile bacterial strain (GW78T) was isolated from forest soil. GW78T was catalase-positive and oxidase-negative. The strain was able to grow optimally at 37 °C and at pH 7.0 in Reasoner's 2A media. The phylogenetic and 16S rRNA gene sequence analysis of GW78T showed its affiliation with the genus Paenibacillus. The 16S rRNA gene sequence of GW78T revealed 98.3 % similarity to its nearest neighbour Paenibacillus mucilaginosus VKPM B-7519T. Its chemotaxonomic properties included MK-7 as the sole menaquinone, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine as major polar lipids, and anteiso-C15 : 0, C16 : 1  ω11c and anteiso-C17 : 0 as predominant fatty acids. Digital DNA-DNA hybridization and average nucleotide identity results with its closest relatives were <74.0 % and <14.0 %, respectively. Overall, 16S rRNA gene sequence comparisons, phylogenetic and genomic evidence, and phenotypic and chemotaxonomic data allow the differentiation of GW78T from other members of the genus Paenibacillus. Thus, we propose that strain GW78T represents a novel species of the genus Paenibacillus, with the name Paenibacillus caseinilyticus sp. nov. The type strain is GW78T (=KCTC 43430T=NBRC 116023T).

Complete genome sequence of Bradyrhizobium NP1, isolated from forest soil

We report the complete genome sequence of Bradyrhizobium strain NP1. This bacterium was isolated from forest soil that had been subject to chronic warming. The genome of this novel isolated bacteria is presented as a single circular contig of 7,712,921 base pairs with 64.14% GC content.

nov., isolated from forest soil in Pyeongchang, Republic of Korea

Rod-shaped Gram-stain-negative, aerobic bacterial strains, designated PC14 and PC15T, were isolated from a forest soil sample collected in Pyeongchang county, Gangwon-do, Republic of Korea. Strains PC14 and PC15T grew at 15-37 °C (optimum, 28-30 °C in tryptone soya agar and Mueller-Hinton agar), hydrolysed chitin and casein, and tolerated pH 8.5 and 2 % (w/v) NaCl. The strains were most closely related to members of the genus Chitinophaga, namely Chitinophaga arvensicola DSM 3695T (98.4 %), Chitinophaga longshanensis Z29T (98.3 %), Chitinophaga ginsengisegetis Gsoil 040T (97.8 %), Chitinophaga polysaccharea MRP-15T (97.8 %) and Chitinophaga niastensis JS16-4T (97.7 %). The type strain grew well on conventional commercial media in the laboratory, including tryptone soya agar, Mueller-Hinton agar, Reasoner's 2A agar, nutrient agar and Luria-Bertani agar. The major polar lipid profile comprised phosphatidylethanolamine, an unidentified aminolipid and unidentified polar lipids. The major respiratory quinone was menaquinone-7. The main fatty acids were iso-C15:0, C16:1 ω5c, C16:0 3-OH, iso-C15:0 3-OH and iso-C17:0 3-OH. The DNA G+C content of the isolated strain based on the whole genome sequence was 46.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strains PC14 and PC15T and the reference type strains ranged from 71.0 to 76.5 %, and from 20.3 to 20.7 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain PC15T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Chitinophaga. Therefore, strain PC15T is considered to represent a novel species, for which the name Chitinophaga nivalis sp. nov. is proposed. The type strain is PC15T (=KACC 22893T=JCM 35788T).

nov., isolated from subtropical forest soil

Four novel bacterial strains, designated RBB1W86^T, RXD159^T, RBB189^T and RLT163^T, were isolated from subtropical forest soil of the Nanling National Nature Reserve located in Guangdong Province, PR China. 16S rRNA gene phylogeny indicated their affiliation to the genus Dyella, among which strains RBB1W86^T and RXD159^T were closely related to Dyella halodurans CGMCC 1.15435^T with 16S rRNA gene sequence similarities of 98.8 and 99.5 %, respectively, and strains RBB189^T and RLT163^T were closely related to Dyella tabacisoli CGMCC 1.16273^T (98.8 %) and Dyella japonica JCM 21530^T (99.4 %), respectively. Phylogenomic analysis based on 92 core genes showed consistent phylogeny with the 16S rRNA gene phylogeny for strains RBB1W86^T, RBB189^T and RLT163^T, while strain RXD159^T showed a closer relationship with D. tabacisoli CGMCC 1.16273^T and strain RBB189^T. The genome-derived average nucleotide identity (ANI) values between the newly isolated strains and their closely related species were 70.18‒90.20 %, and the corresponding digital DNA-DNA hybridization (dDDH) values were 20.80‒40.30 %. Meanwhile, the ANI and dDDH values between each pair of the newly isolated strains were 75.80‒79.77 % and 21.30‒23.30 %, respectively. They all took iso-C_15 : 0 and summed feature 9 (10-methyl C_{16  : 0} and/or iso-C_{17  : 1} ω9c) as the major fatty acids. Moreover, C_16 : 0, iso-C_16 : 0, iso-C_17 : 0 and summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c) were also variously distributed as major components. They all took ubiquinone 8 as the only predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Phosphatidylmethylethanolamine was only present in strain RBB189^T as another major component. Based on the results of phenotypic, genotypic and chemotaxonomic analyses, the newly isolated strains could be clearly distinguished from their closely related species and should represent four distinct novel species of the genus Dyella, for which the names Dyella humicola sp. nov. (type strain RBB1W86^T=GDMCC 1.1901^T=KACC 21988^T), Dyella subtropica sp. nov. (type strain RXD159^T=GDMCC 1.1902^T=KACC 21989^T), Dyella silvatica sp. nov. (type strain RBB189^T=GDMCC 1.1900^T=KACC 21990 ^T) and Dyella silvae sp. nov. (type strain RLT163^T=GDMCC 1.1916^T=KACC 21991^T) are proposed.

Iodide uptake by forest soils is principally related to the activity of extracellular oxidases

¹²⁹I is a nuclear fission decay product of concern because of its long half-life (16 Ma) and propensity to bioaccumulate. Microorganisms impact iodine mobility in soil systems by promoting iodination (covalent binding) of soil organic matter through processes that are not fully understood. Here, we examined iodide uptake by soils collected at two depths (0-10 and 10-20 cm) from 5 deciduous and coniferous forests in Japan and the United States. Autoclaved soils, and soils amended with an enzyme inhibitor (sodium azide) or an antibacterial agent (bronopol), bound significantly less ¹²⁵I tracer (93%, 81%, 61% decrease, respectively) than the untreated control soils, confirming a microbial role in soil iodide uptake. Correlation analyses identified the strongest significant correlation between ¹²⁵I uptake and three explanatory variables, actinobacteria soil biomass (p = 6.04E-04, 1.35E-02 for Kendall-Tau and regression analysis, respectively), soil nitrogen content (p = 4.86E-04, 4.24E-03), and soil oxidase enzyme activity at pH 7.0 using the substrate L-DOPA (p = 2.83E-03, 4.33E-04) and at pH 5.5 using the ABTS (p = 5.09E-03, 3.14E-03). Together, the results suggest that extracellular oxidases, primarily of bacterial origin, are the primary catalyst for soil iodination in aerobic, surface soils of deciduous and coniferous forests, and that soil N content may be indicative of the availability of binding sites for reactive iodine species.

Does Forest Soil Fungal Community Respond to Short-Term Simulated Nitrogen Deposition in Different Forests in Eastern China?

Nitrogen (N) deposition has changed plants and soil microbes remarkably, which deeply alters the structures and functions of terrestrial ecosystems. However, how forest fungal diversity, community compositions, and their potential functions respond to N deposition is still lacking in exploration at a large scale. In this study, we conducted a short-term (4-5 years) experiment of artificial N addition to simulated N deposition in five typical forest ecosystems across eastern China, which includes tropical montane rainforest, subtropical evergreen broadleaved forest, temperate deciduous broadleaved forest, temperate broadleaved and conifer mixed forest, and boreal forest along a latitudinal gradient from tropical to cold temperature zones. Fungal compositions were identified using high-throughput sequencing at the topsoil layer. The results showed that fungal diversity and fungal community compositions among forests varied apparently for both unfertilized and fertilized soils. Generally, soil fungal diversity, communities, and their potential functions responded sluggishly to short-term N addition, whereas the fungal Shannon index was increased in the tropical forest. In addition, environmental heterogeneity explained most of the variation among fungal communities along the latitudinal gradient. Specifically, soil C: N ratio and soil water content were the most important factors driving fungal diversity, whereas mean annual temperature and microbial nutrient limitation mainly shaped fungal community structure and functional compositions. Topsoil fungal communities in eastern forest ecosystems in China were more sensitive to environmental heterogeneity rather than short-term N addition. Our study further emphasized the importance of simultaneously evaluating soil fungal communities in different forest types in response to atmospheric N deposition.

Phosphorus dynamics in litter-soil systems during litter decomposition in larch plantations across the chronosequence

The dynamics of phosphorus (P) in litter-soil systems during litter decomposition across a plantation chronosequence remain to be underinvestigated, especially in terms of the nutrient cycle in plantations. In this study, the P dynamics in a litter-soil system of larch (Larix kaempferi) plantations at three stand ages (10, 25, and 50 years old) were examined through a 4-year in situ decomposition experiment (experiment 1) and a 360-day indoor incubation experiment (experiment 2). The aim of experiment 1 and experiment 2 is to determine the P dynamics in litter and soil, respectively. The results in experiment 1 suggested that litter mass retained 34.1%-42.5% of the initial mass after a 4-year decomposition period, and the turnover time (t_0.95) of the decomposition was 11.3, 13.9, and 11.8 years for 10-, 25- and 50-year-old stand larch plantations, respectively. Litter exhibited a net P decrease during the first 180 days, followed by a phase of a net P increase. The lowest P accumulation rate was found in the 25-year-old stand during the P immobilization stage. This immobilization phase was followed by a slow litter P decrease. Highly correlated relations were found between the litter decomposition rate and the initial litter N concentration and C/N, whereas the P accumulation rate was noticeably correlated with the initial litter P and C/P. The results in experiment 2 showed that litter addition promoted the accumulation of the highly labile P (resin P, NaHCO₃-P_i, and NaHCO₃-P_o), as well as moderately labile P_i (NaOH-P_i) in the soil. The findings obtained suggest that soil microbial biomass P and acid phosphatase activity were the primary factors driving the activation of soil P during litter decomposition. These findings would be beneficial to the systematic understanding of the nutrient cycle in plant-soil systems and litter management during the development of larch plantations.

[Simulated nitrogen deposition reduces potential nitrous oxide emissions in a natural Castanopsis carlesii forest soil]

The reactive nitrogen deposition in subtropical region of China has been increasing annually, which affects biogeochemical processes in forest soils. In this study, three treatments were established, including control (no N addition, CK), low nitrogen deposition (40 kg·hm^-2·a^-1, LN), and high nitrogen deposition (80 kg·hm^-2·a^-1, HN) to study the response of denitrifying functional genes and potential N₂O emissions to simulated nitrogen deposition in the soils of a natural Castanopsis carlesii forest. Results showed that HN significantly decreased soil potential N₂O emission, while 8-year nitrogen deposition did not affect the abundances of nirS, nirK, nosZ Ⅰ and nosZ Ⅱ. However, the abundance of nosZ Ⅰwas significantly higher than nosZ Ⅱ in all the treatments, indicating that nosZ Ⅰ dominated over nosZ Ⅱ in the acidic soils. HN significantly decreased the ratio of (nirK+nirS)/(nosZ Ⅰ+nosZ Ⅱ), which was positively correlated with soil pH. The results suggested that long-term high nitrogen deposition reduced soil pH and the abundance ratio of (nirK+nirS)/(nosZ Ⅰ+nosZ Ⅱ), which subsequently reduced the potential N₂O emission.

Biological Soil Crust From Mesic Forests Promote a Specific Bacteria Community

Biological soil crusts (biocrusts) harbor a diverse community of various microorganisms with microalgae as primary producers and bacteria living in close association. In mesic regions, biocrusts emerge rapidly on disturbed surface soil in forest, typically after clear-cut or windfall. It is unclear whether the bacterial community in biocrusts is similar to the community of the surrounding soil or if biocrust formation promotes a specific bacterial community. Also, many of the interactions between bacteria and algae in biocrusts are largely unknown. Through high-throughput-sequencing analysis of the bacterial community composition, correlated drivers, and the interpretation of biological interactions in a biocrust of a forest ecosystem, we show that the bacterial community in the biocrust represents a subset of the community of the neighboring soil. Bacterial families connected with degradation of large carbon molecules, like cellulose and chitin, and the bacterivore Bdellovibrio were more abundant in the biocrust compared to bulk soil. This points to a closer interaction and nutrient recycling in the biocrust compared to bulk soil. Furthermore, the bacterial richness was positively correlated with the content of mucilage producing algae. The bacteria likely profit from the mucilage sheaths of the algae, either as a carbon source or protectant from grazing or desiccation. Comparative sequence analyses revealed pronounced differences between the biocrust bacterial microbiome. It seems that the bacterial community of the biocrust is recruited from the local soil, resulting in specific bacterial communities in different geographic regions.

Methylocystis silviterrae sp.nov., a high-affinity methanotrophic bacterium isolated from the boreal forest soil

A novel species is proposed for a high-affinity methanotrophic representative of the genus Methylocystis. Strain FS^T was isolated from a weakly acidic (pH 5.3) mixed forest soil of the southern Moscow area. Cells of FS^T are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. Only methane and methanol are used as carbon sources. FS^T grew at a temperature range of 4-37 °C (optimum 25-30 °C) and a pH range of 4.5 to 7.5 (optimum pH 6.0-6.5). The major fatty acids were C_{18  :  1}ω8c, C_{18  :  1}ω7c and C_{18  :  0}; the major quinone as Q-8. FS^T displays 16S rRNA gene sequences similarity to other taxonomically recognized members of the genus Methylocystis, with Methylocystis hirsuta CSC1^T (99.6 % similarity) and Methylocystis rosea SV97^T (99.3 % similarity) as its closest relatives. The genome comprises 3.85 Mbp and has a DNA G+C content of 62.6 mol%. Genomic analyses and DNA-DNA relatedness with genome-sequenced members of the genus Methylocystis demonstrated that FS^T could be separated from its closest relatives. FS^T possesses two particulate methane monooxygenases (pMMO): low-affinity pMMO1 and high-affinity pMMO2. In laboratory experiments, it was demonstrated that FS^T might oxidize methane at atmospheric concentration. The genome contained various genes for nitrogen fixation, polyhydroxybutyrate synthesis, antibiotic resistance and detoxification of arsenic, cyanide and mercury. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Methylocystis silviterrae sp. nov. The type strain is FS^T (=KCTC 82935^T=VKM B-3535^T).

nov., isolated from forest soil

A bacterial strain, named For3^T, was isolated from forest soil sampled in Champenoux, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Streptomycetaceae and, more specifically, to the genus Streptomyces. The strain had 99.93% 16S rRNA gene sequence similarity to its closest relative strains Streptomyces pratensis ATCC 33331^T, Streptomyces anulatus ATCC 27416^T, Streptomyces setonii NRRL ISP-5322^T and Kitasatospora papulosa NRRL B-16504^T. The phylogenomic tree using the genome blast distance phylogeny method showed that the closest relative strain was Streptomyces atroolivaceus NRRL ISP-5137^T and that For3^T represents a new branch among the Streptomyces. Genome relatedness indexes revealed that the average nucleotide identity and digital DNA-DNA hybridization values between For3^T and its closest phylogenomic relative (S. atroolivaceus NRRL ISP-5137^T) were 88.39 and 39.2 %, respectively. The G+C content of the genome was 71.4 mol% and its size was 7.96 Mb with 7492 protein-coding genes. Strain For3^T harboured complete metabolic pathways absent in the closest relative strains such as cellulose biosynthesis, glycogen degradation I, glucosylglycerate biosynthesis I. Anteiso-C_15:0, iso-C_15:0, anteiso-C_17:0 and MK-9(H4)/MK-9(H6) were the predominant cellular fatty acids and respiratory quinones, respectively. Phenotypic and genomic data supported the assignment of strain For3^T to a novel species Streptomyces silvae sp. nov., within the genus Streptomyces, for which the type strain is For3^T (=CIP 111908^T=LMG 32186^T).

High historical variability weakens the effects of current climate differentiation on microbial community dissimilarity and assembly

Understanding the influences of global climate change on soil microbial communities is essential in evaluating the terrestrial biosphere's feedback to this alarming anthropogenic disturbance. However, little is known about how intra-site historical climate variability can mediate the influences of current climate differences on community dissimilarity and assembly. To fill this gap, we examined and disentangled the interactive effects of historical climate variability and current climate differences on the soil bacterial community dissimilarity and stochasticity of community assembly among 143 sites from 28 forests across eastern China. We hypothesize that the relative importance of stochasticity and community dissimilarity are related to historical climate variability and that an increasing sum of intra-site historical variability enhances stochasticity while reduces dissimilarity between two communities. To test our hypothesis, we statistically controlled for covariates between sites including differences in soil chemistry, plant diversity, spatial distance, and seasonal climate variations at annual timescales. We observed that an increase in inter-site current climate differences led to a reduced impact of stochasticity in community assembly and a pronounced divergence between communities. In stark contrast, when communities were subjected to a high level of intra-site historical climate fluctuation, the observed impact incurred from current climate differences was substantially weakened. Moreover, the influence of increased historical variability was consistent along the gradient of current temperature differences between sites. However, effects induced by historical fluctuation in precipitation were disproportional and only evident when small inter-site differences were observed. Consequently, if the prior climate variability is ignored, especially regarding environmental factors like temperature, we assert that the influence current climate differentiation has on regulating community dissimilarity and assembly stochasticity will be underestimated. Together, our findings highlight the importance and need of explicitly controlling the mean and the historical variability of climate factors for the next "generation" of climate change experiments to come.

Description of antibiotic-producing novel bacteria Paraburkholderia antibiotica sp. nov. and Paraburkholderia polaris sp. nov

Two white colony-forming, Gram-stain-negative, non-sporulating and motile bacteria, designated G-4-1-8^T and RP-4-7^T, were isolated from forest soil and Arctic soil, respectively. Both strains showed antimicrobial activity against Gram-negative pathogens (Pseudomonas aeruginosa and Escherichia coli) and could grow at a pH range of pH 4.0-11.0 (optimum, pH 7.0-9.0). Phylogenetic analyses based on their 16S rRNA gene sequences indicated that strains G-4-1-8^T and RP-4-7^T formed a lineage within the family Burkholderiaceae and were clustered as members of the genus Paraburkholderia. Strain G-4-1-8^T showed the highest 16S rRNA sequence similarity to Paraburkholderia monticola JC2948^T (98.1 %), while strain RP-4-7^T showed the highest similarity to Paraburkholderia metrosideri DNBP6-1^T (98.8 %). The only respiratory quinone in both strains was ubiquinone Q-8. Their principal cellular fatty acids were C_16 : 0, cyclo-C_17 : 0, summed feature 3 (iso-C_15 :0 2-OH and/or C_16 :1 ω7c) and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). Their major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. The DNA G+C content of strains G-4-1-8^T and RP-4-7^T were 63.7 and 61.3 mol%, respectively, while their genome lengths were 7.44 and 9.67 Mb, respectively. The genomes of both strains showed at least 12 putative biosynthetic gene clusters. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values between both strains and most closely related Paraburkholderia species were below the species threshold values. Based on a polyphasic study, these isolated strains represent novel species belonging to the genus Paraburkholderia, for which the names Paraburkholderia antibiotica sp. nov. (G-4-1-8^T= KACC 21617^T=NBRC 114603^T) and Paraburkholderia polaris sp. nov. (RP-4-7^T=KACC 21621^T=NBRC 114605^T) are proposed.

nov., two novel species isolated from forest soil

Three aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains RXD178^T, RXD172-2 and RLT1W51^T, 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 RXD178^T, RXD172-2 and RLT1W51^T 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^T were 98.27 and 83.50 %, respectively. The three novel strains contained C_16 : 0, C_17 : 0 cyclo and summed feature 3 (C_16 : 1 ω6c and/or C_16 : 1 ω7c) as the major fatty acids, and summed feature 8 (C_18 : 1 ω6c and/or C_18 : 1 ω7c) comprised a relative higher proportion in strain RXD178^T than in other strains. Both strains RXD172-2 and RLT1W51^T 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^T. Ubiquinone 8 was the predominant quinone. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, strain RXD178^T should be considered as representing one novel species within the genus Collimonas and strains RXD172-2 and RLT1W51^T as another one, for which the names Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov. are proposed, with RXD178^T (=GDMCC 1.1925^T=KACC 21987^T) and RLT1W51^T (=GDMCC 1.1923^T=KACC 21985^T) as the type strains, respectively.

nov., novel actinobacteria isolated from pine forest soil in Poland

The taxonomic status of two filamentous actinobacteria, isolates NF23 and NL8^T, 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 Catenulispora. They formed a well supported lineage within the Catenulispora 16S rRNA gene tree and were most closely related to the type strains of Catenulispora acidiphila (99.1%), Catenulispora pinisilvae (99.9 %) and Catenulispora rubra (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^T and their phylogenetic neighbours showed that they formed a distinct branch in the Catenulispora clade that was most closely related to C. pinisilvae DSM 111109^T. 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 C. acidiphila, C. pinisilvae and C. rubra 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 Catenulispora as C. pinistramenti sp. nov. with isolate NL8^T (=DSM 111110^T=PCM 3045^T) as the type strain. The genomes of strains NF23 and NL8^T are rich in natural product-biosynthetic gene clusters hence these strains have the potential to synthesize new specialised metabolites.

Contrasting Effects of Forest Type and Stand Age on Soil Microbial Activities: An Analysis of Local Scale Variability

Simple Summary

The potentially important role of forests in climate change mitigation suggests a strong need for a more detailed understanding of these ecosystems. Besides climatic conditions, diverse forest vegetation creates varied conditions for the activity of soil microorganisms, and particular attention should be focused on a comprehensive study on the influence of different forest types on microbial activities. We conducted an experiment on six different forest soils (two coniferous, two deciduous, and two mixed sites comprising trees of different ages) collected from the same region (Lublin Upland, Poland) to assess the relationship between forest type and seasonal changes in microbial parameters. The annual mean values of the soil microbial indicators suggest that the mature deciduous stand was the most sustainable in microbial activities among the forest soils investigated. The diversity of the forest environment and the multifactorial dependence of the microbiological activity of forest soils necessitates further research in this field, especially using the same soil types. An understanding of forest ecosystem functioning can also be useful for forest management.

Abstract

Understanding the functioning of different forest ecosystems is important due to their key role in strategies for climate change mitigation, especially through soil C sequestration. In controlled laboratory conditions, we conducted a preliminary study on six different forest soils (two coniferous, two deciduous, and two mixed sites comprising trees of different ages) collected from the same region. The aim was to explore any differences and assess seasonal changes in soil microbial parameters (basal respiration BR, microbial biomass C_mic, metabolic quotient qCO₂, dehydrogenase activity DHA, and C_mic:C_org ratio). Indicator- and forest-specific seasonality was assessed. In addition to litter input, soil parameters (pH, nutrient content, texture and moisture) strongly regulated the analyzed microbial indicators. PCA analysis indicated similarity between mature mixed and deciduous forests. Among annual mean values, high C_mic and DHA with simultaneously low qCO₂ suggest that the mature deciduous stand was the most sustainable in microbial activities among the investigated forest soils. Research on the interrelationship between soil parameters and forest types with different tree ages needs to be continued and extended to analyze a greater number of forest and soil types.

nov., isolated from forest soil

Two Gram-stain-negative, yellow-pigmented and strictly aerobic bacteria, designated strains SE-s27^T and SE-s28^T, were isolated from forest soil. Both strains were non-motile rods that were catalase-positive and oxidase-negative and grew optimally at 25-30 °C, pH 8.0 and with 0 % (w/v) NaCl. Strain SE-s28^T produced flexirubin-type pigments, but strain SE-s27^T did not produce them. Both strains contained menaquinone-6 as the sole respiratory quinone and phosphatidylethanolamine as a major polar lipid. As the major cellular fatty acids (>10 %), SE-s27^T contained iso-C_15 : 1 and iso-C_15 : 1G, whereas SE-s28^T contained iso-C_15 : 0 and summed feature 3 comprising C_16 : 1ω7c and/or C_16 : 1ω6c and/or iso-C_15 : 0 2-OH. The DNA G+C contents of strains SE-s27^T and SE-s28^T were 33.1 and 44.3 mol%, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that SE-s27^T and SE-s28^T formed respective distinct phylogenetic lineages within the genus Flavobacterium. Strains SE-s27^T and SE-s28^T were most closely related to Flavobacterium macrobrachii an-8^T and Flavobacterium piscinae ICH-30^T with 98.0 and 94.5 % 16S rRNA gene sequence similarities, respectively. In conclusion, strains SE-s27^T and SE-s28^T represent novel species of the genus Flavobacterium, for which the names Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov. are proposed. The type strains of F. solisilvae and F. silvaticum are SE-s27^T (=KACC 18802^T=JCM 31544^T) and SE-s28^T (=KACC 18803^T=JCM 31545^T), respectively.

EPR Spectroscopy as a Tool to Characterize the Maturity Degree of Humic Acids

The major indicator of soil fertility and productivity are humic acids (HAs) arising from decomposition of organic matter. The structure and properties of HAs depend, among others climate factors, on soil and anthropogenic factors, i.e., methods of soil management. The purpose of the research undertaken in this paper is to study humic acids resulting from the decomposition of crop residues of wheat (Triticum aestivum L.) and plant material of thuja (Thuja plicata D.Don.ex. Lamb) using electron paramagnetic resonance (EPR) spectroscopy. In the present paper, we report EPR studies carried out on two types of HAs extracted from forest soil and incubated samples of plant material (mixture of wheat straw and roots), both without soil and mixed with soil. EPR signals obtained from these samples were subjected to numerical analysis, which showed that the EPR spectra of each sample could be deconvoluted into Lorentzian and Gaussian components. It can be shown that the origin of HAs has a significant impact on the parameters of their EPR spectra. The parameters of EPR spectra of humic acids depend strongly on their origin. The HA samples isolated from forest soils are characterized by higher spin concentration and lower peak-to-peak width of EPR spectra in comparison to those of HAs incubated from plant material.

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 km2, 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 (R2≥ 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 (R2≥ 0.57, RPIQ ≥ 2.42) and Ah horizon (R2≥ 0.54, RPIQ ≥2.15). When combining Oh and Ah horizons, we achieved good prediction results using the MEMS sensors and Cubist (R2≥ 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 R2 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.

nov., a Nitrogen-Fixing Bacterium Isolated From Forest Soil by Using Optimized Culture Method

A bacterial strain, designated strain G-1-1-14^T, was isolated from Kyonggi University forest soil during a study of previously uncultured bacterium. The cells of strain G-1-1-14^T were motile by means of peritrichous flagella, Gram-stain-negative, rod-shaped, and able to grow autotrophically with hydrogen and fix nitrogen. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain G-1-1-14^T belonged to the genus Azohydromonas. The closest species of strain G-1-1-14^T were Azohydromonas ureilytica UCM-80^T (98.4% sequence similarity), Azohydromonas lata IAM 12599^T (97.5%), Azohydromonas riparia UCM-11^T (97.1%), and Azohydromonas australica IAM 12664^T (97.0%). The genome of strain G-1-1-14^T was 6,654,139 bp long with 5,865 protein-coding genes. The genome consisted of N₂-fixing genes (nifH) and various regulatory genes for CO₂ fixation and H₂ utilization. The principal respiratory quinone was ubiquinone-8, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The major fatty acids were summed feature 3 (iso-C_15:0 2-OH and/or C_16:1ω7c), C_16:0, summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), and cyclo-C_17:0. The DNA G + C content was 69.9%. The average nucleotide identity (OrthoANI), in silico DNA–DNA hybridization (dDDH), and conventional DDH relatedness values were below the species demarcation values for novel species. Based on genomic, genetic, phylogenetic, phenotypic, and chemotaxonomic characterizations, strain G-1-1-14^T represents a novel species within the genus Azohydromonas, for which the name Azohydromonas caseinilytica sp. nov. is proposed. The type strain is G-1-1-14^T (= KACC 21615^T = NBRC 114390^T).

Bacteria but not fungi respond to soil acidification rapidly and consistently in both a spruce and beech forest

Anthropogenically enhanced atmospheric sulphur (S) and nitrogen (N) deposition has acidified and eutrophied forest ecosystems worldwide. However, both S and N mechanisms have an impact on microbial communities and the consequences for microbially driven soil functioning differ. We conducted a two-forest stand (Norway spruce and European beech) field experiment involving acidification (sulphuric acid addition) and N (ammonium nitrate) loading and their combination. For 4 years, we monitored separate responses of soil microbial communities to the treatments and investigated the relationship to changes in the activity of extracellular enzymes. We observed that acidification selected for acidotolerant and oligotrophic taxa of Acidobacteria and Actinobacteria decreased bacterial community richness and diversity in both stands in parallel, disregarding their original dissimilarities in soil chemistry and composition of microbial communities. The shifts in bacterial community influenced the stoichiometry and magnitude of enzymatic activity. The bacterial response to experimental N addition was much weaker, likely due to historically enhanced N availability. Fungi were not influenced by any treatment during 4-year manipulation. We suggest that in the onset of acidification when fungi remain irresponsive, bacterial reaction might govern the changes in soil enzymatic activity.

nov., isolated from forest soil

A Gram-stain-positive, aerobic and rod-shaped bacterial strain, designated JH1-1^T, was isolated from a forest soil sample collected in Suwon, Gyeonggi-do, Republic of Korea. Strain JH1-1^T could grow at 10-35 °C (optimum, 28-30 °C), pH 4.5-8.5 and tolerated 5 % (w/v) NaCl. Strain JH1-1^T was most closely related to members of the genus Arthrobacter, namely Arthrobacter alkaliphilus LC6^T (98.5 % similarity), Arthrobacter methylotrophus TGA^T (98.4 %), Arthrobacter ramosus CCM 1646^T (97.8 %), Arthrobacter bambusae THG-GM18^T (97.5 %) and Arthrobacter pokkalii P3B162^T (97.3 %). The strain grew well on Reasoner's 2A agar, tryptone soya agar, nutrient agar, Mueller-Hinton agar and Luria-Bertani agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, unidentified phospholipid and unidentified glycolipids. The major respiratory quinone was MK-9(H₂). The main fatty acids were C_15 : 0 anteiso, C_15 : 0 iso, C_16 : 0 iso and C_17 :0 anteiso. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain JH1-1^T and its reference type strains ranged from 81.3 to 85.4 % and from 21.1 to 29.1 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain JH1-1^T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Arthrobacter. Therefore, strain JH1-1^T is considered to represent a novel species, for which the name Arthrobacter terricola sp. nov. is proposed. The type strain is JH1-1^T (=KACC 21385^T=JCM 33641^T).

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp.

IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana

Two bacterial strains, 1N^T and 5N^T, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1N^T (0.65×1.85 µm) and 5N^T (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5N^T elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1N^T and 5N^T occurred at 25-30 °C, pH 6.5-7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1N^T and 5N^T were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11^T, Paraburkholderia aspalathi LMG 27731^T and Paraburkholderia caffeinilytica CF1^T. The genomes of 1N^T and 5N^T had an average nucleotide identity (91.6 and 91.3%) and in silico DNA-DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1N^T and 5N^T from each other and their closest relatives. The only ubiquinone present in strains 1N^T and 5N^T was Q-8. The major cellular fatty acids were C_{16 : 0}, 3OH-C_{16 : 0}, C_{17 : 0} cyclo, C_{19 : 0} cyclo ω8c and summed features 2 (3OH-C_{14 : 0} / C_{16 : 1} iso I), 3 (C_{16 : 1} ω6c/ω7c) and 8 (C_{18 : 1} ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana. Our polyphasic approach demonstrated that strains 1N^T and 5N^T represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1N^T=DSM 110721^T=LMG 31704^T) and Paraburkholderia elongata sp. nov. (type strain 5N^T=DSM 110722^T=LMG 31705^T) are proposed.

<i>Pseudomonas stutzeri </i> CM1, Novel Thermotolerant Cellulase- Producing Bacteria Isolated from Forest Soil

BACKGROUND AND OBJECTIVE

Cellulase is an important enzyme that useful for agricultural residue hydrolysis such as plant stover, molasse, rice straw. Thermotolerant cellulases are required to apply in textile, food, detergent, biofuels and pharmaceutical applications. This research aimed to isolate the thermotolerant cellulase-producing bacteria from forest soil and to determine cellulase activity from isolated bacteria.

MATERIALS AND METHODS

Soil samples were collected from the Roi Et Rajabhat University forest. One gram of soil sample was mixed with Luria-Bertani (LB) broth medium and incubated at 37°C with shaking at 150 rpm for 24 h. The cultured broth was streaked on LB agar plate and incubated at 37°C for 24 h. Cellulase-producing bacteria were isolated using Carboxymethylcellulose (CMC) agar plate. Four bacterial isolates which presented a clear zone on CMC agar plate after flooded with iodine solution, named CM1, CM2, CM3 and CM4. Cellulase activity of 4 isolated bacteria was determined against various pH (pH 4-8) and temperature (50-100°C).

RESULTS

The results indicated that CM1 isolate showed the highest cellulase activity at 0.074 unit mL-1 at 80°C and pH5. All isolates were identified using 16S rRNA gene sequencing. The results indicated that CM1, CM3 and CM4 were identified as Pseudomonas stutzeri. while isolate CM2 was Bacillus subtilis.

CONCLUSION

This is the first report presenting the thermotolerant cellulase produced by Pseudomonas stutzeri. The thermotolerant cellulase produced from Pseudomonas stutzeri in this study will be useful in many industrial processes using cellulase at high temperatures.

Chemical sequential extraction of O horizon samples from Fukushima forests: Assessment for degradability and radiocesium retention capacity of organic matters

To investigate how radiocesium (¹³⁷Cs) is retained in the O horizon via interactions with organic matter, we collected O horizon samples in Japanese cedar (Cryptomeria japonica) and konara oak (Quercus serrata) forest sites in Fukushima during the 8 years following the Fukushima Dai-ichi Nuclear Power Plant accident. To assess degradability and ¹³⁷Cs retention capacity of organic matter, we conducted chemical sequential extraction with organic solvent and sulfuric acid, collecting the following fractions: organic solvent extractives (Fraction 1), acid-soluble carbohydrates (Fraction 3), and acid-insoluble residue (Fraction 4). In all samples, across sampling years and sites, ¹³⁷Cs content in Fractions 1, 3, and 4, as a proportion of the total ¹³⁷Cs content, was 0.0-23.6%, 18.4-42.9%, and 44.8-76.0%, respectively. Generally, ¹³⁷Cs is considered to be electrostatically bound to organic matter and relatively mobile, making it easily extractable by sulfuric acid treatment. However, we observed a relatively high proportion of ¹³⁷Cs in Fraction 4, suggesting strong retention of ¹³⁷Cs and their immobility in the O horizon. Complex organic matter such as lignin or tannin may contribute this retention. We also noted that some part of ¹³⁷Cs may be also retained by clay minerals in the O horizon. Although organic matter in Fractions 1 and 3 is considered to decompose faster than that in Fraction 4, over the observation period the ¹³⁷Cs proportion and net rate of decrease in ¹³⁷Cs content (in total and in each fraction) remained nearly constant. This result implies that decomposition of organic matter and the consequent release of bound ¹³⁷Cs may be partly compensated by additional input of ¹³⁷Cs from the canopy and ¹³⁷Cs recycling by soil microorganisms. Our study highlights the potential role of organic matter in the O horizon as a temporary reservoir of ¹³⁷Cs and a driver of the ¹³⁷Cs cycle in forest ecosystems.

nov., a N2-fixing bacterium isolated from forest soil and emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera

A motile, Gram-stain-negative, rod-shaped bacterium, designated G-4-1-14^T, was obtained from forest soil sampled at Gwanggyo mountain, Gyeonggi-do, Republic of Korea. Cells were colourless, aerobic, grew optimally at 28-35 °C and hydrolysed DNA and casein. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-4-1-14^T formed a lineage within the genus Zoogloea. The closest members were Zoogloea resiniphila ATCC 70068^T (98.6 % sequence similarity), Zoogloea caeni EMB43^T (98.2 %), Zoogloea oryzae A-7^T (97.7 %), Zoogloea ramigera IAM 12136^T (96.9 %) and Zoogloea oleivorans Buc^T (96.2 %). The major respiratory quinone was ubiquinone-8 and the principal polar lipids were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The predominant cellular fatty acids were summed feature 3 (iso-C_15 :0 2-OH/C_{16  : 1} ω7c) and C_16 : 0. The DNA G+C content was 65.9 mol%. The average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain G-4-1-14^T and other type strains were ≤81.6 and ≤24.9 %, respectively, which are below the species demarcation thresholds. Based on the results of phenotypic, phylogenetic and genomic analyses, strain G-4-1-14^T represents a novel species in the genus Zoogloea, for which the name Zoogloea dura sp. nov. is proposed. The type strain is G-4-1-14^T (=KACC 21618^T=NBRC 114358^T). In addition, we propose emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera.

nov., a xylan-degrading bacterium isolated from decaying forest soil

A xylanolytic bacterial strain, named A59^T, was isolated from a forest soil consortium in southern Argentina. Strain A59^T is a Gram-stain-positive, facultative anaerobic, endospore-forming and rod-shaped bacterium. Its optimal growth conditions are 30 °C (range, 28-37 °C), pH 7 (range, pH 5-10) and it tolerates up to 7 % of NaCl (range, 2-7 %). Chemotaxonomic analysis revealed that strain A59^Tpossesses meso-diaminopimelic acid in the cell wall. It contains menaquinone MK-7 as the predominant isoprenoid quinone and the major fatty acid is anteiso-C_15 : 0 (35.1 %), with a moderate amount of C_16 : 0 (6.9 %). According to 16S RNA gene sequence analysis, the isolate is phylogenetically placed in the same cluster as Paenibacillus taichungensis BCRC 17757^T (99.7 % nucleotide sequence identity) and Paenibacillus pabuli NBRC 13638^T (99.1 %) and is closely related to Paenibacillus tundrae A10b^T (98.8 %). However, phylogenetic studies based on the housekeeping gyrB gene placed A59^T in a separate branch from all other related type strains. Furthermore, the results of whole genome average nucleotide identity analysis (gANI) with related type strains was lower than 91.10 % and the digital DNA-DNA hybridization value was lower than 44.30 %, which are below the threshold values for separating two species. The DNA G+C content was estimated as 46.09 mol%, based on genome sequencing. On the basis of these results, A59^T represents a new species of the genus Paenibacillus, and we propose the name Paenibacillusxylanivorans sp. nov. The type strain is A59^T (=DSM 107920^T=NCIMB 15123^T).

[Effects of litter removal and nitrogen addition on carbon and nitrogen in different soil fractions in a subtropical broad-leaved forest.]

The increasing nitrogen deposition due to human activities has impacted forest ecosystems to a large extent. The organic carbon and nitrogen released from decomposing litters play an important role in the formation, stability and transformation of soil organic carbon and nitrogen. We collected soil samples from a subtropical evergreen broadleaved forest experiment with nitrogen deposition [control (0), LN (75 kg·hm^-2·a^-1), HN (150 kg·hm^-2·a^-1)] and litter control (litter retained and litter removal) for eight years. After extracted by solution of K₂SO₄, Na₂B₄O₇, Na₄P₂O₇, NaOH, H₂SO₄, Na₂S₂O₄ and HF step by step, carbon and nitrogen in each extraction was analyzed. The results showed that overall most of soil carbon and nitrogen existed in the Humin fraction, accounting for 33.5% of the total carbon and 33.3% of the total nitrogen. The soluble total carbon and nitrogen extracted by Na₂B₄O₇ solution was the highest, followed by NaOH and Na₄P₂O₇ solution. The soluble total carbon, soluble total nitrogen and soluble organic nitrogen of soil extracted by three reagents accounted for 46.2%, 47.9%, and 76.5% of the total extractions, respectively. In addition, nitrogen addition significantly increased carbon and nitrogen content in Na₂S₂O₄ and Humin fractions. Litter removal reduced carbon content in Na₂B₄O₇, H₂SO₄, Na₂S₂O₄ and Humin fractions, and nitrogen content in NaOH, HF and Humin fractions. The nitrogen content in the K₂SO₄ extraction was significantly increased by both litter remained and nitrogen addition. Our results demonstrated that litter and nitrogen added could mutually affect carbon and nitrogen concentration of soil fractions with different chemical stability, with consequences on the process of soil carbon and nitrogen.

Emissions of CO2, CH4, and N2O Fluxes from Forest Soil in Permafrost Region of Daxing'an Mountains, Northeast China

With global warming, the large amount of greenhouse gas emissions released by permafrost degradation is important in the global carbon and nitrogen cycle. To study the feedback effect of greenhouse gases on climate change in permafrost regions, emissions of CO₂, CH₄, and N₂O were continuously measured by using the static chamber-gas chromatograph method, in three forest soil ecosystems (Larix gmelinii, Pinus sylvestris var. mongolica, and Betula platyphylla) of the Daxing’an Mountains, northeast China, from May 2016 to April 2018. Their dynamic characteristics, as well as the key environmental affecting factors, were also analyzed. The results showed that the flux variation ranges of CO₂, CH₄, and N₂O were 7.92 ± 1.30~650.93 ± 28.12 mg·m⁻²·h⁻¹, −57.71 ± 4.65~32.51 ± 13.03 ug·m⁻²·h⁻¹, and −3.87 ± 1.35~31.1 ± 2.92 ug·m⁻²·h⁻¹, respectively. The three greenhouse gas fluxes showed significant seasonal variations, and differences in soil CO₂ and CH₄ fluxes between different forest types were significant. The calculation fluxes indicated that the permafrost soil of the Daxing’an Mountains may be a potential source of CO₂ and N₂O, and a sink of CH₄. Each greenhouse gas was controlled using different key environmental factors. Based on the analysis of Q₁₀ values and global warming potential, the obtained results demonstrated that greenhouse gas emissions from forest soil ecosystems in the permafrost region of the Daxing’an Mountains, northeast China, promote the global greenhouse effect.

nov., isolated from forest soil

During a study of the Kyonggi University soil bacterial diversity, an aerobic, non-motile, Gram-stain-negative, non-spore-forming, rod-shaped, yellow pigmented bacterium, designated strain RD-2-33^T was isolated. Strain RD-2-33^T grew optimally at 28-35 °C and pH 7.0-7.5; hydrolysed gelatin and DNA; and tolerated 1 % of NaCl. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RD-2-33^T clustered with the genus Flavobacterium. The closest member was Flavobacterium dankookense ARSA-19^T (97.1 % sequence similarity) and Flavobacterium cheonhonense ARSA-15^T (96.7 %). Sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine and an unidentified polar lipid. The major cellular fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH, and iso-C_15 : 1 G. The DNA G+C content was 38.6 mol%. The average nucleotide identity (ANI) and in silico DNA-DNA hybridisation relatedness between strain RD-2-33^T and Flavobacterium dankookense DSM 25687^T were 75.2 and 19.3 %, respectively. Based on the polyphasic and phylogenetic data, strain RD-2-33^T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium silvisoli sp. nov. is proposed. The type strain is RD-2-33^T (=KEMB 9005-742^T=KACC 21178^T=NBRC 113789^T).

[Co-accumulation characters of soil organic carbon and nitrogen under broadleaved Korean pine and Betula platyphylla secondary forests in Changbai Mountain, China.]

The retrogressive succession is an important driver for dynamics of soil organic carbon (SOC) and total nitrogen (TN). We studied the quantitative distribution and synergistic accumulation characteristics of soil organic carbon and nitrogen in the primary broadleaved Korean pine (KP) forest and Betula platyphylla (BP) secondary forest in Changbai Mountain through paired plot approach. Further, we analyzed the changes of carbon pool and carbon sink effect in temperate forest soil caused by secondary succession and their carbon-nitrogen coupling mechanism. The results showed that the BP forest accumulated more organic carbon and nitrogen in the surface and subsurface soil (0-20 cm) than the KP forest, with relatively low soil C/N. Compared with KP forest, soil organic carbon storage in BP forest (0-20 cm) was higher by 14.7 t·hm^-2, equivalent to a soil carbon sink gain of 29.4 g·m^-2·a^-1. SOC and TN concentrations were positively correlated in each soil layer of all forest types, causing a co-accumulative relationship between SOC and TN. The coefficient of determination (R²) between SOC and TN in the upper soil layers of BP forest was significantly higher than that of the KP forest, indicating that SOC accumulation under the relatively N-rich BP forest was more dependent on the accumulation of organic nitrogen. In the upper soil layers (0-10 cm) where organic matter concentrated, there was no significant difference in light fraction organic carbon and nitrogen stock between the two forest types, whereas the content, stock, and allocation percentage of heavy fraction organic carbon and nitrogen of BP forest were all significantly higher than that of the KP forest, with an average increment of 8.5 t·hm^-2 in heavy fraction organic carbon stock. Those results indicated that the increase of soil organic carbon and nitrogen during secondary succession was mainly due to the increases of soil organic carbon and nitrogen pools in mineral-bound stability. The carbon-nitrogen coupling mechanisms in litter decomposition and soil organic matter formation was an important driving mechanisms underlying the changes of soil organic carbon and nitrogen pools during secondary succession.

[Effects of global change on methane uptake in forest soils and its mechanisms: A revie]

Elevated atmospheric CO₂ concentration, altered precipitation regime, increased nitrogen deposition, and land cover change have not only changed the physical and chemical properties of forest soils, but also affected plant growth and microbial activity, with concequences on soil carbon and nitrogen cycles, including soil CH₄ uptake. In this study, we summarized the important role of soil CH₄ uptake in forests under global change scenarios. The differences of responses as well as the underlying mechanisms of soil CH₄ uptake in forests to global change were reviewed. Elevated atmospheric CO₂ concentration inhibits soil CH₄ uptake. Reduced precipitation tends to promote soil CH₄ uptake. Increased nitrogen input inhibits soil CH₄ uptake in nitrogen-rich forests, but promotes or has no effects on soil CH₄ uptake in nitrogen-poor forests. Conversion of forests to grassland, farmland, or plantations would reduce soil CH₄ uptake, while afforestation increases soil CH₄ uptake. The future research should explore the long-term and multiple effects of global changes on forest soil CH₄ uptake. In addition, molecular biology methods should be developed to explore the microbial mechanism of soil CH₄ uptake.

[Characteristics of Soil Organic Carbon and Mineralization with Different Stands in Jinyun Mountain]

Soil organic carbon (SOC) is the largest organic carbon stock on land, and slight changes in SOC can significantly affect the atmospheric CO₂ concentration, among which forest soil carbon reservoir accounts for approximately 70% of the global soil carbon stock. Therefore, the implementation of efficient management for SOC stock in the forest ecosystem has become a popular research subject. The mineralized characteristics of SOC in different soil layers (0-20, 20-40,40-60, and 60-100 cm) were analyzed in five typical stands of Jinyun Mountain:broadleaf forest, coniferous forest, coniferous and broadleaf mixed forest, bamboo forest, and 15a abandoned grassland (control soils) in the study area. The results showed that forest type, cultivation duration, and soil depth had significant effects on the SOC mineralization rate. The mineralization rate of SOC in different forest stands decreased with the deepening soil layer, among which the mineralization rate at the 0-20 cm soil layer[11.97-25.12 mg·(kg·d)^-1] was significantly higher than that of other soil layers (P<0.05), and there were no significant differences between the mineralization rates of other soil layers[4.79-6.51 mg·(kg·d)^-1]. The accumulated mineralization of SOC in the five forests decreased with the deepening soil layer. The accumulated mineralization of SOC in the bamboo forest and broadleaf forest in the 0-20 cm soil layer was the highest at 177.66 mg·kg^-1 and 120.38 mg·kg^-1, respectively. With the deepening soil layer in the 60-100 cm soil layer, the accumulated SOC mineralization in the coniferous forest reached the highest (46.96 mg·kg^-1). The SOC mineralization process in the different stands of Jinyun Mountain can be well fitted by the double reservoir first-level kinetic equation. The content of easily decomposable SOC in different forest stands decreased with the deepening soil layer. Coniferous forest soil exhibited a stronger mineralization ability and higher utilization degree of refractory organic carbon stock, while bamboo forest and broadleaf forest soils had higher microbial activity, which could effectively promote the carbon cycle and improve the soil carbon fixation ability.

Impact of vegetation on the methane budget of a temperate forest

Upland forest soils are known to be the main biological sink for methane, but studies have shown that net methane uptake of a forest ecosystem can be reduced when methane emissions by vegetation are considered. We estimated the methane budget of a young oak plantation by considering tree stems but also the understorey vegetation. Automated chambers connected to a laser-based gas analyser, on tree stems, bare soil and soil covered with understorey vegetation, recorded CH₄ fluxes for 7 months at 3 h intervals. Tree stem emissions were low and equated to only 0.1% of the soil sink. Conversely, the presence of understorey vegetation increased soil methane uptake. This plant-driven enhancement of CH₄ uptake occurred when the soil was consuming methane. At the stand level, the methane budget shifted from -1.4 ± 0.4 kg C ha^-1 when we upscaled data obtained only on bare soil, to -2.9 ± 0.6 kg C ha^-1 when we considered soil area that was covered with understorey vegetation. These results indicate that aerenchymatous plant species, which are known to reduce the methane sink in wetlands, actually increase soil methane uptake two-fold in an upland forest by enhancing methane and oxygen transport and/or by promoting growth of methanotrophic populations.

nov., isolated from monsoon evergreen broad-leaved forest soil

A Gram-stain-negative, aerobic, non-motile strain, K3CV102501^T, was isolated from a soil sample collected from the monsoon evergreen broad-leaved forest of Dinghushan Biosphere Reserve located in Guangdong Province, PR China. The primal colony of strain K3CV102501^T was very similar to the fruiting body of myxobacteria on the original isolation plates. Young cultures of strain K3CV102501^T contained long (2-4×0.4-0.5 µm) filamentous cells and divided into rod shapes (0.7-1.0×0.6-0.8 µm) after 4 days of incubation at 28 °C. Strain K3CV102501^T grew at pH 6.0-9.5 (optimum, pH 6.5-7.5) and 7-42 °C (optimum, 28-35 °C). Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain K3CV102501^T belonged to the genus Chitinophagaand showed the highest similarity to C.hitinophaga jiangningensis JCM 19354^T (96.9 %). The DNA G+C content of the type strain was 46.6 mol%. The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and an unidentified aminolipid. Menaquinone-7 was the predominant quinone. The phenotypic, chemotaxonomic and phylogenetic data clearly showed that strain K3CV102501^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga flava sp. nov. is proposed. The type strain is K3CV102501^T (=KCTC 62435^T=GDMCC 1.1325^T).

nov., a novel bacterium isolated from forest soil and emended description of the genus Microvirga

An aerobic, Gram-stain-negative, motile and rod-shaped bacterium, designated c27j1^T, was isolated from a forest soil sample from the Chebaling National Nature Reserve in Guangdong Province, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain c27j1^T belongs to the genus Microvirga and was most closely related to Microvirga aerophila DSM 21344^T (97.7 %) and Microvirga subterranea DSM 14364^T (96.7 %). The average nucleotide identity and digital DNA-DNA hybridization values based on whole genome sequences of strain c27j1 ^T and M. aerophila DSM 21344^T were 77.2 and 22.4 %, respectively. It contained ubiquinone 10 as the predominant quinone, and C19 : 0 cycloω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids. The polar lipids consisted of phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified glycolipids. The genomic DNA G+C content based on the whole genome sequence was 62.2 mol%. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strain c27j1^T should represent a novel species of the genus Microvirga, for which the name Microvirgaflavescens sp. nov. is proposed. The type strain is c27j1^T (=GDMCC 1.1356^T=KCTC 62433^T). The description of the genus Microvirga is also emended, including the major fatty acids, genome size and DNA G+C content.

Pontibacter silvestris sp. nov., isolated from the soil of a Populus euphratica forest and emended description of the genus Pontibacter

Strain XAAS-R86^T, a Gram-stain-negative, short rod-shaped, non-motile, aerobic bacterium, was isolated from a Populus euphratica forest near the city of Hotan, Xinjiang, PR China. The cells were found to be positive for catalase and oxidase activities. Growth occurred optimally at 28-30 °C, pH 7.0-7.5 and in the presence of 0.5-2.0 % NaCl (w/v). The results of phylogenetic analysis of the 16S rRNA gene indicated that XAAS-R86^T represents a member of the genus Pontibacter within the family Hymenobacteraceae. Pontibacter akesuensis CCTCC AB 206086^T is the most closely related species with a validly published name, based on 16S rRNA gene sequence identity (95.7 %). The DNA G+C content of the strain is 43.9 mol%. The main respiratory quinone is MK-7 and the major cellular fatty acids are summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B) and iso-C15 : 0 and its major polar lipids are phosphatidylethanolamine and two unidentified lipids. On the basis of the results of tests performed using a polyphasic approach, XAAS-R86^T represents a novel species of the genus Pontibacter, for which the name Pontibactersilvestris sp. nov. is proposed, with the type strain XAAS-R86^T (=CCTCC AB 2017165^T=KCTC 62047^T).

[Effects of storage temperature and time on the contents of different nitrogen forms in fresh soil samples.]

Soil nitrogen forms and contents are of great importance in ecological studies. The storage methods of soil samples have great effects on the accuracy of determination of nitrogen contents. We aimed to select a reasonable storage method for soil samples with forest soil of Castanopsis faberi fore-st at Wanmulin Nature Reserve in Jian'ou City as an example. The contents of soil ammonium, nitrate, total nitrogen, soluble organic nitrogen, amino acid nitrogen and microbial biomass nitrogen were measured in soil samples under the storage conditions of different temperature (at 25, 4 and -20 ℃) and different times (0, 7 and 30 days). The nitrogen contents during the process of cultivating under the room temperature after being frozen were also measured. The results showed that the contents of all nitrogen forms except for amino acid nitrogen were increased in the soil samples that stored at the room temperature for seven days. There were no significant differences between the contents of all the tested nitrogen forms in the refrigerated or frozen samples and the fresh soil samples. The changes of nitrogen content in soil samples at refrigerated and frozen storage were more stable than those at room temperature storage. The low temperature storage could stimulate soil mineralization. Hence, after stored for 30 days, contents of all the tested nitrogen forms in the refri-gerated and frozen storage soil samples were significantly higher than those in the fresh samples except for the soluble organic nitrogen, whereas there was no significant difference between the refrigerated and frozen storage methods. Therefore, fresh samples should be promptly processed when taken back to the laboratory. If the samples needed to storage, it should not be stored more than half a month. If the samples need a longer storage time, it must be placed in lower temperature (at -40 or -80 ℃). Pre-incubation treatment was required when the low temperature storage soil sample was subjected to an experiment. In the process of pre-incubation, the contents of all the tested nitrogen form in soil samples gradually approached the level of fresh soil sample with the increases of incubation time except for that of nitrate which decreased firstly and then increased rapidly. After incubation for about one week, the nitrogen content of soil sample returned to the level that was close to that of the fresh soil. In combination with studies previously reported, soil samples collected from field and air dried samples needed a pre-incubation for 5-14 days, and the pre-incubation time for the cold storage sample should not be less than one week.

nov., a novel DNA- and tyrosine-hydrolysing gammaproteobacterium isolated from forest soil

A bacterial isolate, designated G-5-5^T, was isolated from forest soil at Kyonggi University. Strain G-5-5^T was acid-tolerant and alkali-tolerant. Cells were strictly aerobic, Gram-stain-negative, catalase- and oxidase-positive, non-motile, non-spore-forming, rod-shaped, and yellow-coloured. Strain G-5-5^T hydrolysed DNA and tyrosine; assimilated d-glucose, maltose, N-acetyl-glucosamine and l-fucose; and tolerated only 0.5 % NaCl (w/v). Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-5-5^T formed a lineage within the family Rhodanobacteraceae and that it grouped with but was distinct from various members of the genus Rhodanobacter. The closest member was Rhodanobacter umsongensis GR24-2^T (97.8 % sequence similarity). The sole respiratory quinone was Q-8. The major polar lipids of strain G-5-5^T were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major cellular fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. The DNA G+C content of strain G-5-5^T was 64.1 mol%. DNA-DNA hybridization relatedness between strain G-5-5^T and other close members of the genus Rhodanobacter ranged from 19 % to 45 %. On the basis of the polyphasic characterization and phylogenetic analyses, strain G-5-5^T represents a novel species of the genus Rhodanobacter, for which the name Rhodanobacter hydrolyticus sp. nov. is proposed. The type strain is G-5-5^T (=KEMB 9005-533^T=KACC 19113^T=NBRC 112685^T).

nov., isolated from forest soil

A Gram-stain-negative, aerobic, non-motile bacterium, designated strain 10-7W-9003^T, was isolated from the forest soil of Limushan National Forest Park, south-east China (19° 10' 42″ N, 109° 44' 45″ E). Strain 10-7W-9003^T showed a shape change during the course of culture from long filamentous cells (5-10×0.4-0.5 µm) at 5-36 h, to rod shaped (1.0-1.5×0.5-0.7 µm) with inoculation after 2 days. It grew optimally at 28-30 °C and pH 6.5-7.5. On the basis of 16S rRNA gene sequence analysis, it belongs to the genus Chitinophaga and is most closely related to Chitinophaga eiseniae KACC 13774^T and Chitinophaga qingshengii JCM 30026^T, with 16S rRNA gene sequences similarities of 98.8 and 98.3 %, respectively. However, the DNA-DNA hybridization study showed that strain 10-7W-9003^T shared relatively low relatedness values with KACC 13774^T (21.8 %) and JCM 30026^T (20.4 %), respectively. The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The genomic DNA G+C content was 50.7 mol%. It contained MK-7 as the major quinone. The phenotypic, chemotaxonomic and phylogenetic data clearly showed that strain 10-7W-9003^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga varians sp. nov. is proposed. The type strain is 10-7W-9003^T (=GDMCC 1.1252^T=KACC 19415^T=KCTC 52926^T).

nov., a bacterium isolated from forest soil and emended description of the genus Fluviicola

A novel bacterium, designated strain CA-1^T, was isolated from forest soil in Kyonggi University. Cells were strictly aerobic, Gram-stain-negative, catalase-positive, oxidase-negative, non-motile, non-spore-forming, rod-shaped and red-orange-pigmented. Strain CA-1^T hydrolysed casein and DNA. It was able to grow at 15-37 °C, pH 5.5-9.0 and at 0-2 % (w/v) NaCl concentration. Flexirubin-type pigments were present. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain CA-1^T formed a lineage within the family Crocinitomicaceae of the phylum Bacteroidetes that was distinct from Fluviicola hefeinensis MYL-8^T (96.8 % sequence similarity) and Fluviicola taffensis DSM 16823^T (96.1 %). Strain CA-1^T contained menaquinone-6 as a sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, unidentified aminolipids, an unidentified aminophospholipid and an unidentified lipid. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C15 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 1 G. The DNA G+C content of strain CA-1^T was 44.1 mol%. The polyphasic characterization revealed that strain CA-1^T represents a novel species in the genus Fluviicola, for which the name Fluviicola kyonggii sp. nov. is proposed. The type strain is CA-1^T (=KEMB 9005-526^T=KACC 19148^T=NBRC 112684^T).

Acacia Changes Microbial Indicators and Increases C and N in Soil Organic Fractions in Intercropped Eucalyptus Plantations

Intercropping forest plantations of Eucalyptus with nitrogen-fixing trees can increase soil N inputs and stimulate soil organic matter (OM) cycling. However, microbial indicators and their correlation in specific fractions of soil OM are unclear in the tropical sandy soils. Here, we examined the microbial indicators associated with C and N in the soil resulting from pure and intercropped Eucalyptus grandis and Acacia mangium plantations. We hypothesized that introduction of A. mangium in a Eucalyptus plantation promotes changes in microbial indicators and increases C and N concentrations on labile fractions of the soil OM, when compared to pure eucalyptus plantations. We determined the microbial and enzymatic activity, and the potential for C degradation by the soil microbial community. Additionally, we evaluated soil OM fractions and litter parameters. Soil (0–20 cm) and litter samples were collected at 27 and 39 months after planting from the following treatments: pure E. grandis (E) and A. mangium (A) plantations, pure E. grandis plantations with N fertilizer (E+N) and an E. grandis, and A. mangium intercropped plantations (E+A). The results showed that intercropped plantations (E+A) increase 3, 45, and 70% microbial biomass C as compared to A, E+N, and E, at 27 months after planting. The metabolic quotient (qCO₂) showed a tendency toward stressful values in pure E. grandis plantations and a strong correlation with dehydrogenase activity. A and E+A treatments also exhibited the highest organic fractions (OF) and C and N contents. A canonical redundancy analysis revealed positive correlations between microbial indicators of soil and litter attributes, and a strong effect of C and N variables in differentiating A and E+A from E and E+N treatments. The results suggested that a significant role of A. mangium enhance the dynamics of soil microbial indicators which help in the accumulation of C and N in soil OF in intercropped E. grandis plantations. Our results are mostly relevant to plantations in sandy soil areas with low levels of OM, suggesting and efficient method for improving nutrient availability in the soil and optimizing eucalyptus growth and development.

nov., isolated from forest soil and emended description of the genus Actinotalea

A Gram-stain-positive, aerobic, non-motile and short-rod-shaped actinobacterium, designated THG-T121^T, was isolated from forest soil. Growth occurred at 10-40 °C (optimum 28-30 °C), at pH 6-8 (optimum 7) and at 0-4 % NaCl (optimum 1 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T121^T were identified as Actinotalea ferrariae KCTC 29134^T (97.9 %), Actinotalea fermentans KCTC 3251^T (97.3 %), Cellulomonas carbonis KCTC 19824^T (97.2 %). 16S rRNA gene sequence similarities among strain THG-T121^T and other recognized species were lower than 97.0 %. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two phosphatidylinositol mannosides, one unidentified phospholipid, three unidentified glycolipids and one unidentified lipid. The isoprenoid quinone was menaquinone (MK-10(H4)). The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1 A, C16 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0. The whole-cell sugars of strain THG-T121^T were rhamnose, ribose, mannose and glucose. The peptidoglycan type of strain THG-T121^T is A4β, containing l-Orn-D-Ser-L-Asp. The DNA G+C content of strain THG-T121^T was 72.4 mol%. DNA-DNA hybridization values between strain THG-T121^T and A. ferrariae KCTC 29134^T, A. fermentans KCTC 3251^T and C. carbonis KCTC 19824^T were 30.2 % (27.3 %, reciprocal analysis), 28.4 %, (17.3 %) and 16.9 %, (9.3 %), respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-T121^T represents a novel species of the genus Actinotalea, for which the name Actinotaleasolisilvae sp. nov. is proposed. The type strain is THG-T121^T (=KACC 19191^T=CGMCC 4.7389^T).