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Mixed forests often increase their stability and species richness in comparison to pure stands. However, a comprehensive understanding of the effects of mixed forests on soil properties, bacterial community diversity, and soil nitrogen cycling remains elusive. This study investigated soil samples from pure Robinia pseudoacacia stands, pure Quercus variabilis stands, and mixed stands of both species in the southern foothills of the Taihang Mountains. Utilizing high-throughput sequencing and real-time fluorescence quantitative PCR, this study analyzed the bacterial community structure and the abundance of nitrogen-cycling functional genes within soils from different stands. The results demonstrated that Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacterial groups across all three forest soil types. The mixed-forest soil exhibited a higher relative abundance of Firmicutes and Bacteroidetes, while Nitrospirae and Crenarchaeota were most abundant in the pure R. pseudoacacia stand soils. Employing FAPROTAX for predictive bacterial function analysis in various soil layers, this study found that nitrogen-cycling processes such as nitrification and denitrification were most prominent in pure R. pseudoacacia soils. Whether in surface or deeper soil layers, the abundance of AOB amoA, nirS, and nirK genes was typically highest in pure R. pseudoacacia stand soils. In conclusion, the mixed forest of R. pseudoacacia and Q. variabilis can moderate the intensity of nitrification and denitrification processes, consequently reducing soil nitrogen loss. [ABSTRACT FROM AUTHOR]

The life strategies of bacterial communities determine their structure and function and are an important driver of biogeochemical cycling. However, the variations in these strategies under different soil resource conditions remain largely unknown. We explored the bacterial life strategies and changes in structure and functions between Antarctic soils and forest (temperate, subtropical, and tropical) soils. The results showed that the weighted mean rRNA operon copy number in temperate soils was 19.5% lower than that in Antarctic soils, whereas no significant differences were observed among Antarctic, subtropical, and tropical soils. An unexpected result was that bacterial communities in Antarctic soils tended to be copiotrophs, such as Actinobacteriota and Bacteroidota, whereas those in temperate soils tended to be oligotrophs, such as Acidobacteriota and Chloroflexi. Functional predictions showed that in comparison to copiotrophs in Antarctic soils, temperate-inhabiting oligotrophic bacteria exhibited an 84.2–91.1% lower abundance of labile C decomposition genes (hemicellulose, cellulose, monosaccharides, and disaccharides), whereas a 74.4% higher abundance of stable C decomposition (lignin). Genes involved in N cycling (nitrogen fixation, assimilatory nitrate reduction, and denitrification) were 24.3–64.4% lower in temperate soils than in Antarctic soils. Collectively, our study provides a framework for describing the life strategies of soil bacteria, which are crucial to global biogeochemical cycles. [ABSTRACT FROM AUTHOR]

The deposition of nitrogen in soil may be influenced by the presence of different nitrogen components, which may affect the accessibility of soil nitrogen and invasive plant–soil microbe interactions. This, in turn, may alter the success of invasive plants. This study aimed to clarify the influences of the invasive plant Bidens pilosa L. on the physicochemical properties, carbon and nitrogen contents, enzymatic activities, and bacterial communities in soil in comparison to the native plant Pterocypsela laciniata (Houtt.) Shih treated with simulated nitrogen deposition at 5 g nitrogen m−2 yr−1 in four forms (nitrate, ammonium, urea, and mixed nitrogen). Monocultural B. pilosa resulted in a notable increase in soil pH but a substantial decrease in the moisture, electrical conductivity, ammonium content, and the activities of polyphenol oxidase, β-xylosidase, FDA hydrolase, and sucrase in soil in comparison to the control. Co-cultivating B. pilosa and P. laciniata resulted in a notable increase in total soil organic carbon content in comparison to the control. Monocultural B. pilosa resulted in a notable decrease in soil bacterial alpha diversity in comparison to monocultural P. laciniata. Soil FDA hydrolase activity and soil bacterial alpha diversity, especially the indices of Shannon's diversity, Simpson's dominance, and Pielou's evenness, exhibited a notable decline under co-cultivated B. pilosa and P. laciniata treated with nitrate in comparison to those treated with ammonium, urea, and mixed nitrogen. [ABSTRACT FROM AUTHOR]

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil–root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root–soil continuum. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Urban forest soil is often disturbed by frequent human activity. Organic mulching is effective for improving soil quality; however, the effects of organic mulching on soil bacterial communities in urban forests are still largely unexplored. This study evaluated how organic mulching changed the urban forest soil bacterial community through an incubation experiment. Four treatments were applied: (1) no organic mulch (CK); (2) wood chips alone (5 g, Mw); (3) wood compost alone (5 g, Mc); and (4) wood chips + wood compost (This mulch was divided into two layers, i.e., the upper layer of wood chips (2.5 g) and the lower layer wood compost (2.5 g, Mw+c).) We found significant differences in the soil physicochemical properties under organic mulching after incubation. Overall, organic mulching can alter soil bacterial community structure. Soil alkali-hydrolyzable nitrogen, soil organic carbon, soil total nitrogen, and carbon-nitrogen ratio were the main factors affecting soil microbial community structures. Soil bacterial groups under organic mulching treatments mainly acted on the C and N cycling of functional pathways in soil. This study suggests that organic mulching could maintain the development of soil bacteria, which establishes a theoretical foundation for enhancing the microbiological environment of urban forest soils. [ABSTRACT FROM AUTHOR]

Pollutants can exist in the soil for a long time and alter the bacterial community. Using lubricants to prevent the wear of chainsaw blades is necessary for thinning activities and wood harvesting. We investigated the influences of soil contamination with chainsaw lubricants on soil bacterial communities. Bio-oil, mineral oil, and recycled oil were scattered on each treatment to investigate variations in soil bacterial structure during treated periods using the Illumina MiSeq sequencing platform. The results obtained were 5943 ASVs, 5112 ASVs, and 6136 ASVs after treatment at one month, six months, and twelve months, respectively. There was a significant difference in Shannon and Simpson indices between treatments and controls. A total of 46 bacterial genera with an average relative abundance of more than 1.0% were detected in all soil samples. Massilia was the most common genus detected in control at one month, with an average relative abundance of 14.99%, while Chthoniobacter was the most abundant genus detected in bio-oil, mineral oil, and recycled oil treatments at one month, with an average relative abundance of 13.39%, 14.32%, and 10.47%, respectively. Among the three chainsaw lubricants, bio-oil and mineral oil had fewer impacts than recycled oil. The abundances of several functional bacteria groups in the bio-oil treatment were higher than in other treatments and controls. Our results indicated that different chainsaw lubricants and their time of application affected the soil bacterial community composition. [ABSTRACT FROM AUTHOR]

Mixed forests often increase their stability and species richness in comparison to pure stands. However, a comprehensive understanding of the effects of mixed forests on soil properties, bacterial community diversity, and soil nitrogen cycling remains elusive. This study investigated soil samples from pure Robinia pseudoacacia stands, pure Quercus variabilis stands, and mixed stands of both species in the southern foothills of the Taihang Mountains. Utilizing high-throughput sequencing and real-time fluorescence quantitative PCR, this study analyzed the bacterial community structure and the abundance of nitrogen-cycling functional genes within soils from different stands. The results demonstrated that Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacterial groups across all three forest soil types. The mixed-forest soil exhibited a higher relative abundance of Firmicutes and Bacteroidetes, while Nitrospirae and Crenarchaeota were most abundant in the pure R. pseudoacacia stand soils. Employing FAPROTAX for predictive bacterial function analysis in various soil layers, this study found that nitrogen-cycling processes such as nitrification and denitrification were most prominent in pure R. pseudoacacia soils. Whether in surface or deeper soil layers, the abundance of AOB amoA, nirS, and nirK genes was typically highest in pure R. pseudoacacia stand soils. In conclusion, the mixed forest of R. pseudoacacia and Q. variabilis can moderate the intensity of nitrification and denitrification processes, consequently reducing soil nitrogen loss.

The deposition of nitrogen in soil may be influenced by the presence of different nitrogen components, which may affect the accessibility of soil nitrogen and invasive plant–soil microbe interactions. This, in turn, may alter the success of invasive plants. This study aimed to clarify the influences of the invasive plant Bidens pilosa L. on the physicochemical properties, carbon and nitrogen contents, enzymatic activities, and bacterial communities in soil in comparison to the native plant Pterocypsela laciniata (Houtt.) Shih treated with simulated nitrogen deposition at 5 g nitrogen m−2 yr−1 in four forms (nitrate, ammonium, urea, and mixed nitrogen). Monocultural B. pilosa resulted in a notable increase in soil pH but a substantial decrease in the moisture, electrical conductivity, ammonium content, and the activities of polyphenol oxidase, β-xylosidase, FDA hydrolase, and sucrase in soil in comparison to the control. Co-cultivating B. pilosa and P. laciniata resulted in a notable increase in total soil organic carbon content in comparison to the control. Monocultural B. pilosa resulted in a notable decrease in soil bacterial alpha diversity in comparison to monocultural P. laciniata. Soil FDA hydrolase activity and soil bacterial alpha diversity, especially the indices of Shannon’s diversity, Simpson’s dominance, and Pielou’s evenness, exhibited a notable decline under co-cultivated B. pilosa and P. laciniata treated with nitrate in comparison to those treated with ammonium, urea, and mixed nitrogen.

The life strategies of bacterial communities determine their structure and function and are an important driver of biogeochemical cycling. However, the variations in these strategies under different soil resource conditions remain largely unknown. We explored the bacterial life strategies and changes in structure and functions between Antarctic soils and forest (temperate, subtropical, and tropical) soils. The results showed that the weighted mean rRNA operon copy number in temperate soils was 19.5% lower than that in Antarctic soils, whereas no significant differences were observed among Antarctic, subtropical, and tropical soils. An unexpected result was that bacterial communities in Antarctic soils tended to be copiotrophs, such as Actinobacteriota and Bacteroidota, whereas those in temperate soils tended to be oligotrophs, such as Acidobacteriota and Chloroflexi. Functional predictions showed that in comparison to copiotrophs in Antarctic soils, temperate-inhabiting oligotrophic bacteria exhibited an 84.2–91.1% lower abundance of labile C decomposition genes (hemicellulose, cellulose, monosaccharides, and disaccharides), whereas a 74.4% higher abundance of stable C decomposition (lignin). Genes involved in N cycling (nitrogen fixation, assimilatory nitrate reduction, and denitrification) were 24.3–64.4% lower in temperate soils than in Antarctic soils. Collectively, our study provides a framework for describing the life strategies of soil bacteria, which are crucial to global biogeochemical cycles.

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil–root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root–soil continuum.

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.

Pollutants can exist in the soil for a long time and alter the bacterial community. Using lubricants to prevent the wear of chainsaw blades is necessary for thinning activities and wood harvesting. We investigated the influences of soil contamination with chainsaw lubricants on soil bacterial communities. Bio-oil, mineral oil, and recycled oil were scattered on each treatment to investigate variations in soil bacterial structure during treated periods using the Illumina MiSeq sequencing platform. The results obtained were 5943 ASVs, 5112 ASVs, and 6136 ASVs after treatment at one month, six months, and twelve months, respectively. There was a significant difference in Shannon and Simpson indices between treatments and controls. A total of 46 bacterial genera with an average relative abundance of more than 1.0% were detected in all soil samples. Massilia was the most common genus detected in control at one month, with an average relative abundance of 14.99%, while Chthoniobacter was the most abundant genus detected in bio-oil, mineral oil, and recycled oil treatments at one month, with an average relative abundance of 13.39%, 14.32%, and 10.47%, respectively. Among the three chainsaw lubricants, bio-oil and mineral oil had fewer impacts than recycled oil. The abundances of several functional bacteria groups in the bio-oil treatment were higher than in other treatments and controls. Our results indicated that different chainsaw lubricants and their time of application affected the soil bacterial community composition.

Urban forest soil is often disturbed by frequent human activity. Organic mulching is effective for improving soil quality; however, the effects of organic mulching on soil bacterial communities in urban forests are still largely unexplored. This study evaluated how organic mulching changed the urban forest soil bacterial community through an incubation experiment. Four treatments were applied: (1) no organic mulch (CK); (2) wood chips alone (5 g, Mw); (3) wood compost alone (5 g, Mc); and (4) wood chips + wood compost (This mulch was divided into two layers, i.e., the upper layer of wood chips (2.5 g) and the lower layer wood compost (2.5 g, Mw+c).) We found significant differences in the soil physicochemical properties under organic mulching after incubation. Overall, organic mulching can alter soil bacterial community structure. Soil alkali-hydrolyzable nitrogen, soil organic carbon, soil total nitrogen, and carbon-nitrogen ratio were the main factors affecting soil microbial community structures. Soil bacterial groups under organic mulching treatments mainly acted on the C and N cycling of functional pathways in soil. This study suggests that organic mulching could maintain the development of soil bacteria, which establishes a theoretical foundation for enhancing the microbiological environment of urban forest soils.

Soil microorganisms play vital roles in ecosystem functions, and soil microbial communities might be affected by heavy metal contamination caused by the anthropogenic activities associated with the coal-based industry. This study explored the effects of heavy metal contamination on soil bacterial and fungal communities surrounding different coal-based industrial fields (the coal mining industry, coal preparation industry, coal-based chemical industry, and coal-fired power industry) in Shanxi province, North China. Moreover, soil samples from farmland and parks away from all the industrial plants were collected as references. The results showed that the concentrations of most heavy metals were greater than the local background values, particularly for arsenic (As), lead (Pb), cadmium (Cd), and mercury (Hg). There were significant differences in soil cellulase and alkaline phosphatase activities among sampling fields. The composition, diversity, and abundance of soil microbial communities among all sampling fields were significantly different, particularly for the fungal community. Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were the predominant bacterial phyla, while Ascomycota, Mortierellomycota, and Basidiomycota dominated the studied fungal community in this coal-based industrially intensive region. A redundancy analysis, variance partitioning analysis, and Spearman correlation analysis revealed that the soil microbial community structure was significantly affected by Cd, total carbon, total nitrogen, and alkaline phosphatase activity. This study profiles the basic features of the soil physicochemical properties, the multiple heavy metal concentrations, and the microbial communities in a coal-based industrial region in North China. [ABSTRACT FROM AUTHOR]

Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near six different characteristic areas of Ny-Ålesund in 2018 were taken as the research objects, and high-throughput sequencing of V3–V4 regions of all samples were performed using 16S rDNA. Among the soil samples of six glacial meltwater areas in Ny-Ålesund, Arctic, the meltwater area near the reservoir bay had the highest bacterial abundance, and the meltwater area near the sand had the lowest one. The dominant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria. The NH4+-N content in intertidal soil was higher than that in subtidal soil. Through WGCNA analysis and LEFSE analysis, it was found that the core bacteria significantly related to NH4+-N were basically distributed in the intertidal area. For example, Nitrosomonadaceae, Nitrospira and Sphingomonas were the core bacteria showed significant different abundance in the intertidal area, which have the ability to metabolize NH4+-N. Our findings suggest that NH4+-N plays an important role in soil bacterial community structure in the Arctic meltwater areas. [ABSTRACT FROM AUTHOR]

The increasing amount of agricultural applications of controlled-release urea (CRU) and fulvic acids (FA) demands a better understanding of FA's effects on microbially mediated nitrogen (N) nutrient cycling. Herein, a 0–60 day laboratory experiment and a consecutive pot experiment (2016–2018) were carried out to reveal the effects of using CRU on soil microbial N-cycling processes and soil fertility, with and without the application of FA. Compared to the CRU treatment, the CRU+FA treatment boosted wheat yield by 22.1%. To reveal the mechanism of CRU+FA affecting the soil fertility, soil nutrient supply and microbial community were assessed and contrasted in this research. From 0–60 days, compared with the CRU treatment, leaching NO3−-N content of CRU+FA was dramatically decreased by 12.7–84.2% in the 20 cm depth of soil column. Different fertilizers and the day of fertilization both have an impact on the soil microbiota. The most dominant bacterial phyla Actinobacteria and Proteobacteria were increased with CRU+FA treatment during 0–60 days. Network analysis revealed that microbial co-occurrence grew more intensive during the CRU+FA treatment, and the environmental change enhanced the microbial community. The CRU+FA treatment, in particular, significantly decreased the relative abundance of Sphingomonas, Lysobacter and Nitrospira associated with nitrification reactions, Nocardioides and Gaiella related to denitrification reactions. Meanwhile, the CRU+FA treatment grew the relative abundance of Ensifer, Blastococcus, and Pseudolabrys that function in N fixation, and then could reduce NH4+-N and NO3−-N leaching and improve the soil nutrient supply. In conclusion, the synergistic effects of slow nutrition release of CRU and growth promoting of FA could improve the soil microbial community of N cycle, reduce the loss of nutrients, and increase the wheat yield. [ABSTRACT FROM AUTHOR]

Japanese larch (Larix kaempferi), a non-native tree species, has been widely planted in the Qinling Mountains since the last century, but it does not meet the habitat needs of giant pandas (Ailuropoda melanoleuca), mainly because of food, further causing habitat degradation and fragmentation. However, how soil microorganisms, considered as predictors of the soil environment, respond to Japanese larch remains poorly explored, especially compared with native forests. Here, we collected 40 soil samples from plantation, bamboo, and natural (excluding bamboo) forests in the Changqing Nature Reserve and Foping Nature Reserve in Qinling to compare soil bacterial community composition and diversity using high-throughput sequencing of bacterial 16S rRNA genes. The soil chemical properties and bacterial communities differed noticeably under forest-type classification patterns. The soil of the Japanese larch planted forests underwent substantial degradation, with higher acidity, lower alpha diversity, and more significant enrichment in the oligotrophic bacteria Acidobacteria and Verrucomicrobia, in contrast to the other two primary forests with elevated soil nutrient levels. The application of PICRUSt2 indicated the down-regulation of amino acid-related metabolism in planted forests. Moreover, pH was the primary factor determining the whole bacterial community structures. To avoid the uncertainty of a single sampling region, we chose different sampling sites that could be considered as geographical factors, possibly due to environmental heterogeneity or dispersal limitations, which also explained the specific community patterns of microorganisms. Overall, this paper may help provide a scientific basis for future revegetation in giant panda habitats, highlighting the urgent need for ecological restoration and sustainable forestry management. [ABSTRACT FROM AUTHOR]

In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome. [ABSTRACT FROM AUTHOR]

Soil microorganisms play vital roles in ecosystem functions, and soil microbial communities might be affected by heavy metal contamination caused by the anthropogenic activities associated with the coal-based industry. This study explored the effects of heavy metal contamination on soil bacterial and fungal communities surrounding different coal-based industrial fields (the coal mining industry, coal preparation industry, coal-based chemical industry, and coal-fired power industry) in Shanxi province, North China. Moreover, soil samples from farmland and parks away from all the industrial plants were collected as references. The results showed that the concentrations of most heavy metals were greater than the local background values, particularly for arsenic (As), lead (Pb), cadmium (Cd), and mercury (Hg). There were significant differences in soil cellulase and alkaline phosphatase activities among sampling fields. The composition, diversity, and abundance of soil microbial communities among all sampling fields were significantly different, particularly for the fungal community. Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were the predominant bacterial phyla, while Ascomycota, Mortierellomycota, and Basidiomycota dominated the studied fungal community in this coal-based industrially intensive region. A redundancy analysis, variance partitioning analysis, and Spearman correlation analysis revealed that the soil microbial community structure was significantly affected by Cd, total carbon, total nitrogen, and alkaline phosphatase activity. This study profiles the basic features of the soil physicochemical properties, the multiple heavy metal concentrations, and the microbial communities in a coal-based industrial region in North China.

The quantity of grass-root exudates varies by season, suggesting temporal shifts in soil microbial community composition and activity across a growing season. We hypothesized that bacterial community and nitrogen cycle-associated prokaryotic gene expressions shift across three phases of the growing season. To test this hypothesis, we quantified gene and transcript copy number of nitrogen fixation (nifH), ammonia oxidation (amoA, hao, nxrB), denitrification (narG, napA, nirK, nirS, norB, nosZ), dissimilatory nitrate reduction to ammonia (nrfA), and anaerobic ammonium oxidation (hzs, hdh) using the pre-optimized Nitrogen Cycle Evaluation (NiCE) chip. Bacterial community composition was characterized using V3-V4 of the 16S rRNA gene, and PICRUSt2 was used to draw out functional inferences. Surprisingly, the nitrogen cycle genes and transcript quantities were largely stable and unresponsive to seasonal changes. We found that genes and transcripts related to ammonia oxidation and denitrification were different for only one or two time points across the seasons (p < 0.05). However, overall, the nitrogen cycling genes did not show drastic variations. Similarly, the bacterial community also did not vary across the seasons. In contrast, the predicted functional potential was slightly low for May and remained constant for other months. Moreover, soil chemical properties showed a seasonal pattern only for nitrate and ammonium concentrations, while ammonia oxidation and denitrification transcripts were strongly correlated with each other. Hence, the results refuted our assumptions, showing stability in N cycling and bacterial community across growing seasons in a natural grassland. [ABSTRACT FROM AUTHOR]

Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near six different characteristic areas of Ny-Ålesund in 2018 were taken as the research objects, and high-throughput sequencing of V3–V4 regions of all samples were performed using 16S rDNA. Among the soil samples of six glacial meltwater areas in Ny-Ålesund, Arctic, the meltwater area near the reservoir bay had the highest bacterial abundance, and the meltwater area near the sand had the lowest one. The dominant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria. The NH4+-N content in intertidal soil was higher than that in subtidal soil. Through WGCNA analysis and LEFSE analysis, it was found that the core bacteria significantly related to NH4+-N were basically distributed in the intertidal area. For example, Nitrosomonadaceae, Nitrospira and Sphingomonas were the core bacteria showed significant different abundance in the intertidal area, which have the ability to metabolize NH4+-N. Our findings suggest that NH4+-N plays an important role in soil bacterial community structure in the Arctic meltwater areas.

Japanese larch (Larix kaempferi), a non-native tree species, has been widely planted in the Qinling Mountains since the last century, but it does not meet the habitat needs of giant pandas (Ailuropoda melanoleuca), mainly because of food, further causing habitat degradation and fragmentation. However, how soil microorganisms, considered as predictors of the soil environment, respond to Japanese larch remains poorly explored, especially compared with native forests. Here, we collected 40 soil samples from plantation, bamboo, and natural (excluding bamboo) forests in the Changqing Nature Reserve and Foping Nature Reserve in Qinling to compare soil bacterial community composition and diversity using high-throughput sequencing of bacterial 16S rRNA genes. The soil chemical properties and bacterial communities differed noticeably under forest-type classification patterns. The soil of the Japanese larch planted forests underwent substantial degradation, with higher acidity, lower alpha diversity, and more significant enrichment in the oligotrophic bacteria Acidobacteria and Verrucomicrobia, in contrast to the other two primary forests with elevated soil nutrient levels. The application of PICRUSt2 indicated the down-regulation of amino acid-related metabolism in planted forests. Moreover, pH was the primary factor determining the whole bacterial community structures. To avoid the uncertainty of a single sampling region, we chose different sampling sites that could be considered as geographical factors, possibly due to environmental heterogeneity or dispersal limitations, which also explained the specific community patterns of microorganisms. Overall, this paper may help provide a scientific basis for future revegetation in giant panda habitats, highlighting the urgent need for ecological restoration and sustainable forestry management.

The increasing amount of agricultural applications of controlled-release urea (CRU) and fulvic acids (FA) demands a better understanding of FA’s effects on microbially mediated nitrogen (N) nutrient cycling. Herein, a 0–60 day laboratory experiment and a consecutive pot experiment (2016–2018) were carried out to reveal the effects of using CRU on soil microbial N-cycling processes and soil fertility, with and without the application of FA. Compared to the CRU treatment, the CRU+FA treatment boosted wheat yield by 22.1%. To reveal the mechanism of CRU+FA affecting the soil fertility, soil nutrient supply and microbial community were assessed and contrasted in this research. From 0–60 days, compared with the CRU treatment, leaching NO3−-N content of CRU+FA was dramatically decreased by 12.7–84.2% in the 20 cm depth of soil column. Different fertilizers and the day of fertilization both have an impact on the soil microbiota. The most dominant bacterial phyla Actinobacteria and Proteobacteria were increased with CRU+FA treatment during 0–60 days. Network analysis revealed that microbial co-occurrence grew more intensive during the CRU+FA treatment, and the environmental change enhanced the microbial community. The CRU+FA treatment, in particular, significantly decreased the relative abundance of Sphingomonas, Lysobacter and Nitrospira associated with nitrification reactions, Nocardioides and Gaiella related to denitrification reactions. Meanwhile, the CRU+FA treatment grew the relative abundance of Ensifer, Blastococcus, and Pseudolabrys that function in N fixation, and then could reduce NH4+-N and NO3−-N leaching and improve the soil nutrient supply. In conclusion, the synergistic effects of slow nutrition release of CRU and growth promoting of FA could improve the soil microbial community of N cycle, reduce the loss of nutrients, and increase the wheat yield.

In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome.

The quantity of grass-root exudates varies by season, suggesting temporal shifts in soil microbial community composition and activity across a growing season. We hypothesized that bacterial community and nitrogen cycle-associated prokaryotic gene expressions shift across three phases of the growing season. To test this hypothesis, we quantified gene and transcript copy number of nitrogen fixation (nifH), ammonia oxidation (amoA, hao, nxrB), denitrification (narG, napA, nirK, nirS, norB, nosZ), dissimilatory nitrate reduction to ammonia (nrfA), and anaerobic ammonium oxidation (hzs, hdh) using the pre-optimized Nitrogen Cycle Evaluation (NiCE) chip. Bacterial community composition was characterized using V3-V4 of the 16S rRNA gene, and PICRUSt2 was used to draw out functional inferences. Surprisingly, the nitrogen cycle genes and transcript quantities were largely stable and unresponsive to seasonal changes. We found that genes and transcripts related to ammonia oxidation and denitrification were different for only one or two time points across the seasons (p < 0.05). However, overall, the nitrogen cycling genes did not show drastic variations. Similarly, the bacterial community also did not vary across the seasons. In contrast, the predicted functional potential was slightly low for May and remained constant for other months. Moreover, soil chemical properties showed a seasonal pattern only for nitrate and ammonium concentrations, while ammonia oxidation and denitrification transcripts were strongly correlated with each other. Hence, the results refuted our assumptions, showing stability in N cycling and bacterial community across growing seasons in a natural grassland.

Myxobacteria are abundant micropredators in soil, and are social bacteria with multicellular behavior and producers of versatile secondary metabolites. The interaction between predator and prey populations is an important component in the soil microbial food web, and this is expected to shape the composition and dynamics of microbial communities. Here we hypothesize the regulation of bacterial abundance and community composition on soil myxobacterial community. Field investigation indicated that the relative abundance of Myxococcales in subtropical and tropical forest soil from South China was 1.49−4.74% of all the 16S rRNA gene sequences, and myxobacterial community composition differed between subtropical and tropical forest. The canonical correspondence analysis and variation partitioning analysis indicated that biotic factor (bacterial community composition) showed slightly stronger explanation for variation of myxobacteria than soil properties (soil pH and soil organic matter). Based on the rhizosphere bacterial network, the greenhouse mesocosm experiment showed that most of the myxobacterial links were with Gram-negative bacteria, except that some nodes from Haliangiacea and Polyangiaceae interacted with actinomycetes and actinomycetes-like Gram-positive bacteria. We inferred that myxobacteria preferential predation on specific bacterial taxa may explain the influence of bacteria on myxobacterial community. Further study confirming the biological process of myxobacterial predation in situ is necessary to advance the understanding of the ecological role of predation behavior in the microbial world.

The Yellow River Delta (YRD) region is an important production base in Shandong Province. It encompasses an array of diversified crop systems, including the corn−wheat rotation system (Wheat−Corn), soybean−corn rotation system (Soybean−Corn), fruits or vegetables system (Fruit), cotton system (Cotton) and rice system (Rice). In this study, the communities of ammonia oxidizer−, denitrifier− and nitrogen (N)−fixing bacteria in those cropping systems were investigated by Illumina Miseq sequencing. We found that Rice soil exhibited significantly higher diversity indices of investigated N−cycling microbial communities than other crop soils, possibly due to its high soil water content. Wheat−Corn soils had higher abundances of nitrification gene amoA and denitrification genes nirK and nirS, and exhibited higher soil potential nitrification rate (PNR), compared with Soybean−Corn, Cotton and Fruit soils. Consistently, redundancy analysis (RDA) showed that soil water content (SWC), electrical conductivity (EC), and total nitrogen (TN) were the most important influencing factors of the diversity and structure of the investigated N−cycling microbial.

Myxobacteria are abundant micropredators in soil, and are social bacteria with multicellular behavior and producers of versatile secondary metabolites. The interaction between predator and prey populations is an important component in the soil microbial food web, and this is expected to shape the composition and dynamics of microbial communities. Here we hypothesize the regulation of bacterial abundance and community composition on soil myxobacterial community. Field investigation indicated that the relative abundance of Myxococcales in subtropical and tropical forest soil from South China was 1.49−4.74% of all the 16S rRNA gene sequences, and myxobacterial community composition differed between subtropical and tropical forest. The canonical correspondence analysis and variation partitioning analysis indicated that biotic factor (bacterial community composition) showed slightly stronger explanation for variation of myxobacteria than soil properties (soil pH and soil organic matter). Based on the rhizosphere bacterial network, the greenhouse mesocosm experiment showed that most of the myxobacterial links were with Gram-negative bacteria, except that some nodes from Haliangiacea and Polyangiaceae interacted with actinomycetes and actinomycetes-like Gram-positive bacteria. We inferred that myxobacteria preferential predation on specific bacterial taxa may explain the influence of bacteria on myxobacterial community. Further study confirming the biological process of myxobacterial predation in situ is necessary to advance the understanding of the ecological role of predation behavior in the microbial world. [ABSTRACT FROM AUTHOR]

The Yellow River Delta (YRD) region is an important production base in Shandong Province. It encompasses an array of diversified crop systems, including the corn–wheat rotation system (Wheat–Corn), soybean–corn rotation system (Soybean–Corn), fruits or vegetables system (Fruit), cotton system (Cotton) and rice system (Rice). In this study, the communities of ammonia oxidizer–, denitrifier– and nitrogen (N)–fixing bacteria in those cropping systems were investigated by Illumina Miseq sequencing. We found that Rice soil exhibited significantly higher diversity indices of investigated N–cycling microbial communities than other crop soils, possibly due to its high soil water content. Wheat–Corn soils had higher abundances of nitrification gene amoA and denitrification genes nirK and nirS, and exhibited higher soil potential nitrification rate (PNR), compared with Soybean–Corn, Cotton and Fruit soils. Consistently, redundancy analysis (RDA) showed that soil water content (SWC), electrical conductivity (EC), and total nitrogen (TN) were the most important influencing factors of the diversity and structure of the investigated N–cycling microbial. [ABSTRACT FROM AUTHOR]