Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use

Toxic response of antimony in the Comamonas testosteroni and its application in soil antimony bioremediation

Antimony (Sb) is toxic to ecosystems and potentially to public health via its accumulation in the food chain. Bioavailability and toxicity of Sb have been reduced using various methods for the remediation of Sb-contaminated soil in most studies. However, Sb-contaminated soil remediation by microbial agents has been rarely evaluated. In this study, we evaluated the potential for the use of Comamonas testosteroni JL40 in the bioremediation of Sb-contamination. Strain JL40 immobilized more than 30 % of the Sb(III) in solution and oxidized over 18 % to Sb(V) for detoxification. Meanwhile, strain JL40 responds to Sb toxicity through such as Sb efflux, intracellular accumulation, biofilm production, and scavenging of reactive oxygen species (ROS), etc. The results of the pot experiment showed the average Sb content of the brown rice was decreased by 59.1%, 38.8%, and 48.4%, for 1.8, 50, and 100 mg/kg Sb spiked soils, respectively. In addition, the results of plant, soil enzyme activity, and rice agronomic trait observations showed that the application of strain JL40 could maintain the health of plants and soil and improve rice production. The single-step and sequential extraction of Sb from rhizosphere soil showed that strain JL40 also plays a role in Sb immobilization and oxidation in the soil environment. During rice potted cultivation, bacterial community analysis and plate counting showed that the strain JL40 could still maintain 103 CFU/g after 30 days of inoculation. With phenotypic and differential proteomics analysis, strain JL40 conferred Sb(III) tolerance by a combination of immobilization, oxidation, efflux and scavenging of ROS, etc. Our study demonstrates the application of Sb-immobilizing and oxidizing bacteria to lower soil Sb and reduce accumulation of Sb in rice. Our results provide guidance for bacterial remediation of Sb-contaminated soil.

Fallopia japonica and Impatiens glandulifera are colonized by species-poor root-associated fungal communities but have minor impacts on soil properties in riparian habitats

Fallopia japonica and Impatiens glandulifera are major plant invaders on a global scale that often become dominant in riparian areas. However, little is known about how these species affect interactions in soil–plant systems. The aim of this study was to investigate the impact of both species on abiotic and biotic soil properties, with a special focus on fungi. We investigated eight sites along small streams invaded by F. japonica and I. glandulifera, respectively, and compared each with nearby sites dominated by the native species Urtica dioica. Three different types of samples were collected: bulk soil, rhizosphere soil and roots from invasive and native stands at each site. Bulk soil samples were analysed for soil physicochemical, microbial properties (soil microbial respiration and ergosterol) and soil arthropod abundance (Acari and Collembola). Soil respiration was also evaluated in rhizosphere samples. The fungal community composition of both bulk soil and roots were analysed using a metabarcoding approach. Soil physicochemical properties as well as soil microbial activity, fungal biomass and soil fungal operational unit taxonomic unit (OTU) richness did not differ between invaded and native riparian habitats, indicating only minor belowground impacts of the two invasive plant species. Soil microbial activity, fungal biomass and soil fungal OTU richness were rather related to the soil physicochemical properties. In contrast, Acari abundance decreased by 68% in the presence of F. japonica, while Collembola abundance increased by 11% in I. glandulifera sites. Moreover, root-associated fungal communities differed between the invasive and native plants. In F. japonica roots, fungal OTU richness of all investigated ecological groups (mycorrhiza, endophytes, parasites, saprobes) were lower compared to U. dioica. However, in I. glandulifera roots only the OTU richness of mycorrhiza and saprobic fungi was lower. Overall, our findings show that F. japonica and I. glandulifera can influence the abundance of soil arthropods and are characterized by lower OTU richness of root-associated fungi.

Dynamic Evaluation of Intensive Land Use Based on Objective Empowerment by Entropy Method and Neural Network Algorithm

In the past, the extreme value standardization of indicators, the traditional weighting method, and the multifactor comprehensive model of land intensive use inevitably linearly correlate the evaluation indicators with the evaluation objects, ignoring the direction differences of different indicators in different intervals. At the same time, these methods are also difficult to meet the change of evaluation index weight value with land use type, and cannot adapt to the actual situation of land use environment level and dynamic change. Considering the objectivity of nonlinear correlation moderate index and weight assignment, based on the standardization of quadratic function index and entropy assignment, this paper studies the intensive and dynamic use of land in development zones by different regions to improve the realistic fit of the evaluation model. The results show that the overall level of land intensive use in Chongqing center district and western Chongqing is better than that in northeast Chongqing and southeast Chongqing, roughly showing the state of "high in west and low in east."

A review on effective soil health bio-indicators for ecosystem restoration and sustainability

Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.

Changes of Microbial Diversity in Rhizosphere of Different Cadmium-Gradients Soil under Irrigation with Reclaimed Water

Water scarcity and the uneven distribution of water resources in China have resulted in water shortages for agricultural irrigation in arid and semi-arid areas. Reclaimed water used for agricultural irrigation has become an effective solution in the context of the global water shortage. In order to improve soil productivity and solve the shortage of water resources, we carried out reclaimed water irrigation experiments on polluted soil. Compared with full irrigation treatments, the EC value of reclaimed water under deficit irrigation treatments decreased by 2.89–42.90%, and the content of organic matter increased by 6.31–12.10%. The proportion of Acidobacteria community in soils with different cadmium concentration gradients irrigated with reclaimed water ranged from 13.6% to 30.5%, its relative abundance decreased with the increase of soil cadmium concentration. In particular, the relative abundance of Pseudomonas pathogens in deficit irrigation treatments was lower than that of the full irrigation treatments. RDA analysis showed that the environmental factors that played a leading role in the change of microbial community structure were organic matter and pH. Furthermore, the metabolic function potential of the rhizosphere soil bacterial community in deficit irrigation treatments was higher than that of full irrigation treatments with reclaimed water. This study proved that reclaimed water irrigation for cadmium contaminated soil did not aggravate the pollution level and promoted the soil ecological environment with better microbial community diversity.

Composition and Diversity of Soil Microbial Community Associated With Land Use Types in the Agro-Pastoral Area in the Upper Yellow River Basin

The microorganisms of soil are sensitive to their living microenvironment, and their community structure and function will change with the environmental conditions. In the agro-pastoral area on the Qinghai-Tibet Plateau, revealing the diversity of the soil microbial communities and its response to different soil physicochemical properties and environmental factors are important for ecosystem management. The microbial (bacteria and archaea) community composition and diversity under different land use types (cultivated land, grazing grassland and planted forest) were analyzed by 16S rRNA (V4 region) method in a typical agro-pastoral region in the upper Yellow River basin. Also, the soil nutrients were studied and correlated with the microbial community. The results showed that the soil nutrient contents in grassland were low, but the available nutrients were relatively high. There was a great spatial variability under different distances to the river. The microbial community diversity was lower in the grassland than the cultivated land and forest land closer to the river. For all land uses, the dominant phyla of soil microorganisms included Proteobacteria, Actinobacteria, and Bacteroidetes, while the abundance of Clostridia was significantly higher than that of the other groups, indicating that Clostridia dominated the Firmicutes and affected soil microbial community composition. The linear discriminant analysis (LDA) effect size (LefSe) analysis showed different biomarkers were more abundant in grassland than other land use types, suggesting that the structure and diversity of soil microorganisms in grassland were significantly different compared with cultivated land and forest land. The distance-based redundancy analysis (db-RDA) results showed that the total phosphorus (TP) and calcium (Ca) were the key environmental factors affecting the diversity and abundance of the soil microbial community in cultivated land and forestland, respectively. However, the microbial diversity in grassland was more related to spatial distance of the river. These results provided a theoretical basis for the changes in the composition, structure, and function of soil microbial communities in agro-pastoral areas.

Impacts of short-term tillage and crop residue incorporation managements on soil microbial community in a double-cropping rice field

Soil microbial community were usually reconsidered as a sensitive indicator in soil quality and soil environment change of paddy field. However, the effects of different tillage and crop residue incorporation managements on soil bacterial community under the double-cropping rice cropping system were still need to further investigated. Therefore, the impacts of different tillage and crop residue incorporation managements on soil bacterial community under the double-cropping rice cropping system in southern of China were studied by using phospholipid fatty acids (PLFAs) profile method in the present paper. The experiment included four different tillage treatments: rotary tillage without crop residue input as a control (RTO), no-tillage with crop residue retention (NT), rotary tillage with crop residue incorporation (RT), and conventional tillage with crop residue incorporation (CT). Compared with RTO treatment, grain yield of rice with NT, RT and CT treatments increased by 1.21%, 3.13% and 6.40%, respectively. This results showed that soil aC15:0, C16:0, iC17:0, C19:0c9, 10 fatty acids with CT and RT treatments were higher than that of RTO treatment, while soil C16:1ω6c and C18:1ω9t fatty acids with NT treatment were higher than that of RTO treatment, respectively. Soil G⁺ and G⁻ bacteria PLFAs contents with CT treatment were higher than that of NT, RT and RTO treatments, while the value of soil G⁺/G⁻ bacteria PLFAs with NT treatment were higher than that of CT, RT and RTO treatments. This results indicated that Richness and McIntosh indices with CT treatment were significantly higher than that of RTO treatment. Principal component analysis (PCA) results showed that the first and second principal components (PC1 and PC2) were explained 93.2% of total variance with all tillage treatments. Except C12:0, C14:0 2OH and C18:2ω6, all unsaturated and cyclopropyl PLFAs contents were belong to PC1. PC1 and PC2 were explained 88.4% of total variance with all tillage treatments. There had significantly positive correlation between soil Richness, Shannon indices and soil PLFAs, G⁺ bacteria, G⁻ bacteria, fungi contents. As a result, it were benefit practices for increasing soil bacterial community structure in the double-cropping rice field of southern China by combined application of rotary, conventional tillage with crop residue incorporation managements.

Maize (Zea mays L.) Seedlings Rhizosphere Microbial Community as Responded to Acidic Biochar Amendment Under Saline Conditions

Biochar has extensively been used for multiple purposes in agriculture, including improving soil microbial biomass. The current study aimed to investigate the effect of acidic biochar on maize seedlings’ rhizosphere bacterial abundance under salinity. There were seven treatments and three replicates in a controlled greenhouse coded as B0S1, B1S1, and B2S1 and B0S2, B1S2, and B2S2. CK is control (free of biochar and salt); B0, B1, and B2 are 0, 15, and 30 g biochar (kg soil)^–1; and S1 and S2 are 2.5 and 5 g salt pot^–1 that were amended, respectively. After harvesting the maize seedlings, the soil samples were collected and analyzed for soil microbial biomass, bacterial abundance, and diversity. The results revealed that relative abundance of Proteobacteria, Actinobacteria, and Chloroflexi increased on phylum level, whereas Actinomarinales, Alphaproteobacteria, and Streptomyces enhanced on genus level, respectively, in B2S1 and B2S2, when compared with CK and non-biochar amended soil under saline conditions. The relative abundance of Actinomarinales was positively correlated with total potassium (TK) and Gematimonadetes negatively correlated with total phosphorus (TP). Biochar addition slightly altered the Ace1, Chao1, and alpha diversity. Principal component analysis corresponded to the changes in soil bacterial community that were closely associated with biochar when compared with CK and salt-treated soils. In conclusion, acidic biochar showed an improved soil microbial community under salinity.

An emerging chemical fumigant: two-sided effects of dazomet on soil microbial environment and plant response

Methyl bromide has been banned worldwide because it causes damage to the ozone layer and the environment. To find a substitute for methyl bromide, the relationships among fumigation, plant growth, and the microbial community in replant soil require further study. We performed pot and field experiments to investigate the effects of dazomet fumigation on soil properties and plant performance. Changes in soil microbial community structure and diversity were assessed using high-throughput sequencing, and plant physiological performance and soil physicochemical properties were also measured. Dazomet fumigation enhanced photosynthesis and promoted plant growth in replant soil; it altered soil physical and chemical properties and reduced soil enzyme activities, although these parameters gradually recovered over time. After dazomet fumigation, the dominant soil phyla changed, microbial diversity decreased significantly, the relative abundance of biocontrol bacteria such as Mortierella increased, and the relative abundance of pathogenic bacteria such as Fusarium decreased. Over the course of the experiment, the soil microbial flora changed dynamically, and soil enzyme activities and other physical and chemical properties also recovered to a certain extent. This result suggested that the effect of dazomet on soil microorganisms was temporary. However, fumigation also led to an increase in some resistant pathogens, such as Trichosporon, that affect soil function and health. Therefore, it is necessary to consider potential negative impacts of dazomet on the soil environment and to perform active environmental risk management in China.

Degradation activity of fungal communities on avocado peel (Persea americana Mill.) in a solid-state process: mycobiota successions and trophic guild shifts

To explore the capability of soil mycobiota to degrade avocado peel waste and identify relevant successions and trophic guild shifts, fungal communities from three environments with different land uses were evaluated in a solid-state process. Soil samples used as inoculum were collected from a pristine mature tropical forest, a traditionally managed Mayan land, and an intensively managed monospecific avocado plantation. Soil-substrate mixes were evaluated for 52 weeks to evaluate organic matter decay and the carbon-to-nitrogen ratio. Amplicon-based high-throughput sequencing from internally transcribed spacer (ITS) analysis revealed significant differences in fungal communities widely dominated by Fusarium sp. and Clonostachys sp.; however, less represented taxa showed relevant shifts concomitantly with organic matter content drops. Trophic guild assignment revealed different behaviors in fungal communities between treatments over the 52 weeks, suggesting distinct preconditioning of fungal communities in these environments. Overall, the results lead to the identification of promising degradation moments and inoculum sources for further consortia enrichment or bioprospecting efforts.

Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing

There is a special interaction between the environment, soil microorganisms, and tea plants, which constitute the ecosystem of tea plantations. Influenced by environmental factors and human management, the changes in soil microbial community affected the growth, quality, and yield of tea plants. However, little is known about the composition and structure of soil bacterial and fungal communities in 100-year-old tea plantations and the mechanisms by which they are affected. In this regard, we characterized the microbiome of tea plantation soils by considering the bacterial and fungal communities in 448 soil samples from 101 ancient tea plantations in eight counties of Lincang city, which is one of the tea domestication centers in the world. 16S and Internal Transcribed Spacer (ITS) rRNA high-throughput amplicon sequencing techniques were applied in this study. The results showed that the abundance, diversity, and composition of the bacterial and fungal communities have different sensitivity with varying pH, altitude, and latitude. pH and altitude affect soil microbial communities, and bacterial communities are more sensitive than fungi in terms of abundance and diversity to pH. The highest α-diversity of bacterial communities is shown in the pH 4.50–5.00 and 2,200-m group, and fungi peaked in the pH 5.00–5.50 and 900-m group. Because of environmental and geographical factors, all microbes are similarly changing, and further correlations showed that the composition and structure of bacterial communities are more sensitive than fungal communities, which were affected by latitude and altitude. In conclusion, the interference of anthropogenic activities plays a more important role in governing fungal community selection than environmental or geographical factors, whereas for the bacterial community, it is more selective to environment adaptation than to adaptation to human activities.

Diversity and structural characteristics of soil microbial communities in different habitats of wild Lilium regale Wilson in Wenchuan area

Lilium regale Wilson (L.regale), originated in the Minjiang River basin in Sichuan, China, has different phenotypic characteristics in different environments. To analyze the correlation between the phenotypes of L.regale and its soil micro-ecological environment, wild habitat soil of L.regale at the two altitudes were selected to analyze the diversity and community structure of microorganisms in soil, and measure the soil physicochemical factors and enzyme activities. The structural composition and diversity of fungal and bacterial communities in hillside and valley soils were significantly different (p < 0.01). Soil available potassium (AK) and soil enzyme activities such as urease (S_UE), sucrase (S_SC), and catalase (S_CAT) differed significantly different between hillsides and valleys (p < 0.01), while organic matter (OM), total phosphorus (TP), and polyphenol oxidase (S_PPO) had no great variances. Correlation analysis was conducted between the common and differential microorganisms and the morphological characteristics, soil physicochemical factors and soil enzyme activities of L.regale in both hillside and valley. The results showed that both of the fungal and bacterial could be clustered into two distinct groups by positive and negative correlations, suggesting that the representative microorganism may have structural characteristics that are directly related to soil physicochemical properties and enzyme activities, which conversely affect the phenotype of Lily. Therefore, the study on the native species of horticultural plants and the local soil microhabitat environment will benefit the conservation of wild Lily and provide theoretical guidance for the domestication and breeding of horticultural plants.

Castro I, Soares R, Brito DRA, Mbanze AA, Chaúque A, Máguas C, Ezeokoli OT, Ribeiro NS, Marques I, Ribeiro-Barros AI. The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique

(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.

Changes in soil ammonia oxidizers and potential nitrification after clear-cutting of boreal forests in China

The Korean pine and broad-leaved mixed forests are the most typical and complete ecosystem among the global boreal forests, with extremely important ecological functions. However, few studies on the changes of soil ammonia oxidizers and potential nitrification after clear-cutting of forests are reported. In this study, in contrast to primary Korean pine forests, nitrate (NO₃^-) was significantly higher in secondary broad-leaved forests, while ammonium (NH₄⁺) was on the contrary. The abundance of ammonia-oxidizing bacteria (AOB) was greatly higher in secondary broad-leaved forests, while levels of ammonia-oxidizing archaea (AOA) were not significantly different between them. The significant differences of community structure of AOA and AOB were observed in different forest types and soil layers. Compared with AOA, community compositions of AOB was more sensitive to forest type. The dominant groups of AOA were Nitrososphaera and Nitrosotalea, and the dominant group of AOB was Nitrosospira, of which Nitrosospira cluster 2 and 4 were functional groups with highly activity. Soil potential nitrification rate (PNR) was higher in secondary broad-leaved forests. Furthermore, PNR and AOB abundance had a significant positive correlation, but no significant correlation with AOA abundance. These results provide insights into the soil nitrogen balance and effects on forest restoration after clear-cutting.

Effects of Residue Retention and Removal Following Thinning on Soil Bacterial Community Composition and Diversity in a Larix olgensis Plantation, Northeast China

Thinning is an important management practice for reducing plant competition and improving wood production in forests. The residues from thinning can contain large amounts of carbon (C) and nitrogen (N), and the management methods applied directly after thinning can affect the input of nutrients to soil, change the availability of substrates to soil bacterial communities, and thus affect soil bacterial community structure. Our objective was to determine the effects of different thinning residue treatments on soil bacterial community structure and diversity. Illumina high-throughput sequencing technology was used to sequence the bacterial 16SrRNA V3–V4 variable region of the soil (0–10 cm) of a Larix olgensis plantation to compare the composition and diversity of soil bacterial communities following removal of thinning residues (tree stems plus tree crowns) (RM) and retention of thinning residues (crowns retained with stem removal) (RT) treatments. Total soil carbon (TC) and nitrogen (TN) content in the residue retention treatment were significantly greater than in residue removal treatments (p < 0.05). The relative abundance of the dominant soil bacteria phyla were, in descending order: Proteobacteria, Verrucomicrobia, Acidobacteria, Chloroflexi, Actinobacteria, Nitrospirae, Planctomycetes, Gemmatimonadetes, and Bacteroidetes, with a total relative abundance of more than 80%. Acidobacteria were enriched in the RM treatment, while Proteobateria, Actinobacteria and Bacteroidetes were greater in the RT treatment. Rhizobiales and Rhodospirillales (belonging to the α-Proteobacteria) were enriched in the RM treatment. Soil bacteria α diversity was not significantly different among different treatments. Spearman correlation analysis showed that the α diversity index was significantly negatively correlated with TC and TN. Lefse analysis revealed that 42 significant soil bacteria from phylum to genus were found in the two different thinning residue treatments. Redundancy analysis showed that soil TC and TN were the major drivers of variation in soil bacterial community structure. Overall, thinning residue retention increased the availability of resources to the soil bacterial community, thus changing bacterial community structure. This research provides a theoretical basis for the regulation of plantation forest soil fertility and quality.

Flood Pulse Irrigation of Meadows Shapes Soil Chemical and Microbial Parameters More Than Mineral Fertilization

While mineral fertilization increases agricultural yields, it also bears the risk of contaminating non-target ecosystems and negatively affecting soil chemical parameters and microbial communities. This calls for alternative and more sustainable agricultural practices that reduce the use of fertilizers. Flood pulse irrigation could be an alternative to mineral fertilization of hay meadows, since it increases the yield with little or no application of fertilizer. However, the positive and negative implications of flood pulse irrigation on soil chemical parameters and particularly soil microbial communities are still largely unknown. In this study, we assessed shifts in soil microbial communities (SMC) as a response to changes in soil chemical parameters after flood pulse irrigation and/or fertilization of meadows. We determined soil chemical (Corg, Ntot, water extractable N, P, K, pH) and microbial (phospholipid-derived fatty acids, PLFA) parameters of 12 meadows in a 2 × 2 factorial design, comprising flood pulse irrigation and fertilization. Corg, Ntot, and water content as well as microbial biomass were higher in flood-irrigated than in non-flooded soils. Soil microbial biomass positively correlated with Corg, Ntot, and water extractable N. Gram-negative bacteria significantly increased, whereas the fungi/bacteria ratio significantly decreased in flood-irrigated soils compared to non-flooded soils. Arbuscular mycorrhizal fungi were positively correlated with soil pH. Flood pulse irrigation seemed to promote the build-up of a larger soil carbon and nitrogen pool as well as higher water content and microbial biomass. By this, it potentially mitigated negative mineral fertilization effects such as changed soil pH and reduced carbon use efficiency. We conclude that flood pulse irrigation may represent a sustainable alternative to mineral fertilization.

Effect of land use on soil properties, microbial abundance and diversity of four different crop lands in central Myanmar

Changing land use systems impact on local edaphic factors and microbial abundance and diversity, however, the information on it in central Myanmar's soils is still lacking. Therefore, soils with four different land uses were analyzed; WAP (soil from perennial tree orchard), PNON (soil from crop rotation of peanut and onion), SESA (soil from mono-crop of sesame) and CHON (soil from mono-crop of onion for 3 years consecutively). Soil organic carbon (SOC), total nitrogen (TN), dissolved organic carbon (DOC), ammonium nitrogen (NH₄ ⁺-N) and pH showed the highest in PNON soil, which suggested crop rotation with high fertilizer input and irrigation had positive effect on the edaphic factors of soil. CHON soil showed the lowest in most soil properties and microbial abundance as a result of intensive use of fertilizer and irrigation, no crop rotation and no input of manures. Microbial community composition showed differences among tested soils and relative abundance of Chloroflexi was the highest in CHON soil whereas that of Basidiomycota was the highest in WAP soil. The abundances of bacteria and fungi were significantly affected by Olsen P, whereas the abundances of archaea were influenced by SOC. Our results suggested crop rotation and manure fertilization (PNON soil) enhanced soil properties and microbial abundance although long-time onion mono-crop (CHON soil) reduced soil fertility. This study can provide information to improve soil quality and sustainability of agro-ecosystems using appropriate agricultural management.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02705-y.

Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages

Background

Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored.

Methods

Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity.

Results

The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng.

Conclusion

Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-020-02081-2.

Effects of Chemical and Solar Soil-Disinfection Methods on Soil Bacterial Communities

The actctivated carbon + solar radiation membrane is an eco-friendly soil disinfestations method for managing soil-borne plant pathogens. However, little was known the impact of Activated carbon + solar radiation membrane on bacterial community structure in strawberry production systems under field conditions. A comprehensive evaluation of the impacts of different soil disinfection methods on the bacterial community structure is fundamental to understand the role of disinfection in maintaining soil health. The changes in the soil bacterial diversity and community composition were detected using realtime fluorescence quantitative PCR (RTFQ PCR) and next-generation sequencing techniques to better understand the effect of soil disinfection. The bacterial community composition was monitored after disinfection using dazomet (DZ), chloropicrin (CP), 100 kg/ha activated carbon + solar radiation membrane (AC1), 200 kg/ha activated carbon + solar radiation membrane (AC2), and 300 kg/ha activated carbon + solar radiation membrane (AC3) and compared with the control (CT). The results indicated that the different dosages of activated carbon (AC1, AC2, and AC3) did not affect the bacterial community structure. On the other hand, DZ and CP considerably reduced the soil biomass and abundance of bacterial species. Chemical fumigants influenced the bacterial community structure, with DZ treatment leading to the dominance of the phylum Firmicutes, accounting for approximately 54%. After fumigation with CP, Proteobacteria and Acidobacteria were the dominant phyla. Beta diversity analysis and principal coordinate analysis revealed that the bacterial communities in the soil treated with DZ and CP formed clusters. Redundancy analysis indicated that soil pH, available potassium, and available phosphorus were the key factors influencing microbial metabolic functional diversity. Thus, it was verified that the damage caused by activated carbon + solar radiation membrane—a potential alternative for chemical fumigant—to the soil bacterial community was less than that caused by chemicals DZ and CP.

From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential

Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization

An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers.

Urease activity and microbial biomass of carbon in hydrocarbon contaminated soils. A case study of cheshmeh-khosh oil field, Iran

Crude oil contamination in soils may result in destructive effects on soil microorganisms and plants and act as a source of groundwater contamination. The objective of this study was to evaluate the biological activities for a better understanding of ecological risks. A couple of biological assays, including soil microbial biomass of carbon (SMBC) and urease activity (UA), were used to evaluate the microbial activities in soils. The chemical analysis demonstrated different values of total petroleum hydrocarbons (TPHs) concentrations (from 0.12 to 2.99 mg/kg of dry soil) and relatively high quantities of Nickel (from 32 to 136.8 mg/kg of dry soil) and cadmium (from 0 to 4 mg/kg of dry soil) in samples. UA and SMBC values were comparatively lower in close distances to oil wells, pipelines, and especially drilling sediments pool. The spatial variability maps using the interpolation module by GIS specified the line from northwest to the southeast of the area as a more affected area by TPHs and Ni + Cd.

Trichloroethylene inhibits nitrogen transformation and microbial community structure in Mollisol

Trichloroethylene (TCE) is the most ubiquitous halogenated organic pollutant in the environment, it is one of the 129 priority control pollutants. In order to clarify the influence of TCE on microorganisms and nitrogen transformation in Mollisol is the core purpose of this study. Results showed that 10 mg kg^-1 TCE is the concentration limit of ammonification in Mollisol. When the concentration of TCE reached 10 mg kg^-1 and the effect lasted for over 7 days, the process of ammonia oxidation to nitric acid in Mollisol will be affected. TCE affected the process of nitrate (NO₃^-) transformation into nitrite (NO₂^-) by affecting the activity of nitrate reductase, thereby affected the denitrification process in soil. When the concentration of TCE is more than 10 mg kg^-1 it reduced the ability of soil microorganisms to obtain nitrogen, thereby affecting soil nitrogen transformation. RDA (Redundancy analysis) showed that the activity of nitrate reductase and the number of nitrifying bacteria and denitrifying bacteria in soil was negatively correlated with the incubation of TCE. In addition, soil nitrate reductase, nitrite reductase, peroxidase activity, ammonifying bacteria, nitrifying bacteria and denitrifying bacteria were negatively correlated with TCE concentration. Beyond that PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) of functional gene structure depend on KEGG (Kyoto Encyclopedia of Genes and Genomes) showed that 20 mg kg^-1 TCE significantly inhibited the metabolism of energy and other substances in Mollisol. Based on the above, it is found that TCE significantly affected nitrification and denitrification in Mollisol, thus the nitrogen transformation in Mollisol was affected by TCE contamination.

Evaluating the impact of turf-care products on soil biological health

Golf courses require extensive use of inputs to meet the needs of playability and aesthetics. The impact of these inputs on soil biological health is largely unknown. Two field trials were conducted at a golf course in Georgia to evaluate short-term effects of wetting agents (Cascade Plus and Duplex [C+D], Revolution [Rev]), plant growth regulators (PrimoMaxx [PM] and Cutless [CL]), and a product called PlantHelper (PH) on soil biological health by measuring microbial abundance and function. Quantitative polymerase chain reaction was used to measure microbial abundance, which included total bacteria, total fungi, and ammonia-oxidizing prokaryotes. Soil respiration and enzyme assays were used as additional indicators of soil health. In bentgrass putting green, total bacteria and ammonia-oxidizing bacteria decreased in abundance in response to the wetting agents and PH, indicating their sensitivity to the products. Whereas C+D stimulated urease activity, Rev and PH caused a short-lived but immediate increase in respiration, indicating that they acted as labile carbon sources. In a bermudagrass fairway, PM was the only product that caused an increase in total bacteria abundance. PrimoMaxx and CL caused a delayed increase in respiration, suggesting that they may have affected the microorganisms indirectly through their impact on root growth and exudate production later. Although CL caused a decrease in urease activity, none of the products significantly affected phosphatase activity. Overall, the products did not seem to have a lasting impact on soil biological health, although long-term studies are needed to confirm these observations.

Effects of soil heavy metal pollution on microbial activities and community diversity in different land use types in mining areas

Microbial activities and community structures play crucial roles in the soil environment and can be served as effective indicators to assess the ecological influence of heavy metal pollution in soil. This article selected soil samples from five land use types (mining area, mineral processing area, heap mining area, tailing area, and vegetable area) in the Shizishan mining area in Tongling, Anhui Province, China. The physicochemical properties, pollution characteristics, enzyme activities (catalase, urease, alkaline phosphatase, neutral phosphatase, cellulase, and sucrase), microbial biomass carbon (MBC), basal respiration (SBR), and metabolic entropy (qCO₂) in soil were determined and compared, and the relationship between environmental factors and the microbial activities and community diversity was analyzed. The results showed that, according to the Nemerow's Pollution Index (P_N), the values were the heap mining area (24.47) > mineral processing area (12.55) > mining area (9.81) > tailings area (6.02) > vegetable area (4.51). With the increase of heavy metal contamination in the sampling area, the six enzyme activities, MBC and SBR decreased, but the qCO₂ increased. Principal coordinate analysis (PCoA) and canonical correlation analysis (CCA) showed that the land use types, soil moisture content (MC), heavy metal content, pH, MBC, SBR, and qCO₂ were significantly affected by the microbial community. The most dominant phyla were Proteobacteria (34.73%), Bacteroidetes (9.25%), Acidobacteria (8.99%), and Chloroflexi (8.68%) at the phylum (0.01) level by a total of 18 phyla. It was also found that Firmicutes and Phormidium were more tolerant to heavy metals. These results contributed to an insight into key environmental variables shaping the microbial activities, community structure, and diversity under various land use types in mining area.

Seasonal Change in Microbial Diversity and Its Relationship with Soil Chemical Properties in an Orchard

This study aimed to determine the microbial diversity at different soil depths (0–5 and 5–20 cm) in a subtropical orchard during different seasons (i.e., spring, summer and autumn) to advance knowledge of the roles of microbes in orchard ecosystem balance. In tracking experiments conducted in an orchard (established in 1996), the phospholipid fatty acid (PLFA) biomarker method was employed to determine the soil microbial system. The total PLFA concentration did not vary significantly between soil depths but changed between seasons. It peaked in the summer at 258.97 ± 23.48 μg g soil^-1 from 0–5 cm and at 270.99 ± 58.94 μg g soil^-1 from 5–20 cm. A total of 33 microbial fatty acid biomarkers were observed and identified in the sampled soil. The quantities of PLFAs for 29 microbial groups varied significantly between seasons, except for 15:0 iso 3OH, 15:1 iso G, 16:0 2OH, and 17:0 iso 3OH. The bacterial PLFAs and fungal and actinomycetic PLFAs in the orchard soil collected in summer were significantly more abundant than those collected in the spring or autumn (P < 0.01). The number of soil microorganism species (richness) and the Simpson and Shannon-Wiener indexes were all highest in summer. The total PLFAs, bacterial PLFAs, fungal PLFAs, actinomycetic PLFAs, richness, and Simpson and Shannon-Wiener indexes were all significantly negatively correlated with soil pH, total organic carbon (TOC), total nitrogen (TN) and the cation exchange capacity (CEC) (P < 0.05).

The soil microbial community of turf: linear and nonlinear changes of taxa and N-cycling gene abundances over a century-long turf development

Turf, consisting of closely spaced grasses and the subtending soil, is a unique ecosystem subject to intense management. Yet soil organic matter accumulates quickly and reaches equilibrium after 20 to 50 years. Resource availability is an important driver of species richness and theoretically their relationship is expected to be unimodal. In this work, we examined the effects of turf development (i.e. a 1, 15, 20 and 109 year-old chronosequence) on microbial taxon richness, community composition, and abundances of genes putatively involved in N cycling through 16S rRNA gene and ITS region amplicon sequencing. Microbial alpha-diversity remained relatively stable although soil organic C and N increased by up to 3-fold over a century-long turf development. However, both bacterial and fungal community compositions changed substantially from those in the previous land use, pine stands and along turf development. Youngest turf was closer to the oldest turf than to middle-aged ones, specifically for bacterial community. Microbial changes to resource availability were also taxonomically specific. The relative abundance of Proteobacteria was independent of resource availability; Nitrospirae increased monotonically, and Bacteroidetes, Actinobacteria and Glomeromycota varied curvilinearly. However, abundances of most taxa from the phylum to operational taxonomic unit level and N-cycling genes varied nonlinearly with turf development.

Stoichiometric control on riparian wetland carbon and nutrient dynamics under different land uses

Riparian wetland provides important ecosystem function, such as water filtration and nutrient retention. When land use change in upland from native forest to sugarcane cultivation have important impacts on carbon (C) and nutrient availability in downstream wetland systems. Here, we examined concentrations and stoichiometry of C and nutrients in total, labile, biomass pools in upland soil, riparian wetland and sediment along two distinct transects (sugarcane versus forest). Sugarcane cultivation significantly reduced total C, nitrogen (N), labile C and N in riparian soils by 69%, 62%, 33% and 45%, respectively, but significantly increased NO₃^--N and δ¹⁵N by 99% and 56% in riparian areas. The presence of native forest resulted in significantly higher NH₄⁺-N concentrations in downstream wetlands. Concentrations of microbial biomass C and N were generally lower, but the abundance of genes associated with nitrifiers (ammonia oxidizing bacteria and archaea) was higher in the sugarcane transect than in the forest transect. These significantly differences between two transects could be attributed to different organic inputs and biogeochemical processes associated with the different vegetation types and management practices in the upland systems. Difference in δ¹³C signature from the two transects further confirmed the significant influence of vegetation type on downstream wetlands. Sugarcane cultivation led to a consistent stoichiometric shift in both resource and microbial biomass towards lower C:P and N:P ratios across upland soils, wetlands and sediment, compared with the forest transect. The average total and microbial biomass C:N:P ratios in soil under sugarcane were 136:9:1 and 180:33:1, respectively. The average total and microbial biomass C:N:P ratios in soil under forest were 410:22:1 and 594:76:1, respectively. It is concluded that since microbial demand of C and nutrients is driven by the stoichiometry of the biomass, which is regulated by the resource stoichiometry, a change of resource induced by upland land use change leads to a shift in the stoichiometry of microbial biomass C, N and P.

Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress

An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.

Significant Impacts of Both Total Amount and Availability of Heavy Metals on the Functions and Assembly of Soil Microbial Communities in Different Land Use Patterns

Land use change alters the accumulation of heavy metals (HMs) in soils and might have significant influence on the assembly and functions of soil microbial community. Although numerous studies have discussed the impacts of either total amounts or availability of metals on soil microbes in land change, there is still limited understanding on which one is more critical. In the present study, soils from three land use types (forest, mining field, and operating factory) located in Shaoguan city (Guangdong Province, China) were collected to investigate the impacts of soil HMs on soil enzyme activities and bacterial community structures. Mining activities remarkably increased the concentrations of HMs in soils, and land use patterns changed soil properties and nutrition level. Soil pH, total and available HMs (Cu, Pb, Zn, and Cd) and organic matters (SOM) were identified as the key influential factors shaping soil ecological functions (soil enzyme activities) and community assembly (bacterial community composition), explained by HMs accumulation and soil acidification caused by human activities. In addition, total amount and availability of some metals (Zn, Pb, Cu, and Cd) showed similar and significant effects on soil bacterial communities. Our findings provide new clues for reassessing the environmental risks of HMs in soils with different land use.

Effects of diet on gut microbiota of soil collembolans

The importance of diet in regulating the gut microbiome of globally distributed and functionally important soil generalist invertebrates such as collembolans remain poorly understood. Here, we studied a model collembolan (Folsomia candida) and found that diet (bacteria, plant litters, yeast, mixed food) is a critical factor in regulating the microbial diversity and community composition of this important soil organism. Collembolans fed with litter exhibited the lowest bacterial diversity and were dominated by Ochrobactrum. Conversely, collembolans fed with mixed diets resulted in the highest bacterial diversity. Our findings further suggest that microbial communities associated with different diets are linked to different levels of collembolan fitness. For example, the relative abundance of the genera of unclassified Thermogemmatisporaceae, Brevibacillus, and Novosphingobium were positively correlated with growth of the collembolans. Together, our work provides evidence that diet is a major force controlling the gut microbiome of collembolans, and is a good environmental predictor for collembolan growth, with implications for ecosystem functioning in terrestrial environments.

Hierarchical drivers of soil microbial community structure variability in "Monte Perdido" Massif (Central Pyrenees)

Microbial activity is highly dependent on climatic factors (moisture and temperature) and edaphic characteristics in temperate ecosystems. Moreover, soil microbial community composition in high mountain areas is less known when compared to plant communities. In this study we investigated the soil microbial community from a functional perspective using PLFA (phospholipid fatty acid) methods in the four aspects of four summits (2,242 – 3,012 m above sea level) in the Spanish Central Pyrenees. Soil organic carbon (C), microbial biomass and nutrient dynamics (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{H}_{4}^{+}$$\end{document}NH4+ + \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{O}_{3}^{-}$$\end{document}NO3−, N mineralization and nitrification potential) were also determined. Microbial biomass C was highest in the lowermost summit and decreased by approximately 50, 14 and 12% with increasing altitude. In each summit soil \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{H}_{4}^{+}$$\end{document}NH4+ and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{O}_{3}^{-}$$\end{document}NO3− concentrations differed significantly among summits and aspects. Soil nitrification potential varied significantly between the factors summit and aspects, e.g., southerly vs. northerly, easterly vs. westerly aspects. Gram negative bacteria and Actinobacteria functional groups dominated the microbial community, with almost 40% of the total PLFA. Non-metric multidimensional scale (NMS) analysis showed that most of the PLFA functional groups were present in all summits and aspects, although with specific biomarkers. A high abundance of biomarkers 16:1ω9c and 16:0 2OH (gram negative bacteria) were obtained in the lowermost summit, while the biomarkers 16.1ω7cDMA (anaerobes) and 19:3ω6c (Eukaryote) were only found in the uppermost summit. Linear mixed model (lmm) analysis was used with summit as fixed effect and aspect as random effect. In general, our results demonstrate a fundamental role for environment, principally moisture, temperature and organic matter in explaining the pattern observed for soil PLFA biomarkers. Under a global change scenario, we need to shed light on the relationships between soil microbial functional groups and soil nutrient-related variables in order to identify the associated patterns of decomposition rates and soil processes driven by microbial communities in mountain areas. The results could thus be used in global predictive models on climate change impact on C or N cycles in these environments.

Soil Microbial Communities and Enzyme Activities after Long-Term Application of Inorganic and Organic Fertilizers at Different Depths of the Soil Profile

Fertilization is a key factor for sustaining productivity in agroecosystems. A long-term experiment in cambisol following periodical application of several types of fertilization has been running at the experimental site since 1954. In this study, we determined the impact of applied inorganic and/or organic fertilizers on the activity of soil enzymes and on the structure of microorganisms at depths of 0–30 cm and 30–60 cm. Single-factor comparison showed that use of inorganic and/or organic fertilizer had an insignificant effect on the activities of soil enzymes (at depths 0–30 cm and 30–60 cm) and also on the structure of microbial communities at both depths studied. Only soil respirations exhibited stimulation by combined fertilization. The results, irrespective of sampling depth (0–60 cm), showed that application of combined organic and inorganic fertilization stimulated the activity of glucosidases and use of inorganic fertilizer inhibited the activity of arylsulphatases. Respirations were stimulated by application of organic fertilizer and combined fertilization. Nevertheless, principal component analyses, which calculate with multidimensional data, revealed differences in samples treated by sole mineral fertilizer compared to other variants, especially in the lower layer. In general, our results indicate that use of combined fertilization may improve biological characteristics in deeper parts of soil profile and possibly increase biological activity in agroecosystems.

Response of Soil Microbes to Vegetation Restoration in Coal Mining Subsidence Areas at Huaibei Coal Mine, China

Vegetation restoration is an available way to ameliorate degraded lands. In order to study the response of soil microbes to vegetation restoration in coal mining subsidence areas, the composition and distribution of soil microbes were discussed through three plots: unsubsided area (CA), new subsided area (NSA), and old subsided area (OSA) with different vegetation restoration time in Huabei coal mine. Meanwhile, changes in soil catalase and urease activity were explored and the correlation between soil bacteria, fungi, and environmental factors was analysed. The results demonstrated that Nitrospira was the dominant bacteria in all areas sampled. Microorganisms in the 0–20 cm and 40–60 cm soil layers of OSA had the highest Simpson index, whereas the index in NSA was lowest (at all soil depths). The catalase activity in NSA was significantly higher than that in CA, and there was no significant difference in catalase activity with soil depth, while the urease activity declined gradually with increasing soil depth. The urease activity in the 20–60 cm soil layer of NSA and OSA was significantly higher than that of CA. Furthermore, the distribution of bacteria was mainly affected by soil organic matter, available potassium, available phosphorus, and alkali-hydrolyzable nitrogen, whereas pH and catalase activity mainly affected fungal distribution. These results implied that soil catalase activity in NSA and urease activity in the 20–40 cm soil layer of NSA and OSA were significantly enhanced after vegetation restoration, and that long-term plant restoration could improve soil fertility and soil microbial community diversity in coal mining areas.

Restoration of Long-Term Monoculture Degraded Tea Orchard by Green and Goat Manures Applications System

Tea is an economic shrubby plant in tropical and subtropical regions of the world. To obtain high yield in tea cultivation, chemical fertilizer application rates have generally been used. However, a large quantity of chemical fertilizer application in a long-term continuously ratooned and monoculture tea orchard can inevitably lead to soil acidification and a decline in fertility. Therefore, the restoration of soil fertility and the sustainable development of tea planting by organic ways are critical for the tea industry. In this study, field trials were conducted in the tea orchard that was continuously ratooned and mono-cultured for 20 years. Nitrogen fertilizer (NF), Laredo soybeans green manure (LF), and goat manure (GM) treatments were applied to restore optimum acidity, soil fertility, microbial activity, and the community structure of a long-term continuously monoculture tea orchard. This paper investigated that the pH value was increased from 4.23 to 4.32 in GM and LF, respectively. Similarly, the content of exchangeable acidity (EA) was decreased by 1.21 and 1.46 cmol·kg−1 in GM and LF, respectively. Available nutrient results indicated that the content of NH4+-N was increased by 3.96, 4.38, NO3−-N by 1.07, 2.16, AP by 3.46, 6.86, AK by 0.26, 0.3 mg kg−1 in GM and LF treatments, respectively. Enzyme analysis revealed that the activity of urease and sucrase was promoted by 7.98 mg·g−1·24 h−1 and 6.77 mg·g−1·24 h−1, respectively, in LF treatment. Likewise, the activity of acid phosphatase and polyphenol oxidase was sharply increased by 2.3 mg·g−1 h−1 and 63.07 mg·g−1 h−1 in LF treatments. Additionally, the activity of urease, sucrase, acidic phosphatase, polyphenol oxidase, and peroxidase were also significantly increased by applying GM treatments. Meanwhile, LF and GM treatments significantly improved soil microbial biomass as well as low weight organic acid content in degraded tea rhizosphere. Furthermore, high throughput sequence results illustrated that the relative abundance of Rhizobiaceae and Bradyrhizobiaceae families increased in LF and GM treatments, respectively, which are mostly a kind of nitrogen fixer and plant growth promoting bacteria. Taken together, the physiological traits of the new sprouts and the biochemical components of new tea leaves were also significantly improved by GM and LF treatments. From this study, it is concluded that LF and GM are good agriculture management practices, which promote plant growth, yield, and nutrient availability by maintaining and improving pH, enhancing available nutrients status, improving the secretion of low molecular weight organic acids, and balancing the microbial community structure in the long-term mono-cultured tea orchard.

The cytochrome P450BM-1 of Bacillus megaterium A14K is induced by 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin: Biophysical, molecular and biochemical determinants

The current study describes biological changes in Bacillus megaterium A14K cells growing in the presence of 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin (TCDD), the most potent congener of dioxins. The results indicate that the metabolizing of 2,3,7,8-TCDD by BmA14K was accompanied with a novel morphological and biophysical profile typified by the growth of single cells with high levels of biosurfactant production, surface hydrophobicity and cell membrane permeability. Moreover, the TCDD-grown bacteria exhibited a specific fatty acid profile characterized by low ratios of branched/straight chain fatty acids (BCFAs/SCFAs) and saturated/unsaturated fatty acids (SFAs/USFAs) with a specific "signature" due to the presence of branched chain unsaturated fatty acids (BCUFAs). This was synchronized with a significant induction of P450_BM-1, an unsaturated fatty acid-metabolizing enzyme in B. megaterium. Subsequently, the profile of oxygenated fatty acids in the TCDD-grown bacteria was typified by the presence of 5,6-epoxy derived from unsaturated C15, C16 and C17 fatty acids, that were absent in control bacteria. A net increase was also detected in both hydroxylated and epoxidized fatty acids, especially those derived from C15:0 and C16:1, respectively, suggesting a specific TCDD-induced "signature" of oxygenated fatty acids in BmA14K. Overall, this study sheds light on the use of B. megaterium A14K as a promising bioindicator/biodegrader of dioxins.

Soil pH effects on the toxicity of zinc oxide nanoparticles to soil microbial community

We conducted an experiment with two agricultural soils with acidic and alkaline pH levels to assess the effects of zinc oxide nanoparticles (nZnO) on the bacterial community. The effect of the nZnO concentrations (0, 0.1, 1, 10, 100, 1000 mg Zn/kg soil) and contact time between nanoparticles and soil (180 days) was considered. We measured the microbial respiration rate, nitrogen transformation, enzymatic activities (dehydrogenase (DH), acidic phosphatase (ACP), and alkaline phosphatase (ALP)), and the community-level physiological profile (CLPP) soil parameters. Respiration potential and nitrogen transformation were negatively affected only at the highest nZnO concentration. The changes in enzymatic activities were very variable with time and between both soils. A stimulating effect of the nanoparticles on microbial activity was clearly shown at 30 days after the nZnO application in both soils, except for the 1000 mg/kg in calcareous soil, after which time in the latter, the functional richness of the bacterial community was reduced to virtually zero. However, values of the enzymatic activities demonstrated that there was self-adaptation of microbial communities over the study period (180 days). The nZnO 1000 mg/kg dose produced an increase in bacterial growth in the acidic soil, without apparent changes in their metabolic profiles over time. A good correlation was found between microbial respiration rates (calcareous and acidic soils) and microbial metabolic activity (acidic soil) based on extracted Zn concentrations. Our findings suggest the necessity of additional studies to examine the effects of nZnO in natural microorganism populations in soil with different pH levels for extended periods of time.

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.

Soil pH Is the Primary Factor Correlating With Soil Microbiome in Karst Rocky Desertification Regions in the Wushan County, Chongqing, China

Karst rocky desertification (KRD) is a process of land degradation, which causes desert-like landscapes, deconstruction of endemic biomass, and declined soil quality. The relationship of KRD progression with above-ground communities (e.g. vegetation and animal) is well-studied. Interaction of soil desertification with underground communities, such as soil microbiome, however, is vastly unknown. This study characterizes change in soil bacterial community in response to KRD progression. Soil bacterial communities were surveyed by deep sequencing of 16S amplicons. Eight soil properties, pH, soil organic matter (SOM), total and available nitrogen (TN and AN), total and available phosphorus (TP and AP), and total and available potassium (TK and AK), were measured to assess soil quality. We find that the overall soil quality decreases along with KRD progressive gradient. Soil bacterial community compositions are distinguishingly different in KRD stages. The richness and diversity in bacterial community do not significantly change with KRD progression although a slight increase in diversity was observed. A slight decrease in richness was seen in SKRD areas. Soil pH primarily correlates with bacterial community composition. We identified a core microbiome for KRD soils consisting of; Acidobacteria, Alpha-Proteobacteria, Planctomycetes, Beta-Proteobacteria, Actinobacteria, Firmicutes, Delta-Proteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Gemmatimonadetes in this study. Phylum Cyanobacteria is significantly abundant in non-degraded soils, suggesting that Cyanobacterial activities might be correlated to soil quality. Our results suggest that Proteobacteria are sensitive to changes in soil properties caused by the KRD progression. Alpha- and beta-Proteobacteria significantly predominated in SKRD compared to NKRD, suggesting that Proteobacteria, along with many others in the core microbiome (Acidobacteria, Actinobacteria, Firmicutes, and Nitrospirae), were active in nutrient limiting degraded soils. This study demonstrates the relationship of soil properties with bacterial community in KRD areas. Our results fill the gap of knowledge on change in soil bacterial community during KRD progression.

Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils

A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L^-1) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application. In contrast, dehydrogenase activity was stimulated in the 1000 μg treatment, and a stimulatory effect also occurred with soil respiration in contaminated soil. The metabolic profiles of the microbial communities indicated that overall carbon metabolic activity in the soils treated with high microcystin concentrations was inhibited, and high concentrations of microcystin also led to different patterns of potential carbon utilization. High microcystin concentrations (100, 1000 μg eq. MC-LR L^-1 in Soil A; 10, 100 1000 μg eq. MC-LR L^-1 in Soil B) significantly decreased soil potential nitrification rate. Furthermore, the decrease in soil potential nitrification rate was positively correlated with the decrease of the amoA gene abundance, which corresponds to the ammonia-oxidizing bacterial community. We conclude that application of microcystin-enriched irrigation water can significantly impact soil microbial community structure and function.

Contribution of aerobic anoxygenic phototrophic bacteria to total organic carbon pool in aquatic system of subtropical karst catchments, Southwest China: evidence from hydrochemical and microbiological study

Aerobic anoxygenic phototrophic bacteria may play a particular role in carbon cycling of aquatic systems. However, little is known about the interaction between aerobic anoxygenic phototrophic bacteria and hydrochemistry in groundwater-surface water exchange systems of subtropical karst catchments. We carried out a detailed study on the abundance of aerobic anoxygenic phototrophic bacteria and bacterioplankton, hydrochemistry and taxonomy of bacterioplankton in the Maocun watershed, Southwest China, an area with karst geological background. Our results revealed that bacteria are the important contributors to total organic carbon source/sequestration in the groundwater-surface water of this area. The aerobic anoxygenic phototrophic bacteria, including β-Proteobacteria, also appear in the studied water system. In addition to that, the genus Polynucleobacter of the phototropic β-Proteobacteria shows a close link with those sampling sites by presenting bacterial origin organic carbon on CCA biplot and is found to be positively correlated with total nitrogen, dissolved oxygen and pH (r = 0.860, 0.747 and 0.813, respectively) in the Maocun watershed. The results suggest that Polynucleobacter might be involved in the production of organic carbon and might act as the negative feedback on global warming.

Diversity and functional properties of acid-tolerant bacteria isolated from tea plantation soil of Assam

In this study, we report on the bacterial diversity and their functional properties prevalent in tea garden soils of Assam that have low pH (3.8-5.5). Culture-dependent studies and phospholipid fatty acid analysis revealed a high abundance of Gram-positive bacteria. Further, 70 acid-tolerant bacterial isolates characterized using a polyphasic taxonomy approach could be grouped to the genus Bacillus, Lysinibacillus, Staphylococcus, Brevundimonas, Alcaligenes, Enterobacter, Klebsiella, Escherichia, and Aeromonas. Among the 70 isolates, 47 most promising isolates were tested for their plant growth promoting activity based on the production of Indole Acetic Acid (IAA), siderophore, and HCN as well as solubilization of phosphate, zinc, and potassium. Out of the 47 isolates, 10 isolates tested positive for the entire aforesaid plant growth promoting tests and further tested for quantitative analyses for production of IAA, siderophore, and phosphate solubilization at the acidic and neutral condition. Results indicated that IAA and siderophore production, as well as phosphate solubilization efficiency of the isolates decreased significantly (P ≤ 0.05) in the acidic environment. This study revealed that low soil pH influences bacterial community structure and their functional properties.