Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling

Rhizosphere priming promotes plant nitrogen acquisition by microbial necromass recycling

Nitrogen availability in the rhizosphere relies on root-microorganism interactions, where root exudates trigger soil organic matter (SOM) decomposition through the rhizosphere priming effect (RPE). Though microbial necromass contribute significantly to organically bound soil nitrogen (N), the role of RPEs in regulating necromass recycling and plant nitrogen acquisition has received limited attention. We used 15N natural abundance as a proxy for necromass-N since necromass is enriched in 15N compared to other soil-N forms. We combined studies using the same experimental design for continuous 13CO2 labelling of various plant species and the same soil type, but considering top- and subsoil. RPE were quantified as difference in SOM-decomposition between planted and unplanted soils. Results showed higher plant N uptake as RPEs increased. The positive relationship between 15N-enrichment of shoots and roots and RPEs indicated an enhanced necromass-N turnover by RPE. Moreover, our data revealed that RPEs were saturated with increasing carbon (C) input via rhizodeposition in topsoil. In subsoil, RPEs increased linearly within a small range of C input indicating a strong effect of root-released C on decomposition rates in deeper soil horizons. Overall, this study confirmed the functional importance of rhizosphere C input for plant N acquisition through enhanced necromass turnover by RPEs.

Effects of γ-polyglutamic acid supplementation on alfalfa growth and rhizosphere soil microorganisms in sandy soil

This study aimed at exploring the effects of γ-polyglutamic acid on the growth of desert alfalfa and the soil microorganisms in the rhizosphere. The study examined the effects of varying concentrations of γ-polyglutamic acid (0%-CK, 2%-G1, 4%-G2, 6%-G3) on sandy soil, the research investigated its impact on the growth characteristics of alfalfa, nutrient content in the rhizosphere soil, and the composition of bacterial communities. The results indicated that there were no significant differences in soil organic matter, total nitrogen, total phosphorus, total potassium, and available phosphorus content among the G1, G2, and G3 treatments. Compared to CK, the soil nutrient content in the G2 treatment increased by 14.81-186.67%, showing the highest enhancement. In terms of alfalfa growth, the G2 treatment demonstrated the best performance, significantly increasing plant height, chlorophyll content, above-ground biomass, and underground biomass by 54.91-154.84%. Compared to the CK treatment, the number of OTUs (operational taxonomic units) in the G1, G2, and G3 treatments increased by 14.54%, 8.27%, and 6.84%, respectively. The application of γ-polyglutamic acid altered the composition and structure of the bacterial community, with Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota accounting for 84.14-87.89% of the total bacterial community. The G2 treatment significantly enhanced the diversity and evenness of soil bacteria in the rhizosphere. Redundancy analysis revealed that organic matter, total nitrogen, total potassium, moisture content, and pH were the primary factors influencing the structure of bacterial phyla. At the genus level, moisture content emerged as the most influential factor on the bacterial community. Notably, moisture content exhibited a strong positive correlation with Acidobacteriota, which in turn was positively associated with indicators of alfalfa growth. In summary, the application of γ-polyglutamic acid at a 4% ratio has the potential for improving sandy soil quality, promoting plant growth, and regulating the rhizosphere microbial community.

Phototrophic Biofilms Transform Soil-Dissolved Organic Matter Similarly Despite Compositional and Environmental Differences

Dissolved organic matter (DOM) is the most reactive pool of organic carbon in soil and one of the most important components of the global carbon cycle. Phototrophic biofilms growing at the soil-water interface in periodically flooding-drying soils like paddy fields consume and produce DOM during their growth and decomposition. However, the effects of phototrophic biofilms on DOM remain poorly understood in these settings. Here, we found that phototrophic biofilms transformed DOM similarly despite differences in soil types and initial DOM compositions, with stronger effects on DOM molecular composition than soil organic carbon and nutrient contents. Specifically, growth of phototrophic biofilms, especially those genera belonging to Proteobacteria and Cyanobacteria, increased the abundance of labile DOM compounds and richness of molecular formulae, while biofilm decomposition decreased the relative abundance of labile components. After a growth and decomposition cycle, phototrophic biofilms universally drove the accumulation of persistent DOM compounds in soil. Our results revealed how phototrophic biofilms shape the richness and changes in soil DOM at the molecular level and provide a reference for using phototrophic biofilms to increase DOM bioactivity and soil fertility in agricultural settings.

Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil

Carbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking 13 C from supplied carbon sources into metabolite pools and biomass.

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.

Bacterial Diversity and Potential Functions in Response to Long-Term Nitrogen Fertilizer on the Semiarid Loess Plateau

Bacterial diversity and its functions are essential to soil health. N fertilization changes bacterial communities and interferes with the soil biogeochemical N cycle. In this study, bacterial community and soil physicochemical properties were studied in 2018 after applying N fertilizers (0, 52.5, 105, 157.5, and 210 kg N ha⁻¹) for a long (2003–2018) and a short (2003–2004) duration in a wheat field on the Loess Plateau of China. Soil bacteria were determined using 16S rRNA Illumina-MiSeq^®, and the prediction function was analyzed through PICRUSt. The study showed that N fertilizer significantly changed the diversity and abundance of bacterial communities. The phyla Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were most abundant, accounting for 74–80% of the bacterial community abundance. The optimum rates of N fertilizer application (N105) maintain soil health by promoting soil microbial diversity and abundance. The bacterial population abundance was higher after short-term N application than after N application for a long duration and lowest with the high N-fertilizer treatment (N210). High N enrichment led to more heterotrophic N-fixing microorganisms (Alphaproteobacteria), in which metabolism and genetic information processing dominated, while cellular processes, genetic information processing, metabolism, and organismal systems were the main functional categories under low N. The phyla Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Chloroflexi were the key bacteria in the co-occurrence network. The genus Saccharimonadales of the superphylum Patescibacteria has a more significant impact under low N treatment. Long-term N fertilization affected the soil pH, NO₃-N, and other physicochemical properties, and soil NO₃-N was the highest indicator, contributing 81% of the bacterial community function under different N fertilizer treatments.

Effects of Conventional and Organic Agriculture on Soil Arbuscular Mycorrhizal Fungal Community in Low-Quality Farmland

Arbuscular mycorrhizal (AM) fungi have promising applications in low-quality farmlands all over the world, but research on their responses to conventional and organic farming systems in low-quality soil is limited. We hypothesized that the colonization activity and community diversity of AM fungi in conventional farming systems may not be lower than in organic farming on low-quality farmlands where beneficial symbiosis is required. We collected soil and maize root samples from medium to low fertility farmlands with conventional or organic farming systems in western Jilin Province, China. The colonization percentage and intensity, taxonomic and phylogenetic diversity, community composition of soil AM fungi, and soil factors were detected and compared between the two farming systems. The colonization intensity and operational taxonomic unit (OTU) taxonomic diversity on conventional farms were higher than on organic farms. Glomus was the most common genus on conventional farms, whereas Paraglomus and Glomus were the most common on organic farms. We also found a simpler AM fungal network structure with lower OTU phylogenetic diversity on conventional farms. Our findings suggested that though the conventional farming system resulted in different compositions and simpler structures of soil AM fungal community, there are potential diverse OTU resources currently present on conventional farms. This work has potential impacts on understanding the influence of different farming systems on soil AM fungi in low-quality farmlands and the development of efficient mycorrhizal inoculant production.

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.

The Proportion of Soil-Borne Fungal Pathogens Increases with Elevated Organic Carbon in Agricultural Soils

Soil-borne fungal phytopathogens are important threats to soil and crop health. However, their community composition and environmental determinants remain unclear. Here, we explored the effects of agricultural fertilization regime (i.e., organic material application) on soil fungal phytopathogens, using data sets from a combination of field survey and long-term experiment. We found that soil organic carbon was the key factor that affected the diversity and relative abundance of fungal phytopathogens in agricultural soils. The dominant genera of phytopathogens including Monographella was also strongly associated with soil organic carbon. In addition, the elevated soil organic carbon enhanced the node proportion of phytopathogens and the positive interactions within the fungal community in the network. Results of the long-term experiment revealed that applications of crop straw and fresh livestock manure significantly increased the proportion of phytopathogens, which were associated with the elevated soil organic carbon. This work offers new insights into the occurrence and environmental factors of fungal phytopathogens in agricultural soils, which are fundamental to control their impacts on the soil and crop systems. IMPORTANCE Fungal phytopathogens are important threats to soil and crop health, but their community composition and environmental determinants remain unclear. We found that soil organic carbon is the key factor of the prevalence of fungal phytopathogens through a field survey, which is also supported by our long-term (6-year) experiment showing the applications of crop straw and fresh livestock manure significantly increased the proportion of fungal phytopathogens. These findings advance our understanding of the occurrence and environmental drivers of soil-borne fungal phytopathogens under agricultural fertilization regime and have important implications for the control of soil-borne pathogens.

Intercropping Walnut and Tea: Effects on Soil Nutrients, Enzyme Activity, and Microbial Communities

The practice of intercropping, which involves growing more than one crop simultaneously during the same growing season, is becoming more important for increasing soil quality, land-use efficiency, and subsequently crop productivity. The present study examined changes in soil physicochemical properties, enzymatic activity, and microbial community composition when walnut (Juglans spp.) was intercropped with tea (Camellia sinensis L.) plants in a forest and compared with a walnut and tea monocropping system. The results showed that walnut–tea intercropping improved the soil nutrient profile and enzymatic activity. The soil available nitrogen (AN), available phosphorus (AP), available potassium (AK), organic matter (OM) content, and sucrase activity were significantly boosted in intercropped walnut and tea than in monocropping forests. The interaction between crops further increased bacterial and fungal diversity when compared to monoculture tea forests. Proteobacteria, Bacteroidetes, Firmicutes, Chlamydiae, Rozellomycota, and Zoopagomycota were found in greater abundance in an intercropping pattern than in monoculture walnut and tea forest plantations. The walnut–tea intercropping system also markedly impacted the abundance of several bacterial and fungal operational taxonomic units (OTUs), which were previously shown to support nutrient cycling, prevent diseases, and ameliorate abiotic stress. The results of this study suggest that intercropping walnut with tea increased host fitness and growth by positively influencing soil microbial populations.

Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.

Glucose addition promotes C fixation and bacteria diversity in C-poor soils, improves root morphology, and enhances key N metabolism in apple roots

The interaction between plant, soil and microorganism plays a crucial role in sustainable development of terrestrial ecosystem function and diversity. However, little information is known about how plant growth, soil organic carbon (C) fractions and microorganism respond to exogenous C addition in soils with low organic C content. Three levels of ¹³C-glucose (equal to 0, 100% and 500% of initial microbial biomass C) were added to non-sterilized (corresponding to treatment abbreviation of CK, Glu-1, Glu-2, respectively) and sterilized soils (corresponding to treatment abbreviation of SS, SS+Glu-1, SS+Glu-2, respectively) planted with apple rootstock (Malus baccata (L.) Borkh.) seedings. The objectives of this study were to analyse the dynamics of soil organic C (SOC) fractions and soil bacterial community diversity with glucose levels and soil sterilization, and to explore the morphology of roots and nitrogen (N) metabolism by plant after glucose addition to sterilized/non-sterilized soils. Results showed that the contents of labile organic C fractions were significantly varied (P<0.05) with the levels of glucose addition and soil sterilization. SS+Glu-2 and Glu-2 treatments increased the contents of labile organic C fractions, on average, by 48.47% and 35.33% compared with no glucose addition, respectively. About 21.42% and 16.17% of glucose-C remained in sterilized and non-sterilized soils, respectively at the end of experiment (day 45). Regardless of soil sterilized or not, the glucose addition increased the richness and diversity indices of soil bacterial community compared with no-glucose addition. The glucose addition optimized root zone conditions, and enhanced root vitality, morphology and biomass. Both SS+Glu-2 and Glu-2 treatments significantly enhanced (P<0.05) the contents of nitrate (NO₃^—N) and nitrite (NO₂^—N), but sharply decreased (P<0.05) the ammonium (NH₄⁺-N) content compared with no glucose addition. Also, these two treatments significantly (P<0.05) increased the enzymic activities and gene transcript levels involved in root N metabolism, which demonstrated that the high level of glucose addition promoted N assimilation and transformation into free amino acids by root. Overall, the addition of exogenous C to not only promotes its fixation and bacterial community diversity in C-poor soils, but also improves root morphology and N absorption by plant.

Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling

Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. We employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 d. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds composed of taxa that had similar 13C assimilation dynamics. We show that C-source bioavailability explained significant variation in both C mineralization dynamics and guild structure, and that the growth dynamics of bacterial guilds differed significantly in response to C addition. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. These results suggest that an understanding of in situ growth dynamics is essential for understanding microbial contributions to soil C cycling. We interpret these findings in the context of bacterial life history strategies and their relationship to terrestrial C cycling.

Soil Organic Carbon Enrichment Triggers In Situ Nitrogen Interception by Phototrophic Biofilms at the Soil-Water Interface: From Regional Scale to Microscale

Phototrophic biofilms are easy to grow at sediment/soil-water interfaces (SWIs) in shallow aquatic ecosystems and greatly impact nutrient biogeochemical cycles. However, the pathways by which they contribute to nitrogen interception and interact with sediment/soil remains largely unknown. Here, we conducted a field investigation in paddy fields in various regions of China and found that nitrogen immobilized in biofilm biomass significantly positively correlated with soil organic carbon (SOC) content. A microcosm experiment showed that this was due to increased bacterial and algal diversity, biomass accumulation, and inorganic nitrogen assimilation at high SOC, especially high dissolved organic carbon (DOC) levels. The metatranscriptomics results further verified that many KO groups of PSII, PSI, AP, and PC in antenna proteins and glutamate synthesis were distinctly expressed at elevated SOC and DOC levels. Our results elucidated the effects and possible pathways of how SOC enrichment triggers photosynthesis and nitrogen immobilization by phototrophic biofilms. The results will provide meaningful information for in situ nitrogen interception by using phototrophic biofilms at the SWI in human-made wetlands to change internal nitrogen cycling.

Conservation management improves agroecosystem function and resilience of soil nitrogen cycling in response to seasonal changes in climate

Understanding how conservation agricultural management improves soil nitrogen (N) stability in the face of climate change can help increase agroecosystem productivity and mitigate runoff, leaching and downstream water quality issues. We conducted a 2-year field study in a 36-year-old rain-fed cotton production system to evaluate the impacts of changing climatic factors (temperature and precipitation) on soil N under conservation management, including moderate inorganic N fertilizer application (0 and 67 kg N ha^-1), winter cover crops (fallow; winter wheat, Triticum aestivum L.; hairy vetch, Vicia villosa Roth), and reduced tillage (no-till; disk tillage). Structural equation modeling (SEM) was used to quantify and compare the effects of conservation management and climatic factors on soil N concentrations. Fertilizer and vetch cover crops increased soil total N concentration by 16% and 18%, respectively, and also increased microbial N transformation rate by 41% and 168%. In addition, vetch cover crops also increased soil labile N concentrations by 57%, 21%, and 79%, i.e., extractable organic N, ammonium, and nitrate, respectively. The highest soil δ¹⁵N value (6.4 ± 0.3‰) was observed under the 67 kg N ha^-1 fertilizer-wheat-disk tillage treatment, and the lowest value (4.8 ± 0.3‰) under the zero-fertilizer-wheat-no-till treatment, indicating fertilizer and tillage might accelerate microbial N transformation. The SEM showed positive effects of temperature and precipitation on labile N concentrations, suggesting destabilization of soil N and the potential for soil N loss under increased temperature and intensified precipitation. Fertilizer and vetch use might mitigate some of the effects of temperature by accelerating microbial N transformations, with vetch having a larger effect than fertilizer (0.35 vs. 0.15, Table 1). No-till can reduce some of the effects of precipitation on soil labile N by maintaining soil structure. Our study suggests that fertilizer, vetch cover crop, and no-till might help improve function and resilience of agroecosystems in relation to soil N cycling. Soil N stabilization in cropping systems can be enhanced by adjusting agricultural management.

Urbanization pressures alter tree rhizosphere microbiomes

The soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban-rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural-urban gradient indicate pH, Ca⁺, and organic matter are largely responsible for driving relative abundance of specific SMC members.

Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil

Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing ¹³C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most ¹³C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed ¹³C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and ¹³C labeling (i.e., partial labeling or labeling at later stages). Major ¹³C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.

Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota

Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics.

The relationship between bacterial diversity and organic carbon mineralization in soft rock and sand compound soil

The soil organic carbon (SOC) mineralization rate in sandy soil plays an important role in improving soil quality, and a research is needed to determine management practices that optimize the mineralization rate. When sandy soil is improved by adding soft rock, the specific promotion process of bacterium to SOC mineralization remain unclear. To investigate these mechanisms, we selected four treatments with soft rock to sand volume ratios of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3) to study. The mineralization rate of organic carbon was measured using the lye absorption method. High-throughput sequencing and scanning electron microscopy were used to determine the bacterial community structure and soil microstructure, respectively. The results showed that the organic carbon content of the sandy soil increased significantly (182.22-276.43%) after using the soft rock treatments. The SOC mineralization rate could be divided into two stages: a rapid decline during days 1-8 and a slow decline during days 8-60. With increased incubation time, the intensity of the cumulative release of organic carbon gradually weakened. Compared with the CK treatment, the SOC mineralization accumulation (Ct) and the potential mineralizable organic carbon content (C₀) in the C1, C2, and C3 treatments increased significantly, by 106.98-225.94% and 112.22-254.08%, respectively. The cumulative mineralization rate (Cr) was 18.11% and 21.38% smaller with treatments C2 and C3, respectively. The SOC mineralization rate constant (k) decreased significantly after the addition of soft rock, while the half-turnover period (Th) changed inversely with k. Compared with the CK treatment, the number of gene copies of the soil bacteria increased by 15.38-272.53% after adding soft rock, with the most significant increase in treatment C3. The bacterial diversity index also increased significantly under treatment C3. The three dominant bacteria were Proteobacteria, Actinobacteria, and Chloroflexi. The correlation between C_r and one of the non-dominant bacteria, Firmicutes, was large, and the bacteria had a significant positive correlation with k. At the same time, the abundance of Firmicutes under treatments C2 and C3 was small. As the proportion of soft rock increased, the soil particles changed from point contact to surface contact, and the adhesion on the surface of the particles gradually increased. Results from this study show that the retention time of SOC can be increased and the carbon sequestration effect is better when the ratio of soft rock to sand is set to 1:2.

Response of organic carbon mineralization and bacterial communities to soft rock additions in sandy soils

Bacteria play a vital role in biotransformation of soil organic carbon (SOC). However, mechanisms of bacterium and organic carbon mineralization remain unclear during improvement of sandy soil using soft rock additions. In this study, four treatments with differing ratios of soft rock to sand of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3) were selected for mineralization incubation and high-throughput sequencing. The results showed that SOC, total nitrogen (TN), available phosphorus (AP), nitrate nitrogen (NO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{3}^{-}$\end{document}3−-N), and mass water content (WC) of sandy soil increased significantly after addition of soft rock (P < 0.05). Compared with the CK treatment, cumulative mineralization and potential mineralized organic carbon content of C1, C2 and C3 increased by 71.79%–183.86% and 71.08%–173.33%. The cumulative mineralization rates of organic carbon treated with C1 and C2 were lower, 16.96% and 17.78%, respectively (P > 0.05). The three dominant bacteria were Actinobacteria, Proteobacteria and Chloroflexi, among which Proteobacteria was negatively correlated with mineralization of organic carbon (P < 0.01). The mineralization rate constant (k) was positively correlated and negatively correlated with Cyanobacteria and Nitrospirae, respectively. Under C2 treatment, Proteobacteria and Nitrospirae had the largest increase, and Cyanobacteria had the largest decrease. Compared with other treatments, C2 treatment significantly increased bacterial diversity index, richness index and evenness index, and the richness index had a negative correlation with k value. In conclusion, when the ratio of soft rock to sand was 1:2, the k of SOC could be reduced. In addition, the retention time of SOC can be increased, and resulting carbon fixation was improved.

Plant growth rate and nitrogen uptake shape rhizosphere bacterial community composition and activity in an agricultural field

Plant-microbial interactions in the rhizosphere are an essential link in soil nitrogen (N) cycling and plant N supply. Plant phenotype and genotype interact with the soil environment to determine rhizosphere community structure and activity. However, the relative contributions of plant identity, phenology and soil resource availability in shaping rhizosphere effects are not well understood. Four summer annuals and a collection of maize hybrids were grown in a common garden experiment conducted at two levels of organic nutrient availability. Plant biomass, N accumulation, rhizosphere bacterial community composition, and rhizosphere potential extracellular enzyme activity were assessed at vegetative, flowering and grain-filling stages of maize. Plant N uptake was strongly coupled with protease activity in the rhizosphere. Temporal trends in rhizosphere community composition varied between plant species. Changes in rhizosphere community composition could be explained by variation in plant growth dynamics. These findings indicate that species-level variation in plant growth dynamics and resource acquisition drive variation in rhizosphere bacterial community composition and activity linked to plant N uptake.

Soil characteristics and land-use drive bacterial community assembly patterns

Land-use and soil characteristics drive variation in soil community composition, but the influences of these factors on dispersal and community assembly at regional scale remain poorly characterized. Land-use remains a consistent driver of soil community composition even when exhibiting patchy spatial distribution at regional scale. In addition, disturbed and early successional soils often exhibit stochastic community assembly patterns. These observations suggest local community composition is influenced by dispersal and assembly from regional species pools. We examined bacterial community assembly within agricultural cropland, old-field, and forested sites across 10 landscapes in the region around Ithaca, New York (USA). We found that the Sloan neutral model explained assembly well at regional scale (R2 = 0.763), but that both soil pH and land-use imposed selection that shaped community composition. We show that homogeneous selection was a dominant assembly process with respect to both soil pH and land-use regime, but that these two factors interacted in their effects on bacterial community assembly. We conclude that bacterial community assembly at a regional scale is driven by dispersal from regional species pools and local selection on the basis of soil pH and other soil characteristics that vary with land-use.

Feedbacks between nitrogen fixation and soil organic matter increase ecosystem functions in diversified agroecosystems

Nitrogen (N) losses from intensified agriculture are a major cause of global change, due to nitrate (NO₃^- ) export and the eutrophication of aquatic systems as well as emissions of nitrous oxide (N₂ O) into the atmosphere. Diversified agroecosystems with legume cover crops couple N and carbon (C) inputs to soil and reduce N pollution, but there is a need to identify controls on legume N₂ fixation across ecosystems with variable soil conditions. Here, I tested the hypothesis that N mineralization from turnover of soil organic matter (SOM) regulates legume N₂ fixation across 10 farms that spanned a gradient of SOM levels. I separated soil samples into two SOM fractions, based on size and density, which are indicators of soil nutrient cycling and N availability (free particulate organic matter and intra-aggregate particulate organic matter [POM]). This study indicates downregulation of legume N₂ fixation in diversified agroecosystems with increasing N availability in intra-aggregate POM and increasing N mineralization. Intercropping the legume with a grass weakened the relationship between N in POM and N₂ fixation due to N assimilation by the grass. Further, mean rates of N and C mineralization across sites increased with two seasons of a legume-grass cover crop mixture, which could enhance this stabilizing feedback between soil N availability and N₂ fixation over time. These results suggest a potential mechanism for the diversity-ecosystem-function relationships measured in long-term studies of agroecosystems, in which regular use of legume cover crops increases total soil organic C and N and reduces negative environmental impacts of crop production.

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO₃-N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity.IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.

Factors governing extracellular DNA degradation dynamics in soil

We examined the impacts of soil moisture, temperature, agricultural management and habitat type on the degradation dynamics of eDNA in soils. Synthetic eDNA was added to soil microcosms, and its disappearance over time was measured using both high-throughput sequencing and qPCR. The synthetic eDNA was degraded rapidly, but a small fraction remained detectable throughout the experiments (39-80 days). The eDNA degradation rate was positively correlated with moisture and temperature, but negatively correlated with soil organic carbon content. End-point stabilization of eDNA was highest at low moisture and temperature, but exhibited no relationship with soil organic carbon. Tilled soils had higher rates of degradation and less stabilization than no-till soils. Among different habitats we observed that forest soils had the slowest degradation rate, and meadow soils had the greatest stabilization of eDNA. While eDNA was detectable by qPCR in all treatments across all time-points, it became inconsistently detectable with high-throughput gene sequencing in less than 1 week. We conclude that eDNA degradation and stabilization dynamics vary with moisture, temperature and habitat characteristics, that small amounts of eDNA may persist in soils indefinitely, and that the ability of persistent eDNA to impact microbial community estimates depends on method sensitivity and experimental objectives.

Effects of permafrost collapse on soil bacterial communities in a wet meadow on the northern Qinghai-Tibetan Plateau

Background

Permafrost degradation may develop thermokarst landforms, which substantially change physico–chemical characteristics in the soil as well as the soil carbon stock. However, little is known about changes of bacterial community among the microfeatures within thermokarst area.

Results

We investigated bacterial communities using the Illumina sequencing method and examined their relationships with soil parameters in a thermokarst feature on the northern Qinghai-Tibetan Plateau. We categorized the ground surface into three different micro-relief patches based on the type and extent of permafrost collapse (control, collapsing and subsided areas). Permafrost collapse significantly decreased the soil carbon density and moisture content in the upper 10 cm samples in the collapsing areas. The highest loading factors for the first principal component (PC) extracted from the soil parameters were soil carbon and nitrogen contents, while soil moisture content and C:N ratios were the highest loading factors for the second PC. The relative abundance of Acidobacteria decreased with depth. Bacterial diversity in subsided areas was higher than that in control areas.

Conclusions

Bacterial community structure was significantly affected by pH and depth. The relative abundance of Gemmatimonadetes and Firmicutes were significantly correlated with the first and second PCs extracted from multiple soil parameters, suggesting these phyla could be used as indicators for the soil parameters in the thermokarst terrain.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0183-y) contains supplementary material, which is available to authorized users.

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field

Rhizosphere microbial communities are critically important for soil nitrogen cycling and plant productivity. There is evidence that plant species and genotypes select distinct rhizosphere communities, however, knowledge of the drivers and extent of this variation remains limited. We grew 11 annual species and 11 maize (Zea mays subsp. mays) inbred lines in a common garden experiment to assess the influence of host phylogeny, growth, and nitrogen metabolism on rhizosphere communities. Growth characteristics, bacterial community composition and potential activity of extracellular enzymes were assayed at time of flowering, when plant nitrogen demand is maximal. Bacterial community composition varied significantly between different plant species and genotypes. Rhizosphere beta-diversity was positively correlated with phylogenetic distance between plant species, but not genetic distance within a plant species. In particular, life history traits associated with plant resource acquisition (e.g., longer lifespan, high nitrogen use efficiency, and larger seed size) were correlated with variation in bacterial community composition and enzyme activity. These results indicate that plant evolutionary history and life history strategy influence rhizosphere bacterial community composition and activity. Thus, incorporating phylogenetic or functional diversity into crop rotations may be a tool to manipulate plant-microbe interactions in agricultural systems.

Distinct respiratory responses of soils to complex organic substrate are governed predominantly by soil architecture and its microbial community

Factors governing the turnover of organic matter (OM) added to soils, including substrate quality, climate, environment and biology, are well known, but their relative importance has been difficult to ascertain due to the interconnected nature of the soil system. This has made their inclusion in mechanistic models of OM turnover or nutrient cycling difficult despite the potential power of these models to unravel complex interactions. Using high temporal-resolution respirometery (6 min measurement intervals), we monitored the respiratory response of 67 soils sampled from across England and Wales over a 5 day period following the addition of a complex organic substrate (green barley powder). Four respiratory response archetypes were observed, characterised by different rates of respiration as well as different time-dependent patterns. We also found that it was possible to predict, with 95% accuracy, which type of respiratory behaviour a soil would exhibit based on certain physical and chemical soil properties combined with the size and phenotypic structure of the microbial community. Bulk density, microbial biomass carbon, water holding capacity and microbial community phenotype were identified as the four most important factors in predicting the soils' respiratory responses using a Bayesian belief network. These results show that the size and constitution of the microbial community are as important as physico-chemical properties of a soil in governing the respiratory response to OM addition. Such a combination suggests that the 'architecture' of the soil, i.e. the integration of the spatial organisation of the environment and the interactions between the communities living and functioning within the pore networks, is fundamentally important in regulating such processes.

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols

Changes in microbial community structure are widely known to occur after soil amendment with low-molecular-weight organic compounds; however, there is little information on concurrent changes in soil microbial functional diversity and enzyme activities, especially following sorbitol and mannitol amendment. Soil microbial functional diversity and enzyme activities can be impacted by sorbitol and mannitol, which in turn can alter soil fertility and quality. The objective of this study was to investigate the effects of sorbitol and mannitol addition on microbial functional diversity and enzyme activities. The results demonstrated that sorbitol and mannitol addition altered the soil microbial community structure and improved enzyme activities. Specifically, the addition of sorbitol enhanced the community-level physiological profile (CLPP) compared with the control, whereas the CLPP was significantly inhibited by the addition of mannitol. The results of a varimax rotated component matrix demonstrated that carbohydrates, polymers, and carboxylic acids affected the soil microbial functional structure. Additionally, we found that enzyme activities were affected by both the concentration and type of inputs. In the presence of high concentrations of sorbitol, the urease, catalase, alkaline phosphatase, β-glucosidase, and N-acetyl-β-d-glucosaminidase activities were significantly increased, while invertase activity was decreased. Similarly, this increase in invertase, catalase, and alkaline phosphatase and N-acetyl-β-d-glucosaminidase activities was especially evident after mannitol addition, and urease activity was only slightly affected. In contrast, β-glucosidase activity was suppressed at the highest concentration. These results indicate that microbial community diversity and enzyme activities are significantly affected by soil amendment with sorbitol and mannitol.

Soil C and N models that integrate microbial diversity

Industrial agriculture is yearly responsible for the loss of 55-100 Pg of historical soil carbon and 9.9 Tg of reactive nitrogen worldwide. Therefore, management practices should be adapted to preserve ecological processes and reduce inputs and environmental impacts. In particular, the management of soil organic matter (SOM) is a key factor influencing C and N cycles. Soil microorganisms play a central role in SOM dynamics. For instance, microbial diversity may explain up to 77 % of carbon mineralisation activities. However, soil microbial diversity is actually rarely taken into account in models of C and N dynamics. Here, we review the influence of microbial diversity on C and N dynamics, and the integration of microbial diversity in soil C and N models. We found that a gain of microbial richness and evenness enhances soil C and N dynamics on the average, though the improvement of C and N dynamics depends on the composition of microbial community. We reviewed 50 models integrating soil microbial diversity. More than 90 % of models integrate microbial diversity with discrete compartments representing conceptual functional groups (64 %) or identified taxonomic groups interacting in a food web (28 %). Half of the models have not been tested against an empirical dataset while the other half mainly consider fixed parameters. This is due to the difficulty to link taxonomic and functional diversity.

Diversity Enhances NPP, N Retention, and Soil Microbial Diversity in Experimental Urban Grassland Assemblages

Urban grasslands, landscapes dominated by turfgrasses for aesthetic or recreational groundcovers, are rapidly expanding in the United States and globally. These managed ecosystems are often less diverse than the natural or agricultural lands they replace, leading to potential losses in ecosystem functioning. Research in non-urban systems has provided evidence for increases in multiple ecosystem functions associated with greater plant diversity. To test if biodiversity-ecosystem function findings are applicable to urban grasslands, we examined the effect of plant species and genotypic diversity on three ecosystem functions, using grassland assemblages of increasing diversity that were grown within a controlled environment facility. We found positive effects of plant diversity on reduced nitrate leaching and plant productivity. Soil microbial diversity (Mean Shannon Diversity, H') of bacteria and fungi were also enhanced in multi-species plantings, suggesting that moderate increments in plant diversity influence the composition of soil biota. The results from this study indicate that plant diversity impacts multiple functions that are important in urban ecosystems; therefore, further tests of urban grassland biodiversity should be examined in situ to determine the feasibility of manipulating plant diversity as an explicit landscape design and function trait.

Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either (13)C-xylose or (13)C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for (13)C-incorporation into DNA from (13)C-xylose and (13)C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated (13)C in the (13)C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These (13)C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes.

Effects of Land Use Changes from Paddy Fields on Soil Bacterial Communities in a Hilly and Mountainous Area

Soil bacterial community structures in terraced rice fields and abandoned lands in a hilly and mountainous area were analyzed using 16S rRNA gene sequences. The DGGE band patterns of each soil were similar. Based on pyrosequencing data, the richness and diversity of bacterial species were slightly higher in paddy fields than in other soils. A beta-diversity analysis clearly indicated that the bacterial community structure in paddy fields differed from those in non-paddy field lands and crop fields that had not been used as a paddy field. These results may reflect the history of land use.

Changes of diet and dominant intestinal microbes in farmland frogs

BACKGROUND

Agricultural activities inevitably result in anthropogenic interference with natural habitats. The diet and the gut microbiota of farmland wildlife can be altered due to the changes in food webs within agricultural ecosystems. In this work, we compared the diet and intestinal microbiota of the frog Fejervarya limnocharis in natural and farmland habitats in order to understand how custom farming affects the health of in vivo microbial ecosystems.

RESULTS

The occurrence, abundance, and the numbers of prey categories of stomach content were significantly different between the frogs inhabiting natural and farmland habitats. In addition, differences in the abundance, species richness, and alpha-diversity of intestinal microbial communities were also statistically significant. The microbial composition, and particularly the composition of dominant microbes living in intestines, indicated that the land use practices might be one of factors affecting the gut microbial community composition. Although the first three dominant microbial phyla Bacteroidetes, Firmicutes, and Proteobacteria found in the intestines of frogs were classified as generalists among habitats, the most dominant gut bacterial phylum Bacteroidetes in natural environments was replaced by the microbial phylum Firmicutes in farmland frogs. Increased intestinal microbial richness of the farmland frogs, which is mostly contributed by numerous microbial species of Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, not only reflects the possible shifts in microbial community composition through the alteration of external ecosystem, but also indicates the higher risk of invasion by disease-related microbes.

CONCLUSIONS

This study indicates that anthropogenic activities, such as the custom farming, have not only affected the food resources of frogs, but also influenced the health and in vivo microbial ecosystem of wildlife.

Long-term oil contamination causes similar changes in microbial communities of two distinct soils

Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of contamination.

Bacterial Community Features Are Shaped by Geographic Location, Physicochemical Properties, and Oil Contamination of Soil in Main Oil Fields of China

Geographic location and physicochemical properties are thought to represent major factors that shape soil bacterial community abundance and diversity. Crude oil contamination is becoming a notable concern with respect to soil property variation; however, the quantifiable influences of geographic location, physicochemical properties, and oil contamination are still poorly understood. In this study, the 16S ribosomal RNA genes of bacteria in the four oil fields in China were analyzed by using pyrosequencing. Results showed that physicochemical properties were the most dominant factor of bacterial community distribution, followed by geographical location. Oil contamination was a driving factor whose indirect influence was stronger than its direct influence. Under the impact of these three factors, different oil fields presented diversified and distinguishable bacterial community features. The soil of sites with the highest total petroleum hydrocarbon content (HB), nitrogen content (DQ), and phosphorus content (XJ) contained the largest proportion of functional groups participating in hydrocarbon degradation, nitrogen turnover, and phosphorus turnover, respectively. The first dominant phylum of the site with loam soil texture (HB) was Actinobacteria instead of Proteobacteria in other sites with sandy or sandy loam soil texture (DQ, SL, XJ). The site with the highest salinization and alkalization (SL) exhibited the largest proportion of unique local bacteria. The site that was located in the desert with extremely low precipitation (XJ) had the most diversified bacteria distribution. The bacterial community diversity was strongly influenced by soil physicochemical properties.

Differences in Arbuscular Mycorrhizal Fungal Community Composition in Soils of Three Land Use Types in Subtropical Hilly Area of Southern China

Land use type is key factor in restoring the degraded soils due to its impact on soil chemical properties and microbial community. In this study, the influences of land use type on arbuscular mycorrhizal fungal (AMF) community and soil chemical properties were assessed in a long-run experimental station in subtropical hilly area of southern China. Soil samples were collected from forest land, orchard and vegetable field. Soil chemical properties were analyzed, and PCR-DGGE was performed to explore the AMF community structure. Cloning and sequencing of DGGE bands were conducted to monitor AMF community composition. Results indicate that the contents of total P, available P and available K were the highest while the contents of soil organic matter, total N, total K and available N were the lowest in vegetable field soils, with forest land soils vice versa. According to DGGE profiling, AMF community in forest soils was more closely related to that in orchard soils than that in vegetable field soils. Sequencing indicated that 45 out of 53 excised bands were AMF and 64.4% of AMF belonged to Glomeraceae, including some “generalists” present in all soils and some “specialists” present only in soils of particular land use. Category principle component analysis demonstrated that total N, soil organic matter and available P were the most important factors affecting AMF community, and some AMF phylotypes were closely associated with particular soil chemical properties. Our data suggest that AMF communities are different with different land use types.

Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems

Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil microbiotic properties. More research will expand our understanding of combined effects of these alternatives on feedbacks between soil microbiotic properties and SOC accrual.

Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity

Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.