Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling

Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes

The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.

Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land management

The soil bacterial community is critical for understanding biological processes in soils and is used for agricultural soil management. The understanding of microorganisms and ecology in different soil groups classified based on soil properties (e.g., minerals, soil texture, location, nitrogen, phosphorus, organic carbon and pH, among others), is limited. To suggest soil management strategies using bacterial data, we classified soils into four groups based on physical-chemical characteristics and elucidated their relationships with soil nutrient characteristics and the bacterial community in agricultural fields in Saraburi Province, Thailand. Results show that soil groups with high bacterial diversity had positive correlations with total Kjeldahl nitrogen and available phosphorus but were negatively affected by total organic carbon and pH levels. Dominant bacterial genera included Lactobacillus, Phascolarctobacterium, Prevotella, Clostridium, Gaiellales and Blautia. Significant key biomarkers were found (p < 0.05). Nutrient-rich soil groups (high available P, acidic pH) were found with genus Agromyces, while low nutrient soil groups (low available P, basic pH) were found with Hydrogenispora, Ignavibacterium and Bauldia. Based on co-occurrence networks, organic degrading bacteria functioned with other bacteria at high degrees of interconnections, suggesting organic amendment, biostimulation and biodegradation using nutrient-rich organic substrates could be used for agricultural soil improvements.

Combined System of Organic Substrate and Straw-Degrading Microbial Agents Improved Soil Organic Matter Levels and Microbial Abundance in a Rice-Wheat Rotation

Rice-wheat rotation is one of the most intensive agricultural planting modes in China and is pivotal to develop optimized straw-returning management in situ to improve soil fertility and productivity in agricultural ecosystems. Previous studies have mainly focused on the effects of straw return with a single application of organic fertilizers. The integrated management of different fertilizers in improving the management of straw return in situ is not well known. In this study, a field experiment was conducted from 2017 to 2019 to explore the effects of a combined system of modified organic substrate (MOS) and straw-degrading compound microbial agent (CMA) on soil physiochemical properties, labile organic carbon, microbial activities, and soil microbial community composition under the background of direct crop straw return and chemical fertilizer utilization. Four treatments were designed: (1) control check; (2) CMA; (3) MOS; and (4) MOS + CMA. The results showed that the MOS + CMA treatment had the combined advantages of soil organic matter (SOM) accumulation, soil nutrient increase and soil microbial community alteration, which may be more suitable for improving the quality and fertility of sandy loam soil. This study provides novel insights for further understanding the effects of organic substrates and composite microbial agents on SOM changes and microbial community composition and function in the field, which has important implications for sustainable crop production and agricultural development.

Comparison of the Responses of Soil Fungal Community to Straw, Inorganic Fertilizer, and Compost in a Farmland in the Loess Plateau

The Loess Plateau is located in the arid and semi-arid regions in northern China. The ecosystem is particularly sensitive to natural and anthropogenic disturbances. Fungi can produce extracellular enzymes, decompose a variety of organic matter, and regulate carbon and nutrient balance. We studied the changes of soil fungal community compositions in response to straw, inorganic fertilizer, and compost in a typical farmland in the Loess Plateau. Our results demonstrated that the addition of straw significantly reduces the Shannon index of the fungal community, in addition, the participation of straw significantly affects the composition of the fungal community. Functional prediction based on FUNGuild showed that straw significantly reduced the relative abundance of saprotrophs, pathotrophs, symbiotrophs, lichenized, ectomycorrhizal, and plant pathogens. Although fertilization practices destroyed the co-occurrence pattern among the fungal species, the addition of straw alleviated this affect. No significant effect of straw, compost, and inorganic fertilizers on the co-occurrence pattern among species in the soil fungal community was observed. Compared with compost and inorganic fertilizer, the addition of straw shaped the community composition by changing the relative abundance of fungal functional taxa. Thus, in the fragile Loess Plateau environment, over-fertilizing or non-order-fertilizing may destroy the co-occurrence pattern of the fungal communities and Loess Plateau ecosystem. IMPORTANCE Determining the response of soil fungi in sensitive ecosystems to external environmental disturbances is an important, yet little-known, topic in microbial ecology. In this study, we evaluated the impact of traditional fertilization management practices on the composition, co-occurrence pattern, and functional groups of fungal communities in loessial soil. Our results show that in the fragile Loess Plateau environment, fertilizer management changed the composition of the fungal community and disrupted the co-occurrence pattern between fungi. The application of straw alleviates the destroying of the co-occurrence pattern. The current research emphasizes the necessity of rational fertilization of farmland in loessial soil.

Dynamic changes of rhizosphere soil bacterial community and nutrients in cadmium polluted soils with soybean-corn intercropping

BACKGROUND

Soybean-corn intercropping is widely practised by farmers in Southwest China. Although rhizosphere microorganisms are important in nutrient cycling processes, the differences in rhizosphere microbial communities between intercropped soybean and corn and their monoculture are poorly known. Additionally, the effects of cadmium (Cd) pollution on these differences have not been examined. Therefore, a field experiment was conducted in Cd-polluted soil to determine the effects of monocultures and soybean-corn intercropping systems on Cd concentrations in plants, on rhizosphere bacterial communities, soil nutrients and Cd availability. Plants and soils were examined five times in the growing season, and Illumina sequencing of 16S rRNA genes was used to analyze the rhizosphere bacterial communities.

RESULTS

Intercropping did not alter Cd concentrations in corn and soybean, but changed soil available Cd (ACd) concentrations and caused different effects in the rhizosphere soils of the two crop species. However, there was little difference in bacterial community diversity for the same crop species under the two planting modes. Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria and Firmicutes were the dominant phyla in the soybean and corn rhizospheres. In ecological networks of bacterial communities, intercropping soybean (IS) had more module hubs and connectors, whereas intercropped corn (IC) had fewer module hubs and connectors than those of corresponding monoculture crops. Soil organic matter (SOM) was the key factor affecting soybean rhizosphere bacterial communities, whereas available nutrients (N, P, K) were the key factors affecting those in corn rhizosphere. During the cropping season, the concentration of soil available phosphorus (AP) in the intercropped soybean-corn was significantly higher than that in corresponding monocultures. In addition, the soil available potassium (AK) concentration was higher in intercropped soybean than that in monocropped soybean.

CONCLUSIONS

Intercropped soybean-corn lead to an increase in the AP concentration during the growing season, and although crop absorption of Cd was not affected in the Cd-contaminated soil, soil ACd concentration was affected. Intercropped soybean-corn also affected the soil physicochemical properties and rhizosphere bacterial community structure. Thus, intercropped soybean-corn was a key factor in determining changes in microbial community composition and networks. These results provide a basic ecological framework for soil microbial function in Cd-contaminated soil.

Effects of Biogas Slurry Combined With Chemical Fertilizer on Soil Bacterial and Fungal Community Composition in a Paddy Field

The application of biogas slurry and chemical fertilizer in paddy fields can be a practical method to reduce the environmental risk and utilize the nutrients of biogas slurry. The responses of bacterial and fungal communities to the application of biogas slurry and chemical fertilizer are important reflections of the quality of the ecological environment. In this study, based on a 3-year field experiment with different ratios of biogas slurry and chemical fertilizer (applying the same pure nitrogen amount), the Illumina MiSeq platform was used to investigate the bacterial and fungal community diversity and composition in paddy soil. Our results revealed that compared with the observations under regular chemical fertilization, on the basis of stable paddy yield, the application of biogas slurry combined with chemical fertilizer significantly enhanced the soil nutrient availability and bacterial community diversity and reduced the fungal community diversity. Dissolved organic carbon (DOC), DOC/SOC (soil organic carbon), available nitrogen (AN) and available phosphorus (AP) were positively correlated with the bacterial community diversity, but no soil property was significantly associated with the fungal community. The bacterial community was primarily driven by the application of biogas slurry combined with chemical fertilizer (40.78%), while the fungal community was almost equally affected by the addition of pure biogas slurry, chemical fertilizer and biogas slurry combined with chemical fertilizer (25.65–28.72%). Biogas slurry combined with chemical fertilizer significantly enriched Proteobacteria, Acidobacteria, Planctomycetes, Rokubacteria, and Ascomycota and depleted Chloroflexi, Bacteroidetes, Crenarchaeota, Basidiomycota, and Glomeromycota. The observation of the alteration of some bacteria- and fungus-specific taxa provides insights for the proper application of biogas slurry combined with chemical fertilizer, which has the potential to promote crop growth and inhibit pathogens.

Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico

The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.

Drivers and ecological consequences of dominance in periurban phytoplankton communities using networks approaches

Evaluating the causes and consequences of dominance by a limited number of taxa in phytoplankton communities is of huge importance in the current context of increasing anthropogenic pressures on natural ecosystems. This is of particular concern in densely populated urban areas where usages and impacts of human populations on water ecosystems are strongly interconnected. Microbial biodiversity is commonly used as a bioindicator of environmental quality and ecosystem functioning, but there are few studies at the regional scale that integrate the drivers of dominance in phytoplankton communities and their consequences on the structure and functioning of these communities. Here, we studied the causes and consequences of phytoplankton dominance in 50 environmentally contrasted waterbodies, sampled over four summer campaigns in the highly-populated Île-de-France region (IDF). Phytoplankton dominance was observed in 32-52% of the communities and most cases were attributed to Chlorophyta (35.5-40.6% of cases) and Cyanobacteria (30.3-36.5%). The best predictors of dominance were identified using multinomial logistic regression and included waterbody features (surface, depth and connection to the hydrological network) and water column characteristics (total N, TN:TP ratio, water temperature and stratification). The consequences of dominance were dependent on the identity of the dominant organisms and included modifications of biological attributes (richness, cohesion) and functioning (biomass, RUE) of phytoplankton communities. We constructed co-occurrence networks using high resolution phytoplankton biomass and demonstrated that networks under dominance by Chlorophyta and Cyanobacteria exhibited significantly different structure compared with networks without dominance. Furthermore, dominance by Cyanobacteria was associated with more profound network modifications (e.g. cohesion, size, density, efficiency and proportion of negative links), suggesting a stronger disruption of the structure and functioning of phytoplankton communities in the conditions in which this group dominates. Finally, we provide a synthesis on the relationships between environmental drivers, dominance status, community attributes and network structure.

Plant functional diversity drives carbon storage following vegetation restoration in Loess Plateau, China

Ongoing climatic changes induced by human activities increases in atmospheric carbon dioxide (CO₂), which have considerable effects on the structure and function of ecosystems, including carbon (C) storage, plant functional traits and therefore on a wide set of ecosystem services. Plant functional diversity is benefit to improve plant photosynthesis and enhance C efficiency and therefore decrease CO₂. Here, the focus of this article is on integrating of plant functional diversity and C storage, which aims to contribute to C sequestration for climate change mitigation following vegetation restoration in Loess Plateau, China. Firstly, the CWM (plant community-weighted mean) traits of the most abundant plant species can account for C storage in AGBC (above-ground biomass C), ALC (above-ground litter C), STC (soil total carbon) and TEC (total ecosystem carbon). Secondly, the CWM of plant height and LCC (leaf carbon concentration) had a positive effect C storage in different part (AGBC, ALC, STC and TEC), while the CWM of LNC (leaf nitrogen concentration) and SLA (specific leaf area) had a negative effect on C storage in different part. Further, the CWM of plant height, LCC, SLA and plant functional dispersion (FDis) can be used to predict C storage by multiple linear regression analysis. Finally, the positive association between FDis and C storage was found in SEM, shedding light on the key role of plant functional diversity driving C storage following vegetation restoration. The findings presented here highlight the importance of both plant traits of dominant species and plant functional diversity in regulating C storage, and show that favorable climate conditions, particularly vegetation restoration, tend to increase C storage and plant functional diversity, which have important implications for improving global C cycling and ecosystem services.

Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202

Maintenance of a beneficial microbial community, especially in the rhizosphere, is indispensable for plant growth and agricultural sustainability. In this sense, plant growth-promoting rhizobacteria (PGPR) have been extensively studied for their role in plant growth promotion and disease resistance. However, the impact of introducing PGPR strains into rhizosphere microbial communities is still underexplored. We previously found that the Proteus vulgaris JBLS202 strain (JBLS202) promoted growth of Kimchi cabbage and altered the relative abundance of total bacteria and Pseudomonas spp. in the treated rhizosphere. To extend these findings, we used pyrosequencing to analyze the changes in bacterial communities in the rhizosphere of Kimchi cabbage after introduction of JBLS202. The alterations were also evaluated by taxon-specific real-time PCR (qPCR). The pyrosequencing data revealed an increase in total bacteria abundance, including specific groups such as Proteobacteria, Acidobacteria, and Actinobacteria, in the treated rhizosphere. Time-course qPCR analysis confirmed the increase in the abundance of Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. Furthermore, genes involved in nitrogen cycling were upregulated by JBLS202 treatment indicating changes in ecological function of the rhizosphere soil. Overall, these results indicate that introduction of JBLS202 alters both the composition and function of the rhizosphere bacterial community, which can have direct and indirect effects on plant growth. Therefore, we propose that long-term changes in bacterial composition and community-level function need to be considered for practical use of PGPRs.

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau

Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems.

Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area

Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area.